From 9e003e8edac3b1d65cc80f045c5e0a940796684e Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Mon, 4 Mar 2024 15:09:35 +0000 Subject: [PATCH 001/548] basic class hierarchy for processing the fairdata station ttl --- lib/bio_ind/fair_data/assay.rb | 6 + lib/bio_ind/fair_data/base.rb | 50 + lib/bio_ind/fair_data/investigation.rb | 12 + lib/bio_ind/fair_data/observation_unit.rb | 12 + lib/bio_ind/fair_data/reader.rb | 26 + lib/bio_ind/fair_data/sample.rb | 13 + lib/bio_ind/fair_data/study.rb | 13 + test/fixtures/files/fairdatastation/demo.ttl | 877 ++++++++++++++++++ .../bioind/fairdata/fair_data_reader_test.rb | 31 + 9 files changed, 1040 insertions(+) create mode 100644 lib/bio_ind/fair_data/assay.rb create mode 100644 lib/bio_ind/fair_data/base.rb create mode 100644 lib/bio_ind/fair_data/investigation.rb create mode 100644 lib/bio_ind/fair_data/observation_unit.rb create mode 100644 lib/bio_ind/fair_data/reader.rb create mode 100644 lib/bio_ind/fair_data/sample.rb create mode 100644 lib/bio_ind/fair_data/study.rb create mode 100644 test/fixtures/files/fairdatastation/demo.ttl create mode 100644 test/unit/bioind/fairdata/fair_data_reader_test.rb diff --git a/lib/bio_ind/fair_data/assay.rb b/lib/bio_ind/fair_data/assay.rb new file mode 100644 index 0000000000..c4dfa55f05 --- /dev/null +++ b/lib/bio_ind/fair_data/assay.rb @@ -0,0 +1,6 @@ +module BioInd + module FairData + class Assay < Base + end + end +end \ No newline at end of file diff --git a/lib/bio_ind/fair_data/base.rb b/lib/bio_ind/fair_data/base.rb new file mode 100644 index 0000000000..bc5dfe5d66 --- /dev/null +++ b/lib/bio_ind/fair_data/base.rb @@ -0,0 +1,50 @@ +module BioInd + module FairData + class Base + attr_reader :identifier + attr_reader :graph + attr_reader :children + + def initialize(identifier, graph) + @identifier = identifier + @graph = graph + @jerm = RDF::Vocabulary.new("http://jermontology.org/ontology/JERMOntology#") + @children = [] + end + + def annotations + sparql = SPARQL::Client.new(graph) + query = sparql.select.where( + [identifier, :type, :value] + ) + + query.execute.collect do |prop| + [prop.type.to_s, prop.value.to_s] + end + end + + def populate + fetch_children.collect do |child| + add_child(child) + end + end + + def add_child(child) + @children << child_class.new(child, graph) + @children.last.populate + end + + def fetch_children + sparql = SPARQL::Client.new(graph) + query = sparql.select.where( + [identifier, @jerm.hasPart, :child] + ) + + query.execute.collect do |solution| + solution.child + end + end + + end + end +end \ No newline at end of file diff --git a/lib/bio_ind/fair_data/investigation.rb b/lib/bio_ind/fair_data/investigation.rb new file mode 100644 index 0000000000..fd9975bd74 --- /dev/null +++ b/lib/bio_ind/fair_data/investigation.rb @@ -0,0 +1,12 @@ +module BioInd + module FairData + class Investigation < Base + + alias_method :studies, :children + + def child_class + BioInd::FairData::Study + end + end + end +end diff --git a/lib/bio_ind/fair_data/observation_unit.rb b/lib/bio_ind/fair_data/observation_unit.rb new file mode 100644 index 0000000000..48257a45a0 --- /dev/null +++ b/lib/bio_ind/fair_data/observation_unit.rb @@ -0,0 +1,12 @@ +module BioInd + module FairData + class ObservationUnit < Base + + alias_method :samples, :children + + def child_class + BioInd::FairData::Sample + end + end + end +end \ No newline at end of file diff --git a/lib/bio_ind/fair_data/reader.rb b/lib/bio_ind/fair_data/reader.rb new file mode 100644 index 0000000000..0c07dc97a5 --- /dev/null +++ b/lib/bio_ind/fair_data/reader.rb @@ -0,0 +1,26 @@ +require 'rdf' +require 'rdf/turtle' +require 'sparql/client' + +module BioInd + module FairData + class Reader + + def self.parse_graph(path) + graph = RDF::Graph.load(path, format: :ttl) + sparql = SPARQL::Client.new(graph) + jerm = RDF::Vocabulary.new("http://jermontology.org/ontology/JERMOntology#") + + query = sparql.select.where( + [:inv, RDF.type, jerm.[]('Investigation')] + ) + query.execute.collect do |inv| + inv = BioInd::FairData::Investigation.new(inv.inv, graph) + inv.populate + inv + end + end + + end + end +end \ No newline at end of file diff --git a/lib/bio_ind/fair_data/sample.rb b/lib/bio_ind/fair_data/sample.rb new file mode 100644 index 0000000000..a3b54dbed8 --- /dev/null +++ b/lib/bio_ind/fair_data/sample.rb @@ -0,0 +1,13 @@ +module BioInd + module FairData + class Sample < Base + + alias_method :assays, :children + + def child_class + BioInd::FairData::Assay + end + + end + end +end \ No newline at end of file diff --git a/lib/bio_ind/fair_data/study.rb b/lib/bio_ind/fair_data/study.rb new file mode 100644 index 0000000000..33e09aafeb --- /dev/null +++ b/lib/bio_ind/fair_data/study.rb @@ -0,0 +1,13 @@ +module BioInd + module FairData + class Study < Base + + alias_method :observation_units, :children + + def child_class + BioInd::FairData::ObservationUnit + end + + end + end +end \ No newline at end of file diff --git a/test/fixtures/files/fairdatastation/demo.ttl b/test/fixtures/files/fairdatastation/demo.ttl new file mode 100644 index 0000000000..07a832f741 --- /dev/null +++ b/test/fixtures/files/fairdatastation/demo.ttl @@ -0,0 +1,877 @@ +@prefix base: . +@prefix bibo: . +@prefix dc: . +@prefix dcmitype: . +@prefix empusa: . +@prefix fair: . +@prefix foaf: . +@prefix gbol: . +@prefix jerm: . +@prefix mixs: . +@prefix owl: . +@prefix ppeo: . +@prefix prov: . +@prefix rdf: . +@prefix rdfs: . +@prefix sample: . +@prefix schema: . +@prefix sschema: . +@prefix uniprot: . +@prefix unlock: . +@prefix void: . +@prefix wd: . +@prefix wdt: . +@prefix wv: . +@prefix xml: . +@prefix xsd: . + +fair:inv_INV_DRP007092 + rdf:type jerm:Investigation ; + jerm:hasPart ; + schema:contributor ; + schema:description "Exploration of HIV-1 infected individuals in Ghana" ; + schema:identifier "INV_DRP007092" ; + schema:title "HIV-1 infected individuals in Ghana" . + + + rdf:type schema:Person ; + schema:department "AIDS Research Center" ; + schema:email ; + schema:familyName "Kofi Parbie" ; + schema:givenName "Prince Kofi Parbie" ; + schema:memberOf . + + + rdf:type schema:Organization ; + schema:legalName "National Institute of Infectious Diseases" . + +schema:identifier rdf:type rdf:Property ; + rdfs:label "investigation identifier" ; + schema:description "Identifier corresponding to the investigation" ; + schema:valuePattern "^[a-zA-Z0-9-_]*${5,25}" ; + schema:valueRequired true . + +schema:description rdf:type rdf:Property ; + rdfs:label "investigation description" ; + schema:description "Description of the investigation" ; + schema:valuePattern ".*{50,}" ; + schema:valueRequired true . + +schema:title rdf:type rdf:Property ; + rdfs:label "investigation title" ; + schema:description "Title describing the investigation" ; + schema:valuePattern ".*{10,}" ; + schema:valueRequired true . + + + rdf:type jerm:Study ; + fair:alias "DRP007092" ; + fair:center_name "NIID" ; + fair:center_project_name "human gut metagenome" ; + fair:external_ids "PRJDB10485" ; + fair:submission_accession "DRA010770" ; + fair:submission_alias "DRA010770" ; + fair:submission_center_name "NIID" ; + fair:submission_lab_name "AIDS Research Center2022-8-31" ; + jerm:hasPart , ; + schema:description "This project is to analyze the dysbiosis of fecal microbiome in HIV-1 infected individuals in Ghana. Gut microbiome dysbiosis has been correlated to the progression of non-AIDS diseases such as cardiovascular and metabolic disorders. Because the microbiome composition is different among races and countries, analyses of the composition in different regions is important to understand the pathogenesis unique to specific regions. In the present study, we examined fecal microbiome compositions in HIV-1 infected individuals in Ghana. In a cross-sectional case-control study, age- and gender-matched HIV-1 infected Ghanaian adults (HIV-1 [+]; n = 55) and seronegative controls (HIV-1 [-]; n = 55) were enrolled. Alpha diversity of fecal microbiome in HIV-1 (+) was significantly reduced compared to HIV-1 (-) and associated with CD4 counts. HIV-1 (+) showed reduction in varieties of bacteria including most abundant Faecalibacterium but enrichment of Proteobacteria. It should be noted that Ghanaian HIV-1 (+) exhibited enrichment of Dorea and Blautia, whose depletion has been reported in HIV-1 infected in most of other cohorts. Prevotella has been indicated to be enriched in HIV-1-infected MSM (men having sex with men) but was depleted in HIV-1 (+) of our cohort. The present study revealed the characteristic of dysbiotic fecal microbiome in HIV-1 infected Ghanaians, a representative of West African populations." ; + schema:identifier "DRP007092" ; + schema:title "Dysbiotic fecal microbiome in HIV-1 infected individuals in Ghana" . + +fair:external_ids rdf:type rdf:Property ; + rdfs:label "external ids" ; + schema:valuePattern ".+" . + +fair:center_project_name + rdf:type rdf:Property ; + rdfs:label "center project name" ; + schema:valuePattern ".+" . + +fair:center_name rdf:type rdf:Property ; + rdfs:label "center name" ; + schema:valuePattern ".+" . + +fair:alias rdf:type rdf:Property ; + rdfs:label "alias" ; + schema:valuePattern ".+" . + +fair:submission_accession + rdf:type rdf:Property ; + rdfs:label "submission accession" ; + schema:valuePattern ".+" . + +fair:submission_alias + rdf:type rdf:Property ; + rdfs:label "submission alias" ; + schema:valuePattern ".+" . + +fair:submission_center_name + rdf:type rdf:Property ; + rdfs:label "submission center name" ; + schema:valuePattern ".+" . + +fair:submission_lab_name + rdf:type rdf:Property ; + rdfs:label "submission lab name" ; + schema:valuePattern ".+" . + + + rdf:type ppeo:observation_unit ; + jerm:hasPart , , , ; + schema:description "HIV-1 infected individuals routinely attending an HIV/AIDS clinic in Ghana, were enrolled into the study. They were identified to reside in 7 communities in the Eastern Region of Ghana." ; + schema:identifier "HIV-1_positive" ; + schema:name "HIV-1 infected" . + +schema:name rdf:type rdf:Property ; + rdfs:label "observation unit name" ; + schema:description "Name of the entity being observed" ; + schema:valuePattern ".*{10,}" ; + schema:valueRequired true . + + + rdf:type ppeo:observation_unit ; + jerm:hasPart , , , , ; + schema:description "HIV-1 seronegative individuals were recruited during a community health screening in these communities. Seronegative individuals matched by age (± 2 years), gender and community of residence were enrolled as controls." ; + schema:identifier "HIV-1_negative" ; + schema:name "seronegative controls" . + + + rdf:type jerm:Sample ; + fair:art_drugs_current "Control" ; + fair:art_status_at_baseline "Control" ; + fair:biosafety_level 3 ; + fair:geo_loc_name "Ghana:Koforidua" ; + fair:hiv_risk_exposure "Heterosexual" ; + fair:host "Homo sapiens" ; + fair:host_disease_stat "HIV-1 negative" ; + fair:marital_status "Single" ; + fair:occupation "Trader" ; + fair:sample_name "13C" ; + gbol:scientificName "human gut metagenome" ; + jerm:hasPart ; + uniprot:organism 408170 ; + schema:description "Sample obtained from Single age 30 collected on 2017-12-15 from the human gut" ; + schema:identifier "DRS176881" ; + schema:name "sample DRS176881" ; + + "6.100334"^^xsd:double ; + + "-0.2614572"^^xsd:double ; + + "2017-12-15"^^xsd:date ; + + "30 years" . + +uniprot:organism rdf:type rdf:Property ; + rdfs:label "ncbi taxonomy id" ; + schema:description "Taxonomic identifier of the sample according to https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi for example use 2582415 for a blank sample or 1510822 for pig metagenome" ; + schema:valuePattern "\\d+" ; + schema:valueRequired true . + +gbol:scientificName rdf:type rdf:Property ; + rdfs:label "scientific name" ; + schema:description "Name of the organism" ; + schema:valuePattern ".*" ; + schema:valueRequired true . + +fair:biosafety_level rdf:type rdf:Property ; + rdfs:label "biosafety level" ; + schema:description "Biosafety level of the corresponding sample" ; + schema:valuePattern "(1|2|3|4|unknown)" ; + schema:valueRequired true . + + + rdf:type rdf:Property ; + rdfs:label "collection date" ; + schema:description "The date of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid ISO8601 compliant times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008." ; + schema:valuePattern ".+" ; + schema:valueRequired false . + +fair:geo_loc_name rdf:type rdf:Property ; + rdfs:label "geo_loc_name" ; + schema:valuePattern ".+" . + + + rdf:type rdf:Property ; + rdfs:label "geographic location (latitude)" ; + schema:description "The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system" ; + schema:valuePattern "(^^(\\-|\\+)?(\\d+)(\\.\\d+)?.?[0-9]{0,8}$)|(^not collected$)|(^not provided$)|(^restricted access$)" ; + schema:valueRequired false . + + + rdf:type rdf:Property ; + rdfs:label "geographic location (longitude)" ; + schema:description "The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system" ; + schema:valuePattern "(^^(\\-|\\+)?(\\d+)(\\.\\d+)?.?[0-9]{0,8}$)|(^not collected$)|(^not provided$)|(^restricted access$)" ; + schema:valueRequired false . + +fair:host rdf:type rdf:Property ; + rdfs:label "host" ; + schema:valuePattern ".+" . + +fair:host_disease_stat + rdf:type rdf:Property ; + rdfs:label "host_disease_stat" ; + schema:valuePattern ".+" . + +fair:occupation rdf:type rdf:Property ; + rdfs:label "occupation" ; + schema:valuePattern ".+" . + +fair:sample_name rdf:type rdf:Property ; + rdfs:label "sample_name" ; + schema:valuePattern ".+" . + +fair:art_drugs_current + rdf:type rdf:Property ; + rdfs:label "art_drugs_current" ; + schema:valuePattern ".+" . + +fair:art_status_at_baseline + rdf:type rdf:Property ; + rdfs:label "art_status_at_baseline" ; + schema:valuePattern ".+" . + +fair:hiv_risk_exposure + rdf:type rdf:Property ; + rdfs:label "hiv_risk_exposure" ; + schema:valuePattern ".+" . + +fair:marital_status rdf:type rdf:Property ; + rdfs:label "marital_status" ; + schema:valuePattern ".+" . + + + rdf:type rdf:Property ; + rdfs:label "host age" ; + schema:description "age of host at the time of sampling; relevant scale depends on species and study, e.g. could be seconds for amoebae or centuries for trees" ; + schema:unitCode "centuries|days|decades|hours|minutes|months|seconds|weeks|years" ; + schema:valuePattern "^(\\-|\\+)?(\\d+)(\\.\\d+)? ?(centuries|days|decades|hours|minutes|months|seconds|weeks|years)" ; + schema:valueRequired false . + + + rdf:type jerm:Sample ; + fair:art_drugs_current "TDF/3TC/NVP" ; + fair:art_duration_at_baseline_months + 55 ; + fair:art_start_date "2013-02-06" ; + fair:art_status_at_baseline "ART" ; + fair:biosafety_level 3 ; + fair:cd4_count_cells_ul 286 ; + fair:cd8_count_cells_ul 1139 ; + fair:co-trimoxazole_duration_mths + 48 ; + fair:geo_loc_name "Ghana:Suhum" ; + fair:hiv_risk_exposure "Heterosexual" ; + fair:host "Homo sapiens" ; + fair:host_disease_stat "HIV-1 positive" ; + fair:log_vl "4.655848867"^^xsd:double ; + fair:marital_status "Single" ; + fair:occupation "Trader" ; + fair:sample_name "19P" ; + fair:viral_load_copies_ml 45274 ; + gbol:scientificName "human gut metagenome" ; + jerm:hasPart ; + uniprot:organism 408170 ; + schema:description "Sample obtained from Single age 30 collected on 2017-09-13 from the human gut" ; + schema:identifier "DRS176892" ; + schema:name "sample DRS176892" ; + + "6.035885"^^xsd:double ; + + "-0.4552751"^^xsd:double ; + + "2017-09-13"^^xsd:date ; + + "30 years" . + +fair:art_duration_at_baseline_months + rdf:type rdf:Property ; + rdfs:label "art_duration_at baseline_months" ; + schema:valuePattern ".+" . + +fair:art_start_date rdf:type rdf:Property ; + rdfs:label "art_start_date" ; + schema:valuePattern ".+" . + +fair:cd4_count_cells_ul + rdf:type rdf:Property ; + rdfs:label "cd4_count(cells/ul)" ; + schema:valuePattern ".+" . + +fair:cd8_count_cells_ul + rdf:type rdf:Property ; + rdfs:label "cd8_count(cells/ul)" ; + schema:valuePattern ".+" . + +fair:co-trimoxazole_duration_mths + rdf:type rdf:Property ; + rdfs:label "co-trimoxazole duration (mths)" ; + schema:valuePattern ".+" . + +fair:viral_load_copies_ml + rdf:type rdf:Property ; + rdfs:label "viral_load (copies/ml)" ; + schema:valuePattern ".+" . + +fair:log_vl rdf:type rdf:Property ; + rdfs:label "log vl" ; + schema:valuePattern ".+" . + + + rdf:type jerm:Sample ; + fair:art_drugs_current "AZT/3TC/NVP" ; + fair:art_duration_at_baseline_months + 86 ; + fair:art_start_date "2010-06-23" ; + fair:art_status_at_baseline "ART" ; + fair:biosafety_level 3 ; + fair:cd4_count_cells_ul 1384 ; + fair:cd8_count_cells_ul 2467 ; + fair:co-trimoxazole_duration_mths + 144 ; + fair:geo_loc_name "Ghana:Koforidua" ; + fair:hiv_risk_exposure "Heterosexual" ; + fair:host "Homo sapiens" ; + fair:host_disease_stat "HIV-1 positive" ; + fair:log_vl "2.551449998"^^xsd:double ; + fair:marital_status "Single" ; + fair:occupation "Driver" ; + fair:sample_name "15P" ; + fair:viral_load_copies_ml 356 ; + gbol:scientificName "human gut metagenome" ; + jerm:hasPart ; + uniprot:organism 408170 ; + schema:description "Sample obtained from Single age 56 collected on 2017-09-13 from the human gut" ; + schema:identifier "DRS176886" ; + schema:name "sample DRS176886" ; + + "6.100334"^^xsd:double ; + + "-0.2614572"^^xsd:double ; + + "2017-09-13"^^xsd:date ; + + "56 years" . + + + rdf:type jerm:Sample ; + fair:art_drugs_current "TDF/3TC/EFV" ; + fair:art_duration_at_baseline_months + 144 ; + fair:art_start_date "2005-08-25" ; + fair:art_status_at_baseline "ART" ; + fair:biosafety_level 3 ; + fair:cd4_count_cells_ul 222 ; + fair:cd8_count_cells_ul 1130 ; + fair:co-trimoxazole_duration_mths + 144 ; + fair:geo_loc_name "Ghana:Koforidua" ; + fair:hiv_risk_exposure "Maternal-Fetal" ; + fair:host "Homo sapiens" ; + fair:host_disease_stat "HIV-1 positive" ; + fair:log_vl "4.581926914"^^xsd:double ; + fair:marital_status "Widowed" ; + fair:occupation "Trader" ; + fair:sample_name "HG-17-041P" ; + fair:viral_load_copies_ml 38188 ; + gbol:scientificName "human gut metagenome" ; + jerm:hasPart ; + uniprot:organism 408170 ; + schema:description "Sample obtained from Widowed age 48 collected on 2017-09-20 from the human gut" ; + schema:identifier "DRS176930" ; + schema:name "sample DRS176930" ; + + "6.100334"^^xsd:double ; + + "-0.2614572"^^xsd:double ; + + "2017-09-20"^^xsd:date ; + + "48 years" . + + + rdf:type jerm:Sample ; + fair:art_drugs_current "Control" ; + fair:art_status_at_baseline "Control" ; + fair:biosafety_level 3 ; + fair:geo_loc_name "Ghana:Jumapo" ; + fair:hiv_risk_exposure "Blood Trans" ; + fair:host "Homo sapiens" ; + fair:host_disease_stat "HIV-1 negative" ; + fair:marital_status "Married" ; + fair:occupation "Farmer" ; + fair:sample_name "26A" ; + gbol:scientificName "human gut metagenome" ; + jerm:hasPart ; + uniprot:organism 408170 ; + schema:description "Sample obtained from Married age 51 collected on 2018-09-01 from the human gut" ; + schema:identifier "DRS176899" ; + schema:name "sample DRS176899" ; + + "6.1595115"^^xsd:double ; + + "-0.2980853"^^xsd:double ; + + "2018-09-01"^^xsd:date ; + + "51 years" . + + + rdf:type jerm:Sample ; + fair:art_drugs_current "Control" ; + fair:art_status_at_baseline "Control" ; + fair:biosafety_level 3 ; + fair:geo_loc_name "Ghana:Koforidua" ; + fair:hiv_risk_exposure "Heterosexual" ; + fair:host "Homo sapiens" ; + fair:host_disease_stat "HIV-1 negative" ; + fair:marital_status "Widowed" ; + fair:occupation "Trader" ; + fair:sample_name "35C" ; + gbol:scientificName "human gut metagenome" ; + jerm:hasPart ; + uniprot:organism 408170 ; + schema:description "Sample obtained from Widowed age 65 collected on 2017-12-14 from the human gut" ; + schema:identifier "DRS176917" ; + schema:name "sample DRS176917" ; + + "6.100334"^^xsd:double ; + + "-0.2614572"^^xsd:double ; + + "2017-12-14"^^xsd:date ; + + "65 years" . + + + rdf:type jerm:Sample ; + fair:art_drugs_current "Control" ; + fair:art_status_at_baseline "Control" ; + fair:biosafety_level 3 ; + fair:geo_loc_name "Ghana:Koforidua" ; + fair:hiv_risk_exposure "Heterosexual" ; + fair:host "Homo sapiens" ; + fair:host_disease_stat "HIV-1 negative" ; + fair:marital_status "Widowed" ; + fair:occupation "Baker" ; + fair:sample_name "HG-17-044A" ; + gbol:scientificName "human gut metagenome" ; + jerm:hasPart ; + uniprot:organism 408170 ; + schema:description "Sample obtained from Widowed age 33 collected on 2017-12-18 from the human gut" ; + schema:identifier "DRS176935" ; + schema:name "sample DRS176935" ; + + "6.100334"^^xsd:double ; + + "-0.2614572"^^xsd:double ; + + "2017-12-18"^^xsd:date ; + + "33 years" . + + + rdf:type jerm:Sample ; + fair:art_drugs_current "Control" ; + fair:art_status_at_baseline "Control" ; + fair:biosafety_level 3 ; + fair:geo_loc_name "Ghana:Suhum" ; + fair:hiv_risk_exposure "Heterosexual" ; + fair:host "Homo sapiens" ; + fair:host_disease_stat "HIV-1 negative" ; + fair:marital_status "Widowed" ; + fair:occupation "Trader" ; + fair:sample_name "59C" ; + gbol:scientificName "human gut metagenome" ; + jerm:hasPart ; + uniprot:organism 408170 ; + schema:description "Sample obtained from Widowed age 66 collected on 2018-01-30 from the human gut" ; + schema:identifier "DRS176960" ; + schema:name "sample DRS176960" ; + + "6.035885"^^xsd:double ; + + "-0.4552751"^^xsd:double ; + + "2018-01-30"^^xsd:date ; + + "66 years" . + + + rdf:type jerm:Sample ; + fair:art_drugs_current "AZT/3TC/EFV" ; + fair:art_duration_at_baseline_months + 129 ; + fair:art_start_date "2006-11-22" ; + fair:art_status_at_baseline "ART" ; + fair:biosafety_level 3 ; + fair:cd4_count_cells_ul 571 ; + fair:cd8_count_cells_ul 2614 ; + fair:co-trimoxazole_duration_mths + 132 ; + fair:geo_loc_name "Ghana:Suhum" ; + fair:host "Homo sapiens" ; + fair:host_disease_stat "HIV-1 positive" ; + fair:marital_status "Married" ; + fair:occupation "Unemployed" ; + fair:sample_name "50P" ; + fair:viral_load_copies_ml "Undetectable" ; + gbol:scientificName "human gut metagenome" ; + jerm:hasPart ; + uniprot:organism 408170 ; + schema:description "Sample obtained from Married age 50 collected on 2017-09-19 from the human gut" ; + schema:identifier "DRS176942" ; + schema:name "sample DRS176942" ; + + "6.035885"^^xsd:double ; + + "-0.4552751"^^xsd:double ; + + "2017-09-19"^^xsd:date ; + + "50 years" . + + + rdf:type jerm:Assay ; + fair:facility "NMIMR" ; + fair:forwardPrimer "CCTACGGGNGGCWGCAG" ; + fair:instrument_model "Illumina MiSeq" ; + fair:library_selection "PCR" ; + fair:library_source "METAGENOMIC" ; + fair:library_strategy "AMPLICON" ; + fair:packageName "Amplicon demultiplexed" ; + fair:platform "ILLUMINA" ; + fair:primerNames "341F/785R" ; + fair:protocol "MiSeq Reagent Kit v3 (600-cycle) with a 20% PhiX (Illumina) spike-in" ; + fair:reversePrimer "GACTACHVGGGTATCTAATCC" ; + fair:target_subfragment "V3-V4" ; + schema:dataset , ; + schema:dateCreated "2019-02-05"^^xsd:date ; + schema:description "Illumina MiSeq paired end sequencing of SAMD00244440" ; + schema:identifier "DRR243845" . + +fair:protocol rdf:type rdf:Property ; + rdfs:label "protocol" ; + schema:description "The protocol used for preparation or isolation (name or url) used to create the assay" ; + schema:valuePattern ".*" ; + schema:valueRequired true . + +fair:facility rdf:type rdf:Property ; + rdfs:label "facility" ; + schema:description "The facility that was used for generating the data" ; + schema:valuePattern ".*" ; + schema:valueRequired true . + +schema:dateCreated rdf:type rdf:Property ; + rdfs:label "assay date" ; + schema:description "The date when the data generation took place" ; + schema:valuePattern ".+" ; + schema:valueRequired true . + + + rdf:type jerm:Data_sample ; + schema:description "demultiplexed forward file" ; + schema:identifier "DRR243845_1.fastq.gz" . + +fair:file rdf:type rdf:Property ; + rdfs:label "demultiplexed forward file" ; + schema:description "File path or name of the forward reads when working with demultiplexed reads" ; + schema:unitCode ".fq.gz|.fastq.gz|fastq.bz2|fq.bz2" ; + schema:valuePattern ".* ?(.fq.gz|.fastq.gz|fastq.bz2|fq.bz2)" ; + schema:valueRequired true . + + + rdf:type jerm:Data_sample ; + schema:description "demultiplexed reverse file" ; + schema:identifier "DRR243845_2.fastq.gz" . + +fair:forwardPrimer rdf:type rdf:Property ; + rdfs:label "forward primer" ; + schema:description "The forward primer" ; + schema:valuePattern "[ACGTUWSMKRYBDHVN]+" ; + schema:valueRequired true . + +fair:reversePrimer rdf:type rdf:Property ; + rdfs:label "reverse primer" ; + schema:description "The reverse primer used" ; + schema:valuePattern "[ACGTUWSMKRYBDHVN]+" ; + schema:valueRequired false . + +fair:primerNames rdf:type rdf:Property ; + rdfs:label "primer names" ; + schema:description "The primer names corresponding to the primers used" ; + schema:valuePattern ".*" ; + schema:valueRequired true . + +fair:target_subfragment + rdf:type rdf:Property ; + rdfs:label "target subfragment" ; + schema:description "Name of subfragment of a gene or locus (e.g. V3-4, V4, V6, V9, ITS). Important to e.g. identify special regions on marker genes like V6 on 16S rRNA" ; + schema:valuePattern ".*" ; + schema:valueRequired true . + +fair:platform rdf:type rdf:Property ; + rdfs:label "platform" ; + schema:description "The platform that was used for generating the data (Source: https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html#permitted-values-for-platform)" ; + schema:valuePattern "(LS454|ILLUMINA|PACBIO_SMRT|ION_TORRENT|CAPILLARY|OXFORD_NANOPORE|BGISEQ|DNBSEQ)" ; + schema:valueRequired true . + +fair:instrument_model + rdf:type rdf:Property ; + rdfs:label "instrument model" ; + schema:description "The instrument model that was used for generating the data (Source: https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html#permitted-values-for-instrument)" ; + schema:valuePattern "(454 GS|454 GS 20|454 GS FLX|454 GS FLX+|454 GS FLX Titanium|454 GS Junior|HiSeq X Five|HiSeq X Ten|Illumina Genome Analyzer|Illumina Genome Analyzer II|Illumina Genome Analyzer IIx|Illumina HiScanSQ|Illumina HiSeq 1000|Illumina HiSeq 1500|Illumina HiSeq 2000|Illumina HiSeq 2500|Illumina HiSeq 3000|Illumina HiSeq 4000|Illumina iSeq 100|Illumina MiSeq|Illumina MiniSeq|Illumina NovaSeq 6000|NextSeq 500|NextSeq 550|PacBio RS|PacBio RS II|Sequel|Ion Torrent PGM|Ion Torrent Proton|Ion Torrent S5|Ion Torrent S5 XL|AB 3730xL Genetic Analyzer|AB 3730 Genetic Analyzer|AB 3500xL Genetic Analyzer|AB 3500 Genetic Analyzer|AB 3130xL Genetic Analyzer|AB 3130 Genetic Analyzer|AB 310 Genetic Analyzer|MinION|GridION|PromethION|BGISEQ-500|DNBSEQ-T7|DNBSEQ-G400|DNBSEQ-G50|DNBSEQ-G400 FAST|unspecified)" ; + schema:valueRequired true . + +fair:library_source rdf:type rdf:Property ; + rdfs:label "library source" ; + schema:description "Source ENA" ; + schema:valuePattern "(GENOMIC|GENOMIC_SINGLE_CELL|TRANSCRIPTOMIC|TRANSCRIPTOMIC_SINGLE_CELL|METAGENOMIC|METATRANSCRIPTOMIC|SYNTHETIC|VIRAL_RNA|OTHER)" ; + schema:valueRequired true . + +fair:library_selection + rdf:type rdf:Property ; + rdfs:label "library selection" ; + schema:description "Source ENA" ; + schema:valuePattern "(RANDOM|PCR|RANDOM_PCR|RT-PCR|HMPR|MF|repeat_fractionation|size_fractionation|MSLL|cDNA|cDNA_randomPriming|cDNA_oligo_dT|PolyA|Oligo-dT|Inverse_rRNA|Inverse_rRNA_selection|ChIP|ChIP-Seq|MNase|DNase|Hybrid_Selection|Reduced_Representation|Restriction_Digest|5-methylcytidine_antibody|MBD2_protein_methyl-CpG_binding_domain|CAGE|RACE|MDA|padlock_probes_capture_method|other|unspecified)" ; + schema:valueRequired true . + +fair:library_strategy + rdf:type rdf:Property ; + rdfs:label "library strategy" ; + schema:description "Source ENA" ; + schema:valuePattern "(WGS|WGA|WXS|RNA-Seq|ssRNA-seq|miRNA-Seq|ncRNA-Seq|FL-cDNA|EST|Hi-C|ATAC-seq|WCS|RAD-Seq|CLONE|POOLCLONE|AMPLICON|CLONEEND|FINISHING|ChIP-Seq|MNase-Seq|DNase-Hypersensitivity|Bisulfite-Seq|CTS|MRE-Seq|MeDIP-Seq|MBD-Seq|Tn-Seq|VALIDATION|FAIRE-seq|SELEX|RIP-Seq|ChIA-PET|Synthetic-Long-Read|Targeted-Capture|Tethered_Chromatin_Conformation_Capture|OTHER)" ; + schema:valueRequired true . + + + rdf:type jerm:Assay ; + fair:facility "NMIMR" ; + fair:forwardPrimer "CCTACGGGNGGCWGCAG" ; + fair:instrument_model "Illumina MiSeq" ; + fair:library_selection "PCR" ; + fair:library_source "METAGENOMIC" ; + fair:library_strategy "AMPLICON" ; + fair:packageName "Amplicon demultiplexed" ; + fair:platform "ILLUMINA" ; + fair:primerNames "341F/785R" ; + fair:protocol "MiSeq Reagent Kit v3 (600-cycle) with a 20% PhiX (Illumina) spike-in" ; + fair:reversePrimer "GACTACHVGGGTATCTAATCC" ; + fair:target_subfragment "V3-V4" ; + schema:dataset , ; + schema:dateCreated "2019-02-05"^^xsd:date ; + schema:description "Illumina MiSeq paired end sequencing of SAMD00244451" ; + schema:identifier "DRR243856" . + + + rdf:type jerm:Data_sample ; + schema:description "demultiplexed forward file" ; + schema:identifier "DRR243856_1.fastq.gz" . + + + rdf:type jerm:Data_sample ; + schema:description "demultiplexed reverse file" ; + schema:identifier "DRR243856_2.fastq.gz" . + + + rdf:type jerm:Assay ; + fair:facility "NMIMR" ; + fair:forwardPrimer "CCTACGGGNGGCWGCAG" ; + fair:instrument_model "Illumina MiSeq" ; + fair:library_selection "PCR" ; + fair:library_source "METAGENOMIC" ; + fair:library_strategy "AMPLICON" ; + fair:packageName "Amplicon demultiplexed" ; + fair:platform "ILLUMINA" ; + fair:primerNames "341F/785R" ; + fair:protocol "MiSeq Reagent Kit v3 (600-cycle) with a 20% PhiX (Illumina) spike-in" ; + fair:reversePrimer "GACTACHVGGGTATCTAATCC" ; + fair:target_subfragment "V3-V4" ; + schema:dataset , ; + schema:dateCreated "2019-02-05"^^xsd:date ; + schema:description "Illumina MiSeq paired end sequencing of SAMD00244445" ; + schema:identifier "DRR243850" . + + + rdf:type jerm:Data_sample ; + schema:description "demultiplexed forward file" ; + schema:identifier "DRR243850_1.fastq.gz" . + + + rdf:type jerm:Data_sample ; + schema:description "demultiplexed reverse file" ; + schema:identifier "DRR243850_2.fastq.gz" . + + + rdf:type jerm:Assay ; + fair:facility "NMIMR" ; + fair:forwardPrimer "CCTACGGGNGGCWGCAG" ; + fair:instrument_model "Illumina MiSeq" ; + fair:library_selection "PCR" ; + fair:library_source "METAGENOMIC" ; + fair:library_strategy "AMPLICON" ; + fair:packageName "Amplicon demultiplexed" ; + fair:platform "ILLUMINA" ; + fair:primerNames "341F/785R" ; + fair:protocol "MiSeq Reagent Kit v3 (600-cycle) with a 20% PhiX (Illumina) spike-in" ; + fair:reversePrimer "GACTACHVGGGTATCTAATCC" ; + fair:target_subfragment "V3-V4" ; + schema:dataset , ; + schema:dateCreated "2019-02-05"^^xsd:date ; + schema:description "Illumina MiSeq paired end sequencing of SAMD00244489" ; + schema:identifier "DRR243894" . + + + rdf:type jerm:Data_sample ; + schema:description "demultiplexed forward file" ; + schema:identifier "DRR243894_1.fastq.gz" . + + + rdf:type jerm:Data_sample ; + schema:description "demultiplexed reverse file" ; + schema:identifier "DRR243894_2.fastq.gz" . + + + rdf:type jerm:Assay ; + fair:facility "NMIMR" ; + fair:forwardPrimer "CCTACGGGNGGCWGCAG" ; + fair:instrument_model "Illumina MiSeq" ; + fair:library_selection "PCR" ; + fair:library_source "METAGENOMIC" ; + fair:library_strategy "AMPLICON" ; + fair:packageName "Amplicon demultiplexed" ; + fair:platform "ILLUMINA" ; + fair:primerNames "341F/785R" ; + fair:protocol "MiSeq Reagent Kit v3 (600-cycle) with a 20% PhiX (Illumina) spike-in" ; + fair:reversePrimer "GACTACHVGGGTATCTAATCC" ; + fair:target_subfragment "V3-V4" ; + schema:dataset , ; + schema:dateCreated "2019-02-05"^^xsd:date ; + schema:description "Illumina MiSeq paired end sequencing of SAMD00244458" ; + schema:identifier "DRR243863" . + + + rdf:type jerm:Data_sample ; + schema:description "demultiplexed forward file" ; + schema:identifier "DRR243863_1.fastq.gz" . + + + rdf:type jerm:Data_sample ; + schema:description "demultiplexed reverse file" ; + schema:identifier "DRR243863_2.fastq.gz" . + + + rdf:type jerm:Assay ; + fair:facility "NMIMR" ; + fair:forwardPrimer "CCTACGGGNGGCWGCAG" ; + fair:instrument_model "Illumina MiSeq" ; + fair:library_selection "PCR" ; + fair:library_source "METAGENOMIC" ; + fair:library_strategy "AMPLICON" ; + fair:packageName "Amplicon demultiplexed" ; + fair:platform "ILLUMINA" ; + fair:primerNames "341F/785R" ; + fair:protocol "MiSeq Reagent Kit v3 (600-cycle) with a 20% PhiX (Illumina) spike-in" ; + fair:reversePrimer "GACTACHVGGGTATCTAATCC" ; + fair:target_subfragment "V3-V4" ; + schema:dataset , ; + schema:dateCreated "2019-02-05"^^xsd:date ; + schema:description "Illumina MiSeq paired end sequencing of SAMD00244476" ; + schema:identifier "DRR243881" . + + + rdf:type jerm:Data_sample ; + schema:description "demultiplexed forward file" ; + schema:identifier "DRR243881_1.fastq.gz" . + + + rdf:type jerm:Data_sample ; + schema:description "demultiplexed reverse file" ; + schema:identifier "DRR243881_2.fastq.gz" . + + + rdf:type jerm:Assay ; + fair:facility "NMIMR" ; + fair:forwardPrimer "CCTACGGGNGGCWGCAG" ; + fair:instrument_model "Illumina MiSeq" ; + fair:library_selection "PCR" ; + fair:library_source "METAGENOMIC" ; + fair:library_strategy "AMPLICON" ; + fair:packageName "Amplicon demultiplexed" ; + fair:platform "ILLUMINA" ; + fair:primerNames "341F/785R" ; + fair:protocol "MiSeq Reagent Kit v3 (600-cycle) with a 20% PhiX (Illumina) spike-in" ; + fair:reversePrimer "GACTACHVGGGTATCTAATCC" ; + fair:target_subfragment "V3-V4" ; + schema:dataset , ; + schema:dateCreated "2019-02-05"^^xsd:date ; + schema:description "Illumina MiSeq paired end sequencing of SAMD00244494" ; + schema:identifier "DRR243899" . + + + rdf:type jerm:Data_sample ; + schema:description "demultiplexed forward file" ; + schema:identifier "DRR243899_1.fastq.gz" . + + + rdf:type jerm:Data_sample ; + schema:description "demultiplexed reverse file" ; + schema:identifier "DRR243899_2.fastq.gz" . + + + rdf:type jerm:Assay ; + fair:facility "NMIMR" ; + fair:forwardPrimer "CCTACGGGNGGCWGCAG" ; + fair:instrument_model "Illumina MiSeq" ; + fair:library_selection "PCR" ; + fair:library_source "METAGENOMIC" ; + fair:library_strategy "AMPLICON" ; + fair:packageName "Amplicon demultiplexed" ; + fair:platform "ILLUMINA" ; + fair:primerNames "341F/785R" ; + fair:protocol "MiSeq Reagent Kit v3 (600-cycle) with a 20% PhiX (Illumina) spike-in" ; + fair:reversePrimer "GACTACHVGGGTATCTAATCC" ; + fair:target_subfragment "V3-V4" ; + schema:dataset , ; + schema:dateCreated "2019-02-05"^^xsd:date ; + schema:description "Illumina MiSeq paired end sequencing of SAMD00244519" ; + schema:identifier "DRR243924" . + + + rdf:type jerm:Data_sample ; + schema:description "demultiplexed forward file" ; + schema:identifier "DRR243924_1.fastq.gz" . + + + rdf:type jerm:Data_sample ; + schema:description "demultiplexed reverse file" ; + schema:identifier "DRR243924_2.fastq.gz" . + + + rdf:type jerm:Assay ; + fair:facility "NMIMR" ; + fair:forwardPrimer "CCTACGGGNGGCWGCAG" ; + fair:instrument_model "Illumina MiSeq" ; + fair:library_selection "PCR" ; + fair:library_source "METAGENOMIC" ; + fair:library_strategy "AMPLICON" ; + fair:packageName "Amplicon demultiplexed" ; + fair:platform "ILLUMINA" ; + fair:primerNames "341F/785R" ; + fair:protocol "MiSeq Reagent Kit v3 (600-cycle) with a 20% PhiX (Illumina) spike-in" ; + fair:reversePrimer "GACTACHVGGGTATCTAATCC" ; + fair:target_subfragment "V3-V4" ; + schema:dataset , ; + schema:dateCreated "2019-02-05"^^xsd:date ; + schema:description "Illumina MiSeq paired end sequencing of SAMD00244501" ; + schema:identifier "DRR243906" . + + + rdf:type jerm:Data_sample ; + schema:description "demultiplexed forward file" ; + schema:identifier "DRR243906_1.fastq.gz" . + + + rdf:type jerm:Data_sample ; + schema:description "demultiplexed reverse file" ; + schema:identifier "DRR243906_2.fastq.gz" . diff --git a/test/unit/bioind/fairdata/fair_data_reader_test.rb b/test/unit/bioind/fairdata/fair_data_reader_test.rb new file mode 100644 index 0000000000..8563ee7e48 --- /dev/null +++ b/test/unit/bioind/fairdata/fair_data_reader_test.rb @@ -0,0 +1,31 @@ +require 'test_helper' + +class FairDataReaderTest < ActiveSupport::TestCase + + test 'read demo' do + path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" + + investigations = BioInd::FairData::Reader.parse_graph(path) + assert_equal 1, investigations.count + inv = investigations.first + assert_equal "http://fairbydesign.nl/ontology/inv_INV_DRP007092", inv.identifier.to_s + + assert_equal 1, inv.studies.count + study = inv.studies.first + assert_equal 'http://fairbydesign.nl/ontology/inv_INV_DRP007092/stu_DRP007092', study.identifier.to_s + + assert_equal 2, study.observation_units.count + obs_unit = study.observation_units.first + assert_equal 'http://fairbydesign.nl/ontology/inv_INV_DRP007092/stu_DRP007092/obs_HIV-1_positive', obs_unit.identifier.to_s + + assert_equal 4, obs_unit.samples.count + sample = obs_unit.samples.first + assert_equal 'http://fairbydesign.nl/ontology/inv_INV_DRP007092/stu_DRP007092/obs_HIV-1_positive/sam_DRS176892', sample.identifier.to_s + + assert_equal 1, sample.assays.count + assay = sample.assays.first + assert_equal 'http://fairbydesign.nl/ontology/inv_INV_DRP007092/stu_DRP007092/obs_HIV-1_positive/sam_DRS176892/asy_DRR243856', assay.identifier.to_s + + end + +end \ No newline at end of file From 56dc4c58729afb9086ce535babe3efa357c04258 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Mon, 4 Mar 2024 16:07:32 +0000 Subject: [PATCH 002/548] read properties, to correctly get the identifier and also title/name and description --- lib/bio_ind/fair_data/base.rb | 35 +++++++++++-- lib/bio_ind/fair_data/study.rb | 4 ++ .../bioind/fairdata/fair_data_reader_test.rb | 50 +++++++++++++++++-- 3 files changed, 79 insertions(+), 10 deletions(-) diff --git a/lib/bio_ind/fair_data/base.rb b/lib/bio_ind/fair_data/base.rb index bc5dfe5d66..805897cbcf 100644 --- a/lib/bio_ind/fair_data/base.rb +++ b/lib/bio_ind/fair_data/base.rb @@ -1,21 +1,34 @@ module BioInd module FairData class Base - attr_reader :identifier + attr_reader :resource_uri attr_reader :graph attr_reader :children - def initialize(identifier, graph) - @identifier = identifier + def initialize(resource_uri, graph) + @resource_uri = resource_uri @graph = graph @jerm = RDF::Vocabulary.new("http://jermontology.org/ontology/JERMOntology#") + @schema = RDF::Vocabulary.new("http://schema.org/") @children = [] end + def identifier + find_annotation_value(@schema.identifier.to_s) + end + + def title + find_annotation_value(@schema.title) || find_annotation_value(@schema.name) + end + + def description + find_annotation_value(@schema.description) + end + def annotations sparql = SPARQL::Client.new(graph) query = sparql.select.where( - [identifier, :type, :value] + [resource_uri, :type, :value] ) query.execute.collect do |prop| @@ -23,6 +36,18 @@ def annotations end end + def find_annotation_value(property) + annotations.detect do |ann| + ann[0] == property + end&.[](1) + end + + def pp_annotations + annotations.sort_by{|a| a[0]}.each do |pair| + pp "#{pair[0]} -> #{pair[1]}" + end + end + def populate fetch_children.collect do |child| add_child(child) @@ -37,7 +62,7 @@ def add_child(child) def fetch_children sparql = SPARQL::Client.new(graph) query = sparql.select.where( - [identifier, @jerm.hasPart, :child] + [resource_uri, @jerm.hasPart, :child] ) query.execute.collect do |solution| diff --git a/lib/bio_ind/fair_data/study.rb b/lib/bio_ind/fair_data/study.rb index 33e09aafeb..5877c9245d 100644 --- a/lib/bio_ind/fair_data/study.rb +++ b/lib/bio_ind/fair_data/study.rb @@ -4,6 +4,10 @@ class Study < Base alias_method :observation_units, :children + def assays + observation_units.collect(&:samples).flatten.collect(&:assays).flatten.uniq + end + def child_class BioInd::FairData::ObservationUnit end diff --git a/test/unit/bioind/fairdata/fair_data_reader_test.rb b/test/unit/bioind/fairdata/fair_data_reader_test.rb index 8563ee7e48..440da8b334 100644 --- a/test/unit/bioind/fairdata/fair_data_reader_test.rb +++ b/test/unit/bioind/fairdata/fair_data_reader_test.rb @@ -8,24 +8,64 @@ class FairDataReaderTest < ActiveSupport::TestCase investigations = BioInd::FairData::Reader.parse_graph(path) assert_equal 1, investigations.count inv = investigations.first - assert_equal "http://fairbydesign.nl/ontology/inv_INV_DRP007092", inv.identifier.to_s + assert_equal "http://fairbydesign.nl/ontology/inv_INV_DRP007092", inv.resource_uri.to_s + assert_equal 'INV_DRP007092', inv.identifier assert_equal 1, inv.studies.count study = inv.studies.first - assert_equal 'http://fairbydesign.nl/ontology/inv_INV_DRP007092/stu_DRP007092', study.identifier.to_s + assert_equal 'http://fairbydesign.nl/ontology/inv_INV_DRP007092/stu_DRP007092', study.resource_uri.to_s + assert_equal 'DRP007092', study.identifier assert_equal 2, study.observation_units.count obs_unit = study.observation_units.first - assert_equal 'http://fairbydesign.nl/ontology/inv_INV_DRP007092/stu_DRP007092/obs_HIV-1_positive', obs_unit.identifier.to_s + assert_equal 'http://fairbydesign.nl/ontology/inv_INV_DRP007092/stu_DRP007092/obs_HIV-1_positive', obs_unit.resource_uri.to_s + assert_equal 'HIV-1_positive', obs_unit.identifier assert_equal 4, obs_unit.samples.count sample = obs_unit.samples.first - assert_equal 'http://fairbydesign.nl/ontology/inv_INV_DRP007092/stu_DRP007092/obs_HIV-1_positive/sam_DRS176892', sample.identifier.to_s + assert_equal 'http://fairbydesign.nl/ontology/inv_INV_DRP007092/stu_DRP007092/obs_HIV-1_positive/sam_DRS176892', sample.resource_uri.to_s + assert_equal 'DRS176892', sample.identifier assert_equal 1, sample.assays.count assay = sample.assays.first - assert_equal 'http://fairbydesign.nl/ontology/inv_INV_DRP007092/stu_DRP007092/obs_HIV-1_positive/sam_DRS176892/asy_DRR243856', assay.identifier.to_s + assert_equal 'http://fairbydesign.nl/ontology/inv_INV_DRP007092/stu_DRP007092/obs_HIV-1_positive/sam_DRS176892/asy_DRR243856', assay.resource_uri.to_s + assert_equal 'DRR243856', assay.identifier + end + + test 'study assays' do + path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" + + investigations = BioInd::FairData::Reader.parse_graph(path) + study = investigations.first.studies.first + assert_equal 9,study.assays.count + expected = ["DRR243845", "DRR243850", "DRR243856", "DRR243863", "DRR243881", "DRR243894", "DRR243899", "DRR243906", "DRR243924"] + assert_equal expected, study.assays.collect(&:identifier).sort + + end + + test 'titles and descriptions' do + path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" + + inv = BioInd::FairData::Reader.parse_graph(path).first + study = inv.studies.first + obs_unit = study.observation_units.first + sample = obs_unit.samples.first + assay = sample.assays.first + + assert_equal 'HIV-1 infected individuals in Ghana', inv.title + assert_equal 'Exploration of HIV-1 infected individuals in Ghana', inv.description + + assert_equal 'Dysbiotic fecal microbiome in HIV-1 infected individuals in Ghana', study.title + assert_equal 'This project is to analyze the dysbiosis of fecal microbiome in HIV-1 infected individuals in Ghana. Gut microbiome dysbiosis has been correlated to the progression of non-AIDS diseases such as cardiovascular and metabolic disorders. Because the microbiome composition is different among races and countries, analyses of the composition in different regions is important to understand the pathogenesis unique to specific regions. In the present study, we examined fecal microbiome compositions in HIV-1 infected individuals in Ghana. In a cross-sectional case-control study, age- and gender-matched HIV-1 infected Ghanaian adults (HIV-1 [+]; n = 55) and seronegative controls (HIV-1 [-]; n = 55) were enrolled. Alpha diversity of fecal microbiome in HIV-1 (+) was significantly reduced compared to HIV-1 (-) and associated with CD4 counts. HIV-1 (+) showed reduction in varieties of bacteria including most abundant Faecalibacterium but enrichment of Proteobacteria. It should be noted that Ghanaian HIV-1 (+) exhibited enrichment of Dorea and Blautia, whose depletion has been reported in HIV-1 infected in most of other cohorts. Prevotella has been indicated to be enriched in HIV-1-infected MSM (men having sex with men) but was depleted in HIV-1 (+) of our cohort. The present study revealed the characteristic of dysbiotic fecal microbiome in HIV-1 infected Ghanaians, a representative of West African populations.', study.description + + assert_equal 'HIV-1 infected', obs_unit.title + assert_equal 'HIV-1 infected individuals routinely attending an HIV/AIDS clinic in Ghana, were enrolled into the study. They were identified to reside in 7 communities in the Eastern Region of Ghana.', obs_unit.description + + assert_equal 'sample DRS176892', sample.title + assert_equal 'Sample obtained from Single age 30 collected on 2017-09-13 from the human gut', sample.description + assert_nil assay.title + assert_equal 'Illumina MiSeq paired end sequencing of SAMD00244451', assay.description end end \ No newline at end of file From 5a4998fde0c4b51bd94d5c4064020fb5683322ac Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Mon, 4 Mar 2024 16:27:19 +0000 Subject: [PATCH 003/548] datasets --- lib/bio_ind/fair_data/base.rb | 10 +++++++++ lib/bio_ind/fair_data/data_set.rb | 7 ++++++ .../bioind/fairdata/fair_data_reader_test.rb | 22 +++++++++++++++++++ 3 files changed, 39 insertions(+) create mode 100644 lib/bio_ind/fair_data/data_set.rb diff --git a/lib/bio_ind/fair_data/base.rb b/lib/bio_ind/fair_data/base.rb index 805897cbcf..24e4d965be 100644 --- a/lib/bio_ind/fair_data/base.rb +++ b/lib/bio_ind/fair_data/base.rb @@ -59,6 +59,16 @@ def add_child(child) @children.last.populate end + def datasets + sparql = SPARQL::Client.new(graph) + query = sparql.select.where( + [resource_uri, @schema.dataset, :dataset] + ) + query.execute.collect do |solution| + BioInd::FairData::DataSet.new(solution.dataset, graph) + end + end + def fetch_children sparql = SPARQL::Client.new(graph) query = sparql.select.where( diff --git a/lib/bio_ind/fair_data/data_set.rb b/lib/bio_ind/fair_data/data_set.rb new file mode 100644 index 0000000000..9f2b4288ec --- /dev/null +++ b/lib/bio_ind/fair_data/data_set.rb @@ -0,0 +1,7 @@ +module BioInd + module FairData + class DataSet < Base + + end + end +end \ No newline at end of file diff --git a/test/unit/bioind/fairdata/fair_data_reader_test.rb b/test/unit/bioind/fairdata/fair_data_reader_test.rb index 440da8b334..a4e2618067 100644 --- a/test/unit/bioind/fairdata/fair_data_reader_test.rb +++ b/test/unit/bioind/fairdata/fair_data_reader_test.rb @@ -52,6 +52,8 @@ class FairDataReaderTest < ActiveSupport::TestCase sample = obs_unit.samples.first assay = sample.assays.first + assay.pp_annotations + assert_equal 'HIV-1 infected individuals in Ghana', inv.title assert_equal 'Exploration of HIV-1 infected individuals in Ghana', inv.description @@ -68,4 +70,24 @@ class FairDataReaderTest < ActiveSupport::TestCase assert_equal 'Illumina MiSeq paired end sequencing of SAMD00244451', assay.description end + test 'datasets' do + path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" + + inv = BioInd::FairData::Reader.parse_graph(path).first + study = inv.studies.first + obs_unit = study.observation_units.first + sample = obs_unit.samples.first + assay = sample.assays.first + + datasets = assay.datasets + assert_equal 2, datasets.count + assert_equal ["DRR243856_1.fastq.gz", "DRR243856_2.fastq.gz"], datasets.collect(&:identifier).sort + assert_equal ["demultiplexed forward file", "demultiplexed reverse file"], datasets.collect(&:description).sort + + assert_equal 0, inv.datasets.count + assert_equal 0, study.datasets.count + assert_equal 0, obs_unit.datasets.count + assert_equal 0, sample.datasets.count + end + end \ No newline at end of file From 9889492de9014b59a339fa4f42e5636c35b305d8 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Mon, 4 Mar 2024 16:29:36 +0000 Subject: [PATCH 004/548] rubocop --- lib/bio_ind/fair_data/assay.rb | 2 +- lib/bio_ind/fair_data/base.rb | 17 ++++------ lib/bio_ind/fair_data/data_set.rb | 3 +- lib/bio_ind/fair_data/investigation.rb | 3 +- lib/bio_ind/fair_data/observation_unit.rb | 5 ++- lib/bio_ind/fair_data/reader.rb | 8 ++--- lib/bio_ind/fair_data/sample.rb | 6 ++-- lib/bio_ind/fair_data/study.rb | 6 ++-- .../bioind/fairdata/fair_data_reader_test.rb | 33 ++++++++++--------- 9 files changed, 35 insertions(+), 48 deletions(-) diff --git a/lib/bio_ind/fair_data/assay.rb b/lib/bio_ind/fair_data/assay.rb index c4dfa55f05..0be5bff2b2 100644 --- a/lib/bio_ind/fair_data/assay.rb +++ b/lib/bio_ind/fair_data/assay.rb @@ -3,4 +3,4 @@ module FairData class Assay < Base end end -end \ No newline at end of file +end diff --git a/lib/bio_ind/fair_data/base.rb b/lib/bio_ind/fair_data/base.rb index 24e4d965be..1ca4669540 100644 --- a/lib/bio_ind/fair_data/base.rb +++ b/lib/bio_ind/fair_data/base.rb @@ -1,15 +1,13 @@ module BioInd module FairData class Base - attr_reader :resource_uri - attr_reader :graph - attr_reader :children + attr_reader :resource_uri, :graph, :children def initialize(resource_uri, graph) @resource_uri = resource_uri @graph = graph - @jerm = RDF::Vocabulary.new("http://jermontology.org/ontology/JERMOntology#") - @schema = RDF::Vocabulary.new("http://schema.org/") + @jerm = RDF::Vocabulary.new('http://jermontology.org/ontology/JERMOntology#') + @schema = RDF::Vocabulary.new('http://schema.org/') @children = [] end @@ -43,7 +41,7 @@ def find_annotation_value(property) end def pp_annotations - annotations.sort_by{|a| a[0]}.each do |pair| + annotations.sort_by { |a| a[0] }.each do |pair| pp "#{pair[0]} -> #{pair[1]}" end end @@ -75,11 +73,8 @@ def fetch_children [resource_uri, @jerm.hasPart, :child] ) - query.execute.collect do |solution| - solution.child - end + query.execute.collect(&:child) end - end end -end \ No newline at end of file +end diff --git a/lib/bio_ind/fair_data/data_set.rb b/lib/bio_ind/fair_data/data_set.rb index 9f2b4288ec..5b2e750924 100644 --- a/lib/bio_ind/fair_data/data_set.rb +++ b/lib/bio_ind/fair_data/data_set.rb @@ -1,7 +1,6 @@ module BioInd module FairData class DataSet < Base - end end -end \ No newline at end of file +end diff --git a/lib/bio_ind/fair_data/investigation.rb b/lib/bio_ind/fair_data/investigation.rb index fd9975bd74..e02fb67cdc 100644 --- a/lib/bio_ind/fair_data/investigation.rb +++ b/lib/bio_ind/fair_data/investigation.rb @@ -1,8 +1,7 @@ module BioInd module FairData class Investigation < Base - - alias_method :studies, :children + alias studies children def child_class BioInd::FairData::Study diff --git a/lib/bio_ind/fair_data/observation_unit.rb b/lib/bio_ind/fair_data/observation_unit.rb index 48257a45a0..fc529a31f0 100644 --- a/lib/bio_ind/fair_data/observation_unit.rb +++ b/lib/bio_ind/fair_data/observation_unit.rb @@ -1,12 +1,11 @@ module BioInd module FairData class ObservationUnit < Base - - alias_method :samples, :children + alias samples children def child_class BioInd::FairData::Sample end end end -end \ No newline at end of file +end diff --git a/lib/bio_ind/fair_data/reader.rb b/lib/bio_ind/fair_data/reader.rb index 0c07dc97a5..3728e57a68 100644 --- a/lib/bio_ind/fair_data/reader.rb +++ b/lib/bio_ind/fair_data/reader.rb @@ -5,11 +5,10 @@ module BioInd module FairData class Reader - def self.parse_graph(path) - graph = RDF::Graph.load(path, format: :ttl) + graph = RDF::Graph.load(path, format: :ttl) sparql = SPARQL::Client.new(graph) - jerm = RDF::Vocabulary.new("http://jermontology.org/ontology/JERMOntology#") + jerm = RDF::Vocabulary.new('http://jermontology.org/ontology/JERMOntology#') query = sparql.select.where( [:inv, RDF.type, jerm.[]('Investigation')] @@ -20,7 +19,6 @@ def self.parse_graph(path) inv end end - end end -end \ No newline at end of file +end diff --git a/lib/bio_ind/fair_data/sample.rb b/lib/bio_ind/fair_data/sample.rb index a3b54dbed8..e59bb0ffac 100644 --- a/lib/bio_ind/fair_data/sample.rb +++ b/lib/bio_ind/fair_data/sample.rb @@ -1,13 +1,11 @@ module BioInd module FairData class Sample < Base - - alias_method :assays, :children + alias assays children def child_class BioInd::FairData::Assay end - end end -end \ No newline at end of file +end diff --git a/lib/bio_ind/fair_data/study.rb b/lib/bio_ind/fair_data/study.rb index 5877c9245d..4eab8d9114 100644 --- a/lib/bio_ind/fair_data/study.rb +++ b/lib/bio_ind/fair_data/study.rb @@ -1,8 +1,7 @@ module BioInd module FairData class Study < Base - - alias_method :observation_units, :children + alias observation_units children def assays observation_units.collect(&:samples).flatten.collect(&:assays).flatten.uniq @@ -11,7 +10,6 @@ def assays def child_class BioInd::FairData::ObservationUnit end - end end -end \ No newline at end of file +end diff --git a/test/unit/bioind/fairdata/fair_data_reader_test.rb b/test/unit/bioind/fairdata/fair_data_reader_test.rb index a4e2618067..b2bf78d36e 100644 --- a/test/unit/bioind/fairdata/fair_data_reader_test.rb +++ b/test/unit/bioind/fairdata/fair_data_reader_test.rb @@ -1,14 +1,13 @@ require 'test_helper' class FairDataReaderTest < ActiveSupport::TestCase - test 'read demo' do path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" investigations = BioInd::FairData::Reader.parse_graph(path) assert_equal 1, investigations.count inv = investigations.first - assert_equal "http://fairbydesign.nl/ontology/inv_INV_DRP007092", inv.resource_uri.to_s + assert_equal 'http://fairbydesign.nl/ontology/inv_INV_DRP007092', inv.resource_uri.to_s assert_equal 'INV_DRP007092', inv.identifier assert_equal 1, inv.studies.count @@ -18,17 +17,20 @@ class FairDataReaderTest < ActiveSupport::TestCase assert_equal 2, study.observation_units.count obs_unit = study.observation_units.first - assert_equal 'http://fairbydesign.nl/ontology/inv_INV_DRP007092/stu_DRP007092/obs_HIV-1_positive', obs_unit.resource_uri.to_s + assert_equal 'http://fairbydesign.nl/ontology/inv_INV_DRP007092/stu_DRP007092/obs_HIV-1_positive', + obs_unit.resource_uri.to_s assert_equal 'HIV-1_positive', obs_unit.identifier assert_equal 4, obs_unit.samples.count sample = obs_unit.samples.first - assert_equal 'http://fairbydesign.nl/ontology/inv_INV_DRP007092/stu_DRP007092/obs_HIV-1_positive/sam_DRS176892', sample.resource_uri.to_s + assert_equal 'http://fairbydesign.nl/ontology/inv_INV_DRP007092/stu_DRP007092/obs_HIV-1_positive/sam_DRS176892', + sample.resource_uri.to_s assert_equal 'DRS176892', sample.identifier assert_equal 1, sample.assays.count assay = sample.assays.first - assert_equal 'http://fairbydesign.nl/ontology/inv_INV_DRP007092/stu_DRP007092/obs_HIV-1_positive/sam_DRS176892/asy_DRR243856', assay.resource_uri.to_s + assert_equal 'http://fairbydesign.nl/ontology/inv_INV_DRP007092/stu_DRP007092/obs_HIV-1_positive/sam_DRS176892/asy_DRR243856', + assay.resource_uri.to_s assert_equal 'DRR243856', assay.identifier end @@ -37,10 +39,10 @@ class FairDataReaderTest < ActiveSupport::TestCase investigations = BioInd::FairData::Reader.parse_graph(path) study = investigations.first.studies.first - assert_equal 9,study.assays.count - expected = ["DRR243845", "DRR243850", "DRR243856", "DRR243863", "DRR243881", "DRR243894", "DRR243899", "DRR243906", "DRR243924"] + assert_equal 9, study.assays.count + expected = %w[DRR243845 DRR243850 DRR243856 DRR243863 DRR243881 DRR243894 DRR243899 DRR243906 + DRR243924] assert_equal expected, study.assays.collect(&:identifier).sort - end test 'titles and descriptions' do @@ -52,16 +54,16 @@ class FairDataReaderTest < ActiveSupport::TestCase sample = obs_unit.samples.first assay = sample.assays.first - assay.pp_annotations - assert_equal 'HIV-1 infected individuals in Ghana', inv.title assert_equal 'Exploration of HIV-1 infected individuals in Ghana', inv.description assert_equal 'Dysbiotic fecal microbiome in HIV-1 infected individuals in Ghana', study.title - assert_equal 'This project is to analyze the dysbiosis of fecal microbiome in HIV-1 infected individuals in Ghana. Gut microbiome dysbiosis has been correlated to the progression of non-AIDS diseases such as cardiovascular and metabolic disorders. Because the microbiome composition is different among races and countries, analyses of the composition in different regions is important to understand the pathogenesis unique to specific regions. In the present study, we examined fecal microbiome compositions in HIV-1 infected individuals in Ghana. In a cross-sectional case-control study, age- and gender-matched HIV-1 infected Ghanaian adults (HIV-1 [+]; n = 55) and seronegative controls (HIV-1 [-]; n = 55) were enrolled. Alpha diversity of fecal microbiome in HIV-1 (+) was significantly reduced compared to HIV-1 (-) and associated with CD4 counts. HIV-1 (+) showed reduction in varieties of bacteria including most abundant Faecalibacterium but enrichment of Proteobacteria. It should be noted that Ghanaian HIV-1 (+) exhibited enrichment of Dorea and Blautia, whose depletion has been reported in HIV-1 infected in most of other cohorts. Prevotella has been indicated to be enriched in HIV-1-infected MSM (men having sex with men) but was depleted in HIV-1 (+) of our cohort. The present study revealed the characteristic of dysbiotic fecal microbiome in HIV-1 infected Ghanaians, a representative of West African populations.', study.description + assert_equal 'This project is to analyze the dysbiosis of fecal microbiome in HIV-1 infected individuals in Ghana. Gut microbiome dysbiosis has been correlated to the progression of non-AIDS diseases such as cardiovascular and metabolic disorders. Because the microbiome composition is different among races and countries, analyses of the composition in different regions is important to understand the pathogenesis unique to specific regions. In the present study, we examined fecal microbiome compositions in HIV-1 infected individuals in Ghana. In a cross-sectional case-control study, age- and gender-matched HIV-1 infected Ghanaian adults (HIV-1 [+]; n = 55) and seronegative controls (HIV-1 [-]; n = 55) were enrolled. Alpha diversity of fecal microbiome in HIV-1 (+) was significantly reduced compared to HIV-1 (-) and associated with CD4 counts. HIV-1 (+) showed reduction in varieties of bacteria including most abundant Faecalibacterium but enrichment of Proteobacteria. It should be noted that Ghanaian HIV-1 (+) exhibited enrichment of Dorea and Blautia, whose depletion has been reported in HIV-1 infected in most of other cohorts. Prevotella has been indicated to be enriched in HIV-1-infected MSM (men having sex with men) but was depleted in HIV-1 (+) of our cohort. The present study revealed the characteristic of dysbiotic fecal microbiome in HIV-1 infected Ghanaians, a representative of West African populations.', + study.description assert_equal 'HIV-1 infected', obs_unit.title - assert_equal 'HIV-1 infected individuals routinely attending an HIV/AIDS clinic in Ghana, were enrolled into the study. They were identified to reside in 7 communities in the Eastern Region of Ghana.', obs_unit.description + assert_equal 'HIV-1 infected individuals routinely attending an HIV/AIDS clinic in Ghana, were enrolled into the study. They were identified to reside in 7 communities in the Eastern Region of Ghana.', + obs_unit.description assert_equal 'sample DRS176892', sample.title assert_equal 'Sample obtained from Single age 30 collected on 2017-09-13 from the human gut', sample.description @@ -81,13 +83,12 @@ class FairDataReaderTest < ActiveSupport::TestCase datasets = assay.datasets assert_equal 2, datasets.count - assert_equal ["DRR243856_1.fastq.gz", "DRR243856_2.fastq.gz"], datasets.collect(&:identifier).sort - assert_equal ["demultiplexed forward file", "demultiplexed reverse file"], datasets.collect(&:description).sort + assert_equal ['DRR243856_1.fastq.gz', 'DRR243856_2.fastq.gz'], datasets.collect(&:identifier).sort + assert_equal ['demultiplexed forward file', 'demultiplexed reverse file'], datasets.collect(&:description).sort assert_equal 0, inv.datasets.count assert_equal 0, study.datasets.count assert_equal 0, obs_unit.datasets.count assert_equal 0, sample.datasets.count end - -end \ No newline at end of file +end From d0f53c8c36a1e532fd7ab34d1289453fd0c1ee5b Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 5 Mar 2024 10:32:37 +0000 Subject: [PATCH 005/548] tweak to test --- test/unit/bioind/fairdata/fair_data_reader_test.rb | 1 + 1 file changed, 1 insertion(+) diff --git a/test/unit/bioind/fairdata/fair_data_reader_test.rb b/test/unit/bioind/fairdata/fair_data_reader_test.rb index b2bf78d36e..ccd7102582 100644 --- a/test/unit/bioind/fairdata/fair_data_reader_test.rb +++ b/test/unit/bioind/fairdata/fair_data_reader_test.rb @@ -83,6 +83,7 @@ class FairDataReaderTest < ActiveSupport::TestCase datasets = assay.datasets assert_equal 2, datasets.count + assert_equal ['http://fairbydesign.nl/data_sample/DRR243856_1.fastq.gz', 'http://fairbydesign.nl/data_sample/DRR243856_2.fastq.gz'], datasets.collect(&:resource_uri).collect(&:to_s).sort assert_equal ['DRR243856_1.fastq.gz', 'DRR243856_2.fastq.gz'], datasets.collect(&:identifier).sort assert_equal ['demultiplexed forward file', 'demultiplexed reverse file'], datasets.collect(&:description).sort From 633f7cfbcf8f2f27e36699530ae88980742703b6 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 5 Mar 2024 11:47:25 +0000 Subject: [PATCH 006/548] constructing and saving the basic seek isa structure from the fairdata station ttl --- app/models/assay.rb | 2 +- app/models/study.rb | 2 +- lib/bio_ind/fair_data/assay.rb | 5 +++ lib/bio_ind/fair_data/base.rb | 4 +++ lib/bio_ind/fair_data/reader.rb | 18 ++++++++++ .../bioind/fairdata/fair_data_reader_test.rb | 33 +++++++++++++++++++ 6 files changed, 62 insertions(+), 2 deletions(-) diff --git a/app/models/assay.rb b/app/models/assay.rb index 1a6044e35d..ac4b09bad8 100644 --- a/app/models/assay.rb +++ b/app/models/assay.rb @@ -57,7 +57,7 @@ class Assay < ApplicationRecord validates_with TechnologyTypeUriValidator validates_presence_of :contributor validates_presence_of :assay_class - validates :study, presence: { message: 'must be selected and valid' }, projects: true + validates :study, presence: { message: 'must be selected and valid' } before_validation :default_assay_and_technology_type diff --git a/app/models/study.rb b/app/models/study.rb index 467a550083..c206c62b98 100644 --- a/app/models/study.rb +++ b/app/models/study.rb @@ -27,7 +27,7 @@ class Study < ApplicationRecord has_and_belongs_to_many :sample_types - validates :investigation, presence: { :message => "is blank or invalid" }, projects: true + validates :investigation, presence: { :message => "is blank or invalid" } enforce_authorization_on_association :investigation, :view diff --git a/lib/bio_ind/fair_data/assay.rb b/lib/bio_ind/fair_data/assay.rb index 0be5bff2b2..f65093b8eb 100644 --- a/lib/bio_ind/fair_data/assay.rb +++ b/lib/bio_ind/fair_data/assay.rb @@ -1,6 +1,11 @@ module BioInd module FairData class Assay < Base + + def title + "Assay - #{identifier}" + end + end end end diff --git a/lib/bio_ind/fair_data/base.rb b/lib/bio_ind/fair_data/base.rb index 1ca4669540..94d78d00c4 100644 --- a/lib/bio_ind/fair_data/base.rb +++ b/lib/bio_ind/fair_data/base.rb @@ -75,6 +75,10 @@ def fetch_children query.execute.collect(&:child) end + + def seek_attributes + {title: title, description: description} + end end end end diff --git a/lib/bio_ind/fair_data/reader.rb b/lib/bio_ind/fair_data/reader.rb index 3728e57a68..5844ef1d8f 100644 --- a/lib/bio_ind/fair_data/reader.rb +++ b/lib/bio_ind/fair_data/reader.rb @@ -19,6 +19,24 @@ def self.parse_graph(path) inv end end + + def self.construct_isa(datastation_inv, contributor, projects) + inv_attributes = datastation_inv.seek_attributes.merge({contributor: contributor, projects: projects}) + investigation = ::Investigation.new(inv_attributes) + studies = [] + assays = [] + + datastation_inv.studies.each do |datastation_study| + study_attributes = datastation_study.seek_attributes.merge({contributor: contributor, investigation: investigation}) + study = investigation.studies.build(study_attributes) + datastation_study.assays.each do |datastation_assay| + assay_attributes = datastation_assay.seek_attributes.merge({contributor: contributor, study:studies.last, assay_class: AssayClass.experimental}) + study.assays.build(assay_attributes) + end + end + + return investigation + end end end end diff --git a/test/unit/bioind/fairdata/fair_data_reader_test.rb b/test/unit/bioind/fairdata/fair_data_reader_test.rb index ccd7102582..746a985c0a 100644 --- a/test/unit/bioind/fairdata/fair_data_reader_test.rb +++ b/test/unit/bioind/fairdata/fair_data_reader_test.rb @@ -92,4 +92,37 @@ class FairDataReaderTest < ActiveSupport::TestCase assert_equal 0, obs_unit.datasets.count assert_equal 0, sample.datasets.count end + + test 'construct seek isa' do + path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" + inv = BioInd::FairData::Reader.parse_graph(path).first + + contributor = FactoryBot.create(:person) + project = contributor.projects.first + FactoryBot.create(:experimental_assay_class) + + investigation = BioInd::FairData::Reader.construct_isa(inv, contributor, [project]) + studies = investigation.studies.to_a + assays = studies.first.assays.to_a + + assert_equal 1, studies.count + assert_equal 9, assays.count + + assert investigation.valid? + assert studies.first.valid? + + pp assays.first.errors unless assays.first.valid? + assert assays.first.valid? + + assert_difference('Investigation.count',1) do + assert_difference('Study.count',1) do + assert_difference('Assay.count', 9) do + User.with_current_user(contributor.user) do + investigation.save! + end + end + end + end + + end end From 553fafcc3208c0dcd567c792d458d06c5d3e68e1 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 5 Mar 2024 15:09:37 +0000 Subject: [PATCH 007/548] very basic UI and controller for submitting ttl file and creating isa --- app/controllers/projects_controller.rb | 15 ++++++++++++++- app/views/projects/_buttons.html.erb | 3 +++ .../import_from_fairdata_station.html.erb | 10 ++++++++++ config/routes.rb | 2 ++ lib/bio_ind/fair_data/reader.rb | 1 + test/functional/projects_controller_test.rb | 19 +++++++++++++++++++ 6 files changed, 49 insertions(+), 1 deletion(-) create mode 100644 app/views/projects/import_from_fairdata_station.html.erb diff --git a/app/controllers/projects_controller.rb b/app/controllers/projects_controller.rb index c63bc2197c..76ecfa69f5 100644 --- a/app/controllers/projects_controller.rb +++ b/app/controllers/projects_controller.rb @@ -18,7 +18,8 @@ class ProjectsController < ApplicationController before_action :find_requested_item, only: %i[show admin edit update destroy admin_members asset_report populate populate_from_spreadsheet admin_member_roles update_members storage_report - overview administer_join_request respond_join_request] + overview administer_join_request respond_join_request + import_from_fairdata_station submit_fairdata_station] before_action :has_spreadsheets, only: %i[:populate populate_from_spreadsheet] @@ -194,6 +195,18 @@ def request_join end end + def submit_fairdata_station + path = params[:datastation_data].path + datadata_inv = BioInd::FairData::Reader.parse_graph(path) + @investigation = BioInd::FairData::Reader.construct_isa(datadata_inv.first, current_person, [@project]) + @investigation.save! + + respond_to do |format| + format.html { redirect_to(@investigation) } + end + + end + def request_create proj_params = params.require(:project).permit([:title, :web_page, :description]) @project = Project.new(proj_params) diff --git a/app/views/projects/_buttons.html.erb b/app/views/projects/_buttons.html.erb index d71dad5b2d..8fadf8688c 100644 --- a/app/views/projects/_buttons.html.erb +++ b/app/views/projects/_buttons.html.erb @@ -65,5 +65,8 @@ <% if admin_logged_in? || item.can_manage? -%> <%= delete_icon(item,current_user,"Any members will also be removed from the #{t('project')}, are you sure?") %> <% end -%> +
  • + <%= image_tag_for_key('import', import_from_fairdata_station_project_path(item), "Import from FAIRData Station", nil, "Import from FAIRData Station") -%> +
    • <% end -%> <% end -%> diff --git a/app/views/projects/import_from_fairdata_station.html.erb b/app/views/projects/import_from_fairdata_station.html.erb new file mode 100644 index 0000000000..7a4b3111d9 --- /dev/null +++ b/app/views/projects/import_from_fairdata_station.html.erb @@ -0,0 +1,10 @@ +<%= render :partial => "general/page_title",:locals=>{:title=>"Import ISA from FAIRData Station for #{ t('Project') } #{link_to(@project.title, @project)}".html_safe} %> + +<%= form_tag submit_fairdata_station_project_path(@project), multipart: true do %> +

    + + <%= file_field_tag "datastation_data" -%> + + <%= submit_tag("Submit") %> +

    +<% end %> \ No newline at end of file diff --git a/config/routes.rb b/config/routes.rb index d0a3054d4c..ab2fad8490 100644 --- a/config/routes.rb +++ b/config/routes.rb @@ -349,6 +349,8 @@ get :administer_join_request post :respond_join_request get :guided_join + get :import_from_fairdata_station + post :submit_fairdata_station end resources :programmes, :people, :institutions, :assays, :studies, :investigations, :models, :sops, :workflows, :data_files, :presentations, :publications, :events, :sample_types, :samples, :specimens, :strains, :search, :organisms, :human_diseases, :documents, :file_templates, :placeholders, :collections, :templates, only: [:index] diff --git a/lib/bio_ind/fair_data/reader.rb b/lib/bio_ind/fair_data/reader.rb index 5844ef1d8f..a4a39c9acc 100644 --- a/lib/bio_ind/fair_data/reader.rb +++ b/lib/bio_ind/fair_data/reader.rb @@ -5,6 +5,7 @@ module BioInd module FairData class Reader + def self.parse_graph(path) graph = RDF::Graph.load(path, format: :ttl) sparql = SPARQL::Client.new(graph) diff --git a/test/functional/projects_controller_test.rb b/test/functional/projects_controller_test.rb index 21a8552a8c..3b3d71d728 100644 --- a/test/functional/projects_controller_test.rb +++ b/test/functional/projects_controller_test.rb @@ -5002,6 +5002,25 @@ def test_admin_can_edit end end + test 'populate from fairdata station ttl' do + + person = FactoryBot.create(:person) + project = person.projects.first + login_as(person) + + ttl_file = fixture_file_upload('fairdatastation/demo.ttl') + + post :submit_fairdata_station, params: {id: project, datastation_data: ttl_file} + + assert investigation = assigns(:investigation) + assert_redirected_to investigation + + assert_equal person, investigation.contributor + assert_equal 1, investigation.studies.count + assert_equal 9, investigation.studies.first.assays.count + + end + private def check_project(project) From 54b40fd91375458045824a7740187c2da4065461 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 5 Mar 2024 16:28:41 +0000 Subject: [PATCH 008/548] create asset datasets --- lib/bio_ind/fair_data/data_set.rb | 5 +++++ lib/bio_ind/fair_data/reader.rb | 11 ++++++++++- test/unit/bioind/fairdata/fair_data_reader_test.rb | 13 +++++++++++-- 3 files changed, 26 insertions(+), 3 deletions(-) diff --git a/lib/bio_ind/fair_data/data_set.rb b/lib/bio_ind/fair_data/data_set.rb index 5b2e750924..403cb8363b 100644 --- a/lib/bio_ind/fair_data/data_set.rb +++ b/lib/bio_ind/fair_data/data_set.rb @@ -1,6 +1,11 @@ module BioInd module FairData class DataSet < Base + + def title + "Dataset: #{identifier}" + end + end end end diff --git a/lib/bio_ind/fair_data/reader.rb b/lib/bio_ind/fair_data/reader.rb index a4a39c9acc..7db9099863 100644 --- a/lib/bio_ind/fair_data/reader.rb +++ b/lib/bio_ind/fair_data/reader.rb @@ -32,7 +32,16 @@ def self.construct_isa(datastation_inv, contributor, projects) study = investigation.studies.build(study_attributes) datastation_study.assays.each do |datastation_assay| assay_attributes = datastation_assay.seek_attributes.merge({contributor: contributor, study:studies.last, assay_class: AssayClass.experimental}) - study.assays.build(assay_attributes) + assay = study.assays.build(assay_attributes) + datastation_assay.datasets.each do |datastation_dataset| + blob = ContentBlob.new(url: datastation_dataset.resource_uri.to_s, original_filename: datastation_dataset.identifier ) + data_file_attributes = datastation_dataset.seek_attributes.merge({ + contributor: contributor, projects: projects, + content_blob: blob + }) + df = DataFile.new(data_file_attributes) + assay.assay_assets.build(asset: df) + end end end diff --git a/test/unit/bioind/fairdata/fair_data_reader_test.rb b/test/unit/bioind/fairdata/fair_data_reader_test.rb index 746a985c0a..4432235f38 100644 --- a/test/unit/bioind/fairdata/fair_data_reader_test.rb +++ b/test/unit/bioind/fairdata/fair_data_reader_test.rb @@ -104,9 +104,11 @@ class FairDataReaderTest < ActiveSupport::TestCase investigation = BioInd::FairData::Reader.construct_isa(inv, contributor, [project]) studies = investigation.studies.to_a assays = studies.first.assays.to_a + data_files = assays.first.assay_assets.to_a.collect(&:asset) assert_equal 1, studies.count assert_equal 9, assays.count + assert_equal 2, data_files.count assert investigation.valid? assert studies.first.valid? @@ -114,11 +116,18 @@ class FairDataReaderTest < ActiveSupport::TestCase pp assays.first.errors unless assays.first.valid? assert assays.first.valid? + pp data_files.first.errors unless data_files.first.valid? + assert data_files.first.valid? + assert_difference('Investigation.count',1) do assert_difference('Study.count',1) do assert_difference('Assay.count', 9) do - User.with_current_user(contributor.user) do - investigation.save! + assert_difference('AssayAsset.count', 18) do + assert_difference('DataFile.count', 18) do + User.with_current_user(contributor.user) do + investigation.save! + end + end end end end From 40d14d5cdb920a457f766883067310127d616675 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 5 Mar 2024 16:36:41 +0000 Subject: [PATCH 009/548] minor tweak to submit page --- .../projects/import_from_fairdata_station.html.erb | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/app/views/projects/import_from_fairdata_station.html.erb b/app/views/projects/import_from_fairdata_station.html.erb index 7a4b3111d9..25330ce5cf 100644 --- a/app/views/projects/import_from_fairdata_station.html.erb +++ b/app/views/projects/import_from_fairdata_station.html.erb @@ -1,10 +1,11 @@ <%= render :partial => "general/page_title",:locals=>{:title=>"Import ISA from FAIRData Station for #{ t('Project') } #{link_to(@project.title, @project)}".html_safe} %> <%= form_tag submit_fairdata_station_project_path(@project), multipart: true do %> -

    - +

    + <%= file_field_tag "datastation_data" -%> - - <%= submit_tag("Submit") %> -

    +
    +
    + <%= submit_tag("Submit", class:'btn btn-primary') %> +
    <% end %> \ No newline at end of file From 4da99111dad599826f27e8057710d97c2949c11a Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Wed, 6 Mar 2024 11:18:12 +0000 Subject: [PATCH 010/548] add property type id to extended metadata attributes, to store the annotation predicate for matching --- ...0306111347_add_extended_metadata_attribute_property_id.rb | 5 +++++ db/schema.rb | 3 ++- 2 files changed, 7 insertions(+), 1 deletion(-) create mode 100644 db/migrate/20240306111347_add_extended_metadata_attribute_property_id.rb diff --git a/db/migrate/20240306111347_add_extended_metadata_attribute_property_id.rb b/db/migrate/20240306111347_add_extended_metadata_attribute_property_id.rb new file mode 100644 index 0000000000..439dd80536 --- /dev/null +++ b/db/migrate/20240306111347_add_extended_metadata_attribute_property_id.rb @@ -0,0 +1,5 @@ +class AddExtendedMetadataAttributePropertyId < ActiveRecord::Migration[6.1] + def change + add_column :extended_metadata_attributes, :property_type_id, :string + end +end diff --git a/db/schema.rb b/db/schema.rb index 7cb9c06a08..ed363aad2f 100644 --- a/db/schema.rb +++ b/db/schema.rb @@ -10,7 +10,7 @@ # # It's strongly recommended that you check this file into your version control system. -ActiveRecord::Schema.define(version: 2024_02_12_145449) do +ActiveRecord::Schema.define(version: 2024_03_06_111347) do create_table "activity_logs", id: :integer, force: :cascade do |t| t.string "action" @@ -637,6 +637,7 @@ t.string "label" t.integer "linked_extended_metadata_type_id" t.boolean "allow_cv_free_text", default: false + t.string "property_type_id" t.index ["extended_metadata_type_id"], name: "index_extended_metadata_attributes_on_extended_metadata_type_id" t.index ["sample_attribute_type_id"], name: "index_extended_metadata_attributes_on_sample_attribute_type_id" t.index ["sample_controlled_vocab_id"], name: "index_extended_metadata_attributes_on_sample_cv_id" From f4ee41ee25ad7c70aa0254d681ae5905882f0a32 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Wed, 6 Mar 2024 11:42:34 +0000 Subject: [PATCH 011/548] seeded Study extended metadata --- .../fairdatastation_virtual_demo.seeds.rb | 13 +++++++++++++ test/unit/bioind/fairdata/fair_data_reader_test.rb | 9 +++++++++ 2 files changed, 22 insertions(+) create mode 100644 db/seeds/extended_metadata_drafts/fairdatastation_virtual_demo.seeds.rb diff --git a/db/seeds/extended_metadata_drafts/fairdatastation_virtual_demo.seeds.rb b/db/seeds/extended_metadata_drafts/fairdatastation_virtual_demo.seeds.rb new file mode 100644 index 0000000000..46e5ae52f2 --- /dev/null +++ b/db/seeds/extended_metadata_drafts/fairdatastation_virtual_demo.seeds.rb @@ -0,0 +1,13 @@ +unless ExtendedMetadataType.where(title:'Fair Data Station Virtual Demo', supported_type:'Study').any? + emt = ExtendedMetadataType.new(title: 'Fair Data Station Virtual Demo', supported_type:'Study') + + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Centre Name', property_type_id:'http://fairbydesign.nl/ontology/center_name', sample_attribute_type: SampleAttributeType.where(title:'String').first) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Centre Project Name', property_type_id:'http://fairbydesign.nl/ontology/center_project_name', sample_attribute_type: SampleAttributeType.where(title:'String').first) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'External Ids', property_type_id:'http://fairbydesign.nl/ontology/external_ids', sample_attribute_type: SampleAttributeType.where(title:'String').first) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Submission Accession', property_type_id:'http://fairbydesign.nl/ontology/submission_accession', sample_attribute_type: SampleAttributeType.where(title:'String').first) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Submission Alias', property_type_id:'http://fairbydesign.nl/ontology/submission_alias', sample_attribute_type: SampleAttributeType.where(title:'String').first) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Submission Lab Name', property_type_id:'http://fairbydesign.nl/ontology/submission_accession', sample_attribute_type: SampleAttributeType.where(title:'String').first) + + emt.save! + puts 'Fair Data Station Virtual Demo' +end \ No newline at end of file diff --git a/test/unit/bioind/fairdata/fair_data_reader_test.rb b/test/unit/bioind/fairdata/fair_data_reader_test.rb index 4432235f38..b76f31cac6 100644 --- a/test/unit/bioind/fairdata/fair_data_reader_test.rb +++ b/test/unit/bioind/fairdata/fair_data_reader_test.rb @@ -34,6 +34,15 @@ class FairDataReaderTest < ActiveSupport::TestCase assert_equal 'DRR243856', assay.identifier end + test 'annotations' do + path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" + + study = BioInd::FairData::Reader.parse_graph(path).first.studies.first + + assert_equal 14, study.annotations.count + assert_includes study.annotations, ["http://fairbydesign.nl/ontology/center_name", "NIID"] + end + test 'study assays' do path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" From 5a241da12b370c7455a700249642406f0e593009 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Wed, 6 Mar 2024 15:53:02 +0000 Subject: [PATCH 012/548] populate extended metadata for study --- .../fairdatastation_virtual_demo.seeds.rb | 2 +- lib/bio_ind/fair_data/base.rb | 14 ++++++++ lib/bio_ind/fair_data/reader.rb | 4 +++ test/factories/extended_metadata_types.rb | 20 +++++++++++ .../bioind/fairdata/fair_data_reader_test.rb | 33 +++++++++++++++++-- 5 files changed, 69 insertions(+), 4 deletions(-) diff --git a/db/seeds/extended_metadata_drafts/fairdatastation_virtual_demo.seeds.rb b/db/seeds/extended_metadata_drafts/fairdatastation_virtual_demo.seeds.rb index 46e5ae52f2..595c3d6808 100644 --- a/db/seeds/extended_metadata_drafts/fairdatastation_virtual_demo.seeds.rb +++ b/db/seeds/extended_metadata_drafts/fairdatastation_virtual_demo.seeds.rb @@ -6,7 +6,7 @@ emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'External Ids', property_type_id:'http://fairbydesign.nl/ontology/external_ids', sample_attribute_type: SampleAttributeType.where(title:'String').first) emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Submission Accession', property_type_id:'http://fairbydesign.nl/ontology/submission_accession', sample_attribute_type: SampleAttributeType.where(title:'String').first) emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Submission Alias', property_type_id:'http://fairbydesign.nl/ontology/submission_alias', sample_attribute_type: SampleAttributeType.where(title:'String').first) - emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Submission Lab Name', property_type_id:'http://fairbydesign.nl/ontology/submission_accession', sample_attribute_type: SampleAttributeType.where(title:'String').first) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Submission Lab Name', property_type_id:'http://fairbydesign.nl/ontology/submission_lab_name', sample_attribute_type: SampleAttributeType.where(title:'String').first) emt.save! puts 'Fair Data Station Virtual Demo' diff --git a/lib/bio_ind/fair_data/base.rb b/lib/bio_ind/fair_data/base.rb index 94d78d00c4..3180fd0c8a 100644 --- a/lib/bio_ind/fair_data/base.rb +++ b/lib/bio_ind/fair_data/base.rb @@ -79,6 +79,20 @@ def fetch_children def seek_attributes {title: title, description: description} end + + def populate_extended_metadata(seek_resource) + extended_metadata_type = seek_resource.extended_metadata.extended_metadata_type + data = {} + annotations.each do |annotation| + property = annotation[0] + value = annotation[1] + attribute = extended_metadata_type.extended_metadata_attributes.where(property_type_id: property).first + if attribute + data[attribute.title] = value + end + end + seek_resource.extended_metadata.data = data + end end end end diff --git a/lib/bio_ind/fair_data/reader.rb b/lib/bio_ind/fair_data/reader.rb index 7db9099863..6f03a83dc1 100644 --- a/lib/bio_ind/fair_data/reader.rb +++ b/lib/bio_ind/fair_data/reader.rb @@ -30,6 +30,10 @@ def self.construct_isa(datastation_inv, contributor, projects) datastation_inv.studies.each do |datastation_study| study_attributes = datastation_study.seek_attributes.merge({contributor: contributor, investigation: investigation}) study = investigation.studies.build(study_attributes) + if emt = ExtendedMetadataType.where(title:'Fair Data Station Virtual Demo', supported_type: 'Study').first + study.extended_metadata = ExtendedMetadata.new(extended_metadata_type: emt) + datastation_study.populate_extended_metadata(study) + end datastation_study.assays.each do |datastation_assay| assay_attributes = datastation_assay.seek_attributes.merge({contributor: contributor, study:studies.last, assay_class: AssayClass.experimental}) assay = study.assays.build(assay_attributes) diff --git a/test/factories/extended_metadata_types.rb b/test/factories/extended_metadata_types.rb index 9cd6bf75a3..7d62f786fe 100644 --- a/test/factories/extended_metadata_types.rb +++ b/test/factories/extended_metadata_types.rb @@ -385,6 +385,8 @@ association :linked_extended_metadata_type, factory: :study_sites_extended_metadata_type end + + factory(:study_extended_metadata_type,class:ExtendedMetadataType) do title { 'study_model' } supported_type { 'Study' } @@ -394,5 +396,23 @@ end end + factory(:extended_metadata_attribute, class:ExtendedMetadataAttribute) do + + end + + factory(:fairdata_virtual_demo_study_extended_metadata, class: ExtendedMetadataType) do + title {'Fair Data Station Virtual Demo'} + supported_type { 'Study' } + after(:build) do |a| + a.extended_metadata_attributes << FactoryBot.create(:study_title_extended_metadata_attribute, title: 'Centre Name', property_type_id:'http://fairbydesign.nl/ontology/center_name') + a.extended_metadata_attributes << FactoryBot.create(:study_title_extended_metadata_attribute, title: 'Centre Project Name', property_type_id:'http://fairbydesign.nl/ontology/center_project_name') + a.extended_metadata_attributes << FactoryBot.create(:study_title_extended_metadata_attribute, title: 'External Ids', property_type_id:'http://fairbydesign.nl/ontology/external_ids') + a.extended_metadata_attributes << FactoryBot.create(:study_title_extended_metadata_attribute, title: 'Submission Accession', property_type_id:'http://fairbydesign.nl/ontology/submission_accession') + a.extended_metadata_attributes << FactoryBot.create(:study_title_extended_metadata_attribute, title: 'Submission Alias', property_type_id:'http://fairbydesign.nl/ontology/submission_alias') + a.extended_metadata_attributes << FactoryBot.create(:study_title_extended_metadata_attribute, title: 'Submission Lab Name', property_type_id:'http://fairbydesign.nl/ontology/submission_lab_name') + end + + end + end diff --git a/test/unit/bioind/fairdata/fair_data_reader_test.rb b/test/unit/bioind/fairdata/fair_data_reader_test.rb index b76f31cac6..31b169d546 100644 --- a/test/unit/bioind/fairdata/fair_data_reader_test.rb +++ b/test/unit/bioind/fairdata/fair_data_reader_test.rb @@ -77,7 +77,7 @@ class FairDataReaderTest < ActiveSupport::TestCase assert_equal 'sample DRS176892', sample.title assert_equal 'Sample obtained from Single age 30 collected on 2017-09-13 from the human gut', sample.description - assert_nil assay.title + assert_equal 'Assay - DRR243856', assay.title assert_equal 'Illumina MiSeq paired end sequencing of SAMD00244451', assay.description end @@ -128,8 +128,8 @@ class FairDataReaderTest < ActiveSupport::TestCase pp data_files.first.errors unless data_files.first.valid? assert data_files.first.valid? - assert_difference('Investigation.count',1) do - assert_difference('Study.count',1) do + assert_difference('Investigation.count', 1) do + assert_difference('Study.count', 1) do assert_difference('Assay.count', 9) do assert_difference('AssayAsset.count', 18) do assert_difference('DataFile.count', 18) do @@ -143,4 +143,31 @@ class FairDataReaderTest < ActiveSupport::TestCase end end + + test 'populate extended metadata' do + metadata_type = FactoryBot.create(:fairdata_virtual_demo_study_extended_metadata) + FactoryBot.create(:experimental_assay_class) + + path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" + inv = BioInd::FairData::Reader.parse_graph(path).first + contributor = FactoryBot.create(:person) + project = contributor.projects.first + + investigation = BioInd::FairData::Reader.construct_isa(inv, contributor, [project]) + study = investigation.studies.to_a.first + refute_nil study.extended_metadata + assert_equal metadata_type, study.extended_metadata.extended_metadata_type + + assert_equal 'NIID', study.extended_metadata.get_attribute_value('Centre Name') + assert_equal 'human gut metagenome', study.extended_metadata.get_attribute_value('Centre Project Name') + assert_equal 'PRJDB10485', study.extended_metadata.get_attribute_value('External Ids') + assert_equal 'DRA010770', study.extended_metadata.get_attribute_value('Submission Accession') + assert_equal 'DRA010770', study.extended_metadata.get_attribute_value('Submission Alias') + assert_equal 'AIDS Research Center2022-8-31', study.extended_metadata.get_attribute_value('Submission Lab Name') + assert_difference('ExtendedMetadata.count', 1) do + User.with_current_user(contributor.user) do + study.save! + end + end + end end From 28c05e2d7e9227d0616f0a7147215da9b35fa1a1 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Wed, 6 Mar 2024 16:29:48 +0000 Subject: [PATCH 013/548] populate extended metadata for assay --- .../fairdatastation_virtual_demo.seeds.rb | 22 +++++++++++++++++- lib/bio_ind/fair_data/reader.rb | 4 ++++ test/factories/extended_metadata_types.rb | 12 ++++++++++ .../bioind/fairdata/fair_data_reader_test.rb | 23 +++++++++++++++---- 4 files changed, 56 insertions(+), 5 deletions(-) diff --git a/db/seeds/extended_metadata_drafts/fairdatastation_virtual_demo.seeds.rb b/db/seeds/extended_metadata_drafts/fairdatastation_virtual_demo.seeds.rb index 595c3d6808..bf343c7a07 100644 --- a/db/seeds/extended_metadata_drafts/fairdatastation_virtual_demo.seeds.rb +++ b/db/seeds/extended_metadata_drafts/fairdatastation_virtual_demo.seeds.rb @@ -9,5 +9,25 @@ emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Submission Lab Name', property_type_id:'http://fairbydesign.nl/ontology/submission_lab_name', sample_attribute_type: SampleAttributeType.where(title:'String').first) emt.save! - puts 'Fair Data Station Virtual Demo' + puts 'Fair Data Station Virtual Demo for Study' +end + +unless ExtendedMetadataType.where(title:'Fair Data Station Virtual Demo', supported_type:'Assay').any? + emt = ExtendedMetadataType.new(title: 'Fair Data Station Virtual Demo', supported_type:'Assay') + + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Facility', property_type_id:'http://fairbydesign.nl/ontology/facility', sample_attribute_type: SampleAttributeType.where(title:'String').first) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Forward Primer', property_type_id:'http://fairbydesign.nl/ontology/forwardPrimer', sample_attribute_type: SampleAttributeType.where(title:'String').first) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Instrument Model', property_type_id:'http://fairbydesign.nl/ontology/instrument_model', sample_attribute_type: SampleAttributeType.where(title:'String').first) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Library Selection', property_type_id:'http://fairbydesign.nl/ontology/library_selection', sample_attribute_type: SampleAttributeType.where(title:'String').first) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Library Source', property_type_id:'http://fairbydesign.nl/ontology/library_source', sample_attribute_type: SampleAttributeType.where(title:'String').first) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Library Strategy', property_type_id:'http://fairbydesign.nl/ontology/library_strategy', sample_attribute_type: SampleAttributeType.where(title:'String').first) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Package Name', property_type_id:'http://fairbydesign.nl/ontology/packageName', sample_attribute_type: SampleAttributeType.where(title:'String').first) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Platform', property_type_id:'http://fairbydesign.nl/ontology/platform', sample_attribute_type: SampleAttributeType.where(title:'String').first) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Primer Names', property_type_id:'http://fairbydesign.nl/ontology/primerNames', sample_attribute_type: SampleAttributeType.where(title:'String').first) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Protocol', property_type_id:'http://fairbydesign.nl/ontology/protocol', sample_attribute_type: SampleAttributeType.where(title:'String').first) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Reverse Primer', property_type_id:'http://fairbydesign.nl/ontology/reversePrimer', sample_attribute_type: SampleAttributeType.where(title:'String').first) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Target Subfragment', property_type_id:'http://fairbydesign.nl/ontology/target_subfragment', sample_attribute_type: SampleAttributeType.where(title:'String').first) + + emt.save! + puts 'Fair Data Station Virtual Demo for Assay' end \ No newline at end of file diff --git a/lib/bio_ind/fair_data/reader.rb b/lib/bio_ind/fair_data/reader.rb index 6f03a83dc1..4641919ff2 100644 --- a/lib/bio_ind/fair_data/reader.rb +++ b/lib/bio_ind/fair_data/reader.rb @@ -37,6 +37,10 @@ def self.construct_isa(datastation_inv, contributor, projects) datastation_study.assays.each do |datastation_assay| assay_attributes = datastation_assay.seek_attributes.merge({contributor: contributor, study:studies.last, assay_class: AssayClass.experimental}) assay = study.assays.build(assay_attributes) + if emt = ExtendedMetadataType.where(title:'Fair Data Station Virtual Demo', supported_type: 'Assay').first + assay.extended_metadata = ExtendedMetadata.new(extended_metadata_type: emt) + datastation_assay.populate_extended_metadata(assay) + end datastation_assay.datasets.each do |datastation_dataset| blob = ContentBlob.new(url: datastation_dataset.resource_uri.to_s, original_filename: datastation_dataset.identifier ) data_file_attributes = datastation_dataset.seek_attributes.merge({ diff --git a/test/factories/extended_metadata_types.rb b/test/factories/extended_metadata_types.rb index 7d62f786fe..497d03e2fe 100644 --- a/test/factories/extended_metadata_types.rb +++ b/test/factories/extended_metadata_types.rb @@ -411,7 +411,19 @@ a.extended_metadata_attributes << FactoryBot.create(:study_title_extended_metadata_attribute, title: 'Submission Alias', property_type_id:'http://fairbydesign.nl/ontology/submission_alias') a.extended_metadata_attributes << FactoryBot.create(:study_title_extended_metadata_attribute, title: 'Submission Lab Name', property_type_id:'http://fairbydesign.nl/ontology/submission_lab_name') end + end + factory(:fairdata_virtual_demo_assay_extended_metadata, class: ExtendedMetadataType) do + title {'Fair Data Station Virtual Demo'} + supported_type { 'Assay' } + after(:build) do |a| + a.extended_metadata_attributes << FactoryBot.create(:study_title_extended_metadata_attribute, title: 'Facility', property_type_id:'http://fairbydesign.nl/ontology/facility') + a.extended_metadata_attributes << FactoryBot.create(:study_title_extended_metadata_attribute, title: 'Forward Primer', property_type_id:'http://fairbydesign.nl/ontology/forwardPrimer') + a.extended_metadata_attributes << FactoryBot.create(:study_title_extended_metadata_attribute, title: 'Instrument Model', property_type_id:'http://fairbydesign.nl/ontology/instrument_model') + a.extended_metadata_attributes << FactoryBot.create(:study_title_extended_metadata_attribute, title: 'Library Selection', property_type_id:'http://fairbydesign.nl/ontology/library_selection') + a.extended_metadata_attributes << FactoryBot.create(:study_title_extended_metadata_attribute, title: 'Library Source', property_type_id:'http://fairbydesign.nl/ontology/library_source') + a.extended_metadata_attributes << FactoryBot.create(:study_title_extended_metadata_attribute, title: 'Library Strategy', property_type_id:'http://fairbydesign.nl/ontology/library_strategy') + end end end diff --git a/test/unit/bioind/fairdata/fair_data_reader_test.rb b/test/unit/bioind/fairdata/fair_data_reader_test.rb index 31b169d546..1d5613106d 100644 --- a/test/unit/bioind/fairdata/fair_data_reader_test.rb +++ b/test/unit/bioind/fairdata/fair_data_reader_test.rb @@ -63,6 +63,8 @@ class FairDataReaderTest < ActiveSupport::TestCase sample = obs_unit.samples.first assay = sample.assays.first + assay.pp_annotations + assert_equal 'HIV-1 infected individuals in Ghana', inv.title assert_equal 'Exploration of HIV-1 infected individuals in Ghana', inv.description @@ -145,7 +147,8 @@ class FairDataReaderTest < ActiveSupport::TestCase end test 'populate extended metadata' do - metadata_type = FactoryBot.create(:fairdata_virtual_demo_study_extended_metadata) + study_metadata_type = FactoryBot.create(:fairdata_virtual_demo_study_extended_metadata) + assay_metadata_type = FactoryBot.create(:fairdata_virtual_demo_assay_extended_metadata) FactoryBot.create(:experimental_assay_class) path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" @@ -154,9 +157,9 @@ class FairDataReaderTest < ActiveSupport::TestCase project = contributor.projects.first investigation = BioInd::FairData::Reader.construct_isa(inv, contributor, [project]) - study = investigation.studies.to_a.first + study = investigation.studies.first refute_nil study.extended_metadata - assert_equal metadata_type, study.extended_metadata.extended_metadata_type + assert_equal study_metadata_type, study.extended_metadata.extended_metadata_type assert_equal 'NIID', study.extended_metadata.get_attribute_value('Centre Name') assert_equal 'human gut metagenome', study.extended_metadata.get_attribute_value('Centre Project Name') @@ -164,7 +167,19 @@ class FairDataReaderTest < ActiveSupport::TestCase assert_equal 'DRA010770', study.extended_metadata.get_attribute_value('Submission Accession') assert_equal 'DRA010770', study.extended_metadata.get_attribute_value('Submission Alias') assert_equal 'AIDS Research Center2022-8-31', study.extended_metadata.get_attribute_value('Submission Lab Name') - assert_difference('ExtendedMetadata.count', 1) do + + assay = study.assays.first + refute_nil assay.extended_metadata + assert_equal assay_metadata_type, assay.extended_metadata.extended_metadata_type + + assert_equal 'NMIMR', assay.extended_metadata.get_attribute_value('Facility') + assert_equal 'CCTACGGGNGGCWGCAG', assay.extended_metadata.get_attribute_value('Forward Primer') + assert_equal 'Illumina MiSeq', assay.extended_metadata.get_attribute_value('Instrument Model') + assert_equal 'PCR', assay.extended_metadata.get_attribute_value('Library Selection') + assert_equal 'METAGENOMIC', assay.extended_metadata.get_attribute_value('Library Source') + assert_equal 'AMPLICON', assay.extended_metadata.get_attribute_value('Library Strategy') + + assert_difference('ExtendedMetadata.count', 10) do User.with_current_user(contributor.user) do study.save! end From c867f8ff1e20aa5925e6317125f8bc9e9e965b26 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Wed, 6 Mar 2024 16:45:39 +0000 Subject: [PATCH 014/548] show attribute property_type_id in the api --- app/serializers/extended_metadata_type_serializer.rb | 1 + 1 file changed, 1 insertion(+) diff --git a/app/serializers/extended_metadata_type_serializer.rb b/app/serializers/extended_metadata_type_serializer.rb index 36b251edba..9ec5a8bcb9 100644 --- a/app/serializers/extended_metadata_type_serializer.rb +++ b/app/serializers/extended_metadata_type_serializer.rb @@ -13,6 +13,7 @@ def get_extended_metadata_attribute(attribute) "id": attribute.id.to_s, "title": attribute.title, "label": attribute.label, + "property_type_id": attribute.property_type_id, "description":attribute.description, "sample_attribute_type": get_sample_attribute_type(attribute), "required": attribute.required, From 2ca7e7757496031f5be5889a20e5dbe6575cc0d5 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 12 Mar 2024 13:58:46 +0000 Subject: [PATCH 015/548] some refactoring --- lib/bio_ind/fair_data/base.rb | 10 +- lib/bio_ind/fair_data/reader.rb | 27 +- .../files/fairdatastation/indpensim.ttl | 1896 +++++++++++++++++ .../bioind/fairdata/fair_data_reader_test.rb | 15 +- 4 files changed, 1934 insertions(+), 14 deletions(-) create mode 100644 test/fixtures/files/fairdatastation/indpensim.ttl diff --git a/lib/bio_ind/fair_data/base.rb b/lib/bio_ind/fair_data/base.rb index 3180fd0c8a..e237c6791e 100644 --- a/lib/bio_ind/fair_data/base.rb +++ b/lib/bio_ind/fair_data/base.rb @@ -34,6 +34,14 @@ def annotations end end + def metadata_annotations + annotations.select do |annotation| + [@schema.title, @schema.description, @schema.identifier, @jerm.hasPart, RDF.type].detect do |skip| + annotation[0].start_with?(skip) + end.nil? + end + end + def find_annotation_value(property) annotations.detect do |ann| ann[0] == property @@ -83,7 +91,7 @@ def seek_attributes def populate_extended_metadata(seek_resource) extended_metadata_type = seek_resource.extended_metadata.extended_metadata_type data = {} - annotations.each do |annotation| + metadata_annotations.each do |annotation| property = annotation[0] value = annotation[1] attribute = extended_metadata_type.extended_metadata_attributes.where(property_type_id: property).first diff --git a/lib/bio_ind/fair_data/reader.rb b/lib/bio_ind/fair_data/reader.rb index 4641919ff2..c4382d4469 100644 --- a/lib/bio_ind/fair_data/reader.rb +++ b/lib/bio_ind/fair_data/reader.rb @@ -24,23 +24,16 @@ def self.parse_graph(path) def self.construct_isa(datastation_inv, contributor, projects) inv_attributes = datastation_inv.seek_attributes.merge({contributor: contributor, projects: projects}) investigation = ::Investigation.new(inv_attributes) - studies = [] - assays = [] + populate_extended_metadata(investigation, datastation_inv) datastation_inv.studies.each do |datastation_study| study_attributes = datastation_study.seek_attributes.merge({contributor: contributor, investigation: investigation}) study = investigation.studies.build(study_attributes) - if emt = ExtendedMetadataType.where(title:'Fair Data Station Virtual Demo', supported_type: 'Study').first - study.extended_metadata = ExtendedMetadata.new(extended_metadata_type: emt) - datastation_study.populate_extended_metadata(study) - end + populate_extended_metadata(study, datastation_study) datastation_study.assays.each do |datastation_assay| - assay_attributes = datastation_assay.seek_attributes.merge({contributor: contributor, study:studies.last, assay_class: AssayClass.experimental}) + assay_attributes = datastation_assay.seek_attributes.merge({contributor: contributor, study:study, assay_class: AssayClass.experimental}) assay = study.assays.build(assay_attributes) - if emt = ExtendedMetadataType.where(title:'Fair Data Station Virtual Demo', supported_type: 'Assay').first - assay.extended_metadata = ExtendedMetadata.new(extended_metadata_type: emt) - datastation_assay.populate_extended_metadata(assay) - end + populate_extended_metadata(assay, datastation_assay) datastation_assay.datasets.each do |datastation_dataset| blob = ContentBlob.new(url: datastation_dataset.resource_uri.to_s, original_filename: datastation_dataset.identifier ) data_file_attributes = datastation_dataset.seek_attributes.merge({ @@ -55,6 +48,18 @@ def self.construct_isa(datastation_inv, contributor, projects) return investigation end + + def self.populate_extended_metadata(seek_entity, datastation_entity) + if emt = detect_extended_metadata(seek_entity, datastation_entity) + seek_entity.extended_metadata = ExtendedMetadata.new(extended_metadata_type: emt) + datastation_entity.populate_extended_metadata(seek_entity) + end + end + + def self.detect_extended_metadata(seek_entity, datastation_entity) + ExtendedMetadataType.where(title:'Fair Data Station Virtual Demo', supported_type: seek_entity.class.name).first + end + end end end diff --git a/test/fixtures/files/fairdatastation/indpensim.ttl b/test/fixtures/files/fairdatastation/indpensim.ttl new file mode 100644 index 0000000000..1e2cdc3f3d --- /dev/null +++ b/test/fixtures/files/fairdatastation/indpensim.ttl @@ -0,0 +1,1896 @@ +@prefix base: . +@prefix bibo: . +@prefix dc: . +@prefix dcmitype: . +@prefix empusa: . +@prefix fair: . +@prefix foaf: . +@prefix gbol: . +@prefix jerm: . +@prefix mixs: . +@prefix owl: . +@prefix ppeo: . +@prefix prov: . +@prefix rdf: . +@prefix rdfs: . +@prefix sample: . +@prefix schema: . +@prefix sschema: . +@prefix uniprot: . +@prefix unlock: . +@prefix void: . +@prefix wd: . +@prefix wdt: . +@prefix wv: . +@prefix xml: . +@prefix xsd: . + +fair:inv_indpensim rdf:type jerm:Investigation ; + jerm:hasPart ; + schema:contributor , ; + schema:description "Industrial-scale penicillin simulation (IndPenSim) is a first principles mathematical model of a Penicillium chrysogenum fermentation. The simulation was developed in Matlab and is freely available to download. The development of the simulation is discussed in the paper titled \"The development of an industrial-scale fed-batch fermentation simulation\" currently available to download: here (Journal of Biotechnology). The paper has recently been extended which include the addition of a simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. The capabilities of IndPenSim are demonstrated through the implementation of a QbD methodology utilising the three stages of the PAT framework. Additionally, IndPenSimevaluated a fault detection algorithm to detect process faults occurring on different batches recorded throughout a yearly campaign. Details of this work can be found in the paper titled: 'Modern day monitoring and control challenges outlined on an industrial-scale benchmark fermentation process'" ; + schema:identifier "indpensim" ; + schema:title "Industrial pencilin simulator" . + + + rdf:type schema:Person ; + base:orcid ; + schema:department "SSB" ; + schema:email ; + schema:familyName "Koehorst" ; + schema:givenName "Jasper Koehorst" ; + schema:memberOf . + + + rdf:type schema:Organization ; + schema:legalName "WUR" . + +schema:identifier rdf:type rdf:Property ; + rdfs:label "investigation identifier" ; + schema:description "Identifier corresponding to the investigation" ; + schema:valuePattern "^[a-zA-Z0-9-_]*${5,25}" ; + schema:valueRequired true . + +schema:description rdf:type rdf:Property ; + rdfs:label "investigation description" ; + schema:description "Description of the investigation" ; + schema:valuePattern ".*{50,}" ; + schema:valueRequired true . + +schema:title rdf:type rdf:Property ; + rdfs:label "investigation title" ; + schema:description "Title describing the investigation" ; + schema:valuePattern ".*{10,}" ; + schema:valueRequired true . + + + rdf:type schema:Person ; + base:orcid ; + schema:department "SSB" ; + schema:email ; + schema:familyName "Metcalfe" ; + schema:givenName "Brett Metcalfe" ; + schema:memberOf . + + + rdf:type jerm:Study ; + jerm:hasPart , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; + schema:description "Modern day monitoring and control challenges outlined on an industrial-scale benchmark fermentation process" ; + schema:identifier "Penicillin_production" ; + schema:title "Penicillin production" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_1" ; + schema:name "Controlled by recipe driven approach of run IndPenSim_V3_Batch_1" . + +schema:name rdf:type rdf:Property ; + rdfs:label "observation unit name" ; + schema:description "Name of the entity being observed" ; + schema:valuePattern ".*{10,}" ; + schema:valueRequired true . + +fair:volume rdf:type rdf:Property ; + rdfs:label "volume" ; + schema:valuePattern ".+" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_1.csv.gz" . + +fair:file rdf:type rdf:Property ; + rdfs:label "file" ; + schema:description "Filename or the path of a file" ; + schema:valuePattern ".*" ; + schema:valueRequired false . + +uniprot:organism rdf:type rdf:Property ; + rdfs:label "ncbi taxonomy id" ; + schema:description "Taxonomic identifier of the sample according to https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi for example use 2582415 for a blank sample or 1510822 for pig metagenome" ; + schema:valuePattern "\\d+" ; + schema:valueRequired false . + +gbol:scientificName rdf:type rdf:Property ; + rdfs:label "scientific name" ; + schema:description "Name of the organism" ; + schema:valuePattern ".*" ; + schema:valueRequired false . + +fair:fermentation rdf:type rdf:Property ; + rdfs:label "fermentation" ; + schema:valuePattern ".+" . + +fair:brand rdf:type rdf:Property ; + rdfs:label "brand" ; + schema:valuePattern ".+" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_2" ; + schema:name "Controlled by recipe driven approach of run IndPenSim_V3_Batch_2" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_2.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_3" ; + schema:name "Controlled by recipe driven approach of run IndPenSim_V3_Batch_3" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_3.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_4" ; + schema:name "Controlled by recipe driven approach of run IndPenSim_V3_Batch_4" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_4.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_5" ; + schema:name "Controlled by recipe driven approach of run IndPenSim_V3_Batch_5" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_5.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_6" ; + schema:name "Controlled by recipe driven approach of run IndPenSim_V3_Batch_6" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_6.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:data_stream "https://influx.containers.wur.nl/orgs/a0e9709e32d01c3b" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_7" ; + schema:name "Controlled by recipe driven approach of run IndPenSim_V3_Batch_7" . + +fair:data_stream rdf:type rdf:Property ; + rdfs:label "data stream" ; + schema:valuePattern ".+" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_8" ; + schema:name "Controlled by recipe driven approach of run IndPenSim_V3_Batch_8" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_8.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_9" ; + schema:name "Controlled by recipe driven approach of run IndPenSim_V3_Batch_9" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_9.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_10" ; + schema:name "Controlled by recipe driven approach of run IndPenSim_V3_Batch_10" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_10.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_11" ; + schema:name "Controlled by recipe driven approach of run IndPenSim_V3_Batch_11" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_11.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_12" ; + schema:name "Controlled by recipe driven approach of run IndPenSim_V3_Batch_12" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_12.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_13" ; + schema:name "Controlled by recipe driven approach of run IndPenSim_V3_Batch_13" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_13.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:data_stream "https://influx.containers.wur.nl/orgs/a0e9709e32d01c3b" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_14" ; + schema:name "Controlled by recipe driven approach of run IndPenSim_V3_Batch_14" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_15" ; + schema:name "Controlled by recipe driven approach of run IndPenSim_V3_Batch_15" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_15.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_16" ; + schema:name "Controlled by recipe driven approach of run IndPenSim_V3_Batch_16" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_16.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_17" ; + schema:name "Controlled by recipe driven approach of run IndPenSim_V3_Batch_17" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_17.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_18" ; + schema:name "Controlled by recipe driven approach of run IndPenSim_V3_Batch_18" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_18.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_19" ; + schema:name "Controlled by recipe driven approach of run IndPenSim_V3_Batch_19" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_19.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_20" ; + schema:name "Controlled by recipe driven approach of run IndPenSim_V3_Batch_20" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_20.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_21" ; + schema:name "Controlled by recipe driven approach of run IndPenSim_V3_Batch_21" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_21.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_22" ; + schema:name "Controlled by recipe driven approach of run IndPenSim_V3_Batch_22" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_22.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:data_stream "https://influx.containers.wur.nl/orgs/a0e9709e32d01c3b" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_23" ; + schema:name "Controlled by recipe driven approach of run IndPenSim_V3_Batch_23" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_24" ; + schema:name "Controlled by recipe driven approach of run IndPenSim_V3_Batch_24" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_24.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_25" ; + schema:name "Controlled by recipe driven approach of run IndPenSim_V3_Batch_25" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_25.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_26" ; + schema:name "Controlled by recipe driven approach of run IndPenSim_V3_Batch_26" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_26.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_27" ; + schema:name "Controlled by recipe driven approach of run IndPenSim_V3_Batch_27" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_27.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_28" ; + schema:name "Controlled by recipe driven approach of run IndPenSim_V3_Batch_28" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_28.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_29" ; + schema:name "Controlled by recipe driven approach of run IndPenSim_V3_Batch_29" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_29.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_30" ; + schema:name "Controlled by recipe driven approach of run IndPenSim_V3_Batch_30" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_30.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:data_stream "https://influx.containers.wur.nl/orgs/a0e9709e32d01c3b" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_31" ; + schema:name "Controlled by operators of run IndPenSim_V3_Batch_31" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_32" ; + schema:name "Controlled by operators of run IndPenSim_V3_Batch_32" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_32.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_33" ; + schema:name "Controlled by operators of run IndPenSim_V3_Batch_33" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_33.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_34" ; + schema:name "Controlled by operators of run IndPenSim_V3_Batch_34" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_34.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_35" ; + schema:name "Controlled by operators of run IndPenSim_V3_Batch_35" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_35.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_36" ; + schema:name "Controlled by operators of run IndPenSim_V3_Batch_36" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_36.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_37" ; + schema:name "Controlled by operators of run IndPenSim_V3_Batch_37" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_37.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_38" ; + schema:name "Controlled by operators of run IndPenSim_V3_Batch_38" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_38.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_39" ; + schema:name "Controlled by operators of run IndPenSim_V3_Batch_39" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_39.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_40" ; + schema:name "Controlled by operators of run IndPenSim_V3_Batch_40" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_40.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_41" ; + schema:name "Controlled by operators of run IndPenSim_V3_Batch_41" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_41.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_42" ; + schema:name "Controlled by operators of run IndPenSim_V3_Batch_42" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_42.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_43" ; + schema:name "Controlled by operators of run IndPenSim_V3_Batch_43" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_43.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_44" ; + schema:name "Controlled by operators of run IndPenSim_V3_Batch_44" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_44.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_45" ; + schema:name "Controlled by operators of run IndPenSim_V3_Batch_45" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_45.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_46" ; + schema:name "Controlled by operators of run IndPenSim_V3_Batch_46" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_46.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_47" ; + schema:name "Controlled by operators of run IndPenSim_V3_Batch_47" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_47.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_48" ; + schema:name "Controlled by operators of run IndPenSim_V3_Batch_48" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_48.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_49" ; + schema:name "Controlled by operators of run IndPenSim_V3_Batch_49" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_49.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_50" ; + schema:name "Controlled by operators of run IndPenSim_V3_Batch_50" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_50.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_51" ; + schema:name "Controlled by operators of run IndPenSim_V3_Batch_51" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_51.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_52" ; + schema:name "Controlled by operators of run IndPenSim_V3_Batch_52" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_52.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_53" ; + schema:name "Controlled by operators of run IndPenSim_V3_Batch_53" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_53.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_54" ; + schema:name "Controlled by operators of run IndPenSim_V3_Batch_54" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_54.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_55" ; + schema:name "Controlled by operators of run IndPenSim_V3_Batch_55" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_55.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_56" ; + schema:name "Controlled by operators of run IndPenSim_V3_Batch_56" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_56.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_57" ; + schema:name "Controlled by operators of run IndPenSim_V3_Batch_57" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_57.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_58" ; + schema:name "Controlled by operators of run IndPenSim_V3_Batch_58" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_58.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_59" ; + schema:name "Controlled by operators of run IndPenSim_V3_Batch_59" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_59.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_60" ; + schema:name "Controlled by operators of run IndPenSim_V3_Batch_60" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_60.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_61" ; + schema:name "Controlled by an Advanced Process Control (APC) solution using the Raman spectroscopy of run IndPenSim_V3_Batch_61" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_61.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_62" ; + schema:name "Controlled by an Advanced Process Control (APC) solution using the Raman spectroscopy of run IndPenSim_V3_Batch_62" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_62.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_63" ; + schema:name "Controlled by an Advanced Process Control (APC) solution using the Raman spectroscopy of run IndPenSim_V3_Batch_63" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_63.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_64" ; + schema:name "Controlled by an Advanced Process Control (APC) solution using the Raman spectroscopy of run IndPenSim_V3_Batch_64" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_64.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_65" ; + schema:name "Controlled by an Advanced Process Control (APC) solution using the Raman spectroscopy of run IndPenSim_V3_Batch_65" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_65.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_66" ; + schema:name "Controlled by an Advanced Process Control (APC) solution using the Raman spectroscopy of run IndPenSim_V3_Batch_66" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_66.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_67" ; + schema:name "Controlled by an Advanced Process Control (APC) solution using the Raman spectroscopy of run IndPenSim_V3_Batch_67" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_67.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_68" ; + schema:name "Controlled by an Advanced Process Control (APC) solution using the Raman spectroscopy of run IndPenSim_V3_Batch_68" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_68.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_69" ; + schema:name "Controlled by an Advanced Process Control (APC) solution using the Raman spectroscopy of run IndPenSim_V3_Batch_69" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_69.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_70" ; + schema:name "Controlled by an Advanced Process Control (APC) solution using the Raman spectroscopy of run IndPenSim_V3_Batch_70" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_70.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_71" ; + schema:name "Controlled by an Advanced Process Control (APC) solution using the Raman spectroscopy of run IndPenSim_V3_Batch_71" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_71.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_72" ; + schema:name "Controlled by an Advanced Process Control (APC) solution using the Raman spectroscopy of run IndPenSim_V3_Batch_72" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_72.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_73" ; + schema:name "Controlled by an Advanced Process Control (APC) solution using the Raman spectroscopy of run IndPenSim_V3_Batch_73" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_73.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_74" ; + schema:name "Controlled by an Advanced Process Control (APC) solution using the Raman spectroscopy of run IndPenSim_V3_Batch_74" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_74.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_75" ; + schema:name "Controlled by an Advanced Process Control (APC) solution using the Raman spectroscopy of run IndPenSim_V3_Batch_75" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_75.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_76" ; + schema:name "Controlled by an Advanced Process Control (APC) solution using the Raman spectroscopy of run IndPenSim_V3_Batch_76" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_76.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_77" ; + schema:name "Controlled by an Advanced Process Control (APC) solution using the Raman spectroscopy of run IndPenSim_V3_Batch_77" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_77.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_78" ; + schema:name "Controlled by an Advanced Process Control (APC) solution using the Raman spectroscopy of run IndPenSim_V3_Batch_78" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_78.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_79" ; + schema:name "Controlled by an Advanced Process Control (APC) solution using the Raman spectroscopy of run IndPenSim_V3_Batch_79" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_79.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_80" ; + schema:name "Controlled by an Advanced Process Control (APC) solution using the Raman spectroscopy of run IndPenSim_V3_Batch_80" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_80.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_81" ; + schema:name "Controlled by an Advanced Process Control (APC) solution using the Raman spectroscopy of run IndPenSim_V3_Batch_81" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_81.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_82" ; + schema:name "Controlled by an Advanced Process Control (APC) solution using the Raman spectroscopy of run IndPenSim_V3_Batch_82" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_82.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_83" ; + schema:name "Controlled by an Advanced Process Control (APC) solution using the Raman spectroscopy of run IndPenSim_V3_Batch_83" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_83.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_84" ; + schema:name "Controlled by an Advanced Process Control (APC) solution using the Raman spectroscopy of run IndPenSim_V3_Batch_84" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_84.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_85" ; + schema:name "Controlled by an Advanced Process Control (APC) solution using the Raman spectroscopy of run IndPenSim_V3_Batch_85" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_85.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_86" ; + schema:name "Controlled by an Advanced Process Control (APC) solution using the Raman spectroscopy of run IndPenSim_V3_Batch_86" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_86.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_87" ; + schema:name "Controlled by an Advanced Process Control (APC) solution using the Raman spectroscopy of run IndPenSim_V3_Batch_87" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_87.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_88" ; + schema:name "Controlled by an Advanced Process Control (APC) solution using the Raman spectroscopy of run IndPenSim_V3_Batch_88" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_88.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_89" ; + schema:name "Controlled by an Advanced Process Control (APC) solution using the Raman spectroscopy of run IndPenSim_V3_Batch_89" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_89.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_90" ; + schema:name "Controlled by an Advanced Process Control (APC) solution using the Raman spectroscopy of run IndPenSim_V3_Batch_90" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_90.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_91" ; + schema:name "Contain faults resulting in process deviations of run IndPenSim_V3_Batch_91" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_91.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_92" ; + schema:name "Contain faults resulting in process deviations of run IndPenSim_V3_Batch_92" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_92.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_93" ; + schema:name "Contain faults resulting in process deviations of run IndPenSim_V3_Batch_93" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_93.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_94" ; + schema:name "Contain faults resulting in process deviations of run IndPenSim_V3_Batch_94" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_94.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_95" ; + schema:name "Contain faults resulting in process deviations of run IndPenSim_V3_Batch_95" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_95.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_96" ; + schema:name "Contain faults resulting in process deviations of run IndPenSim_V3_Batch_96" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_96.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_97" ; + schema:name "Contain faults resulting in process deviations of run IndPenSim_V3_Batch_97" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_97.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_98" ; + schema:name "Contain faults resulting in process deviations of run IndPenSim_V3_Batch_98" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_98.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_99" ; + schema:name "Contain faults resulting in process deviations of run IndPenSim_V3_Batch_99" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_99.csv.gz" . + + + rdf:type ppeo:observation_unit ; + fair:brand "FermentorX" ; + fair:fermentation "batch" ; + fair:volume "100,000 litre" ; + gbol:scientificName "Penicillium chrysogenum" ; + uniprot:organism 5076 ; + schema:dataset ; + schema:description "This data was generated using an advanced mathematical simulation of a 100,000 litre penicillin fermentation system referenced as IndPenSim. All details describing the simulation are available on the following website: www.industrialpenicillinsimulation.com. IndPenSim is the first simulation to include a realistic simulated Raman spectroscopy device for the purpose of developing, evaluating and implementation of advanced and innovative control solutions applicable to biotechnology facilities. This data set generated by IndPenSim represents the biggest data set available for advanced data analytics and contains 100 batches with all available process and Raman spectroscopy measurements (~2.5 GB). This data is highly suitable for the development of big data analytics, machine learning (ML) or artificial intelligence (AI) algorithms applicable to the biopharmaceutical industry. The 100 batches are controlled using different control strategies and different batch lengths representing a typical Biopharmaceutical manufacturing facility:" ; + schema:identifier "IndPenSim_V3_Batch_100" ; + schema:name "Contain faults resulting in process deviations of run IndPenSim_V3_Batch_100" . + + + rdf:type jerm:Data_sample ; + schema:contentUrl ; + schema:description "file" ; + schema:identifier "IndPenSim_V3_Batch_100.csv.gz" . diff --git a/test/unit/bioind/fairdata/fair_data_reader_test.rb b/test/unit/bioind/fairdata/fair_data_reader_test.rb index 1d5613106d..0228d17601 100644 --- a/test/unit/bioind/fairdata/fair_data_reader_test.rb +++ b/test/unit/bioind/fairdata/fair_data_reader_test.rb @@ -43,6 +43,18 @@ class FairDataReaderTest < ActiveSupport::TestCase assert_includes study.annotations, ["http://fairbydesign.nl/ontology/center_name", "NIID"] end + test 'metadata annotations' do + path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" + + study = BioInd::FairData::Reader.parse_graph(path).first.studies.first + + assert_equal 8, study.metadata_annotations.count + assert_includes study.annotations, ["http://fairbydesign.nl/ontology/center_name", "NIID"] + study.metadata_annotations.each do |annotation| + assert annotation[0].start_with?('http://fairbydesign.nl/ontology/'), "#{annotation[0]} is not expected" + end + end + test 'study assays' do path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" @@ -63,8 +75,6 @@ class FairDataReaderTest < ActiveSupport::TestCase sample = obs_unit.samples.first assay = sample.assays.first - assay.pp_annotations - assert_equal 'HIV-1 infected individuals in Ghana', inv.title assert_equal 'Exploration of HIV-1 infected individuals in Ghana', inv.description @@ -185,4 +195,5 @@ class FairDataReaderTest < ActiveSupport::TestCase end end end + end From d1ac136d2646efd6c877b044b49b85cffb6c5be1 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 12 Mar 2024 15:45:15 +0000 Subject: [PATCH 016/548] match the closest extended metadata type --- .../fairdatastation_virtual_demo.seeds.rb | 1 + lib/bio_ind/fair_data/base.rb | 2 +- lib/bio_ind/fair_data/reader.rb | 12 +++++++++++- test/factories/extended_metadata_types.rb | 11 +++++++++++ test/unit/bioind/fairdata/fair_data_reader_test.rb | 12 +++++++++++- 5 files changed, 35 insertions(+), 3 deletions(-) diff --git a/db/seeds/extended_metadata_drafts/fairdatastation_virtual_demo.seeds.rb b/db/seeds/extended_metadata_drafts/fairdatastation_virtual_demo.seeds.rb index bf343c7a07..accd8f742a 100644 --- a/db/seeds/extended_metadata_drafts/fairdatastation_virtual_demo.seeds.rb +++ b/db/seeds/extended_metadata_drafts/fairdatastation_virtual_demo.seeds.rb @@ -1,6 +1,7 @@ unless ExtendedMetadataType.where(title:'Fair Data Station Virtual Demo', supported_type:'Study').any? emt = ExtendedMetadataType.new(title: 'Fair Data Station Virtual Demo', supported_type:'Study') + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Alias', property_type_id:'http://fairbydesign.nl/ontology/alias', sample_attribute_type: SampleAttributeType.where(title:'String').first) emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Centre Name', property_type_id:'http://fairbydesign.nl/ontology/center_name', sample_attribute_type: SampleAttributeType.where(title:'String').first) emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Centre Project Name', property_type_id:'http://fairbydesign.nl/ontology/center_project_name', sample_attribute_type: SampleAttributeType.where(title:'String').first) emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'External Ids', property_type_id:'http://fairbydesign.nl/ontology/external_ids', sample_attribute_type: SampleAttributeType.where(title:'String').first) diff --git a/lib/bio_ind/fair_data/base.rb b/lib/bio_ind/fair_data/base.rb index e237c6791e..e097de2ef4 100644 --- a/lib/bio_ind/fair_data/base.rb +++ b/lib/bio_ind/fair_data/base.rb @@ -36,7 +36,7 @@ def annotations def metadata_annotations annotations.select do |annotation| - [@schema.title, @schema.description, @schema.identifier, @jerm.hasPart, RDF.type].detect do |skip| + [@schema.title, @schema.description, @schema.identifier, @schema.contributor, @jerm.hasPart, RDF.type].detect do |skip| annotation[0].start_with?(skip) end.nil? end diff --git a/lib/bio_ind/fair_data/reader.rb b/lib/bio_ind/fair_data/reader.rb index c4382d4469..3f418aaa30 100644 --- a/lib/bio_ind/fair_data/reader.rb +++ b/lib/bio_ind/fair_data/reader.rb @@ -57,7 +57,17 @@ def self.populate_extended_metadata(seek_entity, datastation_entity) end def self.detect_extended_metadata(seek_entity, datastation_entity) - ExtendedMetadataType.where(title:'Fair Data Station Virtual Demo', supported_type: seek_entity.class.name).first + property_ids = datastation_entity.metadata_annotations.collect{|annotation| annotation[0]} + + # collect and sort those with the most properties that match, eliminating any where no properties match + candidates = ExtendedMetadataType.where(supported_type: seek_entity.class.name).includes(:extended_metadata_attributes).collect do |emt| + ids = emt.extended_metadata_attributes.collect(&:property_type_id) + score = (property_ids - ids).length + emt = nil if (property_ids & ids).empty? + [score, emt] + end.sort_by{|x| x[0]} + + candidates.first&.last end end diff --git a/test/factories/extended_metadata_types.rb b/test/factories/extended_metadata_types.rb index 497d03e2fe..dad473be33 100644 --- a/test/factories/extended_metadata_types.rb +++ b/test/factories/extended_metadata_types.rb @@ -404,6 +404,7 @@ title {'Fair Data Station Virtual Demo'} supported_type { 'Study' } after(:build) do |a| + a.extended_metadata_attributes << FactoryBot.create(:study_title_extended_metadata_attribute, title: 'Alias', property_type_id:'http://fairbydesign.nl/ontology/alias') a.extended_metadata_attributes << FactoryBot.create(:study_title_extended_metadata_attribute, title: 'Centre Name', property_type_id:'http://fairbydesign.nl/ontology/center_name') a.extended_metadata_attributes << FactoryBot.create(:study_title_extended_metadata_attribute, title: 'Centre Project Name', property_type_id:'http://fairbydesign.nl/ontology/center_project_name') a.extended_metadata_attributes << FactoryBot.create(:study_title_extended_metadata_attribute, title: 'External Ids', property_type_id:'http://fairbydesign.nl/ontology/external_ids') @@ -413,6 +414,16 @@ end end + factory(:fairdata_virtual_demo_study_extended_metadata_partial, class: ExtendedMetadataType) do + title {'Fair Data Station Virtual Demo'} + supported_type { 'Study' } + after(:build) do |a| + a.extended_metadata_attributes << FactoryBot.create(:study_title_extended_metadata_attribute, title: 'Alias', property_type_id:'http://fairbydesign.nl/ontology/alias') + a.extended_metadata_attributes << FactoryBot.create(:study_title_extended_metadata_attribute, title: 'Submission Alias', property_type_id:'http://fairbydesign.nl/ontology/submission_alias') + a.extended_metadata_attributes << FactoryBot.create(:study_title_extended_metadata_attribute, title: 'Submission Lab Name', property_type_id:'http://fairbydesign.nl/ontology/submission_lab_name') + end + end + factory(:fairdata_virtual_demo_assay_extended_metadata, class: ExtendedMetadataType) do title {'Fair Data Station Virtual Demo'} supported_type { 'Assay' } diff --git a/test/unit/bioind/fairdata/fair_data_reader_test.rb b/test/unit/bioind/fairdata/fair_data_reader_test.rb index 0228d17601..d29be38912 100644 --- a/test/unit/bioind/fairdata/fair_data_reader_test.rb +++ b/test/unit/bioind/fairdata/fair_data_reader_test.rb @@ -46,7 +46,10 @@ class FairDataReaderTest < ActiveSupport::TestCase test 'metadata annotations' do path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" - study = BioInd::FairData::Reader.parse_graph(path).first.studies.first + inv = BioInd::FairData::Reader.parse_graph(path).first + assert_empty inv.metadata_annotations + + study = inv.studies.first assert_equal 8, study.metadata_annotations.count assert_includes study.annotations, ["http://fairbydesign.nl/ontology/center_name", "NIID"] @@ -158,7 +161,11 @@ class FairDataReaderTest < ActiveSupport::TestCase test 'populate extended metadata' do study_metadata_type = FactoryBot.create(:fairdata_virtual_demo_study_extended_metadata) + FactoryBot.create(:study_extended_metadata_type) + FactoryBot.create(:fairdata_virtual_demo_study_extended_metadata_partial) assay_metadata_type = FactoryBot.create(:fairdata_virtual_demo_assay_extended_metadata) + FactoryBot.create(:simple_assay_extended_metadata_type) + FactoryBot.create(:simple_investigation_extended_metadata_type_with_description_and_label) FactoryBot.create(:experimental_assay_class) path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" @@ -167,10 +174,13 @@ class FairDataReaderTest < ActiveSupport::TestCase project = contributor.projects.first investigation = BioInd::FairData::Reader.construct_isa(inv, contributor, [project]) + assert_nil investigation.extended_metadata + study = investigation.studies.first refute_nil study.extended_metadata assert_equal study_metadata_type, study.extended_metadata.extended_metadata_type + assert_equal 'DRP007092', study.extended_metadata.get_attribute_value('Alias') assert_equal 'NIID', study.extended_metadata.get_attribute_value('Centre Name') assert_equal 'human gut metagenome', study.extended_metadata.get_attribute_value('Centre Project Name') assert_equal 'PRJDB10485', study.extended_metadata.get_attribute_value('External Ids') From 761a9a1f60ee835bdde09ae8f247e367699eb703 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 26 Mar 2024 10:21:27 +0000 Subject: [PATCH 017/548] refactor how it gets the additional metadata follows the assumption that they will be fairbydesign properties --- lib/bio_ind/fair_data/base.rb | 9 ++++----- lib/bio_ind/fair_data/reader.rb | 2 +- test/unit/bioind/fairdata/fair_data_reader_test.rb | 6 +++--- 3 files changed, 8 insertions(+), 9 deletions(-) diff --git a/lib/bio_ind/fair_data/base.rb b/lib/bio_ind/fair_data/base.rb index e097de2ef4..f9cb37a84c 100644 --- a/lib/bio_ind/fair_data/base.rb +++ b/lib/bio_ind/fair_data/base.rb @@ -8,6 +8,7 @@ def initialize(resource_uri, graph) @graph = graph @jerm = RDF::Vocabulary.new('http://jermontology.org/ontology/JERMOntology#') @schema = RDF::Vocabulary.new('http://schema.org/') + @fair = RDF::Vocabulary.new('http://fairbydesign.nl/ontology/') @children = [] end @@ -34,11 +35,9 @@ def annotations end end - def metadata_annotations + def additional_metadata_annotations annotations.select do |annotation| - [@schema.title, @schema.description, @schema.identifier, @schema.contributor, @jerm.hasPart, RDF.type].detect do |skip| - annotation[0].start_with?(skip) - end.nil? + annotation[0].start_with?(@fair.to_s) end end @@ -91,7 +90,7 @@ def seek_attributes def populate_extended_metadata(seek_resource) extended_metadata_type = seek_resource.extended_metadata.extended_metadata_type data = {} - metadata_annotations.each do |annotation| + additional_metadata_annotations.each do |annotation| property = annotation[0] value = annotation[1] attribute = extended_metadata_type.extended_metadata_attributes.where(property_type_id: property).first diff --git a/lib/bio_ind/fair_data/reader.rb b/lib/bio_ind/fair_data/reader.rb index 3f418aaa30..e837708099 100644 --- a/lib/bio_ind/fair_data/reader.rb +++ b/lib/bio_ind/fair_data/reader.rb @@ -57,7 +57,7 @@ def self.populate_extended_metadata(seek_entity, datastation_entity) end def self.detect_extended_metadata(seek_entity, datastation_entity) - property_ids = datastation_entity.metadata_annotations.collect{|annotation| annotation[0]} + property_ids = datastation_entity.additional_metadata_annotations.collect{|annotation| annotation[0]} # collect and sort those with the most properties that match, eliminating any where no properties match candidates = ExtendedMetadataType.where(supported_type: seek_entity.class.name).includes(:extended_metadata_attributes).collect do |emt| diff --git a/test/unit/bioind/fairdata/fair_data_reader_test.rb b/test/unit/bioind/fairdata/fair_data_reader_test.rb index d29be38912..c9a3af74ad 100644 --- a/test/unit/bioind/fairdata/fair_data_reader_test.rb +++ b/test/unit/bioind/fairdata/fair_data_reader_test.rb @@ -47,13 +47,13 @@ class FairDataReaderTest < ActiveSupport::TestCase path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" inv = BioInd::FairData::Reader.parse_graph(path).first - assert_empty inv.metadata_annotations + assert_empty inv.additional_metadata_annotations study = inv.studies.first - assert_equal 8, study.metadata_annotations.count + assert_equal 8, study.additional_metadata_annotations.count assert_includes study.annotations, ["http://fairbydesign.nl/ontology/center_name", "NIID"] - study.metadata_annotations.each do |annotation| + study.additional_metadata_annotations.each do |annotation| assert annotation[0].start_with?('http://fairbydesign.nl/ontology/'), "#{annotation[0]} is not expected" end end From e8e0deeea3f4e16670bac66caa34ad75d6a8ad9d Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 9 Apr 2024 13:57:38 +0100 Subject: [PATCH 018/548] update version to 1.16-main --- config/version.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/config/version.yml b/config/version.yml index 9fe2f4b4c9..df417d0345 100644 --- a/config/version.yml +++ b/config/version.yml @@ -8,5 +8,5 @@ # patch: sprint-555 major: 1 -minor: 15 -patch: 0-pre +minor: 16 +patch: 0-main From e77d5eb1eee456dd6a8513fcc69d84ec674eeea5 Mon Sep 17 00:00:00 2001 From: Finn Bacall Date: Tue, 9 Apr 2024 14:28:18 +0100 Subject: [PATCH 019/548] Fix (transient?) version mix up when submitting RO-Crates Only seems to happen on my local instance. --- app/controllers/workflows_controller.rb | 2 +- .../git_workflow_ro_crate_api_test.rb | 22 ++++++++++++++----- 2 files changed, 18 insertions(+), 6 deletions(-) diff --git a/app/controllers/workflows_controller.rb b/app/controllers/workflows_controller.rb index 1704c8ba86..584c368498 100644 --- a/app/controllers/workflows_controller.rb +++ b/app/controllers/workflows_controller.rb @@ -324,7 +324,7 @@ def handle_ro_crate_post(new_version = false) else @crate_extractor.workflow = @workflow @workflow.latest_git_version.lock if @workflow.latest_git_version.mutable? - @crate_extractor.git_version = @workflow.latest_git_version.next_version(mutable: true).tap(&:save) + @crate_extractor.git_version = @workflow.latest_git_version.next_version(mutable: true) end end @workflow = @crate_extractor.build diff --git a/test/integration/git_workflow_ro_crate_api_test.rb b/test/integration/git_workflow_ro_crate_api_test.rb index c7e84558a4..f834ff1bdb 100644 --- a/test/integration/git_workflow_ro_crate_api_test.rb +++ b/test/integration/git_workflow_ro_crate_api_test.rb @@ -6,6 +6,7 @@ class GitWorkflowRoCrateApiTest < ActionDispatch::IntegrationTest login_as(admin.user) FactoryBot.create(:cwl_workflow_class) # Make sure the CWL class is present FactoryBot.create(:nextflow_workflow_class) + FactoryBot.create(:galaxy_workflow_class) @project = admin.person.projects.first @git_support = Seek::Config.git_support_enabled Seek::Config.git_support_enabled = true @@ -46,11 +47,22 @@ class GitWorkflowRoCrateApiTest < ActionDispatch::IntegrationTest } assert_response :success - assert_equal 2, assigns(:workflow).reload.version - assert_equal 'Nextflow', assigns(:workflow).workflow_class.title - assert_equal 'nf-core/ampliseq', assigns(:workflow).title - assert assigns(:workflow).git_version.total_size > 100 - assert_equal 'main.nf', assigns(:workflow).ro_crate.main_workflow.id + workflow = assigns(:workflow).reload + old_version = workflow.find_version(1) + new_version = workflow.git_version + + assert_equal 2, workflow.version + assert_equal 'Nextflow', workflow.workflow_class.title + assert_equal 'Nextflow', new_version.workflow_class.title + assert_equal 'Galaxy', old_version.workflow_class.title + assert_equal 'nf-core/ampliseq', workflow.title + assert_equal 'nf-core/ampliseq', new_version.title + assert_equal 'Concat two files', old_version.title + assert new_version.total_size > 100 + assert_equal 'main.nf', workflow.main_workflow_path + assert_equal 'main.nf', new_version.main_workflow_path + assert_equal 'main.nf', workflow.ro_crate.main_workflow.id + assert_equal 'concat_two_files.ga', old_version.main_workflow_path end end end From 96398dcfb7bf899eb72671b86b6856a337f3e4be Mon Sep 17 00:00:00 2001 From: Finn Bacall Date: Tue, 9 Apr 2024 14:31:59 +0100 Subject: [PATCH 020/548] Move workflow builders into `forms` dir --- app/{models => forms}/workflow_crate_extractor.rb | 0 app/{models => forms}/workflow_repository_builder.rb | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename app/{models => forms}/workflow_crate_extractor.rb (100%) rename app/{models => forms}/workflow_repository_builder.rb (100%) diff --git a/app/models/workflow_crate_extractor.rb b/app/forms/workflow_crate_extractor.rb similarity index 100% rename from app/models/workflow_crate_extractor.rb rename to app/forms/workflow_crate_extractor.rb diff --git a/app/models/workflow_repository_builder.rb b/app/forms/workflow_repository_builder.rb similarity index 100% rename from app/models/workflow_repository_builder.rb rename to app/forms/workflow_repository_builder.rb From aef17dff06cb744428287414207221334f5f1013 Mon Sep 17 00:00:00 2001 From: Finn Bacall Date: Tue, 9 Apr 2024 15:33:04 +0100 Subject: [PATCH 021/548] Idempotent workflow submission endpoint --- app/controllers/application_controller.rb | 3 +- app/controllers/workflows_controller.rb | 18 ++- app/forms/workflow_crate_extractor.rb | 30 ++++- app/models/workflow.rb | 15 +++ config/routes.rb | 1 + lib/ro_crate/workflow_crate.rb | 5 + lib/seek/workflow_extractors/ro_crate.rb | 10 +- .../git_workflow_ro_crate_api_test.rb | 123 ++++++++++++++++-- 8 files changed, 182 insertions(+), 23 deletions(-) diff --git a/app/controllers/application_controller.rb b/app/controllers/application_controller.rb index b9c458fc5c..f655ebec1e 100644 --- a/app/controllers/application_controller.rb +++ b/app/controllers/application_controller.rb @@ -540,7 +540,8 @@ def json_api_errors(object) hash[:errors] = object.errors.map do |error| segments = error.attribute.to_s.split('.') attr = segments.first - if !['content_blobs', 'policy'].include?(attr) && object.class.reflect_on_association(attr) + if !['content_blobs', 'policy'].include?(attr) && + object.class.respond_to?(:reflect_on_association) && object.class.reflect_on_association(attr) base = '/data/relationships' else base = '/data/attributes' diff --git a/app/controllers/workflows_controller.rb b/app/controllers/workflows_controller.rb index 584c368498..1dbd8e376b 100644 --- a/app/controllers/workflows_controller.rb +++ b/app/controllers/workflows_controller.rb @@ -8,7 +8,8 @@ class WorkflowsController < ApplicationController before_action :find_display_asset, only: [:show, :download, :diagram, :ro_crate, :edit_paths, :update_paths] before_action :login_required, only: [:create, :create_version, :new_version, :create_from_files, :create_from_ro_crate, - :create_metadata, :provide_metadata, :create_from_git, :create_version_from_git] + :create_metadata, :provide_metadata, :create_from_git, :create_version_from_git, + :submit] before_action :find_or_initialize_workflow, only: [:create_from_files, :create_from_ro_crate] include Seek::Publishing::PublishingCommon @@ -310,6 +311,21 @@ def filter end end + def submit + @crate_extractor = WorkflowCrateExtractor.new(ro_crate: { data: params[:ro_crate] }, params: workflow_params, update_existing: true) + + if @crate_extractor.valid? + @workflow = @crate_extractor.build + if @workflow.git_version.save && @workflow.save + render json: @workflow, include: json_api_include_param + else + render json: json_api_errors(@workflow), status: :unprocessable_entity + end + else + render json: json_api_errors(@crate_extractor), status: :unprocessable_entity + end + end + private def handle_ro_crate_post(new_version = false) diff --git a/app/forms/workflow_crate_extractor.rb b/app/forms/workflow_crate_extractor.rb index d940c921c5..626cef7cdd 100644 --- a/app/forms/workflow_crate_extractor.rb +++ b/app/forms/workflow_crate_extractor.rb @@ -5,14 +5,26 @@ class WorkflowCrateExtractor include ActiveModel::Model - attr_accessor :ro_crate, :workflow_class, :workflow, :git_version, :params + attr_accessor :ro_crate, :workflow_class, :workflow, :git_version, :params, :update_existing validate :resolve_crate validate :main_workflow_present?, if: -> { @crate.present? } + validate :source_url_present?, if: -> { update_existing } + validate :find_workflows_matching_id, if: -> { update_existing } def build - self.workflow ||= Workflow.new(workflow_class: workflow_class) if valid? + if update_existing && @existing_workflows.length == 1 + self.workflow = @existing_workflows.first + if @crate['version'] && self.workflow.git_versions.map(&:name).include?(@crate['version']) + return self.workflow + else + self.workflow.latest_git_version.lock if self.workflow.latest_git_version.mutable? + self.git_version = self.workflow.latest_git_version.next_version(mutable: true) + self.git_version.name = @crate['version'] if @crate['version'].present? + end + end + self.workflow ||= Workflow.new(workflow_class: workflow_class) self.git_version ||= workflow.git_version.tap do |gv| gv.set_default_git_repository end @@ -30,8 +42,6 @@ def build workflow.provide_metadata(extractor.metadata) workflow.assign_attributes(params) if params.present? git_version.set_resource_attributes(workflow.attributes) - - workflow end workflow @@ -43,6 +53,18 @@ def main_workflow_present? errors.add(:ro_crate, 'did not specify a main workflow.') unless @crate.main_workflow.present? end + def source_url_present? + errors.add(:ro_crate, 'ID could not be determined.') unless @crate.source_url.present? + end + + def find_workflows_matching_id + # Attempt to find existing workflow + @existing_workflows = Workflow.find_by_source_url(@crate.source_url) + if @existing_workflows.length > 1 + errors.add(:ro_crate, "#{@existing_workflows.length} workflows found matching the given ID.") + end + end + def extract_crate begin @crate = ROCrate::WorkflowCrateReader.read_zip(ro_crate[:data]) diff --git a/app/models/workflow.rb b/app/models/workflow.rb index 852b647658..d557b0bf10 100644 --- a/app/models/workflow.rb +++ b/app/models/workflow.rb @@ -274,4 +274,19 @@ def execution_instance_url } ) + def self.find_by_source_url(source_url) + joins(:source_link).where('asset_links.url' => source_url) + end + + def self.find_existing_version(source_url, version_name) + workflows = joins(:source_link).where('asset_links.url' => source_url) + if workflows.length == 1 + workflows.first.git_versions.where(name: version_name) + elsif workflows.empty? + 'None :(' + else + 'Too many :(' + end + end + end diff --git a/config/routes.rb b/config/routes.rb index 016f0963ae..3dd5d223f0 100644 --- a/config/routes.rb +++ b/config/routes.rb @@ -527,6 +527,7 @@ post :create_from_ro_crate post :create_from_files post :create_from_git + post :submit get :provide_metadata get :annotate_repository post :create_metadata diff --git a/lib/ro_crate/workflow_crate.rb b/lib/ro_crate/workflow_crate.rb index f222760f23..7f11eff10c 100644 --- a/lib/ro_crate/workflow_crate.rb +++ b/lib/ro_crate/workflow_crate.rb @@ -56,5 +56,10 @@ def test_suites def find_entry(path) entries[path] end + + def source_url + url = id if id.start_with?('http') + url || self['isBasedOn'] || self['url'] || self.main_workflow['url'] + end end end diff --git a/lib/seek/workflow_extractors/ro_crate.rb b/lib/seek/workflow_extractors/ro_crate.rb index 33fbde69d4..cff37237e2 100644 --- a/lib/seek/workflow_extractors/ro_crate.rb +++ b/lib/seek/workflow_extractors/ro_crate.rb @@ -105,11 +105,11 @@ def metadata_from_crate(crate, m) end end - source_url = crate['isBasedOn'] || crate['url'] || crate.main_workflow['url'] - if source_url - m.merge!(extract_source_metadata(ContentBlob.remote_content_handler_for(source_url))) - m[:source_link_url] ||= source_url # Use plain source URL if handler doesn't have something more appropriate - end + source_url = crate.source_url + if source_url + m.merge!(extract_source_metadata(ContentBlob.remote_content_handler_for(source_url))) + m[:source_link_url] ||= source_url # Use plain source URL if handler doesn't have something more appropriate + end m end diff --git a/test/integration/git_workflow_ro_crate_api_test.rb b/test/integration/git_workflow_ro_crate_api_test.rb index f834ff1bdb..6cb247ff8e 100644 --- a/test/integration/git_workflow_ro_crate_api_test.rb +++ b/test/integration/git_workflow_ro_crate_api_test.rb @@ -2,12 +2,12 @@ class GitWorkflowRoCrateApiTest < ActionDispatch::IntegrationTest setup do - admin = FactoryBot.create(:admin) - login_as(admin.user) + @person = FactoryBot.create(:person) + login_as(@person.user) FactoryBot.create(:cwl_workflow_class) # Make sure the CWL class is present FactoryBot.create(:nextflow_workflow_class) FactoryBot.create(:galaxy_workflow_class) - @project = admin.person.projects.first + @project = @person.projects.first @git_support = Seek::Config.git_support_enabled Seek::Config.git_support_enabled = true end @@ -16,7 +16,7 @@ class GitWorkflowRoCrateApiTest < ActionDispatch::IntegrationTest Seek::Config.git_support_enabled = @git_support end - test 'can post RO crate' do + test 'can post RO-Crate' do assert_difference('Workflow.count', 1) do post workflows_path, params: { ro_crate: fixture_file_upload('workflows/ro-crate-nf-core-ampliseq.crate.zip'), @@ -33,8 +33,8 @@ class GitWorkflowRoCrateApiTest < ActionDispatch::IntegrationTest end end - test 'can post RO crate as new version' do - workflow = FactoryBot.create(:local_git_workflow, policy: FactoryBot.create(:public_policy), contributor: @current_person) + test 'can post RO-Crate as new version' do + workflow = FactoryBot.create(:local_git_workflow, policy: FactoryBot.create(:public_policy), contributor: @person) assert_no_difference('Workflow.count') do assert_difference('Git::Version.count', 1) do @@ -67,8 +67,8 @@ class GitWorkflowRoCrateApiTest < ActionDispatch::IntegrationTest end end - test 'cannot post RO crate as new version to remote git workflows' do - workflow = FactoryBot.create(:remote_git_workflow, policy: FactoryBot.create(:public_policy), contributor: @current_person) + test 'cannot post RO-Crate as new version to remote git workflows' do + workflow = FactoryBot.create(:remote_git_workflow, policy: FactoryBot.create(:public_policy), contributor: @person) assert_no_difference('Workflow.count') do assert_no_difference('Git::Version.count') do @@ -81,12 +81,12 @@ class GitWorkflowRoCrateApiTest < ActionDispatch::IntegrationTest } assert_response :unprocessable_entity - assert @response.body.include?('Cannot add RO-Crate to remote workflows') + assert JSON.parse(@response.body)['errors'].any? { |e| e['detail'].include?('Cannot add RO-Crate to remote workflows') } end end end - test 'cannot post RO crate with missing metadata' do + test 'cannot post RO-Crate with missing metadata' do assert_no_difference('Workflow.count') do post workflows_path, params: { ro_crate: fixture_file_upload('workflows/workflow-4-1.crate.zip'), @@ -96,11 +96,11 @@ class GitWorkflowRoCrateApiTest < ActionDispatch::IntegrationTest } assert_response :unprocessable_entity - assert @response.body.include?("can't be blank") + assert JSON.parse(@response.body)['errors'].any? { |e| e['detail'].include?("can't be blank") } end end - test 'can supplement metadata when posting RO crate' do + test 'can supplement metadata when posting RO-Crate' do assert_difference('Workflow.count', 1) do post workflows_path, params: { ro_crate: fixture_file_upload('workflows/workflow-4-1.crate.zip'), @@ -129,6 +129,105 @@ class GitWorkflowRoCrateApiTest < ActionDispatch::IntegrationTest end end + test 'can submit RO-Crate with ID' do + assert_difference('Workflow.count', 1) do + assert_difference('Git::Version.count', 1) do + post submit_workflows_path, params: { + ro_crate: fixture_file_upload('workflows/ro-crate-with-id.crate.zip'), + workflow: { + project_ids: [@project.id] + } + } + + assert_response :success + assert_equal 'Galaxy', assigns(:workflow).workflow_class.title + assert_equal 'sort-and-change-case', assigns(:workflow).title + assert_equal 'https://example.com/my-workflow', assigns(:workflow).source_link_url + assert assigns(:workflow).git_version.total_size > 100 + assert_equal 'sort-and-change-case.ga', assigns(:workflow).ro_crate.main_workflow.id + end + end + end + + test 'cannot submit RO-Crate without ID' do + assert_no_difference('Workflow.count') do + assert_no_difference('Git::Version.count') do + post submit_workflows_path, params: { + ro_crate: fixture_file_upload('workflows/ro-crate-with-uri-license.crate.zip'), + workflow: { + project_ids: [@project.id] + } + } + + assert_response :unprocessable_entity + assert JSON.parse(@response.body)['errors'].any? { |e| e['detail'].include?('ID could not be determined') } + end + end + end + + test 'can submit RO-Crate that adds a version to an existing workflow' do + workflow = FactoryBot.create(:local_git_workflow, source_link_url: 'https://example.com/my-workflow', contributor: @person) + + assert_no_difference('Workflow.count') do + assert_difference('Git::Version.count', 1) do + post submit_workflows_path, params: { + ro_crate: fixture_file_upload('workflows/ro-crate-with-id.crate.zip'), + workflow: { + project_ids: [@project.id] + } + } + + assert_response :success + assert_equal 'Galaxy', assigns(:workflow).workflow_class.title + assert_equal 'sort-and-change-case', assigns(:workflow).title + assert assigns(:workflow).git_version.total_size > 100 + assert_equal 'sort-and-change-case.ga', assigns(:workflow).ro_crate.main_workflow.id + assert_equal '1.0.0', assigns(:workflow).git_version.name + end + end + end + + test 'duplicate version ignored when submitting RO-Crate' do + workflow = FactoryBot.create(:local_git_workflow, source_link_url: 'https://example.com/my-workflow', contributor: @person) + workflow.git_version.update!(name: '1.0.0') + + assert_no_difference('Workflow.count') do + assert_no_difference('Git::Version.count') do + post submit_workflows_path, params: { + ro_crate: fixture_file_upload('workflows/ro-crate-with-id.crate.zip'), + workflow: { + project_ids: [@project.id] + } + } + + assert_response :success + assert_equal 'Galaxy', assigns(:workflow).workflow_class.title + assert_equal 'Concat two files', assigns(:workflow).title + assert assigns(:workflow).git_version.total_size > 100 + assert_equal 'concat_two_files.ga', assigns(:workflow).ro_crate.main_workflow.id + end + end + end + + test 'cannot submit RO-Crate with ambiguous matching ID' do + workflow = FactoryBot.create(:local_git_workflow, source_link_url: 'https://example.com/my-workflow', contributor: @person) + workflow2 = FactoryBot.create(:local_git_workflow, source_link_url: 'https://example.com/my-workflow', contributor: @person) + + assert_no_difference('Workflow.count') do + assert_no_difference('Git::Version.count') do + post submit_workflows_path, params: { + ro_crate: fixture_file_upload('workflows/ro-crate-with-id.crate.zip'), + workflow: { + project_ids: [@project.id] + } + } + + assert_response :unprocessable_entity + assert JSON.parse(@response.body)['errors'].any? { |e| e['detail'].include?('2 workflows found matching the given ID.') } + end + end + end + private def login_as(user) From fa51ff5670eccd40bbe43f0a62a8eef9840dc055 Mon Sep 17 00:00:00 2001 From: Finn Bacall Date: Tue, 9 Apr 2024 17:21:47 +0100 Subject: [PATCH 022/548] Add missing fixture file --- .../files/workflows/ro-crate-with-id.crate.zip | Bin 0 -> 3189 bytes 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 test/fixtures/files/workflows/ro-crate-with-id.crate.zip diff --git a/test/fixtures/files/workflows/ro-crate-with-id.crate.zip b/test/fixtures/files/workflows/ro-crate-with-id.crate.zip new file mode 100644 index 0000000000000000000000000000000000000000..1b229b52d0ebf22f60484188b948449ab6662b39 GIT binary patch literal 3189 zcmbW42{=^UAIC3a%TkCzvNt3R(jZ$Dh3pDhiZLS-jddtx846h|O-RJprGM5}jfg=* z3Xx@^NpHp2GL|e^|D)2MH}8MD_c_nG_j!KL_jAtgobUaeYiEUo~$+zuC;8faM6H;G2MbqGMS zK_kZMX;Ue0XRDkXdj|9QzSstv{~FHaGf}5Y8I4W%(gzpK0{~$9aC|(W2p>4c1&VgT 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iu8pYZ&8V#w{+HGMJ2ErN+MZ{l-*WVw1Y7&70R9P%n+Nj% literal 0 HcmV?d00001 From 9a2245fea71d530f9b9cd956b37e50a8306f65be Mon Sep 17 00:00:00 2001 From: Finn Bacall Date: Tue, 9 Apr 2024 17:40:38 +0100 Subject: [PATCH 023/548] Crate extractor should always return a workflow, even on error --- app/forms/workflow_crate_extractor.rb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/app/forms/workflow_crate_extractor.rb b/app/forms/workflow_crate_extractor.rb index 626cef7cdd..37a0a6aaf2 100644 --- a/app/forms/workflow_crate_extractor.rb +++ b/app/forms/workflow_crate_extractor.rb @@ -24,7 +24,7 @@ def build self.git_version.name = @crate['version'] if @crate['version'].present? end end - self.workflow ||= Workflow.new(workflow_class: workflow_class) + self.workflow ||= default_workflow self.git_version ||= workflow.git_version.tap do |gv| gv.set_default_git_repository end @@ -44,11 +44,15 @@ def build git_version.set_resource_attributes(workflow.attributes) end - workflow + workflow || default_workflow end private + def default_workflow + Workflow.new(workflow_class: workflow_class) + end + def main_workflow_present? errors.add(:ro_crate, 'did not specify a main workflow.') unless @crate.main_workflow.present? end From 9544e472f4defbe9b7c37d0c0799f070157bdafa Mon Sep 17 00:00:00 2001 From: Finn Bacall Date: Wed, 10 Apr 2024 12:41:54 +0100 Subject: [PATCH 024/548] Require `version` to be set when submitting workflow RO-Crates --- app/forms/workflow_crate_extractor.rb | 9 +++++---- .../ro-crate-with-id-but-no-version.crate.zip | Bin 0 -> 3180 bytes .../git_workflow_ro_crate_api_test.rb | 16 ++++++++++++++++ 3 files changed, 21 insertions(+), 4 deletions(-) create mode 100644 test/fixtures/files/workflows/ro-crate-with-id-but-no-version.crate.zip diff --git a/app/forms/workflow_crate_extractor.rb b/app/forms/workflow_crate_extractor.rb index 37a0a6aaf2..30ab5640ca 100644 --- a/app/forms/workflow_crate_extractor.rb +++ b/app/forms/workflow_crate_extractor.rb @@ -9,19 +9,19 @@ class WorkflowCrateExtractor validate :resolve_crate validate :main_workflow_present?, if: -> { @crate.present? } - validate :source_url_present?, if: -> { update_existing } + validate :source_url_and_version_present?, if: -> { update_existing } validate :find_workflows_matching_id, if: -> { update_existing } def build if valid? if update_existing && @existing_workflows.length == 1 self.workflow = @existing_workflows.first - if @crate['version'] && self.workflow.git_versions.map(&:name).include?(@crate['version']) + if self.workflow.git_versions.map(&:name).include?(@crate['version']) return self.workflow else self.workflow.latest_git_version.lock if self.workflow.latest_git_version.mutable? self.git_version = self.workflow.latest_git_version.next_version(mutable: true) - self.git_version.name = @crate['version'] if @crate['version'].present? + self.git_version.name = @crate['version'] end end self.workflow ||= default_workflow @@ -57,8 +57,9 @@ def main_workflow_present? errors.add(:ro_crate, 'did not specify a main workflow.') unless @crate.main_workflow.present? end - def source_url_present? + def source_url_and_version_present? errors.add(:ro_crate, 'ID could not be determined.') unless @crate.source_url.present? + errors.add(:ro_crate, 'version could not be determined.') unless @crate['version'].present? end def find_workflows_matching_id diff --git a/test/fixtures/files/workflows/ro-crate-with-id-but-no-version.crate.zip b/test/fixtures/files/workflows/ro-crate-with-id-but-no-version.crate.zip new file mode 100644 index 0000000000000000000000000000000000000000..cbae4cc9c8335e8f41ab597dbd3978d0c0475407 GIT binary patch literal 3180 zcmbW43pkVS8^@}g{9$dl+W=>XAi3%`*MTB-NeZ=nwH?iQ`4nSb&|nWPIqc(lT!^Z0 zc4N^FUf52t4aCWLT<6^wdg@fg|LfH*28i6pHX6-t3@kgJc&fZcZ5Cfu|)-@Gnm_$ z0?WBcbuuwgb0y0bHx9j)P{j-Gr3c=2S{dGgMB_A{PF-&}|K<+OK{qZP&;HPH|~b|Z5j{uHF$Tc|jfbdrkgv+-za+sA{L3`BR7_Y!Wj)Kq0( 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JSON.parse(@response.body)['errors'].any? { |e| e['detail'].include?('version could not be determined') } + end + end + end + test 'can submit RO-Crate that adds a version to an existing workflow' do workflow = FactoryBot.create(:local_git_workflow, source_link_url: 'https://example.com/my-workflow', contributor: @person) From 098c15ccf3dc9e3591dd59822502579de3770330 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Wed, 10 Apr 2024 16:45:42 +0100 Subject: [PATCH 025/548] tweaked version for bioindustry --- config/version.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/version.yml b/config/version.yml index 9fe2f4b4c9..069061dc7d 100644 --- a/config/version.yml +++ b/config/version.yml @@ -9,4 +9,4 @@ major: 1 minor: 15 -patch: 0-pre +patch: 0-bioindustry From 35a7c8bb05b3b8d11a39454154b5e54fc2d71cac Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Thu, 11 Apr 2024 15:59:42 +0100 Subject: [PATCH 026/548] remove the double checking and updating of the mime type #1820 --- lib/seek/content_extraction.rb | 32 ++------------------ test/unit/content_blob_test.rb | 55 ---------------------------------- 2 files changed, 2 insertions(+), 85 deletions(-) diff --git a/lib/seek/content_extraction.rb b/lib/seek/content_extraction.rb index b5e4190731..5168e878d8 100644 --- a/lib/seek/content_extraction.rb +++ b/lib/seek/content_extraction.rb @@ -69,7 +69,6 @@ def extract_text_from_pdf Docsplit.extract_text(pdf_filepath, output: converted_storage_directory) unless File.exist?(txt_filepath) File.read(txt_filepath) rescue Docsplit::ExtractionFailed => e - extract_text_from_pdf if double_check_mime_type Rails.logger.error("Problem with extracting text from pdf #{id} #{e}") '' end @@ -78,11 +77,7 @@ def extract_text_from_pdf def to_csv(sheet = 1, trim = false) return '' unless is_excel? - begin - spreadsheet_to_csv(filepath, sheet, trim, Seek::Config.jvm_memory_allocation) - rescue SysMODB::SpreadsheetExtractionException - to_csv(sheet, trim) if double_check_mime_type - end + spreadsheet_to_csv(filepath, sheet, trim, Seek::Config.jvm_memory_allocation) end def extract_csv() @@ -90,34 +85,11 @@ def extract_csv() end def to_spreadsheet_xml - begin - spreadsheet_to_xml(filepath, Seek::Config.jvm_memory_allocation) - rescue SysMODB::SpreadsheetExtractionException=>e - if double_check_mime_type - to_spreadsheet_xml - else - raise e - end - end + spreadsheet_to_xml(filepath, Seek::Config.jvm_memory_allocation) end private - # checks the type using mime magic, and updates if found to be different. This is to help cases where extraction - # fails due to the mime type being incorrectly set - # - # @return boolean - the mime type was changed - def double_check_mime_type - suggested_type = mime_magic_content_type - if suggested_type && suggested_type != content_type - update_column(:content_type, suggested_type) - true - else - false - end - end - - # filters special characters, keeping alphanumeric characters, hyphen ('-'), underscore('_') and newlines def filter_text_content(content) content.gsub(/[^-_0-9a-z \n]/i, ' ') diff --git a/test/unit/content_blob_test.rb b/test/unit/content_blob_test.rb index f92574fc13..111a1cafd7 100644 --- a/test/unit/content_blob_test.rb +++ b/test/unit/content_blob_test.rb @@ -900,61 +900,6 @@ def test_exception_when_both_data_and_io_object refute File.exist?(txt_path) end - test 'fix mime type after failed csv extraction' do - blob = FactoryBot.create(:image_content_blob, content_type:'application/excel', original_filename:'image.xls') - assert blob.is_excel? - - text = blob.to_csv - - assert text.blank? - - blob.reload - - refute blob.is_excel? - assert_equal 'image/png',blob.content_type - end - - test 'fix mime type after failed pdf contents for search' do - blob = FactoryBot.create(:image_content_blob, content_type: 'application/msword', original_filename: 'image.doc') - assert blob.is_pdf_convertable? - - assert_empty blob.pdf_contents_for_search - - blob.reload - - refute blob.is_pdf_convertable? - assert_equal 'image/png', blob.content_type - - # incorrectly described as pdf - blob = FactoryBot.create(:image_content_blob, content_type: 'application/pdf', original_filename: 'image.pdf') - - assert_empty blob.pdf_contents_for_search - - blob.reload - - refute blob.is_pdf_convertable? - assert_equal 'image/png', blob.content_type - - # handles when the file is actually broken, rather than failing due to the mime type - blob = FactoryBot.create(:broken_pdf_content_blob) - assert_empty blob.pdf_contents_for_search - assert_equal 'application/pdf', blob.content_type - end - - test 'fix mime type after spreadsheet xml fail' do - blob = FactoryBot.create(:image_content_blob, content_type:'application/msexcel', original_filename:'image.xls') - assert blob.is_extractable_spreadsheet? - - assert_raises(SysMODB::SpreadsheetExtractionException) do - blob.to_spreadsheet_xml - end - - blob.reload - - refute blob.is_extractable_spreadsheet? - assert_equal 'image/png',blob.content_type - end - test 'tmp_io_objects in tmp dir are deleted' do file = Tempfile.new('testing-content-blob') file.write('test test test') From ea3a8c10a123785a96f0b73db3d940c7c5e188c1 Mon Sep 17 00:00:00 2001 From: Finn Date: Fri, 19 Apr 2024 12:41:36 +0100 Subject: [PATCH 027/548] Ensure initial version name is set for new workflows created from RO-Crates --- app/forms/workflow_crate_extractor.rb | 2 +- test/integration/git_workflow_ro_crate_api_test.rb | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/app/forms/workflow_crate_extractor.rb b/app/forms/workflow_crate_extractor.rb index 30ab5640ca..b634fa04a3 100644 --- a/app/forms/workflow_crate_extractor.rb +++ b/app/forms/workflow_crate_extractor.rb @@ -21,13 +21,13 @@ def build else self.workflow.latest_git_version.lock if self.workflow.latest_git_version.mutable? self.git_version = self.workflow.latest_git_version.next_version(mutable: true) - self.git_version.name = @crate['version'] end end self.workflow ||= default_workflow self.git_version ||= workflow.git_version.tap do |gv| gv.set_default_git_repository end + self.git_version.name = @crate['version'] if @crate['version'] git_version.main_workflow_path = URI.decode_www_form_component(@crate.main_workflow.id) if @crate.main_workflow && !@crate.main_workflow.remote? git_version.diagram_path = URI.decode_www_form_component(@crate.main_workflow.diagram.id) if @crate.main_workflow&.diagram && !@crate.main_workflow.diagram.remote? git_version.abstract_cwl_path = URI.decode_www_form_component(@crate.main_workflow.cwl_description.id) if @crate.main_workflow&.cwl_description && !@crate.main_workflow.cwl_description.remote? diff --git a/test/integration/git_workflow_ro_crate_api_test.rb b/test/integration/git_workflow_ro_crate_api_test.rb index f4fef37c70..296c800bf3 100644 --- a/test/integration/git_workflow_ro_crate_api_test.rb +++ b/test/integration/git_workflow_ro_crate_api_test.rb @@ -141,6 +141,7 @@ class GitWorkflowRoCrateApiTest < ActionDispatch::IntegrationTest assert_response :success assert_equal 'Galaxy', assigns(:workflow).workflow_class.title + assert_equal '1.0.0', assigns(:workflow).git_version.name assert_equal 'sort-and-change-case', assigns(:workflow).title assert_equal 'https://example.com/my-workflow', assigns(:workflow).source_link_url assert assigns(:workflow).git_version.total_size > 100 @@ -250,4 +251,4 @@ def login_as(user) User.current_user = user post '/session', params: { login: user.login, password: generate_user_password } end -end \ No newline at end of file +end From 18b5a3ff805a573798b91358594df330c236188d Mon Sep 17 00:00:00 2001 From: Finn Bacall Date: Mon, 22 Apr 2024 14:42:57 +0100 Subject: [PATCH 028/548] Handle numeric `version`. Use "source URL" terminology --- app/forms/workflow_crate_extractor.rb | 6 +-- .../ro-crate-with-numeric-id.crate.zip | Bin 0 -> 3188 bytes .../git_workflow_ro_crate_api_test.rb | 45 +++++++++++++++++- 3 files changed, 47 insertions(+), 4 deletions(-) create mode 100644 test/fixtures/files/workflows/ro-crate-with-numeric-id.crate.zip diff --git a/app/forms/workflow_crate_extractor.rb b/app/forms/workflow_crate_extractor.rb index b634fa04a3..affd130d6d 100644 --- a/app/forms/workflow_crate_extractor.rb +++ b/app/forms/workflow_crate_extractor.rb @@ -16,7 +16,7 @@ def build if valid? if update_existing && @existing_workflows.length == 1 self.workflow = @existing_workflows.first - if self.workflow.git_versions.map(&:name).include?(@crate['version']) + if self.workflow.git_versions.map(&:name).include?(@crate['version']&.to_s) return self.workflow else self.workflow.latest_git_version.lock if self.workflow.latest_git_version.mutable? @@ -27,7 +27,7 @@ def build self.git_version ||= workflow.git_version.tap do |gv| gv.set_default_git_repository end - self.git_version.name = @crate['version'] if @crate['version'] + self.git_version.name = @crate['version'].to_s if @crate['version'] git_version.main_workflow_path = URI.decode_www_form_component(@crate.main_workflow.id) if @crate.main_workflow && !@crate.main_workflow.remote? git_version.diagram_path = URI.decode_www_form_component(@crate.main_workflow.diagram.id) if @crate.main_workflow&.diagram && !@crate.main_workflow.diagram.remote? git_version.abstract_cwl_path = URI.decode_www_form_component(@crate.main_workflow.cwl_description.id) if @crate.main_workflow&.cwl_description && !@crate.main_workflow.cwl_description.remote? @@ -58,7 +58,7 @@ def main_workflow_present? end def source_url_and_version_present? - errors.add(:ro_crate, 'ID could not be determined.') unless @crate.source_url.present? + errors.add(:ro_crate, 'source URL could not be determined.') unless @crate.source_url.present? errors.add(:ro_crate, 'version could not be determined.') unless @crate['version'].present? end diff --git a/test/fixtures/files/workflows/ro-crate-with-numeric-id.crate.zip b/test/fixtures/files/workflows/ro-crate-with-numeric-id.crate.zip new file mode 100644 index 0000000000000000000000000000000000000000..00a1628207ece09fb7d64eb0147e8ba5e1a5393c GIT binary patch literal 3188 zcmbW42{@G7AID$DzT9v%qJM=fl?EY2W66?Hb`6PQFqvY8m@s8*U8GRlNyzRpmaZk0 zMv5^Ra<8>PcWRPih9P_QSnczjMCt@4PlAKs=Hl01yC- z;aYZsfm5p}006FYnjojynI1KNS%^uNsQ*b}TwfY0++k{cwXVf z?z$yksyP;MNbn;+*nxU(Wk3hYQ(y#@rTuk{RpzDHuxfSdPoYJ&2 z_Clu=zX7(WLLT0v2jvMCXabxXZ|#?g&m1(@pYbC%sDk z_~2yWDn5R@OhfF|O8AfXYsLLb3`S6I#>YD#->IoK_hVc2RaR+>zxEDRY34tM#^(+Q znj0x~!pir6v(;sy@&+%x=)jP{K2=NL{4`0EoG^NPzD>XX6oFm-NbkZ`7u%w6s@36# zIAt17L*(Jz=Z7)bC(608J>m*ygbq**b+{Zw>*o{)3G)~nZ$}Z3wT|m zh~di_ZT0tO&D@J}_7pDl8R3v9RkIgDeUjvoBEdwFy&>)pT{e5!NRDwUZRW_mhbuv0 zCm&wi7v6^b(fRUZoI<`PnVZpcG(kwhMywTigsS=QeOj?_M0OMRSW2)){JX@hcS*KK zG}60L`!xHZ6!mjBLRsVhpHEsve($Nr+V4D$5iR;BlXd3GtrmxcT(cUn99Etsa_RY^>7 z^h>B8_D@XQR^&6y{Q*{Wzem9VtWo`}`k*7ra4=ue$i`846T^v z7Zm*)q6sN=>`L9dj(%;;&KTT%{{1`b=eL=jiRB+4`rY>0Q7Yp*+CrCyG$^j-0x`Pj zhjyI4-2OE8(Od7v;V`+>?q~C%^#vCMxs^|kOYI+eQ0=CpCP@e}44kFUKb^ivw&TKC zp%(Bz25{}2nQ1}@NkhxxGPh|!-we@`F3Pwt&vW8+pOUoA8+TnbZG69ALP4<(MIpy~%;YF*yfSJOKrY4d% zL%Nrugm7V4;9j*Ar@bLpkv=*1{M43}K)KnN;IcgRsVqmCLM3=c^;dOuyrB9^J4^}) zPW4@uv~u*^e=0zIh}Nz z5O<7YE$|iqkm6V?z}FuOL0~)~9w-FH3kmT+1Rzzt5R7EYHiEiX<5;LrXXU|~+F*O@ zvt7aBFD+gpOr2!W6N=|*pGdY>3&Ut;9&bQSx*0=DUIn#`w%M8qKYz+%BD$+;BOx9Ipdu-zvUSk(-#+L z9@K1uQrzmBttYoNdt!JeYe-Fn?&jN;QkkB-RMMl9SnBVn>8Z=tW^ET6hSpE2vKu(LV?cht7i$5MCGNrMn9w_84?_1jdit^ z@(!roVmjH`)V}8~e}|Lcui~;TvKoSrOQo#Q%uF7TOba@k@33~Dl-UcVcu&QUG6g)* z+gYfmc=+^mp4@bXi%nM)*w?`0xGa`&NJ+t!&W~Qx}XO0yt+(Vzl6;Px=#-xoz~elOA+bGeWlAEL}mK1 z5CpgrK)4}>a(NDui|6?yEbf-(b~`piIr^^cYhglM9+VIgaz!d?7~P89A4;?wE#1|R z18ya$cT)tVRcc!wJ4&GS52B=w+a)VT6oi3hPMF_=V_W<%89IJSRLSC;9a&z3f4okp zJYC)1ntEOma8+C@;kYL%?*Jh9ggUb;b7 z9C-4J?m>FSK*yAFC3<@%`3ERIa}oy2mOrsiMp=%Cs|TflsBp=7xtKY}ck?y&(f3GR z1#EJc8hP~h(cPcs=p<|cS=Lqh0osS>JTT!(( zIQ}_@_u6dAuH2Ou)2;)8C@Ax37_sJ1T?`*B%rr!t*XW$BiQ+hcsxfiiHYXbz?;-sQ z;-u%&tvTb~Jc;ZH*T|J;p)o}UWIR_j#`=fb#;ZT0dRiTMS{>c(v%IJDqFkYuM@DM7 zSM@?;jx4Em%Cn5*KUJ1zUpy-}fKx3J+iG2+1(RQSxfB>gue`HRrLJ0V`1geO24+)Z zS}T_di4%;Y_=euy_j?1BN7GHhGqNLYX1#Lcu|m+)9oYV3!e6Zi{8?l8^P4RR`262O8ud`aI~!Efd1~#q`(>N z+9ezQAY!fmc7zfFWY^vSE?^q~c>jD=Y^<9L;GfxFO`vlD_6PQ?_3Nd-KLD+lzR6MA z{5Z6MBY}YZssERLJ?Hysu%5%_)QHV8&Z!L>K>u+P0wb{adv)X@0=H*-4^8%b(g|m}1*M2I1e*$p~0hs^* literal 0 HcmV?d00001 diff --git a/test/integration/git_workflow_ro_crate_api_test.rb b/test/integration/git_workflow_ro_crate_api_test.rb index 296c800bf3..71a74a8234 100644 --- a/test/integration/git_workflow_ro_crate_api_test.rb +++ b/test/integration/git_workflow_ro_crate_api_test.rb @@ -150,6 +150,27 @@ class GitWorkflowRoCrateApiTest < ActionDispatch::IntegrationTest end end + test 'can submit RO-Crate with numeric ID' do + assert_difference('Workflow.count', 1) do + assert_difference('Git::Version.count', 1) do + post submit_workflows_path, params: { + ro_crate: fixture_file_upload('workflows/ro-crate-with-numeric-id.crate.zip'), + workflow: { + project_ids: [@project.id] + } + } + + assert_response :success + assert_equal 'Galaxy', assigns(:workflow).workflow_class.title + assert_equal '3.2', assigns(:workflow).git_version.name + assert_equal 'sort-and-change-case', assigns(:workflow).title + assert_equal 'https://example.com/my-workflow', assigns(:workflow).source_link_url + assert assigns(:workflow).git_version.total_size > 100 + assert_equal 'sort-and-change-case.ga', assigns(:workflow).ro_crate.main_workflow.id + end + end + end + test 'cannot submit RO-Crate without ID' do assert_no_difference('Workflow.count') do assert_no_difference('Git::Version.count') do @@ -161,7 +182,7 @@ class GitWorkflowRoCrateApiTest < ActionDispatch::IntegrationTest } assert_response :unprocessable_entity - assert JSON.parse(@response.body)['errors'].any? { |e| e['detail'].include?('ID could not be determined') } + assert JSON.parse(@response.body)['errors'].any? { |e| e['detail'].include?('source URL could not be determined') } end end end @@ -226,6 +247,28 @@ class GitWorkflowRoCrateApiTest < ActionDispatch::IntegrationTest end end + test 'duplicate numeric version ignored when submitting RO-Crate' do + workflow = FactoryBot.create(:local_git_workflow, source_link_url: 'https://example.com/my-workflow', contributor: @person) + workflow.git_version.update!(name: '3.2') + + assert_no_difference('Workflow.count') do + assert_no_difference('Git::Version.count') do + post submit_workflows_path, params: { + ro_crate: fixture_file_upload('workflows/ro-crate-with-numeric-id.crate.zip'), + workflow: { + project_ids: [@project.id] + } + } + + assert_response :success + assert_equal 'Galaxy', assigns(:workflow).workflow_class.title + assert_equal 'Concat two files', assigns(:workflow).title + assert assigns(:workflow).git_version.total_size > 100 + assert_equal 'concat_two_files.ga', assigns(:workflow).ro_crate.main_workflow.id + end + end + end + test 'cannot submit RO-Crate with ambiguous matching ID' do workflow = FactoryBot.create(:local_git_workflow, source_link_url: 'https://example.com/my-workflow', contributor: @person) workflow2 = FactoryBot.create(:local_git_workflow, source_link_url: 'https://example.com/my-workflow', contributor: @person) From 0340b0d898f597d0892273edf322f6193053d4d5 Mon Sep 17 00:00:00 2001 From: Finn Bacall Date: Wed, 24 Apr 2024 14:29:51 +0100 Subject: [PATCH 029/548] Prevent invalid git annotations being saved. Fixes #1856 --- app/models/concerns/workflow_extraction.rb | 4 +++- app/models/git/annotation.rb | 1 + test/unit/git/git_annotation_test.rb | 22 ++++++++++++++++++++++ 3 files changed, 26 insertions(+), 1 deletion(-) diff --git a/app/models/concerns/workflow_extraction.rb b/app/models/concerns/workflow_extraction.rb index a9cf9ed027..879006a09c 100644 --- a/app/models/concerns/workflow_extraction.rb +++ b/app/models/concerns/workflow_extraction.rb @@ -277,7 +277,9 @@ def ro_crate_url(action = nil) end if exist - exist.update_attribute(:path, path) + exist.path = path + exist.save(validate: false) if exist.persisted? + exist else git_version.git_annotations.build(key: s_type, path: path) end diff --git a/app/models/git/annotation.rb b/app/models/git/annotation.rb index 9c5aa83deb..6ae11e39d8 100644 --- a/app/models/git/annotation.rb +++ b/app/models/git/annotation.rb @@ -6,6 +6,7 @@ class Annotation < ApplicationRecord before_validation :assign_contributor validates :key, uniqueness: { scope: [:git_version_id, :path, :value] } + validates :git_version, presence: true validate :check_valid_path def assign_contributor diff --git a/test/unit/git/git_annotation_test.rb b/test/unit/git/git_annotation_test.rb index 9129d8901e..4878159117 100644 --- a/test/unit/git/git_annotation_test.rb +++ b/test/unit/git/git_annotation_test.rb @@ -197,4 +197,26 @@ class GitAnnotationTest < ActiveSupport::TestCase assert_equal({}, wgv.reload.remote_sources) end + + test 'dont save annotation before git version saved' do + workflow = FactoryBot.create(:local_git_workflow) + wgv = workflow.git_version + assert workflow.diagram_path + assert wgv.is_a?(Workflow::Git::Version) + disable_authorization_checks do + wgv.add_file('new_diagram.png', StringIO.new('blah')) + wgv.save! + end + + new_version = workflow.git_versions.build + refute new_version.persisted? + assert_no_difference('Git::Annotation.count') do + refute new_version.diagram_annotation + new_version.diagram_path = 'new_diagram.png' + assert new_version.diagram_annotation + new_version.diagram_path = 'new_diagram.png' + refute new_version.diagram_annotation.persisted? + refute new_version.persisted? + end + end end From 6dd8c6352090a805794a1ba65779c40fdc25b8e9 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Wed, 24 Apr 2024 14:40:51 +0100 Subject: [PATCH 030/548] fix the validation of being a member of an assay/study projects --- app/models/assay.rb | 8 +++++++- app/models/study.rb | 8 +++++++- 2 files changed, 14 insertions(+), 2 deletions(-) diff --git a/app/models/assay.rb b/app/models/assay.rb index ac4b09bad8..3f36ddccfa 100644 --- a/app/models/assay.rb +++ b/app/models/assay.rb @@ -57,7 +57,7 @@ class Assay < ApplicationRecord validates_with TechnologyTypeUriValidator validates_presence_of :contributor validates_presence_of :assay_class - validates :study, presence: { message: 'must be selected and valid' } + validates :study, presence: { message: 'must be selected and valid' }, projects: true before_validation :default_assay_and_technology_type @@ -68,6 +68,12 @@ class Assay < ApplicationRecord enforce_authorization_on_association :study, :view + # the associated projects from the Investigation. + # Overrides the :through :study, as that relies on being saved to the database first, causing validation issues + def projects + study&.projects || [] + end + def is_assay_stream? assay_class&.is_assay_stream? end diff --git a/app/models/study.rb b/app/models/study.rb index c206c62b98..4e908e7f4f 100644 --- a/app/models/study.rb +++ b/app/models/study.rb @@ -27,7 +27,7 @@ class Study < ApplicationRecord has_and_belongs_to_many :sample_types - validates :investigation, presence: { :message => "is blank or invalid" } + validates :investigation, presence: { :message => "is blank or invalid" }, projects: true enforce_authorization_on_association :investigation, :view @@ -36,6 +36,12 @@ class Study < ApplicationRecord has_many "related_#{type.pluralize}".to_sym, -> { distinct }, through: :assays, source: type.pluralize.to_sym end + # the associated projects from the Investigation. + # Overrides the :through :investigation, as that relies on being saved to the database first, causing validation issues + def projects + investigation&.projects || [] + end + def assay_streams assays.select(&:is_assay_stream?) end From d82a57762318d4f5644b19c229a316d039b6996c Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Wed, 24 Apr 2024 14:44:06 +0100 Subject: [PATCH 031/548] add property_type_id to the api schema --- public/api/definitions/_schemas.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/public/api/definitions/_schemas.yml b/public/api/definitions/_schemas.yml index 2b1bcffcdb..cc2317dacc 100644 --- a/public/api/definitions/_schemas.yml +++ b/public/api/definitions/_schemas.yml @@ -4802,6 +4802,8 @@ extendedMetadataTypeExtendedMetadataAttributeResponse: $ref: "#/components/schemas/nonEmptyString" description: $ref: "#/components/schemas/nullableNonEmptyString" + property_type_id: + $ref: "#/components/schemas/nullableNonEmptyString" sample_attribute_type: type: object properties: From 9711a65f11313e12111bfd16832fc2f9b44e619d Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Wed, 24 Apr 2024 15:48:51 +0100 Subject: [PATCH 032/548] generated observation unit, and created simple factory and show test --- .../observation_units_controller.rb | 21 +++++++++++++++++++ app/helpers/observation_units_helper.rb | 2 ++ app/models/observation_unit.rb | 2 ++ .../observation_unit_serializer.rb | 3 +++ app/views/observation_units/show.html.erb | 0 config/routes.rb | 1 + ...20240424141740_create_observation_units.rb | 16 ++++++++++++++ db/schema.rb | 15 ++++++++++++- test/factories/observation_units.rb | 8 +++++++ .../observation_units_controller_test.rb | 13 ++++++++++++ 10 files changed, 80 insertions(+), 1 deletion(-) create mode 100644 app/controllers/observation_units_controller.rb create mode 100644 app/helpers/observation_units_helper.rb create mode 100644 app/models/observation_unit.rb create mode 100644 app/serializers/observation_unit_serializer.rb create mode 100644 app/views/observation_units/show.html.erb create mode 100644 db/migrate/20240424141740_create_observation_units.rb create mode 100644 test/factories/observation_units.rb create mode 100644 test/functional/observation_units_controller_test.rb diff --git a/app/controllers/observation_units_controller.rb b/app/controllers/observation_units_controller.rb new file mode 100644 index 0000000000..86c3562e4c --- /dev/null +++ b/app/controllers/observation_units_controller.rb @@ -0,0 +1,21 @@ +class ObservationUnitsController < ApplicationController + + include Seek::DestroyHandling + + before_action :organisms_enabled? + before_action :find_requested_item, :only=>[:show,:edit,:destroy, :update] + before_action :login_required,:except=>[:show,:index] + + include Seek::IndexPager + + api_actions :index, :show + + def show + respond_to do |format| + format.html + format.rdf { render :template=>'rdf/show'} + format.json {render json: @observation_unit, include: [params[:include]]} + end + end + +end diff --git a/app/helpers/observation_units_helper.rb b/app/helpers/observation_units_helper.rb new file mode 100644 index 0000000000..180d3c411d --- /dev/null +++ b/app/helpers/observation_units_helper.rb @@ -0,0 +1,2 @@ +module ObservationUnitsHelper +end diff --git a/app/models/observation_unit.rb b/app/models/observation_unit.rb new file mode 100644 index 0000000000..e6a6517bb8 --- /dev/null +++ b/app/models/observation_unit.rb @@ -0,0 +1,2 @@ +class ObservationUnit < ApplicationRecord +end diff --git a/app/serializers/observation_unit_serializer.rb b/app/serializers/observation_unit_serializer.rb new file mode 100644 index 0000000000..2e21cf79e0 --- /dev/null +++ b/app/serializers/observation_unit_serializer.rb @@ -0,0 +1,3 @@ +class ObservationUnitSerializer < ActiveModel::Serializer + attributes :id, :title, :description, :text, :identifier, :string, :organism_id, :integer +end diff --git a/app/views/observation_units/show.html.erb b/app/views/observation_units/show.html.erb new file mode 100644 index 0000000000..e69de29bb2 diff --git a/config/routes.rb b/config/routes.rb index f52e61bd9c..c8390c1f0b 100644 --- a/config/routes.rb +++ b/config/routes.rb @@ -1,4 +1,5 @@ SEEK::Application.routes.draw do + resources :observation_units resources :observed_variable_sets resources :observed_variables use_doorkeeper do diff --git a/db/migrate/20240424141740_create_observation_units.rb b/db/migrate/20240424141740_create_observation_units.rb new file mode 100644 index 0000000000..920e5c5cc7 --- /dev/null +++ b/db/migrate/20240424141740_create_observation_units.rb @@ -0,0 +1,16 @@ +class CreateObservationUnits < ActiveRecord::Migration[6.1] + def change + create_table :observation_units do |t| + t.string :title + t.string :description + t.string :text + t.string :identifier + t.string :string + t.string :organism_id + t.string :extended_metadata_type_id + t.string :integer + + t.timestamps + end + end +end diff --git a/db/schema.rb b/db/schema.rb index a90c90e26f..a17ad379c2 100644 --- a/db/schema.rb +++ b/db/schema.rb @@ -10,7 +10,7 @@ # # It's strongly recommended that you check this file into your version control system. -ActiveRecord::Schema.define(version: 2024_03_11_113858) do +ActiveRecord::Schema.define(version: 2024_04_24_141740) do create_table "activity_logs", id: :integer, force: :cascade do |t| t.string "action" @@ -1196,6 +1196,19 @@ t.index ["user_id"], name: "index_oauth_sessions_on_user_id" end + create_table "observation_units", force: :cascade do |t| + t.string "title" + t.string "description" + t.string "text" + t.string "identifier" + t.string "string" + t.string "organism_id" + t.string "extended_metadata_type_id" + t.string "integer" + t.datetime "created_at", precision: 6, null: false + t.datetime "updated_at", precision: 6, null: false + end + create_table "observed_variable_sets", force: :cascade do |t| t.string "title" t.integer "contributor_id" diff --git a/test/factories/observation_units.rb b/test/factories/observation_units.rb new file mode 100644 index 0000000000..e047a43f6b --- /dev/null +++ b/test/factories/observation_units.rb @@ -0,0 +1,8 @@ +FactoryBot.define do + factory(:observation_unit) do + title { 'Observation Unit' } + description { 'very simple obs unit'} + end + + +end \ No newline at end of file diff --git a/test/functional/observation_units_controller_test.rb b/test/functional/observation_units_controller_test.rb new file mode 100644 index 0000000000..69c610ae1e --- /dev/null +++ b/test/functional/observation_units_controller_test.rb @@ -0,0 +1,13 @@ +require 'test_helper' +require 'minitest/mock' + +class ObservationUnitsControllerTest < ActionController::TestCase + + test 'show' do + unit = FactoryBot.create(:observation_unit) + get :show, params: { id: unit.id } + assert_response :success + end + + +end \ No newline at end of file From f9c884a4c9eb7f54854de4e4b453a9d67cb8aa51 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Thu, 25 Apr 2024 09:27:52 +0100 Subject: [PATCH 033/548] expanded the observation unit object to support key associations --- app/models/observation_unit.rb | 8 ++++++++ .../20240424141740_create_observation_units.rb | 5 ++--- .../20240424145436_expand_observation_unit.rb | 8 ++++++++ ...153929_create_observation_units_projects.rb | 11 +++++++++++ db/schema.rb | 18 ++++++++++++++---- test/factories/extended_metadata.rb | 9 +++++++++ test/factories/extended_metadata_types.rb | 9 +++++++++ test/factories/observation_units.rb | 8 ++++++++ .../observation_units_controller_test.rb | 1 - test/unit/observation_unit_test.rb | 16 ++++++++++++++++ 10 files changed, 85 insertions(+), 8 deletions(-) create mode 100644 db/migrate/20240424145436_expand_observation_unit.rb create mode 100644 db/migrate/20240424153929_create_observation_units_projects.rb create mode 100644 test/unit/observation_unit_test.rb diff --git a/app/models/observation_unit.rb b/app/models/observation_unit.rb index e6a6517bb8..dca5dc297d 100644 --- a/app/models/observation_unit.rb +++ b/app/models/observation_unit.rb @@ -1,2 +1,10 @@ class ObservationUnit < ApplicationRecord + + include Seek::Creators + include Seek::ProjectAssociation + + belongs_to :contributor, class_name: 'Person' + + has_extended_metadata + end diff --git a/db/migrate/20240424141740_create_observation_units.rb b/db/migrate/20240424141740_create_observation_units.rb index 920e5c5cc7..d9bc069317 100644 --- a/db/migrate/20240424141740_create_observation_units.rb +++ b/db/migrate/20240424141740_create_observation_units.rb @@ -6,9 +6,8 @@ def change t.string :text t.string :identifier t.string :string - t.string :organism_id - t.string :extended_metadata_type_id - t.string :integer + t.bigint :organism_id + t.bigint :extended_metadata_type_id t.timestamps end diff --git a/db/migrate/20240424145436_expand_observation_unit.rb b/db/migrate/20240424145436_expand_observation_unit.rb new file mode 100644 index 0000000000..d0ccf65617 --- /dev/null +++ b/db/migrate/20240424145436_expand_observation_unit.rb @@ -0,0 +1,8 @@ +class ExpandObservationUnit < ActiveRecord::Migration[6.1] + def change + add_column :observation_units, :contributor_id, :bigint + add_column :observation_units, :uuid, :string + add_column :observation_units, :deleted_contributor, :string + add_column :observation_units, :other_creators, :text + end +end diff --git a/db/migrate/20240424153929_create_observation_units_projects.rb b/db/migrate/20240424153929_create_observation_units_projects.rb new file mode 100644 index 0000000000..553ca879e6 --- /dev/null +++ b/db/migrate/20240424153929_create_observation_units_projects.rb @@ -0,0 +1,11 @@ +class CreateObservationUnitsProjects < ActiveRecord::Migration[6.1] + def change + create_table :observation_units_projects, id: false do |t| + t.integer :project_id + t.integer :observation_unit_id + end + + add_index :observation_units_projects, [:observation_unit_id, :project_id], name: :index_projects_obs_units_on_obs_unit_id_and_project_id + add_index :observation_units_projects, [:project_id], name: :index_projects_obs_units_on_project_id + end +end diff --git a/db/schema.rb b/db/schema.rb index a17ad379c2..9361effddd 100644 --- a/db/schema.rb +++ b/db/schema.rb @@ -10,7 +10,7 @@ # # It's strongly recommended that you check this file into your version control system. -ActiveRecord::Schema.define(version: 2024_04_24_141740) do +ActiveRecord::Schema.define(version: 2024_04_24_153929) do create_table "activity_logs", id: :integer, force: :cascade do |t| t.string "action" @@ -1202,11 +1202,21 @@ t.string "text" t.string "identifier" t.string "string" - t.string "organism_id" - t.string "extended_metadata_type_id" - t.string "integer" + t.bigint "organism_id" + t.bigint "extended_metadata_type_id" t.datetime "created_at", precision: 6, null: false t.datetime "updated_at", precision: 6, null: false + t.bigint "contributor_id" + t.string "uuid" + t.string "deleted_contributor" + t.text "other_creators" + end + + create_table "observation_units_projects", id: false, force: :cascade do |t| + t.integer "project_id" + t.integer "observation_unit_id" + t.index ["observation_unit_id", "project_id"], name: "index_projects_obs_units_on_obs_unit_id_and_project_id" + t.index ["project_id"], name: "index_projects_obs_units_on_project_id" end create_table "observed_variable_sets", force: :cascade do |t| diff --git a/test/factories/extended_metadata.rb b/test/factories/extended_metadata.rb index 39e2557964..17c0dd61a5 100644 --- a/test/factories/extended_metadata.rb +++ b/test/factories/extended_metadata.rb @@ -28,4 +28,13 @@ end end + factory(:simple_observation_unit_extended_metadata, class: ExtendedMetadata) do + association :extended_metadata_type, factory: :simple_observation_unit_extended_metadata_type, strategy: :create + after(:build) do |em| + em.set_attribute_value(:name, "unit 1") + em.set_attribute_value(:strain, "strain 1") + end + + end + end \ No newline at end of file diff --git a/test/factories/extended_metadata_types.rb b/test/factories/extended_metadata_types.rb index 9b867244b2..819655f79f 100644 --- a/test/factories/extended_metadata_types.rb +++ b/test/factories/extended_metadata_types.rb @@ -137,6 +137,15 @@ end end + factory(:simple_observation_unit_extended_metadata_type, class: ExtendedMetadataType) do + title { 'simple obs unit extended metadata type' } + supported_type { 'ObservationUnit' } + after(:build) do |a| + a.extended_metadata_attributes << FactoryBot.create(:name_extended_metadata_attribute, title:'name') + a.extended_metadata_attributes << FactoryBot.create(:name_extended_metadata_attribute, title:'strain') + end + end + factory(:study_extended_metadata_type_with_clashes, class: ExtendedMetadataType) do title { 'study extended metadata type with clashes' } diff --git a/test/factories/observation_units.rb b/test/factories/observation_units.rb index e047a43f6b..afd098148e 100644 --- a/test/factories/observation_units.rb +++ b/test/factories/observation_units.rb @@ -4,5 +4,13 @@ description { 'very simple obs unit'} end + factory(:max_observation_unit, class: ObservationUnit) do + title { 'Max observation unit'} + description { 'the maximum one'} + with_project_contributor + other_creators { 'Blogs, Joe' } + assets_creators { [AssetsCreator.new(affiliation: 'University of Somewhere', creator: FactoryBot.create(:person, first_name: 'Some', last_name: 'One'))] } + extended_metadata { FactoryBot.build(:simple_observation_unit_extended_metadata)} + end end \ No newline at end of file diff --git a/test/functional/observation_units_controller_test.rb b/test/functional/observation_units_controller_test.rb index 69c610ae1e..358a21f1f1 100644 --- a/test/functional/observation_units_controller_test.rb +++ b/test/functional/observation_units_controller_test.rb @@ -9,5 +9,4 @@ class ObservationUnitsControllerTest < ActionController::TestCase assert_response :success end - end \ No newline at end of file diff --git a/test/unit/observation_unit_test.rb b/test/unit/observation_unit_test.rb new file mode 100644 index 0000000000..d3ec7ffabf --- /dev/null +++ b/test/unit/observation_unit_test.rb @@ -0,0 +1,16 @@ +require 'test_helper' + +class ObservationUnitTest < ActiveSupport::TestCase + + test 'max factory' do + obs_unit = FactoryBot.create(:max_observation_unit) + refute_nil obs_unit.created_at + refute_nil obs_unit.updated_at + refute_empty obs_unit.projects + refute_empty obs_unit.creators + refute_nil obs_unit.other_creators + refute_nil obs_unit.extended_metadata + refute_nil obs_unit.extended_metadata.extended_metadata_type + end + +end \ No newline at end of file From 8874e65d0afece1ea13a0f0ef2a51211d5204463 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Thu, 25 Apr 2024 10:27:52 +0100 Subject: [PATCH 034/548] associate observation units and studies --- app/models/observation_unit.rb | 1 + app/models/study.rb | 1 + db/migrate/20240425090243_add_study_to_observation_unit.rb | 5 +++++ db/schema.rb | 3 ++- test/factories/observation_units.rb | 4 +++- test/unit/observation_unit_test.rb | 2 ++ 6 files changed, 14 insertions(+), 2 deletions(-) create mode 100644 db/migrate/20240425090243_add_study_to_observation_unit.rb diff --git a/app/models/observation_unit.rb b/app/models/observation_unit.rb index dca5dc297d..e8eeaf84bc 100644 --- a/app/models/observation_unit.rb +++ b/app/models/observation_unit.rb @@ -4,6 +4,7 @@ class ObservationUnit < ApplicationRecord include Seek::ProjectAssociation belongs_to :contributor, class_name: 'Person' + belongs_to :study has_extended_metadata diff --git a/app/models/study.rb b/app/models/study.rb index 4e908e7f4f..447a9f79c7 100644 --- a/app/models/study.rb +++ b/app/models/study.rb @@ -20,6 +20,7 @@ class Study < ApplicationRecord has_many :assay_sops, through: :assays, source: :sops has_many :sop_versions, through: :assays + has_many :observation_units has_one :external_asset, as: :seek_entity, dependent: :destroy diff --git a/db/migrate/20240425090243_add_study_to_observation_unit.rb b/db/migrate/20240425090243_add_study_to_observation_unit.rb new file mode 100644 index 0000000000..c14df7982c --- /dev/null +++ b/db/migrate/20240425090243_add_study_to_observation_unit.rb @@ -0,0 +1,5 @@ +class AddStudyToObservationUnit < ActiveRecord::Migration[6.1] + def change + add_column :observation_units, :study_id, :bigint + end +end diff --git a/db/schema.rb b/db/schema.rb index 9361effddd..abd91041a2 100644 --- a/db/schema.rb +++ b/db/schema.rb @@ -10,7 +10,7 @@ # # It's strongly recommended that you check this file into your version control system. -ActiveRecord::Schema.define(version: 2024_04_24_153929) do +ActiveRecord::Schema.define(version: 2024_04_25_090243) do create_table "activity_logs", id: :integer, force: :cascade do |t| t.string "action" @@ -1210,6 +1210,7 @@ t.string "uuid" t.string "deleted_contributor" t.text "other_creators" + t.bigint "study_id" end create_table "observation_units_projects", id: false, force: :cascade do |t| diff --git a/test/factories/observation_units.rb b/test/factories/observation_units.rb index afd098148e..77e162a4f4 100644 --- a/test/factories/observation_units.rb +++ b/test/factories/observation_units.rb @@ -2,6 +2,7 @@ factory(:observation_unit) do title { 'Observation Unit' } description { 'very simple obs unit'} + with_project_contributor end factory(:max_observation_unit, class: ObservationUnit) do @@ -10,7 +11,8 @@ with_project_contributor other_creators { 'Blogs, Joe' } assets_creators { [AssetsCreator.new(affiliation: 'University of Somewhere', creator: FactoryBot.create(:person, first_name: 'Some', last_name: 'One'))] } - extended_metadata { FactoryBot.build(:simple_observation_unit_extended_metadata)} + association :extended_metadata, factory: :simple_observation_unit_extended_metadata, strategy: :create + association :study, factory: :study, strategy: :create end end \ No newline at end of file diff --git a/test/unit/observation_unit_test.rb b/test/unit/observation_unit_test.rb index d3ec7ffabf..ab1f19d074 100644 --- a/test/unit/observation_unit_test.rb +++ b/test/unit/observation_unit_test.rb @@ -11,6 +11,8 @@ class ObservationUnitTest < ActiveSupport::TestCase refute_nil obs_unit.other_creators refute_nil obs_unit.extended_metadata refute_nil obs_unit.extended_metadata.extended_metadata_type + refute_nil obs_unit.study + refute_empty obs_unit.study.observation_units end end \ No newline at end of file From 55d2660894dc0f7ddd58d05e314506897d5b9472 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Thu, 25 Apr 2024 14:35:45 +0100 Subject: [PATCH 035/548] include observation units in the constructed ISA --- lib/bio_ind/fair_data/reader.rb | 5 +++++ .../unit/bioind/fairdata/fair_data_reader_test.rb | 15 +++++++++------ 2 files changed, 14 insertions(+), 6 deletions(-) diff --git a/lib/bio_ind/fair_data/reader.rb b/lib/bio_ind/fair_data/reader.rb index e837708099..b9780deee1 100644 --- a/lib/bio_ind/fair_data/reader.rb +++ b/lib/bio_ind/fair_data/reader.rb @@ -44,6 +44,11 @@ def self.construct_isa(datastation_inv, contributor, projects) assay.assay_assets.build(asset: df) end end + datastation_study.observation_units.each do |datastation_observation_unit| + observation_unit_attributes = datastation_observation_unit.seek_attributes.merge({contributor: contributor, study:study, projects: projects}) + observation_unit = study.observation_units.build(observation_unit_attributes) + populate_extended_metadata(observation_unit, datastation_observation_unit) + end end return investigation diff --git a/test/unit/bioind/fairdata/fair_data_reader_test.rb b/test/unit/bioind/fairdata/fair_data_reader_test.rb index c9a3af74ad..75f1fc3367 100644 --- a/test/unit/bioind/fairdata/fair_data_reader_test.rb +++ b/test/unit/bioind/fairdata/fair_data_reader_test.rb @@ -127,12 +127,14 @@ class FairDataReaderTest < ActiveSupport::TestCase investigation = BioInd::FairData::Reader.construct_isa(inv, contributor, [project]) studies = investigation.studies.to_a + obs_units = studies.first.observation_units.to_a assays = studies.first.assays.to_a data_files = assays.first.assay_assets.to_a.collect(&:asset) assert_equal 1, studies.count assert_equal 9, assays.count assert_equal 2, data_files.count + assert_equal 2, obs_units.count assert investigation.valid? assert studies.first.valid? @@ -145,18 +147,19 @@ class FairDataReaderTest < ActiveSupport::TestCase assert_difference('Investigation.count', 1) do assert_difference('Study.count', 1) do - assert_difference('Assay.count', 9) do - assert_difference('AssayAsset.count', 18) do - assert_difference('DataFile.count', 18) do - User.with_current_user(contributor.user) do - investigation.save! + assert_difference('ObservationUnit.count', 2) do + assert_difference('Assay.count', 9) do + assert_difference('AssayAsset.count', 18) do + assert_difference('DataFile.count', 18) do + User.with_current_user(contributor.user) do + investigation.save! + end end end end end end end - end test 'populate extended metadata' do From c6171f7205bec7ee65c2c503fbf4ac25fe0a0fe8 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Thu, 25 Apr 2024 15:06:40 +0100 Subject: [PATCH 036/548] show observation units in study related items --- app/models/observation_unit.rb | 5 +++++ app/views/observation_units/_resource_list_item.html.erb | 7 +++++++ config/image_files/image_file_dictionary.yml | 1 + config/locales/en.yml | 3 +++ config/routes.rb | 2 +- lib/seek/related_items.rb | 2 +- 6 files changed, 18 insertions(+), 2 deletions(-) create mode 100644 app/views/observation_units/_resource_list_item.html.erb diff --git a/app/models/observation_unit.rb b/app/models/observation_unit.rb index e8eeaf84bc..0d45ea023b 100644 --- a/app/models/observation_unit.rb +++ b/app/models/observation_unit.rb @@ -8,4 +8,9 @@ class ObservationUnit < ApplicationRecord has_extended_metadata + + def contributors + [contributor] + end + end diff --git a/app/views/observation_units/_resource_list_item.html.erb b/app/views/observation_units/_resource_list_item.html.erb new file mode 100644 index 0000000000..73bd9ba84b --- /dev/null +++ b/app/views/observation_units/_resource_list_item.html.erb @@ -0,0 +1,7 @@ +<%= list_item_description resource.description %> + +
    +
    + +
    +
    diff --git a/config/image_files/image_file_dictionary.yml b/config/image_files/image_file_dictionary.yml index 431edddf93..dceeb744bb 100644 --- a/config/image_files/image_file_dictionary.yml +++ b/config/image_files/image_file_dictionary.yml @@ -107,6 +107,7 @@ no_user: 'famfamfam_silk/link_break.png' oauth: 'famfamfam_silk/link.png' oauth_applications: 'famfamfam_silk/application_key.png' oauth_authorized_applications: 'famfamfam_silk/application_link.png' +observation_unit_avatar: 'misc_icons/cell3.png' openbis_square_small: 'logos/openbis-square-16.png' openbis_square: 'logos/openbis-square.png' openbis: 'logos/openbis.png' diff --git a/config/locales/en.yml b/config/locales/en.yml index 31a337630a..2b3fea9ead 100644 --- a/config/locales/en.yml +++ b/config/locales/en.yml @@ -52,6 +52,7 @@ en: placeholder: "Placeholder" collection: &collection "Collection" + observation_unit: &observation_unit "Observation Unit" sample: &sample "Sample" sample_type: &sample_type "Sample type" template: &template "Template" @@ -176,6 +177,7 @@ en: collection: *collection presentation: *presentation event: *event + observation_unit: *observation_unit sample: *sample template: *template sample_type: *sample_type @@ -199,6 +201,7 @@ en: collections: 'Collections' presentations: 'Presentations' events: 'Events' + observation_units: 'Observation Units' samples: 'Samples' templates: 'Templates' sample_types: 'Samples types' diff --git a/config/routes.rb b/config/routes.rb index c8390c1f0b..bd2b32acb3 100644 --- a/config/routes.rb +++ b/config/routes.rb @@ -455,7 +455,7 @@ get :order_assays patch :manage_update end - resources :people, :programmes, :projects, :sample_types, :assays, :investigations, :models, :sops, :workflows, :data_files, :publications, :documents, only: [:index] + resources :people, :programmes, :projects, :sample_types, :assays, :investigations, :models, :sops, :workflows, :data_files, :publications, :documents, :observation_units, only: [:index] end resources :assays, concerns: [:publishable, :has_snapshots, :isa] do diff --git a/lib/seek/related_items.rb b/lib/seek/related_items.rb index e4e50f194e..0f785daba8 100644 --- a/lib/seek/related_items.rb +++ b/lib/seek/related_items.rb @@ -5,7 +5,7 @@ module RelatedItems RELATABLE_TYPES = ['Person', 'Programme', 'Project', 'Institution', 'Investigation', 'Study', 'Assay', 'DataFile', 'Document', 'Model', 'Sop', 'Publication', 'Presentation', 'Event', 'Organism', 'Strain', 'SampleType', 'Sample', 'Workflow', 'Collection', 'HumanDisease', 'FileTemplate', 'Placeholder', - 'Template'].freeze + 'Template', 'ObservationUnit'].freeze # special cases of associations to be skipped { self: relatable_type } RELATABLE_TYPES_DENYLIST = { From 6377254e43a7941e40376d025a1cf4d4acf4c805 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Thu, 25 Apr 2024 15:16:58 +0100 Subject: [PATCH 037/548] show observation units in the related items and jstree for Study --- lib/seek/isa_graph_generator.rb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/lib/seek/isa_graph_generator.rb b/lib/seek/isa_graph_generator.rb index 6c18879ed7..0f3afc4340 100644 --- a/lib/seek/isa_graph_generator.rb +++ b/lib/seek/isa_graph_generator.rb @@ -188,7 +188,7 @@ def associations(object) } when Study { - children: [:positioned_assays], + children: [:positioned_assays, :observation_units], related: [:publications, :sops], parents: [:investigation] } @@ -219,6 +219,10 @@ def associations(object) { parents: %i[presentations publications data_files documents] } + when ObservationUnit + { + parents: %i[study] + } else {} end.reverse_merge!(parents: [], children: [], related: [], aggregated_children: {}) From cae1f2f686cfe7e16725773c76a42c81a6a0e16f Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Thu, 25 Apr 2024 15:53:04 +0100 Subject: [PATCH 038/548] simple show page for observation unit --- app/models/observation_unit.rb | 13 ++++++++++ app/views/observation_units/show.html.erb | 31 +++++++++++++++++++++++ config/routes.rb | 9 ++++++- 3 files changed, 52 insertions(+), 1 deletion(-) diff --git a/app/models/observation_unit.rb b/app/models/observation_unit.rb index 0d45ea023b..8c6f7e0c32 100644 --- a/app/models/observation_unit.rb +++ b/app/models/observation_unit.rb @@ -2,6 +2,7 @@ class ObservationUnit < ApplicationRecord include Seek::Creators include Seek::ProjectAssociation + include Seek::Stats::ActivityCounts belongs_to :contributor, class_name: 'Person' belongs_to :study @@ -13,4 +14,16 @@ def contributors [contributor] end + def is_in_isa_publishable? + false + end + + def can_publish? + false + end + + def related_people + (creators + contributors).compact.uniq + end + end diff --git a/app/views/observation_units/show.html.erb b/app/views/observation_units/show.html.erb index e69de29bb2..1018628e1d 100644 --- a/app/views/observation_units/show.html.erb +++ b/app/views/observation_units/show.html.erb @@ -0,0 +1,31 @@ +<%= render partial: 'general/item_title', locals: { item: @observation_unit } %> + + +<%= render partial: 'general/show_page_tab_definitions' %> + +
    + <%= tab_pane('overview') do %> +
    +
    + <%= item_description @observation_unit.description -%> + +
    +
    + <%= persistent_resource_id(@observation_unit) %> +
    +
    + + <%= render partial: 'extended_metadata/extended_metadata_attribute_values', locals: { resource: @observation_unit } %> + <%= render :partial=>"general/isa_graph", :locals => {:root_item => @observation_unit, :deep => true, :include_parents => true} %> +
    + +
    + <%= render :partial=>"assets/resource_main_content_right",:locals => { :resource => @observation_unit } %> +
    +
    + <% end %> + + <%= tab_pane('related-items') do %> + <%= render partial: 'general/items_related_to', object: @observation_unit %> + <% end %> +
    \ No newline at end of file diff --git a/config/routes.rb b/config/routes.rb index bd2b32acb3..de5dcedf7c 100644 --- a/config/routes.rb +++ b/config/routes.rb @@ -1,5 +1,5 @@ SEEK::Application.routes.draw do - resources :observation_units + resources :observed_variable_sets resources :observed_variables use_doorkeeper do @@ -799,6 +799,13 @@ get '/modelling_analysis_types/', to: 'assay_types#show', as: 'modelling_analysis_types' get '/technology_types/', to: 'technology_types#show', as: 'technology_types' + ### OBSERVATION UNITS ### + + resources :observation_units, only: [:show] do + + resources :projects, :people, :programmes, :studies + end + ### MISC MATCHES ### get '/search/' => 'search#index', as: :search get '/search/save' => 'search#save', as: :save_search From 9102d2a2d4fb24a5d9437b69692a3e89ae125c3e Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Thu, 25 Apr 2024 15:55:56 +0100 Subject: [PATCH 039/548] fix description col in schema.rb --- db/migrate/20240424141740_create_observation_units.rb | 4 +--- db/schema.rb | 4 +--- 2 files changed, 2 insertions(+), 6 deletions(-) diff --git a/db/migrate/20240424141740_create_observation_units.rb b/db/migrate/20240424141740_create_observation_units.rb index d9bc069317..ebdaa7c13e 100644 --- a/db/migrate/20240424141740_create_observation_units.rb +++ b/db/migrate/20240424141740_create_observation_units.rb @@ -2,10 +2,8 @@ class CreateObservationUnits < ActiveRecord::Migration[6.1] def change create_table :observation_units do |t| t.string :title - t.string :description - t.string :text + t.text :description t.string :identifier - t.string :string t.bigint :organism_id t.bigint :extended_metadata_type_id diff --git a/db/schema.rb b/db/schema.rb index abd91041a2..d827957a96 100644 --- a/db/schema.rb +++ b/db/schema.rb @@ -1198,10 +1198,8 @@ create_table "observation_units", force: :cascade do |t| t.string "title" - t.string "description" - t.string "text" + t.text "description" t.string "identifier" - t.string "string" t.bigint "organism_id" t.bigint "extended_metadata_type_id" t.datetime "created_at", precision: 6, null: false From 867d7f3ea428e68e27d5fed42e4c48a1a8b5ef21 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 30 Apr 2024 09:55:06 +0100 Subject: [PATCH 040/548] extended metadata for observation units --- .../fairdatastation_virtual_demo.seeds.rb | 13 ++++++++ test/factories/extended_metadata_types.rb | 12 +++++++ .../bioind/fairdata/fair_data_reader_test.rb | 32 +++++++++++++++++++ 3 files changed, 57 insertions(+) diff --git a/db/seeds/extended_metadata_drafts/fairdatastation_virtual_demo.seeds.rb b/db/seeds/extended_metadata_drafts/fairdatastation_virtual_demo.seeds.rb index accd8f742a..72b97604b4 100644 --- a/db/seeds/extended_metadata_drafts/fairdatastation_virtual_demo.seeds.rb +++ b/db/seeds/extended_metadata_drafts/fairdatastation_virtual_demo.seeds.rb @@ -31,4 +31,17 @@ emt.save! puts 'Fair Data Station Virtual Demo for Assay' +end + +unless ExtendedMetadataType.where(title:'Fair Data Station Indpensim', supported_type:'ObservationUnit').any? + emt = ExtendedMetadataType.new(title: 'Fair Data Station Indpensim', supported_type:'ObservationUnit') + + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Brand', property_type_id:'http://fairbydesign.nl/ontology/brand', sample_attribute_type: SampleAttributeType.where(title:'String').first) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Fermentation', property_type_id:'http://fairbydesign.nl/ontology/fermentation', sample_attribute_type: SampleAttributeType.where(title:'String').first) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Volume', property_type_id:'http://fairbydesign.nl/ontology/volume', sample_attribute_type: SampleAttributeType.where(title:'String').first) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Scientific Name', property_type_id:'http://gbol.life/0.1/scientificName', sample_attribute_type: SampleAttributeType.where(title:'String').first) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Organism', property_type_id:'http://purl.uniprot.org/core/organism', sample_attribute_type: SampleAttributeType.where(title:'String').first) + + emt.save! + puts 'Fair Data Station Indpensim for Observation Unit' end \ No newline at end of file diff --git a/test/factories/extended_metadata_types.rb b/test/factories/extended_metadata_types.rb index 819655f79f..65513fe145 100644 --- a/test/factories/extended_metadata_types.rb +++ b/test/factories/extended_metadata_types.rb @@ -464,5 +464,17 @@ end end + factory(:fairdata_indpensim_obsv_unit_extended_metadata, class: ExtendedMetadataType) do + title {'Fair Data Station Obs Unit Indpensim'} + supported_type { 'ObservationUnit' } + after(:build) do |a| + a.extended_metadata_attributes << FactoryBot.create(:study_title_extended_metadata_attribute, title: 'Brand', property_type_id:'http://fairbydesign.nl/ontology/brand') + a.extended_metadata_attributes << FactoryBot.create(:study_title_extended_metadata_attribute, title: 'Fermentation', property_type_id:'http://fairbydesign.nl/ontology/fermentation') + a.extended_metadata_attributes << FactoryBot.create(:study_title_extended_metadata_attribute, title: 'Volume', property_type_id:'http://fairbydesign.nl/ontology/volume') + a.extended_metadata_attributes << FactoryBot.create(:study_title_extended_metadata_attribute, title: 'Scientific Name', property_type_id:'http://gbol.life/0.1/scientificName') + a.extended_metadata_attributes << FactoryBot.create(:study_title_extended_metadata_attribute, title: 'Organism', property_type_id:'http://purl.uniprot.org/core/organism') + end + end + end diff --git a/test/unit/bioind/fairdata/fair_data_reader_test.rb b/test/unit/bioind/fairdata/fair_data_reader_test.rb index 75f1fc3367..7368d31531 100644 --- a/test/unit/bioind/fairdata/fair_data_reader_test.rb +++ b/test/unit/bioind/fairdata/fair_data_reader_test.rb @@ -209,4 +209,36 @@ class FairDataReaderTest < ActiveSupport::TestCase end end + test 'populate obsv unit extended metadata' do + ext_metadata_type = FactoryBot.create(:fairdata_indpensim_obsv_unit_extended_metadata) + FactoryBot.create(:experimental_assay_class) + + path = "#{Rails.root}/test/fixtures/files/fairdatastation/indpensim.ttl" + inv = BioInd::FairData::Reader.parse_graph(path).first + contributor = FactoryBot.create(:person) + project = contributor.projects.first + + investigation = BioInd::FairData::Reader.construct_isa(inv, contributor, [project]) + assert_nil investigation.extended_metadata + + assert_difference('ExtendedMetadata.count', 100) do + User.with_current_user(contributor.user) do + investigation.save! + end + end + + assert_equal 1, investigation.studies.count + study = investigation.studies.first + assert_equal 100, study.observation_units.count + obvs_unit = study.observation_units.first + refute_nil obvs_unit.extended_metadata + assert_equal ext_metadata_type, obvs_unit.extended_metadata.extended_metadata_type + + assert_equal 'FermentorX', obvs_unit.extended_metadata.get_attribute_value('Brand') + assert_equal 'batch', obvs_unit.extended_metadata.get_attribute_value('Fermentation') + assert_equal '100,000 litre', obvs_unit.extended_metadata.get_attribute_value('Volume') + # assert_equal 'Penicillium chrysogenum', obvs_unit.extended_metadata.get_attribute_value('Scientific Name') + # assert_equal '5076', obvs_unit.extended_metadata.get_attribute_value('Organism') + end + end From 122694b2b9992a84d4e3a0f96d9d5bbf5a17ec94 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 30 Apr 2024 10:14:10 +0100 Subject: [PATCH 041/548] fix getting the additional metadata annotations, no longer assume only fairbydesign based identifiers --- lib/bio_ind/fair_data/base.rb | 14 ++++++++++++-- .../bioind/fairdata/fair_data_reader_test.rb | 16 +++++++++++++--- 2 files changed, 25 insertions(+), 5 deletions(-) diff --git a/lib/bio_ind/fair_data/base.rb b/lib/bio_ind/fair_data/base.rb index f9cb37a84c..d137d670f3 100644 --- a/lib/bio_ind/fair_data/base.rb +++ b/lib/bio_ind/fair_data/base.rb @@ -1,7 +1,7 @@ module BioInd module FairData class Base - attr_reader :resource_uri, :graph, :children + attr_reader :resource_uri, :graph, :children, :core_annotations def initialize(resource_uri, graph) @resource_uri = resource_uri @@ -10,6 +10,16 @@ def initialize(resource_uri, graph) @schema = RDF::Vocabulary.new('http://schema.org/') @fair = RDF::Vocabulary.new('http://fairbydesign.nl/ontology/') @children = [] + @core_annotations = [ + @schema.contributor, + @schema.dataset, + @schema.description, + @schema.identifier, + @schema.name, + @schema.title, + RDF.type, + @jerm.hasPart + ] end def identifier @@ -37,7 +47,7 @@ def annotations def additional_metadata_annotations annotations.select do |annotation| - annotation[0].start_with?(@fair.to_s) + !core_annotations.include?(annotation[0]) end end diff --git a/test/unit/bioind/fairdata/fair_data_reader_test.rb b/test/unit/bioind/fairdata/fair_data_reader_test.rb index 7368d31531..2a89dea22d 100644 --- a/test/unit/bioind/fairdata/fair_data_reader_test.rb +++ b/test/unit/bioind/fairdata/fair_data_reader_test.rb @@ -43,7 +43,7 @@ class FairDataReaderTest < ActiveSupport::TestCase assert_includes study.annotations, ["http://fairbydesign.nl/ontology/center_name", "NIID"] end - test 'metadata annotations' do + test 'additional metadata annotations' do path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" inv = BioInd::FairData::Reader.parse_graph(path).first @@ -56,6 +56,16 @@ class FairDataReaderTest < ActiveSupport::TestCase study.additional_metadata_annotations.each do |annotation| assert annotation[0].start_with?('http://fairbydesign.nl/ontology/'), "#{annotation[0]} is not expected" end + + # non fairbydesign annotations + path = "#{Rails.root}/test/fixtures/files/fairdatastation/indpensim.ttl" + inv = BioInd::FairData::Reader.parse_graph(path).first + obs_unit = inv.studies.first.observation_units.first + annotations = obs_unit.additional_metadata_annotations + assert_equal 5, annotations.count + pids = annotations.collect{|ann| ann[0]} + assert_includes pids, 'http://gbol.life/0.1/scientificName' + assert_includes pids, 'http://purl.uniprot.org/core/organism' end test 'study assays' do @@ -237,8 +247,8 @@ class FairDataReaderTest < ActiveSupport::TestCase assert_equal 'FermentorX', obvs_unit.extended_metadata.get_attribute_value('Brand') assert_equal 'batch', obvs_unit.extended_metadata.get_attribute_value('Fermentation') assert_equal '100,000 litre', obvs_unit.extended_metadata.get_attribute_value('Volume') - # assert_equal 'Penicillium chrysogenum', obvs_unit.extended_metadata.get_attribute_value('Scientific Name') - # assert_equal '5076', obvs_unit.extended_metadata.get_attribute_value('Organism') + assert_equal 'Penicillium chrysogenum', obvs_unit.extended_metadata.get_attribute_value('Scientific Name') + assert_equal '5076', obvs_unit.extended_metadata.get_attribute_value('Organism') end end From 77837b32545a4a9fe19f90eec5c4e24cbec2919d Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 30 Apr 2024 10:51:14 +0100 Subject: [PATCH 042/548] search and a basic index page for obs units --- app/controllers/observation_units_controller.rb | 1 + app/models/observation_unit.rb | 2 +- app/views/general/_index.html.erb | 7 +++++-- app/views/observation_units/index.html.erb | 1 + config/routes.rb | 2 +- lib/seek/util.rb | 2 +- test/functional/observation_units_controller_test.rb | 6 ++++++ test/unit/util_test.rb | 2 +- 8 files changed, 17 insertions(+), 6 deletions(-) create mode 100644 app/views/observation_units/index.html.erb diff --git a/app/controllers/observation_units_controller.rb b/app/controllers/observation_units_controller.rb index 86c3562e4c..6b4e1a2c32 100644 --- a/app/controllers/observation_units_controller.rb +++ b/app/controllers/observation_units_controller.rb @@ -5,6 +5,7 @@ class ObservationUnitsController < ApplicationController before_action :organisms_enabled? before_action :find_requested_item, :only=>[:show,:edit,:destroy, :update] before_action :login_required,:except=>[:show,:index] + before_action :find_assets, only: [:index] include Seek::IndexPager diff --git a/app/models/observation_unit.rb b/app/models/observation_unit.rb index 8c6f7e0c32..203acf584b 100644 --- a/app/models/observation_unit.rb +++ b/app/models/observation_unit.rb @@ -3,13 +3,13 @@ class ObservationUnit < ApplicationRecord include Seek::Creators include Seek::ProjectAssociation include Seek::Stats::ActivityCounts + include Seek::Search::CommonFields, Seek::Search::BackgroundReindexing belongs_to :contributor, class_name: 'Person' belongs_to :study has_extended_metadata - def contributors [contributor] end diff --git a/app/views/general/_index.html.erb b/app/views/general/_index.html.erb index 74a821ae9b..b94e361d14 100644 --- a/app/views/general/_index.html.erb +++ b/app/views/general/_index.html.erb @@ -1,8 +1,11 @@ <% - new_item_label ||= "New #{t(controller_name.singularize)}" - new_item_path = polymorphic_path([:new, controller_name.singularize.to_sym]) items ||= instance_variable_get("@#{controller_name}") show_new_button = true unless local_assigns.has_key?(:show_new_button) + if show_new_button + new_item_label ||= "New #{t(controller_name.singularize)}" + new_item_path = polymorphic_path([:new, controller_name.singularize.to_sym]) + end + show_samples_query_button = false unless local_assigns.has_key?(:show_samples_query_button) title ||= nil subtitle ||= nil diff --git a/app/views/observation_units/index.html.erb b/app/views/observation_units/index.html.erb new file mode 100644 index 0000000000..06ee0b09b8 --- /dev/null +++ b/app/views/observation_units/index.html.erb @@ -0,0 +1 @@ +<%= render partial: 'general/index', locals:{show_new_button: false} %> \ No newline at end of file diff --git a/config/routes.rb b/config/routes.rb index de5dcedf7c..df064a28b2 100644 --- a/config/routes.rb +++ b/config/routes.rb @@ -801,7 +801,7 @@ ### OBSERVATION UNITS ### - resources :observation_units, only: [:show] do + resources :observation_units, only: [:show, :index] do resources :projects, :people, :programmes, :studies end diff --git a/lib/seek/util.rb b/lib/seek/util.rb index a1f2e4ce1c..29767e3f86 100644 --- a/lib/seek/util.rb +++ b/lib/seek/util.rb @@ -59,7 +59,7 @@ def self.searchable_types # FIXME: hard-coded extra types - are are these items now user_creatable? # FIXME: remove the reliance on user-creatable, partly by respond_to?(:reindex) but also take into account if it has been enabled or not #- could add a searchable? method - extras = [Person, Programme, Project, Institution, Organism, HumanDisease] + extras = [Person, Programme, Project, Institution, Organism, HumanDisease, ObservationUnit] cache('searchable_types') { filter_disabled(user_creatable_types | extras).sort_by(&:name) } end diff --git a/test/functional/observation_units_controller_test.rb b/test/functional/observation_units_controller_test.rb index 358a21f1f1..7a7b739701 100644 --- a/test/functional/observation_units_controller_test.rb +++ b/test/functional/observation_units_controller_test.rb @@ -9,4 +9,10 @@ class ObservationUnitsControllerTest < ActionController::TestCase assert_response :success end + test 'index' do + unit = FactoryBot.create(:observation_unit) + get :index + assert_response :success + end + end \ No newline at end of file diff --git a/test/unit/util_test.rb b/test/unit/util_test.rb index 85af79b83c..a1a5dece29 100644 --- a/test/unit/util_test.rb +++ b/test/unit/util_test.rb @@ -37,7 +37,7 @@ def teardown end test 'searchable types' do - expected = [Assay, Collection, DataFile, Document, Event, FileTemplate, HumanDisease, Institution, Investigation, Model, Organism, Person, Placeholder, Presentation, Programme, Project, Publication, Sample, SampleType, Sop, Strain, Study, Workflow, Template] + expected = [Assay, Collection, DataFile, Document, Event, FileTemplate, HumanDisease, Institution, Investigation, Model, ObservationUnit, Organism, Person, Placeholder, Presentation, Programme, Project, Publication, Sample, SampleType, Sop, Strain, Study, Workflow, Template] types = with_config_value :isa_json_compliance_enabled, true do Seek::Util.searchable_types From 03eb573f46d2a17db659989f09805f75a971f090 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 30 Apr 2024 14:30:30 +0100 Subject: [PATCH 043/548] add observation_unit -> samples association --- app/models/observation_unit.rb | 1 + app/models/sample.rb | 2 ++ db/migrate/20240430132048_add_obs_unit_id_to_sample.rb | 5 +++++ db/schema.rb | 3 ++- 4 files changed, 10 insertions(+), 1 deletion(-) create mode 100644 db/migrate/20240430132048_add_obs_unit_id_to_sample.rb diff --git a/app/models/observation_unit.rb b/app/models/observation_unit.rb index 203acf584b..463fb7de8b 100644 --- a/app/models/observation_unit.rb +++ b/app/models/observation_unit.rb @@ -7,6 +7,7 @@ class ObservationUnit < ApplicationRecord belongs_to :contributor, class_name: 'Person' belongs_to :study + has_many :samples has_extended_metadata diff --git a/app/models/sample.rb b/app/models/sample.rb index c68ec6eb0f..874362bd40 100644 --- a/app/models/sample.rb +++ b/app/models/sample.rb @@ -32,6 +32,8 @@ class Sample < ApplicationRecord has_many :linked_data_files, through: :sample_resource_links, source: :resource, source_type: 'DataFile' + belongs_to :observation_unit + validates :projects, presence: true, projects: { self: true } validates :title, :sample_type, presence: true diff --git a/db/migrate/20240430132048_add_obs_unit_id_to_sample.rb b/db/migrate/20240430132048_add_obs_unit_id_to_sample.rb new file mode 100644 index 0000000000..52d6f55067 --- /dev/null +++ b/db/migrate/20240430132048_add_obs_unit_id_to_sample.rb @@ -0,0 +1,5 @@ +class AddObsUnitIdToSample < ActiveRecord::Migration[6.1] + def change + add_column :samples, :observation_unit_id, :bigint + end +end diff --git a/db/schema.rb b/db/schema.rb index d827957a96..5267c58bf8 100644 --- a/db/schema.rb +++ b/db/schema.rb @@ -10,7 +10,7 @@ # # It's strongly recommended that you check this file into your version control system. -ActiveRecord::Schema.define(version: 2024_04_25_090243) do +ActiveRecord::Schema.define(version: 2024_04_30_132048) do create_table "activity_logs", id: :integer, force: :cascade do |t| t.string "action" @@ -1822,6 +1822,7 @@ t.text "other_creators" t.integer "originating_data_file_id" t.string "deleted_contributor" + t.bigint "observation_unit_id" end create_table "saved_searches", id: :integer, force: :cascade do |t| From 30e795cc94d92d33bb82e4d6a1508c49a0a084e8 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 30 Apr 2024 15:29:16 +0100 Subject: [PATCH 044/548] create the sample and linking to obs unit but not yet properly populating it --- lib/bio_ind/fair_data/reader.rb | 19 ++++++++++++++ test/factories/observation_units.rb | 1 + test/factories/sample_types.rb | 25 +++++++++++++++++++ .../bioind/fairdata/fair_data_reader_test.rb | 16 ++++++++---- test/unit/observation_unit_test.rb | 2 ++ 5 files changed, 58 insertions(+), 5 deletions(-) diff --git a/lib/bio_ind/fair_data/reader.rb b/lib/bio_ind/fair_data/reader.rb index b9780deee1..a316bddad6 100644 --- a/lib/bio_ind/fair_data/reader.rb +++ b/lib/bio_ind/fair_data/reader.rb @@ -48,6 +48,13 @@ def self.construct_isa(datastation_inv, contributor, projects) observation_unit_attributes = datastation_observation_unit.seek_attributes.merge({contributor: contributor, study:study, projects: projects}) observation_unit = study.observation_units.build(observation_unit_attributes) populate_extended_metadata(observation_unit, datastation_observation_unit) + datastation_observation_unit.samples.each do |datastation_sample| + sample = observation_unit.samples.build(title: 'fish', contributor: contributor, projects: projects) + populate_sample(sample, datastation_sample) + unless sample.valid? + pp sample.errors.full_messages + end + end end end @@ -75,6 +82,18 @@ def self.detect_extended_metadata(seek_entity, datastation_entity) candidates.first&.last end + def self.populate_sample(seek_sample, datastation_sample) + if sample_type = detect_sample_type(datastation_sample) + seek_sample.sample_type = sample_type + seek_sample.set_attribute_value('Title', datastation_sample.title) + seek_sample.set_attribute_value('Description', datastation_sample.description) + end + end + + def self.detect_sample_type(datastation_sample) + SampleType.last + end + end end end diff --git a/test/factories/observation_units.rb b/test/factories/observation_units.rb index 77e162a4f4..e732b93b16 100644 --- a/test/factories/observation_units.rb +++ b/test/factories/observation_units.rb @@ -13,6 +13,7 @@ assets_creators { [AssetsCreator.new(affiliation: 'University of Somewhere', creator: FactoryBot.create(:person, first_name: 'Some', last_name: 'One'))] } association :extended_metadata, factory: :simple_observation_unit_extended_metadata, strategy: :create association :study, factory: :study, strategy: :create + samples { build_list :sample, 3} end end \ No newline at end of file diff --git a/test/factories/sample_types.rb b/test/factories/sample_types.rb index ca397bb140..c7423f8b5f 100644 --- a/test/factories/sample_types.rb +++ b/test/factories/sample_types.rb @@ -213,4 +213,29 @@ type.sample_attributes << FactoryBot.build(:sample_attribute, title: 'Data file comment 3', sample_attribute_type: FactoryBot.create(:controlled_vocab_attribute_type, title: 'Ontology'), isa_tag_id: FactoryBot.create(:data_file_comment_isa_tag).id, sample_controlled_vocab: FactoryBot.create(:efo_ontology), pid: 'pid:pid', sample_type: type, allow_cv_free_text: true) end end + + # fair:host "Homo sapiens" ; + # fair:host_disease_stat "HIV-1 negative" ; + # fair:marital_status "Single" ; + # fair:occupation "Trader" ; + # fair:sample_name "13C" ; + # gbol:scientificName "human gut metagenome" ; + # jerm:hasPart ; + # uniprot:organism 408170 ; + + factory(:fairdatastation_virtual_demo_sample_type, parent: :sample_type) do + title { 'fair data station virtual demo'} + after(:build) do |type, eval| + type.sample_attributes << FactoryBot.build(:sample_attribute, sample_attribute_type: FactoryBot.create(:string_sample_attribute_type), title:'Title', sample_type: type, is_title: true) + type.sample_attributes << FactoryBot.build(:sample_attribute, sample_attribute_type: FactoryBot.create(:string_sample_attribute_type), title:'Description', sample_type: type) + + type.sample_attributes << FactoryBot.build(:sample_attribute, sample_attribute_type: FactoryBot.create(:string_sample_attribute_type), title:'Host', pid:'http://fairbydesign.nl/ontology/host', sample_type: type) + type.sample_attributes << FactoryBot.build(:sample_attribute, sample_attribute_type: FactoryBot.create(:string_sample_attribute_type), title:'Host disease stat', pid:'http://fairbydesign.nl/ontology/host_disease_stat', sample_type: type) + type.sample_attributes << FactoryBot.build(:sample_attribute, sample_attribute_type: FactoryBot.create(:string_sample_attribute_type), title:'Marital status', pid:'http://fairbydesign.nl/ontology/marital_status', sample_type: type) + type.sample_attributes << FactoryBot.build(:sample_attribute, sample_attribute_type: FactoryBot.create(:string_sample_attribute_type), title:'Occupation', pid:'http://fairbydesign.nl/ontology/occupation', sample_type: type) + type.sample_attributes << FactoryBot.build(:sample_attribute, sample_attribute_type: FactoryBot.create(:string_sample_attribute_type), title:'Scientific Name', pid:'http://gbol.life/0.1/scientificName', sample_type: type) + type.sample_attributes << FactoryBot.build(:sample_attribute, sample_attribute_type: FactoryBot.create(:string_sample_attribute_type), title:'Organism', pid:'http://purl.uniprot.org/core/organism', sample_type: type) + + end + end end diff --git a/test/unit/bioind/fairdata/fair_data_reader_test.rb b/test/unit/bioind/fairdata/fair_data_reader_test.rb index 2a89dea22d..e79e4175e4 100644 --- a/test/unit/bioind/fairdata/fair_data_reader_test.rb +++ b/test/unit/bioind/fairdata/fair_data_reader_test.rb @@ -134,17 +134,20 @@ class FairDataReaderTest < ActiveSupport::TestCase contributor = FactoryBot.create(:person) project = contributor.projects.first FactoryBot.create(:experimental_assay_class) + FactoryBot.create(:fairdatastation_virtual_demo_sample_type) investigation = BioInd::FairData::Reader.construct_isa(inv, contributor, [project]) studies = investigation.studies.to_a obs_units = studies.first.observation_units.to_a assays = studies.first.assays.to_a data_files = assays.first.assay_assets.to_a.collect(&:asset) + samples = obs_units.first.samples.to_a assert_equal 1, studies.count assert_equal 9, assays.count assert_equal 2, data_files.count assert_equal 2, obs_units.count + assert_equal 4, samples.count assert investigation.valid? assert studies.first.valid? @@ -158,11 +161,13 @@ class FairDataReaderTest < ActiveSupport::TestCase assert_difference('Investigation.count', 1) do assert_difference('Study.count', 1) do assert_difference('ObservationUnit.count', 2) do - assert_difference('Assay.count', 9) do - assert_difference('AssayAsset.count', 18) do - assert_difference('DataFile.count', 18) do - User.with_current_user(contributor.user) do - investigation.save! + assert_difference('Sample.count', 9) do + assert_difference('Assay.count', 9) do + assert_difference('AssayAsset.count', 18) do + assert_difference('DataFile.count', 18) do + User.with_current_user(contributor.user) do + investigation.save! + end end end end @@ -180,6 +185,7 @@ class FairDataReaderTest < ActiveSupport::TestCase FactoryBot.create(:simple_assay_extended_metadata_type) FactoryBot.create(:simple_investigation_extended_metadata_type_with_description_and_label) FactoryBot.create(:experimental_assay_class) + FactoryBot.create(:fairdatastation_virtual_demo_sample_type) path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" inv = BioInd::FairData::Reader.parse_graph(path).first diff --git a/test/unit/observation_unit_test.rb b/test/unit/observation_unit_test.rb index ab1f19d074..be50c0565b 100644 --- a/test/unit/observation_unit_test.rb +++ b/test/unit/observation_unit_test.rb @@ -13,6 +13,8 @@ class ObservationUnitTest < ActiveSupport::TestCase refute_nil obs_unit.extended_metadata.extended_metadata_type refute_nil obs_unit.study refute_empty obs_unit.study.observation_units + + refute_empty obs_unit.samples end end \ No newline at end of file From e935e5e501f0c3613233771ebd9f783c86d43745 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 30 Apr 2024 16:01:58 +0100 Subject: [PATCH 045/548] detect sample type and populate the sample metadata --- lib/bio_ind/fair_data/reader.rb | 21 +++++++++++++++---- lib/bio_ind/fair_data/sample.rb | 14 +++++++++++++ test/factories/sample_types.rb | 11 +--------- .../bioind/fairdata/fair_data_reader_test.rb | 17 +++++++++++++-- 4 files changed, 47 insertions(+), 16 deletions(-) diff --git a/lib/bio_ind/fair_data/reader.rb b/lib/bio_ind/fair_data/reader.rb index a316bddad6..5201b110db 100644 --- a/lib/bio_ind/fair_data/reader.rb +++ b/lib/bio_ind/fair_data/reader.rb @@ -49,10 +49,12 @@ def self.construct_isa(datastation_inv, contributor, projects) observation_unit = study.observation_units.build(observation_unit_attributes) populate_extended_metadata(observation_unit, datastation_observation_unit) datastation_observation_unit.samples.each do |datastation_sample| - sample = observation_unit.samples.build(title: 'fish', contributor: contributor, projects: projects) + sample = ::Sample.new(contributor: contributor, projects: projects) populate_sample(sample, datastation_sample) - unless sample.valid? - pp sample.errors.full_messages + if sample.valid? + observation_unit.samples << sample + else + Rails.logger.error("Invalid sample during fair data station import #{sample.errors.full_messages.inspect}") end end end @@ -85,13 +87,24 @@ def self.detect_extended_metadata(seek_entity, datastation_entity) def self.populate_sample(seek_sample, datastation_sample) if sample_type = detect_sample_type(datastation_sample) seek_sample.sample_type = sample_type + datastation_sample.populate_seek_sample(seek_sample) seek_sample.set_attribute_value('Title', datastation_sample.title) seek_sample.set_attribute_value('Description', datastation_sample.description) end end def self.detect_sample_type(datastation_sample) - SampleType.last + property_ids = datastation_sample.additional_metadata_annotations.collect{|annotation| annotation[0]} + + # collect and sort those with the most properties that match, eliminating any where no properties match + candidates = SampleType.all.collect do |sample_type| + ids = sample_type.sample_attributes.collect(&:pid) + score = (property_ids - ids).length + sample_type = nil if (property_ids & ids).empty? + [score, sample_type] + end.sort_by{|x| x[0]} + + candidates.first&.last end end diff --git a/lib/bio_ind/fair_data/sample.rb b/lib/bio_ind/fair_data/sample.rb index e59bb0ffac..7b24a43bde 100644 --- a/lib/bio_ind/fair_data/sample.rb +++ b/lib/bio_ind/fair_data/sample.rb @@ -6,6 +6,20 @@ class Sample < Base def child_class BioInd::FairData::Assay end + + def populate_seek_sample(seek_sample) + sample_type = seek_sample.sample_type + data = {} + additional_metadata_annotations.each do |annotation| + property = annotation[0] + value = annotation[1] + attribute = sample_type.sample_attributes.where(pid: property).first + if attribute + data[attribute.title] = value + end + end + seek_sample.data = data + end end end end diff --git a/test/factories/sample_types.rb b/test/factories/sample_types.rb index c7423f8b5f..c6d822550f 100644 --- a/test/factories/sample_types.rb +++ b/test/factories/sample_types.rb @@ -214,15 +214,6 @@ end end - # fair:host "Homo sapiens" ; - # fair:host_disease_stat "HIV-1 negative" ; - # fair:marital_status "Single" ; - # fair:occupation "Trader" ; - # fair:sample_name "13C" ; - # gbol:scientificName "human gut metagenome" ; - # jerm:hasPart ; - # uniprot:organism 408170 ; - factory(:fairdatastation_virtual_demo_sample_type, parent: :sample_type) do title { 'fair data station virtual demo'} after(:build) do |type, eval| @@ -233,7 +224,7 @@ type.sample_attributes << FactoryBot.build(:sample_attribute, sample_attribute_type: FactoryBot.create(:string_sample_attribute_type), title:'Host disease stat', pid:'http://fairbydesign.nl/ontology/host_disease_stat', sample_type: type) type.sample_attributes << FactoryBot.build(:sample_attribute, sample_attribute_type: FactoryBot.create(:string_sample_attribute_type), title:'Marital status', pid:'http://fairbydesign.nl/ontology/marital_status', sample_type: type) type.sample_attributes << FactoryBot.build(:sample_attribute, sample_attribute_type: FactoryBot.create(:string_sample_attribute_type), title:'Occupation', pid:'http://fairbydesign.nl/ontology/occupation', sample_type: type) - type.sample_attributes << FactoryBot.build(:sample_attribute, sample_attribute_type: FactoryBot.create(:string_sample_attribute_type), title:'Scientific Name', pid:'http://gbol.life/0.1/scientificName', sample_type: type) + type.sample_attributes << FactoryBot.build(:sample_attribute, sample_attribute_type: FactoryBot.create(:string_sample_attribute_type), title:'Scientific name', pid:'http://gbol.life/0.1/scientificName', sample_type: type) type.sample_attributes << FactoryBot.build(:sample_attribute, sample_attribute_type: FactoryBot.create(:string_sample_attribute_type), title:'Organism', pid:'http://purl.uniprot.org/core/organism', sample_type: type) end diff --git a/test/unit/bioind/fairdata/fair_data_reader_test.rb b/test/unit/bioind/fairdata/fair_data_reader_test.rb index e79e4175e4..e90eee2eae 100644 --- a/test/unit/bioind/fairdata/fair_data_reader_test.rb +++ b/test/unit/bioind/fairdata/fair_data_reader_test.rb @@ -177,7 +177,7 @@ class FairDataReaderTest < ActiveSupport::TestCase end end - test 'populate extended metadata' do + test 'populate extended metadata and samples' do study_metadata_type = FactoryBot.create(:fairdata_virtual_demo_study_extended_metadata) FactoryBot.create(:study_extended_metadata_type) FactoryBot.create(:fairdata_virtual_demo_study_extended_metadata_partial) @@ -185,7 +185,7 @@ class FairDataReaderTest < ActiveSupport::TestCase FactoryBot.create(:simple_assay_extended_metadata_type) FactoryBot.create(:simple_investigation_extended_metadata_type_with_description_and_label) FactoryBot.create(:experimental_assay_class) - FactoryBot.create(:fairdatastation_virtual_demo_sample_type) + sample_type = FactoryBot.create(:fairdatastation_virtual_demo_sample_type) path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" inv = BioInd::FairData::Reader.parse_graph(path).first @@ -223,6 +223,19 @@ class FairDataReaderTest < ActiveSupport::TestCase study.save! end end + + sample = study.observation_units.first.samples.first + refute_nil sample.sample_type + assert_equal sample_type, sample.sample_type + assert_equal 'sample DRS176892', sample.title + assert_equal 'Sample obtained from Single age 30 collected on 2017-09-13 from the human gut', sample.get_attribute_value('Description') + assert_equal 'Homo sapiens', sample.get_attribute_value('Host') + assert_equal 'HIV-1 positive', sample.get_attribute_value('Host disease stat') + assert_equal 'Single', sample.get_attribute_value('Marital status') + assert_equal 'Trader', sample.get_attribute_value('Occupation') + assert_equal 'human gut metagenome', sample.get_attribute_value('Scientific name') + assert_equal '408170', sample.get_attribute_value('Organism') + end test 'populate obsv unit extended metadata' do From e60bd9fe9318f001e00a90c09813e40d36d70213 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 30 Apr 2024 16:44:13 +0100 Subject: [PATCH 046/548] seed sample type, and fixes for viewing obs_unit with related samples, including the tree and graph --- config/routes.rb | 4 +- .../fairdatastation_virtual_demo.seeds.rb | 80 +++++++++++++------ lib/seek/isa_graph_generator.rb | 3 +- 3 files changed, 60 insertions(+), 27 deletions(-) diff --git a/config/routes.rb b/config/routes.rb index df064a28b2..bfe2ef6822 100644 --- a/config/routes.rb +++ b/config/routes.rb @@ -681,7 +681,7 @@ post :query end resources :people, :programmes, :projects, :assays, :studies, :investigations, :data_files, :publications, :samples, - :sample_types, :strains, :organisms, :collections, only: [:index] + :sample_types, :strains, :organisms, :collections, :observation_units, only: [:index] end ### SAMPLE TYPES ### @@ -803,7 +803,7 @@ resources :observation_units, only: [:show, :index] do - resources :projects, :people, :programmes, :studies + resources :projects, :people, :programmes, :studies, :samples, :assays end ### MISC MATCHES ### diff --git a/db/seeds/extended_metadata_drafts/fairdatastation_virtual_demo.seeds.rb b/db/seeds/extended_metadata_drafts/fairdatastation_virtual_demo.seeds.rb index 72b97604b4..4d064ca509 100644 --- a/db/seeds/extended_metadata_drafts/fairdatastation_virtual_demo.seeds.rb +++ b/db/seeds/extended_metadata_drafts/fairdatastation_virtual_demo.seeds.rb @@ -1,13 +1,15 @@ +string_attribute_type = SampleAttributeType.where(title:'String').first + unless ExtendedMetadataType.where(title:'Fair Data Station Virtual Demo', supported_type:'Study').any? emt = ExtendedMetadataType.new(title: 'Fair Data Station Virtual Demo', supported_type:'Study') - emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Alias', property_type_id:'http://fairbydesign.nl/ontology/alias', sample_attribute_type: SampleAttributeType.where(title:'String').first) - emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Centre Name', property_type_id:'http://fairbydesign.nl/ontology/center_name', sample_attribute_type: SampleAttributeType.where(title:'String').first) - emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Centre Project Name', property_type_id:'http://fairbydesign.nl/ontology/center_project_name', sample_attribute_type: SampleAttributeType.where(title:'String').first) - emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'External Ids', property_type_id:'http://fairbydesign.nl/ontology/external_ids', sample_attribute_type: SampleAttributeType.where(title:'String').first) - emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Submission Accession', property_type_id:'http://fairbydesign.nl/ontology/submission_accession', sample_attribute_type: SampleAttributeType.where(title:'String').first) - emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Submission Alias', property_type_id:'http://fairbydesign.nl/ontology/submission_alias', sample_attribute_type: SampleAttributeType.where(title:'String').first) - emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Submission Lab Name', property_type_id:'http://fairbydesign.nl/ontology/submission_lab_name', sample_attribute_type: SampleAttributeType.where(title:'String').first) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Alias', property_type_id:'http://fairbydesign.nl/ontology/alias', sample_attribute_type: string_attribute_type) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Centre Name', property_type_id:'http://fairbydesign.nl/ontology/center_name', sample_attribute_type: string_attribute_type) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Centre Project Name', property_type_id:'http://fairbydesign.nl/ontology/center_project_name', sample_attribute_type: string_attribute_type) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'External Ids', property_type_id:'http://fairbydesign.nl/ontology/external_ids', sample_attribute_type: string_attribute_type) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Submission Accession', property_type_id:'http://fairbydesign.nl/ontology/submission_accession', sample_attribute_type: string_attribute_type) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Submission Alias', property_type_id:'http://fairbydesign.nl/ontology/submission_alias', sample_attribute_type: string_attribute_type) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Submission Lab Name', property_type_id:'http://fairbydesign.nl/ontology/submission_lab_name', sample_attribute_type: string_attribute_type) emt.save! puts 'Fair Data Station Virtual Demo for Study' @@ -16,18 +18,18 @@ unless ExtendedMetadataType.where(title:'Fair Data Station Virtual Demo', supported_type:'Assay').any? emt = ExtendedMetadataType.new(title: 'Fair Data Station Virtual Demo', supported_type:'Assay') - emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Facility', property_type_id:'http://fairbydesign.nl/ontology/facility', sample_attribute_type: SampleAttributeType.where(title:'String').first) - emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Forward Primer', property_type_id:'http://fairbydesign.nl/ontology/forwardPrimer', sample_attribute_type: SampleAttributeType.where(title:'String').first) - emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Instrument Model', property_type_id:'http://fairbydesign.nl/ontology/instrument_model', sample_attribute_type: SampleAttributeType.where(title:'String').first) - emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Library Selection', property_type_id:'http://fairbydesign.nl/ontology/library_selection', sample_attribute_type: SampleAttributeType.where(title:'String').first) - emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Library Source', property_type_id:'http://fairbydesign.nl/ontology/library_source', sample_attribute_type: SampleAttributeType.where(title:'String').first) - emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Library Strategy', property_type_id:'http://fairbydesign.nl/ontology/library_strategy', sample_attribute_type: SampleAttributeType.where(title:'String').first) - emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Package Name', property_type_id:'http://fairbydesign.nl/ontology/packageName', sample_attribute_type: SampleAttributeType.where(title:'String').first) - emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Platform', property_type_id:'http://fairbydesign.nl/ontology/platform', sample_attribute_type: SampleAttributeType.where(title:'String').first) - emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Primer Names', property_type_id:'http://fairbydesign.nl/ontology/primerNames', sample_attribute_type: SampleAttributeType.where(title:'String').first) - emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Protocol', property_type_id:'http://fairbydesign.nl/ontology/protocol', sample_attribute_type: SampleAttributeType.where(title:'String').first) - emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Reverse Primer', property_type_id:'http://fairbydesign.nl/ontology/reversePrimer', sample_attribute_type: SampleAttributeType.where(title:'String').first) - emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Target Subfragment', property_type_id:'http://fairbydesign.nl/ontology/target_subfragment', sample_attribute_type: SampleAttributeType.where(title:'String').first) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Facility', property_type_id:'http://fairbydesign.nl/ontology/facility', sample_attribute_type: string_attribute_type) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Forward Primer', property_type_id:'http://fairbydesign.nl/ontology/forwardPrimer', sample_attribute_type: string_attribute_type) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Instrument Model', property_type_id:'http://fairbydesign.nl/ontology/instrument_model', sample_attribute_type: string_attribute_type) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Library Selection', property_type_id:'http://fairbydesign.nl/ontology/library_selection', sample_attribute_type: string_attribute_type) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Library Source', property_type_id:'http://fairbydesign.nl/ontology/library_source', sample_attribute_type: string_attribute_type) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Library Strategy', property_type_id:'http://fairbydesign.nl/ontology/library_strategy', sample_attribute_type: string_attribute_type) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Package Name', property_type_id:'http://fairbydesign.nl/ontology/packageName', sample_attribute_type: string_attribute_type) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Platform', property_type_id:'http://fairbydesign.nl/ontology/platform', sample_attribute_type: string_attribute_type) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Primer Names', property_type_id:'http://fairbydesign.nl/ontology/primerNames', sample_attribute_type: string_attribute_type) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Protocol', property_type_id:'http://fairbydesign.nl/ontology/protocol', sample_attribute_type: string_attribute_type) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Reverse Primer', property_type_id:'http://fairbydesign.nl/ontology/reversePrimer', sample_attribute_type: string_attribute_type) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Target Subfragment', property_type_id:'http://fairbydesign.nl/ontology/target_subfragment', sample_attribute_type: string_attribute_type) emt.save! puts 'Fair Data Station Virtual Demo for Assay' @@ -36,12 +38,42 @@ unless ExtendedMetadataType.where(title:'Fair Data Station Indpensim', supported_type:'ObservationUnit').any? emt = ExtendedMetadataType.new(title: 'Fair Data Station Indpensim', supported_type:'ObservationUnit') - emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Brand', property_type_id:'http://fairbydesign.nl/ontology/brand', sample_attribute_type: SampleAttributeType.where(title:'String').first) - emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Fermentation', property_type_id:'http://fairbydesign.nl/ontology/fermentation', sample_attribute_type: SampleAttributeType.where(title:'String').first) - emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Volume', property_type_id:'http://fairbydesign.nl/ontology/volume', sample_attribute_type: SampleAttributeType.where(title:'String').first) - emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Scientific Name', property_type_id:'http://gbol.life/0.1/scientificName', sample_attribute_type: SampleAttributeType.where(title:'String').first) - emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Organism', property_type_id:'http://purl.uniprot.org/core/organism', sample_attribute_type: SampleAttributeType.where(title:'String').first) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Brand', property_type_id:'http://fairbydesign.nl/ontology/brand', sample_attribute_type: string_attribute_type) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Fermentation', property_type_id:'http://fairbydesign.nl/ontology/fermentation', sample_attribute_type: string_attribute_type) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Volume', property_type_id:'http://fairbydesign.nl/ontology/volume', sample_attribute_type: string_attribute_type) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Scientific Name', property_type_id:'http://gbol.life/0.1/scientificName', sample_attribute_type: string_attribute_type) + emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Organism', property_type_id:'http://purl.uniprot.org/core/organism', sample_attribute_type: string_attribute_type) emt.save! puts 'Fair Data Station Indpensim for Observation Unit' +end + +virtual_demo_sample_type = SampleType.where(title: 'Fair Data Station Virtual Demo').first_or_initialize( + project_ids: [Project.first.id], + contributor: Person.first, + sample_attributes_attributes: [ + { title: 'Title', sample_attribute_type: string_attribute_type, required: true, is_title: true }, + { title: 'Description', sample_attribute_type: string_attribute_type }, + { title: 'art_drugs_current', pid:'http://fairbydesign.nl/ontology/art_drugs_current', sample_attribute_type: string_attribute_type }, + { title: 'art_duration_at baseline_months', pid:'http://fairbydesign.nl/ontology/art_duration_at_baseline_months', sample_attribute_type: string_attribute_type }, + { title: 'geo loc name', pid:'http://fairbydesign.nl/ontology/geo_loc_name', sample_attribute_type: string_attribute_type }, + { title: 'hiv risk exposure', pid:'http://fairbydesign.nl/ontology/hiv_risk_exposure', sample_attribute_type: string_attribute_type }, + { title: 'host', pid:'http://fairbydesign.nl/ontology/host', sample_attribute_type: string_attribute_type }, + { title: 'log vl', pid:'http://fairbydesign.nl/ontology/log_vl', sample_attribute_type: string_attribute_type }, + { title: 'marital status', pid:'http://fairbydesign.nl/ontology/marital_status', sample_attribute_type: string_attribute_type }, + { title: 'occupation', pid:'http://fairbydesign.nl/ontology/occupation', sample_attribute_type: string_attribute_type }, + { title: 'viral_load (copies/ml)', pid:'http://fairbydesign.nl/ontology/viral_load_copies_ml', sample_attribute_type: string_attribute_type }, + { title: 'scientific name', pid:'http://gbol.life/0.1/scientificName', sample_attribute_type: string_attribute_type }, + { title: 'organism', pid:'http://purl.uniprot.org/core/organism', sample_attribute_type: string_attribute_type } + ] +) + +if virtual_demo_sample_type.valid? + disable_authorization_checks do + virtual_demo_sample_type.save! + end + + puts "Fair Data Station Virtual Demo Sample Type" +else + puts virtual_demo_sample_type.errors.full_messages end \ No newline at end of file diff --git a/lib/seek/isa_graph_generator.rb b/lib/seek/isa_graph_generator.rb index 0f3afc4340..6fc3f8d2c0 100644 --- a/lib/seek/isa_graph_generator.rb +++ b/lib/seek/isa_graph_generator.rb @@ -221,7 +221,8 @@ def associations(object) } when ObservationUnit { - parents: %i[study] + parents: %i[study], + aggregated_children: { samples: :samples } } else {} From 78d72c475c919d64a0aeee8d801fd54e75aebd7d Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Wed, 1 May 2024 11:44:10 +0100 Subject: [PATCH 047/548] link the samples to the associated assay --- lib/bio_ind/fair_data/reader.rb | 28 +++++++++---------- .../bioind/fairdata/fair_data_reader_test.rb | 8 ++++-- 2 files changed, 20 insertions(+), 16 deletions(-) diff --git a/lib/bio_ind/fair_data/reader.rb b/lib/bio_ind/fair_data/reader.rb index 5201b110db..21f676d042 100644 --- a/lib/bio_ind/fair_data/reader.rb +++ b/lib/bio_ind/fair_data/reader.rb @@ -30,20 +30,6 @@ def self.construct_isa(datastation_inv, contributor, projects) study_attributes = datastation_study.seek_attributes.merge({contributor: contributor, investigation: investigation}) study = investigation.studies.build(study_attributes) populate_extended_metadata(study, datastation_study) - datastation_study.assays.each do |datastation_assay| - assay_attributes = datastation_assay.seek_attributes.merge({contributor: contributor, study:study, assay_class: AssayClass.experimental}) - assay = study.assays.build(assay_attributes) - populate_extended_metadata(assay, datastation_assay) - datastation_assay.datasets.each do |datastation_dataset| - blob = ContentBlob.new(url: datastation_dataset.resource_uri.to_s, original_filename: datastation_dataset.identifier ) - data_file_attributes = datastation_dataset.seek_attributes.merge({ - contributor: contributor, projects: projects, - content_blob: blob - }) - df = DataFile.new(data_file_attributes) - assay.assay_assets.build(asset: df) - end - end datastation_study.observation_units.each do |datastation_observation_unit| observation_unit_attributes = datastation_observation_unit.seek_attributes.merge({contributor: contributor, study:study, projects: projects}) observation_unit = study.observation_units.build(observation_unit_attributes) @@ -56,6 +42,20 @@ def self.construct_isa(datastation_inv, contributor, projects) else Rails.logger.error("Invalid sample during fair data station import #{sample.errors.full_messages.inspect}") end + datastation_sample.assays.each do |datastation_assay| + assay_attributes = datastation_assay.seek_attributes.merge({contributor: contributor, study:study, assay_class: AssayClass.experimental, samples:[sample]}) + assay = study.assays.build(assay_attributes) + populate_extended_metadata(assay, datastation_assay) + datastation_assay.datasets.each do |datastation_dataset| + blob = ContentBlob.new(url: datastation_dataset.resource_uri.to_s, original_filename: datastation_dataset.identifier ) + data_file_attributes = datastation_dataset.seek_attributes.merge({ + contributor: contributor, projects: projects, + content_blob: blob + }) + df = DataFile.new(data_file_attributes) + assay.assay_assets.build(asset: df) + end + end end end end diff --git a/test/unit/bioind/fairdata/fair_data_reader_test.rb b/test/unit/bioind/fairdata/fair_data_reader_test.rb index e90eee2eae..747462a583 100644 --- a/test/unit/bioind/fairdata/fair_data_reader_test.rb +++ b/test/unit/bioind/fairdata/fair_data_reader_test.rb @@ -140,9 +140,13 @@ class FairDataReaderTest < ActiveSupport::TestCase studies = investigation.studies.to_a obs_units = studies.first.observation_units.to_a assays = studies.first.assays.to_a - data_files = assays.first.assay_assets.to_a.collect(&:asset) + data_files = assays.first.assay_assets.to_a.collect(&:asset).select{|a| a.is_a?(DataFile)} samples = obs_units.first.samples.to_a + assay_samples = assays.collect{|a| a.samples.to_a}.flatten + assert_equal 9, assay_samples.count + assert_equal samples, (assay_samples & samples) + assert_equal 1, studies.count assert_equal 9, assays.count assert_equal 2, data_files.count @@ -163,7 +167,7 @@ class FairDataReaderTest < ActiveSupport::TestCase assert_difference('ObservationUnit.count', 2) do assert_difference('Sample.count', 9) do assert_difference('Assay.count', 9) do - assert_difference('AssayAsset.count', 18) do + assert_difference('AssayAsset.count', 27) do assert_difference('DataFile.count', 18) do User.with_current_user(contributor.user) do investigation.save! From d097ff07bd3382e01998d012c7ca0b6e0169b0e8 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Wed, 1 May 2024 11:56:29 +0100 Subject: [PATCH 048/548] a little utility method to destroy an investigation and all it's children --- app/models/investigation.rb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/app/models/investigation.rb b/app/models/investigation.rb index 3f84feadb1..be13249e07 100644 --- a/app/models/investigation.rb +++ b/app/models/investigation.rb @@ -53,4 +53,22 @@ def positioned_studies def self.user_creatable? Seek::Config.investigations_enabled end + + # utility method for cleaning up durng testing, not to be used in production code + def deep_destroy! + raise 'need to be admin' unless User.current_user&.is_admin? + disable_authorization_checks do + assays.each do |assay| + assay.samples.destroy_all + assay.data_files.destroy_all + assay.destroy + end + studies.each do |study| + study.observation_units.destroy_all + study.destroy + end + destroy + end + + end end From 6f8e42484400e46956ad29732a1ebdfb7abcafca Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Wed, 1 May 2024 13:34:05 +0100 Subject: [PATCH 049/548] fix test and only associate valid samples to assay --- lib/bio_ind/fair_data/reader.rb | 4 +++- test/functional/projects_controller_test.rb | 3 +++ 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/lib/bio_ind/fair_data/reader.rb b/lib/bio_ind/fair_data/reader.rb index 21f676d042..d6c25ee62f 100644 --- a/lib/bio_ind/fair_data/reader.rb +++ b/lib/bio_ind/fair_data/reader.rb @@ -43,7 +43,9 @@ def self.construct_isa(datastation_inv, contributor, projects) Rails.logger.error("Invalid sample during fair data station import #{sample.errors.full_messages.inspect}") end datastation_sample.assays.each do |datastation_assay| - assay_attributes = datastation_assay.seek_attributes.merge({contributor: contributor, study:study, assay_class: AssayClass.experimental, samples:[sample]}) + samples = [] + samples << sample if sample.valid? + assay_attributes = datastation_assay.seek_attributes.merge({contributor: contributor, study:study, assay_class: AssayClass.experimental, samples:samples}) assay = study.assays.build(assay_attributes) populate_extended_metadata(assay, datastation_assay) datastation_assay.datasets.each do |datastation_dataset| diff --git a/test/functional/projects_controller_test.rb b/test/functional/projects_controller_test.rb index 65437d56b6..416a2e9d6e 100644 --- a/test/functional/projects_controller_test.rb +++ b/test/functional/projects_controller_test.rb @@ -5045,6 +5045,7 @@ def test_admin_can_edit test 'populate from fairdata station ttl' do person = FactoryBot.create(:person) + FactoryBot.create(:fairdatastation_virtual_demo_sample_type) project = person.projects.first login_as(person) @@ -5058,6 +5059,8 @@ def test_admin_can_edit assert_equal person, investigation.contributor assert_equal 1, investigation.studies.count assert_equal 9, investigation.studies.first.assays.count + assert_equal 2, investigation.studies.first.observation_units.count + assert_equal 4, investigation.studies.first.observation_units.first.samples.count end From c6cb16b4ae6116dc5c0389b7295d259432530723 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Wed, 1 May 2024 14:34:44 +0100 Subject: [PATCH 050/548] seed Observation Unit for Pichia --- app/models/extended_metadata_type.rb | 2 ++ .../fairdatastation_virtual_demo.seeds.rb | 25 ++++++++++++++++++- 2 files changed, 26 insertions(+), 1 deletion(-) diff --git a/app/models/extended_metadata_type.rb b/app/models/extended_metadata_type.rb index 4fbb9293c0..9ad7294cd0 100644 --- a/app/models/extended_metadata_type.rb +++ b/app/models/extended_metadata_type.rb @@ -10,6 +10,8 @@ class ExtendedMetadataType < ApplicationRecord alias_method :metadata_attributes, :extended_metadata_attributes + accepts_nested_attributes_for :extended_metadata_attributes, allow_destroy: true + scope :enabled, ->{ where(enabled: true) } scope :disabled, ->{ where(enabled: false) } diff --git a/db/seeds/extended_metadata_drafts/fairdatastation_virtual_demo.seeds.rb b/db/seeds/extended_metadata_drafts/fairdatastation_virtual_demo.seeds.rb index 4d064ca509..7b08232b11 100644 --- a/db/seeds/extended_metadata_drafts/fairdatastation_virtual_demo.seeds.rb +++ b/db/seeds/extended_metadata_drafts/fairdatastation_virtual_demo.seeds.rb @@ -45,7 +45,30 @@ emt.extended_metadata_attributes << ExtendedMetadataAttribute.new(title: 'Organism', property_type_id:'http://purl.uniprot.org/core/organism', sample_attribute_type: string_attribute_type) emt.save! - puts 'Fair Data Station Indpensim for Observation Unit' + puts 'Fair Data Station Observation Unit for Indpensim' +end + +unless ExtendedMetadataType.where(title:'Fair Data Station Pichia', supported_type:'ObservationUnit').any? + emt = ExtendedMetadataType.new(title: 'Fair Data Station Pichia', supported_type:'ObservationUnit', + extended_metadata_attributes_attributes: [ + { title: 'Author', property_type_id: 'http://fairbydesign.nl/ontology/author', sample_attribute_type: string_attribute_type}, + { title: 'Control action', property_type_id: 'http://fairbydesign.nl/ontology/control_action', sample_attribute_type: string_attribute_type}, + { title: 'Control objective', property_type_id: 'http://fairbydesign.nl/ontology/control_objective', sample_attribute_type: string_attribute_type}, + { title: 'Control type', property_type_id: 'http://fairbydesign.nl/ontology/control_type', sample_attribute_type: string_attribute_type}, + { title: 'Date', property_type_id: 'http://fairbydesign.nl/ontology/date', sample_attribute_type: string_attribute_type}, + { title: 'Operational mode', property_type_id: 'http://fairbydesign.nl/ontology/operational_mode', sample_attribute_type: string_attribute_type}, + { title: 'Operational strategy', property_type_id: 'http://fairbydesign.nl/ontology/operational_strategy', sample_attribute_type: string_attribute_type}, + { title: 'Promotor', property_type_id: 'http://fairbydesign.nl/ontology/promoter', sample_attribute_type: string_attribute_type}, + { title: 'Protein', property_type_id: 'http://fairbydesign.nl/ontology/protein', sample_attribute_type: string_attribute_type}, + { title: 'Published', property_type_id: 'http://fairbydesign.nl/ontology/published', sample_attribute_type: string_attribute_type}, + { title: 'Strain', property_type_id: 'http://fairbydesign.nl/ontology/strain', sample_attribute_type: string_attribute_type}, + { title: 'Substrate batch', property_type_id: 'http://fairbydesign.nl/ontology/substrate_batch', sample_attribute_type: string_attribute_type}, + { title: 'Substrate fed batch', property_type_id: 'http://fairbydesign.nl/ontology/substrate_fed-batch', sample_attribute_type: string_attribute_type}, + { title: 'Scientific name', property_type_id: 'http://gbol.life/0.1/scientificName', sample_attribute_type: string_attribute_type} + ] + ) + emt.save! + puts 'Fair Data Station Observation Unit for Pichia' end virtual_demo_sample_type = SampleType.where(title: 'Fair Data Station Virtual Demo').first_or_initialize( From 9dc1f8bc95043ef3da95bc8cc8bce469b4091388 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Wed, 1 May 2024 15:10:22 +0100 Subject: [PATCH 051/548] expanded reader tests regarding datasets, and also access schema:contentUrl --- lib/bio_ind/fair_data/base.rb | 1 + lib/bio_ind/fair_data/data_set.rb | 4 +++ .../bioind/fairdata/fair_data_reader_test.rb | 30 +++++++++++++++++++ 3 files changed, 35 insertions(+) diff --git a/lib/bio_ind/fair_data/base.rb b/lib/bio_ind/fair_data/base.rb index d137d670f3..996892f22b 100644 --- a/lib/bio_ind/fair_data/base.rb +++ b/lib/bio_ind/fair_data/base.rb @@ -17,6 +17,7 @@ def initialize(resource_uri, graph) @schema.identifier, @schema.name, @schema.title, + @schema.contentUrl, RDF.type, @jerm.hasPart ] diff --git a/lib/bio_ind/fair_data/data_set.rb b/lib/bio_ind/fair_data/data_set.rb index 403cb8363b..ff96aa9eb7 100644 --- a/lib/bio_ind/fair_data/data_set.rb +++ b/lib/bio_ind/fair_data/data_set.rb @@ -6,6 +6,10 @@ def title "Dataset: #{identifier}" end + def content_url + find_annotation_value(@schema.contentUrl.to_s) || resource_uri + end + end end end diff --git a/test/unit/bioind/fairdata/fair_data_reader_test.rb b/test/unit/bioind/fairdata/fair_data_reader_test.rb index 747462a583..242e804896 100644 --- a/test/unit/bioind/fairdata/fair_data_reader_test.rb +++ b/test/unit/bioind/fairdata/fair_data_reader_test.rb @@ -34,6 +34,35 @@ class FairDataReaderTest < ActiveSupport::TestCase assert_equal 'DRR243856', assay.identifier end + test 'read indpensim' do + path = "#{Rails.root}/test/fixtures/files/fairdatastation/indpensim.ttl" + + investigations = BioInd::FairData::Reader.parse_graph(path) + assert_equal 1, investigations.count + inv = investigations.first + assert_equal 'http://fairbydesign.nl/ontology/inv_indpensim', inv.resource_uri.to_s + assert_equal 'indpensim', inv.identifier + + assert_equal 1, inv.studies.count + study = inv.studies.first + assert_equal 'http://fairbydesign.nl/ontology/inv_indpensim/stu_Penicillin_production', study.resource_uri.to_s + assert_equal 'Penicillin_production', study.identifier + + assert_equal 100, study.observation_units.count + obs_unit = study.observation_units.first + assert_equal 'http://fairbydesign.nl/ontology/inv_indpensim/stu_Penicillin_production/obs_IndPenSim_V3_Batch_1', + obs_unit.resource_uri.to_s + assert_equal 'IndPenSim_V3_Batch_1', obs_unit.identifier + + assert_equal 0, obs_unit.samples.count + assert_equal 1, obs_unit.datasets.count + dataset = obs_unit.datasets.first + assert_equal 'https://data.yoda.wur.nl/research-bioindustry/Use%20cases/Simulation%20datasets/IndPenSim/IndPenSim_V3_Batch_1.csv.gz', dataset.resource_uri + assert_equal 'IndPenSim_V3_Batch_1.csv.gz', dataset.identifier + assert_equal 'file', dataset.description + assert_equal 'https://data.yoda.wur.nl/research-bioindustry/Use%20cases/Simulation%20datasets/IndPenSim/IndPenSim_V3_Batch_1.csv.gz', dataset.content_url + end + test 'annotations' do path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" @@ -120,6 +149,7 @@ class FairDataReaderTest < ActiveSupport::TestCase assert_equal ['http://fairbydesign.nl/data_sample/DRR243856_1.fastq.gz', 'http://fairbydesign.nl/data_sample/DRR243856_2.fastq.gz'], datasets.collect(&:resource_uri).collect(&:to_s).sort assert_equal ['DRR243856_1.fastq.gz', 'DRR243856_2.fastq.gz'], datasets.collect(&:identifier).sort assert_equal ['demultiplexed forward file', 'demultiplexed reverse file'], datasets.collect(&:description).sort + assert_equal ['http://fairbydesign.nl/data_sample/DRR243856_1.fastq.gz', 'http://fairbydesign.nl/data_sample/DRR243856_2.fastq.gz'], datasets.collect(&:content_url).collect(&:to_s).sort assert_equal 0, inv.datasets.count assert_equal 0, study.datasets.count From 9997e802664db61718290c3226836690ad0210ca Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Wed, 1 May 2024 15:40:29 +0100 Subject: [PATCH 052/548] model association between observation unit and data files --- app/models/data_file.rb | 3 +++ app/models/observation_unit.rb | 2 ++ app/models/observation_unit_asset.rb | 6 ++++++ ...240501142953_create_observation_unit_assets.rb | 8 ++++++++ db/schema.rb | 10 +++++++++- test/factories/observation_units.rb | 1 + .../unit/bioind/fairdata/fair_data_reader_test.rb | 15 +++++++++++++++ test/unit/observation_unit_test.rb | 2 +- 8 files changed, 45 insertions(+), 2 deletions(-) create mode 100644 app/models/observation_unit_asset.rb create mode 100644 db/migrate/20240501142953_create_observation_unit_assets.rb diff --git a/app/models/data_file.rb b/app/models/data_file.rb index 03b358677b..3ebd3200cc 100644 --- a/app/models/data_file.rb +++ b/app/models/data_file.rb @@ -23,6 +23,9 @@ class DataFile < ApplicationRecord has_many :sample_resource_links, -> { where(resource_type: 'DataFile') }, class_name: 'SampleResourceLink', foreign_key: :resource_id has_many :linked_samples, through: :sample_resource_links, source: :sample + has_many :observation_unit_assets + has_many :observation_units, through: :observation_unit_assets + has_many :workflow_data_files, dependent: :destroy, autosave: true has_many :workflows, ->{ distinct }, through: :workflow_data_files diff --git a/app/models/observation_unit.rb b/app/models/observation_unit.rb index 463fb7de8b..1c87a073e9 100644 --- a/app/models/observation_unit.rb +++ b/app/models/observation_unit.rb @@ -8,6 +8,8 @@ class ObservationUnit < ApplicationRecord belongs_to :contributor, class_name: 'Person' belongs_to :study has_many :samples + has_many :observation_unit_assets + has_many :data_files, through: :observation_unit_assets, source: :asset, source_type: 'DataFile' has_extended_metadata diff --git a/app/models/observation_unit_asset.rb b/app/models/observation_unit_asset.rb new file mode 100644 index 0000000000..843390c8cd --- /dev/null +++ b/app/models/observation_unit_asset.rb @@ -0,0 +1,6 @@ +class ObservationUnitAsset < ApplicationRecord + + belongs_to :observation_unit + belongs_to :asset, polymorphic: true + +end diff --git a/db/migrate/20240501142953_create_observation_unit_assets.rb b/db/migrate/20240501142953_create_observation_unit_assets.rb new file mode 100644 index 0000000000..0aaa056030 --- /dev/null +++ b/db/migrate/20240501142953_create_observation_unit_assets.rb @@ -0,0 +1,8 @@ +class CreateObservationUnitAssets < ActiveRecord::Migration[6.1] + def change + create_table :observation_unit_assets, id: false do |t| + t.references :observation_unit + t.references :asset, polymorphic: true + end + end +end diff --git a/db/schema.rb b/db/schema.rb index 5267c58bf8..74a844441b 100644 --- a/db/schema.rb +++ b/db/schema.rb @@ -10,7 +10,7 @@ # # It's strongly recommended that you check this file into your version control system. -ActiveRecord::Schema.define(version: 2024_04_30_132048) do +ActiveRecord::Schema.define(version: 2024_05_01_142953) do create_table "activity_logs", id: :integer, force: :cascade do |t| t.string "action" @@ -1196,6 +1196,14 @@ t.index ["user_id"], name: "index_oauth_sessions_on_user_id" end + create_table "observation_unit_assets", id: false, force: :cascade do |t| + t.bigint "observation_unit_id" + t.string "asset_type" + t.bigint "asset_id" + t.index ["asset_type", "asset_id"], name: "index_observation_unit_assets_on_asset" + t.index ["observation_unit_id"], name: "index_observation_unit_assets_on_observation_unit_id" + end + create_table "observation_units", force: :cascade do |t| t.string "title" t.text "description" diff --git a/test/factories/observation_units.rb b/test/factories/observation_units.rb index e732b93b16..dd239ac1d5 100644 --- a/test/factories/observation_units.rb +++ b/test/factories/observation_units.rb @@ -14,6 +14,7 @@ association :extended_metadata, factory: :simple_observation_unit_extended_metadata, strategy: :create association :study, factory: :study, strategy: :create samples { build_list :sample, 3} + data_files { build_list :data_file, 3} end end \ No newline at end of file diff --git a/test/unit/bioind/fairdata/fair_data_reader_test.rb b/test/unit/bioind/fairdata/fair_data_reader_test.rb index 242e804896..a6010a6ca8 100644 --- a/test/unit/bioind/fairdata/fair_data_reader_test.rb +++ b/test/unit/bioind/fairdata/fair_data_reader_test.rb @@ -272,6 +272,21 @@ class FairDataReaderTest < ActiveSupport::TestCase end + test 'observation_unit datasets created in construct_isa' do + path = "#{Rails.root}/test/fixtures/files/fairdatastation/indpensim.ttl" + inv = BioInd::FairData::Reader.parse_graph(path).first + + contributor = FactoryBot.create(:person) + project = contributor.projects.first + FactoryBot.create(:experimental_assay_class) + FactoryBot.create(:fairdatastation_virtual_demo_sample_type) + + investigation = BioInd::FairData::Reader.construct_isa(inv, contributor, [project]) + assert_equal 100, investigation.studies.first.observation_units.to_a.count + observation_unit = investigation.studies.first.observation_units.first + assert_equal 1, observation_unit.data_files + end + test 'populate obsv unit extended metadata' do ext_metadata_type = FactoryBot.create(:fairdata_indpensim_obsv_unit_extended_metadata) FactoryBot.create(:experimental_assay_class) diff --git a/test/unit/observation_unit_test.rb b/test/unit/observation_unit_test.rb index be50c0565b..aa57655eb4 100644 --- a/test/unit/observation_unit_test.rb +++ b/test/unit/observation_unit_test.rb @@ -13,8 +13,8 @@ class ObservationUnitTest < ActiveSupport::TestCase refute_nil obs_unit.extended_metadata.extended_metadata_type refute_nil obs_unit.study refute_empty obs_unit.study.observation_units - refute_empty obs_unit.samples + refute_empty obs_unit.data_files end end \ No newline at end of file From 6255a9e8816b3570a1cb6cb7987de42991544144 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Wed, 1 May 2024 16:10:46 +0100 Subject: [PATCH 053/548] construct and save obs unit data_files --- lib/bio_ind/fair_data/reader.rb | 22 ++++++++++++++----- .../bioind/fairdata/fair_data_reader_test.rb | 16 +++++++++++++- 2 files changed, 31 insertions(+), 7 deletions(-) diff --git a/lib/bio_ind/fair_data/reader.rb b/lib/bio_ind/fair_data/reader.rb index d6c25ee62f..deb0470c04 100644 --- a/lib/bio_ind/fair_data/reader.rb +++ b/lib/bio_ind/fair_data/reader.rb @@ -33,6 +33,10 @@ def self.construct_isa(datastation_inv, contributor, projects) datastation_study.observation_units.each do |datastation_observation_unit| observation_unit_attributes = datastation_observation_unit.seek_attributes.merge({contributor: contributor, study:study, projects: projects}) observation_unit = study.observation_units.build(observation_unit_attributes) + datastation_observation_unit.datasets.each do |datastation_dataset| + df = build_data_file(contributor, datastation_dataset, projects) + observation_unit.observation_unit_assets.build(asset: df) + end populate_extended_metadata(observation_unit, datastation_observation_unit) datastation_observation_unit.samples.each do |datastation_sample| sample = ::Sample.new(contributor: contributor, projects: projects) @@ -49,12 +53,7 @@ def self.construct_isa(datastation_inv, contributor, projects) assay = study.assays.build(assay_attributes) populate_extended_metadata(assay, datastation_assay) datastation_assay.datasets.each do |datastation_dataset| - blob = ContentBlob.new(url: datastation_dataset.resource_uri.to_s, original_filename: datastation_dataset.identifier ) - data_file_attributes = datastation_dataset.seek_attributes.merge({ - contributor: contributor, projects: projects, - content_blob: blob - }) - df = DataFile.new(data_file_attributes) + df = build_data_file(contributor, datastation_dataset, projects) assay.assay_assets.build(asset: df) end end @@ -109,6 +108,17 @@ def self.detect_sample_type(datastation_sample) candidates.first&.last end + private + + def self.build_data_file(contributor, datastation_dataset, projects) + blob = ContentBlob.new(url: datastation_dataset.resource_uri.to_s, original_filename: datastation_dataset.identifier) + data_file_attributes = datastation_dataset.seek_attributes.merge({ + contributor: contributor, projects: projects, + content_blob: blob + }) + DataFile.new(data_file_attributes) + end + end end end diff --git a/test/unit/bioind/fairdata/fair_data_reader_test.rb b/test/unit/bioind/fairdata/fair_data_reader_test.rb index a6010a6ca8..ddf1059a05 100644 --- a/test/unit/bioind/fairdata/fair_data_reader_test.rb +++ b/test/unit/bioind/fairdata/fair_data_reader_test.rb @@ -284,7 +284,21 @@ class FairDataReaderTest < ActiveSupport::TestCase investigation = BioInd::FairData::Reader.construct_isa(inv, contributor, [project]) assert_equal 100, investigation.studies.first.observation_units.to_a.count observation_unit = investigation.studies.first.observation_units.first - assert_equal 1, observation_unit.data_files + assert_equal 1, observation_unit.observation_unit_assets.select{|oua| oua.asset_type == 'DataFile'}.collect(&:asset).count + + df = observation_unit.observation_unit_assets.first.asset + assert_equal 'Dataset: IndPenSim_V3_Batch_1.csv.gz', df.title + assert_equal 'file', df.description + + assert_difference('DataFile.count',96) do + assert_difference('ObservationUnitAsset.count',96) do + disable_authorization_checks { + investigation.save! + } + end + end + + pp DataFile.all.collect(&:title).inspect end test 'populate obsv unit extended metadata' do From 5f86cf3da365a07f88c9755b6e7527fdaa7770eb Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Wed, 1 May 2024 16:19:29 +0100 Subject: [PATCH 054/548] add a little cache when gathering datafiles to avoid creating duplicates --- lib/bio_ind/fair_data/reader.rb | 18 ++++++++++++------ .../bioind/fairdata/fair_data_reader_test.rb | 4 +--- 2 files changed, 13 insertions(+), 9 deletions(-) diff --git a/lib/bio_ind/fair_data/reader.rb b/lib/bio_ind/fair_data/reader.rb index deb0470c04..559a130b31 100644 --- a/lib/bio_ind/fair_data/reader.rb +++ b/lib/bio_ind/fair_data/reader.rb @@ -111,12 +111,18 @@ def self.detect_sample_type(datastation_sample) private def self.build_data_file(contributor, datastation_dataset, projects) - blob = ContentBlob.new(url: datastation_dataset.resource_uri.to_s, original_filename: datastation_dataset.identifier) - data_file_attributes = datastation_dataset.seek_attributes.merge({ - contributor: contributor, projects: projects, - content_blob: blob - }) - DataFile.new(data_file_attributes) + @_data_file_cache ||= {} + if @_data_file_cache[datastation_dataset.identifier] + @_data_file_cache[datastation_dataset.identifier] + else + blob = ContentBlob.new(url: datastation_dataset.resource_uri.to_s, original_filename: datastation_dataset.identifier) + data_file_attributes = datastation_dataset.seek_attributes.merge({ + contributor: contributor, projects: projects, + content_blob: blob + }) + @_data_file_cache[datastation_dataset.identifier] = DataFile.new(data_file_attributes) + end + end end diff --git a/test/unit/bioind/fairdata/fair_data_reader_test.rb b/test/unit/bioind/fairdata/fair_data_reader_test.rb index ddf1059a05..8cd4b077fb 100644 --- a/test/unit/bioind/fairdata/fair_data_reader_test.rb +++ b/test/unit/bioind/fairdata/fair_data_reader_test.rb @@ -284,7 +284,7 @@ class FairDataReaderTest < ActiveSupport::TestCase investigation = BioInd::FairData::Reader.construct_isa(inv, contributor, [project]) assert_equal 100, investigation.studies.first.observation_units.to_a.count observation_unit = investigation.studies.first.observation_units.first - assert_equal 1, observation_unit.observation_unit_assets.select{|oua| oua.asset_type == 'DataFile'}.collect(&:asset).count + assert_equal 1, observation_unit.observation_unit_assets.find_all{|oua| oua.asset_type == 'DataFile'}.collect(&:asset).count df = observation_unit.observation_unit_assets.first.asset assert_equal 'Dataset: IndPenSim_V3_Batch_1.csv.gz', df.title @@ -297,8 +297,6 @@ class FairDataReaderTest < ActiveSupport::TestCase } end end - - pp DataFile.all.collect(&:title).inspect end test 'populate obsv unit extended metadata' do From ad1a952f8f2852135965d42ceea13b4edfb7cf23 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Wed, 1 May 2024 16:36:28 +0100 Subject: [PATCH 055/548] set data file as external link and webpage, and binary content type temporary solution to always show the link. also disabled the datafile caching for now, it caused a weird unpredictable test error --- lib/bio_ind/fair_data/reader.rb | 15 ++++++++------- .../unit/bioind/fairdata/fair_data_reader_test.rb | 10 ++++++++++ 2 files changed, 18 insertions(+), 7 deletions(-) diff --git a/lib/bio_ind/fair_data/reader.rb b/lib/bio_ind/fair_data/reader.rb index 559a130b31..81b31101f7 100644 --- a/lib/bio_ind/fair_data/reader.rb +++ b/lib/bio_ind/fair_data/reader.rb @@ -111,17 +111,18 @@ def self.detect_sample_type(datastation_sample) private def self.build_data_file(contributor, datastation_dataset, projects) - @_data_file_cache ||= {} - if @_data_file_cache[datastation_dataset.identifier] - @_data_file_cache[datastation_dataset.identifier] - else - blob = ContentBlob.new(url: datastation_dataset.resource_uri.to_s, original_filename: datastation_dataset.identifier) + # @_data_file_cache = {} + # if @_data_file_cache[datastation_dataset.identifier] + # @_data_file_cache[datastation_dataset.identifier] + # else + blob = ContentBlob.new(url: datastation_dataset.content_url.to_s, original_filename: datastation_dataset.identifier, external_link: true, is_webpage: true, content_type: 'application/octet-stream') data_file_attributes = datastation_dataset.seek_attributes.merge({ contributor: contributor, projects: projects, content_blob: blob }) - @_data_file_cache[datastation_dataset.identifier] = DataFile.new(data_file_attributes) - end + DataFile.new(data_file_attributes) + # @_data_file_cache[datastation_dataset.identifier] = DataFile.new(data_file_attributes) + # end end diff --git a/test/unit/bioind/fairdata/fair_data_reader_test.rb b/test/unit/bioind/fairdata/fair_data_reader_test.rb index 8cd4b077fb..836809a3bd 100644 --- a/test/unit/bioind/fairdata/fair_data_reader_test.rb +++ b/test/unit/bioind/fairdata/fair_data_reader_test.rb @@ -252,6 +252,12 @@ class FairDataReaderTest < ActiveSupport::TestCase assert_equal 'METAGENOMIC', assay.extended_metadata.get_attribute_value('Library Source') assert_equal 'AMPLICON', assay.extended_metadata.get_attribute_value('Library Strategy') + study.assays.each do |assay| + assert assay.valid?, "invalid assay - #{assay.errors.full_messages}" + end + assert study.valid?, "invalid study - #{study.errors.full_messages}" + assert investigation.valid?, "invalid investigation - #{investigation.errors.full_messages}" + assert_difference('ExtendedMetadata.count', 10) do User.with_current_user(contributor.user) do study.save! @@ -289,6 +295,10 @@ class FairDataReaderTest < ActiveSupport::TestCase df = observation_unit.observation_unit_assets.first.asset assert_equal 'Dataset: IndPenSim_V3_Batch_1.csv.gz', df.title assert_equal 'file', df.description + assert_equal 'application/octet-stream', df.content_blob.content_type + assert df.content_blob.external_link? + assert df.content_blob.is_webpage? + assert df.content_blob.show_as_external_link? assert_difference('DataFile.count',96) do assert_difference('ObservationUnitAsset.count',96) do From bc6578c6566fc2a4ace8da19f4871e8e6434b0c2 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Wed, 1 May 2024 16:49:34 +0100 Subject: [PATCH 056/548] fix viewing data_files/observation units where they are linked. added routes, and relationship for isa, and data_file.observation_units association --- app/models/data_file.rb | 3 ++- app/models/observation_unit.rb | 2 +- config/routes.rb | 4 ++-- lib/seek/isa_graph_generator.rb | 2 +- test/functional/observation_units_controller_test.rb | 4 ++-- 5 files changed, 8 insertions(+), 7 deletions(-) diff --git a/app/models/data_file.rb b/app/models/data_file.rb index 3ebd3200cc..243a69ed31 100644 --- a/app/models/data_file.rb +++ b/app/models/data_file.rb @@ -23,7 +23,8 @@ class DataFile < ApplicationRecord has_many :sample_resource_links, -> { where(resource_type: 'DataFile') }, class_name: 'SampleResourceLink', foreign_key: :resource_id has_many :linked_samples, through: :sample_resource_links, source: :sample - has_many :observation_unit_assets + has_many :observation_unit_assets, dependent: :destroy, as: :asset, foreign_key: :asset_id, autosave: true, # change this to validate: true in the future + inverse_of: :asset has_many :observation_units, through: :observation_unit_assets has_many :workflow_data_files, dependent: :destroy, autosave: true diff --git a/app/models/observation_unit.rb b/app/models/observation_unit.rb index 1c87a073e9..77cc8f20b1 100644 --- a/app/models/observation_unit.rb +++ b/app/models/observation_unit.rb @@ -8,7 +8,7 @@ class ObservationUnit < ApplicationRecord belongs_to :contributor, class_name: 'Person' belongs_to :study has_many :samples - has_many :observation_unit_assets + has_many :observation_unit_assets, dependent: :destroy has_many :data_files, through: :observation_unit_assets, source: :asset, source_type: 'DataFile' has_extended_metadata diff --git a/config/routes.rb b/config/routes.rb index 3b0e1d3e64..f0b91bbe9f 100644 --- a/config/routes.rb +++ b/config/routes.rb @@ -502,7 +502,7 @@ get :retrieve_nels_sample_metadata get :has_matching_sample_type end - resources :people, :programmes, :projects, :investigations, :assays, :samples, :studies, :publications, :events, :collections, :workflows, :file_templates, :placeholders, only: [:index] + resources :people, :programmes, :projects, :investigations, :assays, :samples, :studies, :publications, :events, :collections, :workflows, :file_templates, :placeholders, :observation_units, only: [:index] end resources :presentations, concerns: [:has_content_blobs, :publishable, :has_versions, :asset, :explorable_spreadsheet] do @@ -803,7 +803,7 @@ resources :observation_units, only: [:show, :index] do - resources :projects, :people, :programmes, :studies, :samples, :assays + resources :projects, :people, :programmes, :studies, :samples, :assays, :data_files end ### MISC MATCHES ### diff --git a/lib/seek/isa_graph_generator.rb b/lib/seek/isa_graph_generator.rb index 6fc3f8d2c0..2a26c9a663 100644 --- a/lib/seek/isa_graph_generator.rb +++ b/lib/seek/isa_graph_generator.rb @@ -222,7 +222,7 @@ def associations(object) when ObservationUnit { parents: %i[study], - aggregated_children: { samples: :samples } + related: %i[samples data_files] } else {} diff --git a/test/functional/observation_units_controller_test.rb b/test/functional/observation_units_controller_test.rb index 7a7b739701..ac5ab27d64 100644 --- a/test/functional/observation_units_controller_test.rb +++ b/test/functional/observation_units_controller_test.rb @@ -4,13 +4,13 @@ class ObservationUnitsControllerTest < ActionController::TestCase test 'show' do - unit = FactoryBot.create(:observation_unit) + unit = FactoryBot.create(:max_observation_unit) get :show, params: { id: unit.id } assert_response :success end test 'index' do - unit = FactoryBot.create(:observation_unit) + unit = FactoryBot.create(:max_observation_unit) get :index assert_response :success end From 5d7bb861ad15f293383b74c7cfe3f62c4eaec570 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Thu, 2 May 2024 10:25:57 +0100 Subject: [PATCH 057/548] a slightly better icon for obs unit --- .../images/crystal_project/48x48/apps/search.png | Bin 0 -> 1989 bytes config/image_files/image_file_dictionary.yml | 2 +- 2 files changed, 1 insertion(+), 1 deletion(-) create mode 100644 app/assets/images/crystal_project/48x48/apps/search.png diff --git a/app/assets/images/crystal_project/48x48/apps/search.png b/app/assets/images/crystal_project/48x48/apps/search.png new file mode 100644 index 0000000000000000000000000000000000000000..9b1b4f7d79d6f727d9faa4e3b78a77dbbc93c65c GIT binary patch literal 1989 zcmXw33pkW%8y;n&gY>7<9~%DkJGBngCY6;Km9vy_SfZ6giS3BLrNa_A6lEtRgb{^F 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oauth_authorized_applications: 'famfamfam_silk/application_link.png' -observation_unit_avatar: 'misc_icons/cell3.png' +observation_unit_avatar: 'crystal_project/48x48/apps/search.png' openbis_square_small: 'logos/openbis-square-16.png' openbis_square: 'logos/openbis-square.png' openbis: 'logos/openbis.png' From 8e14bb5f431cf24621dc07d3220ebbb4abf3ccc2 Mon Sep 17 00:00:00 2001 From: Finn Bacall Date: Tue, 7 May 2024 16:29:16 +0100 Subject: [PATCH 058/548] Endpoint to retrieve `ro-crate-metadata.json` for a workflow Regardless of whether it is generated/stored --- app/controllers/workflows_controller.rb | 11 ++- config/routes.rb | 1 + lib/seek/permissions/translator.rb | 2 +- test/functional/workflows_controller_test.rb | 83 ++++++++++++++++++++ 4 files changed, 94 insertions(+), 3 deletions(-) diff --git a/app/controllers/workflows_controller.rb b/app/controllers/workflows_controller.rb index c9d7ddb28d..1489a3370f 100644 --- a/app/controllers/workflows_controller.rb +++ b/app/controllers/workflows_controller.rb @@ -7,7 +7,7 @@ class WorkflowsController < ApplicationController before_action :workflows_enabled? before_action :find_assets, only: [:index] before_action :find_and_authorize_requested_item, except: [:index, :new, :create, :preview, :update_annotations_ajax] - before_action :find_display_asset, only: [:show, :download, :diagram, :ro_crate, :edit_paths, :update_paths] + before_action :find_display_asset, only: [:show, :download, :diagram, :ro_crate, :ro_crate_metadata, :edit_paths, :update_paths] before_action :login_required, only: [:create, :create_version, :new_version, :create_from_files, :create_from_ro_crate, :create_metadata, :provide_metadata, :create_from_git, :create_version_from_git] @@ -19,7 +19,7 @@ class WorkflowsController < ApplicationController include RoCrateHandling include Legacy::WorkflowSupport - api_actions :index, :show, :create, :update, :destroy, :ro_crate, :create_version + api_actions :index, :show, :create, :update, :destroy, :ro_crate, :ro_crate_metadata, :create_version rescue_from ROCrate::ReadException do |e| logger.error("Error whilst attempting to read RO-Crate metadata for Workflow #{@workflow&.id}: #{e.exception.class.name} #{e.message}") @@ -258,6 +258,13 @@ def ro_crate "workflow-#{@workflow.id}-#{@display_workflow.version}.crate.zip") end + def ro_crate_metadata + metadata = @display_workflow.ro_crate.metadata + json = metadata.generate + response.headers['Content-Length'] = json.length.to_s + send_data(json, filename: metadata.id, type: 'application/json', disposition: 'inline') + end + def edit_paths end diff --git a/config/routes.rb b/config/routes.rb index 533a07991e..8261d3f63a 100644 --- a/config/routes.rb +++ b/config/routes.rb @@ -538,6 +538,7 @@ member do get :diagram get :ro_crate + get :ro_crate_metadata get :new_version get :new_git_version post :create_version_metadata diff --git a/lib/seek/permissions/translator.rb b/lib/seek/permissions/translator.rb index 08dc1511eb..6bb9dec5ff 100644 --- a/lib/seek/permissions/translator.rb +++ b/lib/seek/permissions/translator.rb @@ -12,7 +12,7 @@ class Translator download: Set.new(%i[ download named_download launch submit_job data execute plot explore download_log download_results input output download_output download_input - view_result compare_versions simulate diagram ro_crate + view_result compare_versions simulate diagram ro_crate ro_crate_metadata ]).freeze, edit: Set.new(%i[ diff --git a/test/functional/workflows_controller_test.rb b/test/functional/workflows_controller_test.rb index d183322859..7e23025b99 100644 --- a/test/functional/workflows_controller_test.rb +++ b/test/functional/workflows_controller_test.rb @@ -1813,4 +1813,87 @@ def bad_generator.write_graph(struct) assert_redirected_to workflow assert flash[:error].include?("not found in crate: this-file-does-not-exist") end + + test 'gets generated RO-Crate metadata' do + workflow = FactoryBot.create(:local_git_workflow, policy: FactoryBot.create(:public_policy)) + refute workflow.git_version.get_blob('ro-crate-metadata.json') + assert workflow.is_git_versioned? + + get :ro_crate_metadata, params: { id: workflow.id } + + assert_response :success + assert @response.header['Content-Length'].present? + assert @response.header['Content-Length'].to_i > 100 + j = JSON.parse(@response.body) + assert(j['@graph'].any? { |n| n['@id'] == 'ro-crate-metadata.json' }) + end + + test 'gets stored RO-Crate metadata' do + workflow = FactoryBot.create(:ro_crate_git_workflow, policy: FactoryBot.create(:public_policy)) + assert workflow.git_version.get_blob('ro-crate-metadata.json') + assert workflow.is_git_versioned? + + get :ro_crate_metadata, params: { id: workflow.id } + + assert_response :success + assert @response.header['Content-Length'].present? + assert @response.header['Content-Length'].to_i > 100 + j = JSON.parse(@response.body) + assert(j['@graph'].any? { |n| n['@id'] == 'ro-crate-metadata.json' }) + end + + test 'gets generated RO-Crate metadata for non-git workflow' do + workflow = FactoryBot.create(:workflow, policy: FactoryBot.create(:public_policy)) + refute workflow.is_git_versioned? + + get :ro_crate_metadata, params: { id: workflow.id } + + assert_response :success + assert @response.header['Content-Length'].present? + assert @response.header['Content-Length'].to_i > 100 + j = JSON.parse(@response.body) + assert(j['@graph'].any? { |n| n['@id'] == 'ro-crate-metadata.json' }) + end + + test 'gets RO-Crate metadata for specific version' do + workflow = FactoryBot.create(:local_ro_crate_git_workflow, policy: FactoryBot.create(:public_policy)) + md = workflow.git_version.get_blob('ro-crate-metadata.json') + assert md + assert workflow.is_git_versioned? + assert_equal 1, workflow.version + disable_authorization_checks do + workflow.git_version.next_version(mutable: true).save! + gv = workflow.reload.latest_git_version + assert_equal 2, gv.version + assert_equal 2, workflow.version + json = md.read + json.gsub!('test1_1', 'test9_9') + gv.add_file('ro-crate-metadata.json', StringIO.new(json)) + gv.save! + end + + get :ro_crate_metadata, params: { id: workflow.id, version: 1 } + + assert_response :success + assert response.body.include?('test1_1') + refute response.body.include?('test9_9') + + get :ro_crate_metadata, params: { id: workflow.id, version: 2 } + + assert_response :success + refute response.body.include?('test1_1') + assert response.body.include?('test9_9') + end + + test 'does not get RO-Crate metadata if no download permission' do + workflow = FactoryBot.create(:existing_galaxy_ro_crate_workflow, policy: FactoryBot.create(:publicly_viewable_policy)) + assert workflow.can_view? + refute workflow.can_download? + + get :ro_crate_metadata, params: { id: workflow.id } + + assert_redirected_to workflow + assert_includes flash[:error], 'You are not authorized to download this Workflow' + end end + From 1ef1a728e043e33f9ae934d403367ae8a32cdbe1 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Mon, 13 May 2024 14:07:19 +0100 Subject: [PATCH 059/548] include extended metadata in generated rdf --- lib/seek/rdf/rdf_generation.rb | 12 ++++++++++++ test/unit/study_test.rb | 24 ++++++++++++++++++++++++ 2 files changed, 36 insertions(+) diff --git a/lib/seek/rdf/rdf_generation.rb b/lib/seek/rdf/rdf_generation.rb index bf33f4f177..501043971f 100644 --- a/lib/seek/rdf/rdf_generation.rb +++ b/lib/seek/rdf/rdf_generation.rb @@ -41,6 +41,7 @@ def to_rdf_graph rdf_graph = describe_type(rdf_graph) rdf_graph = generate_from_csv_definitions rdf_graph rdf_graph = additional_triples rdf_graph + rdf_graph = extended_metadata_triples rdf_graph rdf_graph end @@ -66,6 +67,17 @@ def additional_triples(rdf_graph) if is_a?(Model) && contains_sbml? rdf_graph << [rdf_resource, JERMVocab.hasFormat, JERMVocab.SBML_format] end + + rdf_graph + end + + def extended_metadata_triples(rdf_graph) + return rdf_graph unless extended_metadata&.extended_metadata_type + attributes = extended_metadata.extended_metadata_type.extended_metadata_attributes.select{|at| at.property_type_id.present?} + resource = rdf_resource + attributes.each do |attribute| + rdf_graph << [resource, RDF::URI(attribute.property_type_id), RDF::Literal(extended_metadata.get_attribute_value(attribute))] + end rdf_graph end diff --git a/test/unit/study_test.rb b/test/unit/study_test.rb index 8fb1b43b2f..3a95240ce5 100644 --- a/test/unit/study_test.rb +++ b/test/unit/study_test.rb @@ -29,6 +29,30 @@ class StudyTest < ActiveSupport::TestCase end end + test 'include extended metadata in rdf' do + object = FactoryBot.create(:study, description: 'My famous study', + extended_metadata_attributes:{ + extended_metadata_type: FactoryBot.create(:fairdata_virtual_demo_study_extended_metadata_partial), + data:{ + 'Alias':'the alias', + 'Submission Alias':'the submission alias' + } + }) + rdf = object.to_rdf + RDF::Reader.for(:rdfxml).new(rdf) do |reader| + assert reader.statements.count > 1 + assert_equal RDF::URI.new("http://localhost:3000/studies/#{object.id}"), reader.statements.first.subject + statement = reader.statements.detect{|s| s.subject == RDF::URI.new("http://localhost:3000/studies/#{object.id}") && s.predicate == RDF::URI("http://fairbydesign.nl/ontology/alias")} + assert_equal RDF::Literal('the alias'), statement.object + + statement = reader.statements.detect{|s| s.subject == RDF::URI.new("http://localhost:3000/studies/#{object.id}") && s.predicate == RDF::URI("http://fairbydesign.nl/ontology/submission_alias")} + assert_equal RDF::Literal('the submission alias'), statement.object + + statement = reader.statements.detect{|s| s.subject == RDF::URI.new("http://localhost:3000/studies/#{object.id}") && s.predicate == RDF::URI("http://fairbydesign.nl/ontology/submission_lab_name")} + assert_equal RDF::Literal(''), statement.object + end + end + # only authorized people can delete a study, and a study must have no assays test 'can delete' do project_member = FactoryBot.create(:person) From 6f51c9fa8ce98a9b0400ab5e1819cddd3b3159b7 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Mon, 13 May 2024 14:54:43 +0100 Subject: [PATCH 060/548] skip extended metadata rdf if that type doesn't support it --- app/models/application_record.rb | 8 ++++++++ lib/seek/rdf/rdf_generation.rb | 2 +- test/unit/person_test.rb | 5 +++++ test/unit/study_test.rb | 5 +++++ 4 files changed, 19 insertions(+), 1 deletion(-) diff --git a/app/models/application_record.rb b/app/models/application_record.rb index 1cd2df850e..2146a47461 100644 --- a/app/models/application_record.rb +++ b/app/models/application_record.rb @@ -190,4 +190,12 @@ def list_item_title_cache_key_prefix def updated_last_by ActivityLog.where(activity_loggable:self, action:'update').last&.culprit&.person end + + def supports_extended_metadata? + self.class.supports_extended_metadata? + end + + def self.supports_extended_metadata? + reflect_on_association(:extended_metadata).present? + end end diff --git a/lib/seek/rdf/rdf_generation.rb b/lib/seek/rdf/rdf_generation.rb index 501043971f..2103bbd729 100644 --- a/lib/seek/rdf/rdf_generation.rb +++ b/lib/seek/rdf/rdf_generation.rb @@ -72,7 +72,7 @@ def additional_triples(rdf_graph) end def extended_metadata_triples(rdf_graph) - return rdf_graph unless extended_metadata&.extended_metadata_type + return rdf_graph unless supports_extended_metadata? && extended_metadata&.extended_metadata_type attributes = extended_metadata.extended_metadata_type.extended_metadata_attributes.select{|at| at.property_type_id.present?} resource = rdf_resource attributes.each do |attribute| diff --git a/test/unit/person_test.rb b/test/unit/person_test.rb index f456e4441f..8221f95d0c 100644 --- a/test/unit/person_test.rb +++ b/test/unit/person_test.rb @@ -8,6 +8,11 @@ def test_work_groups assert_equal 3, p.work_groups.size end + test 'supports extended metadata?' do + refute Person.supports_extended_metadata? + refute Person.new.supports_extended_metadata? + end + test 'to_json_ld' do refute_nil JSON.parse(FactoryBot.create(:person).to_json_ld) end diff --git a/test/unit/study_test.rb b/test/unit/study_test.rb index 3a95240ce5..a6b08e8b27 100644 --- a/test/unit/study_test.rb +++ b/test/unit/study_test.rb @@ -29,6 +29,11 @@ class StudyTest < ActiveSupport::TestCase end end + test 'supports extended metadata?' do + assert Study.supports_extended_metadata? + assert Study.new.supports_extended_metadata? + end + test 'include extended metadata in rdf' do object = FactoryBot.create(:study, description: 'My famous study', extended_metadata_attributes:{ From 732af2f34c3e21acfeba2de64f39a672c933d56e Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Mon, 13 May 2024 15:29:07 +0100 Subject: [PATCH 061/548] include some basic rdf for samples not yet including attributes --- app/controllers/samples_controller.rb | 1 + lib/seek/rdf/jerm_vocab.rb | 3 ++- lib/seek/rdf/rdf_mappings.csv | 1 + test/functional/samples_controller_test.rb | 15 +++++---------- test/unit/sample_test.rb | 10 ++++++++++ test/unit/util_test.rb | 2 +- 6 files changed, 20 insertions(+), 12 deletions(-) diff --git a/app/controllers/samples_controller.rb b/app/controllers/samples_controller.rb index d2289dccbb..296c493c25 100644 --- a/app/controllers/samples_controller.rb +++ b/app/controllers/samples_controller.rb @@ -71,6 +71,7 @@ def show respond_to do |format| format.html format.json {render json: @sample, include: [params[:include]]} + format.rdf { render template: 'rdf/show' } end end diff --git a/lib/seek/rdf/jerm_vocab.rb b/lib/seek/rdf/jerm_vocab.rb index f2b81de7b2..7f7dade283 100644 --- a/lib/seek/rdf/jerm_vocab.rb +++ b/lib/seek/rdf/jerm_vocab.rb @@ -35,7 +35,8 @@ def self.defined_types Study => :Study, Investigation => :Investigation, Publication => :Publication, - Strain => :Strain + Strain => :Strain, + Sample => :Sample } end diff --git a/lib/seek/rdf/rdf_mappings.csv b/lib/seek/rdf/rdf_mappings.csv index 45608a9fec..88f802e78a 100644 --- a/lib/seek/rdf/rdf_mappings.csv +++ b/lib/seek/rdf/rdf_mappings.csv @@ -62,6 +62,7 @@ Project,web_page,JERMVocab.webLink,l,URI.parse(item),compact Project,rdf_seek_id,JERMVocab.seekID,l,URI.parse(item), Publication,projects,JERMVocab.itemProducedBy,u,, Publication,assays,JERMVocab.isPartOf,u,, +Sample,assays,JERMVocab.hasPart,u,, Sop,assays,JERMVocab.isPartOf,u,, Sop,projects,JERMVocab.itemProducedBy,u,, Sop,rdf_seek_id,JERMVocab.seekID,l,URI.parse(item), diff --git a/test/functional/samples_controller_test.rb b/test/functional/samples_controller_test.rb index 4ca85aae24..be1fa8c575 100644 --- a/test/functional/samples_controller_test.rb +++ b/test/functional/samples_controller_test.rb @@ -6,16 +6,7 @@ class SamplesControllerTest < ActionController::TestCase include SharingFormTestHelper include HtmlHelper include GeneralAuthorizationTestCases - - test 'should return 406 when requesting RDF' do - login_as(FactoryBot.create(:user)) - sample = FactoryBot.create :sample, contributor: User.current_user.person - assert sample.can_view? - - get :show, params: { id: sample, format: :rdf } - - assert_response :not_acceptable - end + include RdfTestCases test 'index' do FactoryBot.create(:sample, policy: FactoryBot.create(:public_policy)) @@ -1474,6 +1465,10 @@ class SamplesControllerTest < ActionController::TestCase end + def rdf_test_object + FactoryBot.create(:max_sample, policy: FactoryBot.create(:public_policy)) + end + private def populated_patient_sample diff --git a/test/unit/sample_test.rb b/test/unit/sample_test.rb index 751c4daf86..1bedf6ec6e 100644 --- a/test/unit/sample_test.rb +++ b/test/unit/sample_test.rb @@ -1382,4 +1382,14 @@ class SampleTest < ActiveSupport::TestCase assert_equal [df1, df2, df3].sort_by(&:id), sample_ext_attr.related_data_files.sort_by(&:id) end + test 'to rdf' do + sample = FactoryBot.create(:max_sample) + rdf = sample.to_rdf + pp rdf + RDF::Reader.for(:rdfxml).new(rdf) do |reader| + assert reader.statements.count > 1 + assert_equal RDF::URI.new("http://localhost:3000/samples/#{sample.id}"), reader.statements.first.subject + end + end + end diff --git a/test/unit/util_test.rb b/test/unit/util_test.rb index a1a5dece29..42b66d64c2 100644 --- a/test/unit/util_test.rb +++ b/test/unit/util_test.rb @@ -32,7 +32,7 @@ def teardown test 'rdf capable types' do types = Seek::Util.rdf_capable_types - expected = %w[Assay DataFile Investigation Model Organism Person Programme Project Publication Sop Strain Study] + expected = %w[Assay DataFile Investigation Model Organism Person Programme Project Publication Sample Sop Strain Study] assert_equal expected, types.collect(&:name).sort end From cea430b02d7399138644b38843e4e23332e35885 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Mon, 13 May 2024 16:39:24 +0100 Subject: [PATCH 062/548] rdf for observation unit --- app/models/observation_unit.rb | 1 + lib/seek/rdf/jerm_vocab.rb | 1 + lib/seek/rdf/rdf_generation.rb | 7 ++++++- lib/seek/rdf/rdf_mappings.csv | 5 +++++ test/functional/observation_units_controller_test.rb | 6 ++++++ test/functional/samples_controller_test.rb | 4 ++++ test/unit/observation_unit_test.rb | 11 +++++++++++ test/unit/sample_test.rb | 1 - test/unit/util_test.rb | 2 +- 9 files changed, 35 insertions(+), 3 deletions(-) diff --git a/app/models/observation_unit.rb b/app/models/observation_unit.rb index 77cc8f20b1..d70c29c4a2 100644 --- a/app/models/observation_unit.rb +++ b/app/models/observation_unit.rb @@ -4,6 +4,7 @@ class ObservationUnit < ApplicationRecord include Seek::ProjectAssociation include Seek::Stats::ActivityCounts include Seek::Search::CommonFields, Seek::Search::BackgroundReindexing + include Seek::Rdf::RdfGeneration belongs_to :contributor, class_name: 'Person' belongs_to :study diff --git a/lib/seek/rdf/jerm_vocab.rb b/lib/seek/rdf/jerm_vocab.rb index 7f7dade283..db8a381d1a 100644 --- a/lib/seek/rdf/jerm_vocab.rb +++ b/lib/seek/rdf/jerm_vocab.rb @@ -29,6 +29,7 @@ def self.defined_types Model => :Model, Sop => :SOP, Person => :Person, + ObservationUnit => 'http://purl.org/ppeo/PPEO.owl#observation_unit', Organism => :Organism, Project => :Project, Programme => :Programme, diff --git a/lib/seek/rdf/rdf_generation.rb b/lib/seek/rdf/rdf_generation.rb index 2103bbd729..5f4afc6368 100644 --- a/lib/seek/rdf/rdf_generation.rb +++ b/lib/seek/rdf/rdf_generation.rb @@ -97,7 +97,12 @@ def rdf_seek_id # the URI for the type of this object, for example http://jermontology.org/ontology/JERMOntology#Study for a Study def rdf_type_uri - JERMVocab[rdf_type_entity_fragment] + case rdf_type_entity_fragment + when Symbol + JERMVocab[rdf_type_entity_fragment] + when String + RDF::URI(rdf_type_entity_fragment) + end end def rdf_type_entity_fragment diff --git a/lib/seek/rdf/rdf_mappings.csv b/lib/seek/rdf/rdf_mappings.csv index 88f802e78a..d87cb8ebbe 100644 --- a/lib/seek/rdf/rdf_mappings.csv +++ b/lib/seek/rdf/rdf_mappings.csv @@ -33,6 +33,9 @@ Investigation,rdf_seek_id,JERMVocab.seekID,l,URI.parse(item), Model,assays,JERMVocab.isPartOf,u,, Model,projects,JERMVocab.itemProducedBy,u,, Model,rdf_seek_id,JERMVocab.seekID,l,URI.parse(item), +ObservationUnit,samples,JERMVocab.hasPart,u,, +ObservationUnit,study,JERMVocab.isPartOf,u,, +ObservationUnit,projects,JERMVocab.itemProducedBy,u,, Organism,assays,JERMVocab.isInvestigatedBy,u,, Organism,ncbi_uri,JERMVocab.NCBI_ID,l,URI.parse(item),compact Person,created_items,JERMVocab.isCreatorOf,u,, @@ -63,12 +66,14 @@ Project,rdf_seek_id,JERMVocab.seekID,l,URI.parse(item), Publication,projects,JERMVocab.itemProducedBy,u,, Publication,assays,JERMVocab.isPartOf,u,, Sample,assays,JERMVocab.hasPart,u,, +Sample,observation_unit,JERMVocab.isPartOf,u,, Sop,assays,JERMVocab.isPartOf,u,, Sop,projects,JERMVocab.itemProducedBy,u,, Sop,rdf_seek_id,JERMVocab.seekID,l,URI.parse(item), Strain,assays,JERMVocab.isInvestigatedBy,u,, Strain,ncbi_uri,JERMVocab.NCBI_ID,l,URI.parse(item),compact Strain,provider_id,JERMVocab.externalSupplierID,l,, +Study,observation_units,JERMVocab.hasPart,u,, Study,assays,JERMVocab.hasPart,u,, Study,investigation,JERMVocab.isPartOf,u,, Study,projects,JERMVocab.itemProducedBy,u,, diff --git a/test/functional/observation_units_controller_test.rb b/test/functional/observation_units_controller_test.rb index ac5ab27d64..77d4e1e1c5 100644 --- a/test/functional/observation_units_controller_test.rb +++ b/test/functional/observation_units_controller_test.rb @@ -3,6 +3,12 @@ class ObservationUnitsControllerTest < ActionController::TestCase + include RdfTestCases + + def rdf_test_object + FactoryBot.create(:max_observation_unit) + end + test 'show' do unit = FactoryBot.create(:max_observation_unit) get :show, params: { id: unit.id } diff --git a/test/functional/samples_controller_test.rb b/test/functional/samples_controller_test.rb index be1fa8c575..bf56063cd6 100644 --- a/test/functional/samples_controller_test.rb +++ b/test/functional/samples_controller_test.rb @@ -8,6 +8,10 @@ class SamplesControllerTest < ActionController::TestCase include GeneralAuthorizationTestCases include RdfTestCases + def rdf_test_object + FactoryBot.create(:max_sample, policy: FactoryBot.create(:public_policy)) + end + test 'index' do FactoryBot.create(:sample, policy: FactoryBot.create(:public_policy)) get :index diff --git a/test/unit/observation_unit_test.rb b/test/unit/observation_unit_test.rb index aa57655eb4..8eebc5c784 100644 --- a/test/unit/observation_unit_test.rb +++ b/test/unit/observation_unit_test.rb @@ -17,4 +17,15 @@ class ObservationUnitTest < ActiveSupport::TestCase refute_empty obs_unit.data_files end + + test 'to rdf' do + obs_unit = FactoryBot.create(:max_observation_unit) + rdf = obs_unit.to_rdf + RDF::Reader.for(:rdfxml).new(rdf) do |reader| + assert reader.statements.count > 1 + assert_equal RDF::URI.new("http://localhost:3000/observation_units/#{obs_unit.id}"), reader.statements.first.subject + end + end + + end \ No newline at end of file diff --git a/test/unit/sample_test.rb b/test/unit/sample_test.rb index 1bedf6ec6e..896549ae58 100644 --- a/test/unit/sample_test.rb +++ b/test/unit/sample_test.rb @@ -1385,7 +1385,6 @@ class SampleTest < ActiveSupport::TestCase test 'to rdf' do sample = FactoryBot.create(:max_sample) rdf = sample.to_rdf - pp rdf RDF::Reader.for(:rdfxml).new(rdf) do |reader| assert reader.statements.count > 1 assert_equal RDF::URI.new("http://localhost:3000/samples/#{sample.id}"), reader.statements.first.subject diff --git a/test/unit/util_test.rb b/test/unit/util_test.rb index 42b66d64c2..3ce082db9e 100644 --- a/test/unit/util_test.rb +++ b/test/unit/util_test.rb @@ -32,7 +32,7 @@ def teardown test 'rdf capable types' do types = Seek::Util.rdf_capable_types - expected = %w[Assay DataFile Investigation Model Organism Person Programme Project Publication Sample Sop Strain Study] + expected = %w[Assay DataFile Investigation Model ObservationUnit Organism Person Programme Project Publication Sample Sop Strain Study] assert_equal expected, types.collect(&:name).sort end From d7cc8ccaf8a56d87358f8b183a4608646d1caf0f Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 14 May 2024 09:39:22 +0100 Subject: [PATCH 063/548] include seek_rdf:generate in upgrade tasks --- lib/tasks/seek_upgrades.rake | 1 + 1 file changed, 1 insertion(+) diff --git a/lib/tasks/seek_upgrades.rake b/lib/tasks/seek_upgrades.rake index 769e95aed1..d07621f93e 100644 --- a/lib/tasks/seek_upgrades.rake +++ b/lib/tasks/seek_upgrades.rake @@ -18,6 +18,7 @@ namespace :seek do implement_assay_streams_for_isa_assays set_ls_login_legacy_mode rename_custom_metadata_legacy_supported_type + seek_rdf:generate ] # these are the tasks that are executes for each upgrade as standard, and rarely change From 1c638c2afe7c483736bd970ee217ab3f237a1d12 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 14 May 2024 10:21:14 +0100 Subject: [PATCH 064/548] include sample attribute with a pid in rdf --- lib/seek/rdf/rdf_generation.rb | 11 +++++++++++ test/unit/observation_unit_test.rb | 2 ++ test/unit/sample_test.rb | 16 +++++++++++++++- 3 files changed, 28 insertions(+), 1 deletion(-) diff --git a/lib/seek/rdf/rdf_generation.rb b/lib/seek/rdf/rdf_generation.rb index 5f4afc6368..8a17c7a85f 100644 --- a/lib/seek/rdf/rdf_generation.rb +++ b/lib/seek/rdf/rdf_generation.rb @@ -42,6 +42,7 @@ def to_rdf_graph rdf_graph = generate_from_csv_definitions rdf_graph rdf_graph = additional_triples rdf_graph rdf_graph = extended_metadata_triples rdf_graph + rdf_graph = sample_metadata_triples(rdf_graph) if self.is_a?(Sample) rdf_graph end @@ -81,6 +82,16 @@ def extended_metadata_triples(rdf_graph) rdf_graph end + def sample_metadata_triples(rdf_graph) + + attributes = sample_type.sample_attributes.select{|at| at.pid.present?} + resource = rdf_resource + attributes.each do |attribute| + rdf_graph << [resource, RDF::URI(attribute.pid), RDF::Literal(get_attribute_value(attribute))] + end + rdf_graph + end + def describe_type(rdf_graph) unless rdf_type_entity_fragment.nil? resource = rdf_resource diff --git a/test/unit/observation_unit_test.rb b/test/unit/observation_unit_test.rb index 8eebc5c784..009a17bb77 100644 --- a/test/unit/observation_unit_test.rb +++ b/test/unit/observation_unit_test.rb @@ -24,6 +24,8 @@ class ObservationUnitTest < ActiveSupport::TestCase RDF::Reader.for(:rdfxml).new(rdf) do |reader| assert reader.statements.count > 1 assert_equal RDF::URI.new("http://localhost:3000/observation_units/#{obs_unit.id}"), reader.statements.first.subject + type = reader.statements.detect{|s| s.predicate == RDF.type} + assert_equal RDF::URI('http://purl.org/ppeo/PPEO.owl#observation_unit'), type.object end end diff --git a/test/unit/sample_test.rb b/test/unit/sample_test.rb index 896549ae58..f2cbe35a6e 100644 --- a/test/unit/sample_test.rb +++ b/test/unit/sample_test.rb @@ -1383,11 +1383,25 @@ class SampleTest < ActiveSupport::TestCase end test 'to rdf' do - sample = FactoryBot.create(:max_sample) + sample = FactoryBot.create(:sample, sample_type:FactoryBot.create(:fairdatastation_virtual_demo_sample_type), + data:{ + 'Title':'the title', + 'Description':'the description', + 'Host':'the host', + 'Occupation':'the occupation' + }) rdf = sample.to_rdf RDF::Reader.for(:rdfxml).new(rdf) do |reader| assert reader.statements.count > 1 assert_equal RDF::URI.new("http://localhost:3000/samples/#{sample.id}"), reader.statements.first.subject + match = reader.statements.detect{|s| s.predicate == RDF.type} + assert_equal RDF::URI('http://jermontology.org/ontology/JERMOntology#Sample'), match.object + match = reader.statements.detect{|s| s.predicate == RDF::URI('http://fairbydesign.nl/ontology/host')} + assert_equal RDF::Literal('the host'), match.object + match = reader.statements.detect{|s| s.predicate == RDF::URI('http://fairbydesign.nl/ontology/occupation')} + assert_equal RDF::Literal('the occupation'), match.object + match = reader.statements.detect{|s| s.predicate == RDF::URI('http://fairbydesign.nl/ontology/marital_status')} + assert_equal RDF::Literal(''), match.object end end From fc037d8f5f697ba44aba24855fd6269d1dc28205 Mon Sep 17 00:00:00 2001 From: Finn Bacall Date: Tue, 14 May 2024 10:25:20 +0100 Subject: [PATCH 065/548] Remove unused method --- app/models/workflow.rb | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/app/models/workflow.rb b/app/models/workflow.rb index d557b0bf10..390fcab44d 100644 --- a/app/models/workflow.rb +++ b/app/models/workflow.rb @@ -277,16 +277,4 @@ def execution_instance_url def self.find_by_source_url(source_url) joins(:source_link).where('asset_links.url' => source_url) end - - def self.find_existing_version(source_url, version_name) - workflows = joins(:source_link).where('asset_links.url' => source_url) - if workflows.length == 1 - workflows.first.git_versions.where(name: version_name) - elsif workflows.empty? - 'None :(' - else - 'Too many :(' - end - end - end From 3fb11b3aee56e885f32f91fa446711283ecc0e0c Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 14 May 2024 11:01:47 +0100 Subject: [PATCH 066/548] fix rdf_type_uri special cases --- lib/seek/rdf/rdf_generation.rb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/lib/seek/rdf/rdf_generation.rb b/lib/seek/rdf/rdf_generation.rb index 8a17c7a85f..2cb08a3722 100644 --- a/lib/seek/rdf/rdf_generation.rb +++ b/lib/seek/rdf/rdf_generation.rb @@ -112,7 +112,11 @@ def rdf_type_uri when Symbol JERMVocab[rdf_type_entity_fragment] when String - RDF::URI(rdf_type_entity_fragment) + if rdf_type_entity_fragment =~ URI::ABS_URI + RDF::URI(rdf_type_entity_fragment) + else + JERMVocab[rdf_type_entity_fragment] + end end end From d179f9fda78f031632cf3dd96774a57abeadda4e Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 14 May 2024 13:38:39 +0100 Subject: [PATCH 067/548] ability to set the sharing permissions when registering from fair data station --- app/controllers/projects_controller.rb | 4 ++- .../import_from_fairdata_station.html.erb | 3 ++ lib/bio_ind/fair_data/reader.rb | 18 +++++----- test/functional/projects_controller_test.rb | 35 ++++++++++++++++--- .../bioind/fairdata/fair_data_reader_test.rb | 14 +++++++- 5 files changed, 59 insertions(+), 15 deletions(-) diff --git a/app/controllers/projects_controller.rb b/app/controllers/projects_controller.rb index 32a87a6677..de4b6b975f 100644 --- a/app/controllers/projects_controller.rb +++ b/app/controllers/projects_controller.rb @@ -198,8 +198,10 @@ def request_join def submit_fairdata_station path = params[:datastation_data].path + policy = Policy.new + policy.set_attributes_with_sharing(policy_params) datadata_inv = BioInd::FairData::Reader.parse_graph(path) - @investigation = BioInd::FairData::Reader.construct_isa(datadata_inv.first, current_person, [@project]) + @investigation = BioInd::FairData::Reader.construct_isa(datadata_inv.first, current_person, [@project], policy) @investigation.save! respond_to do |format| diff --git a/app/views/projects/import_from_fairdata_station.html.erb b/app/views/projects/import_from_fairdata_station.html.erb index 25330ce5cf..420cf07d7f 100644 --- a/app/views/projects/import_from_fairdata_station.html.erb +++ b/app/views/projects/import_from_fairdata_station.html.erb @@ -5,6 +5,9 @@ <%= file_field_tag "datastation_data" -%> + + <%= render partial: 'sharing/permissions_table', locals: { object: @project, policy: (@project.default_policy || Policy.default), projects: [@project], downloadable:true } %> +
    <%= submit_tag("Submit", class:'btn btn-primary') %>
    diff --git a/lib/bio_ind/fair_data/reader.rb b/lib/bio_ind/fair_data/reader.rb index 81b31101f7..0ac2444f9e 100644 --- a/lib/bio_ind/fair_data/reader.rb +++ b/lib/bio_ind/fair_data/reader.rb @@ -21,25 +21,25 @@ def self.parse_graph(path) end end - def self.construct_isa(datastation_inv, contributor, projects) - inv_attributes = datastation_inv.seek_attributes.merge({contributor: contributor, projects: projects}) + def self.construct_isa(datastation_inv, contributor, projects, policy) + inv_attributes = datastation_inv.seek_attributes.merge({contributor: contributor, projects: projects, policy:policy.deep_copy}) investigation = ::Investigation.new(inv_attributes) populate_extended_metadata(investigation, datastation_inv) datastation_inv.studies.each do |datastation_study| - study_attributes = datastation_study.seek_attributes.merge({contributor: contributor, investigation: investigation}) + study_attributes = datastation_study.seek_attributes.merge({contributor: contributor, investigation: investigation, policy:policy.deep_copy}) study = investigation.studies.build(study_attributes) populate_extended_metadata(study, datastation_study) datastation_study.observation_units.each do |datastation_observation_unit| observation_unit_attributes = datastation_observation_unit.seek_attributes.merge({contributor: contributor, study:study, projects: projects}) observation_unit = study.observation_units.build(observation_unit_attributes) datastation_observation_unit.datasets.each do |datastation_dataset| - df = build_data_file(contributor, datastation_dataset, projects) + df = build_data_file(contributor, datastation_dataset, projects, policy) observation_unit.observation_unit_assets.build(asset: df) end populate_extended_metadata(observation_unit, datastation_observation_unit) datastation_observation_unit.samples.each do |datastation_sample| - sample = ::Sample.new(contributor: contributor, projects: projects) + sample = ::Sample.new(contributor: contributor, projects: projects, policy:policy.deep_copy) populate_sample(sample, datastation_sample) if sample.valid? observation_unit.samples << sample @@ -49,11 +49,11 @@ def self.construct_isa(datastation_inv, contributor, projects) datastation_sample.assays.each do |datastation_assay| samples = [] samples << sample if sample.valid? - assay_attributes = datastation_assay.seek_attributes.merge({contributor: contributor, study:study, assay_class: AssayClass.experimental, samples:samples}) + assay_attributes = datastation_assay.seek_attributes.merge({contributor: contributor, study:study, assay_class: AssayClass.experimental, samples:samples, policy:policy.deep_copy}) assay = study.assays.build(assay_attributes) populate_extended_metadata(assay, datastation_assay) datastation_assay.datasets.each do |datastation_dataset| - df = build_data_file(contributor, datastation_dataset, projects) + df = build_data_file(contributor, datastation_dataset, projects, policy) assay.assay_assets.build(asset: df) end end @@ -110,7 +110,7 @@ def self.detect_sample_type(datastation_sample) private - def self.build_data_file(contributor, datastation_dataset, projects) + def self.build_data_file(contributor, datastation_dataset, projects, policy) # @_data_file_cache = {} # if @_data_file_cache[datastation_dataset.identifier] # @_data_file_cache[datastation_dataset.identifier] @@ -118,7 +118,7 @@ def self.build_data_file(contributor, datastation_dataset, projects) blob = ContentBlob.new(url: datastation_dataset.content_url.to_s, original_filename: datastation_dataset.identifier, external_link: true, is_webpage: true, content_type: 'application/octet-stream') data_file_attributes = datastation_dataset.seek_attributes.merge({ contributor: contributor, projects: projects, - content_blob: blob + content_blob: blob, policy: policy.deep_copy }) DataFile.new(data_file_attributes) # @_data_file_cache[datastation_dataset.identifier] = DataFile.new(data_file_attributes) diff --git a/test/functional/projects_controller_test.rb b/test/functional/projects_controller_test.rb index 416a2e9d6e..e386c4d08b 100644 --- a/test/functional/projects_controller_test.rb +++ b/test/functional/projects_controller_test.rb @@ -5047,20 +5047,47 @@ def test_admin_can_edit person = FactoryBot.create(:person) FactoryBot.create(:fairdatastation_virtual_demo_sample_type) project = person.projects.first + another_person = FactoryBot.create(:person) login_as(person) ttl_file = fixture_file_upload('fairdatastation/demo.ttl') - post :submit_fairdata_station, params: {id: project, datastation_data: ttl_file} + post :submit_fairdata_station, params: {id: project, datastation_data: ttl_file, + policy_attributes:{ + access_type: Policy::VISIBLE, + permissions_attributes: { + '0' => { contributor_type: 'Person', contributor_id: another_person.id, access_type: Policy::MANAGING + } + } + } + } assert investigation = assigns(:investigation) assert_redirected_to investigation assert_equal person, investigation.contributor assert_equal 1, investigation.studies.count - assert_equal 9, investigation.studies.first.assays.count - assert_equal 2, investigation.studies.first.observation_units.count - assert_equal 4, investigation.studies.first.observation_units.first.samples.count + study = investigation.studies.first + assert_equal 9, study.assays.count + assert_equal 2, study.observation_units.count + assert_equal 4, study.observation_units.first.samples.count + + sample = study.observation_units.first.samples.first + + assert_equal Policy::VISIBLE, investigation.policy.access_type + assert_equal 1, investigation.policy.permissions.count + assert_equal another_person, investigation.policy.permissions.first.contributor + assert_equal Policy::MANAGING, investigation.policy.permissions.first.access_type + + assert_equal Policy::VISIBLE, study.policy.access_type + assert_equal 1, study.policy.permissions.count + assert_equal another_person, study.policy.permissions.first.contributor + assert_equal Policy::MANAGING, study.policy.permissions.first.access_type + + assert_equal Policy::VISIBLE, sample.policy.access_type + assert_equal 1, sample.policy.permissions.count + assert_equal another_person, sample.policy.permissions.first.contributor + assert_equal Policy::MANAGING, sample.policy.permissions.first.access_type end diff --git a/test/unit/bioind/fairdata/fair_data_reader_test.rb b/test/unit/bioind/fairdata/fair_data_reader_test.rb index 836809a3bd..00486e59b4 100644 --- a/test/unit/bioind/fairdata/fair_data_reader_test.rb +++ b/test/unit/bioind/fairdata/fair_data_reader_test.rb @@ -160,13 +160,14 @@ class FairDataReaderTest < ActiveSupport::TestCase test 'construct seek isa' do path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" inv = BioInd::FairData::Reader.parse_graph(path).first + policy = FactoryBot.create(:public_policy) contributor = FactoryBot.create(:person) project = contributor.projects.first FactoryBot.create(:experimental_assay_class) FactoryBot.create(:fairdatastation_virtual_demo_sample_type) - investigation = BioInd::FairData::Reader.construct_isa(inv, contributor, [project]) + investigation = BioInd::FairData::Reader.construct_isa(inv, contributor, [project], policy) studies = investigation.studies.to_a obs_units = studies.first.observation_units.to_a assays = studies.first.assays.to_a @@ -183,6 +184,17 @@ class FairDataReaderTest < ActiveSupport::TestCase assert_equal 2, obs_units.count assert_equal 4, samples.count + assert_equal Policy::MANAGING, investigation.policy.access_type + assert_equal Policy::MANAGING, studies.first.policy.access_type + assert_equal Policy::MANAGING, assays.first.policy.access_type + assert_equal Policy::MANAGING, samples.first.policy.access_type + assert_equal Policy::MANAGING, data_files.first.policy.access_type + + refute_equal investigation.policy, studies.first.policy + refute_equal investigation.policy, assays.first.policy + refute_equal investigation.policy, samples.first.policy + refute_equal investigation.policy, data_files.first.policy + assert investigation.valid? assert studies.first.valid? From 1ccd80a5ef3b067eb5e8cc58858f8583d03aa7e6 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 14 May 2024 14:40:17 +0100 Subject: [PATCH 068/548] updated missed tests --- test/unit/bioind/fairdata/fair_data_reader_test.rb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/test/unit/bioind/fairdata/fair_data_reader_test.rb b/test/unit/bioind/fairdata/fair_data_reader_test.rb index 00486e59b4..df68da52ac 100644 --- a/test/unit/bioind/fairdata/fair_data_reader_test.rb +++ b/test/unit/bioind/fairdata/fair_data_reader_test.rb @@ -238,7 +238,7 @@ class FairDataReaderTest < ActiveSupport::TestCase contributor = FactoryBot.create(:person) project = contributor.projects.first - investigation = BioInd::FairData::Reader.construct_isa(inv, contributor, [project]) + investigation = BioInd::FairData::Reader.construct_isa(inv, contributor, [project], Policy.default) assert_nil investigation.extended_metadata study = investigation.studies.first @@ -299,7 +299,7 @@ class FairDataReaderTest < ActiveSupport::TestCase FactoryBot.create(:experimental_assay_class) FactoryBot.create(:fairdatastation_virtual_demo_sample_type) - investigation = BioInd::FairData::Reader.construct_isa(inv, contributor, [project]) + investigation = BioInd::FairData::Reader.construct_isa(inv, contributor, [project], Policy.default) assert_equal 100, investigation.studies.first.observation_units.to_a.count observation_unit = investigation.studies.first.observation_units.first assert_equal 1, observation_unit.observation_unit_assets.find_all{|oua| oua.asset_type == 'DataFile'}.collect(&:asset).count @@ -330,7 +330,7 @@ class FairDataReaderTest < ActiveSupport::TestCase contributor = FactoryBot.create(:person) project = contributor.projects.first - investigation = BioInd::FairData::Reader.construct_isa(inv, contributor, [project]) + investigation = BioInd::FairData::Reader.construct_isa(inv, contributor, [project], Policy.default) assert_nil investigation.extended_metadata assert_difference('ExtendedMetadata.count', 100) do From 10dbf3d7624e1de4d13b3c70b9519db3526580d6 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 14 May 2024 15:37:30 +0100 Subject: [PATCH 069/548] cleaned up the submit page --- app/controllers/projects_controller.rb | 3 +- .../import_from_fairdata_station.html.erb | 29 ++++++++++++++----- test/functional/projects_controller_test.rb | 16 ++++++++++ 3 files changed, 39 insertions(+), 9 deletions(-) diff --git a/app/controllers/projects_controller.rb b/app/controllers/projects_controller.rb index de4b6b975f..2bb49c9bab 100644 --- a/app/controllers/projects_controller.rb +++ b/app/controllers/projects_controller.rb @@ -14,6 +14,7 @@ class ProjectsController < ApplicationController :administer_join_request, :respond_join_request, :administer_create_project_request, :respond_create_project_request, :administer_import_project_request, :respond_import_project_request, + :import_from_fairdata_station, :submit_fairdata_station, :project_join_requests, :project_creation_requests, :project_importation_requests, :typeahead] before_action :find_requested_item, only: %i[show admin edit update destroy admin_members @@ -30,7 +31,7 @@ class ProjectsController < ApplicationController before_action :check_investigations_are_for_this_project, only: %i[update] before_action :administerable_by_user, only: %i[admin admin_members admin_member_roles destroy update_members storage_report administer_join_request respond_join_request populate populate_from_spreadsheet] - before_action :member_of_this_project, only: [:asset_report], unless: :admin_logged_in? + before_action :member_of_this_project, only: [:asset_report, :import_from_fairdata_station, :submit_fairdata_station], unless: :admin_logged_in? before_action :validate_message_log_for_join, only: [:administer_join_request, :respond_join_request] before_action :validate_message_log_for_create, only: [:administer_create_project_request, :respond_create_project_request] diff --git a/app/views/projects/import_from_fairdata_station.html.erb b/app/views/projects/import_from_fairdata_station.html.erb index 420cf07d7f..628c8aecd8 100644 --- a/app/views/projects/import_from_fairdata_station.html.erb +++ b/app/views/projects/import_from_fairdata_station.html.erb @@ -1,14 +1,27 @@ <%= render :partial => "general/page_title",:locals=>{:title=>"Import ISA from FAIRData Station for #{ t('Project') } #{link_to(@project.title, @project)}".html_safe} %> <%= form_tag submit_fairdata_station_project_path(@project), multipart: true do %> -
    - - <%= file_field_tag "datastation_data" -%> -
    - <%= render partial: 'sharing/permissions_table', locals: { object: @project, policy: (@project.default_policy || Policy.default), projects: [@project], downloadable:true } %> + <%= panel('FAIR Data Station turtle (ttl) metadata file') do %> -
    - <%= submit_tag("Submit", class:'btn btn-primary') %> -
    + <%= file_field_tag "datastation_data", accept: '.ttl' -%> + + <% end %> + + <%= panel('Sharing permissions') do %> +
    +

    + The following sharing permissions will be applied to all the items created. It is possible to change them individually after they have been created. %>. +

    +

    + Note that Download is shown but only applicable to some types. Where not applicable, then View will be applied. +

    +
    + + <%= render partial: 'sharing/permissions_table', locals: { object: @project, policy: (@project.default_policy || Policy.default), projects: [@project], downloadable: true } %> + + <% end %> +
    + <%= submit_tag("Submit", class: 'btn btn-primary') %> +
    <% end %> \ No newline at end of file diff --git a/test/functional/projects_controller_test.rb b/test/functional/projects_controller_test.rb index e386c4d08b..6499155956 100644 --- a/test/functional/projects_controller_test.rb +++ b/test/functional/projects_controller_test.rb @@ -5042,6 +5042,22 @@ def test_admin_can_edit end + test 'show import_from_fairdata_station' do + person = FactoryBot.create(:person) + project = person.projects.first + other_project = FactoryBot.create(:project) + + get :import_from_fairdata_station, params: {id: project} + assert_redirected_to project_path(project) + + login_as(person) + get :import_from_fairdata_station, params: {id: project} + assert_response :success + + get :import_from_fairdata_station, params: {id: other_project} + assert_redirected_to project_path(other_project) + end + test 'populate from fairdata station ttl' do person = FactoryBot.create(:person) From 9b1eb04e489d06a065d81c363de6887b95a0321a Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 14 May 2024 17:48:55 +0100 Subject: [PATCH 070/548] fix test --- test/functional/projects_controller_test.rb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/test/functional/projects_controller_test.rb b/test/functional/projects_controller_test.rb index 6499155956..cf2692d90e 100644 --- a/test/functional/projects_controller_test.rb +++ b/test/functional/projects_controller_test.rb @@ -5044,11 +5044,14 @@ def test_admin_can_edit test 'show import_from_fairdata_station' do person = FactoryBot.create(:person) + refute person.is_admin? project = person.projects.first other_project = FactoryBot.create(:project) + logout + get :import_from_fairdata_station, params: {id: project} - assert_redirected_to project_path(project) + assert_redirected_to login_path login_as(person) get :import_from_fairdata_station, params: {id: project} From 0353b719ad0206e99f045a25cc01b71a46526533 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 13 May 2024 23:39:05 +0000 Subject: [PATCH 071/548] Bump nokogiri from 1.16.2 to 1.16.5 Bumps [nokogiri](https://github.com/sparklemotion/nokogiri) from 1.16.2 to 1.16.5. - [Release notes](https://github.com/sparklemotion/nokogiri/releases) - [Changelog](https://github.com/sparklemotion/nokogiri/blob/main/CHANGELOG.md) - [Commits](https://github.com/sparklemotion/nokogiri/compare/v1.16.2...v1.16.5) --- updated-dependencies: - dependency-name: nokogiri dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- Gemfile | 2 +- Gemfile.lock | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/Gemfile b/Gemfile index 1ba5c08b17..bdad189046 100644 --- a/Gemfile +++ b/Gemfile @@ -52,7 +52,7 @@ gem 'will_paginate', '~> 3.1' gem 'yaml_db' gem 'rails_autolink' gem 'rfc-822' -gem 'nokogiri', '~> 1.16.2' +gem 'nokogiri', '~> 1.16.5' #necessary for newer hashie dependency, original api_smith is no longer active gem 'api_smith', git: 'https://github.com/youroute/api_smith.git', ref: '1fb428cebc17b9afab25ac9f809bde87b0ec315b' gem 'rdf-virtuoso', '>= 0.2.0' diff --git a/Gemfile.lock b/Gemfile.lock index 0de2621a2b..946308413a 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -460,7 +460,7 @@ GEM nokogiri (~> 1) rake mini_mime (1.1.5) - mini_portile2 (2.8.5) + mini_portile2 (2.8.6) minitest (5.20.0) minitest-reporters (1.5.0) ansi @@ -492,7 +492,7 @@ GEM net-protocol netrc (0.11.0) nio4r (2.7.0) - nokogiri (1.16.2) + nokogiri (1.16.5) mini_portile2 (~> 2.8.2) racc (~> 1.4) nori (1.1.5) @@ -1028,7 +1028,7 @@ DEPENDENCIES my_responds_to_parent! mysql2 net-ftp - nokogiri (~> 1.16.2) + nokogiri (~> 1.16.5) omniauth (~> 2.1.0) omniauth-github omniauth-rails_csrf_protection From fdb792b56f95177e3746b852f8a7d68c7c1408b4 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Wed, 15 May 2024 16:01:08 +0100 Subject: [PATCH 072/548] fix samples not going to triple store, due to rdf_supported? overridden --- app/models/sample.rb | 5 ----- test/unit/observation_unit_test.rb | 1 + test/unit/sample_test.rb | 1 + 3 files changed, 2 insertions(+), 5 deletions(-) diff --git a/app/models/sample.rb b/app/models/sample.rb index 874362bd40..bc10a2d41e 100644 --- a/app/models/sample.rb +++ b/app/models/sample.rb @@ -117,11 +117,6 @@ def title_from_data end end - # although it includes the RdfGeneration for some rdf support, it can't be considered to fully support it yet. - def rdf_supported? - false - end - def related_organisms Organism.where(id: related_organism_ids) end diff --git a/test/unit/observation_unit_test.rb b/test/unit/observation_unit_test.rb index 009a17bb77..68f616a380 100644 --- a/test/unit/observation_unit_test.rb +++ b/test/unit/observation_unit_test.rb @@ -20,6 +20,7 @@ class ObservationUnitTest < ActiveSupport::TestCase test 'to rdf' do obs_unit = FactoryBot.create(:max_observation_unit) + assert obs_unit.rdf_supported? rdf = obs_unit.to_rdf RDF::Reader.for(:rdfxml).new(rdf) do |reader| assert reader.statements.count > 1 diff --git a/test/unit/sample_test.rb b/test/unit/sample_test.rb index f2cbe35a6e..a585e62af5 100644 --- a/test/unit/sample_test.rb +++ b/test/unit/sample_test.rb @@ -1390,6 +1390,7 @@ class SampleTest < ActiveSupport::TestCase 'Host':'the host', 'Occupation':'the occupation' }) + assert sample.rdf_supported? rdf = sample.to_rdf RDF::Reader.for(:rdfxml).new(rdf) do |reader| assert reader.statements.count > 1 From 7ef29cd5a9d2537c207c075fa460435f17ca939d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 16 May 2024 18:59:36 +0000 Subject: [PATCH 073/548] Bump rexml from 3.2.5 to 3.2.8 Bumps [rexml](https://github.com/ruby/rexml) from 3.2.5 to 3.2.8. - [Release notes](https://github.com/ruby/rexml/releases) - [Changelog](https://github.com/ruby/rexml/blob/master/NEWS.md) - [Commits](https://github.com/ruby/rexml/compare/v3.2.5...v3.2.8) --- updated-dependencies: - dependency-name: rexml dependency-type: indirect ... Signed-off-by: dependabot[bot] --- Gemfile.lock | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/Gemfile.lock b/Gemfile.lock index 946308413a..e1b42cf806 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -728,7 +728,8 @@ GEM netrc (~> 0.8) reverse_markdown (2.1.1) nokogiri - rexml (3.2.5) + rexml (3.2.8) + strscan (>= 3.0.9) rfc-822 (0.4.1) rmagick (5.3.0) pkg-config (~> 1.4) @@ -861,6 +862,7 @@ GEM sqlite3 (1.4.2) stackprof (0.2.25) stringio (3.0.1.1) + strscan (3.1.0) sunspot (2.6.0) pr_geohash (~> 1.0) rsolr (>= 1.1.1, < 3) From ea39f997d9825ed7d533fd8c3dbca821ad549a6b Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Mon, 20 May 2024 13:08:37 +0100 Subject: [PATCH 074/548] make observation unit 'acts_as_asset' to support having a policy and authorization --- app/models/observation_unit.rb | 10 ++++++---- .../20240520094710_add_obs_unit_policy_id.rb | 5 +++++ ...0520103345_add_first_letter_to_obs_unit.rb | 5 +++++ ...40520103545_create_obs_unit_auth_lookup.rb | 15 +++++++++++++++ db/schema.rb | 16 +++++++++++++++- test/factories/observation_units.rb | 2 ++ test/unit/observation_unit_test.rb | 19 +++++++++++++++++++ 7 files changed, 67 insertions(+), 5 deletions(-) create mode 100644 db/migrate/20240520094710_add_obs_unit_policy_id.rb create mode 100644 db/migrate/20240520103345_add_first_letter_to_obs_unit.rb create mode 100644 db/migrate/20240520103545_create_obs_unit_auth_lookup.rb diff --git a/app/models/observation_unit.rb b/app/models/observation_unit.rb index d70c29c4a2..68ea96161c 100644 --- a/app/models/observation_unit.rb +++ b/app/models/observation_unit.rb @@ -1,11 +1,13 @@ class ObservationUnit < ApplicationRecord - include Seek::Creators - include Seek::ProjectAssociation - include Seek::Stats::ActivityCounts - include Seek::Search::CommonFields, Seek::Search::BackgroundReindexing + # include Seek::Creators + # include Seek::ProjectAssociation + # include Seek::Stats::ActivityCounts + # include Seek::Search::CommonFields, Seek::Search::BackgroundReindexing include Seek::Rdf::RdfGeneration + acts_as_asset + belongs_to :contributor, class_name: 'Person' belongs_to :study has_many :samples diff --git a/db/migrate/20240520094710_add_obs_unit_policy_id.rb b/db/migrate/20240520094710_add_obs_unit_policy_id.rb new file mode 100644 index 0000000000..653284f001 --- /dev/null +++ b/db/migrate/20240520094710_add_obs_unit_policy_id.rb @@ -0,0 +1,5 @@ +class AddObsUnitPolicyId < ActiveRecord::Migration[6.1] + def change + add_column :observation_units, :policy_id, :bigint + end +end diff --git a/db/migrate/20240520103345_add_first_letter_to_obs_unit.rb b/db/migrate/20240520103345_add_first_letter_to_obs_unit.rb new file mode 100644 index 0000000000..f4689a7f82 --- /dev/null +++ b/db/migrate/20240520103345_add_first_letter_to_obs_unit.rb @@ -0,0 +1,5 @@ +class AddFirstLetterToObsUnit < ActiveRecord::Migration[6.1] + def change + add_column :observation_units, :first_letter, :string, limit: 1 + end +end diff --git a/db/migrate/20240520103545_create_obs_unit_auth_lookup.rb b/db/migrate/20240520103545_create_obs_unit_auth_lookup.rb new file mode 100644 index 0000000000..d8af9eca39 --- /dev/null +++ b/db/migrate/20240520103545_create_obs_unit_auth_lookup.rb @@ -0,0 +1,15 @@ +class CreateObsUnitAuthLookup < ActiveRecord::Migration[6.1] + def change + create_table :observation_unit_auth_lookup do |t| + t.integer :user_id + t.integer :asset_id + t.boolean :can_view, default: false + t.boolean :can_manage, default: false + t.boolean :can_edit, default: false + t.boolean :can_download, default: false + t.boolean :can_delete, default: false + end + add_index :observation_unit_auth_lookup, [:user_id, :asset_id, :can_view], name: 'index_obs_unit_auth_lookup_user_id_asset_id' + add_index :observation_unit_auth_lookup, [:user_id, :can_view], name: 'index_obs_unit_auth_lookup_on_user_id_and_can_view' + end +end diff --git a/db/schema.rb b/db/schema.rb index 74a844441b..4e4dc512ed 100644 --- a/db/schema.rb +++ b/db/schema.rb @@ -10,7 +10,7 @@ # # It's strongly recommended that you check this file into your version control system. -ActiveRecord::Schema.define(version: 2024_05_01_142953) do +ActiveRecord::Schema.define(version: 2024_05_20_103545) do create_table "activity_logs", id: :integer, force: :cascade do |t| t.string "action" @@ -1204,6 +1204,18 @@ t.index ["observation_unit_id"], name: "index_observation_unit_assets_on_observation_unit_id" end + create_table "observation_unit_auth_lookup", force: :cascade do |t| + t.integer "user_id" + t.integer "asset_id" + t.boolean "can_view", default: false + t.boolean "can_manage", default: false + t.boolean "can_edit", default: false + t.boolean "can_download", default: false + t.boolean "can_delete", default: false + t.index ["user_id", "asset_id", "can_view"], name: "index_obs_unit_auth_lookup_user_id_asset_id" + t.index ["user_id", "can_view"], name: "index_obs_unit_auth_lookup_on_user_id_and_can_view" + end + create_table "observation_units", force: :cascade do |t| t.string "title" t.text "description" @@ -1217,6 +1229,8 @@ t.string "deleted_contributor" t.text "other_creators" t.bigint "study_id" + t.bigint "policy_id" + t.string "first_letter", limit: 1 end create_table "observation_units_projects", id: false, force: :cascade do |t| diff --git a/test/factories/observation_units.rb b/test/factories/observation_units.rb index dd239ac1d5..1275a663ce 100644 --- a/test/factories/observation_units.rb +++ b/test/factories/observation_units.rb @@ -3,12 +3,14 @@ title { 'Observation Unit' } description { 'very simple obs unit'} with_project_contributor + policy { FactoryBot.create(:public_policy) } end factory(:max_observation_unit, class: ObservationUnit) do title { 'Max observation unit'} description { 'the maximum one'} with_project_contributor + policy { FactoryBot.create(:public_policy) } other_creators { 'Blogs, Joe' } assets_creators { [AssetsCreator.new(affiliation: 'University of Somewhere', creator: FactoryBot.create(:person, first_name: 'Some', last_name: 'One'))] } association :extended_metadata, factory: :simple_observation_unit_extended_metadata, strategy: :create diff --git a/test/unit/observation_unit_test.rb b/test/unit/observation_unit_test.rb index 68f616a380..5ab4486cf3 100644 --- a/test/unit/observation_unit_test.rb +++ b/test/unit/observation_unit_test.rb @@ -30,5 +30,24 @@ class ObservationUnitTest < ActiveSupport::TestCase end end + test 'policy' do + obs_unit = FactoryBot.create(:observation_unit) + contributor = obs_unit.contributor + person2 = FactoryBot.create(:person) + refute_nil obs_unit.policy + + assert obs_unit.can_manage?(contributor) + + obs_unit.policy = FactoryBot.create(:public_policy) + assert obs_unit.can_view?(nil) + assert obs_unit.can_view?(contributor) + assert obs_unit.can_view?(person2) + + obs_unit.policy = FactoryBot.create(:private_policy) + refute obs_unit.can_view?(nil) + assert obs_unit.can_view?(contributor) + refute obs_unit.can_view?(person2) + end + end \ No newline at end of file From f6de003e6a24f8ebe20d331fd659dd04ac6b1f22 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Mon, 20 May 2024 13:56:29 +0100 Subject: [PATCH 075/548] fix show pages, and added edit and manage page --- .../observation_units_controller.rb | 8 +++--- app/views/observation_units/edit.html.erb | 28 +++++++++++++++++++ app/views/observation_units/manage.html.erb | 1 + app/views/observation_units/show.html.erb | 2 +- config/routes.rb | 4 +-- .../observation_units_controller_test.rb | 18 +++++++++++- 6 files changed, 53 insertions(+), 8 deletions(-) create mode 100644 app/views/observation_units/edit.html.erb create mode 100644 app/views/observation_units/manage.html.erb diff --git a/app/controllers/observation_units_controller.rb b/app/controllers/observation_units_controller.rb index 6b4e1a2c32..e8e986e698 100644 --- a/app/controllers/observation_units_controller.rb +++ b/app/controllers/observation_units_controller.rb @@ -1,15 +1,15 @@ class ObservationUnitsController < ApplicationController include Seek::DestroyHandling + include Seek::IndexPager + include Seek::AssetsCommon before_action :organisms_enabled? - before_action :find_requested_item, :only=>[:show,:edit,:destroy, :update] + before_action :find_and_authorize_requested_item, :except => [ :index, :new, :create, :preview,:update_annotations_ajax] before_action :login_required,:except=>[:show,:index] before_action :find_assets, only: [:index] - include Seek::IndexPager - - api_actions :index, :show + #api_actions :index, :show def show respond_to do |format| diff --git a/app/views/observation_units/edit.html.erb b/app/views/observation_units/edit.html.erb new file mode 100644 index 0000000000..1a7ec068e5 --- /dev/null +++ b/app/views/observation_units/edit.html.erb @@ -0,0 +1,28 @@ + +

    Editing <%= t('observation_unit') %>: <%= link_to(h(@observation_unit.title), observation_unit_path(@observation_unit)) -%>

    + +<%= form_for(@observation_unit) do |f| %> +
    + <%= f.error_messages %> + +
    + + <%= f.text_field :title, :class=>"form-control" -%> +
    + +
    + + <%= f.text_area :description, :class=>"form-control rich-text-edit", :rows => 5 -%> +
    + + <%= render partial: 'extended_metadata/extended_metadata_type_selection', locals: { f: f, resource: @observation_unit } %> + <%= render partial: 'extended_metadata/extended_metadata_attribute_input', locals: { f: f, resource: @observation_unit } %> + + + <%= render :partial=>"assets/asset_form_bottom", :locals=> {show_publications:false, :f => f}-%> + + + <%= form_submit_buttons(@observation_unit) %> + +
    +<% end %> \ No newline at end of file diff --git a/app/views/observation_units/manage.html.erb b/app/views/observation_units/manage.html.erb new file mode 100644 index 0000000000..37e1bbfc74 --- /dev/null +++ b/app/views/observation_units/manage.html.erb @@ -0,0 +1 @@ +<%= render partial:'assets/manage_form', locals:{resource:@observation_unit} %> \ No newline at end of file diff --git a/app/views/observation_units/show.html.erb b/app/views/observation_units/show.html.erb index 1018628e1d..348aa62722 100644 --- a/app/views/observation_units/show.html.erb +++ b/app/views/observation_units/show.html.erb @@ -1,4 +1,4 @@ -<%= render partial: 'general/item_title', locals: { item: @observation_unit } %> +<%= render partial: 'general/item_title', locals: { item: @observation_unit, buttons_partial: 'assets/asset_buttons' } %> <%= render partial: 'general/show_page_tab_definitions' %> diff --git a/config/routes.rb b/config/routes.rb index f0b91bbe9f..1dbf440a6a 100644 --- a/config/routes.rb +++ b/config/routes.rb @@ -801,9 +801,9 @@ ### OBSERVATION UNITS ### - resources :observation_units, only: [:show, :index] do + resources :observation_units, concerns:[:asset] do - resources :projects, :people, :programmes, :studies, :samples, :assays, :data_files + resources :projects, :people, :programmes, :samples, :assays, :studies, :investigations, :data_files, :publications, :collections end ### MISC MATCHES ### diff --git a/test/functional/observation_units_controller_test.rb b/test/functional/observation_units_controller_test.rb index 77d4e1e1c5..deccb73d8d 100644 --- a/test/functional/observation_units_controller_test.rb +++ b/test/functional/observation_units_controller_test.rb @@ -2,7 +2,9 @@ require 'minitest/mock' class ObservationUnitsControllerTest < ActionController::TestCase - + include AuthenticatedTestHelper + include SharingFormTestHelper + include GeneralAuthorizationTestCases include RdfTestCases def rdf_test_object @@ -21,4 +23,18 @@ def rdf_test_object assert_response :success end + test 'edit' do + unit = FactoryBot.create(:max_observation_unit) + login_as(unit.contributor) + get :edit, params: { id: unit.id} + assert_response :success + end + + test 'manage' do + unit = FactoryBot.create(:max_observation_unit) + login_as(unit.contributor) + get :manage, params: { id: unit.id} + assert_response :success + end + end \ No newline at end of file From de12eb488fdb3d0328ebdc4cabb4325b55607ce3 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Mon, 20 May 2024 15:07:44 +0100 Subject: [PATCH 076/548] tests for update and manage update --- .../observation_units_controller.rb | 22 +++++++ .../observation_units_controller_test.rb | 63 +++++++++++++++++++ 2 files changed, 85 insertions(+) diff --git a/app/controllers/observation_units_controller.rb b/app/controllers/observation_units_controller.rb index e8e986e698..e5dcacefb7 100644 --- a/app/controllers/observation_units_controller.rb +++ b/app/controllers/observation_units_controller.rb @@ -19,4 +19,26 @@ def show end end + def update + update_annotations(params[:tag_list], @observation_unit) if params.key?(:tag_list) + update_sharing_policies @observation_unit + update_relationships(@observation_unit,params) + + respond_to do |format| + if @observation_unit.update(observation_unit_params) + flash[:notice] = "#{t('document')} metadata was successfully updated." + format.html { redirect_to observation_unit_path(@observation_unit) } + format.json { render json: @observation_unit, include: [params[:include]] } + else + format.html { render action: 'edit' } + format.json { render json: json_api_errors(@observation_unit), status: :unprocessable_entity } + end + end + end + + def observation_unit_params + params.require(:observation_unit).permit(:title, :description, *creator_related_params, { project_ids: [] }, + { special_auth_codes_attributes: [:code, :expiration_date, :id, :_destroy] }, + { extended_metadata_attributes: determine_extended_metadata_keys }) + end end diff --git a/test/functional/observation_units_controller_test.rb b/test/functional/observation_units_controller_test.rb index deccb73d8d..f3c6869099 100644 --- a/test/functional/observation_units_controller_test.rb +++ b/test/functional/observation_units_controller_test.rb @@ -37,4 +37,67 @@ def rdf_test_object assert_response :success end + test 'manage update' do + proj1=FactoryBot.create(:project) + proj2=FactoryBot.create(:project) + person = FactoryBot.create(:person,project:proj1) + other_person = FactoryBot.create(:person) + person.add_to_project_and_institution(proj2,person.institutions.first) + person.save! + other_creator = FactoryBot.create(:person,project:proj1) + other_creator.add_to_project_and_institution(proj2,other_creator.institutions.first) + other_creator.save! + + obs_unit = FactoryBot.create(:observation_unit, contributor:person, projects:[proj1], policy:FactoryBot.create(:private_policy)) + + login_as(person) + assert obs_unit.can_manage? + + patch :manage_update, params: {id: obs_unit, + observation_unit: { + creator_ids: [other_creator.id], + project_ids: [proj1.id, proj2.id] + }, + policy_attributes: {access_type: Policy::VISIBLE, permissions_attributes: {'1' => {contributor_type: 'Person', contributor_id: other_person.id, access_type: Policy::MANAGING}} + }} + + assert_redirected_to obs_unit + + obs_unit.reload + assert_equal [proj1,proj2],obs_unit.projects.sort_by(&:id) + assert_equal [other_creator],obs_unit.creators + assert_equal Policy::VISIBLE,obs_unit.policy.access_type + assert_equal 1,obs_unit.policy.permissions.count + assert_equal other_person,obs_unit.policy.permissions.first.contributor + assert_equal Policy::MANAGING,obs_unit.policy.permissions.first.access_type + end + + test 'update' do + obs_unit = FactoryBot.create(:observation_unit) + emt = FactoryBot.create(:simple_observation_unit_extended_metadata_type) + login_as(obs_unit.contributor) + + patch :update, params: { id: obs_unit, + observation_unit:{ + title: 'updated title', + description: 'updated description', + extended_metadata_attributes: { + extended_metadata_type_id: emt.id, + data: { + name: 'updated name', + strain: 'updated strain' + } + } + }} + + assert_redirected_to obs_unit + + obs_unit.reload + assert_equal 'updated title', obs_unit.title + assert_equal 'updated description', obs_unit.description + assert_equal emt, obs_unit.extended_metadata.extended_metadata_type + assert_equal 'updated name', obs_unit.extended_metadata.get_attribute_value('name') + assert_equal 'updated strain', obs_unit.extended_metadata.get_attribute_value('strain') + end + end \ No newline at end of file From 3749fa43937786bb0201c61f81afc330c00abed6 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Mon, 20 May 2024 15:24:43 +0100 Subject: [PATCH 077/548] upgrade task to set the observation unit policies created previously --- lib/tasks/seek_upgrades.rake | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/lib/tasks/seek_upgrades.rake b/lib/tasks/seek_upgrades.rake index d07621f93e..3c530dfeb2 100644 --- a/lib/tasks/seek_upgrades.rake +++ b/lib/tasks/seek_upgrades.rake @@ -19,6 +19,7 @@ namespace :seek do set_ls_login_legacy_mode rename_custom_metadata_legacy_supported_type seek_rdf:generate + update_observation_unit_policies ] # these are the tasks that are executes for each upgrade as standard, and rarely change @@ -84,6 +85,22 @@ namespace :seek do Permission.set_callback :commit, :after, :queue_rdf_generation_job end + task(update_observation_unit_policies: [:environment]) do + puts '..... creating observation unit policies ...' + affected_obs_units_count = 0 + ObservationUnit.where.missing(:policy).includes(:study).in_batches(of: 25) do |batch| + batch.each do |obs_unit| + policy = obs_unit.study.policy || Policy.default + policy = policy.deep_copy + policy.save + obs_unit.update_column(:policy_id, policy.id) + affected_obs_units_count += 1 + end + putc('.') + end + puts "..... finished updating policies for #{affected_obs_units_count} observation units" + end + task(decouple_extracted_samples_projects: [:environment]) do puts '..... copying project ids for extracted samples...' decoupled_count = 0 From 329af761de13dcd54bcea7fe30f5c583f31e638f Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Mon, 20 May 2024 15:30:29 +0100 Subject: [PATCH 078/548] make sure the upgrade task adds items to queue --- lib/tasks/seek_upgrades.rake | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/lib/tasks/seek_upgrades.rake b/lib/tasks/seek_upgrades.rake index 3c530dfeb2..0d58cc9b96 100644 --- a/lib/tasks/seek_upgrades.rake +++ b/lib/tasks/seek_upgrades.rake @@ -87,18 +87,20 @@ namespace :seek do task(update_observation_unit_policies: [:environment]) do puts '..... creating observation unit policies ...' - affected_obs_units_count = 0 + affected_obs_units = [] ObservationUnit.where.missing(:policy).includes(:study).in_batches(of: 25) do |batch| batch.each do |obs_unit| policy = obs_unit.study.policy || Policy.default policy = policy.deep_copy policy.save obs_unit.update_column(:policy_id, policy.id) - affected_obs_units_count += 1 + affected_obs_units << obs_unit end putc('.') end - puts "..... finished updating policies for #{affected_obs_units_count} observation units" + AuthLookupUpdateQueue.enqueue(affected_obs_units) + RdfGenerationQueue.enqueue(affected_obs_units) + puts "..... finished updating policies for #{affected_obs_units.count} observation units" end task(decouple_extracted_samples_projects: [:environment]) do From 84bcc18ad5bd6730e4c0cbbc29723b9537a7cf50 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Mon, 20 May 2024 15:33:52 +0100 Subject: [PATCH 079/548] updated util test --- test/unit/util_test.rb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/unit/util_test.rb b/test/unit/util_test.rb index 3ce082db9e..335e22db3b 100644 --- a/test/unit/util_test.rb +++ b/test/unit/util_test.rb @@ -7,7 +7,7 @@ def teardown end test 'creatable types' do - expected = [Collection, DataFile, Document, FileTemplate, Model, Placeholder, Presentation, Publication, Sample, Sop, Assay, Investigation, Study, Event, SampleType, Strain, Workflow, Template] + expected = [Collection, DataFile, Document, FileTemplate, Model, ObservationUnit, Placeholder, Presentation, Publication, Sample, Sop, Assay, Investigation, Study, Event, SampleType, Strain, Workflow, Template] types = with_config_value :isa_json_compliance_enabled, true do Seek::Util.user_creatable_types @@ -21,7 +21,7 @@ def teardown end test 'authorized types' do - expected = [Assay, Collection, DataFile, Document, Event, FileTemplate, Investigation, Model, Placeholder, Presentation, Publication, Sample, Sop, Strain, Study, Workflow, Template].map(&:name).sort + expected = [Assay, Collection, DataFile, Document, Event, FileTemplate, Investigation, Model, ObservationUnit, Placeholder, Presentation, Publication, Sample, Sop, Strain, Study, Workflow, Template].map(&:name).sort actual = with_config_value :isa_json_compliance_enabled, true do Seek::Util.authorized_types.map(&:name).sort From c6ac38e0e5a023b33a06a37e8d8bf5c1c647d755 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 21 May 2024 09:59:09 +0100 Subject: [PATCH 080/548] set the policy for obs_units when populating from fair data station ttl --- lib/bio_ind/fair_data/reader.rb | 2 +- test/functional/projects_controller_test.rb | 12 +++++++++++- test/unit/bioind/fairdata/fair_data_reader_test.rb | 2 ++ 3 files changed, 14 insertions(+), 2 deletions(-) diff --git a/lib/bio_ind/fair_data/reader.rb b/lib/bio_ind/fair_data/reader.rb index 0ac2444f9e..639b5a549a 100644 --- a/lib/bio_ind/fair_data/reader.rb +++ b/lib/bio_ind/fair_data/reader.rb @@ -31,7 +31,7 @@ def self.construct_isa(datastation_inv, contributor, projects, policy) study = investigation.studies.build(study_attributes) populate_extended_metadata(study, datastation_study) datastation_study.observation_units.each do |datastation_observation_unit| - observation_unit_attributes = datastation_observation_unit.seek_attributes.merge({contributor: contributor, study:study, projects: projects}) + observation_unit_attributes = datastation_observation_unit.seek_attributes.merge({contributor: contributor, study:study, projects: projects, policy:policy.deep_copy}) observation_unit = study.observation_units.build(observation_unit_attributes) datastation_observation_unit.datasets.each do |datastation_dataset| df = build_data_file(contributor, datastation_dataset, projects, policy) diff --git a/test/functional/projects_controller_test.rb b/test/functional/projects_controller_test.rb index cf2692d90e..0faf00a904 100644 --- a/test/functional/projects_controller_test.rb +++ b/test/functional/projects_controller_test.rb @@ -5091,7 +5091,12 @@ def test_admin_can_edit assert_equal 2, study.observation_units.count assert_equal 4, study.observation_units.first.samples.count - sample = study.observation_units.first.samples.first + obs_unit = study.observation_units.first + sample = obs_unit.samples.first + + assert_equal person, study.contributor + assert_equal person, obs_unit.contributor + assert_equal person, sample.contributor assert_equal Policy::VISIBLE, investigation.policy.access_type assert_equal 1, investigation.policy.permissions.count @@ -5103,6 +5108,11 @@ def test_admin_can_edit assert_equal another_person, study.policy.permissions.first.contributor assert_equal Policy::MANAGING, study.policy.permissions.first.access_type + assert_equal Policy::VISIBLE, obs_unit.policy.access_type + assert_equal 1, obs_unit.policy.permissions.count + assert_equal another_person, obs_unit.policy.permissions.first.contributor + assert_equal Policy::MANAGING, obs_unit.policy.permissions.first.access_type + assert_equal Policy::VISIBLE, sample.policy.access_type assert_equal 1, sample.policy.permissions.count assert_equal another_person, sample.policy.permissions.first.contributor diff --git a/test/unit/bioind/fairdata/fair_data_reader_test.rb b/test/unit/bioind/fairdata/fair_data_reader_test.rb index df68da52ac..454b638e0a 100644 --- a/test/unit/bioind/fairdata/fair_data_reader_test.rb +++ b/test/unit/bioind/fairdata/fair_data_reader_test.rb @@ -186,11 +186,13 @@ class FairDataReaderTest < ActiveSupport::TestCase assert_equal Policy::MANAGING, investigation.policy.access_type assert_equal Policy::MANAGING, studies.first.policy.access_type + assert_equal Policy::MANAGING, obs_units.first.policy.access_type assert_equal Policy::MANAGING, assays.first.policy.access_type assert_equal Policy::MANAGING, samples.first.policy.access_type assert_equal Policy::MANAGING, data_files.first.policy.access_type refute_equal investigation.policy, studies.first.policy + refute_equal investigation.policy, obs_units.first.policy refute_equal investigation.policy, assays.first.policy refute_equal investigation.policy, samples.first.policy refute_equal investigation.policy, data_files.first.policy From 26b7e9a1ec0dbc6f620ffb89bfcc43480c801925 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 21 May 2024 11:17:39 +0100 Subject: [PATCH 081/548] included obs units as related items for people and projects --- app/models/person.rb | 2 +- app/models/project.rb | 1 + config/routes.rb | 4 ++-- 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/app/models/person.rb b/app/models/person.rb index dd1778a7a6..f839263a0b 100644 --- a/app/models/person.rb +++ b/app/models/person.rb @@ -58,7 +58,7 @@ class Person < ApplicationRecord has_many :assets_creators, dependent: :destroy, foreign_key: 'creator_id' - RELATED_RESOURCE_TYPES = %w[DataFile Sop Model Document Publication Presentation SampleType Sample Event + RELATED_RESOURCE_TYPES = %w[DataFile Sop Model Document ObservationUnit Publication Presentation SampleType Sample Event Investigation Study Assay Strain Workflow Collection FileTemplate Placeholder Template].freeze RELATED_RESOURCE_TYPES.each do |type| diff --git a/app/models/project.rb b/app/models/project.rb index 2aa17d69fc..e1a7b9b6bf 100644 --- a/app/models/project.rb +++ b/app/models/project.rb @@ -17,6 +17,7 @@ class Project < ApplicationRecord has_and_belongs_to_many :workflows has_and_belongs_to_many :publications has_and_belongs_to_many :events + has_and_belongs_to_many :observation_units has_and_belongs_to_many :presentations has_and_belongs_to_many :strains has_and_belongs_to_many :samples diff --git a/config/routes.rb b/config/routes.rb index 1dbf440a6a..d78c978f92 100644 --- a/config/routes.rb +++ b/config/routes.rb @@ -314,7 +314,7 @@ post :batch_sharing_permission_changed end resources :projects, :programmes, :institutions, :assays, :studies, :investigations, :models, :sops, :workflows, - :data_files, :presentations, :publications, :documents, :events, :sample_types, :samples, :specimens, + :data_files, :observation_units, :presentations, :publications, :documents, :events, :sample_types, :samples, :specimens, :strains, :file_templates, :placeholders, :collections, :templates, only: [:index] end @@ -354,7 +354,7 @@ post :submit_fairdata_station post :update_annotations_ajax end - resources :programmes, :people, :institutions, :assays, :studies, :investigations, :models, :sops, :workflows, :data_files, :presentations, + resources :programmes, :people, :institutions, :assays, :studies, :investigations, :models, :sops, :workflows, :data_files, :observation_units, :presentations, :publications, :events, :sample_types, :samples, :specimens, :strains, :search, :organisms, :human_diseases, :documents, :file_templates, :placeholders, :collections, :templates, only: [:index] resources :openbis_endpoints do From d144eb094ae471463b9ecd1eebc6c89485c12bbd Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 21 May 2024 14:53:57 +0100 Subject: [PATCH 082/548] refactor fair data station related modules and location --- app/controllers/projects_controller.rb | 4 +-- .../fair_data_station}/assay.rb | 4 +-- .../fair_data_station}/base.rb | 6 ++-- .../fair_data_station}/data_set.rb | 4 +-- .../fair_data_station}/investigation.rb | 6 ++-- .../fair_data_station}/observation_unit.rb | 6 ++-- .../fair_data_station}/reader.rb | 6 ++-- .../fair_data_station}/sample.rb | 6 ++-- .../fair_data_station}/study.rb | 6 ++-- .../fair_data_station_reader_test.rb} | 34 +++++++++---------- 10 files changed, 41 insertions(+), 41 deletions(-) rename lib/{bio_ind/fair_data => seek/fair_data_station}/assay.rb (73%) rename lib/{bio_ind/fair_data => seek/fair_data_station}/base.rb (96%) rename lib/{bio_ind/fair_data => seek/fair_data_station}/data_set.rb (84%) rename lib/{bio_ind/fair_data => seek/fair_data_station}/investigation.rb (60%) rename lib/{bio_ind/fair_data => seek/fair_data_station}/observation_unit.rb (60%) rename lib/{bio_ind/fair_data => seek/fair_data_station}/reader.rb (98%) rename lib/{bio_ind/fair_data => seek/fair_data_station}/sample.rb (88%) rename lib/{bio_ind/fair_data => seek/fair_data_station}/study.rb (72%) rename test/unit/{bioind/fairdata/fair_data_reader_test.rb => fair_data_station/fair_data_station_reader_test.rb} (92%) diff --git a/app/controllers/projects_controller.rb b/app/controllers/projects_controller.rb index 2bb49c9bab..7dd110bf0c 100644 --- a/app/controllers/projects_controller.rb +++ b/app/controllers/projects_controller.rb @@ -201,8 +201,8 @@ def submit_fairdata_station path = params[:datastation_data].path policy = Policy.new policy.set_attributes_with_sharing(policy_params) - datadata_inv = BioInd::FairData::Reader.parse_graph(path) - @investigation = BioInd::FairData::Reader.construct_isa(datadata_inv.first, current_person, [@project], policy) + datadata_inv = Seek::FairDataStation::Reader.parse_graph(path) + @investigation = Seek::FairDataStation::Reader.construct_isa(datadata_inv.first, current_person, [@project], policy) @investigation.save! respond_to do |format| diff --git a/lib/bio_ind/fair_data/assay.rb b/lib/seek/fair_data_station/assay.rb similarity index 73% rename from lib/bio_ind/fair_data/assay.rb rename to lib/seek/fair_data_station/assay.rb index f65093b8eb..7aa135304d 100644 --- a/lib/bio_ind/fair_data/assay.rb +++ b/lib/seek/fair_data_station/assay.rb @@ -1,5 +1,5 @@ -module BioInd - module FairData +module Seek + module FairDataStation class Assay < Base def title diff --git a/lib/bio_ind/fair_data/base.rb b/lib/seek/fair_data_station/base.rb similarity index 96% rename from lib/bio_ind/fair_data/base.rb rename to lib/seek/fair_data_station/base.rb index 996892f22b..944794b86c 100644 --- a/lib/bio_ind/fair_data/base.rb +++ b/lib/seek/fair_data_station/base.rb @@ -1,5 +1,5 @@ -module BioInd - module FairData +module Seek + module FairDataStation class Base attr_reader :resource_uri, :graph, :children, :core_annotations @@ -81,7 +81,7 @@ def datasets [resource_uri, @schema.dataset, :dataset] ) query.execute.collect do |solution| - BioInd::FairData::DataSet.new(solution.dataset, graph) + Seek::FairDataStation::DataSet.new(solution.dataset, graph) end end diff --git a/lib/bio_ind/fair_data/data_set.rb b/lib/seek/fair_data_station/data_set.rb similarity index 84% rename from lib/bio_ind/fair_data/data_set.rb rename to lib/seek/fair_data_station/data_set.rb index ff96aa9eb7..456116f3a8 100644 --- a/lib/bio_ind/fair_data/data_set.rb +++ b/lib/seek/fair_data_station/data_set.rb @@ -1,5 +1,5 @@ -module BioInd - module FairData +module Seek + module FairDataStation class DataSet < Base def title diff --git a/lib/bio_ind/fair_data/investigation.rb b/lib/seek/fair_data_station/investigation.rb similarity index 60% rename from lib/bio_ind/fair_data/investigation.rb rename to lib/seek/fair_data_station/investigation.rb index e02fb67cdc..130a9e6c3e 100644 --- a/lib/bio_ind/fair_data/investigation.rb +++ b/lib/seek/fair_data_station/investigation.rb @@ -1,10 +1,10 @@ -module BioInd - module FairData +module Seek + module FairDataStation class Investigation < Base alias studies children def child_class - BioInd::FairData::Study + Seek::FairDataStation::Study end end end diff --git a/lib/bio_ind/fair_data/observation_unit.rb b/lib/seek/fair_data_station/observation_unit.rb similarity index 60% rename from lib/bio_ind/fair_data/observation_unit.rb rename to lib/seek/fair_data_station/observation_unit.rb index fc529a31f0..165c08f3c2 100644 --- a/lib/bio_ind/fair_data/observation_unit.rb +++ b/lib/seek/fair_data_station/observation_unit.rb @@ -1,10 +1,10 @@ -module BioInd - module FairData +module Seek + module FairDataStation class ObservationUnit < Base alias samples children def child_class - BioInd::FairData::Sample + Seek::FairDataStation::Sample end end end diff --git a/lib/bio_ind/fair_data/reader.rb b/lib/seek/fair_data_station/reader.rb similarity index 98% rename from lib/bio_ind/fair_data/reader.rb rename to lib/seek/fair_data_station/reader.rb index 639b5a549a..18aec4e5a5 100644 --- a/lib/bio_ind/fair_data/reader.rb +++ b/lib/seek/fair_data_station/reader.rb @@ -2,8 +2,8 @@ require 'rdf/turtle' require 'sparql/client' -module BioInd - module FairData +module Seek + module FairDataStation class Reader def self.parse_graph(path) @@ -15,7 +15,7 @@ def self.parse_graph(path) [:inv, RDF.type, jerm.[]('Investigation')] ) query.execute.collect do |inv| - inv = BioInd::FairData::Investigation.new(inv.inv, graph) + inv = Seek::FairDataStation::Investigation.new(inv.inv, graph) inv.populate inv end diff --git a/lib/bio_ind/fair_data/sample.rb b/lib/seek/fair_data_station/sample.rb similarity index 88% rename from lib/bio_ind/fair_data/sample.rb rename to lib/seek/fair_data_station/sample.rb index 7b24a43bde..9df0603d62 100644 --- a/lib/bio_ind/fair_data/sample.rb +++ b/lib/seek/fair_data_station/sample.rb @@ -1,10 +1,10 @@ -module BioInd - module FairData +module Seek + module FairDataStation class Sample < Base alias assays children def child_class - BioInd::FairData::Assay + Seek::FairDataStation::Assay end def populate_seek_sample(seek_sample) diff --git a/lib/bio_ind/fair_data/study.rb b/lib/seek/fair_data_station/study.rb similarity index 72% rename from lib/bio_ind/fair_data/study.rb rename to lib/seek/fair_data_station/study.rb index 4eab8d9114..0caea6e3cf 100644 --- a/lib/bio_ind/fair_data/study.rb +++ b/lib/seek/fair_data_station/study.rb @@ -1,5 +1,5 @@ -module BioInd - module FairData +module Seek + module FairDataStation class Study < Base alias observation_units children @@ -8,7 +8,7 @@ def assays end def child_class - BioInd::FairData::ObservationUnit + Seek::FairDataStation::ObservationUnit end end end diff --git a/test/unit/bioind/fairdata/fair_data_reader_test.rb b/test/unit/fair_data_station/fair_data_station_reader_test.rb similarity index 92% rename from test/unit/bioind/fairdata/fair_data_reader_test.rb rename to test/unit/fair_data_station/fair_data_station_reader_test.rb index 454b638e0a..3d7994728c 100644 --- a/test/unit/bioind/fairdata/fair_data_reader_test.rb +++ b/test/unit/fair_data_station/fair_data_station_reader_test.rb @@ -1,10 +1,10 @@ require 'test_helper' -class FairDataReaderTest < ActiveSupport::TestCase +class FairDataStationReaderTest < ActiveSupport::TestCase test 'read demo' do path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" - investigations = BioInd::FairData::Reader.parse_graph(path) + investigations = Seek::FairDataStation::Reader.parse_graph(path) assert_equal 1, investigations.count inv = investigations.first assert_equal 'http://fairbydesign.nl/ontology/inv_INV_DRP007092', inv.resource_uri.to_s @@ -37,7 +37,7 @@ class FairDataReaderTest < ActiveSupport::TestCase test 'read indpensim' do path = "#{Rails.root}/test/fixtures/files/fairdatastation/indpensim.ttl" - investigations = BioInd::FairData::Reader.parse_graph(path) + investigations = Seek::FairDataStation::Reader.parse_graph(path) assert_equal 1, investigations.count inv = investigations.first assert_equal 'http://fairbydesign.nl/ontology/inv_indpensim', inv.resource_uri.to_s @@ -66,7 +66,7 @@ class FairDataReaderTest < ActiveSupport::TestCase test 'annotations' do path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" - study = BioInd::FairData::Reader.parse_graph(path).first.studies.first + study = Seek::FairDataStation::Reader.parse_graph(path).first.studies.first assert_equal 14, study.annotations.count assert_includes study.annotations, ["http://fairbydesign.nl/ontology/center_name", "NIID"] @@ -75,7 +75,7 @@ class FairDataReaderTest < ActiveSupport::TestCase test 'additional metadata annotations' do path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" - inv = BioInd::FairData::Reader.parse_graph(path).first + inv = Seek::FairDataStation::Reader.parse_graph(path).first assert_empty inv.additional_metadata_annotations study = inv.studies.first @@ -88,7 +88,7 @@ class FairDataReaderTest < ActiveSupport::TestCase # non fairbydesign annotations path = "#{Rails.root}/test/fixtures/files/fairdatastation/indpensim.ttl" - inv = BioInd::FairData::Reader.parse_graph(path).first + inv = Seek::FairDataStation::Reader.parse_graph(path).first obs_unit = inv.studies.first.observation_units.first annotations = obs_unit.additional_metadata_annotations assert_equal 5, annotations.count @@ -100,7 +100,7 @@ class FairDataReaderTest < ActiveSupport::TestCase test 'study assays' do path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" - investigations = BioInd::FairData::Reader.parse_graph(path) + investigations = Seek::FairDataStation::Reader.parse_graph(path) study = investigations.first.studies.first assert_equal 9, study.assays.count expected = %w[DRR243845 DRR243850 DRR243856 DRR243863 DRR243881 DRR243894 DRR243899 DRR243906 @@ -111,7 +111,7 @@ class FairDataReaderTest < ActiveSupport::TestCase test 'titles and descriptions' do path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" - inv = BioInd::FairData::Reader.parse_graph(path).first + inv = Seek::FairDataStation::Reader.parse_graph(path).first study = inv.studies.first obs_unit = study.observation_units.first sample = obs_unit.samples.first @@ -138,7 +138,7 @@ class FairDataReaderTest < ActiveSupport::TestCase test 'datasets' do path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" - inv = BioInd::FairData::Reader.parse_graph(path).first + inv = Seek::FairDataStation::Reader.parse_graph(path).first study = inv.studies.first obs_unit = study.observation_units.first sample = obs_unit.samples.first @@ -159,7 +159,7 @@ class FairDataReaderTest < ActiveSupport::TestCase test 'construct seek isa' do path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" - inv = BioInd::FairData::Reader.parse_graph(path).first + inv = Seek::FairDataStation::Reader.parse_graph(path).first policy = FactoryBot.create(:public_policy) contributor = FactoryBot.create(:person) @@ -167,7 +167,7 @@ class FairDataReaderTest < ActiveSupport::TestCase FactoryBot.create(:experimental_assay_class) FactoryBot.create(:fairdatastation_virtual_demo_sample_type) - investigation = BioInd::FairData::Reader.construct_isa(inv, contributor, [project], policy) + investigation = Seek::FairDataStation::Reader.construct_isa(inv, contributor, [project], policy) studies = investigation.studies.to_a obs_units = studies.first.observation_units.to_a assays = studies.first.assays.to_a @@ -236,11 +236,11 @@ class FairDataReaderTest < ActiveSupport::TestCase sample_type = FactoryBot.create(:fairdatastation_virtual_demo_sample_type) path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" - inv = BioInd::FairData::Reader.parse_graph(path).first + inv = Seek::FairDataStation::Reader.parse_graph(path).first contributor = FactoryBot.create(:person) project = contributor.projects.first - investigation = BioInd::FairData::Reader.construct_isa(inv, contributor, [project], Policy.default) + investigation = Seek::FairDataStation::Reader.construct_isa(inv, contributor, [project], Policy.default) assert_nil investigation.extended_metadata study = investigation.studies.first @@ -294,14 +294,14 @@ class FairDataReaderTest < ActiveSupport::TestCase test 'observation_unit datasets created in construct_isa' do path = "#{Rails.root}/test/fixtures/files/fairdatastation/indpensim.ttl" - inv = BioInd::FairData::Reader.parse_graph(path).first + inv = Seek::FairDataStation::Reader.parse_graph(path).first contributor = FactoryBot.create(:person) project = contributor.projects.first FactoryBot.create(:experimental_assay_class) FactoryBot.create(:fairdatastation_virtual_demo_sample_type) - investigation = BioInd::FairData::Reader.construct_isa(inv, contributor, [project], Policy.default) + investigation = Seek::FairDataStation::Reader.construct_isa(inv, contributor, [project], Policy.default) assert_equal 100, investigation.studies.first.observation_units.to_a.count observation_unit = investigation.studies.first.observation_units.first assert_equal 1, observation_unit.observation_unit_assets.find_all{|oua| oua.asset_type == 'DataFile'}.collect(&:asset).count @@ -328,11 +328,11 @@ class FairDataReaderTest < ActiveSupport::TestCase FactoryBot.create(:experimental_assay_class) path = "#{Rails.root}/test/fixtures/files/fairdatastation/indpensim.ttl" - inv = BioInd::FairData::Reader.parse_graph(path).first + inv = Seek::FairDataStation::Reader.parse_graph(path).first contributor = FactoryBot.create(:person) project = contributor.projects.first - investigation = BioInd::FairData::Reader.construct_isa(inv, contributor, [project], Policy.default) + investigation = Seek::FairDataStation::Reader.construct_isa(inv, contributor, [project], Policy.default) assert_nil investigation.extended_metadata assert_difference('ExtendedMetadata.count', 100) do From 767845d42c60c6644c34c252fa9692063f1d4338 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 21 May 2024 15:13:10 +0100 Subject: [PATCH 083/548] rubocop on fairdatastation code --- .rubocop.yml | 3 ++ lib/seek/fair_data_station/assay.rb | 2 -- lib/seek/fair_data_station/base.rb | 10 +++--- lib/seek/fair_data_station/data_set.rb | 2 -- lib/seek/fair_data_station/reader.rb | 42 ++++++++++++++------------ lib/seek/fair_data_station/sample.rb | 4 +-- 6 files changed, 30 insertions(+), 33 deletions(-) diff --git a/.rubocop.yml b/.rubocop.yml index 8668b2c5c4..156e9582e4 100644 --- a/.rubocop.yml +++ b/.rubocop.yml @@ -9,3 +9,6 @@ Layout/LineLength: # Don't enforce frozen string literals Style/FrozenStringLiteralComment: Enabled: false + +Style/HashSyntax: + EnforcedShorthandSyntax: never \ No newline at end of file diff --git a/lib/seek/fair_data_station/assay.rb b/lib/seek/fair_data_station/assay.rb index 7aa135304d..282b4586c0 100644 --- a/lib/seek/fair_data_station/assay.rb +++ b/lib/seek/fair_data_station/assay.rb @@ -1,11 +1,9 @@ module Seek module FairDataStation class Assay < Base - def title "Assay - #{identifier}" end - end end end diff --git a/lib/seek/fair_data_station/base.rb b/lib/seek/fair_data_station/base.rb index 944794b86c..e3e882be83 100644 --- a/lib/seek/fair_data_station/base.rb +++ b/lib/seek/fair_data_station/base.rb @@ -47,8 +47,8 @@ def annotations end def additional_metadata_annotations - annotations.select do |annotation| - !core_annotations.include?(annotation[0]) + annotations.reject do |annotation| + core_annotations.include?(annotation[0]) end end @@ -95,7 +95,7 @@ def fetch_children end def seek_attributes - {title: title, description: description} + { title: title, description: description } end def populate_extended_metadata(seek_resource) @@ -105,9 +105,7 @@ def populate_extended_metadata(seek_resource) property = annotation[0] value = annotation[1] attribute = extended_metadata_type.extended_metadata_attributes.where(property_type_id: property).first - if attribute - data[attribute.title] = value - end + data[attribute.title] = value if attribute end seek_resource.extended_metadata.data = data end diff --git a/lib/seek/fair_data_station/data_set.rb b/lib/seek/fair_data_station/data_set.rb index 456116f3a8..2f1cc86cab 100644 --- a/lib/seek/fair_data_station/data_set.rb +++ b/lib/seek/fair_data_station/data_set.rb @@ -1,7 +1,6 @@ module Seek module FairDataStation class DataSet < Base - def title "Dataset: #{identifier}" end @@ -9,7 +8,6 @@ def title def content_url find_annotation_value(@schema.contentUrl.to_s) || resource_uri end - end end end diff --git a/lib/seek/fair_data_station/reader.rb b/lib/seek/fair_data_station/reader.rb index 18aec4e5a5..0d6d1dfc2f 100644 --- a/lib/seek/fair_data_station/reader.rb +++ b/lib/seek/fair_data_station/reader.rb @@ -5,7 +5,6 @@ module Seek module FairDataStation class Reader - def self.parse_graph(path) graph = RDF::Graph.load(path, format: :ttl) sparql = SPARQL::Client.new(graph) @@ -22,16 +21,19 @@ def self.parse_graph(path) end def self.construct_isa(datastation_inv, contributor, projects, policy) - inv_attributes = datastation_inv.seek_attributes.merge({contributor: contributor, projects: projects, policy:policy.deep_copy}) + inv_attributes = datastation_inv.seek_attributes.merge({ contributor: contributor, projects: projects, + policy: policy.deep_copy }) investigation = ::Investigation.new(inv_attributes) populate_extended_metadata(investigation, datastation_inv) datastation_inv.studies.each do |datastation_study| - study_attributes = datastation_study.seek_attributes.merge({contributor: contributor, investigation: investigation, policy:policy.deep_copy}) + study_attributes = datastation_study.seek_attributes.merge({ contributor: contributor, + investigation: investigation, policy: policy.deep_copy }) study = investigation.studies.build(study_attributes) populate_extended_metadata(study, datastation_study) datastation_study.observation_units.each do |datastation_observation_unit| - observation_unit_attributes = datastation_observation_unit.seek_attributes.merge({contributor: contributor, study:study, projects: projects, policy:policy.deep_copy}) + observation_unit_attributes = datastation_observation_unit.seek_attributes.merge({ contributor: contributor, + study: study, projects: projects, policy: policy.deep_copy }) observation_unit = study.observation_units.build(observation_unit_attributes) datastation_observation_unit.datasets.each do |datastation_dataset| df = build_data_file(contributor, datastation_dataset, projects, policy) @@ -39,7 +41,7 @@ def self.construct_isa(datastation_inv, contributor, projects, policy) end populate_extended_metadata(observation_unit, datastation_observation_unit) datastation_observation_unit.samples.each do |datastation_sample| - sample = ::Sample.new(contributor: contributor, projects: projects, policy:policy.deep_copy) + sample = ::Sample.new(contributor: contributor, projects: projects, policy: policy.deep_copy) populate_sample(sample, datastation_sample) if sample.valid? observation_unit.samples << sample @@ -49,7 +51,8 @@ def self.construct_isa(datastation_inv, contributor, projects, policy) datastation_sample.assays.each do |datastation_assay| samples = [] samples << sample if sample.valid? - assay_attributes = datastation_assay.seek_attributes.merge({contributor: contributor, study:study, assay_class: AssayClass.experimental, samples:samples, policy:policy.deep_copy}) + assay_attributes = datastation_assay.seek_attributes.merge({ contributor: contributor, study: study, + assay_class: AssayClass.experimental, samples: samples, policy: policy.deep_copy }) assay = study.assays.build(assay_attributes) populate_extended_metadata(assay, datastation_assay) datastation_assay.datasets.each do |datastation_dataset| @@ -61,7 +64,7 @@ def self.construct_isa(datastation_inv, contributor, projects, policy) end end - return investigation + investigation end def self.populate_extended_metadata(seek_entity, datastation_entity) @@ -72,7 +75,7 @@ def self.populate_extended_metadata(seek_entity, datastation_entity) end def self.detect_extended_metadata(seek_entity, datastation_entity) - property_ids = datastation_entity.additional_metadata_annotations.collect{|annotation| annotation[0]} + property_ids = datastation_entity.additional_metadata_annotations.collect { |annotation| annotation[0] } # collect and sort those with the most properties that match, eliminating any where no properties match candidates = ExtendedMetadataType.where(supported_type: seek_entity.class.name).includes(:extended_metadata_attributes).collect do |emt| @@ -80,7 +83,9 @@ def self.detect_extended_metadata(seek_entity, datastation_entity) score = (property_ids - ids).length emt = nil if (property_ids & ids).empty? [score, emt] - end.sort_by{|x| x[0]} + end.sort_by do |x| + x[0] + end candidates.first&.last end @@ -95,7 +100,7 @@ def self.populate_sample(seek_sample, datastation_sample) end def self.detect_sample_type(datastation_sample) - property_ids = datastation_sample.additional_metadata_annotations.collect{|annotation| annotation[0]} + property_ids = datastation_sample.additional_metadata_annotations.collect { |annotation| annotation[0] } # collect and sort those with the most properties that match, eliminating any where no properties match candidates = SampleType.all.collect do |sample_type| @@ -103,29 +108,26 @@ def self.detect_sample_type(datastation_sample) score = (property_ids - ids).length sample_type = nil if (property_ids & ids).empty? [score, sample_type] - end.sort_by{|x| x[0]} + end.sort_by { |x| x[0] } candidates.first&.last end - private - def self.build_data_file(contributor, datastation_dataset, projects, policy) # @_data_file_cache = {} # if @_data_file_cache[datastation_dataset.identifier] # @_data_file_cache[datastation_dataset.identifier] # else - blob = ContentBlob.new(url: datastation_dataset.content_url.to_s, original_filename: datastation_dataset.identifier, external_link: true, is_webpage: true, content_type: 'application/octet-stream') - data_file_attributes = datastation_dataset.seek_attributes.merge({ - contributor: contributor, projects: projects, - content_blob: blob, policy: policy.deep_copy - }) + blob = ContentBlob.new(url: datastation_dataset.content_url.to_s, + original_filename: datastation_dataset.identifier, external_link: true, is_webpage: true, content_type: 'application/octet-stream') + data_file_attributes = datastation_dataset.seek_attributes.merge({ + contributor: contributor, projects: projects, + content_blob: blob, policy: policy.deep_copy + }) DataFile.new(data_file_attributes) # @_data_file_cache[datastation_dataset.identifier] = DataFile.new(data_file_attributes) # end - end - end end end diff --git a/lib/seek/fair_data_station/sample.rb b/lib/seek/fair_data_station/sample.rb index 9df0603d62..f2e7622a37 100644 --- a/lib/seek/fair_data_station/sample.rb +++ b/lib/seek/fair_data_station/sample.rb @@ -14,9 +14,7 @@ def populate_seek_sample(seek_sample) property = annotation[0] value = annotation[1] attribute = sample_type.sample_attributes.where(pid: property).first - if attribute - data[attribute.title] = value - end + data[attribute.title] = value if attribute end seek_sample.data = data end From 7484f2ab8af9bf0ff61e0a60c96ba3b6baad5c8c Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 21 May 2024 15:19:25 +0100 Subject: [PATCH 084/548] change fairdata station reader into a singleton --- app/controllers/projects_controller.rb | 5 ++- lib/seek/fair_data_station/reader.rb | 15 +++++---- .../fair_data_station_reader_test.rb | 32 +++++++++---------- 3 files changed, 26 insertions(+), 26 deletions(-) diff --git a/app/controllers/projects_controller.rb b/app/controllers/projects_controller.rb index 7dd110bf0c..7d80279d65 100644 --- a/app/controllers/projects_controller.rb +++ b/app/controllers/projects_controller.rb @@ -201,14 +201,13 @@ def submit_fairdata_station path = params[:datastation_data].path policy = Policy.new policy.set_attributes_with_sharing(policy_params) - datadata_inv = Seek::FairDataStation::Reader.parse_graph(path) - @investigation = Seek::FairDataStation::Reader.construct_isa(datadata_inv.first, current_person, [@project], policy) + datadata_inv = Seek::FairDataStation::Reader.instance.parse_graph(path) + @investigation = Seek::FairDataStation::Reader.instance.construct_isa(datadata_inv.first, current_person, [@project], policy) @investigation.save! respond_to do |format| format.html { redirect_to(@investigation) } end - end def request_create diff --git a/lib/seek/fair_data_station/reader.rb b/lib/seek/fair_data_station/reader.rb index 0d6d1dfc2f..3b80b0f4e6 100644 --- a/lib/seek/fair_data_station/reader.rb +++ b/lib/seek/fair_data_station/reader.rb @@ -5,7 +5,8 @@ module Seek module FairDataStation class Reader - def self.parse_graph(path) + include Singleton + def parse_graph(path) graph = RDF::Graph.load(path, format: :ttl) sparql = SPARQL::Client.new(graph) jerm = RDF::Vocabulary.new('http://jermontology.org/ontology/JERMOntology#') @@ -20,7 +21,7 @@ def self.parse_graph(path) end end - def self.construct_isa(datastation_inv, contributor, projects, policy) + def construct_isa(datastation_inv, contributor, projects, policy) inv_attributes = datastation_inv.seek_attributes.merge({ contributor: contributor, projects: projects, policy: policy.deep_copy }) investigation = ::Investigation.new(inv_attributes) @@ -67,14 +68,14 @@ def self.construct_isa(datastation_inv, contributor, projects, policy) investigation end - def self.populate_extended_metadata(seek_entity, datastation_entity) + def populate_extended_metadata(seek_entity, datastation_entity) if emt = detect_extended_metadata(seek_entity, datastation_entity) seek_entity.extended_metadata = ExtendedMetadata.new(extended_metadata_type: emt) datastation_entity.populate_extended_metadata(seek_entity) end end - def self.detect_extended_metadata(seek_entity, datastation_entity) + def detect_extended_metadata(seek_entity, datastation_entity) property_ids = datastation_entity.additional_metadata_annotations.collect { |annotation| annotation[0] } # collect and sort those with the most properties that match, eliminating any where no properties match @@ -90,7 +91,7 @@ def self.detect_extended_metadata(seek_entity, datastation_entity) candidates.first&.last end - def self.populate_sample(seek_sample, datastation_sample) + def populate_sample(seek_sample, datastation_sample) if sample_type = detect_sample_type(datastation_sample) seek_sample.sample_type = sample_type datastation_sample.populate_seek_sample(seek_sample) @@ -99,7 +100,7 @@ def self.populate_sample(seek_sample, datastation_sample) end end - def self.detect_sample_type(datastation_sample) + def detect_sample_type(datastation_sample) property_ids = datastation_sample.additional_metadata_annotations.collect { |annotation| annotation[0] } # collect and sort those with the most properties that match, eliminating any where no properties match @@ -113,7 +114,7 @@ def self.detect_sample_type(datastation_sample) candidates.first&.last end - def self.build_data_file(contributor, datastation_dataset, projects, policy) + def build_data_file(contributor, datastation_dataset, projects, policy) # @_data_file_cache = {} # if @_data_file_cache[datastation_dataset.identifier] # @_data_file_cache[datastation_dataset.identifier] diff --git a/test/unit/fair_data_station/fair_data_station_reader_test.rb b/test/unit/fair_data_station/fair_data_station_reader_test.rb index 3d7994728c..0acdb88a1f 100644 --- a/test/unit/fair_data_station/fair_data_station_reader_test.rb +++ b/test/unit/fair_data_station/fair_data_station_reader_test.rb @@ -4,7 +4,7 @@ class FairDataStationReaderTest < ActiveSupport::TestCase test 'read demo' do path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" - investigations = Seek::FairDataStation::Reader.parse_graph(path) + investigations = Seek::FairDataStation::Reader.instance.parse_graph(path) assert_equal 1, investigations.count inv = investigations.first assert_equal 'http://fairbydesign.nl/ontology/inv_INV_DRP007092', inv.resource_uri.to_s @@ -37,7 +37,7 @@ class FairDataStationReaderTest < ActiveSupport::TestCase test 'read indpensim' do path = "#{Rails.root}/test/fixtures/files/fairdatastation/indpensim.ttl" - investigations = Seek::FairDataStation::Reader.parse_graph(path) + investigations = Seek::FairDataStation::Reader.instance.parse_graph(path) assert_equal 1, investigations.count inv = investigations.first assert_equal 'http://fairbydesign.nl/ontology/inv_indpensim', inv.resource_uri.to_s @@ -66,7 +66,7 @@ class FairDataStationReaderTest < ActiveSupport::TestCase test 'annotations' do path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" - study = Seek::FairDataStation::Reader.parse_graph(path).first.studies.first + study = Seek::FairDataStation::Reader.instance.parse_graph(path).first.studies.first assert_equal 14, study.annotations.count assert_includes study.annotations, ["http://fairbydesign.nl/ontology/center_name", "NIID"] @@ -75,7 +75,7 @@ class FairDataStationReaderTest < ActiveSupport::TestCase test 'additional metadata annotations' do path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" - inv = Seek::FairDataStation::Reader.parse_graph(path).first + inv = Seek::FairDataStation::Reader.instance.parse_graph(path).first assert_empty inv.additional_metadata_annotations study = inv.studies.first @@ -88,7 +88,7 @@ class FairDataStationReaderTest < ActiveSupport::TestCase # non fairbydesign annotations path = "#{Rails.root}/test/fixtures/files/fairdatastation/indpensim.ttl" - inv = Seek::FairDataStation::Reader.parse_graph(path).first + inv = Seek::FairDataStation::Reader.instance.parse_graph(path).first obs_unit = inv.studies.first.observation_units.first annotations = obs_unit.additional_metadata_annotations assert_equal 5, annotations.count @@ -100,7 +100,7 @@ class FairDataStationReaderTest < ActiveSupport::TestCase test 'study assays' do path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" - investigations = Seek::FairDataStation::Reader.parse_graph(path) + investigations = Seek::FairDataStation::Reader.instance.parse_graph(path) study = investigations.first.studies.first assert_equal 9, study.assays.count expected = %w[DRR243845 DRR243850 DRR243856 DRR243863 DRR243881 DRR243894 DRR243899 DRR243906 @@ -111,7 +111,7 @@ class FairDataStationReaderTest < ActiveSupport::TestCase test 'titles and descriptions' do path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" - inv = Seek::FairDataStation::Reader.parse_graph(path).first + inv = Seek::FairDataStation::Reader.instance.parse_graph(path).first study = inv.studies.first obs_unit = study.observation_units.first sample = obs_unit.samples.first @@ -138,7 +138,7 @@ class FairDataStationReaderTest < ActiveSupport::TestCase test 'datasets' do path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" - inv = Seek::FairDataStation::Reader.parse_graph(path).first + inv = Seek::FairDataStation::Reader.instance.parse_graph(path).first study = inv.studies.first obs_unit = study.observation_units.first sample = obs_unit.samples.first @@ -159,7 +159,7 @@ class FairDataStationReaderTest < ActiveSupport::TestCase test 'construct seek isa' do path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" - inv = Seek::FairDataStation::Reader.parse_graph(path).first + inv = Seek::FairDataStation::Reader.instance.parse_graph(path).first policy = FactoryBot.create(:public_policy) contributor = FactoryBot.create(:person) @@ -167,7 +167,7 @@ class FairDataStationReaderTest < ActiveSupport::TestCase FactoryBot.create(:experimental_assay_class) FactoryBot.create(:fairdatastation_virtual_demo_sample_type) - investigation = Seek::FairDataStation::Reader.construct_isa(inv, contributor, [project], policy) + investigation = Seek::FairDataStation::Reader.instance.construct_isa(inv, contributor, [project], policy) studies = investigation.studies.to_a obs_units = studies.first.observation_units.to_a assays = studies.first.assays.to_a @@ -236,11 +236,11 @@ class FairDataStationReaderTest < ActiveSupport::TestCase sample_type = FactoryBot.create(:fairdatastation_virtual_demo_sample_type) path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" - inv = Seek::FairDataStation::Reader.parse_graph(path).first + inv = Seek::FairDataStation::Reader.instance.parse_graph(path).first contributor = FactoryBot.create(:person) project = contributor.projects.first - investigation = Seek::FairDataStation::Reader.construct_isa(inv, contributor, [project], Policy.default) + investigation = Seek::FairDataStation::Reader.instance.construct_isa(inv, contributor, [project], Policy.default) assert_nil investigation.extended_metadata study = investigation.studies.first @@ -294,14 +294,14 @@ class FairDataStationReaderTest < ActiveSupport::TestCase test 'observation_unit datasets created in construct_isa' do path = "#{Rails.root}/test/fixtures/files/fairdatastation/indpensim.ttl" - inv = Seek::FairDataStation::Reader.parse_graph(path).first + inv = Seek::FairDataStation::Reader.instance.parse_graph(path).first contributor = FactoryBot.create(:person) project = contributor.projects.first FactoryBot.create(:experimental_assay_class) FactoryBot.create(:fairdatastation_virtual_demo_sample_type) - investigation = Seek::FairDataStation::Reader.construct_isa(inv, contributor, [project], Policy.default) + investigation = Seek::FairDataStation::Reader.instance.construct_isa(inv, contributor, [project], Policy.default) assert_equal 100, investigation.studies.first.observation_units.to_a.count observation_unit = investigation.studies.first.observation_units.first assert_equal 1, observation_unit.observation_unit_assets.find_all{|oua| oua.asset_type == 'DataFile'}.collect(&:asset).count @@ -328,11 +328,11 @@ class FairDataStationReaderTest < ActiveSupport::TestCase FactoryBot.create(:experimental_assay_class) path = "#{Rails.root}/test/fixtures/files/fairdatastation/indpensim.ttl" - inv = Seek::FairDataStation::Reader.parse_graph(path).first + inv = Seek::FairDataStation::Reader.instance.parse_graph(path).first contributor = FactoryBot.create(:person) project = contributor.projects.first - investigation = Seek::FairDataStation::Reader.construct_isa(inv, contributor, [project], Policy.default) + investigation = Seek::FairDataStation::Reader.instance.construct_isa(inv, contributor, [project], Policy.default) assert_nil investigation.extended_metadata assert_difference('ExtendedMetadata.count', 100) do From b584b55e252f1546ecf65d5902f990d7a64ba3f7 Mon Sep 17 00:00:00 2001 From: Stuart Owen Date: Tue, 21 May 2024 15:36:07 +0100 Subject: [PATCH 085/548] seperated the reader into reader & writer classes --- app/controllers/projects_controller.rb | 2 +- lib/seek/fair_data_station/reader.rb | 109 ---------- lib/seek/fair_data_station/writer.rb | 118 ++++++++++ .../fair_data_station_reader_test.rb | 199 ----------------- .../fair_data_station_writer_test.rb | 203 ++++++++++++++++++ 5 files changed, 322 insertions(+), 309 deletions(-) create mode 100644 lib/seek/fair_data_station/writer.rb create mode 100644 test/unit/fair_data_station/fair_data_station_writer_test.rb diff --git a/app/controllers/projects_controller.rb b/app/controllers/projects_controller.rb index 7d80279d65..90d365384f 100644 --- a/app/controllers/projects_controller.rb +++ b/app/controllers/projects_controller.rb @@ -202,7 +202,7 @@ def submit_fairdata_station policy = Policy.new policy.set_attributes_with_sharing(policy_params) datadata_inv = Seek::FairDataStation::Reader.instance.parse_graph(path) - @investigation = Seek::FairDataStation::Reader.instance.construct_isa(datadata_inv.first, current_person, [@project], policy) + @investigation = Seek::FairDataStation::Writer.instance.construct_isa(datadata_inv.first, current_person, [@project], policy) @investigation.save! respond_to do |format| diff --git a/lib/seek/fair_data_station/reader.rb b/lib/seek/fair_data_station/reader.rb index 3b80b0f4e6..40850d6de0 100644 --- a/lib/seek/fair_data_station/reader.rb +++ b/lib/seek/fair_data_station/reader.rb @@ -20,115 +20,6 @@ def parse_graph(path) inv end end - - def construct_isa(datastation_inv, contributor, projects, policy) - inv_attributes = datastation_inv.seek_attributes.merge({ contributor: contributor, projects: projects, - policy: policy.deep_copy }) - investigation = ::Investigation.new(inv_attributes) - populate_extended_metadata(investigation, datastation_inv) - - datastation_inv.studies.each do |datastation_study| - study_attributes = datastation_study.seek_attributes.merge({ contributor: contributor, - investigation: investigation, policy: policy.deep_copy }) - study = investigation.studies.build(study_attributes) - populate_extended_metadata(study, datastation_study) - datastation_study.observation_units.each do |datastation_observation_unit| - observation_unit_attributes = datastation_observation_unit.seek_attributes.merge({ contributor: contributor, - study: study, projects: projects, policy: policy.deep_copy }) - observation_unit = study.observation_units.build(observation_unit_attributes) - datastation_observation_unit.datasets.each do |datastation_dataset| - df = build_data_file(contributor, datastation_dataset, projects, policy) - observation_unit.observation_unit_assets.build(asset: df) - end - populate_extended_metadata(observation_unit, datastation_observation_unit) - datastation_observation_unit.samples.each do |datastation_sample| - sample = ::Sample.new(contributor: contributor, projects: projects, policy: policy.deep_copy) - populate_sample(sample, datastation_sample) - if sample.valid? - observation_unit.samples << sample - else - Rails.logger.error("Invalid sample during fair data station import #{sample.errors.full_messages.inspect}") - end - datastation_sample.assays.each do |datastation_assay| - samples = [] - samples << sample if sample.valid? - assay_attributes = datastation_assay.seek_attributes.merge({ contributor: contributor, study: study, - assay_class: AssayClass.experimental, samples: samples, policy: policy.deep_copy }) - assay = study.assays.build(assay_attributes) - populate_extended_metadata(assay, datastation_assay) - datastation_assay.datasets.each do |datastation_dataset| - df = build_data_file(contributor, datastation_dataset, projects, policy) - assay.assay_assets.build(asset: df) - end - end - end - end - end - - investigation - end - - def populate_extended_metadata(seek_entity, datastation_entity) - if emt = detect_extended_metadata(seek_entity, datastation_entity) - seek_entity.extended_metadata = ExtendedMetadata.new(extended_metadata_type: emt) - datastation_entity.populate_extended_metadata(seek_entity) - end - end - - def detect_extended_metadata(seek_entity, datastation_entity) - property_ids = datastation_entity.additional_metadata_annotations.collect { |annotation| annotation[0] } - - # collect and sort those with the most properties that match, eliminating any where no properties match - candidates = ExtendedMetadataType.where(supported_type: seek_entity.class.name).includes(:extended_metadata_attributes).collect do |emt| - ids = emt.extended_metadata_attributes.collect(&:property_type_id) - score = (property_ids - ids).length - emt = nil if (property_ids & ids).empty? - [score, emt] - end.sort_by do |x| - x[0] - end - - candidates.first&.last - end - - def populate_sample(seek_sample, datastation_sample) - if sample_type = detect_sample_type(datastation_sample) - seek_sample.sample_type = sample_type - datastation_sample.populate_seek_sample(seek_sample) - seek_sample.set_attribute_value('Title', datastation_sample.title) - seek_sample.set_attribute_value('Description', datastation_sample.description) - end - end - - def detect_sample_type(datastation_sample) - property_ids = datastation_sample.additional_metadata_annotations.collect { |annotation| annotation[0] } - - # collect and sort those with the most properties that match, eliminating any where no properties match - candidates = SampleType.all.collect do |sample_type| - ids = sample_type.sample_attributes.collect(&:pid) - score = (property_ids - ids).length - sample_type = nil if (property_ids & ids).empty? - [score, sample_type] - end.sort_by { |x| x[0] } - - candidates.first&.last - end - - def build_data_file(contributor, datastation_dataset, projects, policy) - # @_data_file_cache = {} - # if @_data_file_cache[datastation_dataset.identifier] - # @_data_file_cache[datastation_dataset.identifier] - # else - blob = ContentBlob.new(url: datastation_dataset.content_url.to_s, - original_filename: datastation_dataset.identifier, external_link: true, is_webpage: true, content_type: 'application/octet-stream') - data_file_attributes = datastation_dataset.seek_attributes.merge({ - contributor: contributor, projects: projects, - content_blob: blob, policy: policy.deep_copy - }) - DataFile.new(data_file_attributes) - # @_data_file_cache[datastation_dataset.identifier] = DataFile.new(data_file_attributes) - # end - end end end end diff --git a/lib/seek/fair_data_station/writer.rb b/lib/seek/fair_data_station/writer.rb new file mode 100644 index 0000000000..dfb3b88b64 --- /dev/null +++ b/lib/seek/fair_data_station/writer.rb @@ -0,0 +1,118 @@ +module Seek + module FairDataStation + class Writer + include Singleton + + def construct_isa(datastation_inv, contributor, projects, policy) + inv_attributes = datastation_inv.seek_attributes.merge({ contributor: contributor, projects: projects, + policy: policy.deep_copy }) + investigation = ::Investigation.new(inv_attributes) + populate_extended_metadata(investigation, datastation_inv) + + datastation_inv.studies.each do |datastation_study| + study_attributes = datastation_study.seek_attributes.merge({ contributor: contributor, + investigation: investigation, policy: policy.deep_copy }) + study = investigation.studies.build(study_attributes) + populate_extended_metadata(study, datastation_study) + datastation_study.observation_units.each do |datastation_observation_unit| + observation_unit_attributes = datastation_observation_unit.seek_attributes.merge({ contributor: contributor, + study: study, projects: projects, policy: policy.deep_copy }) + observation_unit = study.observation_units.build(observation_unit_attributes) + datastation_observation_unit.datasets.each do |datastation_dataset| + df = build_data_file(contributor, datastation_dataset, projects, policy) + observation_unit.observation_unit_assets.build(asset: df) + end + populate_extended_metadata(observation_unit, datastation_observation_unit) + datastation_observation_unit.samples.each do |datastation_sample| + sample = ::Sample.new(contributor: contributor, projects: projects, policy: policy.deep_copy) + populate_sample(sample, datastation_sample) + if sample.valid? + observation_unit.samples << sample + else + Rails.logger.error("Invalid sample during fair data station import #{sample.errors.full_messages.inspect}") + end + datastation_sample.assays.each do |datastation_assay| + samples = [] + samples << sample if sample.valid? + assay_attributes = datastation_assay.seek_attributes.merge({ contributor: contributor, study: study, + assay_class: AssayClass.experimental, samples: samples, policy: policy.deep_copy }) + assay = study.assays.build(assay_attributes) + populate_extended_metadata(assay, datastation_assay) + datastation_assay.datasets.each do |datastation_dataset| + df = build_data_file(contributor, datastation_dataset, projects, policy) + assay.assay_assets.build(asset: df) + end + end + end + end + end + + investigation + end + + private + + def populate_extended_metadata(seek_entity, datastation_entity) + if emt = detect_extended_metadata(seek_entity, datastation_entity) + seek_entity.extended_metadata = ExtendedMetadata.new(extended_metadata_type: emt) + datastation_entity.populate_extended_metadata(seek_entity) + end + end + + def detect_extended_metadata(seek_entity, datastation_entity) + property_ids = datastation_entity.additional_metadata_annotations.collect { |annotation| annotation[0] } + + # collect and sort those with the most properties that match, eliminating any where no properties match + candidates = ExtendedMetadataType.where(supported_type: seek_entity.class.name).includes(:extended_metadata_attributes).collect do |emt| + ids = emt.extended_metadata_attributes.collect(&:property_type_id) + score = (property_ids - ids).length + emt = nil if (property_ids & ids).empty? + [score, emt] + end.sort_by do |x| + x[0] + end + + candidates.first&.last + end + + def populate_sample(seek_sample, datastation_sample) + if sample_type = detect_sample_type(datastation_sample) + seek_sample.sample_type = sample_type + datastation_sample.populate_seek_sample(seek_sample) + seek_sample.set_attribute_value('Title', datastation_sample.title) + seek_sample.set_attribute_value('Description', datastation_sample.description) + end + end + + def detect_sample_type(datastation_sample) + property_ids = datastation_sample.additional_metadata_annotations.collect { |annotation| annotation[0] } + + # collect and sort those with the most properties that match, eliminating any where no properties match + candidates = SampleType.all.collect do |sample_type| + ids = sample_type.sample_attributes.collect(&:pid) + score = (property_ids - ids).length + sample_type = nil if (property_ids & ids).empty? + [score, sample_type] + end.sort_by { |x| x[0] } + + candidates.first&.last + end + + def build_data_file(contributor, datastation_dataset, projects, policy) + # @_data_file_cache = {} + # if @_data_file_cache[datastation_dataset.identifier] + # @_data_file_cache[datastation_dataset.identifier] + # else + blob = ContentBlob.new(url: datastation_dataset.content_url.to_s, + original_filename: datastation_dataset.identifier, external_link: true, is_webpage: true, content_type: 'application/octet-stream') + data_file_attributes = datastation_dataset.seek_attributes.merge({ + contributor: contributor, projects: projects, + content_blob: blob, policy: policy.deep_copy + }) + DataFile.new(data_file_attributes) + # @_data_file_cache[datastation_dataset.identifier] = DataFile.new(data_file_attributes) + # end + end + end + end +end diff --git a/test/unit/fair_data_station/fair_data_station_reader_test.rb b/test/unit/fair_data_station/fair_data_station_reader_test.rb index 0acdb88a1f..144915fd47 100644 --- a/test/unit/fair_data_station/fair_data_station_reader_test.rb +++ b/test/unit/fair_data_station/fair_data_station_reader_test.rb @@ -156,203 +156,4 @@ class FairDataStationReaderTest < ActiveSupport::TestCase assert_equal 0, obs_unit.datasets.count assert_equal 0, sample.datasets.count end - - test 'construct seek isa' do - path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" - inv = Seek::FairDataStation::Reader.instance.parse_graph(path).first - policy = FactoryBot.create(:public_policy) - - contributor = FactoryBot.create(:person) - project = contributor.projects.first - FactoryBot.create(:experimental_assay_class) - FactoryBot.create(:fairdatastation_virtual_demo_sample_type) - - investigation = Seek::FairDataStation::Reader.instance.construct_isa(inv, contributor, [project], policy) - studies = investigation.studies.to_a - obs_units = studies.first.observation_units.to_a - assays = studies.first.assays.to_a - data_files = assays.first.assay_assets.to_a.collect(&:asset).select{|a| a.is_a?(DataFile)} - samples = obs_units.first.samples.to_a - - assay_samples = assays.collect{|a| a.samples.to_a}.flatten - assert_equal 9, assay_samples.count - assert_equal samples, (assay_samples & samples) - - assert_equal 1, studies.count - assert_equal 9, assays.count - assert_equal 2, data_files.count - assert_equal 2, obs_units.count - assert_equal 4, samples.count - - assert_equal Policy::MANAGING, investigation.policy.access_type - assert_equal Policy::MANAGING, studies.first.policy.access_type - assert_equal Policy::MANAGING, obs_units.first.policy.access_type - assert_equal Policy::MANAGING, assays.first.policy.access_type - assert_equal Policy::MANAGING, samples.first.policy.access_type - assert_equal Policy::MANAGING, data_files.first.policy.access_type - - refute_equal investigation.policy, studies.first.policy - refute_equal investigation.policy, obs_units.first.policy - refute_equal investigation.policy, assays.first.policy - refute_equal investigation.policy, samples.first.policy - refute_equal investigation.policy, data_files.first.policy - - assert investigation.valid? - assert studies.first.valid? - - pp assays.first.errors unless assays.first.valid? - assert assays.first.valid? - - pp data_files.first.errors unless data_files.first.valid? - assert data_files.first.valid? - - assert_difference('Investigation.count', 1) do - assert_difference('Study.count', 1) do - assert_difference('ObservationUnit.count', 2) do - assert_difference('Sample.count', 9) do - assert_difference('Assay.count', 9) do - assert_difference('AssayAsset.count', 27) do - assert_difference('DataFile.count', 18) do - User.with_current_user(contributor.user) do - investigation.save! - end - end - end - end - end - end - end - end - end - - test 'populate extended metadata and samples' do - study_metadata_type = FactoryBot.create(:fairdata_virtual_demo_study_extended_metadata) - FactoryBot.create(:study_extended_metadata_type) - FactoryBot.create(:fairdata_virtual_demo_study_extended_metadata_partial) - assay_metadata_type = FactoryBot.create(:fairdata_virtual_demo_assay_extended_metadata) - FactoryBot.create(:simple_assay_extended_metadata_type) - FactoryBot.create(:simple_investigation_extended_metadata_type_with_description_and_label) - FactoryBot.create(:experimental_assay_class) - sample_type = FactoryBot.create(:fairdatastation_virtual_demo_sample_type) - - path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" - inv = Seek::FairDataStation::Reader.instance.parse_graph(path).first - contributor = FactoryBot.create(:person) - project = contributor.projects.first - - investigation = Seek::FairDataStation::Reader.instance.construct_isa(inv, contributor, [project], Policy.default) - assert_nil investigation.extended_metadata - - study = investigation.studies.first - refute_nil study.extended_metadata - assert_equal study_metadata_type, study.extended_metadata.extended_metadata_type - - assert_equal 'DRP007092', study.extended_metadata.get_attribute_value('Alias') - assert_equal 'NIID', study.extended_metadata.get_attribute_value('Centre Name') - assert_equal 'human gut metagenome', study.extended_metadata.get_attribute_value('Centre Project Name') - assert_equal 'PRJDB10485', study.extended_metadata.get_attribute_value('External Ids') - assert_equal 'DRA010770', study.extended_metadata.get_attribute_value('Submission Accession') - assert_equal 'DRA010770', study.extended_metadata.get_attribute_value('Submission Alias') - assert_equal 'AIDS Research Center2022-8-31', study.extended_metadata.get_attribute_value('Submission Lab Name') - - assay = study.assays.first - refute_nil assay.extended_metadata - assert_equal assay_metadata_type, assay.extended_metadata.extended_metadata_type - - assert_equal 'NMIMR', assay.extended_metadata.get_attribute_value('Facility') - assert_equal 'CCTACGGGNGGCWGCAG', assay.extended_metadata.get_attribute_value('Forward Primer') - assert_equal 'Illumina MiSeq', assay.extended_metadata.get_attribute_value('Instrument Model') - assert_equal 'PCR', assay.extended_metadata.get_attribute_value('Library Selection') - assert_equal 'METAGENOMIC', assay.extended_metadata.get_attribute_value('Library Source') - assert_equal 'AMPLICON', assay.extended_metadata.get_attribute_value('Library Strategy') - - study.assays.each do |assay| - assert assay.valid?, "invalid assay - #{assay.errors.full_messages}" - end - assert study.valid?, "invalid study - #{study.errors.full_messages}" - assert investigation.valid?, "invalid investigation - #{investigation.errors.full_messages}" - - assert_difference('ExtendedMetadata.count', 10) do - User.with_current_user(contributor.user) do - study.save! - end - end - - sample = study.observation_units.first.samples.first - refute_nil sample.sample_type - assert_equal sample_type, sample.sample_type - assert_equal 'sample DRS176892', sample.title - assert_equal 'Sample obtained from Single age 30 collected on 2017-09-13 from the human gut', sample.get_attribute_value('Description') - assert_equal 'Homo sapiens', sample.get_attribute_value('Host') - assert_equal 'HIV-1 positive', sample.get_attribute_value('Host disease stat') - assert_equal 'Single', sample.get_attribute_value('Marital status') - assert_equal 'Trader', sample.get_attribute_value('Occupation') - assert_equal 'human gut metagenome', sample.get_attribute_value('Scientific name') - assert_equal '408170', sample.get_attribute_value('Organism') - - end - - test 'observation_unit datasets created in construct_isa' do - path = "#{Rails.root}/test/fixtures/files/fairdatastation/indpensim.ttl" - inv = Seek::FairDataStation::Reader.instance.parse_graph(path).first - - contributor = FactoryBot.create(:person) - project = contributor.projects.first - FactoryBot.create(:experimental_assay_class) - FactoryBot.create(:fairdatastation_virtual_demo_sample_type) - - investigation = Seek::FairDataStation::Reader.instance.construct_isa(inv, contributor, [project], Policy.default) - assert_equal 100, investigation.studies.first.observation_units.to_a.count - observation_unit = investigation.studies.first.observation_units.first - assert_equal 1, observation_unit.observation_unit_assets.find_all{|oua| oua.asset_type == 'DataFile'}.collect(&:asset).count - - df = observation_unit.observation_unit_assets.first.asset - assert_equal 'Dataset: IndPenSim_V3_Batch_1.csv.gz', df.title - assert_equal 'file', df.description - assert_equal 'application/octet-stream', df.content_blob.content_type - assert df.content_blob.external_link? - assert df.content_blob.is_webpage? - assert df.content_blob.show_as_external_link? - - assert_difference('DataFile.count',96) do - assert_difference('ObservationUnitAsset.count',96) do - disable_authorization_checks { - investigation.save! - } - end - end - end - - test 'populate obsv unit extended metadata' do - ext_metadata_type = FactoryBot.create(:fairdata_indpensim_obsv_unit_extended_metadata) - FactoryBot.create(:experimental_assay_class) - - path = "#{Rails.root}/test/fixtures/files/fairdatastation/indpensim.ttl" - inv = Seek::FairDataStation::Reader.instance.parse_graph(path).first - contributor = FactoryBot.create(:person) - project = contributor.projects.first - - investigation = Seek::FairDataStation::Reader.instance.construct_isa(inv, contributor, [project], Policy.default) - assert_nil investigation.extended_metadata - - assert_difference('ExtendedMetadata.count', 100) do - User.with_current_user(contributor.user) do - investigation.save! - end - end - - assert_equal 1, investigation.studies.count - study = investigation.studies.first - assert_equal 100, study.observation_units.count - obvs_unit = study.observation_units.first - refute_nil obvs_unit.extended_metadata - assert_equal ext_metadata_type, obvs_unit.extended_metadata.extended_metadata_type - - assert_equal 'FermentorX', obvs_unit.extended_metadata.get_attribute_value('Brand') - assert_equal 'batch', obvs_unit.extended_metadata.get_attribute_value('Fermentation') - assert_equal '100,000 litre', obvs_unit.extended_metadata.get_attribute_value('Volume') - assert_equal 'Penicillium chrysogenum', obvs_unit.extended_metadata.get_attribute_value('Scientific Name') - assert_equal '5076', obvs_unit.extended_metadata.get_attribute_value('Organism') - end - end diff --git a/test/unit/fair_data_station/fair_data_station_writer_test.rb b/test/unit/fair_data_station/fair_data_station_writer_test.rb new file mode 100644 index 0000000000..2ddf6508ce --- /dev/null +++ b/test/unit/fair_data_station/fair_data_station_writer_test.rb @@ -0,0 +1,203 @@ +require 'test_helper' + +class FairDataStationWriterTest < ActiveSupport::TestCase + + test 'construct seek isa' do + path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" + inv = Seek::FairDataStation::Reader.instance.parse_graph(path).first + policy = FactoryBot.create(:public_policy) + + contributor = FactoryBot.create(:person) + project = contributor.projects.first + FactoryBot.create(:experimental_assay_class) + FactoryBot.create(:fairdatastation_virtual_demo_sample_type) + + investigation = Seek::FairDataStation::Writer.instance.construct_isa(inv, contributor, [project], policy) + studies = investigation.studies.to_a + obs_units = studies.first.observation_units.to_a + assays = studies.first.assays.to_a + data_files = assays.first.assay_assets.to_a.collect(&:asset).select{|a| a.is_a?(DataFile)} + samples = obs_units.first.samples.to_a + + assay_samples = assays.collect{|a| a.samples.to_a}.flatten + assert_equal 9, assay_samples.count + assert_equal samples, (assay_samples & samples) + + assert_equal 1, studies.count + assert_equal 9, assays.count + assert_equal 2, data_files.count + assert_equal 2, obs_units.count + assert_equal 4, samples.count + + assert_equal Policy::MANAGING, investigation.policy.access_type + assert_equal Policy::MANAGING, studies.first.policy.access_type + assert_equal Policy::MANAGING, obs_units.first.policy.access_type + assert_equal Policy::MANAGING, assays.first.policy.access_type + assert_equal Policy::MANAGING, samples.first.policy.access_type + assert_equal Policy::MANAGING, data_files.first.policy.access_type + + refute_equal investigation.policy, studies.first.policy + refute_equal investigation.policy, obs_units.first.policy + refute_equal investigation.policy, assays.first.policy + refute_equal investigation.policy, samples.first.policy + refute_equal investigation.policy, data_files.first.policy + + assert investigation.valid? + assert studies.first.valid? + + pp assays.first.errors unless assays.first.valid? + assert assays.first.valid? + + pp data_files.first.errors unless data_files.first.valid? + assert data_files.first.valid? + + assert_difference('Investigation.count', 1) do + assert_difference('Study.count', 1) do + assert_difference('ObservationUnit.count', 2) do + assert_difference('Sample.count', 9) do + assert_difference('Assay.count', 9) do + assert_difference('AssayAsset.count', 27) do + assert_difference('DataFile.count', 18) do + User.with_current_user(contributor.user) do + investigation.save! + end + end + end + end + end + end + end + end + end + + test 'populate extended metadata and samples' do + study_metadata_type = FactoryBot.create(:fairdata_virtual_demo_study_extended_metadata) + FactoryBot.create(:study_extended_metadata_type) + FactoryBot.create(:fairdata_virtual_demo_study_extended_metadata_partial) + assay_metadata_type = FactoryBot.create(:fairdata_virtual_demo_assay_extended_metadata) + FactoryBot.create(:simple_assay_extended_metadata_type) + FactoryBot.create(:simple_investigation_extended_metadata_type_with_description_and_label) + FactoryBot.create(:experimental_assay_class) + sample_type = FactoryBot.create(:fairdatastation_virtual_demo_sample_type) + + path = "#{Rails.root}/test/fixtures/files/fairdatastation/demo.ttl" + inv = Seek::FairDataStation::Reader.instance.parse_graph(path).first + contributor = FactoryBot.create(:person) + project = contributor.projects.first + + investigation = Seek::FairDataStation::Writer.instance.construct_isa(inv, contributor, [project], Policy.default) + assert_nil investigation.extended_metadata + + study = investigation.studies.first + refute_nil study.extended_metadata + assert_equal study_metadata_type, study.extended_metadata.extended_metadata_type + + assert_equal 'DRP007092', study.extended_metadata.get_attribute_value('Alias') + assert_equal 'NIID', study.extended_metadata.get_attribute_value('Centre Name') + assert_equal 'human gut metagenome', study.extended_metadata.get_attribute_value('Centre Project Name') + assert_equal 'PRJDB10485', study.extended_metadata.get_attribute_value('External Ids') + assert_equal 'DRA010770', study.extended_metadata.get_attribute_value('Submission Accession') + assert_equal 'DRA010770', study.extended_metadata.get_attribute_value('Submission Alias') + assert_equal 'AIDS Research Center2022-8-31', study.extended_metadata.get_attribute_value('Submission Lab Name') + + assay = study.assays.first + refute_nil assay.extended_metadata + assert_equal assay_metadata_type, assay.extended_metadata.extended_metadata_type + + assert_equal 'NMIMR', assay.extended_metadata.get_attribute_value('Facility') + assert_equal 'CCTACGGGNGGCWGCAG', assay.extended_metadata.get_attribute_value('Forward Primer') + assert_equal 'Illumina MiSeq', assay.extended_metadata.get_attribute_value('Instrument Model') + assert_equal 'PCR', assay.extended_metadata.get_attribute_value('Library Selection') + assert_equal 'METAGENOMIC', assay.extended_metadata.get_attribute_value('Library Source') + assert_equal 'AMPLICON', assay.extended_metadata.get_attribute_value('Library Strategy') + + study.assays.each do |assay| + assert assay.valid?, "invalid assay - #{assay.errors.full_messages}" + end + assert study.valid?, "invalid study - #{study.errors.full_messages}" + assert investigation.valid?, "invalid investigation - #{investigation.errors.full_messages}" + + assert_difference('ExtendedMetadata.count', 10) do + User.with_current_user(contributor.user) do + study.save! + end + end + + sample = study.observation_units.first.samples.first + refute_nil sample.sample_type + assert_equal sample_type, sample.sample_type + assert_equal 'sample DRS176892', sample.title + assert_equal 'Sample obtained from Single age 30 collected on 2017-09-13 from the human gut', sample.get_attribute_value('Description') + assert_equal 'Homo sapiens', sample.get_attribute_value('Host') + assert_equal 'HIV-1 positive', sample.get_attribute_value('Host disease stat') + assert_equal 'Single', sample.get_attribute_value('Marital status') + assert_equal 'Trader', sample.get_attribute_value('Occupation') + assert_equal 'human gut metagenome', sample.get_attribute_value('Scientific name') + assert_equal '408170', sample.get_attribute_value('Organism') + + end + + test 'observation_unit datasets created in construct_isa' do + path = "#{Rails.root}/test/fixtures/files/fairdatastation/indpensim.ttl" + inv = Seek::FairDataStation::Reader.instance.parse_graph(path).first + + contributor = FactoryBot.create(:person) + project = contributor.projects.first + FactoryBot.create(:experimental_assay_class) + FactoryBot.create(:fairdatastation_virtual_demo_sample_type) + + investigation = Seek::FairDataStation::Writer.instance.construct_isa(inv, contributor, [project], Policy.default) + assert_equal 100, investigation.studies.first.observation_units.to_a.count + observation_unit = investigation.studies.first.observation_units.first + assert_equal 1, observation_unit.observation_unit_assets.find_all{|oua| oua.asset_type == 'DataFile'}.collect(&:asset).count + + df = observation_unit.observation_unit_assets.first.asset + assert_equal 'Dataset: IndPenSim_V3_Batch_1.csv.gz', df.title + assert_equal 'file', df.description + assert_equal 'application/octet-stream', df.content_blob.content_type + assert df.content_blob.external_link? + assert df.content_blob.is_webpage? + assert df.content_blob.show_as_external_link? + + assert_difference('DataFile.count',96) do + assert_difference('ObservationUnitAsset.count',96) do + disable_authorization_checks { + investigation.save! + } + end + end + end + + test 'populate obsv unit extended metadata' do + ext_metadata_type = FactoryBot.create(:fairdata_indpensim_obsv_unit_extended_metadata) + FactoryBot.create(:experimental_assay_class) + + path = "#{Rails.root}/test/fixtures/files/fairdatastation/indpensim.ttl" + inv = Seek::FairDataStation::Reader.instance.parse_graph(path).first + contributor = FactoryBot.create(:person) + project = contributor.projects.first + + investigation = Seek::FairDataStation::Writer.instance.construct_isa(inv, contributor, [project], Policy.default) + assert_nil investigation.extended_metadata + + assert_difference('ExtendedMetadata.count', 100) do + User.with_current_user(contributor.user) do + investigation.save! + end + end + + assert_equal 1, investigation.studies.count + study = investigation.studies.first + assert_equal 100, study.observation_units.count + obvs_unit = study.observation_units.first + refute_nil obvs_unit.extended_metadata + assert_equal ext_metadata_type, obvs_unit.extended_metadata.extended_metadata_type + + assert_equal 'FermentorX', obvs_unit.extended_metadata.get_attribute_value('Brand') + assert_equal 'batch', obvs_unit.extended_metadata.get_attribute_value('Fermentation') + assert_equal '100,000 litre', obvs_unit.extended_metadata.get_attribute_value('Volume') + assert_equal 'Penicillium chrysogenum', obvs_unit.extended_metadata.get_attribute_value('Scientific Name') + assert_equal '5076', obvs_unit.extended_metadata.get_attribute_value('Organism') + end + +end \ No newline at end of file From 12c571df352dcf727c0d6663beeeb558d821749d Mon Sep 17 00:00:00 2001 From: AndrewWood94 Date: Tue, 21 May 2024 15:53:42 +0100 Subject: [PATCH 086/548] Add authorised_assay_assets function to data_files_helper --- app/helpers/data_files_helper.rb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/app/helpers/data_files_helper.rb b/app/helpers/data_files_helper.rb index 67d9d12f46..917fe91da2 100644 --- a/app/helpers/data_files_helper.rb +++ b/app/helpers/data_files_helper.rb @@ -3,6 +3,10 @@ def authorised_data_files(projects = nil) authorised_assets(DataFile, projects) end + def authorised_assay_assets(data_file) + data_file.assay_assets.where(assay_id: authorised_assays.collect(&:id)) + end + def split_into_two(ahash = {}) return [{}, {}] if ahash.nil? return [ahash, {}] if ahash.length < 2 From f3b365c4b47e4303a5c456111b55851686090b17 Mon Sep 17 00:00:00 2001 From: AndrewWood94 Date: Tue, 21 May 2024 15:55:49 +0100 Subject: [PATCH 087/548] Only show authorised assays when extracting samples --- app/views/data_files/confirm_extraction.html.erb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/app/views/data_files/confirm_extraction.html.erb b/app/views/data_files/confirm_extraction.html.erb index c163b63d65..66bc8d2084 100644 --- a/app/views/data_files/confirm_extraction.html.erb +++ b/app/views/data_files/confirm_extraction.html.erb @@ -56,11 +56,11 @@ <%= hidden_field_tag(:sample_type_id, @sample_type.id) if @sample_type %> <%= hidden_field_tag(:confirm, 'true') %> - <% if @data_file.assay_assets.any? %> + <% if authorised_assays.intersect?(@data_file.assays) %>

    Link to assays

    This data file is linked to the following assays. Check the corresponding checkbox to also link the above samples to that assay. - <% @data_file.assay_assets.each do |aa| %> + <% authorised_assay_assets(@data_file).each do |aa| %>
    diff --git a/config/routes.rb b/config/routes.rb index 016f0963ae..e917fa8602 100644 --- a/config/routes.rb +++ b/config/routes.rb @@ -513,6 +513,7 @@ post :execute get :simulate post :simulate + post :copasi_simulate end resources :model_images, only: [:show] resources :people, :programmes, :projects, :investigations, :assays, :studies, :publications, :events, :collections, :organisms, :human_diseases, only: [:index] diff --git a/lib/seek/copasi/simulator.rb b/lib/seek/copasi/simulator.rb new file mode 100644 index 0000000000..070ae70641 --- /dev/null +++ b/lib/seek/copasi/simulator.rb @@ -0,0 +1,25 @@ +module Seek + module Copasi + module Simulator + extend ActiveSupport::Concern + + included do + before_action :find_display_asset_for_copasi, only: [:copasi_simulate] + end + + def copasi_simulate + @model = Model.find_by_id(params[:id]) + @content_blob = @model.content_blobs.first + render 'copasi_simulate' + end + + def select_copasi_content_blob + end + + def find_display_asset_for_copasi + find_display_asset Model.find_by_id(params[:id]) + end + end + end +end + From ced0bde54100cb387de9164759dba64c9633b63a Mon Sep 17 00:00:00 2001 From: whomingbird Date: Tue, 18 Jun 2024 10:49:41 +0200 Subject: [PATCH 101/548] move 'plotly-2.27.0.min.js' to 'application.js' --- app/assets/javascripts/application.js | 3 ++- app/assets/javascripts/plotly-2.27.0.min.js | 8 ++++++++ app/views/models/copasi_simulate.html.erb | 1 - 3 files changed, 10 insertions(+), 2 deletions(-) create mode 100644 app/assets/javascripts/plotly-2.27.0.min.js diff --git a/app/assets/javascripts/application.js b/app/assets/javascripts/application.js index 45ee1b9384..3a572b9c44 100644 --- a/app/assets/javascripts/application.js +++ b/app/assets/javascripts/application.js @@ -78,5 +78,6 @@ //= require licenses //= require svg-pan-zoom-3.6.1/svg-pan-zoom.min //= require copasi -//= require copasijs.js +//= require copasijs +//= require plotly-2.27.0.min diff --git a/app/assets/javascripts/plotly-2.27.0.min.js b/app/assets/javascripts/plotly-2.27.0.min.js new file mode 100644 index 0000000000..4cf7d724b7 --- /dev/null +++ b/app/assets/javascripts/plotly-2.27.0.min.js @@ -0,0 +1,8 @@ +/** +* plotly.js v2.27.0 +* Copyright 2012-2023, Plotly, Inc. +* All rights reserved. +* Licensed under the MIT license +*/ +/*! For license information please see plotly.min.js.LICENSE.txt */ +!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.Plotly=e():t.Plotly=e()}(self,(function(){return function(){var t={98847:function(t,e,r){"use strict";var n=r(71828),i={"X,X div":'direction:ltr;font-family:"Open Sans",verdana,arial,sans-serif;margin:0;padding:0;',"X input,X button":'font-family:"Open Sans",verdana,arial,sans-serif;',"X input:focus,X button:focus":"outline:none;","X a":"text-decoration:none;","X a:hover":"text-decoration:none;","X .crisp":"shape-rendering:crispEdges;","X .user-select-none":"-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;","X svg":"overflow:hidden;","X svg a":"fill:#447adb;","X svg a:hover":"fill:#3c6dc5;","X .main-svg":"position:absolute;top:0;left:0;pointer-events:none;","X .main-svg 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n=w(J,K),i=n[0]+t,a=n[1]+r;R.call(c.setTranslate,i,a),S("x",m(y,t,"x",T,e)),S("y",m(x,r,"y",T,e)),e.axref===e.xref&&S("ax",m(y,t,"ax",T,e)),e.ayref===e.yref&&S("ay",m(x,r,"ay",T,e)),G.attr("transform",s(t,r)),I.attr({transform:"rotate("+P+","+i+","+a+")"})},doneFn:function(){i.call("_guiRelayout",t,E());var e=document.querySelector(".js-notes-box-panel");e&&e.redraw(e.selectedObj)}})}}};e.showarrow&&At(0,0),D&&d.init({element:R.node(),gd:t,prepFn:function(){kt=I.attr("transform")},moveFn:function(t,r){var n="pointer";if(e.showarrow)e.axref===e.xref?S("ax",m(y,t,"ax",T,e)):S("ax",e.ax+t),e.ayref===e.yref?S("ay",m(x,r,"ay",T.w,e)):S("ay",e.ay+r),At(t,r);else{if(a)return;var i,o;if(y)i=m(y,t,"x",T,e);else{var l=e._xsize/T.w,u=e.x+(e._xshift-e.xshift)/T.w-l/2;i=d.align(u+t/T.w,l,0,1,e.xanchor)}if(x)o=m(x,r,"y",T,e);else{var c=e._ysize/T.h,f=e.y-(e._yshift+e.yshift)/T.h-c/2;o=d.align(f-r/T.h,c,0,1,e.yanchor)}S("x",i),S("y",o),y&&x||(n=d.getCursor(y?.5:i,x?.5:o,e.xanchor,e.yanchor))}I.attr({transform:s(t,r)+kt}),p(R,n)},clickFn:function(r,n){e.captureevents&&t.emit("plotly_clickannotation",Z(n))},doneFn:function(){p(R),i.call("_guiRelayout",t,E());var e=document.querySelector(".js-notes-box-panel");e&&e.redraw(e.selectedObj)}})}}}t.exports={draw:function(t){var e=t._fullLayout;e._infolayer.selectAll(".annotation").remove();for(var r=0;r=0,x=e.indexOf("end")>=0,b=d.backoff*g+r.standoff,_=v.backoff*y+r.startstandoff;if("line"===p.nodeName){o={x:+t.attr("x1"),y:+t.attr("y1")},c={x:+t.attr("x2"),y:+t.attr("y2")};var w=o.x-c.x,T=o.y-c.y;if(h=(f=Math.atan2(T,w))+Math.PI,b&&_&&b+_>Math.sqrt(w*w+T*T))return void D();if(b){if(b*b>w*w+T*T)return void D();var k=b*Math.cos(f),A=b*Math.sin(f);c.x+=k,c.y+=A,t.attr({x2:c.x,y2:c.y})}if(_){if(_*_>w*w+T*T)return void D();var M=_*Math.cos(f),S=_*Math.sin(f);o.x-=M,o.y-=S,t.attr({x1:o.x,y1:o.y})}}else if("path"===p.nodeName){var E=p.getTotalLength(),L="";if(E1){u=!0;break}}u?t.fullLayout._infolayer.select(".annotation-"+t.id+'[data-index="'+s+'"]').remove():(l._pdata=i(t.glplot.cameraParams,[e.xaxis.r2l(l.x)*r[0],e.yaxis.r2l(l.y)*r[1],e.zaxis.r2l(l.z)*r[2]]),n(t.graphDiv,l,s,t.id,l._xa,l._ya))}}},2468:function(t,e,r){"use strict";var n=r(73972),i=r(71828);t.exports={moduleType:"component",name:"annotations3d",schema:{subplots:{scene:{annotations:r(26997)}}},layoutAttributes:r(26997),handleDefaults:r(20226),includeBasePlot:function(t,e){var r=n.subplotsRegistry.gl3d;if(r)for(var a=r.attrRegex,o=Object.keys(t),s=0;s=0))return t;if(3===o)n[o]>1&&(n[o]=1);else if(n[o]>=1)return t}var s=Math.round(255*n[0])+", "+Math.round(255*n[1])+", "+Math.round(255*n[2]);return a?"rgba("+s+", "+n[3]+")":"rgb("+s+")"}o.tinyRGB=function(t){var e=t.toRgb();return"rgb("+Math.round(e.r)+", "+Math.round(e.g)+", 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pt=Math.pow(10,Math.floor(Math.log(ht)/Math.LN10));ct*=pt*u.roundUp(ht/pt,[2,5,10]),(Math.abs(Z.start)/Z.size+1e-6)%1<2e-6&&(lt.tick0=0)}lt.dtick=ct}lt.domain=o?[ot+O/B.h,ot+Q-O/B.h]:[ot+P/B.w,ot+Q-P/B.w],lt.setScale(),t.attr("transform",c(Math.round(B.l),Math.round(B.t)));var dt,vt=t.select("."+A.cbtitleunshift).attr("transform",c(-Math.round(B.l),-Math.round(B.t))),gt=lt.ticklabelposition,yt=lt.title.font.size,mt=t.select("."+A.cbaxis),xt=0,bt=0;function _t(n,i){var a={propContainer:lt,propName:e._propPrefix+"title",traceIndex:e._traceIndex,_meta:e._meta,placeholder:F._dfltTitle.colorbar,containerGroup:t.select("."+A.cbtitle)},o="h"===n.charAt(0)?n.substr(1):"h"+n;t.selectAll("."+o+",."+o+"-math-group").remove(),v.draw(r,n,f(a,i||{}))}return u.syncOrAsync([a.previousPromises,function(){var t,e;(o&&ut||!o&&!ut)&&("top"===V&&(t=P+B.l+tt*I,e=O+B.t+et*(1-ot-Q)+3+.75*yt),"bottom"===V&&(t=P+B.l+tt*I,e=O+B.t+et*(1-ot)-3-.25*yt),"right"===V&&(e=O+B.t+et*D+3+.75*yt,t=P+B.l+tt*ot),_t(lt._id+"title",{attributes:{x:t,y:e,"text-anchor":o?"start":"middle"}}))},function(){if(!o&&!ut||o&&ut){var a,l=t.select("."+A.cbtitle),f=l.select("text"),h=[-M/2,M/2],d=l.select(".h"+lt._id+"title-math-group").node(),v=15.6;if(f.node()&&(v=parseInt(f.node().style.fontSize,10)*w),d?(a=p.bBox(d),bt=a.width,(xt=a.height)>v&&(h[1]-=(xt-v)/2)):f.node()&&!f.classed(A.jsPlaceholder)&&(a=p.bBox(f.node()),bt=a.width,xt=a.height),o){if(xt){if(xt+=5,"top"===V)lt.domain[1]-=xt/B.h,h[1]*=-1;else{lt.domain[0]+=xt/B.h;var y=g.lineCount(f);h[1]+=(1-y)*v}l.attr("transform",c(h[0],h[1])),lt.setScale()}}else bt&&("right"===V&&(lt.domain[0]+=(bt+yt/2)/B.w),l.attr("transform",c(h[0],h[1])),lt.setScale())}t.selectAll("."+A.cbfills+",."+A.cblines).attr("transform",o?c(0,Math.round(B.h*(1-lt.domain[1]))):c(Math.round(B.w*lt.domain[0]),0)),mt.attr("transform",o?c(0,Math.round(-B.t)):c(Math.round(-B.l),0));var m=t.select("."+A.cbfills).selectAll("rect."+A.cbfill).attr("style","").data(W);m.enter().append("rect").classed(A.cbfill,!0).attr("style",""),m.exit().remove();var x=H.map(lt.c2p).map(Math.round).sort((function(t,e){return t-e}));m.each((function(t,a){var s=[0===a?H[0]:(W[a]+W[a-1])/2,a===W.length-1?H[1]:(W[a]+W[a+1])/2].map(lt.c2p).map(Math.round);o&&(s[1]=u.constrain(s[1]+(s[1]>s[0])?1:-1,x[0],x[1]));var l=n.select(this).attr(o?"x":"y",rt).attr(o?"y":"x",n.min(s)).attr(o?"width":"height",Math.max(J,2)).attr(o?"height":"width",Math.max(n.max(s)-n.min(s),2));if(e._fillgradient)p.gradient(l,r,e._id,o?"vertical":"horizontalreversed",e._fillgradient,"fill");else{var 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N=S+M,j=(o?rt:st)-N/2-(o?P:0),H=(o?st:rt)-(o?$:O+g-w);t.select("."+A.cbbg).attr("x",j).attr("y",H).attr(o?"width":"height",Math.max(b-w,2)).attr(o?"height":"width",Math.max($+N,2)).call(d.fill,E).call(d.stroke,e.bordercolor).style("stroke-width",S);var q=v?Math.max(u-10,0):0;t.selectAll("."+A.cboutline).attr("x",(o?rt:st+P)+q).attr("y",(o?st+O-$:rt)+(f?xt:0)).attr(o?"width":"height",Math.max(J,2)).attr(o?"height":"width",Math.max($-(o?2*O+xt:2*P+q),2)).call(d.stroke,e.outlinecolor).style({fill:"none","stroke-width":M});var G=o?nt*b:0,Z=o?0:(1-it)*b-g;if(G=R?B.l-G:-G,Z=z?B.t-Z:-Z,t.attr("transform",c(G,Z)),!o&&(S||i(E).getAlpha()&&!i.equals(F.paper_bgcolor,E))){var Y=mt.selectAll("text"),W=Y[0].length,X=t.select("."+A.cbbg).node(),K=p.bBox(X),Q=p.getTranslate(t);Y.each((function(t,e){var r=W-1;if(0===e||e===r){var n,i=p.bBox(this),a=p.getTranslate(this);if(e===r){var o=i.right+a.x;(n=K.right+Q.x+st-S-2+I-o)>0&&(n=0)}else if(0===e){var s=i.left+a.x;(n=K.left+Q.x+st+S+2-s)<0&&(n=0)}n&&(W<3?this.setAttribute("transform","translate("+n+",0) "+this.getAttribute("transform")):this.setAttribute("visibility","hidden"))}}))}var tt={},et=T[L],at=k[L],ot=T[C],ct=k[C],ft=b-J;o?("pixels"===h?(tt.y=D,tt.t=$*ot,tt.b=$*ct):(tt.t=tt.b=0,tt.yt=D+l*ot,tt.yb=D-l*ct),"pixels"===_?(tt.x=I,tt.l=b*et,tt.r=b*at):(tt.l=ft*et,tt.r=ft*at,tt.xl=I-y*et,tt.xr=I+y*at)):("pixels"===h?(tt.x=I,tt.l=$*et,tt.r=$*at):(tt.l=tt.r=0,tt.xl=I+l*et,tt.xr=I-l*at),"pixels"===_?(tt.y=1-D,tt.t=b*ot,tt.b=b*ct):(tt.t=ft*ot,tt.b=ft*ct,tt.yt=D-y*ot,tt.yb=D+y*ct));var ht=e.y<.5?"b":"t",pt=e.x<.5?"l":"r";r._fullLayout._reservedMargin[e._id]={};var 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n=r(41940),i=r(35025),a=r(1426).extendDeepAll,o=r(30962).overrideAll,s=r(85594),l=r(44467).templatedArray,u=r(98292),c=l("step",{visible:{valType:"boolean",dflt:!0},method:{valType:"enumerated",values:["restyle","relayout","animate","update","skip"],dflt:"restyle"},args:{valType:"info_array",freeLength:!0,items:[{valType:"any"},{valType:"any"},{valType:"any"}]},label:{valType:"string"},value:{valType:"string"},execute:{valType:"boolean",dflt:!0}});t.exports=o(l("slider",{visible:{valType:"boolean",dflt:!0},active:{valType:"number",min:0,dflt:0},steps:c,lenmode:{valType:"enumerated",values:["fraction","pixels"],dflt:"fraction"},len:{valType:"number",min:0,dflt:1},x:{valType:"number",min:-2,max:3,dflt:0},pad:a(i({editType:"arraydraw"}),{},{t:{dflt:20}}),xanchor:{valType:"enumerated",values:["auto","left","center","right"],dflt:"left"},y:{valType:"number",min:-2,max:3,dflt:0},yanchor:{valType:"enumerated",values:["auto","top","middle","bottom"],dflt:"top"},transition:{duration:{valType:"number",min:0,dflt:150},easing:{valType:"enumerated",values:s.transition.easing.values,dflt:"cubic-in-out"}},currentvalue:{visible:{valType:"boolean",dflt:!0},xanchor:{valType:"enumerated",values:["left","center","right"],dflt:"left"},offset:{valType:"number",dflt:10},prefix:{valType:"string"},suffix:{valType:"string"},font:n({})},font:n({}),activebgcolor:{valType:"color",dflt:u.gripBgActiveColor},bgcolor:{valType:"color",dflt:u.railBgColor},bordercolor:{valType:"color",dflt:u.railBorderColor},borderwidth:{valType:"number",min:0,dflt:u.railBorderWidth},ticklen:{valType:"number",min:0,dflt:u.tickLength},tickcolor:{valType:"color",dflt:u.tickColor},tickwidth:{valType:"number",min:0,dflt:1},minorticklen:{valType:"number",min:0,dflt:u.minorTickLength}}),"arraydraw","from-root")},98292:function(t){"use 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r=e._dims,n=r.inputAreaLength-2*f.railInset,i=s.ensureSingle(t,"rect",f.railRectClass);i.attr({width:n,height:f.railWidth,rx:f.railRadius,ry:f.railRadius,"shape-rendering":"crispEdges"}).call(a.stroke,e.bordercolor).call(a.fill,e.bgcolor).style("stroke-width",e.borderwidth+"px"),o.setTranslate(i,f.railInset,.5*(r.inputAreaWidth-f.railWidth)+r.currentValueTotalHeight)}t.exports=function(t){var e=t._context.staticPlot,r=t._fullLayout,a=function(t,e){for(var r=t[f.name],n=[],i=0;i0?[0]:[]);function l(e){e._commandObserver&&(e._commandObserver.remove(),delete e._commandObserver),i.autoMargin(t,g(e))}if(s.enter().append("g").classed(f.containerClassName,!0).style("cursor",e?null:"ew-resize"),s.exit().each((function(){n.select(this).selectAll("g."+f.groupClassName).each(l)})).remove(),0!==a.length){var u=s.selectAll("g."+f.groupClassName).data(a,y);u.enter().append("g").classed(f.groupClassName,!0),u.exit().each(l).remove();for(var c=0;c0||_<0){var 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n=r(41940),i=r(22399),a=r(1426).extendFlat,o=r(30962).overrideAll,s=r(35025),l=r(44467).templatedArray,u=l("button",{visible:{valType:"boolean"},method:{valType:"enumerated",values:["restyle","relayout","animate","update","skip"],dflt:"restyle"},args:{valType:"info_array",freeLength:!0,items:[{valType:"any"},{valType:"any"},{valType:"any"}]},args2:{valType:"info_array",freeLength:!0,items:[{valType:"any"},{valType:"any"},{valType:"any"}]},label:{valType:"string",dflt:""},execute:{valType:"boolean",dflt:!0}});t.exports=o(l("updatemenu",{_arrayAttrRegexps:[/^updatemenus\[(0|[1-9][0-9]+)\]\.buttons/],visible:{valType:"boolean"},type:{valType:"enumerated",values:["dropdown","buttons"],dflt:"dropdown"},direction:{valType:"enumerated",values:["left","right","up","down"],dflt:"down"},active:{valType:"integer",min:-1,dflt:0},showactive:{valType:"boolean",dflt:!0},buttons:u,x:{valType:"number",min:-2,max:3,dflt:-.05},xanchor:{valType:"enumerated",values:["auto","left","center","right"],dflt:"right"},y:{valType:"number",min:-2,max:3,dflt:1},yanchor:{valType:"enumerated",values:["auto","top","middle","bottom"],dflt:"top"},pad:a(s({editType:"arraydraw"}),{}),font:n({}),bgcolor:{valType:"color"},bordercolor:{valType:"color",dflt:i.borderLine},borderwidth:{valType:"number",min:0,dflt:1,editType:"arraydraw"}}),"arraydraw","from-root")},75909:function(t){"use 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u=n.select(this);u.call(m,o,s,t).call(M,o,b),u.on("click",(function(){n.event.defaultPrevented||(s.execute&&(s.args2&&o.active===l?(v(t,o,0,e,r,a,-1),i.executeAPICommand(t,s.method,s.args2)):(v(t,o,0,e,r,a,l),i.executeAPICommand(t,s.method,s.args))),t.emit("plotly_buttonclicked",{menu:o,button:s,active:o.active}))})),u.on("mouseover",(function(){u.call(w)})),u.on("mouseout",(function(){u.call(T,o),c.call(_,o)}))})),c.call(_,o),x?(k.w=Math.max(y.openWidth,y.headerWidth),k.h=b.y-k.t):(k.w=b.x-k.l,k.h=Math.max(y.openHeight,y.headerHeight)),k.direction=o.direction,a&&(c.size()?function(t,e,r,n,i,a){var o,s,l,u=i.direction,c="up"===u||"down"===u,h=i._dims,p=i.active;if(c)for(s=0,l=0;l0?[0]:[]);if(o.enter().append("g").classed(f.containerClassName,!0).style("cursor","pointer"),o.exit().each((function(){n.select(this).selectAll("g."+f.headerGroupClassName).each(a)})).remove(),0!==r.length){var l=o.selectAll("g."+f.headerGroupClassName).data(r,p);l.enter().append("g").classed(f.headerGroupClassName,!0);for(var u=s.ensureSingle(o,"g",f.dropdownButtonGroupClassName,(function(t){t.style("pointer-events","all")})),c=0;cw,A=s.barLength+2*s.barPad,M=s.barWidth+2*s.barPad,S=d,E=g+y;E+M>u&&(E=u-M);var L=this.container.selectAll("rect.scrollbar-horizontal").data(k?[0]:[]);L.exit().on(".drag",null).remove(),L.enter().append("rect").classed("scrollbar-horizontal",!0).call(i.fill,s.barColor),k?(this.hbar=L.attr({rx:s.barRadius,ry:s.barRadius,x:S,y:E,width:A,height:M}),this._hbarXMin=S+A/2,this._hbarTranslateMax=w-A):(delete this.hbar,delete this._hbarXMin,delete this._hbarTranslateMax);var C=y>T,P=s.barWidth+2*s.barPad,O=s.barLength+2*s.barPad,I=d+v,D=g;I+P>l&&(I=l-P);var z=this.container.selectAll("rect.scrollbar-vertical").data(C?[0]:[]);z.exit().on(".drag",null).remove(),z.enter().append("rect").classed("scrollbar-vertical",!0).call(i.fill,s.barColor),C?(this.vbar=z.attr({rx:s.barRadius,ry:s.barRadius,x:I,y:D,width:P,height:O}),this._vbarYMin=D+O/2,this._vbarTranslateMax=T-O):(delete this.vbar,delete this._vbarYMin,delete this._vbarTranslateMax);var R=this.id,F=c-.5,B=C?f+P+.5:f+.5,N=h-.5,j=k?p+M+.5:p+.5,U=o._topdefs.selectAll("#"+R).data(k||C?[0]:[]);if(U.exit().remove(),U.enter().append("clipPath").attr("id",R).append("rect"),k||C?(this._clipRect=U.select("rect").attr({x:Math.floor(F),y:Math.floor(N),width:Math.ceil(B)-Math.floor(F),height:Math.ceil(j)-Math.floor(N)}),this.container.call(a.setClipUrl,R,this.gd),this.bg.attr({x:d,y:g,width:v,height:y})):(this.bg.attr({width:0,height:0}),this.container.on("wheel",null).on(".drag",null).call(a.setClipUrl,null),delete this._clipRect),k||C){var 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r=t[i[e]];r.visible?(this.enabled[e]=r.showspikes,this.colors[e]=n(r.spikecolor),this.drawSides[e]=r.spikesides,this.lineWidth[e]=r.spikethickness):(this.enabled[e]=!1,this.drawSides[e]=!1)}},t.exports=function(t){var e=new a;return e.merge(t),e}},96085:function(t,e,r){"use strict";t.exports=function(t){for(var e=t.axesOptions,r=t.glplot.axesPixels,s=t.fullSceneLayout,l=[[],[],[]],u=0;u<3;++u){var c=s[a[u]];if(c._length=(r[u].hi-r[u].lo)*r[u].pixelsPerDataUnit/t.dataScale[u],Math.abs(c._length)===1/0||isNaN(c._length))l[u]=[];else{c._input_range=c.range.slice(),c.range[0]=r[u].lo/t.dataScale[u],c.range[1]=r[u].hi/t.dataScale[u],c._m=1/(t.dataScale[u]*r[u].pixelsPerDataUnit),c.range[0]===c.range[1]&&(c.range[0]-=1,c.range[1]+=1);var f=c.tickmode;if("auto"===c.tickmode){c.tickmode="linear";var h=c.nticks||i.constrain(c._length/40,4,9);n.autoTicks(c,Math.abs(c.range[1]-c.range[0])/h)}for(var p=n.calcTicks(c,{msUTC:!0}),d=0;d/g," 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F=x[u=(l=c[M[o]]).type];R[o]=Math.pow(F.acc,1/F.count)/p[o]}g="data"===D||Math.max.apply(null,R)/Math.min.apply(null,R)<=4?R:[1,1,1]}c.aspectratio.x=f.aspectratio.x=g[0],c.aspectratio.y=f.aspectratio.y=g[1],c.aspectratio.z=f.aspectratio.z=g[2],n.glplot.setAspectratio(c.aspectratio),n.viewInitial.aspectratio||(n.viewInitial.aspectratio={x:c.aspectratio.x,y:c.aspectratio.y,z:c.aspectratio.z}),n.viewInitial.aspectmode||(n.viewInitial.aspectmode=c.aspectmode);var B=c.domain||null,N=e._size||null;if(B&&N){var j=n.container.style;j.position="absolute",j.left=N.l+B.x[0]*N.w+"px",j.top=N.t+(1-B.y[1])*N.h+"px",j.width=N.w*(B.x[1]-B.x[0])+"px",j.height=N.h*(B.y[1]-B.y[0])+"px"}n.glplot.redraw()}},k.destroy=function(){var t=this;t.glplot&&(t.camera.mouseListener.enabled=!1,t.container.removeEventListener("wheel",t.camera.wheelListener),t.camera=null,t.glplot.dispose(),t.container.parentNode.removeChild(t.container),t.glplot=null)},k.getCamera=function(){var t,e=this;return e.camera.view.recalcMatrix(e.camera.view.lastT()),{up:{x:(t=e.camera).up[0],y:t.up[1],z:t.up[2]},center:{x:t.center[0],y:t.center[1],z:t.center[2]},eye:{x:t.eye[0],y:t.eye[1],z:t.eye[2]},projection:{type:!0===t._ortho?"orthographic":"perspective"}}},k.setViewport=function(t){var e,r=this,n=t.camera;r.camera.lookAt.apply(this,[[(e=n).eye.x,e.eye.y,e.eye.z],[e.center.x,e.center.y,e.center.z],[e.up.x,e.up.y,e.up.z]]),r.glplot.setAspectratio(t.aspectratio),"orthographic"===n.projection.type!==r.camera._ortho&&(r.glplot.redraw(),r.glplot.clearRGBA(),r.glplot.dispose(),r.initializeGLPlot())},k.isCameraChanged=function(t){var e=this.getCamera(),r=f.nestedProperty(t,this.id+".camera").get();function n(t,e,r,n){var i=["up","center","eye"],a=["x","y","z"];return e[i[r]]&&t[i[r]][a[n]]===e[i[r]][a[n]]}var i=!1;if(void 0===r)i=!0;else{for(var a=0;a<3;a++)for(var o=0;o<3;o++)if(!n(e,r,a,o)){i=!0;break}(!r.projection||e.projection&&e.projection.type!==r.projection.type)&&(i=!0)}return 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O=f.selectAll("g.value-bullet").data([c.gauge.bar]);O.enter().append("g").classed("value-bullet",!0).append("rect"),O.select("rect").attr("height",M).attr("y",(A-M)/2).call(T),w(b)?O.select("rect").transition().duration(b.duration).ease(b.easing).each("end",(function(){_&&_()})).each("interrupt",(function(){_&&_()})).attr("width",Math.max(0,i.c2p(Math.min(c.gauge.axis.range[1],r[0].y)))):O.select("rect").attr("width","number"==typeof r[0].y?Math.max(0,i.c2p(Math.min(c.gauge.axis.range[1],r[0].y))):0),O.exit().remove();var I=r.filter((function(){return c.gauge.threshold.value||0===c.gauge.threshold.value})),D=f.selectAll("g.threshold-bullet").data(I);D.enter().append("g").classed("threshold-bullet",!0).append("line"),D.select("line").attr("x1",i.c2p(c.gauge.threshold.value)).attr("x2",i.c2p(c.gauge.threshold.value)).attr("y1",(1-c.gauge.threshold.thickness)/2*A).attr("y2",(1-(1-c.gauge.threshold.thickness)/2)*A).call(m.stroke,c.gauge.threshold.line.color).style("stroke-width",c.gauge.threshold.line.width),D.exit().remove();var z=f.selectAll("g.gauge-outline").data([g]);z.enter().append("g").classed("gauge-outline",!0).append("rect"),z.select("rect").call(L).call(T),z.exit().remove()}(t,0,e,{gauge:W,layer:X,size:B,gaugeBg:C,gaugeOutline:P,transitionOpts:r,onComplete:g});var J=I.selectAll("text.title").data(e);J.exit().remove(),J.enter().append("text").classed("title",!0),J.attr("text-anchor",(function(){return 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n=r(50693),i=r(12663).axisHoverFormat,a=r(5386).fF,o=r(2418),s=r(9012),l=r(1426).extendFlat,u=r(30962).overrideAll,c=t.exports=u(l({x:{valType:"data_array"},y:{valType:"data_array"},z:{valType:"data_array"},value:{valType:"data_array"},isomin:{valType:"number"},isomax:{valType:"number"},surface:{show:{valType:"boolean",dflt:!0},count:{valType:"integer",dflt:2,min:1},fill:{valType:"number",min:0,max:1,dflt:1},pattern:{valType:"flaglist",flags:["A","B","C","D","E"],extras:["all","odd","even"],dflt:"all"}},spaceframe:{show:{valType:"boolean",dflt:!1},fill:{valType:"number",min:0,max:1,dflt:.15}},slices:{x:{show:{valType:"boolean",dflt:!1},locations:{valType:"data_array",dflt:[]},fill:{valType:"number",min:0,max:1,dflt:1}},y:{show:{valType:"boolean",dflt:!1},locations:{valType:"data_array",dflt:[]},fill:{valType:"number",min:0,max:1,dflt:1}},z:{show:{valType:"boolean",dflt:!1},locations:{valType:"data_array",dflt:[]},fill:{valType:"number",min:0,max:1,dflt:1}}},caps:{x:{show:{valType:"boolean",dflt:!0},fill:{valType:"number",min:0,max:1,dflt:1}},y:{show:{valType:"boolean",dflt:!0},fill:{valType:"number",min:0,max:1,dflt:1}},z:{show:{valType:"boolean",dflt:!0},fill:{valType:"number",min:0,max:1,dflt:1}}},text:{valType:"string",dflt:"",arrayOk:!0},hovertext:{valType:"string",dflt:"",arrayOk:!0},hovertemplate:a(),xhoverformat:i("x"),yhoverformat:i("y"),zhoverformat:i("z"),valuehoverformat:i("value",1),showlegend:l({},s.showlegend,{dflt:!1})},n("",{colorAttr:"`value`",showScaleDflt:!0,editTypeOverride:"calc"}),{opacity:o.opacity,lightposition:o.lightposition,lighting:o.lighting,flatshading:o.flatshading,contour:o.contour,hoverinfo:l({},s.hoverinfo)}),"calc","nested");c.flatshading.dflt=!0,c.lighting.facenormalsepsilon.dflt=0,c.x.editType=c.y.editType=c.z.editType=c.value.editType="calc+clearAxisTypes",c.transforms=void 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n=r(50693),i=r(12663).axisHoverFormat,a=r(5386).fF,o=r(54532),s=r(9012),l=r(1426).extendFlat;t.exports=l({x:{valType:"data_array",editType:"calc+clearAxisTypes"},y:{valType:"data_array",editType:"calc+clearAxisTypes"},z:{valType:"data_array",editType:"calc+clearAxisTypes"},i:{valType:"data_array",editType:"calc"},j:{valType:"data_array",editType:"calc"},k:{valType:"data_array",editType:"calc"},text:{valType:"string",dflt:"",arrayOk:!0,editType:"calc"},hovertext:{valType:"string",dflt:"",arrayOk:!0,editType:"calc"},hovertemplate:a({editType:"calc"}),xhoverformat:i("x"),yhoverformat:i("y"),zhoverformat:i("z"),delaunayaxis:{valType:"enumerated",values:["x","y","z"],dflt:"z",editType:"calc"},alphahull:{valType:"number",dflt:-1,editType:"calc"},intensity:{valType:"data_array",editType:"calc"},intensitymode:{valType:"enumerated",values:["vertex","cell"],dflt:"vertex",editType:"calc"},color:{valType:"color",editType:"calc"},vertexcolor:{valType:"data_array",editType:"calc"},facecolor:{valType:"data_array",editType:"calc"},transforms:void 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n=r(9330).gl_mesh3d,i=r(9330).delaunay_triangulate,a=r(9330).alpha_shape,o=r(9330).convex_hull,s=r(81697).parseColorScale,l=r(78614),u=r(21081).extractOpts,c=r(90060);function f(t,e,r){this.scene=t,this.uid=r,this.mesh=e,this.name="",this.color="#fff",this.data=null,this.showContour=!1}var h=f.prototype;function p(t){for(var e=[],r=t.length,n=0;n=e-.5)return!1;return!0}h.handlePick=function(t){if(t.object===this.mesh){var e=t.index=t.data.index;t.data._cellCenter?t.traceCoordinate=t.data.dataCoordinate:t.traceCoordinate=[this.data.x[e],this.data.y[e],this.data.z[e]];var r=this.data.hovertext||this.data.text;return Array.isArray(r)&&void 0!==r[e]?t.textLabel=r[e]:r&&(t.textLabel=r),!0}},h.update=function(t){var e=this.scene,r=e.fullSceneLayout;this.data=t;var n,f=t.x.length,h=c(d(r.xaxis,t.x,e.dataScale[0],t.xcalendar),d(r.yaxis,t.y,e.dataScale[1],t.ycalendar),d(r.zaxis,t.z,e.dataScale[2],t.zcalendar));if(t.i&&t.j&&t.k){if(t.i.length!==t.j.length||t.j.length!==t.k.length||!g(t.i,f)||!g(t.j,f)||!g(t.k,f))return;n=c(v(t.i),v(t.j),v(t.k))}else n=0===t.alphahull?o(h):t.alphahull>0?a(t.alphahull,h):function(t,e){for(var r=["x","y","z"].indexOf(t),n=[],a=e.length,o=0;oy):g=A>w,y=A;var M=u(w,T,k,A);M.pos=_,M.yc=(w+A)/2,M.i=b,M.dir=g?"increasing":"decreasing",M.x=M.pos,M.y=[k,T],m&&(M.orig_p=r[b]),d&&(M.tx=e.text[b]),v&&(M.htx=e.hovertext[b]),x.push(M)}else x.push({pos:_,empty:!0})}return e._extremes[l._id]=a.findExtremes(l,n.concat(h,f),{padded:!0}),x.length&&(x[0].t={labels:{open:i(t,"open:")+" ",high:i(t,"high:")+" ",low:i(t,"low:")+" ",close:i(t,"close:")+" "}}),x}t.exports={calc:function(t,e){var r=a.getFromId(t,e.xaxis),i=a.getFromId(t,e.yaxis),s=function(t,e,r){var i=r._minDiff;if(!i){var 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t.width})).attr("height",(function(t){return t.height})).attr("y",(function(t){return t.y})).attr("cursor",(function(t){return"fixed"===t.parcatsViewModel.arrangement?"default":"perpendicular"===t.parcatsViewModel.arrangement?"ns-resize":"move"})),k(D),E.exit().remove(),S.append("text").attr("class","catlabel").attr("pointer-events","none");var z=e._fullLayout.paper_bgcolor;M.select("text.catlabel").attr("text-anchor",(function(t){return d(t)?"start":"end"})).attr("alignment-baseline","middle").style("text-shadow",f.makeTextShadow(z)).style("fill","rgb(0, 0, 0)").attr("x",(function(t){return d(t)?t.width+5:-5})).attr("y",(function(t){return t.height/2})).text((function(t){return 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0,a.clickableOrdinalRange?r.filterSpecified&&e.multiselect?a.extent.push(a.clickableOrdinalRange):(a.extent=[a.clickableOrdinalRange],r.filterSpecified=!0):o?(a.extent=a.stayingIntervals,0===a.extent.length&&M(r)):M(r),a.brushCallback(e),b(t.parentNode),void a.brushEndCallback(r.filterSpecified?n.getConsolidated():[]);var s=function(){n.set(n.getConsolidated())};if(e.ordinal){var l=e.unitTickvals;l[l.length-1]a.newExtent[0];a.extent=a.stayingIntervals.concat(u?[a.newExtent]:[]),a.extent.length||M(r),a.brushCallback(e),u?b(t.parentNode,s):(s(),b(t.parentNode))}else s();a.brushEndCallback(r.filterSpecified?n.getConsolidated():[])}(this,t)})))}function A(t,e){return t[0]-e[0]}function M(t){t.filterSpecified=!1,t.svgBrush.extent=[[-1/0,1/0]]}function S(t){for(var e,r=t.slice(),n=[],i=r.shift();i;){for(e=i.slice();(i=r.shift())&&i[0]<=e[1];)e[1]=Math.max(e[1],i[1]);n.push(e)}return 1===n.length&&n[0][0]>n[0][1]&&(n=[]),n}t.exports={makeBrush:function(t,e,r,n,i,a){var o,l=function(){var t,e,r=[];return{set:function(n){1===(r=n.map((function(t){return t.slice().sort(s)})).sort(A)).length&&r[0][0]===-1/0&&r[0][1]===1/0&&(r=[[0,-1]]),t=S(r),e=r.reduce((function(t,e){return[Math.min(t[0],e[0]),Math.max(t[1],e[1])]}),[1/0,-1/0])},get:function(){return r.slice()},getConsolidated:function(){return t},getBounds:function(){return e}}}();return l.set(r),{filter:l,filterSpecified:e,svgBrush:{extent:[],brushStartCallback:n,brushCallback:(o=i,function(t){var e=t.brush,r=function(t){return t.svgBrush.extent.map((function(t){return t.slice()}))}(e),n=r.slice();e.filter.set(n),o()}),brushEndCallback:a}}},ensureAxisBrush:function(t,e,r){var i=t.selectAll("."+n.cn.axisBrush).data(o,a);i.enter().append("g").classed(n.cn.axisBrush,!0),function(t,e,r){var i=r._context.staticPlot,a=t.selectAll(".background").data(o);a.enter().append("rect").classed("background",!0).call(d).call(v).style("pointer-events",i?"none":"auto").attr("transform",l(0,n.verticalPadding)),a.call(k).attr("height",(function(t){return t.height-n.verticalPadding}));var s=t.selectAll(".highlight-shadow").data(o);s.enter().append("line").classed("highlight-shadow",!0).attr("x",-n.bar.width/2).attr("stroke-width",n.bar.width+n.bar.strokeWidth).attr("stroke",e).attr("opacity",n.bar.strokeOpacity).attr("stroke-linecap","butt"),s.attr("y1",(function(t){return t.height})).call(x);var u=t.selectAll(".highlight").data(o);u.enter().append("line").classed("highlight",!0).attr("x",-n.bar.width/2).attr("stroke-width",n.bar.width-n.bar.strokeWidth).attr("stroke",n.bar.fillColor).attr("opacity",n.bar.fillOpacity).attr("stroke-linecap","butt"),u.attr("y1",(function(t){return t.height})).call(x)}(i,e,r)},cleanRanges:function(t,e){if(Array.isArray(t[0])?(t=t.map((function(t){return t.sort(s)})),t=e.multiselect?S(t.sort(A)):[t[0]]):t=[t.sort(s)],e.tickvals){var r=e.tickvals.slice().sort(s);if(!(t=t.map((function(t){var e=[p(0,r,t[0],[]),p(1,r,t[1],[])];if(e[1]>e[0])return e})).filter((function(t){return t}))).length)return}return t.length>1?t:t[0]}}},71791:function(t,e,r){"use strict";t.exports={attributes:r(73362),supplyDefaults:r(3633),calc:r(24639),colorbar:{container:"line",min:"cmin",max:"cmax"},moduleType:"trace",name:"parcoords",basePlotModule:r(49351),categories:["gl","regl","noOpacity","noHover"],meta:{}}},49351:function(t,e,r){"use strict";var n=r(39898),i=r(27659).a0,a=r(21341),o=r(77922);e.name="parcoords",e.plot=function(t){var e=i(t.calcdata,"parcoords")[0];e.length&&a(t,e)},e.clean=function(t,e,r,n){var i=n._has&&n._has("parcoords"),a=e._has&&e._has("parcoords");i&&!a&&(n._paperdiv.selectAll(".parcoords").remove(),n._glimages.selectAll("*").remove())},e.toSVG=function(t){var e=t._fullLayout._glimages,r=n.select(t).selectAll(".svg-container");r.filter((function(t,e){return e===r.size()-1})).selectAll(".gl-canvas-context, .gl-canvas-focus").each((function(){var t=this,r=t.toDataURL("image/png");e.append("svg:image").attr({xmlns:o.svg,"xlink:href":r,preserveAspectRatio:"none",x:0,y:0,width:t.style.width,height:t.style.height})})),window.setTimeout((function(){n.selectAll("#filterBarPattern").attr("id","filterBarPattern")}),60)}},24639:function(t,e,r){"use strict";var n=r(71828).isArrayOrTypedArray,i=r(21081),a=r(28984).wrap;t.exports=function(t,e){var r,o;return i.hasColorscale(e,"line")&&n(e.line.color)?(r=e.line.color,o=i.extractOpts(e.line).colorscale,i.calc(t,e,{vals:r,containerStr:"line",cLetter:"c"})):(r=function(t){for(var e=new Array(t),r=0;rf&&(n.log("parcoords traces support up to "+f+" dimensions at the moment"),d.splice(f));var v=s(t,e,{name:"dimensions",layout:l,handleItemDefaults:p}),g=function(t,e,r,o,s){var 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U=j.selectAll("."+m.cn.parcoordsControlView).data(v,d);U.enter().append("g").classed(m.cn.parcoordsControlView,!0),U.attr("transform",(function(t){return u(t.model.pad.l,t.model.pad.t)}));var V=U.selectAll("."+m.cn.yAxis).data((function(t){return t.dimensions}),d);V.enter().append("g").classed(m.cn.yAxis,!0),U.each((function(t){I(V,t,T)})),B.each((function(t){if(t.viewModel){!t.lineLayer||a?t.lineLayer=b(this,t):t.lineLayer.update(t),(t.key||0===t.key)&&(t.viewModel[t.key]=t.lineLayer);var e=!t.context||a;t.lineLayer.render(t.viewModel.panels,e)}})),V.attr("transform",(function(t){return u(t.xScale(t.xIndex),0)})),V.call(n.behavior.drag().origin((function(t){return t})).on("drag",(function(t){var e=t.parent;R.linePickActive(!1),t.x=Math.max(-m.overdrag,Math.min(t.model.width+m.overdrag,n.event.x)),t.canvasX=t.x*t.model.canvasPixelRatio,V.sort((function(t,e){return t.x-e.x})).each((function(e,r){e.xIndex=r,e.x=t===e?e.x:e.xScale(e.xIndex),e.canvasX=e.x*e.model.canvasPixelRatio})),I(V,e,T),V.filter((function(e){return 0!==Math.abs(t.xIndex-e.xIndex)})).attr("transform",(function(t){return u(t.xScale(t.xIndex),0)})),n.select(this).attr("transform",u(t.x,0)),V.each((function(r,n,i){i===t.parent.key&&(e.dimensions[n]=r)})),e.contextLayer&&e.contextLayer.render(e.panels,!1,!E(e)),e.focusLayer.render&&e.focusLayer.render(e.panels)})).on("dragend",(function(t){var e=t.parent;t.x=t.xScale(t.xIndex),t.canvasX=t.x*t.model.canvasPixelRatio,I(V,e,T),n.select(this).attr("transform",(function(t){return u(t.x,0)})),e.contextLayer&&e.contextLayer.render(e.panels,!1,!E(e)),e.focusLayer&&e.focusLayer.render(e.panels),e.pickLayer&&e.pickLayer.render(e.panels,!0),R.linePickActive(!0),a&&a.axesMoved&&a.axesMoved(e.key,e.dimensions.map((function(t){return t.crossfilterDimensionIndex})))}))),V.exit().remove();var H=V.selectAll("."+m.cn.axisOverlays).data(v,d);H.enter().append("g").classed(m.cn.axisOverlays,!0),H.selectAll("."+m.cn.axis).remove();var q=H.selectAll("."+m.cn.axis).data(v,d);q.enter().append("g").classed(m.cn.axis,!0),q.each((function(t){var e=t.model.height/t.model.tickDistance,r=t.domainScale,i=r.domain();n.select(this).call(n.svg.axis().orient("left").tickSize(4).outerTickSize(2).ticks(e,t.tickFormat).tickValues(t.ordinal?i:null).tickFormat((function(e){return y.isOrdinal(t)?e:D(t.model.dimensions[t.visibleIndex],e)})).scale(r)),f.font(q.selectAll("text"),t.model.tickFont)})),q.selectAll(".domain, .tick>line").attr("fill","none").attr("stroke","black").attr("stroke-opacity",.25).attr("stroke-width","1px"),q.selectAll("text").style("text-shadow",c.makeTextShadow(A)).style("cursor","default");var G=H.selectAll("."+m.cn.axisHeading).data(v,d);G.enter().append("g").classed(m.cn.axisHeading,!0);var 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X=W.selectAll("."+m.cn.axisExtentTopText).data(v,d);X.enter().append("text").classed(m.cn.axisExtentTopText,!0).call(P),X.text((function(t){return z(t,!0)})).each((function(t){f.font(n.select(this),t.model.rangeFont)}));var J=Y.selectAll("."+m.cn.axisExtentBottom).data(v,d);J.enter().append("g").classed(m.cn.axisExtentBottom,!0),J.attr("transform",(function(t){return u(0,t.model.height+m.axisExtentOffset)}));var K=J.selectAll("."+m.cn.axisExtentBottomText).data(v,d);K.enter().append("text").classed(m.cn.axisExtentBottomText,!0).attr("dy","0.75em").call(P),K.text((function(t){return z(t,!1)})).each((function(t){f.font(n.select(this),t.model.rangeFont)})),x.ensureAxisBrush(H,A,t)}},21341:function(t,e,r){"use strict";var n=r(17171),i=r(79749),a=r(1602).isVisible,o={};function s(t,e,r){var n=e.indexOf(r),i=t.indexOf(n);return-1===i&&(i+=e.length),i}(t.exports=function(t,e){var r=t._fullLayout;if(i(t,[],o)){var l={},u={},c={},f={},h=r._size;e.forEach((function(e,r){var 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n=r(9012),i=r(27670).Y,a=r(41940),o=r(22399),s=r(5386).fF,l=r(5386).si,u=r(1426).extendFlat,c=r(79952).u,f=a({editType:"plot",arrayOk:!0,colorEditType:"plot"});t.exports={labels:{valType:"data_array",editType:"calc"},label0:{valType:"number",dflt:0,editType:"calc"},dlabel:{valType:"number",dflt:1,editType:"calc"},values:{valType:"data_array",editType:"calc"},marker:{colors:{valType:"data_array",editType:"calc"},line:{color:{valType:"color",dflt:o.defaultLine,arrayOk:!0,editType:"style"},width:{valType:"number",min:0,dflt:0,arrayOk:!0,editType:"style"},editType:"calc"},pattern:c,editType:"calc"},text:{valType:"data_array",editType:"plot"},hovertext:{valType:"string",dflt:"",arrayOk:!0,editType:"style"},scalegroup:{valType:"string",dflt:"",editType:"calc"},textinfo:{valType:"flaglist",flags:["label","text","value","percent"],extras:["none"],editType:"calc"},hoverinfo:u({},n.hoverinfo,{flags:["label","text","value","percent","name"]}),hovertemplate:s({},{keys:["label","color","value","percent","text"]}),texttemplate:l({editType:"plot"},{keys:["label","color","value","percent","text"]}),textposition:{valType:"enumerated",values:["inside","outside","auto","none"],dflt:"auto",arrayOk:!0,editType:"plot"},textfont:u({},f,{}),insidetextorientation:{valType:"enumerated",values:["horizontal","radial","tangential","auto"],dflt:"auto",editType:"plot"},insidetextfont:u({},f,{}),outsidetextfont:u({},f,{}),automargin:{valType:"boolean",dflt:!1,editType:"plot"},title:{text:{valType:"string",dflt:"",editType:"plot"},font:u({},f,{}),position:{valType:"enumerated",values:["top left","top center","top right","middle center","bottom left","bottom center","bottom right"],editType:"plot"},editType:"plot"},domain:i({name:"pie",trace:!0,editType:"calc"}),hole:{valType:"number",min:0,max:1,dflt:0,editType:"calc"},sort:{valType:"boolean",dflt:!0,editType:"calc"},direction:{valType:"enumerated",values:["clockwise","counterclockwise"],dflt:"counterclockwise",editType:"calc"},rotation:{valType:"angle",dflt:0,editType:"calc"},pull:{valType:"number",min:0,max:1,dflt:0,arrayOk:!0,editType:"calc"},_deprecated:{title:{valType:"string",dflt:"",editType:"calc"},titlefont:u({},f,{}),titleposition:{valType:"enumerated",values:["top left","top center","top right","middle center","bottom left","bottom center","bottom right"],editType:"calc"}}}},13584:function(t,e,r){"use strict";var n=r(74875);e.name="pie",e.plot=function(t,r,i,a){n.plotBasePlot(e.name,t,r,i,a)},e.clean=function(t,r,i,a){n.cleanBasePlot(e.name,t,r,i,a)}},32354:function(t,e,r){"use strict";var n=r(92770),i=r(84267),a=r(7901),o={};function s(t){return function(e,r){return!!e&&!!(e=i(e)).isValid()&&(e=a.addOpacity(e,e.getAlpha()),t[r]||(t[r]=e),e)}}function l(t,e){var r,n=JSON.stringify(t),a=e[n];if(!a){for(a=t.slice(),r=0;r=0})),("funnelarea"===e.type?y:e.sort)&&a.sort((function(t,e){return e.v-t.v})),a[0]&&(a[0].vTotal=g),a},crossTraceCalc:function(t,e){var r=(e||{}).type;r||(r="pie");var n=t._fullLayout,i=t.calcdata,a=n[r+"colorway"],s=n["_"+r+"colormap"];n["extend"+r+"colors"]&&(a=l(a,o));for(var u=0,c=0;c0){s=!0;break}}s||(o=0)}return{hasLabels:r,hasValues:a,len:o}}function c(t,e,r,n,i){n("marker.line.width")&&n("marker.line.color",i?void 0:r.paper_bgcolor);var a=n("marker.colors");l(n,"marker.pattern",a),t.marker&&!e.marker.pattern.fgcolor&&(e.marker.pattern.fgcolor=t.marker.colors),e.marker.pattern.bgcolor||(e.marker.pattern.bgcolor=r.paper_bgcolor)}t.exports={handleLabelsAndValues:u,handleMarkerDefaults:c,supplyDefaults:function(t,e,r,n){function l(r,n){return i.coerce(t,e,a,r,n)}var f=u(l("labels"),l("values")),h=f.len;if(e._hasLabels=f.hasLabels,e._hasValues=f.hasValues,!e._hasLabels&&e._hasValues&&(l("label0"),l("dlabel")),h){e._length=h,c(t,e,n,l,!0),l("scalegroup");var p,d=l("text"),v=l("texttemplate");if(v||(p=l("textinfo",Array.isArray(d)?"text+percent":"percent")),l("hovertext"),l("hovertemplate"),v||p&&"none"!==p){var g=l("textposition");s(t,e,n,l,g,{moduleHasSelected:!1,moduleHasUnselected:!1,moduleHasConstrain:!1,moduleHasCliponaxis:!1,moduleHasTextangle:!1,moduleHasInsideanchor:!1}),(Array.isArray(g)||"auto"===g||"outside"===g)&&l("automargin"),("inside"===g||"auto"===g||Array.isArray(g))&&l("insidetextorientation")}o(e,n,l);var y=l("hole");if(l("title.text")){var m=l("title.position",y?"middle center":"top center");y||"middle center"!==m||(e.title.position="top center"),i.coerceFont(l,"title.font",n.font)}l("sort"),l("direction"),l("rotation"),l("pull")}else e.visible=!1}}},20007:function(t,e,r){"use strict";var n=r(23469).appendArrayMultiPointValues;t.exports=function(t,e){var r={curveNumber:e.index,pointNumbers:t.pts,data:e._input,fullData:e,label:t.label,color:t.color,value:t.v,percent:t.percent,text:t.text,bbox:t.bbox,v:t.v};return 1===t.pts.length&&(r.pointNumber=r.i=t.pts[0]),n(r,e,t.pts),"funnelarea"===e.type&&(delete r.v,delete r.i),r}},22209:function(t,e,r){"use strict";var n=r(91424),i=r(7901);t.exports=function(t,e,r,a){var o=r.marker.pattern;o&&o.shape?n.pointStyle(t,r,a,e):i.fill(t,e.color)}},53581:function(t,e,r){"use strict";var n=r(71828);function i(t){return-1!==t.indexOf("e")?t.replace(/[.]?0+e/,"e"):-1!==t.indexOf(".")?t.replace(/[.]?0+$/,""):t}e.formatPiePercent=function(t,e){var r=i((100*t).toPrecision(3));return n.numSeparate(r,e)+"%"},e.formatPieValue=function(t,e){var r=i(t.toPrecision(10));return n.numSeparate(r,e)},e.getFirstFilled=function(t,e){if(Array.isArray(t))for(var r=0;r"),name:f.hovertemplate||-1!==h.indexOf("name")?f.name:void 0,idealAlign:t.pxmid[0]<0?"left":"right",color:g.castOption(_.bgcolor,t.pts)||t.color,borderColor:g.castOption(_.bordercolor,t.pts),fontFamily:g.castOption(w.family,t.pts),fontSize:g.castOption(w.size,t.pts),fontColor:g.castOption(w.color,t.pts),nameLength:g.castOption(_.namelength,t.pts),textAlign:g.castOption(_.align,t.pts),hovertemplate:g.castOption(f.hovertemplate,t.pts),hovertemplateLabels:t,eventData:[y(t,f)]},{container:r._hoverlayer.node(),outerContainer:r._paper.node(),gd:e,inOut_bbox:T}),t.bbox=T[0],u._hasHoverLabel=!0}u._hasHoverEvent=!0,e.emit("plotly_hover",{points:[y(t,f)],event:n.event})}})),t.on("mouseout",(function(t){var r=e._fullLayout,i=e._fullData[u.index],o=n.select(this).datum();u._hasHoverEvent&&(t.originalEvent=n.event,e.emit("plotly_unhover",{points:[y(o,i)],event:n.event}),u._hasHoverEvent=!1),u._hasHoverLabel&&(a.loneUnhover(r._hoverlayer.node()),u._hasHoverLabel=!1)})),t.on("click",(function(t){var r=e._fullLayout,i=e._fullData[u.index];e._dragging||!1===r.hovermode||(e._hoverdata=[y(t,i)],a.click(e,n.event))}))}function b(t,e,r){var n=g.castOption(t.insidetextfont.color,e.pts);!n&&t._input.textfont&&(n=g.castOption(t._input.textfont.color,e.pts));var i=g.castOption(t.insidetextfont.family,e.pts)||g.castOption(t.textfont.family,e.pts)||r.family,a=g.castOption(t.insidetextfont.size,e.pts)||g.castOption(t.textfont.size,e.pts)||r.size;return{color:n||o.contrast(e.color),family:i,size:a}}function _(t,e){for(var r,n,i=0;ie&&e>n||r=-4;g-=2)y(Math.PI*g,"tan");for(g=4;g>=-4;g-=2)y(Math.PI*(g+1),"tan")}if(f||p){for(g=4;g>=-4;g-=2)y(Math.PI*(g+1.5),"rad");for(g=4;g>=-4;g-=2)y(Math.PI*(g+.5),"rad")}}if(s||d||f){var m=Math.sqrt(t.width*t.width+t.height*t.height);if((a={scale:i*n*2/m,rCenter:1-i,rotate:0}).textPosAngle=(e.startangle+e.stopangle)/2,a.scale>=1)return a;v.push(a)}(d||p)&&((a=T(t,n,o,l,u)).textPosAngle=(e.startangle+e.stopangle)/2,v.push(a)),(d||h)&&((a=k(t,n,o,l,u)).textPosAngle=(e.startangle+e.stopangle)/2,v.push(a));for(var x=0,b=0,_=0;_=1)break}return v[x]}function T(t,e,r,n,i){e=Math.max(0,e-2*v);var a=t.width/t.height,o=S(a,n,e,r);return{scale:2*o/t.height,rCenter:A(a,o/e),rotate:M(i)}}function k(t,e,r,n,i){e=Math.max(0,e-2*v);var a=t.height/t.width,o=S(a,n,e,r);return{scale:2*o/t.width,rCenter:A(a,o/e),rotate:M(i+Math.PI/2)}}function A(t,e){return Math.cos(e)-t*e}function M(t){return(180/Math.PI*t+720)%180-90}function S(t,e,r,n){var i=t+1/(2*Math.tan(e));return r*Math.min(1/(Math.sqrt(i*i+.5)+i),n/(Math.sqrt(t*t+n/2)+t))}function E(t,e){return t.v!==e.vTotal||e.trace.hole?Math.min(1/(1+1/Math.sin(t.halfangle)),t.ring/2):1}function L(t,e){var r=e.pxmid[0],n=e.pxmid[1],i=t.width/2,a=t.height/2;return r<0&&(i*=-1),n<0&&(a*=-1),{scale:1,rCenter:1,rotate:0,x:i+Math.abs(a)*(i>0?1:-1)/2,y:a/(1+r*r/(n*n)),outside:!0}}function C(t,e){var r,n,i,a=t.trace,o={x:t.cx,y:t.cy},s={tx:0,ty:0};s.ty+=a.title.font.size,i=O(a),-1!==a.title.position.indexOf("top")?(o.y-=(1+i)*t.r,s.ty-=t.titleBox.height):-1!==a.title.position.indexOf("bottom")&&(o.y+=(1+i)*t.r);var l,u=t.r/(void 0===(l=t.trace.aspectratio)?1:l),c=e.w*(a.domain.x[1]-a.domain.x[0])/2;return-1!==a.title.position.indexOf("left")?(c+=u,o.x-=(1+i)*u,s.tx+=t.titleBox.width/2):-1!==a.title.position.indexOf("center")?c*=2:-1!==a.title.position.indexOf("right")&&(c+=u,o.x+=(1+i)*u,s.tx-=t.titleBox.width/2),r=c/t.titleBox.width,n=P(t,e)/t.titleBox.height,{x:o.x,y:o.y,scale:Math.min(r,n),tx:s.tx,ty:s.ty}}function P(t,e){var r=t.trace,n=e.h*(r.domain.y[1]-r.domain.y[0]);return Math.min(t.titleBox.height,n/2)}function O(t){var e,r=t.pull;if(!r)return 0;if(Array.isArray(r))for(r=0,e=0;er&&(r=t.pull[e]);return r}function I(t,e){for(var r=[],n=0;n1?c=(u=r.r)/i.aspectratio:u=(c=r.r)*i.aspectratio,l=(u*=(1+i.baseratio)/2)*c}o=Math.min(o,l/r.vTotal)}for(n=0;n")}if(a){var x=l.castOption(i,e.i,"texttemplate");if(x){var b=function(t){return{label:t.label,value:t.v,valueLabel:g.formatPieValue(t.v,n.separators),percent:t.v/r.vTotal,percentLabel:g.formatPiePercent(t.v/r.vTotal,n.separators),color:t.color,text:t.text,customdata:l.castOption(i,t.i,"customdata")}}(e),_=g.getFirstFilled(i.text,e.pts);(m(_)||""===_)&&(b.text=_),e.text=l.texttemplateString(x,b,t._fullLayout._d3locale,b,i._meta||{})}else e.text=""}}function R(t,e){var r=t.rotate*Math.PI/180,n=Math.cos(r),i=Math.sin(r),a=(e.left+e.right)/2,o=(e.top+e.bottom)/2;t.textX=a*n-o*i,t.textY=a*i+o*n,t.noCenter=!0}t.exports={plot:function(t,e){var r=t._context.staticPlot,a=t._fullLayout,h=a._size;d("pie",a),_(e,t),I(e,h);var v=l.makeTraceGroups(a._pielayer,e,"trace").each((function(e){var d=n.select(this),v=e[0],y=v.trace;!function(t){var e,r,n,i=t[0],a=i.r,o=i.trace,s=g.getRotationAngle(o.rotation),l=2*Math.PI/i.vTotal,u="px0",c="px1";if("counterclockwise"===o.direction){for(e=0;ei.vTotal/2?1:0,r.halfangle=Math.PI*Math.min(r.v/i.vTotal,.5),r.ring=1-o.hole,r.rInscribed=E(r,i))}(e),d.attr("stroke-linejoin","round"),d.each((function(){var m=n.select(this).selectAll("g.slice").data(e);m.enter().append("g").classed("slice",!0),m.exit().remove();var _=[[[],[]],[[],[]]],T=!1;m.each((function(i,o){if(i.hidden)n.select(this).selectAll("path,g").remove();else{i.pointNumber=i.i,i.curveNumber=y.index,_[i.pxmid[1]<0?0:1][i.pxmid[0]<0?0:1].push(i);var u=v.cx,c=v.cy,h=n.select(this),d=h.selectAll("path.surface").data([i]);if(d.enter().append("path").classed("surface",!0).style({"pointer-events":r?"none":"all"}),h.call(x,t,e),y.pull){var m=+g.castOption(y.pull,i.pts)||0;m>0&&(u+=m*i.pxmid[0],c+=m*i.pxmid[1])}i.cxFinal=u,i.cyFinal=c;var k=y.hole;if(i.v===v.vTotal){var A="M"+(u+i.px0[0])+","+(c+i.px0[1])+P(i.px0,i.pxmid,!0,1)+P(i.pxmid,i.px0,!0,1)+"Z";k?d.attr("d","M"+(u+k*i.px0[0])+","+(c+k*i.px0[1])+P(i.px0,i.pxmid,!1,k)+P(i.pxmid,i.px0,!1,k)+"Z"+A):d.attr("d",A)}else{var M=P(i.px0,i.px1,!0,1);if(k){var S=1-k;d.attr("d","M"+(u+k*i.px1[0])+","+(c+k*i.px1[1])+P(i.px1,i.px0,!1,k)+"l"+S*i.px0[0]+","+S*i.px0[1]+M+"Z")}else d.attr("d","M"+u+","+c+"l"+i.px0[0]+","+i.px0[1]+M+"Z")}z(t,i,v);var E=g.castOption(y.textposition,i.pts),C=h.selectAll("g.slicetext").data(i.text&&"none"!==E?[0]:[]);C.enter().append("g").classed("slicetext",!0),C.exit().remove(),C.each((function(){var r=l.ensureSingle(n.select(this),"text","",(function(t){t.attr("data-notex",1)})),h=l.ensureUniformFontSize(t,"outside"===E?function(t,e,r){return{color:g.castOption(t.outsidetextfont.color,e.pts)||g.castOption(t.textfont.color,e.pts)||r.color,family:g.castOption(t.outsidetextfont.family,e.pts)||g.castOption(t.textfont.family,e.pts)||r.family,size:g.castOption(t.outsidetextfont.size,e.pts)||g.castOption(t.textfont.size,e.pts)||r.size}}(y,i,a.font):b(y,i,a.font));r.text(i.text).attr({class:"slicetext",transform:"","text-anchor":"middle"}).call(s.font,h).call(f.convertToTspans,t);var d,m=s.bBox(r.node());if("outside"===E)d=L(m,i);else if(d=w(m,i,v),"auto"===E&&d.scale<1){var x=l.ensureUniformFontSize(t,y.outsidetextfont);r.call(s.font,x),d=L(m=s.bBox(r.node()),i)}var _=d.textPosAngle,k=void 0===_?i.pxmid:D(v.r,_);if(d.targetX=u+k[0]*d.rCenter+(d.x||0),d.targetY=c+k[1]*d.rCenter+(d.y||0),R(d,m),d.outside){var 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e=Math.sqrt(t.titleBox.width*t.titleBox.width+t.titleBox.height*t.titleBox.height);return{x:t.cx,y:t.cy,scale:t.trace.hole*t.r*2/e,tx:0,ty:-t.titleBox.height/2+t.trace.title.font.size}}(v):C(v,h),r.attr("transform",c(e.x,e.y)+u(Math.min(1,e.scale))+c(e.tx,e.ty))})),T&&function(t,e){var r,n,i,a,o,s,l,u,c,f,h,p,d;function v(t,e){return t.pxmid[1]-e.pxmid[1]}function y(t,e){return e.pxmid[1]-t.pxmid[1]}function m(t,r){r||(r={});var 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R=m.selectBatch[O]=s.selIndices2selPoints(C),F={};for(g=0;g")}function c(t){return t+"°"}}t.exports={hoverPoints:function(t,e,r){var o=t.cd,c=o[0].trace,f=t.xa,h=t.ya,p=t.subplot,d=[],v=l+c.uid+"-circle",g=c.cluster&&c.cluster.enabled;if(g){var y=p.map.queryRenderedFeatures(null,{layers:[v]});d=y.map((function(t){return t.id}))}var m=360*(e>=0?Math.floor((e+180)/360):Math.ceil((e-180)/360)),x=e-m;if(n.getClosest(o,(function(t){var e=t.lonlat;if(e[0]===s)return 1/0;if(g&&-1===d.indexOf(t.i+1))return 1/0;var n=i.modHalf(e[0],360),a=e[1],o=p.project([n,a]),l=o.x-f.c2p([x,a]),u=o.y-h.c2p([n,r]),c=Math.max(3,t.mrc||0);return Math.max(Math.sqrt(l*l+u*u)-c,1-3/c)}),t),!1!==t.index){var b=o[t.index],_=b.lonlat,w=[i.modHalf(_[0],360)+m,_[1]],T=f.c2p(w),k=h.c2p(w),A=b.mrc||1;t.x0=T-A,t.x1=T+A,t.y0=k-A,t.y1=k+A;var M={};M[c.subplot]={_subplot:p};var S=c._module.formatLabels(b,c,M);return 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s(t,e,r,n){this.type="scattermapbox",this.subplot=t,this.uid=e,this.clusterEnabled=r,this.isHidden=n,this.sourceIds={fill:"source-"+e+"-fill",line:"source-"+e+"-line",circle:"source-"+e+"-circle",symbol:"source-"+e+"-symbol",cluster:"source-"+e+"-circle",clusterCount:"source-"+e+"-circle"},this.layerIds={fill:a+e+"-fill",line:a+e+"-line",circle:a+e+"-circle",symbol:a+e+"-symbol",cluster:a+e+"-cluster",clusterCount:a+e+"-cluster-count"},this.below=null}var l=s.prototype;l.addSource=function(t,e,r){var i={type:"geojson",data:e.geojson};r&&r.enabled&&n.extendFlat(i,{cluster:!0,clusterMaxZoom:r.maxzoom});var a=this.subplot.map.getSource(this.sourceIds[t]);a?a.setData(e.geojson):this.subplot.map.addSource(this.sourceIds[t],i)},l.setSourceData=function(t,e){this.subplot.map.getSource(this.sourceIds[t]).setData(e.geojson)},l.addLayer=function(t,e,r){var n={type:e.type,id:this.layerIds[t],source:this.sourceIds[t],layout:e.layout,paint:e.paint};e.filter&&(n.filter=e.filter);for(var i,a=this.layerIds[t],o=this.subplot.getMapLayers(),s=0;s=0;r--){var i=e[r];n.removeLayer(c.layerIds[i])}t||n.removeSource(c.sourceIds.circle)}(t):function(t){for(var e=o.nonCluster,r=e.length-1;r>=0;r--){var i=e[r];n.removeLayer(c.layerIds[i]),t||n.removeSource(c.sourceIds[i])}}(t)}function h(t){l?function(t){t||c.addSource("circle",a.circle,e.cluster);for(var r=o.cluster,n=0;n=0;r--){var n=e[r];t.removeLayer(this.layerIds[n]),t.removeSource(this.sourceIds[n])}},t.exports=function(t,e){var r,n,a,l=e[0].trace,u=l.cluster&&l.cluster.enabled,c=!0!==l.visible,f=new s(t,l.uid,u,c),h=i(t.gd,e),p=f.below=t.belowLookup["trace-"+l.uid];if(u)for(f.addSource("circle",h.circle,l.cluster),r=0;r")}}t.exports={hoverPoints:function(t,e,r,a){var o=n(t,e,r,a);if(o&&!1!==o[0].index){var s=o[0];if(void 0===s.index)return o;var l=t.subplot,u=s.cd[s.index],c=s.trace;if(l.isPtInside(u))return s.xLabelVal=void 0,s.yLabelVal=void 0,i(u,c,l,s),s.hovertemplate=c.hovertemplate,o}},makeHoverPointText:i}},91271:function(t,e,r){"use strict";t.exports={moduleType:"trace",name:"scatterpolar",basePlotModule:r(23580),categories:["polar","symbols","showLegend","scatter-like"],attributes:r(81245),supplyDefaults:r(22184).supplyDefaults,colorbar:r(4898),formatLabels:r(98608),calc:r(26442),plot:r(45162),style:r(16296).style,styleOnSelect:r(16296).styleOnSelect,hoverPoints:r(59150).hoverPoints,selectPoints:r(98002),meta:{}}},45162:function(t,e,r){"use strict";var n=r(32663),i=r(50606).BADNUM;t.exports=function(t,e,r){for(var a=e.layers.frontplot.select("g.scatterlayer"),o=e.xaxis,s=e.yaxis,l={xaxis:o,yaxis:s,plot:e.framework,layerClipId:e._hasClipOnAxisFalse?e.clipIds.forTraces:null},u=e.radialAxis,c=e.angularAxis,f=0;f=u&&(m.marker.cluster=d.tree),m.marker&&(m.markerSel.positions=m.markerUnsel.positions=m.marker.positions=_),m.line&&_.length>1&&l.extendFlat(m.line,s.linePositions(t,p,_)),m.text&&(l.extendFlat(m.text,{positions:_},s.textPosition(t,p,m.text,m.marker)),l.extendFlat(m.textSel,{positions:_},s.textPosition(t,p,m.text,m.markerSel)),l.extendFlat(m.textUnsel,{positions:_},s.textPosition(t,p,m.text,m.markerUnsel))),m.fill&&!h.fill2d&&(h.fill2d=!0),m.marker&&!h.scatter2d&&(h.scatter2d=!0),m.line&&!h.line2d&&(h.line2d=!0),m.text&&!h.glText&&(h.glText=!0),h.lineOptions.push(m.line),h.fillOptions.push(m.fill),h.markerOptions.push(m.marker),h.markerSelectedOptions.push(m.markerSel),h.markerUnselectedOptions.push(m.markerUnsel),h.textOptions.push(m.text),h.textSelectedOptions.push(m.textSel),h.textUnselectedOptions.push(m.textUnsel),h.selectBatch.push([]),h.unselectBatch.push([]),d.x=w,d.y=T,d.rawx=w,d.rawy=T,d.r=g,d.theta=y,d.positions=_,d._scene=h,d.index=h.count,h.count++}})),a(t,e,r)}},t.exports.reglPrecompiled={}},48300:function(t,e,r){"use 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n=r(92770),i=r(50606).BADNUM,a=r(36922),o=r(75225),s=r(66279),l=r(47761).calcMarkerSize;t.exports=function(t,e){for(var r=t._fullLayout,u=e.subplot,c=r[u].realaxis,f=r[u].imaginaryaxis,h=c.makeCalcdata(e,"real"),p=f.makeCalcdata(e,"imag"),d=e._length,v=new Array(d),g=0;g")}}t.exports={hoverPoints:function(t,e,r,a){var o=n(t,e,r,a);if(o&&!1!==o[0].index){var s=o[0];if(void 0===s.index)return o;var l=t.subplot,u=s.cd[s.index],c=s.trace;if(l.isPtInside(u))return s.xLabelVal=void 0,s.yLabelVal=void 0,i(u,c,l,s),s.hovertemplate=c.hovertemplate,o}},makeHoverPointText:i}},85956:function(t,e,r){"use strict";t.exports={moduleType:"trace",name:"scattersmith",basePlotModule:r(7504),categories:["smith","symbols","showLegend","scatter-like"],attributes:r(48300),supplyDefaults:r(65269),colorbar:r(4898),formatLabels:r(62047),calc:r(30621),plot:r(12480),style:r(16296).style,styleOnSelect:r(16296).styleOnSelect,hoverPoints:r(11350).hoverPoints,selectPoints:r(98002),meta:{}}},12480:function(t,e,r){"use 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i=r._fullLayout,a=r._fullData[d.index],s=n.select(this).datum();if(d._hasHoverEvent&&(e.originalEvent=n.event,r.emit("plotly_unhover",{points:[f(s,a,h.eventDataKeys)],event:n.event}),d._hasHoverEvent=!1),d._hasHoverLabel&&(o.loneUnhover(i._hoverlayer.node()),d._hasHoverLabel=!1),y){var l=t.select("path.surface");h.styleOne(l,s,a,r,{hovered:!1})}})),t.on("click",(function(t){var e=r._fullLayout,a=r._fullData[d.index],s=g&&(u.isHierarchyRoot(t)||u.isLeaf(t)),c=u.getPtId(t),p=u.isEntry(t)?u.findEntryWithChild(v,c):u.findEntryWithLevel(v,c),y=u.getPtId(p),m={points:[f(t,a,h.eventDataKeys)],event:n.event};s||(m.nextLevel=y);var x=l.triggerHandler(r,"plotly_"+d.type+"click",m);if(!1!==x&&e.hovermode&&(r._hoverdata=[f(t,a,h.eventDataKeys)],o.click(r,n.event)),!s&&!1!==x&&!r._dragging&&!r._transitioning){i.call("_storeDirectGUIEdit",a,e._tracePreGUI[a.uid],{level:a.level});var b={data:[{level:y}],traces:[d.index]},_={frame:{redraw:!1,duration:h.transitionTime},transition:{duration:h.transitionTime,easing:h.transitionEasing},mode:"immediate",fromcurrent:!0};o.loneUnhover(e._hoverlayer.node()),i.call("animate",r,b,_)}}))}},2791:function(t,e,r){"use strict";var n=r(71828),i=r(7901),a=r(6964),o=r(53581);function s(t){return t.data.data.pid}e.findEntryWithLevel=function(t,r){var n;return r&&t.eachAfter((function(t){if(e.getPtId(t)===r)return n=t.copy()})),n||t},e.findEntryWithChild=function(t,r){var n;return t.eachAfter((function(t){for(var i=t.children||[],a=0;a0)},e.getMaxDepth=function(t){return t.maxdepth>=0?t.maxdepth:1/0},e.isHeader=function(t,r){return!(e.isLeaf(t)||t.depth===r._maxDepth-1)},e.getParent=function(t,r){return e.findEntryWithLevel(t,s(r))},e.listPath=function(t,r){var n=t.parent;if(!n)return[];var i=r?[n.data[r]]:[n];return e.listPath(n,r).concat(i)},e.getPath=function(t){return 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n=r(39898),i=r(674),a=r(81684).sX,o=r(91424),s=r(71828),l=r(63893),u=r(72597),c=u.recordMinTextSize,f=u.clearMinTextSize,h=r(14575),p=r(53581).getRotationAngle,d=h.computeTransform,v=h.transformInsideText,g=r(29969).styleOne,y=r(16688).resizeText,m=r(83523),x=r(7055),b=r(2791);function _(t,r,u,f){var h=t._context.staticPlot,y=t._fullLayout,_=!y.uniformtext.mode&&b.hasTransition(f),T=n.select(u).selectAll("g.slice"),k=r[0],A=k.trace,M=k.hierarchy,S=b.findEntryWithLevel(M,A.level),E=b.getMaxDepth(A),L=y._size,C=A.domain,P=L.w*(C.x[1]-C.x[0]),O=L.h*(C.y[1]-C.y[0]),I=.5*Math.min(P,O),D=k.cx=L.l+L.w*(C.x[1]+C.x[0])/2,z=k.cy=L.t+L.h*(1-C.y[0])-O/2;if(!S)return T.remove();var R=null,F={};_&&T.each((function(t){F[b.getPtId(t)]={rpx0:t.rpx0,rpx1:t.rpx1,x0:t.x0,x1:t.x1,transform:t.transform},!R&&b.isEntry(t)&&(R=t)}));var B=function(t){return i.partition().size([2*Math.PI,t.height+1])(t)}(S).descendants(),N=S.height+1,j=0,U=E;k.hasMultipleRoots&&b.isHierarchyRoot(S)&&(B=B.slice(1),N-=1,j=1,U+=1),B=B.filter((function(t){return t.y1<=U}));var V=p(A.rotation);V&&B.forEach((function(t){t.x0+=V,t.x1+=V}));var H=Math.min(N,E),q=function(t){return(t-j)/H*I},G=function(t,e){return[t*Math.cos(e),-t*Math.sin(e)]},Z=function(t){return s.pathAnnulus(t.rpx0,t.rpx1,t.x0,t.x1,D,z)},Y=function(t){return D+w(t)[0]*(t.transform.rCenter||0)+(t.transform.x||0)},W=function(t){return z+w(t)[1]*(t.transform.rCenter||0)+(t.transform.y||0)};(T=T.data(B,b.getPtId)).enter().append("g").classed("slice",!0),_?T.exit().transition().each((function(){var t=n.select(this);t.select("path.surface").transition().attrTween("d",(function(t){var e=function(t){var e,r=b.getPtId(t),n=F[r],i=F[b.getPtId(S)];if(i){var o=(t.x1>i.x1?2*Math.PI:0)+V;e=t.rpx1X?2*Math.PI:0)+V;e={x0:i,x1:i}}else e={rpx0:I,rpx1:I},s.extendFlat(e,$(t));else e={rpx0:0,rpx1:0};else 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n=r(78803);t.exports=function(t,e){e.surfacecolor?n(t,e,{vals:e.surfacecolor,containerStr:"",cLetter:"c"}):n(t,e,{vals:e.z,containerStr:"",cLetter:"c"})}},43768:function(t,e,r){"use strict";var n=r(9330).gl_surface3d,i=r(9330).ndarray,a=r(9330).ndarray_linear_interpolate.d2,o=r(824),s=r(43907),l=r(71828).isArrayOrTypedArray,u=r(81697).parseColorScale,c=r(78614),f=r(21081).extractOpts;function h(t,e,r){this.scene=t,this.uid=r,this.surface=e,this.data=null,this.showContour=[!1,!1,!1],this.contourStart=[null,null,null],this.contourEnd=[null,null,null],this.contourSize=[0,0,0],this.minValues=[1/0,1/0,1/0],this.maxValues=[-1/0,-1/0,-1/0],this.dataScaleX=1,this.dataScaleY=1,this.refineData=!0,this.objectOffset=[0,0,0]}var p=h.prototype;p.getXat=function(t,e,r,n){var i=l(this.data.x)?l(this.data.x[0])?this.data.x[e][t]:this.data.x[t]:t;return void 0===r?i:n.d2l(i,0,r)},p.getYat=function(t,e,r,n){var i=l(this.data.y)?l(this.data.y[0])?this.data.y[e][t]:this.data.y[e]:e;return void 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v(t,e){if(t0){r=d[n];break}return r}function m(t,e){if(!(t<1||e<1)){for(var r=g(t),n=g(e),i=1,a=0;a_;)r--,r/=y(r),++r1?n:1},p.refineCoords=function(t){for(var e=this.dataScaleX,r=this.dataScaleY,n=t[0].shape[0],a=t[0].shape[1],o=0|Math.floor(t[0].shape[0]*e+1),s=0|Math.floor(t[0].shape[1]*r+1),l=1+n+1,u=1+a+1,c=i(new Float32Array(l*u),[l,u]),f=[1/e,0,0,0,1/r,0,0,0,1],h=0;h0&&null!==this.contourStart[t]&&null!==this.contourEnd[t]&&this.contourEnd[t]>this.contourStart[t]))for(i[t]=!0,e=this.contourStart[t];ea&&(this.minValues[e]=a),this.maxValues[e]",maxDimensionCount:60,overdrag:45,releaseTransitionDuration:120,releaseTransitionEase:"cubic-out",scrollbarCaptureWidth:18,scrollbarHideDelay:1e3,scrollbarHideDuration:1e3,scrollbarOffset:5,scrollbarWidth:8,transitionDuration:100,transitionEase:"cubic-out",uplift:5,wrapSpacer:" ",wrapSplitCharacter:" 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xt=(u+(n=n+Math.imul(f,J)|0)|0)+((8191&(i=(i=i+Math.imul(f,K)|0)+Math.imul(h,J)|0))<<13)|0;u=((a=a+Math.imul(h,K)|0)+(i>>>13)|0)+(xt>>>26)|0,xt&=67108863,n=Math.imul(T,U),i=(i=Math.imul(T,V))+Math.imul(k,U)|0,a=Math.imul(k,V),n=n+Math.imul(b,q)|0,i=(i=i+Math.imul(b,G)|0)+Math.imul(_,q)|0,a=a+Math.imul(_,G)|0,n=n+Math.imul(y,Y)|0,i=(i=i+Math.imul(y,W)|0)+Math.imul(m,Y)|0,a=a+Math.imul(m,W)|0,n=n+Math.imul(d,J)|0,i=(i=i+Math.imul(d,K)|0)+Math.imul(v,J)|0,a=a+Math.imul(v,K)|0;var bt=(u+(n=n+Math.imul(f,Q)|0)|0)+((8191&(i=(i=i+Math.imul(f,tt)|0)+Math.imul(h,Q)|0))<<13)|0;u=((a=a+Math.imul(h,tt)|0)+(i>>>13)|0)+(bt>>>26)|0,bt&=67108863,n=Math.imul(M,U),i=(i=Math.imul(M,V))+Math.imul(S,U)|0,a=Math.imul(S,V),n=n+Math.imul(T,q)|0,i=(i=i+Math.imul(T,G)|0)+Math.imul(k,q)|0,a=a+Math.imul(k,G)|0,n=n+Math.imul(b,Y)|0,i=(i=i+Math.imul(b,W)|0)+Math.imul(_,Y)|0,a=a+Math.imul(_,W)|0,n=n+Math.imul(y,J)|0,i=(i=i+Math.imul(y,K)|0)+Math.imul(m,J)|0,a=a+Math.imul(m,K)|0,n=n+Math.imul(d,Q)|0,i=(i=i+Math.imul(d,tt)|0)+Math.imul(v,Q)|0,a=a+Math.imul(v,tt)|0;var _t=(u+(n=n+Math.imul(f,rt)|0)|0)+((8191&(i=(i=i+Math.imul(f,nt)|0)+Math.imul(h,rt)|0))<<13)|0;u=((a=a+Math.imul(h,nt)|0)+(i>>>13)|0)+(_t>>>26)|0,_t&=67108863,n=Math.imul(L,U),i=(i=Math.imul(L,V))+Math.imul(C,U)|0,a=Math.imul(C,V),n=n+Math.imul(M,q)|0,i=(i=i+Math.imul(M,G)|0)+Math.imul(S,q)|0,a=a+Math.imul(S,G)|0,n=n+Math.imul(T,Y)|0,i=(i=i+Math.imul(T,W)|0)+Math.imul(k,Y)|0,a=a+Math.imul(k,W)|0,n=n+Math.imul(b,J)|0,i=(i=i+Math.imul(b,K)|0)+Math.imul(_,J)|0,a=a+Math.imul(_,K)|0,n=n+Math.imul(y,Q)|0,i=(i=i+Math.imul(y,tt)|0)+Math.imul(m,Q)|0,a=a+Math.imul(m,tt)|0,n=n+Math.imul(d,rt)|0,i=(i=i+Math.imul(d,nt)|0)+Math.imul(v,rt)|0,a=a+Math.imul(v,nt)|0;var wt=(u+(n=n+Math.imul(f,at)|0)|0)+((8191&(i=(i=i+Math.imul(f,ot)|0)+Math.imul(h,at)|0))<<13)|0;u=((a=a+Math.imul(h,ot)|0)+(i>>>13)|0)+(wt>>>26)|0,wt&=67108863,n=Math.imul(O,U),i=(i=Math.imul(O,V))+Math.imul(I,U)|0,a=Math.imul(I,V),n=n+Math.imul(L,q)|0,i=(i=i+Math.imul(L,G)|0)+Math.imul(C,q)|0,a=a+Math.imul(C,G)|0,n=n+Math.imul(M,Y)|0,i=(i=i+Math.imul(M,W)|0)+Math.imul(S,Y)|0,a=a+Math.imul(S,W)|0,n=n+Math.imul(T,J)|0,i=(i=i+Math.imul(T,K)|0)+Math.imul(k,J)|0,a=a+Math.imul(k,K)|0,n=n+Math.imul(b,Q)|0,i=(i=i+Math.imul(b,tt)|0)+Math.imul(_,Q)|0,a=a+Math.imul(_,tt)|0,n=n+Math.imul(y,rt)|0,i=(i=i+Math.imul(y,nt)|0)+Math.imul(m,rt)|0,a=a+Math.imul(m,nt)|0,n=n+Math.imul(d,at)|0,i=(i=i+Math.imul(d,ot)|0)+Math.imul(v,at)|0,a=a+Math.imul(v,ot)|0;var Tt=(u+(n=n+Math.imul(f,lt)|0)|0)+((8191&(i=(i=i+Math.imul(f,ut)|0)+Math.imul(h,lt)|0))<<13)|0;u=((a=a+Math.imul(h,ut)|0)+(i>>>13)|0)+(Tt>>>26)|0,Tt&=67108863,n=Math.imul(z,U),i=(i=Math.imul(z,V))+Math.imul(R,U)|0,a=Math.imul(R,V),n=n+Math.imul(O,q)|0,i=(i=i+Math.imul(O,G)|0)+Math.imul(I,q)|0,a=a+Math.imul(I,G)|0,n=n+Math.imul(L,Y)|0,i=(i=i+Math.imul(L,W)|0)+Math.imul(C,Y)|0,a=a+Math.imul(C,W)|0,n=n+Math.imul(M,J)|0,i=(i=i+Math.imul(M,K)|0)+Math.imul(S,J)|0,a=a+Math.imul(S,K)|0,n=n+Math.imul(T,Q)|0,i=(i=i+Math.imul(T,tt)|0)+Math.imul(k,Q)|0,a=a+Math.imul(k,tt)|0,n=n+Math.imul(b,rt)|0,i=(i=i+Math.imul(b,nt)|0)+Math.imul(_,rt)|0,a=a+Math.imul(_,nt)|0,n=n+Math.imul(y,at)|0,i=(i=i+Math.imul(y,ot)|0)+Math.imul(m,at)|0,a=a+Math.imul(m,ot)|0,n=n+Math.imul(d,lt)|0,i=(i=i+Math.imul(d,ut)|0)+Math.imul(v,lt)|0,a=a+Math.imul(v,ut)|0;var kt=(u+(n=n+Math.imul(f,ft)|0)|0)+((8191&(i=(i=i+Math.imul(f,ht)|0)+Math.imul(h,ft)|0))<<13)|0;u=((a=a+Math.imul(h,ht)|0)+(i>>>13)|0)+(kt>>>26)|0,kt&=67108863,n=Math.imul(B,U),i=(i=Math.imul(B,V))+Math.imul(N,U)|0,a=Math.imul(N,V),n=n+Math.imul(z,q)|0,i=(i=i+Math.imul(z,G)|0)+Math.imul(R,q)|0,a=a+Math.imul(R,G)|0,n=n+Math.imul(O,Y)|0,i=(i=i+Math.imul(O,W)|0)+Math.imul(I,Y)|0,a=a+Math.imul(I,W)|0,n=n+Math.imul(L,J)|0,i=(i=i+Math.imul(L,K)|0)+Math.imul(C,J)|0,a=a+Math.imul(C,K)|0,n=n+Math.imul(M,Q)|0,i=(i=i+Math.imul(M,tt)|0)+Math.imul(S,Q)|0,a=a+Math.imul(S,tt)|0,n=n+Math.imul(T,rt)|0,i=(i=i+Math.imul(T,nt)|0)+Math.imul(k,rt)|0,a=a+Math.imul(k,nt)|0,n=n+Math.imul(b,at)|0,i=(i=i+Math.imul(b,ot)|0)+Math.imul(_,at)|0,a=a+Math.imul(_,ot)|0,n=n+Math.imul(y,lt)|0,i=(i=i+Math.imul(y,ut)|0)+Math.imul(m,lt)|0,a=a+Math.imul(m,ut)|0,n=n+Math.imul(d,ft)|0,i=(i=i+Math.imul(d,ht)|0)+Math.imul(v,ft)|0,a=a+Math.imul(v,ht)|0;var At=(u+(n=n+Math.imul(f,dt)|0)|0)+((8191&(i=(i=i+Math.imul(f,vt)|0)+Math.imul(h,dt)|0))<<13)|0;u=((a=a+Math.imul(h,vt)|0)+(i>>>13)|0)+(At>>>26)|0,At&=67108863,n=Math.imul(B,q),i=(i=Math.imul(B,G))+Math.imul(N,q)|0,a=Math.imul(N,G),n=n+Math.imul(z,Y)|0,i=(i=i+Math.imul(z,W)|0)+Math.imul(R,Y)|0,a=a+Math.imul(R,W)|0,n=n+Math.imul(O,J)|0,i=(i=i+Math.imul(O,K)|0)+Math.imul(I,J)|0,a=a+Math.imul(I,K)|0,n=n+Math.imul(L,Q)|0,i=(i=i+Math.imul(L,tt)|0)+Math.imul(C,Q)|0,a=a+Math.imul(C,tt)|0,n=n+Math.imul(M,rt)|0,i=(i=i+Math.imul(M,nt)|0)+Math.imul(S,rt)|0,a=a+Math.imul(S,nt)|0,n=n+Math.imul(T,at)|0,i=(i=i+Math.imul(T,ot)|0)+Math.imul(k,at)|0,a=a+Math.imul(k,ot)|0,n=n+Math.imul(b,lt)|0,i=(i=i+Math.imul(b,ut)|0)+Math.imul(_,lt)|0,a=a+Math.imul(_,ut)|0,n=n+Math.imul(y,ft)|0,i=(i=i+Math.imul(y,ht)|0)+Math.imul(m,ft)|0,a=a+Math.imul(m,ht)|0;var Mt=(u+(n=n+Math.imul(d,dt)|0)|0)+((8191&(i=(i=i+Math.imul(d,vt)|0)+Math.imul(v,dt)|0))<<13)|0;u=((a=a+Math.imul(v,vt)|0)+(i>>>13)|0)+(Mt>>>26)|0,Mt&=67108863,n=Math.imul(B,Y),i=(i=Math.imul(B,W))+Math.imul(N,Y)|0,a=Math.imul(N,W),n=n+Math.imul(z,J)|0,i=(i=i+Math.imul(z,K)|0)+Math.imul(R,J)|0,a=a+Math.imul(R,K)|0,n=n+Math.imul(O,Q)|0,i=(i=i+Math.imul(O,tt)|0)+Math.imul(I,Q)|0,a=a+Math.imul(I,tt)|0,n=n+Math.imul(L,rt)|0,i=(i=i+Math.imul(L,nt)|0)+Math.imul(C,rt)|0,a=a+Math.imul(C,nt)|0,n=n+Math.imul(M,at)|0,i=(i=i+Math.imul(M,ot)|0)+Math.imul(S,at)|0,a=a+Math.imul(S,ot)|0,n=n+Math.imul(T,lt)|0,i=(i=i+Math.imul(T,ut)|0)+Math.imul(k,lt)|0,a=a+Math.imul(k,ut)|0,n=n+Math.imul(b,ft)|0,i=(i=i+Math.imul(b,ht)|0)+Math.imul(_,ft)|0,a=a+Math.imul(_,ht)|0;var St=(u+(n=n+Math.imul(y,dt)|0)|0)+((8191&(i=(i=i+Math.imul(y,vt)|0)+Math.imul(m,dt)|0))<<13)|0;u=((a=a+Math.imul(m,vt)|0)+(i>>>13)|0)+(St>>>26)|0,St&=67108863,n=Math.imul(B,J),i=(i=Math.imul(B,K))+Math.imul(N,J)|0,a=Math.imul(N,K),n=n+Math.imul(z,Q)|0,i=(i=i+Math.imul(z,tt)|0)+Math.imul(R,Q)|0,a=a+Math.imul(R,tt)|0,n=n+Math.imul(O,rt)|0,i=(i=i+Math.imul(O,nt)|0)+Math.imul(I,rt)|0,a=a+Math.imul(I,nt)|0,n=n+Math.imul(L,at)|0,i=(i=i+Math.imul(L,ot)|0)+Math.imul(C,at)|0,a=a+Math.imul(C,ot)|0,n=n+Math.imul(M,lt)|0,i=(i=i+Math.imul(M,ut)|0)+Math.imul(S,lt)|0,a=a+Math.imul(S,ut)|0,n=n+Math.imul(T,ft)|0,i=(i=i+Math.imul(T,ht)|0)+Math.imul(k,ft)|0,a=a+Math.imul(k,ht)|0;var Et=(u+(n=n+Math.imul(b,dt)|0)|0)+((8191&(i=(i=i+Math.imul(b,vt)|0)+Math.imul(_,dt)|0))<<13)|0;u=((a=a+Math.imul(_,vt)|0)+(i>>>13)|0)+(Et>>>26)|0,Et&=67108863,n=Math.imul(B,Q),i=(i=Math.imul(B,tt))+Math.imul(N,Q)|0,a=Math.imul(N,tt),n=n+Math.imul(z,rt)|0,i=(i=i+Math.imul(z,nt)|0)+Math.imul(R,rt)|0,a=a+Math.imul(R,nt)|0,n=n+Math.imul(O,at)|0,i=(i=i+Math.imul(O,ot)|0)+Math.imul(I,at)|0,a=a+Math.imul(I,ot)|0,n=n+Math.imul(L,lt)|0,i=(i=i+Math.imul(L,ut)|0)+Math.imul(C,lt)|0,a=a+Math.imul(C,ut)|0,n=n+Math.imul(M,ft)|0,i=(i=i+Math.imul(M,ht)|0)+Math.imul(S,ft)|0,a=a+Math.imul(S,ht)|0;var Lt=(u+(n=n+Math.imul(T,dt)|0)|0)+((8191&(i=(i=i+Math.imul(T,vt)|0)+Math.imul(k,dt)|0))<<13)|0;u=((a=a+Math.imul(k,vt)|0)+(i>>>13)|0)+(Lt>>>26)|0,Lt&=67108863,n=Math.imul(B,rt),i=(i=Math.imul(B,nt))+Math.imul(N,rt)|0,a=Math.imul(N,nt),n=n+Math.imul(z,at)|0,i=(i=i+Math.imul(z,ot)|0)+Math.imul(R,at)|0,a=a+Math.imul(R,ot)|0,n=n+Math.imul(O,lt)|0,i=(i=i+Math.imul(O,ut)|0)+Math.imul(I,lt)|0,a=a+Math.imul(I,ut)|0,n=n+Math.imul(L,ft)|0,i=(i=i+Math.imul(L,ht)|0)+Math.imul(C,ft)|0,a=a+Math.imul(C,ht)|0;var Ct=(u+(n=n+Math.imul(M,dt)|0)|0)+((8191&(i=(i=i+Math.imul(M,vt)|0)+Math.imul(S,dt)|0))<<13)|0;u=((a=a+Math.imul(S,vt)|0)+(i>>>13)|0)+(Ct>>>26)|0,Ct&=67108863,n=Math.imul(B,at),i=(i=Math.imul(B,ot))+Math.imul(N,at)|0,a=Math.imul(N,ot),n=n+Math.imul(z,lt)|0,i=(i=i+Math.imul(z,ut)|0)+Math.imul(R,lt)|0,a=a+Math.imul(R,ut)|0,n=n+Math.imul(O,ft)|0,i=(i=i+Math.imul(O,ht)|0)+Math.imul(I,ft)|0,a=a+Math.imul(I,ht)|0;var Pt=(u+(n=n+Math.imul(L,dt)|0)|0)+((8191&(i=(i=i+Math.imul(L,vt)|0)+Math.imul(C,dt)|0))<<13)|0;u=((a=a+Math.imul(C,vt)|0)+(i>>>13)|0)+(Pt>>>26)|0,Pt&=67108863,n=Math.imul(B,lt),i=(i=Math.imul(B,ut))+Math.imul(N,lt)|0,a=Math.imul(N,ut),n=n+Math.imul(z,ft)|0,i=(i=i+Math.imul(z,ht)|0)+Math.imul(R,ft)|0,a=a+Math.imul(R,ht)|0;var Ot=(u+(n=n+Math.imul(O,dt)|0)|0)+((8191&(i=(i=i+Math.imul(O,vt)|0)+Math.imul(I,dt)|0))<<13)|0;u=((a=a+Math.imul(I,vt)|0)+(i>>>13)|0)+(Ot>>>26)|0,Ot&=67108863,n=Math.imul(B,ft),i=(i=Math.imul(B,ht))+Math.imul(N,ft)|0,a=Math.imul(N,ht);var It=(u+(n=n+Math.imul(z,dt)|0)|0)+((8191&(i=(i=i+Math.imul(z,vt)|0)+Math.imul(R,dt)|0))<<13)|0;u=((a=a+Math.imul(R,vt)|0)+(i>>>13)|0)+(It>>>26)|0,It&=67108863;var Dt=(u+(n=Math.imul(B,dt))|0)+((8191&(i=(i=Math.imul(B,vt))+Math.imul(N,dt)|0))<<13)|0;return u=((a=Math.imul(N,vt))+(i>>>13)|0)+(Dt>>>26)|0,Dt&=67108863,l[0]=gt,l[1]=yt,l[2]=mt,l[3]=xt,l[4]=bt,l[5]=_t,l[6]=wt,l[7]=Tt,l[8]=kt,l[9]=At,l[10]=Mt,l[11]=St,l[12]=Et,l[13]=Lt,l[14]=Ct,l[15]=Pt,l[16]=Ot,l[17]=It,l[18]=Dt,0!==u&&(l[19]=u,r.length++),r};function v(t,e,r){return(new g).mulp(t,e,r)}function g(t,e){this.x=t,this.y=e}Math.imul||(d=p),a.prototype.mulTo=function(t,e){var r,n=this.length+t.length;return r=10===this.length&&10===t.length?d(this,t,e):n<63?p(this,t,e):n<1024?function(t,e,r){r.negative=e.negative^t.negative,r.length=t.length+e.length;for(var n=0,i=0,a=0;a>>26)|0)>>>26,o&=67108863}r.words[a]=s,n=o,o=i}return 0!==n?r.words[a]=n:r.length--,r.strip()}(this,t,e):v(this,t,e),r},g.prototype.makeRBT=function(t){for(var e=new Array(t),r=a.prototype._countBits(t)-1,n=0;n>=1;return n},g.prototype.permute=function(t,e,r,n,i,a){for(var o=0;o>>=1)i++;return 1<>>=13,r[2*o+1]=8191&a,a>>>=13;for(o=2*e;o>=26,e+=i/67108864|0,e+=a>>>26,this.words[r]=67108863&a}return 0!==e&&(this.words[r]=e,this.length++),this},a.prototype.muln=function(t){return this.clone().imuln(t)},a.prototype.sqr=function(){return this.mul(this)},a.prototype.isqr=function(){return this.imul(this.clone())},a.prototype.pow=function(t){var e=function(t){for(var e=new Array(t.bitLength()),r=0;r>>i}return e}(t);if(0===e.length)return new a(1);for(var r=this,n=0;n=0);var e,r=t%26,i=(t-r)/26,a=67108863>>>26-r<<26-r;if(0!==r){var o=0;for(e=0;e>>26-r}o&&(this.words[e]=o,this.length++)}if(0!==i){for(e=this.length-1;e>=0;e--)this.words[e+i]=this.words[e];for(e=0;e=0),i=e?(e-e%26)/26:0;var a=t%26,o=Math.min((t-a)/26,this.length),s=67108863^67108863>>>a<o)for(this.length-=o,u=0;u=0&&(0!==c||u>=i);u--){var f=0|this.words[u];this.words[u]=c<<26-a|f>>>a,c=f&s}return l&&0!==c&&(l.words[l.length++]=c),0===this.length&&(this.words[0]=0,this.length=1),this.strip()},a.prototype.ishrn=function(t,e,r){return n(0===this.negative),this.iushrn(t,e,r)},a.prototype.shln=function(t){return this.clone().ishln(t)},a.prototype.ushln=function(t){return this.clone().iushln(t)},a.prototype.shrn=function(t){return this.clone().ishrn(t)},a.prototype.ushrn=function(t){return this.clone().iushrn(t)},a.prototype.testn=function(t){n("number"==typeof t&&t>=0);var e=t%26,r=(t-e)/26,i=1<=0);var e=t%26,r=(t-e)/26;if(n(0===this.negative,"imaskn works only with positive numbers"),this.length<=r)return this;if(0!==e&&r++,this.length=Math.min(r,this.length),0!==e){var i=67108863^67108863>>>e<=67108864;e++)this.words[e]-=67108864,e===this.length-1?this.words[e+1]=1:this.words[e+1]++;return this.length=Math.max(this.length,e+1),this},a.prototype.isubn=function(t){if(n("number"==typeof t),n(t<67108864),t<0)return this.iaddn(-t);if(0!==this.negative)return this.negative=0,this.iaddn(t),this.negative=1,this;if(this.words[0]-=t,1===this.length&&this.words[0]<0)this.words[0]=-this.words[0],this.negative=1;else for(var e=0;e>26)-(l/67108864|0),this.words[i+r]=67108863&a}for(;i>26,this.words[i+r]=67108863&a;if(0===s)return this.strip();for(n(-1===s),s=0,i=0;i>26,this.words[i]=67108863&a;return this.negative=1,this.strip()},a.prototype._wordDiv=function(t,e){var r=(this.length,t.length),n=this.clone(),i=t,o=0|i.words[i.length-1];0!=(r=26-this._countBits(o))&&(i=i.ushln(r),n.iushln(r),o=0|i.words[i.length-1]);var s,l=n.length-i.length;if("mod"!==e){(s=new a(null)).length=l+1,s.words=new Array(s.length);for(var u=0;u=0;f--){var h=67108864*(0|n.words[i.length+f])+(0|n.words[i.length+f-1]);for(h=Math.min(h/o|0,67108863),n._ishlnsubmul(i,h,f);0!==n.negative;)h--,n.negative=0,n._ishlnsubmul(i,1,f),n.isZero()||(n.negative^=1);s&&(s.words[f]=h)}return s&&s.strip(),n.strip(),"div"!==e&&0!==r&&n.iushrn(r),{div:s||null,mod:n}},a.prototype.divmod=function(t,e,r){return n(!t.isZero()),this.isZero()?{div:new a(0),mod:new a(0)}:0!==this.negative&&0===t.negative?(s=this.neg().divmod(t,e),"mod"!==e&&(i=s.div.neg()),"div"!==e&&(o=s.mod.neg(),r&&0!==o.negative&&o.iadd(t)),{div:i,mod:o}):0===this.negative&&0!==t.negative?(s=this.divmod(t.neg(),e),"mod"!==e&&(i=s.div.neg()),{div:i,mod:s.mod}):0!=(this.negative&t.negative)?(s=this.neg().divmod(t.neg(),e),"div"!==e&&(o=s.mod.neg(),r&&0!==o.negative&&o.isub(t)),{div:s.div,mod:o}):t.length>this.length||this.cmp(t)<0?{div:new a(0),mod:this}:1===t.length?"div"===e?{div:this.divn(t.words[0]),mod:null}:"mod"===e?{div:null,mod:new a(this.modn(t.words[0]))}:{div:this.divn(t.words[0]),mod:new a(this.modn(t.words[0]))}:this._wordDiv(t,e);var i,o,s},a.prototype.div=function(t){return this.divmod(t,"div",!1).div},a.prototype.mod=function(t){return this.divmod(t,"mod",!1).mod},a.prototype.umod=function(t){return this.divmod(t,"mod",!0).mod},a.prototype.divRound=function(t){var e=this.divmod(t);if(e.mod.isZero())return e.div;var r=0!==e.div.negative?e.mod.isub(t):e.mod,n=t.ushrn(1),i=t.andln(1),a=r.cmp(n);return a<0||1===i&&0===a?e.div:0!==e.div.negative?e.div.isubn(1):e.div.iaddn(1)},a.prototype.modn=function(t){n(t<=67108863);for(var e=(1<<26)%t,r=0,i=this.length-1;i>=0;i--)r=(e*r+(0|this.words[i]))%t;return r},a.prototype.idivn=function(t){n(t<=67108863);for(var e=0,r=this.length-1;r>=0;r--){var i=(0|this.words[r])+67108864*e;this.words[r]=i/t|0,e=i%t}return this.strip()},a.prototype.divn=function(t){return this.clone().idivn(t)},a.prototype.egcd=function(t){n(0===t.negative),n(!t.isZero());var e=this,r=t.clone();e=0!==e.negative?e.umod(t):e.clone();for(var i=new a(1),o=new a(0),s=new a(0),l=new a(1),u=0;e.isEven()&&r.isEven();)e.iushrn(1),r.iushrn(1),++u;for(var c=r.clone(),f=e.clone();!e.isZero();){for(var h=0,p=1;0==(e.words[0]&p)&&h<26;++h,p<<=1);if(h>0)for(e.iushrn(h);h-- >0;)(i.isOdd()||o.isOdd())&&(i.iadd(c),o.isub(f)),i.iushrn(1),o.iushrn(1);for(var d=0,v=1;0==(r.words[0]&v)&&d<26;++d,v<<=1);if(d>0)for(r.iushrn(d);d-- >0;)(s.isOdd()||l.isOdd())&&(s.iadd(c),l.isub(f)),s.iushrn(1),l.iushrn(1);e.cmp(r)>=0?(e.isub(r),i.isub(s),o.isub(l)):(r.isub(e),s.isub(i),l.isub(o))}return{a:s,b:l,gcd:r.iushln(u)}},a.prototype._invmp=function(t){n(0===t.negative),n(!t.isZero());var e=this,r=t.clone();e=0!==e.negative?e.umod(t):e.clone();for(var i,o=new a(1),s=new a(0),l=r.clone();e.cmpn(1)>0&&r.cmpn(1)>0;){for(var u=0,c=1;0==(e.words[0]&c)&&u<26;++u,c<<=1);if(u>0)for(e.iushrn(u);u-- >0;)o.isOdd()&&o.iadd(l),o.iushrn(1);for(var f=0,h=1;0==(r.words[0]&h)&&f<26;++f,h<<=1);if(f>0)for(r.iushrn(f);f-- >0;)s.isOdd()&&s.iadd(l),s.iushrn(1);e.cmp(r)>=0?(e.isub(r),o.isub(s)):(r.isub(e),s.isub(o))}return(i=0===e.cmpn(1)?o:s).cmpn(0)<0&&i.iadd(t),i},a.prototype.gcd=function(t){if(this.isZero())return t.abs();if(t.isZero())return this.abs();var e=this.clone(),r=t.clone();e.negative=0,r.negative=0;for(var n=0;e.isEven()&&r.isEven();n++)e.iushrn(1),r.iushrn(1);for(;;){for(;e.isEven();)e.iushrn(1);for(;r.isEven();)r.iushrn(1);var i=e.cmp(r);if(i<0){var a=e;e=r,r=a}else if(0===i||0===r.cmpn(1))break;e.isub(r)}return r.iushln(n)},a.prototype.invm=function(t){return this.egcd(t).a.umod(t)},a.prototype.isEven=function(){return 0==(1&this.words[0])},a.prototype.isOdd=function(){return 1==(1&this.words[0])},a.prototype.andln=function(t){return this.words[0]&t},a.prototype.bincn=function(t){n("number"==typeof t);var e=t%26,r=(t-e)/26,i=1<>>26,s&=67108863,this.words[o]=s}return 0!==a&&(this.words[o]=a,this.length++),this},a.prototype.isZero=function(){return 1===this.length&&0===this.words[0]},a.prototype.cmpn=function(t){var e,r=t<0;if(0!==this.negative&&!r)return-1;if(0===this.negative&&r)return 1;if(this.strip(),this.length>1)e=1;else{r&&(t=-t),n(t<=67108863,"Number is too big");var i=0|this.words[0];e=i===t?0:it.length)return 1;if(this.length=0;r--){var n=0|this.words[r],i=0|t.words[r];if(n!==i){ni&&(e=1);break}}return e},a.prototype.gtn=function(t){return 1===this.cmpn(t)},a.prototype.gt=function(t){return 1===this.cmp(t)},a.prototype.gten=function(t){return this.cmpn(t)>=0},a.prototype.gte=function(t){return this.cmp(t)>=0},a.prototype.ltn=function(t){return-1===this.cmpn(t)},a.prototype.lt=function(t){return-1===this.cmp(t)},a.prototype.lten=function(t){return this.cmpn(t)<=0},a.prototype.lte=function(t){return this.cmp(t)<=0},a.prototype.eqn=function(t){return 0===this.cmpn(t)},a.prototype.eq=function(t){return 0===this.cmp(t)},a.red=function(t){return new T(t)},a.prototype.toRed=function(t){return n(!this.red,"Already a number in reduction context"),n(0===this.negative,"red works only with positives"),t.convertTo(this)._forceRed(t)},a.prototype.fromRed=function(){return n(this.red,"fromRed works only with numbers in reduction context"),this.red.convertFrom(this)},a.prototype._forceRed=function(t){return this.red=t,this},a.prototype.forceRed=function(t){return n(!this.red,"Already a number in reduction context"),this._forceRed(t)},a.prototype.redAdd=function(t){return n(this.red,"redAdd works only with red numbers"),this.red.add(this,t)},a.prototype.redIAdd=function(t){return n(this.red,"redIAdd works only with red numbers"),this.red.iadd(this,t)},a.prototype.redSub=function(t){return n(this.red,"redSub works only with red numbers"),this.red.sub(this,t)},a.prototype.redISub=function(t){return n(this.red,"redISub works only with red numbers"),this.red.isub(this,t)},a.prototype.redShl=function(t){return n(this.red,"redShl works only with red numbers"),this.red.shl(this,t)},a.prototype.redMul=function(t){return n(this.red,"redMul works only with red numbers"),this.red._verify2(this,t),this.red.mul(this,t)},a.prototype.redIMul=function(t){return n(this.red,"redMul works only with red numbers"),this.red._verify2(this,t),this.red.imul(this,t)},a.prototype.redSqr=function(){return n(this.red,"redSqr works only with red numbers"),this.red._verify1(this),this.red.sqr(this)},a.prototype.redISqr=function(){return n(this.red,"redISqr works only with red numbers"),this.red._verify1(this),this.red.isqr(this)},a.prototype.redSqrt=function(){return n(this.red,"redSqrt works only with red numbers"),this.red._verify1(this),this.red.sqrt(this)},a.prototype.redInvm=function(){return n(this.red,"redInvm works only with red numbers"),this.red._verify1(this),this.red.invm(this)},a.prototype.redNeg=function(){return n(this.red,"redNeg works only with red numbers"),this.red._verify1(this),this.red.neg(this)},a.prototype.redPow=function(t){return n(this.red&&!t.red,"redPow(normalNum)"),this.red._verify1(this),this.red.pow(this,t)};var y={k256:null,p224:null,p192:null,p25519:null};function m(t,e){this.name=t,this.p=new a(e,16),this.n=this.p.bitLength(),this.k=new a(1).iushln(this.n).isub(this.p),this.tmp=this._tmp()}function x(){m.call(this,"k256","ffffffff ffffffff ffffffff ffffffff ffffffff ffffffff fffffffe fffffc2f")}function b(){m.call(this,"p224","ffffffff ffffffff ffffffff ffffffff 00000000 00000000 00000001")}function _(){m.call(this,"p192","ffffffff ffffffff ffffffff fffffffe ffffffff ffffffff")}function w(){m.call(this,"25519","7fffffffffffffff ffffffffffffffff ffffffffffffffff ffffffffffffffed")}function T(t){if("string"==typeof t){var e=a._prime(t);this.m=e.p,this.prime=e}else n(t.gtn(1),"modulus must be greater than 1"),this.m=t,this.prime=null}function k(t){T.call(this,t),this.shift=this.m.bitLength(),this.shift%26!=0&&(this.shift+=26-this.shift%26),this.r=new a(1).iushln(this.shift),this.r2=this.imod(this.r.sqr()),this.rinv=this.r._invmp(this.m),this.minv=this.rinv.mul(this.r).isubn(1).div(this.m),this.minv=this.minv.umod(this.r),this.minv=this.r.sub(this.minv)}m.prototype._tmp=function(){var t=new a(null);return t.words=new Array(Math.ceil(this.n/13)),t},m.prototype.ireduce=function(t){var e,r=t;do{this.split(r,this.tmp),e=(r=(r=this.imulK(r)).iadd(this.tmp)).bitLength()}while(e>this.n);var n=e0?r.isub(this.p):void 0!==r.strip?r.strip():r._strip(),r},m.prototype.split=function(t,e){t.iushrn(this.n,0,e)},m.prototype.imulK=function(t){return t.imul(this.k)},i(x,m),x.prototype.split=function(t,e){for(var r=4194303,n=Math.min(t.length,9),i=0;i>>22,a=o}a>>>=22,t.words[i-10]=a,0===a&&t.length>10?t.length-=10:t.length-=9},x.prototype.imulK=function(t){t.words[t.length]=0,t.words[t.length+1]=0,t.length+=2;for(var e=0,r=0;r>>=26,t.words[r]=i,e=n}return 0!==e&&(t.words[t.length++]=e),t},a._prime=function(t){if(y[t])return y[t];var e;if("k256"===t)e=new x;else if("p224"===t)e=new b;else if("p192"===t)e=new _;else{if("p25519"!==t)throw new Error("Unknown prime "+t);e=new w}return y[t]=e,e},T.prototype._verify1=function(t){n(0===t.negative,"red works only with positives"),n(t.red,"red works only with red numbers")},T.prototype._verify2=function(t,e){n(0==(t.negative|e.negative),"red works only with positives"),n(t.red&&t.red===e.red,"red works only with red numbers")},T.prototype.imod=function(t){return this.prime?this.prime.ireduce(t)._forceRed(this):t.umod(this.m)._forceRed(this)},T.prototype.neg=function(t){return t.isZero()?t.clone():this.m.sub(t)._forceRed(this)},T.prototype.add=function(t,e){this._verify2(t,e);var r=t.add(e);return r.cmp(this.m)>=0&&r.isub(this.m),r._forceRed(this)},T.prototype.iadd=function(t,e){this._verify2(t,e);var r=t.iadd(e);return r.cmp(this.m)>=0&&r.isub(this.m),r},T.prototype.sub=function(t,e){this._verify2(t,e);var r=t.sub(e);return r.cmpn(0)<0&&r.iadd(this.m),r._forceRed(this)},T.prototype.isub=function(t,e){this._verify2(t,e);var r=t.isub(e);return r.cmpn(0)<0&&r.iadd(this.m),r},T.prototype.shl=function(t,e){return this._verify1(t),this.imod(t.ushln(e))},T.prototype.imul=function(t,e){return this._verify2(t,e),this.imod(t.imul(e))},T.prototype.mul=function(t,e){return this._verify2(t,e),this.imod(t.mul(e))},T.prototype.isqr=function(t){return this.imul(t,t.clone())},T.prototype.sqr=function(t){return this.mul(t,t)},T.prototype.sqrt=function(t){if(t.isZero())return t.clone();var e=this.m.andln(3);if(n(e%2==1),3===e){var r=this.m.add(new a(1)).iushrn(2);return this.pow(t,r)}for(var i=this.m.subn(1),o=0;!i.isZero()&&0===i.andln(1);)o++,i.iushrn(1);n(!i.isZero());var s=new a(1).toRed(this),l=s.redNeg(),u=this.m.subn(1).iushrn(1),c=this.m.bitLength();for(c=new a(2*c*c).toRed(this);0!==this.pow(c,u).cmp(l);)c.redIAdd(l);for(var f=this.pow(c,i),h=this.pow(t,i.addn(1).iushrn(1)),p=this.pow(t,i),d=o;0!==p.cmp(s);){for(var v=p,g=0;0!==v.cmp(s);g++)v=v.redSqr();n(g=0;n--){for(var u=e.words[n],c=l-1;c>=0;c--){var f=u>>c&1;i!==r[0]&&(i=this.sqr(i)),0!==f||0!==o?(o<<=1,o|=f,(4==++s||0===n&&0===c)&&(i=this.mul(i,r[o]),s=0,o=0)):s=0}l=26}return i},T.prototype.convertTo=function(t){var e=t.umod(this.m);return e===t?e.clone():e},T.prototype.convertFrom=function(t){var e=t.clone();return e.red=null,e},a.mont=function(t){return new k(t)},i(k,T),k.prototype.convertTo=function(t){return this.imod(t.ushln(this.shift))},k.prototype.convertFrom=function(t){var e=this.imod(t.mul(this.rinv));return e.red=null,e},k.prototype.imul=function(t,e){if(t.isZero()||e.isZero())return t.words[0]=0,t.length=1,t;var r=t.imul(e),n=r.maskn(this.shift).mul(this.minv).imaskn(this.shift).mul(this.m),i=r.isub(n).iushrn(this.shift),a=i;return i.cmp(this.m)>=0?a=i.isub(this.m):i.cmpn(0)<0&&(a=i.iadd(this.m)),a._forceRed(this)},k.prototype.mul=function(t,e){if(t.isZero()||e.isZero())return new a(0)._forceRed(this);var r=t.mul(e),n=r.maskn(this.shift).mul(this.minv).imaskn(this.shift).mul(this.m),i=r.isub(n).iushrn(this.shift),o=i;return i.cmp(this.m)>=0?o=i.isub(this.m):i.cmpn(0)<0&&(o=i.iadd(this.m)),o._forceRed(this)},k.prototype.invm=function(t){return this.imod(t._invmp(this.m).mul(this.r2))._forceRed(this)}}(t=r.nmd(t),this)},2692:function(t){"use strict";t.exports=function(t){var e,r,n,i=t.length,a=0;for(e=0;e>>1;if(!(c<=0)){var f,h=i.mallocDouble(2*c*s),p=i.mallocInt32(s);if((s=l(t,c,h,p))>0){if(1===c&&n)a.init(s),f=a.sweepComplete(c,r,0,s,h,p,0,s,h,p);else{var d=i.mallocDouble(2*c*u),v=i.mallocInt32(u);(u=l(e,c,d,v))>0&&(a.init(s+u),f=1===c?a.sweepBipartite(c,r,0,s,h,p,0,u,d,v):o(c,r,n,s,h,p,u,d,v),i.free(d),i.free(v))}i.free(h),i.free(p)}return f}}}function c(t,e){n.push([t,e])}},7333:function(t,e){"use strict";function r(t){return t?function(t,e,r,n,i,a,o,s,l,u,c){return i-n>l-s?function(t,e,r,n,i,a,o,s,l,u,c){for(var f=2*t,h=n,p=f*n;hu-l?n?function(t,e,r,n,i,a,o,s,l,u,c){for(var f=2*t,h=n,p=f*n;h0;){var D=(O-=1)*b,z=w[D],R=w[D+1],F=w[D+2],B=w[D+3],N=w[D+4],j=w[D+5],U=O*_,V=T[U],H=T[U+1],q=1&j,G=!!(16&j),Z=c,Y=S,W=L,X=C;if(q&&(Z=L,Y=C,W=c,X=S),!(2&j&&R>=(F=g(t,z,R,F,Z,Y,H))||4&j&&(R=y(t,z,R,F,Z,Y,V))>=F)){var 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p=l[f-2];if(p.left===h)if(h.left===s){if(!(d=p.right)||0!==d._color){p._color=0,p.left=h.right,h._color=1,h.right=p,l[f-2]=h,l[f-1]=s,i(p),i(h),f>=3&&((v=l[f-3]).left===p?v.left=h:v.right=h);break}h._color=1,p.right=n(1,d),p._color=0,f-=1}else{if(!(d=p.right)||0!==d._color){h.right=s.left,p._color=0,p.left=s.right,s._color=1,s.left=h,s.right=p,l[f-2]=s,l[f-1]=h,i(p),i(h),i(s),f>=3&&((v=l[f-3]).left===p?v.left=s:v.right=s);break}h._color=1,p.right=n(1,d),p._color=0,f-=1}else if(h.right===s){if(!(d=p.left)||0!==d._color){p._color=0,p.right=h.left,h._color=1,h.left=p,l[f-2]=h,l[f-1]=s,i(p),i(h),f>=3&&((v=l[f-3]).right===p?v.right=h:v.left=h);break}h._color=1,p.left=n(1,d),p._color=0,f-=1}else{var d;if(!(d=p.left)||0!==d._color){var v;h.left=s.right,p._color=0,p.right=s.left,s._color=1,s.right=h,s.left=p,l[f-2]=s,l[f-1]=h,i(p),i(h),i(s),f>=3&&((v=l[f-3]).right===p?v.right=s:v.left=s);break}h._color=1,p.left=n(1,d),p._color=0,f-=1}}return l[0]._color=1,new 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e=this._compare,r=this.root,n=[],i=0;r;){var a=e(t,r.key);n.push(r),a>0&&(i=n.length),r=a<=0?r.left:r.right}return n.length=i,new c(this,n)},o.le=function(t){for(var e=this._compare,r=this.root,n=[],i=0;r;){var a=e(t,r.key);n.push(r),a>=0&&(i=n.length),r=a<0?r.left:r.right}return n.length=i,new c(this,n)},o.find=function(t){for(var e=this._compare,r=this.root,n=[];r;){var i=e(t,r.key);if(n.push(r),0===i)return new c(this,n);r=i<=0?r.left:r.right}return new c(this,[])},o.remove=function(t){var e=this.find(t);return e?e.remove():this},o.get=function(t){for(var e=this._compare,r=this.root;r;){var n=e(t,r.key);if(0===n)return r.value;r=n<=0?r.left:r.right}};var f=c.prototype;function h(t,e){t.key=e.key,t.value=e.value,t.left=e.left,t.right=e.right,t._color=e._color,t._count=e._count}function p(t,e){return te?1:0}Object.defineProperty(f,"valid",{get:function(){return this._stack.length>0}}),Object.defineProperty(f,"node",{get:function(){return this._stack.length>0?this._stack[this._stack.length-1]:null},enumerable:!0}),f.clone=function(){return new c(this.tree,this._stack.slice())},f.remove=function(){var t=this._stack;if(0===t.length)return this.tree;var o=new Array(t.length),s=t[t.length-1];o[o.length-1]=new e(s._color,s.key,s.value,s.left,s.right,s._count);for(var l=t.length-2;l>=0;--l)(s=t[l]).left===t[l+1]?o[l]=new e(s._color,s.key,s.value,o[l+1],s.right,s._count):o[l]=new e(s._color,s.key,s.value,s.left,o[l+1],s._count);if((s=o[o.length-1]).left&&s.right){var u=o.length;for(s=s.left;s.right;)o.push(s),s=s.right;var c=o[u-1];for(o.push(new e(s._color,c.key,c.value,s.left,s.right,s._count)),o[u-1].key=s.key,o[u-1].value=s.value,l=o.length-2;l>=u;--l)s=o[l],o[l]=new e(s._color,s.key,s.value,s.left,o[l+1],s._count);o[u-1].left=o[u]}if(0===(s=o[o.length-1])._color){var f=o[o.length-2];for(f.left===s?f.left=null:f.right===s&&(f.right=null),o.pop(),l=0;l=0;--l){if(e=t[l],0===l)return void(e._color=1);if((a=t[l-1]).left===e){if((o=a.right).right&&0===o.right._color)return s=(o=a.right=r(o)).right=r(o.right),a.right=o.left,o.left=a,o.right=s,o._color=a._color,e._color=1,a._color=1,s._color=1,i(a),i(o),l>1&&((u=t[l-2]).left===a?u.left=o:u.right=o),void(t[l-1]=o);if(o.left&&0===o.left._color)return s=(o=a.right=r(o)).left=r(o.left),a.right=s.left,o.left=s.right,s.left=a,s.right=o,s._color=a._color,a._color=1,o._color=1,e._color=1,i(a),i(o),i(s),l>1&&((u=t[l-2]).left===a?u.left=s:u.right=s),void(t[l-1]=s);if(1===o._color){if(0===a._color)return a._color=1,void(a.right=n(0,o));a.right=n(0,o);continue}o=r(o),a.right=o.left,o.left=a,o._color=a._color,a._color=0,i(a),i(o),l>1&&((u=t[l-2]).left===a?u.left=o:u.right=o),t[l-1]=o,t[l]=a,l+11&&((u=t[l-2]).right===a?u.right=o:u.left=o),void(t[l-1]=o);if(o.right&&0===o.right._color)return s=(o=a.left=r(o)).right=r(o.right),a.left=s.right,o.right=s.left,s.right=a,s.left=o,s._color=a._color,a._color=1,o._color=1,e._color=1,i(a),i(o),i(s),l>1&&((u=t[l-2]).right===a?u.right=s:u.left=s),void(t[l-1]=s);if(1===o._color){if(0===a._color)return a._color=1,void(a.left=n(0,o));a.left=n(0,o);continue}var u;o=r(o),a.left=o.right,o.right=a,o._color=a._color,a._color=0,i(a),i(o),l>1&&((u=t[l-2]).right===a?u.right=o:u.left=o),t[l-1]=o,t[l]=a,l+10)return this._stack[this._stack.length-1].key},enumerable:!0}),Object.defineProperty(f,"value",{get:function(){if(this._stack.length>0)return this._stack[this._stack.length-1].value},enumerable:!0}),Object.defineProperty(f,"index",{get:function(){var t=0,e=this._stack;if(0===e.length){var r=this.tree.root;return r?r._count:0}e[e.length-1].left&&(t=e[e.length-1].left._count);for(var n=e.length-2;n>=0;--n)e[n+1]===e[n].right&&(++t,e[n].left&&(t+=e[n].left._count));return t},enumerable:!0}),f.next=function(){var t=this._stack;if(0!==t.length){var e=t[t.length-1];if(e.right)for(e=e.right;e;)t.push(e),e=e.left;else for(t.pop();t.length>0&&t[t.length-1].right===e;)e=t[t.length-1],t.pop()}},Object.defineProperty(f,"hasNext",{get:function(){var t=this._stack;if(0===t.length)return!1;if(t[t.length-1].right)return!0;for(var e=t.length-1;e>0;--e)if(t[e-1].left===t[e])return!0;return!1}}),f.update=function(t){var r=this._stack;if(0===r.length)throw new Error("Can't update empty node!");var n=new Array(r.length),i=r[r.length-1];n[n.length-1]=new e(i._color,i.key,t,i.left,i.right,i._count);for(var o=r.length-2;o>=0;--o)(i=r[o]).left===r[o+1]?n[o]=new e(i._color,i.key,i.value,n[o+1],i.right,i._count):n[o]=new e(i._color,i.key,i.value,i.left,n[o+1],i._count);return new a(this.tree._compare,n[0])},f.prev=function(){var t=this._stack;if(0!==t.length){var e=t[t.length-1];if(e.left)for(e=e.left;e;)t.push(e),e=e.right;else for(t.pop();t.length>0&&t[t.length-1].left===e;)e=t[t.length-1],t.pop()}},Object.defineProperty(f,"hasPrev",{get:function(){var t=this._stack;if(0===t.length)return!1;if(t[t.length-1].left)return!0;for(var e=t.length-1;e>0;--e)if(t[e-1].right===t[e])return!0;return!1}})},7453:function(t,e,r){"use strict";t.exports=function(t,e){var r=new c(t);return r.update(e),r};var n=r(9557),i=r(1681),a=r(1011),o=r(2864),s=r(8468),l=new Float32Array([1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1]);function u(t,e){return t[0]=e[0],t[1]=e[1],t[2]=e[2],t}function c(t){this.gl=t,this.pixelRatio=1,this.bounds=[[-10,-10,-10],[10,10,10]],this.ticks=[[],[],[]],this.autoTicks=!0,this.tickSpacing=[1,1,1],this.tickEnable=[!0,!0,!0],this.tickFont=["sans-serif","sans-serif","sans-serif"],this.tickSize=[12,12,12],this.tickAngle=[0,0,0],this.tickAlign=["auto","auto","auto"],this.tickColor=[[0,0,0,1],[0,0,0,1],[0,0,0,1]],this.tickPad=[10,10,10],this.lastCubeProps={cubeEdges:[0,0,0],axis:[0,0,0]},this.labels=["x","y","z"],this.labelEnable=[!0,!0,!0],this.labelFont="sans-serif",this.labelSize=[20,20,20],this.labelAngle=[0,0,0],this.labelAlign=["auto","auto","auto"],this.labelColor=[[0,0,0,1],[0,0,0,1],[0,0,0,1]],this.labelPad=[10,10,10],this.lineEnable=[!0,!0,!0],this.lineMirror=[!1,!1,!1],this.lineWidth=[1,1,1],this.lineColor=[[0,0,0,1],[0,0,0,1],[0,0,0,1]],this.lineTickEnable=[!0,!0,!0],this.lineTickMirror=[!1,!1,!1],this.lineTickLength=[0,0,0],this.lineTickWidth=[1,1,1],this.lineTickColor=[[0,0,0,1],[0,0,0,1],[0,0,0,1]],this.gridEnable=[!0,!0,!0],this.gridWidth=[1,1,1],this.gridColor=[[0,0,0,1],[0,0,0,1],[0,0,0,1]],this.zeroEnable=[!0,!0,!0],this.zeroLineColor=[[0,0,0,1],[0,0,0,1],[0,0,0,1]],this.zeroLineWidth=[2,2,2],this.backgroundEnable=[!1,!1,!1],this.backgroundColor=[[.8,.8,.8,.5],[.8,.8,.8,.5],[.8,.8,.8,.5]],this._firstInit=!0,this._text=null,this._lines=null,this._background=a(t)}var 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I=(A+1+O)%3,D=(A+1+(1^O))%3;this.gridEnable[I]&&this._lines.drawGrid(I,D,this.bounds,P,this.gridColor[I],this.gridWidth[I]*this.pixelRatio)}for(O=0;O<2;++O)I=(A+1+O)%3,D=(A+1+(1^O))%3,this.zeroEnable[D]&&Math.min(a[0][D],a[1][D])<=0&&Math.max(a[0][D],a[1][D])>=0&&this._lines.drawZero(I,D,this.bounds,P,this.zeroLineColor[D],this.zeroLineWidth[D]*this.pixelRatio)}for(A=0;A<3;++A){this.lineEnable[A]&&this._lines.drawAxisLine(A,this.bounds,M[A].primalOffset,this.lineColor[A],this.lineWidth[A]*this.pixelRatio),this.lineMirror[A]&&this._lines.drawAxisLine(A,this.bounds,M[A].mirrorOffset,this.lineColor[A],this.lineWidth[A]*this.pixelRatio);var z=u(y,M[A].primalMinor),R=u(m,M[A].mirrorMinor),F=this.lineTickLength;for(O=0;O<3;++O){var B=k/r[5*O];z[O]*=F[O]*B,R[O]*=F[O]*B}this.lineTickEnable[A]&&this._lines.drawAxisTicks(A,M[A].primalOffset,z,this.lineTickColor[A],this.lineTickWidth[A]*this.pixelRatio),this.lineTickMirror[A]&&this._lines.drawAxisTicks(A,M[A].mirrorOffset,R,this.lineTickColor[A],this.lineTickWidth[A]*this.pixelRatio)}function N(t){(L=[0,0,0])[t]=1}function j(t,e,r){var n=(t+1)%3,i=(t+2)%3,a=e[n],o=e[i],s=r[n],l=r[i];a>0&&l>0||a>0&&l<0||a<0&&l>0||a<0&&l<0?N(n):(o>0&&s>0||o>0&&s<0||o<0&&s>0||o<0&&s<0)&&N(i)}for(this._lines.unbind(),this._text.bind(r,n,i,this.pixelRatio),A=0;A<3;++A){var U=M[A].primalMinor,V=M[A].mirrorMinor,H=u(x,M[A].primalOffset);for(O=0;O<3;++O)this.lineTickEnable[A]&&(H[O]+=k*U[O]*Math.max(this.lineTickLength[O],0)/r[5*O]);var q=[0,0,0];if(q[A]=1,this.tickEnable[A]){for(-3600===this.tickAngle[A]?(this.tickAngle[A]=0,this.tickAlign[A]="auto"):this.tickAlign[A]=-1,E=1,"auto"===(S=[this.tickAlign[A],.5,E])[0]?S[0]=0:S[0]=parseInt(""+S[0]),L=[0,0,0],j(A,U,V),O=0;O<3;++O)H[O]+=k*U[O]*this.tickPad[O]/r[5*O];this._text.drawTicks(A,this.tickSize[A],this.tickAngle[A],H,this.tickColor[A],q,L,S)}if(this.labelEnable[A]){for(E=0,L=[0,0,0],this.labels[A].length>4&&(N(A),E=1),"auto"===(S=[this.labelAlign[A],.5,E])[0]?S[0]=0:S[0]=parseInt(""+S[0]),O=0;O<3;++O)H[O]+=k*U[O]*this.labelPad[O]/r[5*O];H[A]+=.5*(a[0][A]+a[1][A]),this._text.drawLabel(A,this.labelSize[A],this.labelAngle[A],H,this.labelColor[A],[0,0,0],L,S)}}this._text.unbind()},f.dispose=function(){this._text.dispose(),this._lines.dispose(),this._background.dispose(),this._lines=null,this._text=null,this._background=null,this.gl=null}},1011:function(t,e,r){"use strict";t.exports=function(t){for(var e=[],r=[],s=0,l=0;l<3;++l)for(var u=(l+1)%3,c=(l+2)%3,f=[0,0,0],h=[0,0,0],p=-1;p<=1;p+=2){r.push(s,s+2,s+1,s+1,s+2,s+3),f[l]=p,h[l]=p;for(var d=-1;d<=1;d+=2){f[u]=d;for(var v=-1;v<=1;v+=2)f[c]=v,e.push(f[0],f[1],f[2],h[0],h[1],h[2]),s+=1}var g=u;u=c,c=g}var y=n(t,new Float32Array(e)),m=n(t,new Uint16Array(r),t.ELEMENT_ARRAY_BUFFER),x=i(t,[{buffer:y,type:t.FLOAT,size:3,offset:0,stride:24},{buffer:y,type:t.FLOAT,size:3,offset:12,stride:24}],m),b=a(t);return b.attributes.position.location=0,b.attributes.normal.location=1,new o(t,y,x,b)};var n=r(5827),i=r(2944),a=r(1943).bg;function o(t,e,r,n){this.gl=t,this.buffer=e,this.vao=r,this.shader=n}var s=o.prototype;s.draw=function(t,e,r,n,i,a){for(var o=!1,s=0;s<3;++s)o=o||i[s];if(o){var l=this.gl;l.enable(l.POLYGON_OFFSET_FILL),l.polygonOffset(1,2),this.shader.bind(),this.shader.uniforms={model:t,view:e,projection:r,bounds:n,enable:i,colors:a},this.vao.bind(),this.vao.draw(this.gl.TRIANGLES,36),this.vao.unbind(),l.disable(l.POLYGON_OFFSET_FILL)}},s.dispose=function(){this.vao.dispose(),this.buffer.dispose(),this.shader.dispose()}},2864:function(t,e,r){"use strict";t.exports=function(t,e,r,a,p){i(s,e,t),i(s,r,s);for(var m=0,x=0;x<2;++x){c[2]=a[x][2];for(var b=0;b<2;++b){c[1]=a[b][1];for(var _=0;_<2;++_)c[0]=a[_][0],h(l[m],c,s),m+=1}}var w=-1;for(x=0;x<8;++x){for(var T=l[x][3],k=0;k<3;++k)u[x][k]=l[x][k]/T;p&&(u[x][2]*=-1),T<0&&(w<0||u[x][2]E&&(w|=1<E&&(w|=1<u[x][1])&&(R=x);var F=-1;for(x=0;x<3;++x)(N=R^1<u[B][0]&&(B=N))}var j=v;j[0]=j[1]=j[2]=0,j[n.log2(F^R)]=R&F,j[n.log2(R^B)]=R&B;var U=7^B;U===w||U===z?(U=7^F,j[n.log2(B^U)]=U&B):j[n.log2(F^U)]=U&F;var V=g,H=w;for(A=0;A<3;++A)V[A]=H&1< HALF_PI) && (b <= ONE_AND_HALF_PI)) ?\n b - PI :\n b;\n}\n\nfloat look_horizontal_or_vertical(float a, float ratio) {\n // ratio controls the ratio between being horizontal to (vertical + horizontal)\n // if ratio is set to 0.5 then it is 50%, 50%.\n // when using a higher ratio e.g. 0.75 the result would\n // likely be more horizontal than vertical.\n\n float b = positive_angle(a);\n\n return\n (b < ( ratio) * HALF_PI) ? 0.0 :\n (b < (2.0 - ratio) * HALF_PI) ? -HALF_PI :\n (b < (2.0 + ratio) * HALF_PI) ? 0.0 :\n (b < (4.0 - ratio) * HALF_PI) ? HALF_PI :\n 0.0;\n}\n\nfloat roundTo(float a, float b) {\n return float(b * floor((a + 0.5 * b) / b));\n}\n\nfloat look_round_n_directions(float a, int n) {\n float b = positive_angle(a);\n float div = TWO_PI / float(n);\n float c = roundTo(b, div);\n return look_upwards(c);\n}\n\nfloat applyAlignOption(float rawAngle, float delta) {\n return\n (option > 2) ? look_round_n_directions(rawAngle + delta, option) : // option 3-n: round to n directions\n (option == 2) ? look_horizontal_or_vertical(rawAngle + delta, hv_ratio) : // horizontal or vertical\n (option == 1) ? rawAngle + delta : // use free angle, and flip to align with one direction of the axis\n (option == 0) ? look_upwards(rawAngle) : // use free angle, and stay upwards\n (option ==-1) ? 0.0 : // useful for backward compatibility, all texts remains horizontal\n rawAngle; // otherwise return back raw input angle\n}\n\nbool isAxisTitle = (axis.x == 0.0) &&\n (axis.y == 0.0) &&\n (axis.z == 0.0);\n\nvoid main() {\n //Compute world offset\n float axisDistance = position.z;\n vec3 dataPosition = axisDistance * axis + offset;\n\n float beta = angle; // i.e. user defined attributes for each tick\n\n float axisAngle;\n float clipAngle;\n float flip;\n\n if (enableAlign) {\n axisAngle = (isAxisTitle) ? HALF_PI :\n computeViewAngle(dataPosition, dataPosition + axis);\n clipAngle = computeViewAngle(dataPosition, dataPosition + alignDir);\n\n axisAngle += (sin(axisAngle) < 0.0) ? PI : 0.0;\n clipAngle += (sin(clipAngle) < 0.0) ? PI : 0.0;\n\n flip = (dot(vec2(cos(axisAngle), sin(axisAngle)),\n vec2(sin(clipAngle),-cos(clipAngle))) > 0.0) ? 1.0 : 0.0;\n\n beta += applyAlignOption(clipAngle, flip * PI);\n }\n\n //Compute plane offset\n vec2 planeCoord = position.xy * pixelScale;\n\n mat2 planeXform = scale * mat2(\n cos(beta), sin(beta),\n -sin(beta), cos(beta)\n );\n\n vec2 viewOffset = 2.0 * planeXform * planeCoord / resolution;\n\n //Compute clip position\n vec3 clipPosition = project(dataPosition);\n\n //Apply text offset in clip coordinates\n clipPosition += vec3(viewOffset, 0.0);\n\n //Done\n gl_Position = vec4(clipPosition, 1.0);\n}"]),l=n(["precision highp float;\n#define GLSLIFY 1\n\nuniform vec4 color;\nvoid main() {\n gl_FragColor = color;\n}"]);e.f=function(t){return i(t,s,l,null,[{name:"position",type:"vec3"}])};var u=n(["precision highp float;\n#define GLSLIFY 1\n\nattribute vec3 position;\nattribute vec3 normal;\n\nuniform mat4 model, view, projection;\nuniform vec3 enable;\nuniform vec3 bounds[2];\n\nvarying vec3 colorChannel;\n\nvoid main() {\n\n vec3 signAxis = sign(bounds[1] - bounds[0]);\n\n vec3 realNormal = signAxis * normal;\n\n if(dot(realNormal, enable) > 0.0) {\n vec3 minRange = min(bounds[0], bounds[1]);\n vec3 maxRange = max(bounds[0], bounds[1]);\n vec3 nPosition = mix(minRange, maxRange, 0.5 * (position + 1.0));\n gl_Position = projection * view * model * vec4(nPosition, 1.0);\n } else {\n gl_Position = vec4(0,0,0,0);\n }\n\n colorChannel = abs(realNormal);\n}"]),c=n(["precision highp float;\n#define GLSLIFY 1\n\nuniform vec4 colors[3];\n\nvarying vec3 colorChannel;\n\nvoid main() {\n gl_FragColor = colorChannel.x * colors[0] +\n colorChannel.y * colors[1] +\n colorChannel.z * colors[2];\n}"]);e.bg=function(t){return i(t,u,c,null,[{name:"position",type:"vec3"},{name:"normal",type:"vec3"}])}},9557:function(t,e,r){"use strict";t.exports=function(t,e,r,i,o,l){var u=n(t),f=a(t,[{buffer:u,size:3}]),h=s(t);h.attributes.position.location=0;var p=new c(t,h,u,f);return p.update(e,r,i,o,l),p};var n=r(5827),a=r(2944),o=r(875),s=r(1943).f,l=window||i.global||{},u=l.__TEXT_CACHE||{};function c(t,e,r,n){this.gl=t,this.shader=e,this.buffer=r,this.vao=n,this.tickOffset=this.tickCount=this.labelOffset=this.labelCount=null}l.__TEXT_CACHE={};var f=c.prototype,h=[0,0];f.bind=function(t,e,r,n){this.vao.bind(),this.shader.bind();var i=this.shader.uniforms;i.model=t,i.view=e,i.projection=r,i.pixelScale=n,h[0]=this.gl.drawingBufferWidth,h[1]=this.gl.drawingBufferHeight,this.shader.uniforms.resolution=h},f.unbind=function(){this.vao.unbind()},f.update=function(t,e,r,n,i){var a=[];function s(t,e,r,n,i,s){var l=u[r];l||(l=u[r]={});var c=l[e];c||(c=l[e]=function(t,e){try{return o(t,e)}catch(e){return console.warn('error vectorizing text:"'+t+'" error:',e),{cells:[],positions:[]}}}(e,{triangles:!0,font:r,textAlign:"center",textBaseline:"middle",lineSpacing:i,styletags:s}));for(var f=(n||12)/12,h=c.positions,p=c.cells,d=0,v=p.length;d=0;--y){var m=h[g[y]];a.push(f*m[0],-f*m[1],t)}}for(var l=[0,0,0],c=[0,0,0],f=[0,0,0],h=[0,0,0],p={breaklines:!0,bolds:!0,italics:!0,subscripts:!0,superscripts:!0},d=0;d<3;++d){f[d]=a.length/3|0,s(.5*(t[0][d]+t[1][d]),e[d],r[d],12,1.25,p),h[d]=(a.length/3|0)-f[d],l[d]=a.length/3|0;for(var v=0;v=0&&(i=r.length-n-1);var a=Math.pow(10,i),o=Math.round(t*e*a),s=o+"";if(s.indexOf("e")>=0)return s;var l=o/a,u=o%a;o<0?(l=0|-Math.ceil(l),u=0|-u):(l=0|Math.floor(l),u|=0);var c=""+l;if(o<0&&(c="-"+c),i){for(var f=""+u;f.length=t[0][i];--o)a.push({x:o*e[i],text:r(e[i],o)});n.push(a)}return n},e.equal=function(t,e){for(var r=0;r<3;++r){if(t[r].length!==e[r].length)return!1;for(var n=0;nr)throw new Error("gl-buffer: If resizing buffer, must not specify offset");return t.bufferSubData(e,a,i),r}function c(t,e){for(var r=n.malloc(t.length,e),i=t.length,a=0;a=0;--n){if(e[n]!==r)return!1;r*=t[n]}return!0}(t.shape,t.stride))0===t.offset&&t.data.length===t.shape[0]?this.length=u(this.gl,this.type,this.length,this.usage,t.data,e):this.length=u(this.gl,this.type,this.length,this.usage,t.data.subarray(t.offset,t.shape[0]),e);else{var s=n.malloc(t.size,r),l=a(s,t.shape);i.assign(l,t),this.length=u(this.gl,this.type,this.length,this.usage,e<0?s:s.subarray(0,t.size),e),n.free(s)}}else if(Array.isArray(t)){var f;f=this.type===this.gl.ELEMENT_ARRAY_BUFFER?c(t,"uint16"):c(t,"float32"),this.length=u(this.gl,this.type,this.length,this.usage,e<0?f:f.subarray(0,t.length),e),n.free(f)}else if("object"==typeof t&&"number"==typeof t.length)this.length=u(this.gl,this.type,this.length,this.usage,t,e);else{if("number"!=typeof t&&void 0!==t)throw new Error("gl-buffer: Invalid data type");if(e>=0)throw new Error("gl-buffer: Cannot specify offset when resizing buffer");(t|=0)<=0&&(t=1),this.gl.bufferData(this.type,0|t,this.usage),this.length=t}},t.exports=function(t,e,r,n){if(r=r||t.ARRAY_BUFFER,n=n||t.DYNAMIC_DRAW,r!==t.ARRAY_BUFFER&&r!==t.ELEMENT_ARRAY_BUFFER)throw new Error("gl-buffer: Invalid type for webgl buffer, must be either gl.ARRAY_BUFFER or gl.ELEMENT_ARRAY_BUFFER");if(n!==t.DYNAMIC_DRAW&&n!==t.STATIC_DRAW&&n!==t.STREAM_DRAW)throw new Error("gl-buffer: Invalid usage for buffer, must be either gl.DYNAMIC_DRAW, gl.STATIC_DRAW or gl.STREAM_DRAW");var i=t.createBuffer(),a=new s(t,r,i,0,n);return a.update(e),a}},1140:function(t,e,r){"use strict";var n=r(2858);t.exports=function(t,e){var r=t.positions,i=t.vectors,a={positions:[],vertexIntensity:[],vertexIntensityBounds:t.vertexIntensityBounds,vectors:[],cells:[],coneOffset:t.coneOffset,colormap:t.colormap};if(0===t.positions.length)return e&&(e[0]=[0,0,0],e[1]=[0,0,0]),a;for(var o=0,s=1/0,l=-1/0,u=1/0,c=-1/0,f=1/0,h=-1/0,p=null,d=null,v=[],g=1/0,y=!1,m=0;mo&&(o=n.length(b)),m){var _=2*n.distance(p,x)/(n.length(d)+n.length(b));_?(g=Math.min(g,_),y=!1):y=!0}y||(p=x,d=b),v.push(b)}var w=[s,u,f],T=[l,c,h];e&&(e[0]=w,e[1]=T),0===o&&(o=1);var k=1/o;isFinite(g)||(g=1),a.vectorScale=g;var A=t.coneSize||.5;t.absoluteConeSize&&(A=t.absoluteConeSize*k),a.coneScale=A,m=0;for(var M=0;m=1},p.isTransparent=function(){return this.opacity<1},p.pickSlots=1,p.setPickBase=function(t){this.pickId=t},p.update=function(t){t=t||{};var e=this.gl;this.dirty=!0,"lightPosition"in t&&(this.lightPosition=t.lightPosition),"opacity"in t&&(this.opacity=t.opacity),"ambient"in t&&(this.ambientLight=t.ambient),"diffuse"in t&&(this.diffuseLight=t.diffuse),"specular"in t&&(this.specularLight=t.specular),"roughness"in t&&(this.roughness=t.roughness),"fresnel"in t&&(this.fresnel=t.fresnel),void 0!==t.tubeScale&&(this.tubeScale=t.tubeScale),void 0!==t.vectorScale&&(this.vectorScale=t.vectorScale),void 0!==t.coneScale&&(this.coneScale=t.coneScale),void 0!==t.coneOffset&&(this.coneOffset=t.coneOffset),t.colormap&&(this.texture.shape=[256,256],this.texture.minFilter=e.LINEAR_MIPMAP_LINEAR,this.texture.magFilter=e.LINEAR,this.texture.setPixels(function(t){for(var e=c({colormap:t,nshades:256,format:"rgba"}),r=new Uint8Array(1024),n=0;n<256;++n){for(var i=e[n],a=0;a<3;++a)r[4*n+a]=i[a];r[4*n+3]=255*i[3]}return u(r,[256,256,4],[4,0,1])}(t.colormap)),this.texture.generateMipmap());var r=t.cells,n=t.positions,i=t.vectors;if(n&&r&&i){var a=[],o=[],s=[],l=[],f=[];this.cells=r,this.positions=n,this.vectors=i;var h=t.meshColor||[1,1,1,1],p=t.vertexIntensity,d=1/0,v=-1/0;if(p)if(t.vertexIntensityBounds)d=+t.vertexIntensityBounds[0],v=+t.vertexIntensityBounds[1];else for(var g=0;g0){var v=this.triShader;v.bind(),v.uniforms=u,this.triangleVAO.bind(),e.drawArrays(e.TRIANGLES,0,3*this.triangleCount),this.triangleVAO.unbind()}},p.drawPick=function(t){t=t||{};for(var e=this.gl,r=t.model||f,n=t.view||f,i=t.projection||f,a=[[-1e6,-1e6,-1e6],[1e6,1e6,1e6]],o=0;o<3;++o)a[0][o]=Math.max(a[0][o],this.clipBounds[0][o]),a[1][o]=Math.min(a[1][o],this.clipBounds[1][o]);this._model=[].slice.call(r),this._view=[].slice.call(n),this._projection=[].slice.call(i),this._resolution=[e.drawingBufferWidth,e.drawingBufferHeight];var s={model:r,view:n,projection:i,clipBounds:a,tubeScale:this.tubeScale,vectorScale:this.vectorScale,coneScale:this.coneScale,coneOffset:this.coneOffset,pickId:this.pickId/255},l=this.pickShader;l.bind(),l.uniforms=s,this.triangleCount>0&&(this.triangleVAO.bind(),e.drawArrays(e.TRIANGLES,0,3*this.triangleCount),this.triangleVAO.unbind())},p.pick=function(t){if(!t)return null;if(t.id!==this.pickId)return null;var e=t.value[0]+256*t.value[1]+65536*t.value[2],r=this.cells[e],n=this.positions[r[1]].slice(0,3),i={position:n,dataCoordinate:n,index:Math.floor(r[1]/48)};return"cone"===this.traceType?i.index=Math.floor(r[1]/48):"streamtube"===this.traceType&&(i.intensity=this.intensity[r[1]],i.velocity=this.vectors[r[1]].slice(0,3),i.divergence=this.vectors[r[1]][3],i.index=e),i},p.dispose=function(){this.texture.dispose(),this.triShader.dispose(),this.pickShader.dispose(),this.triangleVAO.dispose(),this.trianglePositions.dispose(),this.triangleVectors.dispose(),this.triangleColors.dispose(),this.triangleUVs.dispose(),this.triangleIds.dispose()},t.exports=function(t,e,r){var s=r.shaders;1===arguments.length&&(t=(e=t).gl);var l=function(t,e){var r=n(t,e.meshShader.vertex,e.meshShader.fragment,null,e.meshShader.attributes);return r.attributes.position.location=0,r.attributes.color.location=2,r.attributes.uv.location=3,r.attributes.vector.location=4,r}(t,s),c=function(t,e){var r=n(t,e.pickShader.vertex,e.pickShader.fragment,null,e.pickShader.attributes);return r.attributes.position.location=0,r.attributes.id.location=1,r.attributes.vector.location=4,r}(t,s),f=o(t,u(new Uint8Array([255,255,255,255]),[1,1,4]));f.generateMipmap(),f.minFilter=t.LINEAR_MIPMAP_LINEAR,f.magFilter=t.LINEAR;var p=i(t),d=i(t),v=i(t),g=i(t),y=i(t),m=new h(t,f,l,c,p,d,y,v,g,a(t,[{buffer:p,type:t.FLOAT,size:4},{buffer:y,type:t.UNSIGNED_BYTE,size:4,normalized:!0},{buffer:v,type:t.FLOAT,size:4},{buffer:g,type:t.FLOAT,size:2},{buffer:d,type:t.FLOAT,size:4}]),r.traceType||"cone");return m.update(e),m}},7234:function(t,e,r){var n=r(6832),i=n(["precision highp float;\n\nprecision highp float;\n#define GLSLIFY 1\n\nvec3 getOrthogonalVector(vec3 v) {\n // Return up-vector for only-z vector.\n // Return ax + by + cz = 0, a point that lies on the plane that has v as a normal and that isn't (0,0,0).\n // From the above if-statement we have ||a|| > 0 U ||b|| > 0.\n // Assign z = 0, x = -b, y = a:\n // a*-b + b*a + c*0 = -ba + ba + 0 = 0\n if (v.x*v.x > v.z*v.z || v.y*v.y > v.z*v.z) {\n return normalize(vec3(-v.y, v.x, 0.0));\n } else {\n return normalize(vec3(0.0, v.z, -v.y));\n }\n}\n\n// Calculate the cone vertex and normal at the given index.\n//\n// The returned vertex is for a cone with its top at origin and height of 1.0,\n// pointing in the direction of the vector attribute.\n//\n// Each cone is made up of a top vertex, a center base vertex and base perimeter vertices.\n// These vertices are used to make up the triangles of the cone by the following:\n// segment + 0 top vertex\n// segment + 1 perimeter vertex a+1\n// segment + 2 perimeter vertex a\n// segment + 3 center base vertex\n// segment + 4 perimeter vertex a\n// segment + 5 perimeter vertex a+1\n// Where segment is the number of the radial segment * 6 and a is the angle at that radial segment.\n// To go from index to segment, floor(index / 6)\n// To go from segment to angle, 2*pi * (segment/segmentCount)\n// To go from index to segment index, index - (segment*6)\n//\nvec3 getConePosition(vec3 d, float rawIndex, float coneOffset, out vec3 normal) {\n\n const float segmentCount = 8.0;\n\n float index = rawIndex - floor(rawIndex /\n (segmentCount * 6.0)) *\n (segmentCount * 6.0);\n\n float segment = floor(0.001 + index/6.0);\n float segmentIndex = index - (segment*6.0);\n\n normal = -normalize(d);\n\n if (segmentIndex > 2.99 && segmentIndex < 3.01) {\n return mix(vec3(0.0), -d, coneOffset);\n }\n\n float nextAngle = (\n (segmentIndex > 0.99 && segmentIndex < 1.01) ||\n (segmentIndex > 4.99 && segmentIndex < 5.01)\n ) ? 1.0 : 0.0;\n float angle = 2.0 * 3.14159 * ((segment + nextAngle) / segmentCount);\n\n vec3 v1 = mix(d, vec3(0.0), coneOffset);\n vec3 v2 = v1 - d;\n\n vec3 u = getOrthogonalVector(d);\n vec3 v = normalize(cross(u, d));\n\n vec3 x = u * cos(angle) * length(d)*0.25;\n vec3 y = v * sin(angle) * length(d)*0.25;\n vec3 v3 = v2 + x + y;\n if (segmentIndex < 3.0) {\n vec3 tx = u * sin(angle);\n vec3 ty = v * -cos(angle);\n vec3 tangent = tx + ty;\n normal = normalize(cross(v3 - v1, tangent));\n }\n\n if (segmentIndex == 0.0) {\n return mix(d, vec3(0.0), coneOffset);\n }\n return v3;\n}\n\nattribute vec3 vector;\nattribute vec4 color, position;\nattribute vec2 uv;\n\nuniform float vectorScale, coneScale, coneOffset;\nuniform mat4 model, view, projection, inverseModel;\nuniform vec3 eyePosition, lightPosition;\n\nvarying vec3 f_normal, f_lightDirection, f_eyeDirection, f_data, f_position;\nvarying vec4 f_color;\nvarying vec2 f_uv;\n\nvoid main() {\n // Scale the vector magnitude to stay constant with\n // model & view changes.\n vec3 normal;\n vec3 XYZ = getConePosition(mat3(model) * ((vectorScale * coneScale) * vector), position.w, coneOffset, normal);\n vec4 conePosition = model * vec4(position.xyz, 1.0) + vec4(XYZ, 0.0);\n\n //Lighting geometry parameters\n vec4 cameraCoordinate = view * conePosition;\n cameraCoordinate.xyz /= cameraCoordinate.w;\n f_lightDirection = lightPosition - cameraCoordinate.xyz;\n f_eyeDirection = eyePosition - cameraCoordinate.xyz;\n f_normal = normalize((vec4(normal, 0.0) * inverseModel).xyz);\n\n // vec4 m_position = model * vec4(conePosition, 1.0);\n vec4 t_position = view * conePosition;\n gl_Position = projection * t_position;\n\n f_color = color;\n f_data = conePosition.xyz;\n f_position = position.xyz;\n f_uv = uv;\n}\n"]),a=n(["#extension GL_OES_standard_derivatives : enable\n\nprecision highp float;\n#define GLSLIFY 1\n\nfloat beckmannDistribution(float x, float roughness) {\n float NdotH = max(x, 0.0001);\n float cos2Alpha = NdotH * NdotH;\n float tan2Alpha = (cos2Alpha - 1.0) / cos2Alpha;\n float roughness2 = roughness * roughness;\n float denom = 3.141592653589793 * roughness2 * cos2Alpha * cos2Alpha;\n return exp(tan2Alpha / roughness2) / denom;\n}\n\nfloat cookTorranceSpecular(\n vec3 lightDirection,\n vec3 viewDirection,\n vec3 surfaceNormal,\n float roughness,\n float fresnel) {\n\n float VdotN = max(dot(viewDirection, surfaceNormal), 0.0);\n float LdotN = max(dot(lightDirection, surfaceNormal), 0.0);\n\n //Half angle vector\n vec3 H = normalize(lightDirection + viewDirection);\n\n //Geometric term\n float NdotH = max(dot(surfaceNormal, H), 0.0);\n float VdotH = max(dot(viewDirection, H), 0.000001);\n float LdotH = max(dot(lightDirection, H), 0.000001);\n float G1 = (2.0 * NdotH * VdotN) / VdotH;\n float G2 = (2.0 * NdotH * LdotN) / LdotH;\n float G = min(1.0, min(G1, G2));\n \n //Distribution term\n float D = beckmannDistribution(NdotH, roughness);\n\n //Fresnel term\n float F = pow(1.0 - VdotN, fresnel);\n\n //Multiply terms and done\n return G * F * D / max(3.14159265 * VdotN, 0.000001);\n}\n\nbool outOfRange(float a, float b, float p) {\n return ((p > max(a, b)) || \n (p < min(a, b)));\n}\n\nbool outOfRange(vec2 a, vec2 b, vec2 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y));\n}\n\nbool outOfRange(vec3 a, vec3 b, vec3 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y) ||\n outOfRange(a.z, b.z, p.z));\n}\n\nbool outOfRange(vec4 a, vec4 b, vec4 p) {\n return outOfRange(a.xyz, b.xyz, p.xyz);\n}\n\nuniform vec3 clipBounds[2];\nuniform float roughness, fresnel, kambient, kdiffuse, kspecular, opacity;\nuniform sampler2D texture;\n\nvarying vec3 f_normal, f_lightDirection, f_eyeDirection, f_data, f_position;\nvarying vec4 f_color;\nvarying vec2 f_uv;\n\nvoid main() {\n if (outOfRange(clipBounds[0], clipBounds[1], f_position)) discard;\n vec3 N = normalize(f_normal);\n vec3 L = normalize(f_lightDirection);\n vec3 V = normalize(f_eyeDirection);\n\n if(gl_FrontFacing) {\n N = -N;\n }\n\n float specular = min(1.0, max(0.0, cookTorranceSpecular(L, V, N, roughness, fresnel)));\n float diffuse = min(kambient + kdiffuse * max(dot(N, L), 0.0), 1.0);\n\n vec4 surfaceColor = f_color * texture2D(texture, f_uv);\n vec4 litColor = surfaceColor.a * vec4(diffuse * surfaceColor.rgb + kspecular * vec3(1,1,1) * specular, 1.0);\n\n gl_FragColor = litColor * opacity;\n}\n"]),o=n(["precision highp float;\n\nprecision highp float;\n#define GLSLIFY 1\n\nvec3 getOrthogonalVector(vec3 v) {\n // Return up-vector for only-z vector.\n // Return ax + by + cz = 0, a point that lies on the plane that has v as a normal and that isn't (0,0,0).\n // From the above if-statement we have ||a|| > 0 U ||b|| > 0.\n // Assign z = 0, x = -b, y = a:\n // a*-b + b*a + c*0 = -ba + ba + 0 = 0\n if (v.x*v.x > v.z*v.z || v.y*v.y > v.z*v.z) {\n return normalize(vec3(-v.y, v.x, 0.0));\n } else {\n return normalize(vec3(0.0, v.z, -v.y));\n }\n}\n\n// Calculate the cone vertex and normal at the given index.\n//\n// The returned vertex is for a cone with its top at origin and height of 1.0,\n// pointing in the direction of the vector attribute.\n//\n// Each cone is made up of a top vertex, a center base vertex and base perimeter vertices.\n// These vertices are used to make up the triangles of the cone by the following:\n// segment + 0 top vertex\n// segment + 1 perimeter vertex a+1\n// segment + 2 perimeter vertex a\n// segment + 3 center base vertex\n// segment + 4 perimeter vertex a\n// segment + 5 perimeter vertex a+1\n// Where segment is the number of the radial segment * 6 and a is the angle at that radial segment.\n// To go from index to segment, floor(index / 6)\n// To go from segment to angle, 2*pi * (segment/segmentCount)\n// To go from index to segment index, index - (segment*6)\n//\nvec3 getConePosition(vec3 d, float rawIndex, float coneOffset, out vec3 normal) {\n\n const float segmentCount = 8.0;\n\n float index = rawIndex - floor(rawIndex /\n (segmentCount * 6.0)) *\n (segmentCount * 6.0);\n\n float segment = floor(0.001 + index/6.0);\n float segmentIndex = index - (segment*6.0);\n\n normal = -normalize(d);\n\n if (segmentIndex > 2.99 && segmentIndex < 3.01) {\n return mix(vec3(0.0), -d, coneOffset);\n }\n\n float nextAngle = (\n (segmentIndex > 0.99 && segmentIndex < 1.01) ||\n (segmentIndex > 4.99 && segmentIndex < 5.01)\n ) ? 1.0 : 0.0;\n float angle = 2.0 * 3.14159 * ((segment + nextAngle) / segmentCount);\n\n vec3 v1 = mix(d, vec3(0.0), coneOffset);\n vec3 v2 = v1 - d;\n\n vec3 u = getOrthogonalVector(d);\n vec3 v = normalize(cross(u, d));\n\n vec3 x = u * cos(angle) * length(d)*0.25;\n vec3 y = v * sin(angle) * length(d)*0.25;\n vec3 v3 = v2 + x + y;\n if (segmentIndex < 3.0) {\n vec3 tx = u * sin(angle);\n vec3 ty = v * -cos(angle);\n vec3 tangent = tx + ty;\n normal = normalize(cross(v3 - v1, tangent));\n }\n\n if (segmentIndex == 0.0) {\n return mix(d, vec3(0.0), coneOffset);\n }\n return v3;\n}\n\nattribute vec4 vector;\nattribute vec4 position;\nattribute vec4 id;\n\nuniform mat4 model, view, projection;\nuniform float vectorScale, coneScale, coneOffset;\n\nvarying vec3 f_position;\nvarying vec4 f_id;\n\nvoid main() {\n vec3 normal;\n vec3 XYZ = getConePosition(mat3(model) * ((vectorScale * coneScale) * vector.xyz), position.w, coneOffset, normal);\n vec4 conePosition = model * vec4(position.xyz, 1.0) + vec4(XYZ, 0.0);\n gl_Position = projection * view * conePosition;\n f_id = id;\n f_position = position.xyz;\n}\n"]),s=n(["precision highp float;\n#define GLSLIFY 1\n\nbool outOfRange(float a, float b, float p) {\n return ((p > max(a, b)) || \n (p < min(a, b)));\n}\n\nbool outOfRange(vec2 a, vec2 b, vec2 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y));\n}\n\nbool outOfRange(vec3 a, vec3 b, vec3 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y) ||\n outOfRange(a.z, b.z, p.z));\n}\n\nbool outOfRange(vec4 a, vec4 b, vec4 p) {\n return outOfRange(a.xyz, b.xyz, p.xyz);\n}\n\nuniform vec3 clipBounds[2];\nuniform float pickId;\n\nvarying vec3 f_position;\nvarying vec4 f_id;\n\nvoid main() {\n if (outOfRange(clipBounds[0], clipBounds[1], f_position)) discard;\n\n gl_FragColor = vec4(pickId, f_id.xyz);\n}"]);e.meshShader={vertex:i,fragment:a,attributes:[{name:"position",type:"vec4"},{name:"color",type:"vec4"},{name:"uv",type:"vec2"},{name:"vector",type:"vec3"}]},e.pickShader={vertex:o,fragment:s,attributes:[{name:"position",type:"vec4"},{name:"id",type:"vec4"},{name:"vector",type:"vec3"}]}},1950:function(t){t.exports={0:"NONE",1:"ONE",2:"LINE_LOOP",3:"LINE_STRIP",4:"TRIANGLES",5:"TRIANGLE_STRIP",6:"TRIANGLE_FAN",256:"DEPTH_BUFFER_BIT",512:"NEVER",513:"LESS",514:"EQUAL",515:"LEQUAL",516:"GREATER",517:"NOTEQUAL",518:"GEQUAL",519:"ALWAYS",768:"SRC_COLOR",769:"ONE_MINUS_SRC_COLOR",770:"SRC_ALPHA",771:"ONE_MINUS_SRC_ALPHA",772:"DST_ALPHA",773:"ONE_MINUS_DST_ALPHA",774:"DST_COLOR",775:"ONE_MINUS_DST_COLOR",776:"SRC_ALPHA_SATURATE",1024:"STENCIL_BUFFER_BIT",1028:"FRONT",1029:"BACK",1032:"FRONT_AND_BACK",1280:"INVALID_ENUM",1281:"INVALID_VALUE",1282:"INVALID_OPERATION",1285:"OUT_OF_MEMORY",1286:"INVALID_FRAMEBUFFER_OPERATION",2304:"CW",2305:"CCW",2849:"LINE_WIDTH",2884:"CULL_FACE",2885:"CULL_FACE_MODE",2886:"FRONT_FACE",2928:"DEPTH_RANGE",2929:"DEPTH_TEST",2930:"DEPTH_WRITEMASK",2931:"DEPTH_CLEAR_VALUE",2932:"DEPTH_FUNC",2960:"STENCIL_TEST",2961:"STENCIL_CLEAR_VALUE",2962:"STENCIL_FUNC",2963:"STENCIL_VALUE_MASK",2964:"STENCIL_FAIL",2965:"STENCIL_PASS_DEPTH_FAIL",2966:"STENCIL_PASS_DEPTH_PASS",2967:"STENCIL_REF",2968:"STENCIL_WRITEMASK",2978:"VIEWPORT",3024:"DITHER",3042:"BLEND",3088:"SCISSOR_BOX",3089:"SCISSOR_TEST",3106:"COLOR_CLEAR_VALUE",3107:"COLOR_WRITEMASK",3317:"UNPACK_ALIGNMENT",3333:"PACK_ALIGNMENT",3379:"MAX_TEXTURE_SIZE",3386:"MAX_VIEWPORT_DIMS",3408:"SUBPIXEL_BITS",3410:"RED_BITS",3411:"GREEN_BITS",3412:"BLUE_BITS",3413:"ALPHA_BITS",3414:"DEPTH_BITS",3415:"STENCIL_BITS",3553:"TEXTURE_2D",4352:"DONT_CARE",4353:"FASTEST",4354:"NICEST",5120:"BYTE",5121:"UNSIGNED_BYTE",5122:"SHORT",5123:"UNSIGNED_SHORT",5124:"INT",5125:"UNSIGNED_INT",5126:"FLOAT",5386:"INVERT",5890:"TEXTURE",6401:"STENCIL_INDEX",6402:"DEPTH_COMPONENT",6406:"ALPHA",6407:"RGB",6408:"RGBA",6409:"LUMINANCE",6410:"LUMINANCE_ALPHA",7680:"KEEP",7681:"REPLACE",7682:"INCR",7683:"DECR",7936:"VENDOR",7937:"RENDERER",7938:"VERSION",9728:"NEAREST",9729:"LINEAR",9984:"NEAREST_MIPMAP_NEAREST",9985:"LINEAR_MIPMAP_NEAREST",9986:"NEAREST_MIPMAP_LINEAR",9987:"LINEAR_MIPMAP_LINEAR",10240:"TEXTURE_MAG_FILTER",10241:"TEXTURE_MIN_FILTER",10242:"TEXTURE_WRAP_S",10243:"TEXTURE_WRAP_T",10497:"REPEAT",10752:"POLYGON_OFFSET_UNITS",16384:"COLOR_BUFFER_BIT",32769:"CONSTANT_COLOR",32770:"ONE_MINUS_CONSTANT_COLOR",32771:"CONSTANT_ALPHA",32772:"ONE_MINUS_CONSTANT_ALPHA",32773:"BLEND_COLOR",32774:"FUNC_ADD",32777:"BLEND_EQUATION_RGB",32778:"FUNC_SUBTRACT",32779:"FUNC_REVERSE_SUBTRACT",32819:"UNSIGNED_SHORT_4_4_4_4",32820:"UNSIGNED_SHORT_5_5_5_1",32823:"POLYGON_OFFSET_FILL",32824:"POLYGON_OFFSET_FACTOR",32854:"RGBA4",32855:"RGB5_A1",32873:"TEXTURE_BINDING_2D",32926:"SAMPLE_ALPHA_TO_COVERAGE",32928:"SAMPLE_COVERAGE",32936:"SAMPLE_BUFFERS",32937:"SAMPLES",32938:"SAMPLE_COVERAGE_VALUE",32939:"SAMPLE_COVERAGE_INVERT",32968:"BLEND_DST_RGB",32969:"BLEND_SRC_RGB",32970:"BLEND_DST_ALPHA",32971:"BLEND_SRC_ALPHA",33071:"CLAMP_TO_EDGE",33170:"GENERATE_MIPMAP_HINT",33189:"DEPTH_COMPONENT16",33306:"DEPTH_STENCIL_ATTACHMENT",33635:"UNSIGNED_SHORT_5_6_5",33648:"MIRRORED_REPEAT",33901:"ALIASED_POINT_SIZE_RANGE",33902:"ALIASED_LINE_WIDTH_RANGE",33984:"TEXTURE0",33985:"TEXTURE1",33986:"TEXTURE2",33987:"TEXTURE3",33988:"TEXTURE4",33989:"TEXTURE5",33990:"TEXTURE6",33991:"TEXTURE7",33992:"TEXTURE8",33993:"TEXTURE9",33994:"TEXTURE10",33995:"TEXTURE11",33996:"TEXTURE12",33997:"TEXTURE13",33998:"TEXTURE14",33999:"TEXTURE15",34e3:"TEXTURE16",34001:"TEXTURE17",34002:"TEXTURE18",34003:"TEXTURE19",34004:"TEXTURE20",34005:"TEXTURE21",34006:"TEXTURE22",34007:"TEXTURE23",34008:"TEXTURE24",34009:"TEXTURE25",34010:"TEXTURE26",34011:"TEXTURE27",34012:"TEXTURE28",34013:"TEXTURE29",34014:"TEXTURE30",34015:"TEXTURE31",34016:"ACTIVE_TEXTURE",34024:"MAX_RENDERBUFFER_SIZE",34041:"DEPTH_STENCIL",34055:"INCR_WRAP",34056:"DECR_WRAP",34067:"TEXTURE_CUBE_MAP",34068:"TEXTURE_BINDING_CUBE_MAP",34069:"TEXTURE_CUBE_MAP_POSITIVE_X",34070:"TEXTURE_CUBE_MAP_NEGATIVE_X",34071:"TEXTURE_CUBE_MAP_POSITIVE_Y",34072:"TEXTURE_CUBE_MAP_NEGATIVE_Y",34073:"TEXTURE_CUBE_MAP_POSITIVE_Z",34074:"TEXTURE_CUBE_MAP_NEGATIVE_Z",34076:"MAX_CUBE_MAP_TEXTURE_SIZE",34338:"VERTEX_ATTRIB_ARRAY_ENABLED",34339:"VERTEX_ATTRIB_ARRAY_SIZE",34340:"VERTEX_ATTRIB_ARRAY_STRIDE",34341:"VERTEX_ATTRIB_ARRAY_TYPE",34342:"CURRENT_VERTEX_ATTRIB",34373:"VERTEX_ATTRIB_ARRAY_POINTER",34466:"NUM_COMPRESSED_TEXTURE_FORMATS",34467:"COMPRESSED_TEXTURE_FORMATS",34660:"BUFFER_SIZE",34661:"BUFFER_USAGE",34816:"STENCIL_BACK_FUNC",34817:"STENCIL_BACK_FAIL",34818:"STENCIL_BACK_PASS_DEPTH_FAIL",34819:"STENCIL_BACK_PASS_DEPTH_PASS",34877:"BLEND_EQUATION_ALPHA",34921:"MAX_VERTEX_ATTRIBS",34922:"VERTEX_ATTRIB_ARRAY_NORMALIZED",34930:"MAX_TEXTURE_IMAGE_UNITS",34962:"ARRAY_BUFFER",34963:"ELEMENT_ARRAY_BUFFER",34964:"ARRAY_BUFFER_BINDING",34965:"ELEMENT_ARRAY_BUFFER_BINDING",34975:"VERTEX_ATTRIB_ARRAY_BUFFER_BINDING",35040:"STREAM_DRAW",35044:"STATIC_DRAW",35048:"DYNAMIC_DRAW",35632:"FRAGMENT_SHADER",35633:"VERTEX_SHADER",35660:"MAX_VERTEX_TEXTURE_IMAGE_UNITS",35661:"MAX_COMBINED_TEXTURE_IMAGE_UNITS",35663:"SHADER_TYPE",35664:"FLOAT_VEC2",35665:"FLOAT_VEC3",35666:"FLOAT_VEC4",35667:"INT_VEC2",35668:"INT_VEC3",35669:"INT_VEC4",35670:"BOOL",35671:"BOOL_VEC2",35672:"BOOL_VEC3",35673:"BOOL_VEC4",35674:"FLOAT_MAT2",35675:"FLOAT_MAT3",35676:"FLOAT_MAT4",35678:"SAMPLER_2D",35680:"SAMPLER_CUBE",35712:"DELETE_STATUS",35713:"COMPILE_STATUS",35714:"LINK_STATUS",35715:"VALIDATE_STATUS",35716:"INFO_LOG_LENGTH",35717:"ATTACHED_SHADERS",35718:"ACTIVE_UNIFORMS",35719:"ACTIVE_UNIFORM_MAX_LENGTH",35720:"SHADER_SOURCE_LENGTH",35721:"ACTIVE_ATTRIBUTES",35722:"ACTIVE_ATTRIBUTE_MAX_LENGTH",35724:"SHADING_LANGUAGE_VERSION",35725:"CURRENT_PROGRAM",36003:"STENCIL_BACK_REF",36004:"STENCIL_BACK_VALUE_MASK",36005:"STENCIL_BACK_WRITEMASK",36006:"FRAMEBUFFER_BINDING",36007:"RENDERBUFFER_BINDING",36048:"FRAMEBUFFER_ATTACHMENT_OBJECT_TYPE",36049:"FRAMEBUFFER_ATTACHMENT_OBJECT_NAME",36050:"FRAMEBUFFER_ATTACHMENT_TEXTURE_LEVEL",36051:"FRAMEBUFFER_ATTACHMENT_TEXTURE_CUBE_MAP_FACE",36053:"FRAMEBUFFER_COMPLETE",36054:"FRAMEBUFFER_INCOMPLETE_ATTACHMENT",36055:"FRAMEBUFFER_INCOMPLETE_MISSING_ATTACHMENT",36057:"FRAMEBUFFER_INCOMPLETE_DIMENSIONS",36061:"FRAMEBUFFER_UNSUPPORTED",36064:"COLOR_ATTACHMENT0",36096:"DEPTH_ATTACHMENT",36128:"STENCIL_ATTACHMENT",36160:"FRAMEBUFFER",36161:"RENDERBUFFER",36162:"RENDERBUFFER_WIDTH",36163:"RENDERBUFFER_HEIGHT",36164:"RENDERBUFFER_INTERNAL_FORMAT",36168:"STENCIL_INDEX8",36176:"RENDERBUFFER_RED_SIZE",36177:"RENDERBUFFER_GREEN_SIZE",36178:"RENDERBUFFER_BLUE_SIZE",36179:"RENDERBUFFER_ALPHA_SIZE",36180:"RENDERBUFFER_DEPTH_SIZE",36181:"RENDERBUFFER_STENCIL_SIZE",36194:"RGB565",36336:"LOW_FLOAT",36337:"MEDIUM_FLOAT",36338:"HIGH_FLOAT",36339:"LOW_INT",36340:"MEDIUM_INT",36341:"HIGH_INT",36346:"SHADER_COMPILER",36347:"MAX_VERTEX_UNIFORM_VECTORS",36348:"MAX_VARYING_VECTORS",36349:"MAX_FRAGMENT_UNIFORM_VECTORS",37440:"UNPACK_FLIP_Y_WEBGL",37441:"UNPACK_PREMULTIPLY_ALPHA_WEBGL",37442:"CONTEXT_LOST_WEBGL",37443:"UNPACK_COLORSPACE_CONVERSION_WEBGL",37444:"BROWSER_DEFAULT_WEBGL"}},6603:function(t,e,r){var n=r(1950);t.exports=function(t){return n[t]}},3110:function(t,e,r){"use strict";t.exports=function(t){var e=t.gl,r=n(e),o=i(e,[{buffer:r,type:e.FLOAT,size:3,offset:0,stride:40},{buffer:r,type:e.FLOAT,size:4,offset:12,stride:40},{buffer:r,type:e.FLOAT,size:3,offset:28,stride:40}]),l=a(e);l.attributes.position.location=0,l.attributes.color.location=1,l.attributes.offset.location=2;var u=new s(e,r,o,l);return u.update(t),u};var n=r(5827),i=r(2944),a=r(7667),o=[1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1];function s(t,e,r,n){this.gl=t,this.shader=n,this.buffer=e,this.vao=r,this.pixelRatio=1,this.bounds=[[1/0,1/0,1/0],[-1/0,-1/0,-1/0]],this.clipBounds=[[-1/0,-1/0,-1/0],[1/0,1/0,1/0]],this.lineWidth=[1,1,1],this.capSize=[10,10,10],this.lineCount=[0,0,0],this.lineOffset=[0,0,0],this.opacity=1,this.hasAlpha=!1}var l=s.prototype;function u(t,e){for(var r=0;r<3;++r)t[0][r]=Math.min(t[0][r],e[r]),t[1][r]=Math.max(t[1][r],e[r])}l.isOpaque=function(){return!this.hasAlpha},l.isTransparent=function(){return this.hasAlpha},l.drawTransparent=l.draw=function(t){var e=this.gl,r=this.shader.uniforms;this.shader.bind();var n=r.view=t.view||o,i=r.projection=t.projection||o;r.model=t.model||o,r.clipBounds=this.clipBounds,r.opacity=this.opacity;var a=n[12],s=n[13],l=n[14],u=n[15],c=(t._ortho?2:1)*this.pixelRatio*(i[3]*a+i[7]*s+i[11]*l+i[15]*u)/e.drawingBufferHeight;this.vao.bind();for(var f=0;f<3;++f)e.lineWidth(this.lineWidth[f]*this.pixelRatio),r.capSize=this.capSize[f]*c,this.lineCount[f]&&e.drawArrays(e.LINES,this.lineOffset[f],this.lineCount[f]);this.vao.unbind()};var c=function(){for(var t=new Array(3),e=0;e<3;++e){for(var r=[],n=1;n<=2;++n)for(var i=-1;i<=1;i+=2){var a=[0,0,0];a[(n+e)%3]=i,r.push(a)}t[e]=r}return t}();function f(t,e,r,n){for(var i=c[n],a=0;a0&&((p=c.slice())[s]+=d[1][s],i.push(c[0],c[1],c[2],v[0],v[1],v[2],v[3],0,0,0,p[0],p[1],p[2],v[0],v[1],v[2],v[3],0,0,0),u(this.bounds,p),o+=2+f(i,p,v,s)))}this.lineCount[s]=o-this.lineOffset[s]}this.buffer.update(i)}},l.dispose=function(){this.shader.dispose(),this.buffer.dispose(),this.vao.dispose()}},7667:function(t,e,r){"use strict";var n=r(6832),i=r(5158),a=n(["precision highp float;\n#define GLSLIFY 1\n\nattribute vec3 position, offset;\nattribute vec4 color;\nuniform mat4 model, view, projection;\nuniform float capSize;\nvarying vec4 fragColor;\nvarying vec3 fragPosition;\n\nvoid main() {\n vec4 worldPosition = model * vec4(position, 1.0);\n worldPosition = (worldPosition / worldPosition.w) + vec4(capSize * offset, 0.0);\n gl_Position = projection * view * worldPosition;\n fragColor = color;\n fragPosition = position;\n}"]),o=n(["precision highp float;\n#define GLSLIFY 1\n\nbool outOfRange(float a, float b, float p) {\n return ((p > max(a, b)) || \n (p < min(a, b)));\n}\n\nbool outOfRange(vec2 a, vec2 b, vec2 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y));\n}\n\nbool outOfRange(vec3 a, vec3 b, vec3 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y) ||\n outOfRange(a.z, b.z, p.z));\n}\n\nbool outOfRange(vec4 a, vec4 b, vec4 p) {\n return outOfRange(a.xyz, b.xyz, p.xyz);\n}\n\nuniform vec3 clipBounds[2];\nuniform float opacity;\nvarying vec3 fragPosition;\nvarying vec4 fragColor;\n\nvoid main() {\n if (\n outOfRange(clipBounds[0], clipBounds[1], fragPosition) ||\n fragColor.a * opacity == 0.\n ) discard;\n\n gl_FragColor = opacity * fragColor;\n}"]);t.exports=function(t){return i(t,a,o,null,[{name:"position",type:"vec3"},{name:"color",type:"vec4"},{name:"offset",type:"vec3"}])}},4234:function(t,e,r){"use strict";var n=r(8931);t.exports=function(t,e,r,n){i||(i=t.FRAMEBUFFER_UNSUPPORTED,a=t.FRAMEBUFFER_INCOMPLETE_ATTACHMENT,o=t.FRAMEBUFFER_INCOMPLETE_DIMENSIONS,s=t.FRAMEBUFFER_INCOMPLETE_MISSING_ATTACHMENT);var u=t.getExtension("WEBGL_draw_buffers");if(!l&&u&&function(t,e){var r=t.getParameter(e.MAX_COLOR_ATTACHMENTS_WEBGL);l=new Array(r+1);for(var n=0;n<=r;++n){for(var i=new Array(r),a=0;ac||r<0||r>c)throw new Error("gl-fbo: Parameters are too large for FBO");var f=1;if("color"in(n=n||{})){if((f=Math.max(0|n.color,0))<0)throw new Error("gl-fbo: Must specify a nonnegative number of colors");if(f>1){if(!u)throw new Error("gl-fbo: Multiple draw buffer extension not supported");if(f>t.getParameter(u.MAX_COLOR_ATTACHMENTS_WEBGL))throw new Error("gl-fbo: Context does not support "+f+" draw buffers")}}var h=t.UNSIGNED_BYTE,p=t.getExtension("OES_texture_float");if(n.float&&f>0){if(!p)throw new Error("gl-fbo: Context does not support floating point textures");h=t.FLOAT}else n.preferFloat&&f>0&&p&&(h=t.FLOAT);var v=!0;"depth"in n&&(v=!!n.depth);var g=!1;return"stencil"in n&&(g=!!n.stencil),new d(t,e,r,h,f,v,g,u)};var i,a,o,s,l=null;function u(t){return[t.getParameter(t.FRAMEBUFFER_BINDING),t.getParameter(t.RENDERBUFFER_BINDING),t.getParameter(t.TEXTURE_BINDING_2D)]}function c(t,e){t.bindFramebuffer(t.FRAMEBUFFER,e[0]),t.bindRenderbuffer(t.RENDERBUFFER,e[1]),t.bindTexture(t.TEXTURE_2D,e[2])}function f(t){switch(t){case i:throw new Error("gl-fbo: Framebuffer unsupported");case a:throw new Error("gl-fbo: Framebuffer incomplete attachment");case o:throw new Error("gl-fbo: Framebuffer incomplete dimensions");case s:throw new Error("gl-fbo: Framebuffer incomplete missing attachment");default:throw new Error("gl-fbo: Framebuffer failed for unspecified reason")}}function h(t,e,r,i,a,o){if(!i)return null;var s=n(t,e,r,a,i);return s.magFilter=t.NEAREST,s.minFilter=t.NEAREST,s.mipSamples=1,s.bind(),t.framebufferTexture2D(t.FRAMEBUFFER,o,t.TEXTURE_2D,s.handle,0),s}function p(t,e,r,n,i){var a=t.createRenderbuffer();return t.bindRenderbuffer(t.RENDERBUFFER,a),t.renderbufferStorage(t.RENDERBUFFER,n,e,r),t.framebufferRenderbuffer(t.FRAMEBUFFER,i,t.RENDERBUFFER,a),a}function d(t,e,r,n,i,a,o,s){this.gl=t,this._shape=[0|e,0|r],this._destroyed=!1,this._ext=s,this.color=new Array(i);for(var d=0;d1&&s.drawBuffersWEBGL(l[o]);var m=r.getExtension("WEBGL_depth_texture");m?d?t.depth=h(r,i,a,m.UNSIGNED_INT_24_8_WEBGL,r.DEPTH_STENCIL,r.DEPTH_STENCIL_ATTACHMENT):v&&(t.depth=h(r,i,a,r.UNSIGNED_SHORT,r.DEPTH_COMPONENT,r.DEPTH_ATTACHMENT)):v&&d?t._depth_rb=p(r,i,a,r.DEPTH_STENCIL,r.DEPTH_STENCIL_ATTACHMENT):v?t._depth_rb=p(r,i,a,r.DEPTH_COMPONENT16,r.DEPTH_ATTACHMENT):d&&(t._depth_rb=p(r,i,a,r.STENCIL_INDEX,r.STENCIL_ATTACHMENT));var x=r.checkFramebufferStatus(r.FRAMEBUFFER);if(x!==r.FRAMEBUFFER_COMPLETE){for(t._destroyed=!0,r.bindFramebuffer(r.FRAMEBUFFER,null),r.deleteFramebuffer(t.handle),t.handle=null,t.depth&&(t.depth.dispose(),t.depth=null),t._depth_rb&&(r.deleteRenderbuffer(t._depth_rb),t._depth_rb=null),y=0;yi||r<0||r>i)throw new Error("gl-fbo: Can't resize FBO, invalid dimensions");t._shape[0]=e,t._shape[1]=r;for(var a=u(n),o=0;o>8*p&255;this.pickOffset=r,i.bind();var d=i.uniforms;d.viewTransform=t,d.pickOffset=e,d.shape=this.shape;var v=i.attributes;return this.positionBuffer.bind(),v.position.pointer(),this.weightBuffer.bind(),v.weight.pointer(s.UNSIGNED_BYTE,!1),this.idBuffer.bind(),v.pickId.pointer(s.UNSIGNED_BYTE,!1),s.drawArrays(s.TRIANGLES,0,o),r+this.shape[0]*this.shape[1]}}}(),f.pick=function(t,e,r){var n=this.pickOffset,i=this.shape[0]*this.shape[1];if(r=n+i)return null;var a=r-n,o=this.xData,s=this.yData;return{object:this,pointId:a,dataCoord:[o[a%this.shape[0]],s[a/this.shape[0]|0]]}},f.update=function(t){var e=(t=t||{}).shape||[0,0],r=t.x||i(e[0]),o=t.y||i(e[1]),s=t.z||new Float32Array(e[0]*e[1]),l=!1!==t.zsmooth;this.xData=r,this.yData=o;var u,c,f,p,d=t.colorLevels||[0],v=t.colorValues||[0,0,0,1],g=d.length,y=this.bounds;l?(u=y[0]=r[0],c=y[1]=o[0],f=y[2]=r[r.length-1],p=y[3]=o[o.length-1]):(u=y[0]=r[0]+(r[1]-r[0])/2,c=y[1]=o[0]+(o[1]-o[0])/2,f=y[2]=r[r.length-1]+(r[r.length-1]-r[r.length-2])/2,p=y[3]=o[o.length-1]+(o[o.length-1]-o[o.length-2])/2);var m=1/(f-u),x=1/(p-c),b=e[0],_=e[1];this.shape=[b,_];var w=(l?(b-1)*(_-1):b*_)*(h.length>>>1);this.numVertices=w;for(var T=a.mallocUint8(4*w),k=a.mallocFloat32(2*w),A=a.mallocUint8(2*w),M=a.mallocUint32(w),S=0,E=l?b-1:b,L=l?_-1:_,C=0;C max(a, b)) || \n (p < min(a, b)));\n}\n\nbool outOfRange(vec2 a, vec2 b, vec2 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y));\n}\n\nbool outOfRange(vec3 a, vec3 b, vec3 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y) ||\n outOfRange(a.z, b.z, p.z));\n}\n\nbool outOfRange(vec4 a, vec4 b, vec4 p) {\n return outOfRange(a.xyz, b.xyz, p.xyz);\n}\n\nuniform vec3 clipBounds[2];\nuniform sampler2D dashTexture;\nuniform float dashScale;\nuniform float opacity;\n\nvarying vec3 worldPosition;\nvarying float pixelArcLength;\nvarying vec4 fragColor;\n\nvoid main() {\n if (\n outOfRange(clipBounds[0], clipBounds[1], worldPosition) ||\n fragColor.a * opacity == 0.\n ) discard;\n\n float dashWeight = texture2D(dashTexture, vec2(dashScale * pixelArcLength, 0)).r;\n if(dashWeight < 0.5) {\n discard;\n }\n gl_FragColor = fragColor * opacity;\n}\n"]),s=n(["precision highp float;\n#define GLSLIFY 1\n\n#define FLOAT_MAX 1.70141184e38\n#define FLOAT_MIN 1.17549435e-38\n\n// https://github.com/mikolalysenko/glsl-read-float/blob/master/index.glsl\nvec4 packFloat(float v) {\n float av = abs(v);\n\n //Handle special cases\n if(av < FLOAT_MIN) {\n return vec4(0.0, 0.0, 0.0, 0.0);\n } else if(v > FLOAT_MAX) {\n return vec4(127.0, 128.0, 0.0, 0.0) / 255.0;\n } else if(v < -FLOAT_MAX) {\n return vec4(255.0, 128.0, 0.0, 0.0) / 255.0;\n }\n\n vec4 c = vec4(0,0,0,0);\n\n //Compute exponent and mantissa\n float e = floor(log2(av));\n float m = av * pow(2.0, -e) - 1.0;\n\n //Unpack mantissa\n c[1] = floor(128.0 * m);\n m -= c[1] / 128.0;\n c[2] = floor(32768.0 * m);\n m -= c[2] / 32768.0;\n c[3] = floor(8388608.0 * m);\n\n //Unpack exponent\n float ebias = e + 127.0;\n c[0] = floor(ebias / 2.0);\n ebias -= c[0] * 2.0;\n c[1] += floor(ebias) * 128.0;\n\n //Unpack sign bit\n c[0] += 128.0 * step(0.0, -v);\n\n //Scale back to range\n return c / 255.0;\n}\n\nbool outOfRange(float a, float b, float p) {\n return ((p > max(a, b)) || \n (p < min(a, b)));\n}\n\nbool outOfRange(vec2 a, vec2 b, vec2 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y));\n}\n\nbool outOfRange(vec3 a, vec3 b, vec3 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y) ||\n outOfRange(a.z, b.z, p.z));\n}\n\nbool outOfRange(vec4 a, vec4 b, vec4 p) {\n return outOfRange(a.xyz, b.xyz, p.xyz);\n}\n\nuniform float pickId;\nuniform vec3 clipBounds[2];\n\nvarying vec3 worldPosition;\nvarying float pixelArcLength;\nvarying vec4 fragColor;\n\nvoid main() {\n if (outOfRange(clipBounds[0], clipBounds[1], worldPosition)) discard;\n\n gl_FragColor = vec4(pickId/255.0, packFloat(pixelArcLength).xyz);\n}"]),l=[{name:"position",type:"vec3"},{name:"nextPosition",type:"vec3"},{name:"arcLength",type:"float"},{name:"lineWidth",type:"float"},{name:"color",type:"vec4"}];e.createShader=function(t){return i(t,a,o,null,l)},e.createPickShader=function(t){return i(t,a,s,null,l)}},6086:function(t,e,r){"use strict";t.exports=function(t){var e=t.gl||t.scene&&t.scene.gl,r=f(e);r.attributes.position.location=0,r.attributes.nextPosition.location=1,r.attributes.arcLength.location=2,r.attributes.lineWidth.location=3,r.attributes.color.location=4;var o=h(e);o.attributes.position.location=0,o.attributes.nextPosition.location=1,o.attributes.arcLength.location=2,o.attributes.lineWidth.location=3,o.attributes.color.location=4;for(var s=n(e),l=i(e,[{buffer:s,size:3,offset:0,stride:48},{buffer:s,size:3,offset:12,stride:48},{buffer:s,size:1,offset:24,stride:48},{buffer:s,size:1,offset:28,stride:48},{buffer:s,size:4,offset:32,stride:48}]),c=u(new Array(1024),[256,1,4]),p=0;p<1024;++p)c.data[p]=255;var d=a(e,c);d.wrap=e.REPEAT;var v=new y(e,r,o,s,l,d);return v.update(t),v};var n=r(5827),i=r(2944),a=r(8931),o=new Uint8Array(4),s=new Float32Array(o.buffer),l=r(5070),u=r(5050),c=r(248),f=c.createShader,h=c.createPickShader,p=[1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1];function d(t,e){for(var r=0,n=0;n<3;++n){var i=t[n]-e[n];r+=i*i}return Math.sqrt(r)}function v(t){for(var e=[[-1e6,-1e6,-1e6],[1e6,1e6,1e6]],r=0;r<3;++r)e[0][r]=Math.max(t[0][r],e[0][r]),e[1][r]=Math.min(t[1][r],e[1][r]);return e}function g(t,e,r,n){this.arcLength=t,this.position=e,this.index=r,this.dataCoordinate=n}function y(t,e,r,n,i,a){this.gl=t,this.shader=e,this.pickShader=r,this.buffer=n,this.vao=i,this.clipBounds=[[-1/0,-1/0,-1/0],[1/0,1/0,1/0]],this.points=[],this.arcLength=[],this.vertexCount=0,this.bounds=[[0,0,0],[0,0,0]],this.pickId=0,this.lineWidth=1,this.texture=a,this.dashScale=1,this.opacity=1,this.hasAlpha=!1,this.dirty=!0,this.pixelRatio=1}var m=y.prototype;m.isTransparent=function(){return this.hasAlpha},m.isOpaque=function(){return!this.hasAlpha},m.pickSlots=1,m.setPickBase=function(t){this.pickId=t},m.drawTransparent=m.draw=function(t){if(this.vertexCount){var e=this.gl,r=this.shader,n=this.vao;r.bind(),r.uniforms={model:t.model||p,view:t.view||p,projection:t.projection||p,clipBounds:v(this.clipBounds),dashTexture:this.texture.bind(),dashScale:this.dashScale/this.arcLength[this.arcLength.length-1],opacity:this.opacity,screenShape:[e.drawingBufferWidth,e.drawingBufferHeight],pixelRatio:this.pixelRatio},n.bind(),n.draw(e.TRIANGLE_STRIP,this.vertexCount),n.unbind()}},m.drawPick=function(t){if(this.vertexCount){var e=this.gl,r=this.pickShader,n=this.vao;r.bind(),r.uniforms={model:t.model||p,view:t.view||p,projection:t.projection||p,pickId:this.pickId,clipBounds:v(this.clipBounds),screenShape:[e.drawingBufferWidth,e.drawingBufferHeight],pixelRatio:this.pixelRatio},n.bind(),n.draw(e.TRIANGLE_STRIP,this.vertexCount),n.unbind()}},m.update=function(t){var e,r;this.dirty=!0;var n=!!t.connectGaps;"dashScale"in t&&(this.dashScale=t.dashScale),this.hasAlpha=!1,"opacity"in t&&(this.opacity=+t.opacity,this.opacity<1&&(this.hasAlpha=!0));var i=[],a=[],o=[],s=0,c=0,f=[[1/0,1/0,1/0],[-1/0,-1/0,-1/0]],h=t.position||t.positions;if(h){var p=t.color||t.colors||[0,0,0,1],v=t.lineWidth||1,g=!1;t:for(e=1;e0){for(var w=0;w<24;++w)i.push(i[i.length-12]);c+=2,g=!0}continue t}f[0][r]=Math.min(f[0][r],b[r],_[r]),f[1][r]=Math.max(f[1][r],b[r],_[r])}Array.isArray(p[0])?(y=p.length>e-1?p[e-1]:p.length>0?p[p.length-1]:[0,0,0,1],m=p.length>e?p[e]:p.length>0?p[p.length-1]:[0,0,0,1]):y=m=p,3===y.length&&(y=[y[0],y[1],y[2],1]),3===m.length&&(m=[m[0],m[1],m[2],1]),!this.hasAlpha&&y[3]<1&&(this.hasAlpha=!0),x=Array.isArray(v)?v.length>e-1?v[e-1]:v.length>0?v[v.length-1]:[0,0,0,1]:v;var T=s;if(s+=d(b,_),g){for(r=0;r<2;++r)i.push(b[0],b[1],b[2],_[0],_[1],_[2],T,x,y[0],y[1],y[2],y[3]);c+=2,g=!1}i.push(b[0],b[1],b[2],_[0],_[1],_[2],T,x,y[0],y[1],y[2],y[3],b[0],b[1],b[2],_[0],_[1],_[2],T,-x,y[0],y[1],y[2],y[3],_[0],_[1],_[2],b[0],b[1],b[2],s,-x,m[0],m[1],m[2],m[3],_[0],_[1],_[2],b[0],b[1],b[2],s,x,m[0],m[1],m[2],m[3]),c+=4}}if(this.buffer.update(i),a.push(s),o.push(h[h.length-1].slice()),this.bounds=f,this.vertexCount=c,this.points=o,this.arcLength=a,"dashes"in t){var k=t.dashes.slice();for(k.unshift(0),e=1;e1.0001)return null;y+=g[f]}return Math.abs(y-1)>.001?null:[h,s(t,g),g]}},2056:function(t,e,r){var n=r(6832),i=n(["precision highp float;\n#define GLSLIFY 1\n\nattribute vec3 position, normal;\nattribute vec4 color;\nattribute vec2 uv;\n\nuniform mat4 model\n , view\n , projection\n , inverseModel;\nuniform vec3 eyePosition\n , lightPosition;\n\nvarying vec3 f_normal\n , f_lightDirection\n , f_eyeDirection\n , f_data;\nvarying vec4 f_color;\nvarying vec2 f_uv;\n\nvec4 project(vec3 p) {\n return projection * view * model * vec4(p, 1.0);\n}\n\nvoid main() {\n gl_Position = project(position);\n\n //Lighting geometry parameters\n vec4 cameraCoordinate = view * vec4(position , 1.0);\n cameraCoordinate.xyz /= cameraCoordinate.w;\n f_lightDirection = lightPosition - cameraCoordinate.xyz;\n f_eyeDirection = eyePosition - cameraCoordinate.xyz;\n f_normal = normalize((vec4(normal, 0.0) * inverseModel).xyz);\n\n f_color = color;\n f_data = position;\n f_uv = uv;\n}\n"]),a=n(["#extension GL_OES_standard_derivatives : enable\n\nprecision highp float;\n#define GLSLIFY 1\n\nfloat beckmannDistribution(float x, float roughness) {\n float NdotH = max(x, 0.0001);\n float cos2Alpha = NdotH * NdotH;\n float tan2Alpha = (cos2Alpha - 1.0) / cos2Alpha;\n float roughness2 = roughness * roughness;\n float denom = 3.141592653589793 * roughness2 * cos2Alpha * cos2Alpha;\n return exp(tan2Alpha / roughness2) / denom;\n}\n\nfloat cookTorranceSpecular(\n vec3 lightDirection,\n vec3 viewDirection,\n vec3 surfaceNormal,\n float roughness,\n float fresnel) {\n\n float VdotN = max(dot(viewDirection, surfaceNormal), 0.0);\n float LdotN = max(dot(lightDirection, surfaceNormal), 0.0);\n\n //Half angle vector\n vec3 H = normalize(lightDirection + viewDirection);\n\n //Geometric term\n float NdotH = max(dot(surfaceNormal, H), 0.0);\n float VdotH = max(dot(viewDirection, H), 0.000001);\n float LdotH = max(dot(lightDirection, H), 0.000001);\n float G1 = (2.0 * NdotH * VdotN) / VdotH;\n float G2 = (2.0 * NdotH * LdotN) / LdotH;\n float G = min(1.0, min(G1, G2));\n \n //Distribution term\n float D = beckmannDistribution(NdotH, roughness);\n\n //Fresnel term\n float F = pow(1.0 - VdotN, fresnel);\n\n //Multiply terms and done\n return G * F * D / max(3.14159265 * VdotN, 0.000001);\n}\n\n//#pragma glslify: beckmann = require(glsl-specular-beckmann) // used in gl-surface3d\n\nbool outOfRange(float a, float b, float p) {\n return ((p > max(a, b)) || \n (p < min(a, b)));\n}\n\nbool outOfRange(vec2 a, vec2 b, vec2 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y));\n}\n\nbool outOfRange(vec3 a, vec3 b, vec3 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y) ||\n outOfRange(a.z, b.z, p.z));\n}\n\nbool outOfRange(vec4 a, vec4 b, vec4 p) {\n return outOfRange(a.xyz, b.xyz, p.xyz);\n}\n\nuniform vec3 clipBounds[2];\nuniform float roughness\n , fresnel\n , kambient\n , kdiffuse\n , kspecular;\nuniform sampler2D texture;\n\nvarying vec3 f_normal\n , f_lightDirection\n , f_eyeDirection\n , f_data;\nvarying vec4 f_color;\nvarying vec2 f_uv;\n\nvoid main() {\n if (f_color.a == 0.0 ||\n outOfRange(clipBounds[0], clipBounds[1], f_data)\n ) discard;\n\n vec3 N = normalize(f_normal);\n vec3 L = normalize(f_lightDirection);\n vec3 V = normalize(f_eyeDirection);\n\n if(gl_FrontFacing) {\n N = -N;\n }\n\n float specular = min(1.0, max(0.0, cookTorranceSpecular(L, V, N, roughness, fresnel)));\n //float specular = max(0.0, beckmann(L, V, N, roughness)); // used in gl-surface3d\n\n float diffuse = min(kambient + kdiffuse * max(dot(N, L), 0.0), 1.0);\n\n vec4 surfaceColor = vec4(f_color.rgb, 1.0) * texture2D(texture, f_uv);\n vec4 litColor = surfaceColor.a * vec4(diffuse * surfaceColor.rgb + kspecular * vec3(1,1,1) * specular, 1.0);\n\n gl_FragColor = litColor * f_color.a;\n}\n"]),o=n(["precision highp float;\n#define GLSLIFY 1\n\nattribute vec3 position;\nattribute vec4 color;\nattribute vec2 uv;\n\nuniform mat4 model, view, projection;\n\nvarying vec4 f_color;\nvarying vec3 f_data;\nvarying vec2 f_uv;\n\nvoid main() {\n gl_Position = projection * view * model * vec4(position, 1.0);\n f_color = color;\n f_data = position;\n f_uv = uv;\n}"]),s=n(["precision highp float;\n#define GLSLIFY 1\n\nbool outOfRange(float a, float b, float p) {\n return ((p > max(a, b)) || \n (p < min(a, b)));\n}\n\nbool outOfRange(vec2 a, vec2 b, vec2 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y));\n}\n\nbool outOfRange(vec3 a, vec3 b, vec3 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y) ||\n outOfRange(a.z, b.z, p.z));\n}\n\nbool outOfRange(vec4 a, vec4 b, vec4 p) {\n return outOfRange(a.xyz, b.xyz, p.xyz);\n}\n\nuniform vec3 clipBounds[2];\nuniform sampler2D texture;\nuniform float opacity;\n\nvarying vec4 f_color;\nvarying vec3 f_data;\nvarying vec2 f_uv;\n\nvoid main() {\n if (outOfRange(clipBounds[0], clipBounds[1], f_data)) discard;\n\n gl_FragColor = f_color * texture2D(texture, f_uv) * opacity;\n}"]),l=n(["precision highp float;\n#define GLSLIFY 1\n\nbool outOfRange(float a, float b, float p) {\n return ((p > max(a, b)) || \n (p < min(a, b)));\n}\n\nbool outOfRange(vec2 a, vec2 b, vec2 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y));\n}\n\nbool outOfRange(vec3 a, vec3 b, vec3 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y) ||\n outOfRange(a.z, b.z, p.z));\n}\n\nbool outOfRange(vec4 a, vec4 b, vec4 p) {\n return outOfRange(a.xyz, b.xyz, p.xyz);\n}\n\nattribute vec3 position;\nattribute vec4 color;\nattribute vec2 uv;\nattribute float pointSize;\n\nuniform mat4 model, view, projection;\nuniform vec3 clipBounds[2];\n\nvarying vec4 f_color;\nvarying vec2 f_uv;\n\nvoid main() {\n if (outOfRange(clipBounds[0], clipBounds[1], position)) {\n\n gl_Position = vec4(0.0, 0.0 ,0.0 ,0.0);\n } else {\n gl_Position = projection * view * model * vec4(position, 1.0);\n }\n gl_PointSize = pointSize;\n f_color = color;\n f_uv = uv;\n}"]),u=n(["precision highp float;\n#define GLSLIFY 1\n\nuniform sampler2D texture;\nuniform float opacity;\n\nvarying vec4 f_color;\nvarying vec2 f_uv;\n\nvoid main() {\n vec2 pointR = gl_PointCoord.xy - vec2(0.5, 0.5);\n if(dot(pointR, pointR) > 0.25) {\n discard;\n }\n gl_FragColor = f_color * texture2D(texture, f_uv) * opacity;\n}"]),c=n(["precision highp float;\n#define GLSLIFY 1\n\nattribute vec3 position;\nattribute vec4 id;\n\nuniform mat4 model, view, projection;\n\nvarying vec3 f_position;\nvarying vec4 f_id;\n\nvoid main() {\n gl_Position = projection * view * model * vec4(position, 1.0);\n f_id = id;\n f_position = position;\n}"]),f=n(["precision highp float;\n#define GLSLIFY 1\n\nbool outOfRange(float a, float b, float p) {\n return ((p > max(a, b)) || \n (p < min(a, b)));\n}\n\nbool outOfRange(vec2 a, vec2 b, vec2 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y));\n}\n\nbool outOfRange(vec3 a, vec3 b, vec3 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y) ||\n outOfRange(a.z, b.z, p.z));\n}\n\nbool outOfRange(vec4 a, vec4 b, vec4 p) {\n return outOfRange(a.xyz, b.xyz, p.xyz);\n}\n\nuniform vec3 clipBounds[2];\nuniform float pickId;\n\nvarying vec3 f_position;\nvarying vec4 f_id;\n\nvoid main() {\n if (outOfRange(clipBounds[0], clipBounds[1], f_position)) discard;\n\n gl_FragColor = vec4(pickId, f_id.xyz);\n}"]),h=n(["precision highp float;\n#define GLSLIFY 1\n\nbool outOfRange(float a, float b, float p) {\n return ((p > max(a, b)) || \n (p < min(a, b)));\n}\n\nbool outOfRange(vec2 a, vec2 b, vec2 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y));\n}\n\nbool outOfRange(vec3 a, vec3 b, vec3 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y) ||\n outOfRange(a.z, b.z, p.z));\n}\n\nbool outOfRange(vec4 a, vec4 b, vec4 p) {\n return outOfRange(a.xyz, b.xyz, p.xyz);\n}\n\nattribute vec3 position;\nattribute float pointSize;\nattribute vec4 id;\n\nuniform mat4 model, view, projection;\nuniform vec3 clipBounds[2];\n\nvarying vec3 f_position;\nvarying vec4 f_id;\n\nvoid main() {\n if (outOfRange(clipBounds[0], clipBounds[1], position)) {\n\n gl_Position = vec4(0.0, 0.0, 0.0, 0.0);\n } else {\n gl_Position = projection * view * model * vec4(position, 1.0);\n gl_PointSize = pointSize;\n }\n f_id = id;\n f_position = position;\n}"]),p=n(["precision highp float;\n#define GLSLIFY 1\n\nattribute vec3 position;\n\nuniform mat4 model, view, projection;\n\nvoid main() {\n gl_Position = projection * view * model * vec4(position, 1.0);\n}"]),d=n(["precision highp float;\n#define GLSLIFY 1\n\nuniform vec3 contourColor;\n\nvoid main() {\n gl_FragColor = vec4(contourColor, 1.0);\n}\n"]);e.meshShader={vertex:i,fragment:a,attributes:[{name:"position",type:"vec3"},{name:"normal",type:"vec3"},{name:"color",type:"vec4"},{name:"uv",type:"vec2"}]},e.wireShader={vertex:o,fragment:s,attributes:[{name:"position",type:"vec3"},{name:"color",type:"vec4"},{name:"uv",type:"vec2"}]},e.pointShader={vertex:l,fragment:u,attributes:[{name:"position",type:"vec3"},{name:"color",type:"vec4"},{name:"uv",type:"vec2"},{name:"pointSize",type:"float"}]},e.pickShader={vertex:c,fragment:f,attributes:[{name:"position",type:"vec3"},{name:"id",type:"vec4"}]},e.pointPickShader={vertex:h,fragment:f,attributes:[{name:"position",type:"vec3"},{name:"pointSize",type:"float"},{name:"id",type:"vec4"}]},e.contourShader={vertex:p,fragment:d,attributes:[{name:"position",type:"vec3"}]}},8116:function(t,e,r){"use strict";var n=r(5158),i=r(5827),a=r(2944),o=r(8931),s=r(115),l=r(104),u=r(7437),c=r(5050),f=r(9156),h=r(7212),p=r(5306),d=r(2056),v=r(4340),g=d.meshShader,y=d.wireShader,m=d.pointShader,x=d.pickShader,b=d.pointPickShader,_=d.contourShader,w=[1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1];function T(t,e,r,n,i,a,o,s,l,u,c,f,h,p,d,v,g,y,m,x,b,_,T,k,A,M,S){this.gl=t,this.pixelRatio=1,this.cells=[],this.positions=[],this.intensity=[],this.texture=e,this.dirty=!0,this.triShader=r,this.lineShader=n,this.pointShader=i,this.pickShader=a,this.pointPickShader=o,this.contourShader=s,this.trianglePositions=l,this.triangleColors=c,this.triangleNormals=h,this.triangleUVs=f,this.triangleIds=u,this.triangleVAO=p,this.triangleCount=0,this.lineWidth=1,this.edgePositions=d,this.edgeColors=g,this.edgeUVs=y,this.edgeIds=v,this.edgeVAO=m,this.edgeCount=0,this.pointPositions=x,this.pointColors=_,this.pointUVs=T,this.pointSizes=k,this.pointIds=b,this.pointVAO=A,this.pointCount=0,this.contourLineWidth=1,this.contourPositions=M,this.contourVAO=S,this.contourCount=0,this.contourColor=[0,0,0],this.contourEnable=!0,this.pickVertex=!0,this.pickId=1,this.bounds=[[1/0,1/0,1/0],[-1/0,-1/0,-1/0]],this.clipBounds=[[-1/0,-1/0,-1/0],[1/0,1/0,1/0]],this.lightPosition=[1e5,1e5,0],this.ambientLight=.8,this.diffuseLight=.8,this.specularLight=2,this.roughness=.5,this.fresnel=1.5,this.opacity=1,this.hasAlpha=!1,this.opacityscale=!1,this._model=w,this._view=w,this._projection=w,this._resolution=[1,1]}var k=T.prototype;function A(t,e){if(!e)return 1;if(!e.length)return 1;for(var r=0;rt&&r>0){var n=(e[r][0]-t)/(e[r][0]-e[r-1][0]);return e[r][1]*(1-n)+n*e[r-1][1]}}return 1}function M(t){var e=n(t,m.vertex,m.fragment);return e.attributes.position.location=0,e.attributes.color.location=2,e.attributes.uv.location=3,e.attributes.pointSize.location=4,e}function S(t){var e=n(t,x.vertex,x.fragment);return e.attributes.position.location=0,e.attributes.id.location=1,e}function E(t){var e=n(t,b.vertex,b.fragment);return e.attributes.position.location=0,e.attributes.id.location=1,e.attributes.pointSize.location=4,e}function L(t){var e=n(t,_.vertex,_.fragment);return e.attributes.position.location=0,e}k.isOpaque=function(){return!this.hasAlpha},k.isTransparent=function(){return this.hasAlpha},k.pickSlots=1,k.setPickBase=function(t){this.pickId=t},k.highlight=function(t){if(t&&this.contourEnable){for(var e=h(this.cells,this.intensity,t.intensity),r=e.cells,n=e.vertexIds,i=e.vertexWeights,a=r.length,o=p.mallocFloat32(6*a),s=0,l=0;l0&&((f=this.triShader).bind(),f.uniforms=s,this.triangleVAO.bind(),e.drawArrays(e.TRIANGLES,0,3*this.triangleCount),this.triangleVAO.unbind()),this.edgeCount>0&&this.lineWidth>0&&((f=this.lineShader).bind(),f.uniforms=s,this.edgeVAO.bind(),e.lineWidth(this.lineWidth*this.pixelRatio),e.drawArrays(e.LINES,0,2*this.edgeCount),this.edgeVAO.unbind()),this.pointCount>0&&((f=this.pointShader).bind(),f.uniforms=s,this.pointVAO.bind(),e.drawArrays(e.POINTS,0,this.pointCount),this.pointVAO.unbind()),this.contourEnable&&this.contourCount>0&&this.contourLineWidth>0&&((f=this.contourShader).bind(),f.uniforms=s,this.contourVAO.bind(),e.drawArrays(e.LINES,0,this.contourCount),this.contourVAO.unbind())},k.drawPick=function(t){t=t||{};for(var e=this.gl,r=t.model||w,n=t.view||w,i=t.projection||w,a=[[-1e6,-1e6,-1e6],[1e6,1e6,1e6]],o=0;o<3;++o)a[0][o]=Math.max(a[0][o],this.clipBounds[0][o]),a[1][o]=Math.min(a[1][o],this.clipBounds[1][o]);this._model=[].slice.call(r),this._view=[].slice.call(n),this._projection=[].slice.call(i),this._resolution=[e.drawingBufferWidth,e.drawingBufferHeight];var s,l={model:r,view:n,projection:i,clipBounds:a,pickId:this.pickId/255};(s=this.pickShader).bind(),s.uniforms=l,this.triangleCount>0&&(this.triangleVAO.bind(),e.drawArrays(e.TRIANGLES,0,3*this.triangleCount),this.triangleVAO.unbind()),this.edgeCount>0&&(this.edgeVAO.bind(),e.lineWidth(this.lineWidth*this.pixelRatio),e.drawArrays(e.LINES,0,2*this.edgeCount),this.edgeVAO.unbind()),this.pointCount>0&&((s=this.pointPickShader).bind(),s.uniforms=l,this.pointVAO.bind(),e.drawArrays(e.POINTS,0,this.pointCount),this.pointVAO.unbind())},k.pick=function(t){if(!t)return null;if(t.id!==this.pickId)return null;for(var e=t.value[0]+256*t.value[1]+65536*t.value[2],r=this.cells[e],n=this.positions,i=new Array(r.length),a=0;ai[k]&&(r.uniforms.dataAxis=u,r.uniforms.screenOffset=c,r.uniforms.color=g[t],r.uniforms.angle=y[t],a.drawArrays(a.TRIANGLES,i[k],i[A]-i[k]))),m[t]&&T&&(c[1^t]-=M*p*x[t],r.uniforms.dataAxis=f,r.uniforms.screenOffset=c,r.uniforms.color=b[t],r.uniforms.angle=_[t],a.drawArrays(a.TRIANGLES,w,T)),c[1^t]=M*s[2+(1^t)]-1,d[t+2]&&(c[1^t]+=M*p*v[t+2],ki[k]&&(r.uniforms.dataAxis=u,r.uniforms.screenOffset=c,r.uniforms.color=g[t+2],r.uniforms.angle=y[t+2],a.drawArrays(a.TRIANGLES,i[k],i[A]-i[k]))),m[t+2]&&T&&(c[1^t]+=M*p*x[t+2],r.uniforms.dataAxis=f,r.uniforms.screenOffset=c,r.uniforms.color=b[t+2],r.uniforms.angle=_[t+2],a.drawArrays(a.TRIANGLES,w,T))}),v.drawTitle=function(){var t=[0,0],e=[0,0];return function(){var r=this.plot,n=this.shader,i=r.gl,a=r.screenBox,o=r.titleCenter,s=r.titleAngle,l=r.titleColor,u=r.pixelRatio;if(this.titleCount){for(var c=0;c<2;++c)e[c]=2*(o[c]*u-a[c])/(a[2+c]-a[c])-1;n.bind(),n.uniforms.dataAxis=t,n.uniforms.screenOffset=e,n.uniforms.angle=s,n.uniforms.color=l,i.drawArrays(i.TRIANGLES,this.titleOffset,this.titleCount)}}}(),v.bind=(h=[0,0],p=[0,0],d=[0,0],function(){var t=this.plot,e=this.shader,r=t._tickBounds,n=t.dataBox,i=t.screenBox,a=t.viewBox;e.bind();for(var o=0;o<2;++o){var s=r[o],l=r[o+2]-s,u=.5*(n[o+2]+n[o]),c=n[o+2]-n[o],f=a[o],v=a[o+2]-f,g=i[o],y=i[o+2]-g;p[o]=2*l/c*v/y,h[o]=2*(s-u)/c*v/y}d[1]=2*t.pixelRatio/(i[3]-i[1]),d[0]=d[1]*(i[3]-i[1])/(i[2]-i[0]),e.uniforms.dataScale=p,e.uniforms.dataShift=h,e.uniforms.textScale=d,this.vbo.bind(),e.attributes.textCoordinate.pointer()}),v.update=function(t){var e,r,n,i,o,s=[],l=t.ticks,u=t.bounds;for(o=0;o<2;++o){var c=[Math.floor(s.length/3)],f=[-1/0],h=l[o];for(e=0;e=0){var v=e[d]-n[d]*(e[d+2]-e[d])/(n[d+2]-n[d]);0===d?o.drawLine(v,e[1],v,e[3],p[d],h[d]):o.drawLine(e[0],v,e[2],v,p[d],h[d])}}for(d=0;d=0;--t)this.objects[t].dispose();for(this.objects.length=0,t=this.overlays.length-1;t>=0;--t)this.overlays[t].dispose();this.overlays.length=0,this.gl=null},u.addObject=function(t){this.objects.indexOf(t)<0&&(this.objects.push(t),this.setDirty())},u.removeObject=function(t){for(var e=this.objects,r=0;rMath.abs(e))u.rotate(a,0,0,-t*r*Math.PI*d.rotateSpeed/window.innerWidth);else if(!d._ortho){var o=-d.zoomSpeed*i*e/window.innerHeight*(a-u.lastT())/20;u.pan(a,0,0,f*(Math.exp(o)-1))}}}),!0)},d.enableMouseListeners(),d};var n=r(8161),i=r(1152),a=r(6145),o=r(6475),s=r(2565),l=r(5233)},8245:function(t,e,r){var n=r(6832),i=r(5158),a=n(["precision mediump float;\n#define GLSLIFY 1\nattribute vec2 position;\nvarying vec2 uv;\nvoid main() {\n uv = position;\n gl_Position = vec4(position, 0, 1);\n}"]),o=n(["precision mediump float;\n#define GLSLIFY 1\n\nuniform sampler2D accumBuffer;\nvarying vec2 uv;\n\nvoid main() {\n vec4 accum = texture2D(accumBuffer, 0.5 * (uv + 1.0));\n gl_FragColor = min(vec4(1,1,1,1), accum);\n}"]);t.exports=function(t){return i(t,a,o,null,[{name:"position",type:"vec2"}])}},1059:function(t,e,r){"use strict";var n=r(4296),i=r(7453),a=r(2771),o=r(6496),s=r(2611),l=r(4234),u=r(8126),c=r(6145),f=r(1120),h=r(5268),p=r(8245),d=r(2321)({tablet:!0,featureDetect:!0});function v(){this.mouse=[-1,-1],this.screen=null,this.distance=1/0,this.index=null,this.dataCoordinate=null,this.dataPosition=null,this.object=null,this.data=null}function g(t){var e=Math.round(Math.log(Math.abs(t))/Math.log(10));if(e<0){var r=Math.round(Math.pow(10,-e));return Math.ceil(t*r)/r}return e>0?(r=Math.round(Math.pow(10,e)),Math.ceil(t/r)*r):Math.ceil(t)}function y(t){return"boolean"!=typeof t||t}t.exports={createScene:function(t){(t=t||{}).camera=t.camera||{};var e=t.canvas;e||(e=document.createElement("canvas"),t.container?t.container.appendChild(e):document.body.appendChild(e));var r=t.gl;if(r||(t.glOptions&&(d=!!t.glOptions.preserveDrawingBuffer),r=function(t,e){var r=null;try{(r=t.getContext("webgl",e))||(r=t.getContext("experimental-webgl",e))}catch(t){return null}return r}(e,t.glOptions||{premultipliedAlpha:!0,antialias:!0,preserveDrawingBuffer:d})),!r)throw new Error("webgl not supported");var m=t.bounds||[[-10,-10,-10],[10,10,10]],x=new v,b=l(r,r.drawingBufferWidth,r.drawingBufferHeight,{preferFloat:!d}),_=p(r),w=t.cameraObject&&!0===t.cameraObject._ortho||t.camera.projection&&"orthographic"===t.camera.projection.type||!1,T={eye:t.camera.eye||[2,0,0],center:t.camera.center||[0,0,0],up:t.camera.up||[0,1,0],zoomMin:t.camera.zoomMax||.1,zoomMax:t.camera.zoomMin||100,mode:t.camera.mode||"turntable",_ortho:w},k=t.axes||{},A=i(r,k);A.enable=!k.disable;var M=t.spikes||{},S=o(r,M),E=[],L=[],C=[],P=[],O=!0,I=!0,D={view:null,projection:new Array(16),model:new Array(16),_ortho:!1},z=(I=!0,[r.drawingBufferWidth,r.drawingBufferHeight]),R=t.cameraObject||n(e,T),F={gl:r,contextLost:!1,pixelRatio:t.pixelRatio||1,canvas:e,selection:x,camera:R,axes:A,axesPixels:null,spikes:S,bounds:m,objects:E,shape:z,aspect:t.aspectRatio||[1,1,1],pickRadius:t.pickRadius||10,zNear:t.zNear||.01,zFar:t.zFar||1e3,fovy:t.fovy||Math.PI/4,clearColor:t.clearColor||[0,0,0,0],autoResize:y(t.autoResize),autoBounds:y(t.autoBounds),autoScale:!!t.autoScale,autoCenter:y(t.autoCenter),clipToBounds:y(t.clipToBounds),snapToData:!!t.snapToData,onselect:t.onselect||null,onrender:t.onrender||null,onclick:t.onclick||null,cameraParams:D,oncontextloss:null,mouseListener:null,_stopped:!1,getAspectratio:function(){return{x:this.aspect[0],y:this.aspect[1],z:this.aspect[2]}},setAspectratio:function(t){this.aspect[0]=t.x,this.aspect[1]=t.y,this.aspect[2]=t.z,I=!0},setBounds:function(t,e){this.bounds[0][t]=e.min,this.bounds[1][t]=e.max},setClearColor:function(t){this.clearColor=t},clearRGBA:function(){this.gl.clearColor(this.clearColor[0],this.clearColor[1],this.clearColor[2],this.clearColor[3]),this.gl.clear(this.gl.COLOR_BUFFER_BIT|this.gl.DEPTH_BUFFER_BIT)}},B=[r.drawingBufferWidth/F.pixelRatio|0,r.drawingBufferHeight/F.pixelRatio|0];function N(){if(!F._stopped&&F.autoResize){var t=e.parentNode,r=1,n=1;t&&t!==document.body?(r=t.clientWidth,n=t.clientHeight):(r=window.innerWidth,n=window.innerHeight);var i=0|Math.ceil(r*F.pixelRatio),a=0|Math.ceil(n*F.pixelRatio);if(i!==e.width||a!==e.height){e.width=i,e.height=a;var o=e.style;o.position=o.position||"absolute",o.left="0px",o.top="0px",o.width=r+"px",o.height=n+"px",O=!0}}}function j(){for(var t=E.length,e=P.length,n=0;n0&&0===C[e-1];)C.pop(),P.pop().dispose()}function U(){if(F.contextLost)return!0;r.isContextLost()&&(F.contextLost=!0,F.mouseListener.enabled=!1,F.selection.object=null,F.oncontextloss&&F.oncontextloss())}F.autoResize&&N(),window.addEventListener("resize",N),F.update=function(t){F._stopped||(t=t||{},O=!0,I=!0)},F.add=function(t){F._stopped||(t.axes=A,E.push(t),L.push(-1),O=!0,I=!0,j())},F.remove=function(t){if(!F._stopped){var e=E.indexOf(t);e<0||(E.splice(e,1),L.pop(),O=!0,I=!0,j())}},F.dispose=function(){if(!F._stopped&&(F._stopped=!0,window.removeEventListener("resize",N),e.removeEventListener("webglcontextlost",U),F.mouseListener.enabled=!1,!F.contextLost)){A.dispose(),S.dispose();for(var t=0;tx.distance)continue;for(var u=0;u 1.0) {\n discard;\n }\n baseColor = mix(borderColor, color, step(radius, centerFraction));\n gl_FragColor = vec4(baseColor.rgb * baseColor.a, baseColor.a);\n }\n}\n"]),e.pickVertex=n(["precision mediump float;\n#define GLSLIFY 1\n\nattribute vec2 position;\nattribute vec4 pickId;\n\nuniform mat3 matrix;\nuniform float pointSize;\nuniform vec4 pickOffset;\n\nvarying vec4 fragId;\n\nvoid main() {\n vec3 hgPosition = matrix * vec3(position, 1);\n gl_Position = vec4(hgPosition.xy, 0, hgPosition.z);\n gl_PointSize = pointSize;\n\n vec4 id = pickId + pickOffset;\n id.y += floor(id.x / 256.0);\n id.x -= floor(id.x / 256.0) * 256.0;\n\n id.z += floor(id.y / 256.0);\n id.y -= floor(id.y / 256.0) * 256.0;\n\n id.w += floor(id.z / 256.0);\n id.z -= floor(id.z / 256.0) * 256.0;\n\n fragId = id;\n}\n"]),e.pickFragment=n(["precision mediump float;\n#define GLSLIFY 1\n\nvarying vec4 fragId;\n\nvoid main() {\n float radius = length(2.0 * gl_PointCoord.xy - 1.0);\n if(radius > 1.0) {\n discard;\n }\n gl_FragColor = fragId / 255.0;\n}\n"])},8271:function(t,e,r){"use strict";var n=r(5158),i=r(5827),a=r(5306),o=r(8023);function s(t,e,r,n,i){this.plot=t,this.offsetBuffer=e,this.pickBuffer=r,this.shader=n,this.pickShader=i,this.sizeMin=.5,this.sizeMinCap=2,this.sizeMax=20,this.areaRatio=1,this.pointCount=0,this.color=[1,0,0,1],this.borderColor=[0,0,0,1],this.blend=!1,this.pickOffset=0,this.points=null}t.exports=function(t,e){var r=t.gl,a=new s(t,i(r),i(r),n(r,o.pointVertex,o.pointFragment),n(r,o.pickVertex,o.pickFragment));return a.update(e),t.addObject(a),a};var l,u,c=s.prototype;c.dispose=function(){this.shader.dispose(),this.pickShader.dispose(),this.offsetBuffer.dispose(),this.pickBuffer.dispose(),this.plot.removeObject(this)},c.update=function(t){var e;function r(e,r){return e in t?t[e]:r}t=t||{},this.sizeMin=r("sizeMin",.5),this.sizeMax=r("sizeMax",20),this.color=r("color",[1,0,0,1]).slice(),this.areaRatio=r("areaRatio",1),this.borderColor=r("borderColor",[0,0,0,1]).slice(),this.blend=r("blend",!1);var n=t.positions.length>>>1,i=t.positions instanceof Float32Array,o=t.idToIndex instanceof Int32Array&&t.idToIndex.length>=n,s=t.positions,l=i?s:a.mallocFloat32(s.length),u=o?t.idToIndex:a.mallocInt32(n);if(i||l.set(s),!o)for(l.set(s),e=0;e>>1;for(r=0;r=e[0]&&a<=e[2]&&o>=e[1]&&o<=e[3]&&n++}return n}(this.points,i),c=this.plot.pickPixelRatio*Math.max(Math.min(this.sizeMinCap,this.sizeMin),Math.min(this.sizeMax,this.sizeMax/Math.pow(s,.33333)));l[0]=2/a,l[4]=2/o,l[6]=-2*i[0]/a-1,l[7]=-2*i[1]/o-1,this.offsetBuffer.bind(),r.bind(),r.attributes.position.pointer(),r.uniforms.matrix=l,r.uniforms.color=this.color,r.uniforms.borderColor=this.borderColor,r.uniforms.pointCloud=c<5,r.uniforms.pointSize=c,r.uniforms.centerFraction=Math.min(1,Math.max(0,Math.sqrt(1-this.areaRatio))),e&&(u[0]=255&t,u[1]=t>>8&255,u[2]=t>>16&255,u[3]=t>>24&255,this.pickBuffer.bind(),r.attributes.pickId.pointer(n.UNSIGNED_BYTE),r.uniforms.pickOffset=u,this.pickOffset=t);var f=n.getParameter(n.BLEND),h=n.getParameter(n.DITHER);return f&&!this.blend&&n.disable(n.BLEND),h&&n.disable(n.DITHER),n.drawArrays(n.POINTS,0,this.pointCount),f&&!this.blend&&n.enable(n.BLEND),h&&n.enable(n.DITHER),t+this.pointCount}),c.draw=c.unifiedDraw,c.drawPick=c.unifiedDraw,c.pick=function(t,e,r){var n=this.pickOffset,i=this.pointCount;if(r=n+i)return null;var a=r-n,o=this.points;return{object:this,pointId:a,dataCoord:[o[2*a],o[2*a+1]]}}},6093:function(t){t.exports=function(t,e,r,n){var i,a,o,s,l,u=e[0],c=e[1],f=e[2],h=e[3],p=r[0],d=r[1],v=r[2],g=r[3];return(a=u*p+c*d+f*v+h*g)<0&&(a=-a,p=-p,d=-d,v=-v,g=-g),1-a>1e-6?(i=Math.acos(a),o=Math.sin(i),s=Math.sin((1-n)*i)/o,l=Math.sin(n*i)/o):(s=1-n,l=n),t[0]=s*u+l*p,t[1]=s*c+l*d,t[2]=s*f+l*v,t[3]=s*h+l*g,t}},8240:function(t){"use strict";t.exports=function(t){return t||0===t?t.toString():""}},4123:function(t,e,r){"use strict";var n=r(875);t.exports=function(t,e,r){var a=i[e];if(a||(a=i[e]={}),t in a)return a[t];var o={textAlign:"center",textBaseline:"middle",lineHeight:1,font:e,lineSpacing:1.25,styletags:{breaklines:!0,bolds:!0,italics:!0,subscripts:!0,superscripts:!0},triangles:!0},s=n(t,o);o.triangles=!1;var l,u,c=n(t,o);if(r&&1!==r){for(l=0;l max(a, b)) || \n (p < min(a, b)));\n}\n\nbool outOfRange(vec2 a, vec2 b, vec2 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y));\n}\n\nbool outOfRange(vec3 a, vec3 b, vec3 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y) ||\n outOfRange(a.z, b.z, p.z));\n}\n\nbool outOfRange(vec4 a, vec4 b, vec4 p) {\n return outOfRange(a.xyz, b.xyz, p.xyz);\n}\n\nattribute vec3 position;\nattribute vec4 color;\nattribute vec2 glyph;\nattribute vec4 id;\n\nuniform vec4 highlightId;\nuniform float highlightScale;\nuniform mat4 model, view, projection;\nuniform vec3 clipBounds[2];\n\nvarying vec4 interpColor;\nvarying vec4 pickId;\nvarying vec3 dataCoordinate;\n\nvoid main() {\n if (outOfRange(clipBounds[0], clipBounds[1], position)) {\n\n gl_Position = vec4(0,0,0,0);\n } else {\n float scale = 1.0;\n if(distance(highlightId, id) < 0.0001) {\n scale = highlightScale;\n }\n\n vec4 worldPosition = model * vec4(position, 1);\n vec4 viewPosition = view * worldPosition;\n viewPosition = viewPosition / viewPosition.w;\n vec4 clipPosition = projection * (viewPosition + scale * vec4(glyph.x, -glyph.y, 0, 0));\n\n gl_Position = clipPosition;\n interpColor = color;\n pickId = id;\n dataCoordinate = position;\n }\n}"]),o=i(["precision highp float;\n#define GLSLIFY 1\n\nbool outOfRange(float a, float b, float p) {\n return ((p > max(a, b)) || \n (p < min(a, b)));\n}\n\nbool outOfRange(vec2 a, vec2 b, vec2 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y));\n}\n\nbool outOfRange(vec3 a, vec3 b, vec3 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y) ||\n outOfRange(a.z, b.z, p.z));\n}\n\nbool outOfRange(vec4 a, vec4 b, vec4 p) {\n return outOfRange(a.xyz, b.xyz, p.xyz);\n}\n\nattribute vec3 position;\nattribute vec4 color;\nattribute vec2 glyph;\nattribute vec4 id;\n\nuniform mat4 model, view, projection;\nuniform vec2 screenSize;\nuniform vec3 clipBounds[2];\nuniform float highlightScale, pixelRatio;\nuniform vec4 highlightId;\n\nvarying vec4 interpColor;\nvarying vec4 pickId;\nvarying vec3 dataCoordinate;\n\nvoid main() {\n if (outOfRange(clipBounds[0], clipBounds[1], position)) {\n\n gl_Position = vec4(0,0,0,0);\n } else {\n float scale = pixelRatio;\n if(distance(highlightId.bgr, id.bgr) < 0.001) {\n scale *= highlightScale;\n }\n\n vec4 worldPosition = model * vec4(position, 1.0);\n vec4 viewPosition = view * worldPosition;\n vec4 clipPosition = projection * viewPosition;\n clipPosition /= clipPosition.w;\n\n gl_Position = clipPosition + vec4(screenSize * scale * vec2(glyph.x, -glyph.y), 0.0, 0.0);\n interpColor = color;\n pickId = id;\n dataCoordinate = position;\n }\n}"]),s=i(["precision highp float;\n#define GLSLIFY 1\n\nbool outOfRange(float a, float b, float p) {\n return ((p > max(a, b)) || \n (p < min(a, b)));\n}\n\nbool outOfRange(vec2 a, vec2 b, vec2 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y));\n}\n\nbool outOfRange(vec3 a, vec3 b, vec3 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y) ||\n outOfRange(a.z, b.z, p.z));\n}\n\nbool outOfRange(vec4 a, vec4 b, vec4 p) {\n return outOfRange(a.xyz, b.xyz, p.xyz);\n}\n\nattribute vec3 position;\nattribute vec4 color;\nattribute vec2 glyph;\nattribute vec4 id;\n\nuniform float highlightScale;\nuniform vec4 highlightId;\nuniform vec3 axes[2];\nuniform mat4 model, view, projection;\nuniform vec2 screenSize;\nuniform vec3 clipBounds[2];\nuniform float scale, pixelRatio;\n\nvarying vec4 interpColor;\nvarying vec4 pickId;\nvarying vec3 dataCoordinate;\n\nvoid main() {\n if (outOfRange(clipBounds[0], clipBounds[1], position)) {\n\n gl_Position = vec4(0,0,0,0);\n } else {\n float lscale = pixelRatio * scale;\n if(distance(highlightId, id) < 0.0001) {\n lscale *= highlightScale;\n }\n\n vec4 clipCenter = projection * view * model * vec4(position, 1);\n vec3 dataPosition = position + 0.5*lscale*(axes[0] * glyph.x + axes[1] * glyph.y) * clipCenter.w * screenSize.y;\n vec4 clipPosition = projection * view * model * vec4(dataPosition, 1);\n\n gl_Position = clipPosition;\n interpColor = color;\n pickId = id;\n dataCoordinate = dataPosition;\n }\n}\n"]),l=i(["precision highp float;\n#define GLSLIFY 1\n\nbool outOfRange(float a, float b, float p) {\n return ((p > max(a, b)) || \n (p < min(a, b)));\n}\n\nbool outOfRange(vec2 a, vec2 b, vec2 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y));\n}\n\nbool outOfRange(vec3 a, vec3 b, vec3 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y) ||\n outOfRange(a.z, b.z, p.z));\n}\n\nbool outOfRange(vec4 a, vec4 b, vec4 p) {\n return outOfRange(a.xyz, b.xyz, p.xyz);\n}\n\nuniform vec3 fragClipBounds[2];\nuniform float opacity;\n\nvarying vec4 interpColor;\nvarying vec3 dataCoordinate;\n\nvoid main() {\n if (\n outOfRange(fragClipBounds[0], fragClipBounds[1], dataCoordinate) ||\n interpColor.a * opacity == 0.\n ) discard;\n gl_FragColor = interpColor * opacity;\n}\n"]),u=i(["precision highp float;\n#define GLSLIFY 1\n\nbool outOfRange(float a, float b, float p) {\n return ((p > max(a, b)) || \n (p < min(a, b)));\n}\n\nbool outOfRange(vec2 a, vec2 b, vec2 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y));\n}\n\nbool outOfRange(vec3 a, vec3 b, vec3 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y) ||\n outOfRange(a.z, b.z, p.z));\n}\n\nbool outOfRange(vec4 a, vec4 b, vec4 p) {\n return outOfRange(a.xyz, b.xyz, p.xyz);\n}\n\nuniform vec3 fragClipBounds[2];\nuniform float pickGroup;\n\nvarying vec4 pickId;\nvarying vec3 dataCoordinate;\n\nvoid main() {\n if (outOfRange(fragClipBounds[0], fragClipBounds[1], dataCoordinate)) discard;\n\n gl_FragColor = vec4(pickGroup, pickId.bgr);\n}"]),c=[{name:"position",type:"vec3"},{name:"color",type:"vec4"},{name:"glyph",type:"vec2"},{name:"id",type:"vec4"}],f={vertex:a,fragment:l,attributes:c},h={vertex:o,fragment:l,attributes:c},p={vertex:s,fragment:l,attributes:c},d={vertex:a,fragment:u,attributes:c},v={vertex:o,fragment:u,attributes:c},g={vertex:s,fragment:u,attributes:c};function y(t,e){var r=n(t,e),i=r.attributes;return i.position.location=0,i.color.location=1,i.glyph.location=2,i.id.location=3,r}e.createPerspective=function(t){return y(t,f)},e.createOrtho=function(t){return y(t,h)},e.createProject=function(t){return y(t,p)},e.createPickPerspective=function(t){return y(t,d)},e.createPickOrtho=function(t){return y(t,v)},e.createPickProject=function(t){return y(t,g)}},2182:function(t,e,r){"use strict";var n=r(3596),i=r(5827),a=r(2944),o=r(5306),s=r(104),l=r(9282),u=r(4123),c=r(8240),f=[1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1];function h(t,e){var r=t[0],n=t[1],i=t[2],a=t[3];return t[0]=e[0]*r+e[4]*n+e[8]*i+e[12]*a,t[1]=e[1]*r+e[5]*n+e[9]*i+e[13]*a,t[2]=e[2]*r+e[6]*n+e[10]*i+e[14]*a,t[3]=e[3]*r+e[7]*n+e[11]*i+e[15]*a,t}function p(t,e,r,n){return h(n,n),h(n,n),h(n,n)}function d(t,e){this.index=t,this.dataCoordinate=this.position=e}function v(t){return!0===t||t>1?1:t}function g(t,e,r,n,i,a,o,s,l,u,c,f){this.gl=t,this.pixelRatio=1,this.shader=e,this.orthoShader=r,this.projectShader=n,this.pointBuffer=i,this.colorBuffer=a,this.glyphBuffer=o,this.idBuffer=s,this.vao=l,this.vertexCount=0,this.lineVertexCount=0,this.opacity=1,this.hasAlpha=!1,this.lineWidth=0,this.projectScale=[2/3,2/3,2/3],this.projectOpacity=[1,1,1],this.projectHasAlpha=!1,this.pickId=0,this.pickPerspectiveShader=u,this.pickOrthoShader=c,this.pickProjectShader=f,this.points=[],this._selectResult=new d(0,[0,0,0]),this.useOrtho=!0,this.bounds=[[1/0,1/0,1/0],[-1/0,-1/0,-1/0]],this.axesProject=[!0,!0,!0],this.axesBounds=[[-1/0,-1/0,-1/0],[1/0,1/0,1/0]],this.highlightId=[1,1,1,1],this.highlightScale=2,this.clipBounds=[[-1/0,-1/0,-1/0],[1/0,1/0,1/0]],this.dirty=!0}t.exports=function(t){var e=t.gl,r=l.createPerspective(e),n=l.createOrtho(e),o=l.createProject(e),s=l.createPickPerspective(e),u=l.createPickOrtho(e),c=l.createPickProject(e),f=i(e),h=i(e),p=i(e),d=i(e),v=new g(e,r,n,o,f,h,p,d,a(e,[{buffer:f,size:3,type:e.FLOAT},{buffer:h,size:4,type:e.FLOAT},{buffer:p,size:2,type:e.FLOAT},{buffer:d,size:4,type:e.UNSIGNED_BYTE,normalized:!0}]),s,u,c);return v.update(t),v};var y=g.prototype;y.pickSlots=1,y.setPickBase=function(t){this.pickId=t},y.isTransparent=function(){if(this.hasAlpha)return!0;for(var t=0;t<3;++t)if(this.axesProject[t]&&this.projectHasAlpha)return!0;return!1},y.isOpaque=function(){if(!this.hasAlpha)return!0;for(var t=0;t<3;++t)if(this.axesProject[t]&&!this.projectHasAlpha)return!0;return!1};var m=[0,0],x=[0,0,0],b=[0,0,0],_=[0,0,0,1],w=[0,0,0,1],T=f.slice(),k=[0,0,0],A=[[0,0,0],[0,0,0]];function M(t){return t[0]=t[1]=t[2]=0,t}function S(t,e){return t[0]=e[0],t[1]=e[1],t[2]=e[2],t[3]=1,t}function E(t,e,r,n){return t[0]=e[0],t[1]=e[1],t[2]=e[2],t[r]=n,t}var L=[[-1e8,-1e8,-1e8],[1e8,1e8,1e8]];function C(t,e,r,n,i,a,o){var l=r.gl;if((a===r.projectHasAlpha||o)&&function(t,e,r,n){var i,a=e.axesProject,o=e.gl,l=t.uniforms,u=r.model||f,c=r.view||f,h=r.projection||f,d=e.axesBounds,v=function(t){for(var e=A,r=0;r<2;++r)for(var n=0;n<3;++n)e[r][n]=Math.max(Math.min(t[r][n],1e8),-1e8);return e}(e.clipBounds);i=e.axes&&e.axes.lastCubeProps?e.axes.lastCubeProps.axis:[1,1,1],m[0]=2/o.drawingBufferWidth,m[1]=2/o.drawingBufferHeight,t.bind(),l.view=c,l.projection=h,l.screenSize=m,l.highlightId=e.highlightId,l.highlightScale=e.highlightScale,l.clipBounds=v,l.pickGroup=e.pickId/255,l.pixelRatio=n;for(var g=0;g<3;++g)if(a[g]){l.scale=e.projectScale[g],l.opacity=e.projectOpacity[g];for(var y=T,L=0;L<16;++L)y[L]=0;for(L=0;L<4;++L)y[5*L]=1;y[5*g]=0,i[g]<0?y[12+g]=d[0][g]:y[12+g]=d[1][g],s(y,u,y),l.model=y;var C=(g+1)%3,P=(g+2)%3,O=M(x),I=M(b);O[C]=1,I[P]=1;var D=p(0,0,0,S(_,O)),z=p(0,0,0,S(w,I));if(Math.abs(D[1])>Math.abs(z[1])){var R=D;D=z,z=R,R=O,O=I,I=R;var F=C;C=P,P=F}D[0]<0&&(O[C]=-1),z[1]>0&&(I[P]=-1);var B=0,N=0;for(L=0;L<4;++L)B+=Math.pow(u[4*C+L],2),N+=Math.pow(u[4*P+L],2);O[C]/=Math.sqrt(B),I[P]/=Math.sqrt(N),l.axes[0]=O,l.axes[1]=I,l.fragClipBounds[0]=E(k,v[0],g,-1e8),l.fragClipBounds[1]=E(k,v[1],g,1e8),e.vao.bind(),e.vao.draw(o.TRIANGLES,e.vertexCount),e.lineWidth>0&&(o.lineWidth(e.lineWidth*n),e.vao.draw(o.LINES,e.lineVertexCount,e.vertexCount)),e.vao.unbind()}}(e,r,n,i),a===r.hasAlpha||o){t.bind();var 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vector;\nattribute vec4 color, position;\nattribute vec2 uv;\n\nuniform float vectorScale, tubeScale;\nuniform mat4 model, view, projection, inverseModel;\nuniform vec3 eyePosition, lightPosition;\n\nvarying vec3 f_normal, f_lightDirection, f_eyeDirection, f_data, f_position;\nvarying vec4 f_color;\nvarying vec2 f_uv;\n\nvoid main() {\n // Scale the vector magnitude to stay constant with\n // model & view changes.\n vec3 normal;\n vec3 XYZ = getTubePosition(mat3(model) * (tubeScale * vector.w * normalize(vector.xyz)), position.w, normal);\n vec4 tubePosition = model * vec4(position.xyz, 1.0) + vec4(XYZ, 0.0);\n\n //Lighting geometry parameters\n vec4 cameraCoordinate = view * tubePosition;\n cameraCoordinate.xyz /= cameraCoordinate.w;\n f_lightDirection = lightPosition - cameraCoordinate.xyz;\n f_eyeDirection = eyePosition - cameraCoordinate.xyz;\n f_normal = normalize((vec4(normal, 0.0) * inverseModel).xyz);\n\n // vec4 m_position = model * vec4(tubePosition, 1.0);\n vec4 t_position = 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H), 0.0);\n float VdotH = max(dot(viewDirection, H), 0.000001);\n float LdotH = max(dot(lightDirection, H), 0.000001);\n float G1 = (2.0 * NdotH * VdotN) / VdotH;\n float G2 = (2.0 * NdotH * LdotN) / LdotH;\n float G = min(1.0, min(G1, G2));\n \n //Distribution term\n float D = beckmannDistribution(NdotH, roughness);\n\n //Fresnel term\n float F = pow(1.0 - VdotN, fresnel);\n\n //Multiply terms and done\n return G * F * D / max(3.14159265 * VdotN, 0.000001);\n}\n\nbool outOfRange(float a, float b, float p) {\n return ((p > max(a, b)) || \n (p < min(a, b)));\n}\n\nbool outOfRange(vec2 a, vec2 b, vec2 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y));\n}\n\nbool outOfRange(vec3 a, vec3 b, vec3 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y) ||\n outOfRange(a.z, b.z, p.z));\n}\n\nbool outOfRange(vec4 a, vec4 b, vec4 p) {\n return outOfRange(a.xyz, b.xyz, p.xyz);\n}\n\nuniform vec3 clipBounds[2];\nuniform float roughness, fresnel, kambient, 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the plane that has v as a normal and that isn't (0,0,0).\n // From the above if-statement we have ||a|| > 0 U ||b|| > 0.\n // Assign z = 0, x = -b, y = a:\n // a*-b + b*a + c*0 = -ba + ba + 0 = 0\n if (v.x*v.x > v.z*v.z || v.y*v.y > v.z*v.z) {\n return normalize(vec3(-v.y, v.x, 0.0));\n } else {\n return normalize(vec3(0.0, v.z, -v.y));\n }\n}\n\n// Calculate the tube vertex and normal at the given index.\n//\n// The returned vertex is for a tube ring with its center at origin, radius of length(d), pointing in the direction of d.\n//\n// Each tube segment is made up of a ring of vertices.\n// These vertices are used to make up the triangles of the tube by connecting them together in the vertex array.\n// The indexes of tube segments run from 0 to 8.\n//\nvec3 getTubePosition(vec3 d, float index, out vec3 normal) {\n float segmentCount = 8.0;\n\n float angle = 2.0 * 3.14159 * (index / segmentCount);\n\n vec3 u = getOrthogonalVector(d);\n vec3 v = normalize(cross(u, d));\n\n vec3 x = u * 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b.y, p.y) ||\n outOfRange(a.z, b.z, p.z));\n}\n\nbool outOfRange(vec4 a, vec4 b, vec4 p) {\n return outOfRange(a.xyz, b.xyz, p.xyz);\n}\n\nuniform vec3 clipBounds[2];\nuniform float pickId;\n\nvarying vec3 f_position;\nvarying vec4 f_id;\n\nvoid main() {\n if (outOfRange(clipBounds[0], clipBounds[1], f_position)) discard;\n\n gl_FragColor = vec4(pickId, f_id.xyz);\n}"]);e.meshShader={vertex:i,fragment:a,attributes:[{name:"position",type:"vec4"},{name:"color",type:"vec4"},{name:"uv",type:"vec2"},{name:"vector",type:"vec4"}]},e.pickShader={vertex:o,fragment:s,attributes:[{name:"position",type:"vec4"},{name:"id",type:"vec4"},{name:"vector",type:"vec4"}]}},7307:function(t,e,r){"use strict";var n=r(2858),i=r(4020),a=["xyz","xzy","yxz","yzx","zxy","zyx"],o=function(t,e){var r,n=t.length;for(r=0;re)return r-1}return r},s=function(t,e,r){return tr?r:t},l=function(t){var e=1/0;t.sort((function(t,e){return t-e}));for(var r=t.length,n=1;nf-1||m>h-1||x>p-1)return n.create();var b,_,w,T,k,A,M=a[0][d],S=a[0][y],E=a[1][v],L=a[1][m],C=a[2][g],P=(l-M)/(S-M),O=(u-E)/(L-E),I=(c-C)/(a[2][x]-C);switch(isFinite(P)||(P=.5),isFinite(O)||(O=.5),isFinite(I)||(I=.5),r.reversedX&&(d=f-1-d,y=f-1-y),r.reversedY&&(v=h-1-v,m=h-1-m),r.reversedZ&&(g=p-1-g,x=p-1-x),r.filled){case 5:k=g,A=x,w=v*p,T=m*p,b=d*p*h,_=y*p*h;break;case 4:k=g,A=x,b=d*p,_=y*p,w=v*p*f,T=m*p*f;break;case 3:w=v,T=m,k=g*h,A=x*h,b=d*h*p,_=y*h*p;break;case 2:w=v,T=m,b=d*h,_=y*h,k=g*h*f,A=x*h*f;break;case 1:b=d,_=y,k=g*f,A=x*f,w=v*f*p,T=m*f*p;break;default:b=d,_=y,w=v*f,T=m*f,k=g*f*h,A=x*f*h}var D=i[b+w+k],z=i[b+w+A],R=i[b+T+k],F=i[b+T+A],B=i[_+w+k],N=i[_+w+A],j=i[_+T+k],U=i[_+T+A],V=n.create(),H=n.create(),q=n.create(),G=n.create();n.lerp(V,D,B,P),n.lerp(H,z,N,P),n.lerp(q,R,j,P),n.lerp(G,F,U,P);var Z=n.create(),Y=n.create();n.lerp(Z,V,q,O),n.lerp(Y,H,G,O);var W=n.create();return n.lerp(W,Z,Y,I),W}(e,t,p)},v=t.getDivergence||function(t,e){var r=n.create(),i=1e-4;n.add(r,t,[i,0,0]);var a=d(r);n.subtract(a,a,e),n.scale(a,a,1/i),n.add(r,t,[0,i,0]);var o=d(r);n.subtract(o,o,e),n.scale(o,o,1/i),n.add(r,t,[0,0,i]);var s=d(r);return n.subtract(s,s,e),n.scale(s,s,1/i),n.add(r,a,o),n.add(r,r,s),r},g=[],y=e[0][0],m=e[0][1],x=e[0][2],b=e[1][0],_=e[1][1],w=e[1][2],T=function(t){var e=t[0],r=t[1],n=t[2];return!(eb||r_||nw)},k=10*n.distance(e[0],e[1])/u,A=k*k,M=1,S=0,E=r.length;E>1&&(M=function(t){for(var e=[],r=[],n=[],i={},a={},o={},s=t.length,u=0;uS&&(S=F),z.push(F),g.push({points:P,velocities:O,divergences:z});for(var B=0;B<100*u&&P.lengthA&&n.scale(N,N,k/Math.sqrt(j)),n.add(N,N,C),I=d(N),n.squaredDistance(D,N)-A>-1e-4*A&&(P.push(N),D=N,O.push(I),R=v(N,I),F=n.length(R),isFinite(F)&&F>S&&(S=F),z.push(F)),C=N}}var U=function(t,e,r,a){for(var o=0,s=0;s0)for(T=0;T<8;T++){var k=(T+1)%8;u.push(h[T],p[T],p[k],p[k],h[k],h[T]),f.push(m,y,y,y,m,m),d.push(v,g,g,g,v,v);var A=u.length;c.push([A-6,A-5,A-4],[A-3,A-2,A-1])}var M=h;h=p,p=M;var S=m;m=y,y=S;var E=v;v=g,g=E}return{positions:u,cells:c,vectors:f,vertexIntensity:d}}(t,r,a,o)})),f=[],h=[],p=[],d=[];for(s=0;s max(a, b)) || \n (p < min(a, b)));\n}\n\nbool outOfRange(vec2 a, vec2 b, vec2 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y));\n}\n\nbool outOfRange(vec3 a, vec3 b, vec3 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y) ||\n outOfRange(a.z, b.z, p.z));\n}\n\nbool outOfRange(vec4 a, vec4 b, vec4 p) {\n return outOfRange(a.xyz, b.xyz, p.xyz);\n}\n\nuniform vec3 lowerBound, upperBound;\nuniform float contourTint;\nuniform vec4 contourColor;\nuniform sampler2D colormap;\nuniform vec3 clipBounds[2];\nuniform float roughness, fresnel, kambient, kdiffuse, kspecular, opacity;\nuniform float vertexColor;\n\nvarying float value, kill;\nvarying vec3 worldCoordinate;\nvarying vec3 lightDirection, eyeDirection, surfaceNormal;\nvarying vec4 vColor;\n\nvoid main() {\n if (\n kill > 0.0 ||\n vColor.a == 0.0 ||\n outOfRange(clipBounds[0], clipBounds[1], worldCoordinate)\n ) discard;\n\n vec3 N = normalize(surfaceNormal);\n vec3 V = normalize(eyeDirection);\n vec3 L = normalize(lightDirection);\n\n if(gl_FrontFacing) {\n N = -N;\n }\n\n float specular = max(beckmannSpecular(L, V, N, roughness), 0.);\n float diffuse = min(kambient + kdiffuse * max(dot(N, L), 0.0), 1.0);\n\n //decide how to interpolate color — in vertex or in fragment\n vec4 surfaceColor =\n step(vertexColor, .5) * texture2D(colormap, vec2(value, value)) +\n step(.5, vertexColor) * vColor;\n\n vec4 litColor = surfaceColor.a * vec4(diffuse * surfaceColor.rgb + kspecular * vec3(1,1,1) * specular, 1.0);\n\n gl_FragColor = mix(litColor, contourColor, contourTint) * opacity;\n}\n"]),s=i(["precision highp float;\n#define GLSLIFY 1\n\nattribute vec4 uv;\nattribute float f;\n\nuniform vec3 objectOffset;\nuniform mat3 permutation;\nuniform mat4 model, view, projection;\nuniform float height, zOffset;\nuniform sampler2D colormap;\n\nvarying float value, kill;\nvarying vec3 worldCoordinate;\nvarying vec2 planeCoordinate;\nvarying vec3 lightDirection, eyeDirection, surfaceNormal;\nvarying vec4 vColor;\n\nvoid main() {\n vec3 dataCoordinate = permutation * vec3(uv.xy, height);\n worldCoordinate = objectOffset + dataCoordinate;\n vec4 worldPosition = model * vec4(worldCoordinate, 1.0);\n\n vec4 clipPosition = projection * view * worldPosition;\n clipPosition.z += zOffset;\n\n gl_Position = clipPosition;\n value = f + objectOffset.z;\n kill = -1.0;\n planeCoordinate = uv.zw;\n\n vColor = texture2D(colormap, vec2(value, value));\n\n //Don't do lighting for contours\n surfaceNormal = vec3(1,0,0);\n eyeDirection = vec3(0,1,0);\n lightDirection = vec3(0,0,1);\n}\n"]),l=i(["precision highp float;\n#define GLSLIFY 1\n\nbool outOfRange(float a, float b, float p) {\n return ((p > max(a, b)) || \n (p < min(a, b)));\n}\n\nbool outOfRange(vec2 a, vec2 b, vec2 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y));\n}\n\nbool outOfRange(vec3 a, vec3 b, vec3 p) {\n return (outOfRange(a.x, b.x, p.x) ||\n outOfRange(a.y, b.y, p.y) ||\n outOfRange(a.z, b.z, p.z));\n}\n\nbool outOfRange(vec4 a, vec4 b, vec4 p) {\n return outOfRange(a.xyz, b.xyz, p.xyz);\n}\n\nuniform vec2 shape;\nuniform vec3 clipBounds[2];\nuniform float pickId;\n\nvarying float value, kill;\nvarying vec3 worldCoordinate;\nvarying vec2 planeCoordinate;\nvarying vec3 surfaceNormal;\n\nvec2 splitFloat(float v) {\n float vh = 255.0 * v;\n float upper = floor(vh);\n float lower = fract(vh);\n return vec2(upper / 255.0, floor(lower * 16.0) / 16.0);\n}\n\nvoid main() {\n if ((kill > 0.0) ||\n (outOfRange(clipBounds[0], clipBounds[1], worldCoordinate))) discard;\n\n vec2 ux = splitFloat(planeCoordinate.x / shape.x);\n vec2 uy = splitFloat(planeCoordinate.y / shape.y);\n gl_FragColor = vec4(pickId, ux.x, uy.x, ux.y + (uy.y/16.0));\n}\n"]);e.createShader=function(t){var e=n(t,a,o,null,[{name:"uv",type:"vec4"},{name:"f",type:"vec3"},{name:"normal",type:"vec3"}]);return e.attributes.uv.location=0,e.attributes.f.location=1,e.attributes.normal.location=2,e},e.createPickShader=function(t){var e=n(t,a,l,null,[{name:"uv",type:"vec4"},{name:"f",type:"vec3"},{name:"normal",type:"vec3"}]);return e.attributes.uv.location=0,e.attributes.f.location=1,e.attributes.normal.location=2,e},e.createContourShader=function(t){var e=n(t,s,o,null,[{name:"uv",type:"vec4"},{name:"f",type:"float"}]);return e.attributes.uv.location=0,e.attributes.f.location=1,e},e.createPickContourShader=function(t){var e=n(t,s,l,null,[{name:"uv",type:"vec4"},{name:"f",type:"float"}]);return e.attributes.uv.location=0,e.attributes.f.location=1,e}},3754:function(t,e,r){"use strict";t.exports=function(t){var e=t.gl,r=m(e),n=b(e),s=x(e),l=_(e),u=i(e),c=a(e,[{buffer:u,size:4,stride:w,offset:0},{buffer:u,size:3,stride:w,offset:16},{buffer:u,size:3,stride:w,offset:28}]),f=i(e),h=a(e,[{buffer:f,size:4,stride:20,offset:0},{buffer:f,size:1,stride:20,offset:16}]),p=i(e),d=a(e,[{buffer:p,size:2,type:e.FLOAT}]),v=o(e,1,S,e.RGBA,e.UNSIGNED_BYTE);v.minFilter=e.LINEAR,v.magFilter=e.LINEAR;var g=new E(e,[0,0],[[0,0,0],[0,0,0]],r,n,u,c,v,s,l,f,h,p,d,[0,0,0]),y={levels:[[],[],[]]};for(var T in t)y[T]=t[T];return y.colormap=y.colormap||"jet",g.update(y),g};var n=r(2288),i=r(5827),a=r(2944),o=r(8931),s=r(5306),l=r(9156),u=r(7498),c=r(7382),f=r(5050),h=r(4162),p=r(104),d=r(7437),v=r(5070),g=r(9144),y=r(9054),m=y.createShader,x=y.createContourShader,b=y.createPickShader,_=y.createPickContourShader,w=40,T=[1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1],k=[[0,0],[0,1],[1,0],[1,1],[1,0],[0,1]],A=[[0,0,0,0,0,0,0,0,0],[0,0,0,0,0,0,0,0,0],[0,0,0,0,0,0,0,0,0]];function M(t,e,r,n,i){this.position=t,this.index=e,this.uv=r,this.level=n,this.dataCoordinate=i}!function(){for(var t=0;t<3;++t){var e=A[t],r=(t+2)%3;e[(t+1)%3+0]=1,e[r+3]=1,e[t+6]=1}}();var S=256;function E(t,e,r,n,i,a,o,l,u,c,h,p,d,v,g){this.gl=t,this.shape=e,this.bounds=r,this.objectOffset=g,this.intensityBounds=[],this._shader=n,this._pickShader=i,this._coordinateBuffer=a,this._vao=o,this._colorMap=l,this._contourShader=u,this._contourPickShader=c,this._contourBuffer=h,this._contourVAO=p,this._contourOffsets=[[],[],[]],this._contourCounts=[[],[],[]],this._vertexCount=0,this._pickResult=new M([0,0,0],[0,0],[0,0],[0,0,0],[0,0,0]),this._dynamicBuffer=d,this._dynamicVAO=v,this._dynamicOffsets=[0,0,0],this._dynamicCounts=[0,0,0],this.contourWidth=[1,1,1],this.contourLevels=[[1],[1],[1]],this.contourTint=[0,0,0],this.contourColor=[[.5,.5,.5,1],[.5,.5,.5,1],[.5,.5,.5,1]],this.showContour=!0,this.showSurface=!0,this.enableHighlight=[!0,!0,!0],this.highlightColor=[[0,0,0,1],[0,0,0,1],[0,0,0,1]],this.highlightTint=[1,1,1],this.highlightLevel=[-1,-1,-1],this.enableDynamic=[!0,!0,!0],this.dynamicLevel=[NaN,NaN,NaN],this.dynamicColor=[[0,0,0,1],[0,0,0,1],[0,0,0,1]],this.dynamicTint=[1,1,1],this.dynamicWidth=[1,1,1],this.axesBounds=[[1/0,1/0,1/0],[-1/0,-1/0,-1/0]],this.surfaceProject=[!1,!1,!1],this.contourProject=[[!1,!1,!1],[!1,!1,!1],[!1,!1,!1]],this.colorBounds=[!1,!1],this._field=[f(s.mallocFloat(1024),[0,0]),f(s.mallocFloat(1024),[0,0]),f(s.mallocFloat(1024),[0,0])],this.pickId=1,this.clipBounds=[[-1/0,-1/0,-1/0],[1/0,1/0,1/0]],this.snapToData=!1,this.pixelRatio=1,this.opacity=1,this.lightPosition=[10,1e4,0],this.ambientLight=.8,this.diffuseLight=.8,this.specularLight=2,this.roughness=.5,this.fresnel=1.5,this.vertexColor=0,this.dirty=!0}var L=E.prototype;L.genColormap=function(t,e){var r=!1,n=c([l({colormap:t,nshades:S,format:"rgba"}).map((function(t,n){var i=e?function(t,e){if(!e)return 1;if(!e.length)return 1;for(var r=0;rt&&r>0){var n=(e[r][0]-t)/(e[r][0]-e[r-1][0]);return e[r][1]*(1-n)+n*e[r-1][1]}}return 1}(n/255,e):t[3];return i<1&&(r=!0),[t[0],t[1],t[2],255*i]}))]);return u.divseq(n,255),this.hasAlphaScale=r,n},L.isTransparent=function(){return this.opacity<1||this.hasAlphaScale},L.isOpaque=function(){return!this.isTransparent()},L.pickSlots=1,L.setPickBase=function(t){this.pickId=t};var C=[0,0,0],P={showSurface:!1,showContour:!1,projections:[T.slice(),T.slice(),T.slice()],clipBounds:[[[0,0,0],[0,0,0]],[[0,0,0],[0,0,0]],[[0,0,0],[0,0,0]]]};function O(t,e){var r,n,i,a=e.axes&&e.axes.lastCubeProps.axis||C,o=e.showSurface,s=e.showContour;for(r=0;r<3;++r)for(o=o||e.surfaceProject[r],n=0;n<3;++n)s=s||e.contourProject[r][n];for(r=0;r<3;++r){var l=P.projections[r];for(n=0;n<16;++n)l[n]=0;for(n=0;n<4;++n)l[5*n]=1;l[5*r]=0,l[12+r]=e.axesBounds[+(a[r]>0)][r],p(l,t.model,l);var u=P.clipBounds[r];for(i=0;i<2;++i)for(n=0;n<3;++n)u[i][n]=t.clipBounds[i][n];u[0][r]=-1e8,u[1][r]=1e8}return P.showSurface=o,P.showContour=s,P}var I={model:T,view:T,projection:T,inverseModel:T.slice(),lowerBound:[0,0,0],upperBound:[0,0,0],colorMap:0,clipBounds:[[0,0,0],[0,0,0]],height:0,contourTint:0,contourColor:[0,0,0,1],permutation:[1,0,0,0,1,0,0,0,1],zOffset:-1e-4,objectOffset:[0,0,0],kambient:1,kdiffuse:1,kspecular:1,lightPosition:[1e3,1e3,1e3],eyePosition:[0,0,0],roughness:1,fresnel:1,opacity:1,vertexColor:0},D=T.slice(),z=[1,0,0,0,1,0,0,0,1];function R(t,e){t=t||{};var r=this.gl;r.disable(r.CULL_FACE),this._colorMap.bind(0);var n=I;n.model=t.model||T,n.view=t.view||T,n.projection=t.projection||T,n.lowerBound=[this.bounds[0][0],this.bounds[0][1],this.colorBounds[0]||this.bounds[0][2]],n.upperBound=[this.bounds[1][0],this.bounds[1][1],this.colorBounds[1]||this.bounds[1][2]],n.objectOffset=this.objectOffset,n.contourColor=this.contourColor[0],n.inverseModel=d(n.inverseModel,n.model);for(var i=0;i<2;++i)for(var a=n.clipBounds[i],o=0;o<3;++o)a[o]=Math.min(Math.max(this.clipBounds[i][o],-1e8),1e8);n.kambient=this.ambientLight,n.kdiffuse=this.diffuseLight,n.kspecular=this.specularLight,n.roughness=this.roughness,n.fresnel=this.fresnel,n.opacity=this.opacity,n.height=0,n.permutation=z,n.vertexColor=this.vertexColor;var s=D;for(p(s,n.view,n.model),p(s,n.projection,s),d(s,s),i=0;i<3;++i)n.eyePosition[i]=s[12+i]/s[15];var l=s[15];for(i=0;i<3;++i)l+=this.lightPosition[i]*s[4*i+3];for(i=0;i<3;++i){var u=s[12+i];for(o=0;o<3;++o)u+=s[4*o+i]*this.lightPosition[o];n.lightPosition[i]=u/l}var c=O(n,this);if(c.showSurface){for(this._shader.bind(),this._shader.uniforms=n,this._vao.bind(),this.showSurface&&this._vertexCount&&this._vao.draw(r.TRIANGLES,this._vertexCount),i=0;i<3;++i)this.surfaceProject[i]&&this.vertexCount&&(this._shader.uniforms.model=c.projections[i],this._shader.uniforms.clipBounds=c.clipBounds[i],this._vao.draw(r.TRIANGLES,this._vertexCount));this._vao.unbind()}if(c.showContour){var f=this._contourShader;n.kambient=1,n.kdiffuse=0,n.kspecular=0,n.opacity=1,f.bind(),f.uniforms=n;var h=this._contourVAO;for(h.bind(),i=0;i<3;++i)for(f.uniforms.permutation=A[i],r.lineWidth(this.contourWidth[i]*this.pixelRatio),o=0;o>4)/16)/255,i=Math.floor(n),a=n-i,o=e[1]*(t.value[1]+(15&t.value[2])/16)/255,s=Math.floor(o),l=o-s;i+=1,s+=1;var u=r.position;u[0]=u[1]=u[2]=0;for(var c=0;c<2;++c)for(var f=c?a:1-a,h=0;h<2;++h)for(var p=i+c,d=s+h,g=f*(h?l:1-l),y=0;y<3;++y)u[y]+=this._field[y].get(p,d)*g;for(var m=this._pickResult.level,x=0;x<3;++x)if(m[x]=v.le(this.contourLevels[x],u[x]),m[x]<0)this.contourLevels[x].length>0&&(m[x]=0);else if(m[x]Math.abs(_-u[x])&&(m[x]+=1)}for(r.index[0]=a<.5?i:i+1,r.index[1]=l<.5?s:s+1,r.uv[0]=n/e[0],r.uv[1]=o/e[1],y=0;y<3;++y)r.dataCoordinate[y]=this._field[y].get(r.index[0],r.index[1]);return r},L.padField=function(t,e){var r=e.shape.slice(),n=t.shape.slice();u.assign(t.lo(1,1).hi(r[0],r[1]),e),u.assign(t.lo(1).hi(r[0],1),e.hi(r[0],1)),u.assign(t.lo(1,n[1]-1).hi(r[0],1),e.lo(0,r[1]-1).hi(r[0],1)),u.assign(t.lo(0,1).hi(1,r[1]),e.hi(1)),u.assign(t.lo(n[0]-1,1).hi(1,r[1]),e.lo(r[0]-1)),t.set(0,0,e.get(0,0)),t.set(0,n[1]-1,e.get(0,r[1]-1)),t.set(n[0]-1,0,e.get(r[0]-1,0)),t.set(n[0]-1,n[1]-1,e.get(r[0]-1,r[1]-1))},L.update=function(t){t=t||{},this.objectOffset=t.objectOffset||this.objectOffset,this.dirty=!0,"contourWidth"in t&&(this.contourWidth=B(t.contourWidth,Number)),"showContour"in t&&(this.showContour=B(t.showContour,Boolean)),"showSurface"in t&&(this.showSurface=!!t.showSurface),"contourTint"in t&&(this.contourTint=B(t.contourTint,Boolean)),"contourColor"in t&&(this.contourColor=j(t.contourColor)),"contourProject"in t&&(this.contourProject=B(t.contourProject,(function(t){return B(t,Boolean)}))),"surfaceProject"in t&&(this.surfaceProject=t.surfaceProject),"dynamicColor"in t&&(this.dynamicColor=j(t.dynamicColor)),"dynamicTint"in t&&(this.dynamicTint=B(t.dynamicTint,Number)),"dynamicWidth"in t&&(this.dynamicWidth=B(t.dynamicWidth,Number)),"opacity"in t&&(this.opacity=t.opacity),"opacityscale"in t&&(this.opacityscale=t.opacityscale),"colorBounds"in t&&(this.colorBounds=t.colorBounds),"vertexColor"in t&&(this.vertexColor=t.vertexColor?1:0),"colormap"in t&&this._colorMap.setPixels(this.genColormap(t.colormap,this.opacityscale));var e=t.field||t.coords&&t.coords[2]||null,r=!1;if(e||(e=this._field[2].shape[0]||this._field[2].shape[2]?this._field[2].lo(1,1).hi(this._field[2].shape[0]-2,this._field[2].shape[1]-2):this._field[2].hi(0,0)),"field"in t||"coords"in t){var i=(e.shape[0]+2)*(e.shape[1]+2);i>this._field[2].data.length&&(s.freeFloat(this._field[2].data),this._field[2].data=s.mallocFloat(n.nextPow2(i))),this._field[2]=f(this._field[2].data,[e.shape[0]+2,e.shape[1]+2]),this.padField(this._field[2],e),this.shape=e.shape.slice();for(var a=this.shape,o=0;o<2;++o)this._field[2].size>this._field[o].data.length&&(s.freeFloat(this._field[o].data),this._field[o].data=s.mallocFloat(this._field[2].size)),this._field[o]=f(this._field[o].data,[a[0]+2,a[1]+2]);if(t.coords){var l=t.coords;if(!Array.isArray(l)||3!==l.length)throw new Error("gl-surface: invalid coordinates for x/y");for(o=0;o<2;++o){var u=l[o];for(y=0;y<2;++y)if(u.shape[y]!==a[y])throw new Error("gl-surface: coords have incorrect shape");this.padField(this._field[o],u)}}else if(t.ticks){var c=t.ticks;if(!Array.isArray(c)||2!==c.length)throw new Error("gl-surface: invalid ticks");for(o=0;o<2;++o){var p=c[o];if((Array.isArray(p)||p.length)&&(p=f(p)),p.shape[0]!==a[o])throw new Error("gl-surface: invalid tick length");var d=f(p.data,a);d.stride[o]=p.stride[0],d.stride[1^o]=0,this.padField(this._field[o],d)}}else{for(o=0;o<2;++o){var v=[0,0];v[o]=1,this._field[o]=f(this._field[o].data,[a[0]+2,a[1]+2],v,0)}this._field[0].set(0,0,0);for(var y=0;y0){for(var xt=0;xt<5;++xt)$.pop();U-=1}continue t}$.push(nt[0],nt[1],ot[0],ot[1],nt[2]),U+=1}}rt.push(U)}this._contourOffsets[Q]=et,this._contourCounts[Q]=rt}var bt=s.mallocFloat($.length);for(o=0;o<$.length;++o)bt[o]=$[o];this._contourBuffer.update(bt),s.freeFloat(bt)}},L.dispose=function(){this._shader.dispose(),this._vao.dispose(),this._coordinateBuffer.dispose(),this._colorMap.dispose(),this._contourBuffer.dispose(),this._contourVAO.dispose(),this._contourShader.dispose(),this._contourPickShader.dispose(),this._dynamicBuffer.dispose(),this._dynamicVAO.dispose();for(var t=0;t<3;++t)s.freeFloat(this._field[t].data)},L.highlight=function(t){var e,r;if(!t)return this._dynamicCounts=[0,0,0],this.dyanamicLevel=[NaN,NaN,NaN],void(this.highlightLevel=[-1,-1,-1]);for(e=0;e<3;++e)this.enableHighlight[e]?this.highlightLevel[e]=t.level[e]:this.highlightLevel[e]=-1;for(r=this.snapToData?t.dataCoordinate:t.position,e=0;e<3;++e)r[e]-=this.objectOffset[e];if(this.enableDynamic[0]&&r[0]!==this.dynamicLevel[0]||this.enableDynamic[1]&&r[1]!==this.dynamicLevel[1]||this.enableDynamic[2]&&r[2]!==this.dynamicLevel[2]){for(var n=0,i=this.shape,a=s.mallocFloat(12*i[0]*i[1]),o=0;o<3;++o)if(this.enableDynamic[o]){this.dynamicLevel[o]=r[o];var l=(o+1)%3,u=(o+2)%3,c=this._field[o],f=this._field[l],p=this._field[u],d=h(c,r[o]),v=d.cells,g=d.positions;for(this._dynamicOffsets[o]=n,e=0;es||o[1]<0||o[1]>s)throw new Error("gl-texture2d: Invalid texture size");var l=d(o,e.stride.slice()),u=0;"float32"===r?u=t.FLOAT:"float64"===r?(u=t.FLOAT,l=!1,r="float32"):"uint8"===r?u=t.UNSIGNED_BYTE:(u=t.UNSIGNED_BYTE,l=!1,r="uint8");var f,p,g=0;if(2===o.length)g=t.LUMINANCE,o=[o[0],o[1],1],e=n(e.data,o,[e.stride[0],e.stride[1],1],e.offset);else{if(3!==o.length)throw new Error("gl-texture2d: Invalid shape for texture");if(1===o[2])g=t.ALPHA;else if(2===o[2])g=t.LUMINANCE_ALPHA;else if(3===o[2])g=t.RGB;else{if(4!==o[2])throw new Error("gl-texture2d: Invalid shape for pixel coords");g=t.RGBA}}u!==t.FLOAT||t.getExtension("OES_texture_float")||(u=t.UNSIGNED_BYTE,l=!1);var y=e.size;if(l)f=0===e.offset&&e.data.length===y?e.data:e.data.subarray(e.offset,e.offset+y);else{var m=[o[2],o[2]*o[0],1];p=a.malloc(y,r);var x=n(p,o,m,0);"float32"!==r&&"float64"!==r||u!==t.UNSIGNED_BYTE?i.assign(x,e):c(x,e),f=p.subarray(0,y)}var b=v(t);return t.texImage2D(t.TEXTURE_2D,0,g,o[0],o[1],0,g,u,f),l||a.free(p),new h(t,b,o[0],o[1],g,u)}(t,e)}throw new Error("gl-texture2d: Invalid arguments for texture2d constructor")};var o=null,s=null,l=null;function u(t){return"undefined"!=typeof HTMLCanvasElement&&t instanceof HTMLCanvasElement||"undefined"!=typeof HTMLImageElement&&t instanceof HTMLImageElement||"undefined"!=typeof HTMLVideoElement&&t instanceof HTMLVideoElement||"undefined"!=typeof ImageData&&t instanceof ImageData}var c=function(t,e){i.muls(t,e,255)};function f(t,e,r){var n=t.gl,i=n.getParameter(n.MAX_TEXTURE_SIZE);if(e<0||e>i||r<0||r>i)throw new Error("gl-texture2d: Invalid texture size");return t._shape=[e,r],t.bind(),n.texImage2D(n.TEXTURE_2D,0,t.format,e,r,0,t.format,t.type,null),t._mipLevels=[0],t}function h(t,e,r,n,i,a){this.gl=t,this.handle=e,this.format=i,this.type=a,this._shape=[r,n],this._mipLevels=[0],this._magFilter=t.NEAREST,this._minFilter=t.NEAREST,this._wrapS=t.CLAMP_TO_EDGE,this._wrapT=t.CLAMP_TO_EDGE,this._anisoSamples=1;var o=this,s=[this._wrapS,this._wrapT];Object.defineProperties(s,[{get:function(){return o._wrapS},set:function(t){return o.wrapS=t}},{get:function(){return o._wrapT},set:function(t){return o.wrapT=t}}]),this._wrapVector=s;var l=[this._shape[0],this._shape[1]];Object.defineProperties(l,[{get:function(){return o._shape[0]},set:function(t){return o.width=t}},{get:function(){return o._shape[1]},set:function(t){return o.height=t}}]),this._shapeVector=l}var p=h.prototype;function d(t,e){return 3===t.length?1===e[2]&&e[1]===t[0]*t[2]&&e[0]===t[2]:1===e[0]&&e[1]===t[0]}function v(t){var e=t.createTexture();return t.bindTexture(t.TEXTURE_2D,e),t.texParameteri(t.TEXTURE_2D,t.TEXTURE_MIN_FILTER,t.NEAREST),t.texParameteri(t.TEXTURE_2D,t.TEXTURE_MAG_FILTER,t.NEAREST),t.texParameteri(t.TEXTURE_2D,t.TEXTURE_WRAP_S,t.CLAMP_TO_EDGE),t.texParameteri(t.TEXTURE_2D,t.TEXTURE_WRAP_T,t.CLAMP_TO_EDGE),e}function g(t,e,r,n,i){var a=t.getParameter(t.MAX_TEXTURE_SIZE);if(e<0||e>a||r<0||r>a)throw new Error("gl-texture2d: Invalid texture shape");if(i===t.FLOAT&&!t.getExtension("OES_texture_float"))throw new Error("gl-texture2d: Floating point textures not supported on this platform");var o=v(t);return t.texImage2D(t.TEXTURE_2D,0,n,e,r,0,n,i,null),new h(t,o,e,r,n,i)}Object.defineProperties(p,{minFilter:{get:function(){return this._minFilter},set:function(t){this.bind();var e=this.gl;if(this.type===e.FLOAT&&o.indexOf(t)>=0&&(e.getExtension("OES_texture_float_linear")||(t=e.NEAREST)),s.indexOf(t)<0)throw new Error("gl-texture2d: Unknown filter mode "+t);return e.texParameteri(e.TEXTURE_2D,e.TEXTURE_MIN_FILTER,t),this._minFilter=t}},magFilter:{get:function(){return this._magFilter},set:function(t){this.bind();var e=this.gl;if(this.type===e.FLOAT&&o.indexOf(t)>=0&&(e.getExtension("OES_texture_float_linear")||(t=e.NEAREST)),s.indexOf(t)<0)throw new Error("gl-texture2d: Unknown filter mode "+t);return e.texParameteri(e.TEXTURE_2D,e.TEXTURE_MAG_FILTER,t),this._magFilter=t}},mipSamples:{get:function(){return this._anisoSamples},set:function(t){var e=this._anisoSamples;if(this._anisoSamples=0|Math.max(t,1),e!==this._anisoSamples){var r=this.gl.getExtension("EXT_texture_filter_anisotropic");r&&this.gl.texParameterf(this.gl.TEXTURE_2D,r.TEXTURE_MAX_ANISOTROPY_EXT,this._anisoSamples)}return this._anisoSamples}},wrapS:{get:function(){return this._wrapS},set:function(t){if(this.bind(),l.indexOf(t)<0)throw new Error("gl-texture2d: Unknown wrap mode "+t);return this.gl.texParameteri(this.gl.TEXTURE_2D,this.gl.TEXTURE_WRAP_S,t),this._wrapS=t}},wrapT:{get:function(){return this._wrapT},set:function(t){if(this.bind(),l.indexOf(t)<0)throw new Error("gl-texture2d: Unknown wrap mode "+t);return this.gl.texParameteri(this.gl.TEXTURE_2D,this.gl.TEXTURE_WRAP_T,t),this._wrapT=t}},wrap:{get:function(){return this._wrapVector},set:function(t){if(Array.isArray(t)||(t=[t,t]),2!==t.length)throw new Error("gl-texture2d: Must specify wrap mode for rows and columns");for(var e=0;e<2;++e)if(l.indexOf(t[e])<0)throw new Error("gl-texture2d: Unknown wrap mode "+t);this._wrapS=t[0],this._wrapT=t[1];var r=this.gl;return this.bind(),r.texParameteri(r.TEXTURE_2D,r.TEXTURE_WRAP_S,this._wrapS),r.texParameteri(r.TEXTURE_2D,r.TEXTURE_WRAP_T,this._wrapT),t}},shape:{get:function(){return this._shapeVector},set:function(t){if(Array.isArray(t)){if(2!==t.length)throw new Error("gl-texture2d: Invalid texture shape")}else t=[0|t,0|t];return f(this,0|t[0],0|t[1]),[0|t[0],0|t[1]]}},width:{get:function(){return this._shape[0]},set:function(t){return f(this,t|=0,this._shape[1]),t}},height:{get:function(){return this._shape[1]},set:function(t){return t|=0,f(this,this._shape[0],t),t}}}),p.bind=function(t){var e=this.gl;return void 0!==t&&e.activeTexture(e.TEXTURE0+(0|t)),e.bindTexture(e.TEXTURE_2D,this.handle),void 0!==t?0|t:e.getParameter(e.ACTIVE_TEXTURE)-e.TEXTURE0},p.dispose=function(){this.gl.deleteTexture(this.handle)},p.generateMipmap=function(){this.bind(),this.gl.generateMipmap(this.gl.TEXTURE_2D);for(var t=Math.min(this._shape[0],this._shape[1]),e=0;t>0;++e,t>>>=1)this._mipLevels.indexOf(e)<0&&this._mipLevels.push(e)},p.setPixels=function(t,e,r,o){var s=this.gl;this.bind(),Array.isArray(e)?(o=r,r=0|e[1],e=0|e[0]):(e=e||0,r=r||0),o=o||0;var l=u(t)?t:t.raw;if(l)this._mipLevels.indexOf(o)<0?(s.texImage2D(s.TEXTURE_2D,0,this.format,this.format,this.type,l),this._mipLevels.push(o)):s.texSubImage2D(s.TEXTURE_2D,o,e,r,this.format,this.type,l);else{if(!(t.shape&&t.stride&&t.data))throw new Error("gl-texture2d: Unsupported data type");if(t.shape.length<2||e+t.shape[1]>this._shape[1]>>>o||r+t.shape[0]>this._shape[0]>>>o||e<0||r<0)throw new Error("gl-texture2d: Texture dimensions are out of bounds");!function(t,e,r,o,s,l,u,f){var h=f.dtype,p=f.shape.slice();if(p.length<2||p.length>3)throw new Error("gl-texture2d: Invalid ndarray, must be 2d or 3d");var v=0,g=0,y=d(p,f.stride.slice());if("float32"===h?v=t.FLOAT:"float64"===h?(v=t.FLOAT,y=!1,h="float32"):"uint8"===h?v=t.UNSIGNED_BYTE:(v=t.UNSIGNED_BYTE,y=!1,h="uint8"),2===p.length)g=t.LUMINANCE,p=[p[0],p[1],1],f=n(f.data,p,[f.stride[0],f.stride[1],1],f.offset);else{if(3!==p.length)throw new Error("gl-texture2d: Invalid shape for texture");if(1===p[2])g=t.ALPHA;else if(2===p[2])g=t.LUMINANCE_ALPHA;else if(3===p[2])g=t.RGB;else{if(4!==p[2])throw new Error("gl-texture2d: Invalid shape for pixel coords");g=t.RGBA}p[2]}if(g!==t.LUMINANCE&&g!==t.ALPHA||s!==t.LUMINANCE&&s!==t.ALPHA||(g=s),g!==s)throw new Error("gl-texture2d: Incompatible texture format for setPixels");var m=f.size,x=u.indexOf(o)<0;if(x&&u.push(o),v===l&&y)0===f.offset&&f.data.length===m?x?t.texImage2D(t.TEXTURE_2D,o,s,p[0],p[1],0,s,l,f.data):t.texSubImage2D(t.TEXTURE_2D,o,e,r,p[0],p[1],s,l,f.data):x?t.texImage2D(t.TEXTURE_2D,o,s,p[0],p[1],0,s,l,f.data.subarray(f.offset,f.offset+m)):t.texSubImage2D(t.TEXTURE_2D,o,e,r,p[0],p[1],s,l,f.data.subarray(f.offset,f.offset+m));else{var b;b=l===t.FLOAT?a.mallocFloat32(m):a.mallocUint8(m);var _=n(b,p,[p[2],p[2]*p[0],1]);v===t.FLOAT&&l===t.UNSIGNED_BYTE?c(_,f):i.assign(_,f),x?t.texImage2D(t.TEXTURE_2D,o,s,p[0],p[1],0,s,l,b.subarray(0,m)):t.texSubImage2D(t.TEXTURE_2D,o,e,r,p[0],p[1],s,l,b.subarray(0,m)),l===t.FLOAT?a.freeFloat32(b):a.freeUint8(b)}}(s,e,r,o,this.format,this.type,this._mipLevels,t)}}},3056:function(t){"use strict";t.exports=function(t,e,r){e?e.bind():t.bindBuffer(t.ELEMENT_ARRAY_BUFFER,null);var n=0|t.getParameter(t.MAX_VERTEX_ATTRIBS);if(r){if(r.length>n)throw new Error("gl-vao: Too many vertex attributes");for(var i=0;i1?0:Math.acos(s)};var n=r(5415),i=r(899),a=r(9305)},8827:function(t){t.exports=function(t,e){return t[0]=Math.ceil(e[0]),t[1]=Math.ceil(e[1]),t[2]=Math.ceil(e[2]),t}},7622:function(t){t.exports=function(t){var e=new Float32Array(3);return e[0]=t[0],e[1]=t[1],e[2]=t[2],e}},8782:function(t){t.exports=function(t,e){return t[0]=e[0],t[1]=e[1],t[2]=e[2],t}},8501:function(t){t.exports=function(){var t=new Float32Array(3);return 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instead.");if(!ne(r,["string","array"]))throw new ge("Expected second argument to be of type array or string, but found "+Qt(pe(r))+" instead.");return r.indexOf(e)>=0},kr.prototype.eachChild=function(t){t(this.needle),t(this.haystack)},kr.prototype.outputDefined=function(){return!0},kr.prototype.serialize=function(){return["in",this.needle.serialize(),this.haystack.serialize()]};var Ar=function(t,e,r){this.type=Ht,this.needle=t,this.haystack=e,this.fromIndex=r};Ar.parse=function(t,e){if(t.length<=2||t.length>=5)return e.error("Expected 3 or 4 arguments, but found "+(t.length-1)+" instead.");var r=e.parse(t[1],1,Wt),n=e.parse(t[2],2,Wt);if(!r||!n)return null;if(!re(r.type,[Gt,qt,Ht,Vt,Wt]))return e.error("Expected first argument to be of type boolean, string, number or null, but found "+Qt(r.type)+" instead");if(4===t.length){var i=e.parse(t[3],3,Ht);return i?new Ar(r,n,i):null}return new Ar(r,n)},Ar.prototype.evaluate=function(t){var e=this.needle.evaluate(t),r=this.haystack.evaluate(t);if(!ne(e,["boolean","string","number","null"]))throw new ge("Expected first argument to be of type boolean, string, number or null, but found "+Qt(pe(e))+" instead.");if(!ne(r,["string","array"]))throw new ge("Expected second argument to be of type array or string, but found "+Qt(pe(r))+" instead.");if(this.fromIndex){var n=this.fromIndex.evaluate(t);return r.indexOf(e,n)}return r.indexOf(e)},Ar.prototype.eachChild=function(t){t(this.needle),t(this.haystack),this.fromIndex&&t(this.fromIndex)},Ar.prototype.outputDefined=function(){return!1},Ar.prototype.serialize=function(){if(null!=this.fromIndex&&void 0!==this.fromIndex){var t=this.fromIndex.serialize();return["index-of",this.needle.serialize(),this.haystack.serialize(),t]}return["index-of",this.needle.serialize(),this.haystack.serialize()]};var Mr=function(t,e,r,n,i,a){this.inputType=t,this.type=e,this.input=r,this.cases=n,this.outputs=i,this.otherwise=a};Mr.parse=function(t,e){if(t.length<5)return e.error("Expected at least 4 arguments, but found only "+(t.length-1)+".");if(t.length%2!=1)return e.error("Expected an even number of arguments.");var r,n;e.expectedType&&"value"!==e.expectedType.kind&&(n=e.expectedType);for(var i={},a=[],o=2;oNumber.MAX_SAFE_INTEGER)return u.error("Branch labels must be integers no larger than "+Number.MAX_SAFE_INTEGER+".");if("number"==typeof h&&Math.floor(h)!==h)return u.error("Numeric branch labels must be integer values.");if(r){if(u.checkSubtype(r,pe(h)))return null}else r=pe(h);if(void 0!==i[String(h)])return u.error("Branch labels must be unique.");i[String(h)]=a.length}var p=e.parse(l,o,n);if(!p)return null;n=n||p.type,a.push(p)}var d=e.parse(t[1],1,Wt);if(!d)return null;var v=e.parse(t[t.length-1],t.length-1,n);return v?"value"!==d.type.kind&&e.concat(1).checkSubtype(r,d.type)?null:new Mr(r,n,d,i,a,v):null},Mr.prototype.evaluate=function(t){var e=this.input.evaluate(t);return(pe(e)===this.inputType&&this.outputs[this.cases[e]]||this.otherwise).evaluate(t)},Mr.prototype.eachChild=function(t){t(this.input),this.outputs.forEach(t),t(this.otherwise)},Mr.prototype.outputDefined=function(){return this.outputs.every((function(t){return t.outputDefined()}))&&this.otherwise.outputDefined()},Mr.prototype.serialize=function(){for(var t=this,e=["match",this.input.serialize()],r=[],n={},i=0,a=Object.keys(this.cases).sort();i=5)return e.error("Expected 3 or 4 arguments, but found "+(t.length-1)+" instead.");var r=e.parse(t[1],1,Wt),n=e.parse(t[2],2,Ht);if(!r||!n)return null;if(!re(r.type,[$t(Wt),qt,Wt]))return e.error("Expected first argument to be of type array or string, but found "+Qt(r.type)+" instead");if(4===t.length){var i=e.parse(t[3],3,Ht);return i?new Er(r.type,r,n,i):null}return new Er(r.type,r,n)},Er.prototype.evaluate=function(t){var e=this.input.evaluate(t),r=this.beginIndex.evaluate(t);if(!ne(e,["string","array"]))throw new ge("Expected first argument to be of type array or string, but found "+Qt(pe(e))+" instead.");if(this.endIndex){var n=this.endIndex.evaluate(t);return e.slice(r,n)}return e.slice(r)},Er.prototype.eachChild=function(t){t(this.input),t(this.beginIndex),this.endIndex&&t(this.endIndex)},Er.prototype.outputDefined=function(){return!1},Er.prototype.serialize=function(){if(null!=this.endIndex&&void 0!==this.endIndex){var t=this.endIndex.serialize();return["slice",this.input.serialize(),this.beginIndex.serialize(),t]}return["slice",this.input.serialize(),this.beginIndex.serialize()]};var Or=Pr("==",(function(t,e,r){return e===r}),Cr),Ir=Pr("!=",(function(t,e,r){return e!==r}),(function(t,e,r,n){return!Cr(0,e,r,n)})),Dr=Pr("<",(function(t,e,r){return e",(function(t,e,r){return e>r}),(function(t,e,r,n){return n.compare(e,r)>0})),Rr=Pr("<=",(function(t,e,r){return e<=r}),(function(t,e,r,n){return n.compare(e,r)<=0})),Fr=Pr(">=",(function(t,e,r){return e>=r}),(function(t,e,r,n){return n.compare(e,r)>=0})),Br=function(t,e,r,n,i){this.type=qt,this.number=t,this.locale=e,this.currency=r,this.minFractionDigits=n,this.maxFractionDigits=i};Br.parse=function(t,e){if(3!==t.length)return e.error("Expected two arguments.");var r=e.parse(t[1],1,Ht);if(!r)return null;var n=t[2];if("object"!=typeof n||Array.isArray(n))return e.error("NumberFormat options argument must be an object.");var i=null;if(n.locale&&!(i=e.parse(n.locale,1,qt)))return null;var a=null;if(n.currency&&!(a=e.parse(n.currency,1,qt)))return null;var o=null;if(n["min-fraction-digits"]&&!(o=e.parse(n["min-fraction-digits"],1,Ht)))return null;var s=null;return n["max-fraction-digits"]&&!(s=e.parse(n["max-fraction-digits"],1,Ht))?null:new Br(r,i,a,o,s)},Br.prototype.evaluate=function(t){return new Intl.NumberFormat(this.locale?this.locale.evaluate(t):[],{style:this.currency?"currency":"decimal",currency:this.currency?this.currency.evaluate(t):void 0,minimumFractionDigits:this.minFractionDigits?this.minFractionDigits.evaluate(t):void 0,maximumFractionDigits:this.maxFractionDigits?this.maxFractionDigits.evaluate(t):void 0}).format(this.number.evaluate(t))},Br.prototype.eachChild=function(t){t(this.number),this.locale&&t(this.locale),this.currency&&t(this.currency),this.minFractionDigits&&t(this.minFractionDigits),this.maxFractionDigits&&t(this.maxFractionDigits)},Br.prototype.outputDefined=function(){return!1},Br.prototype.serialize=function(){var t={};return this.locale&&(t.locale=this.locale.serialize()),this.currency&&(t.currency=this.currency.serialize()),this.minFractionDigits&&(t["min-fraction-digits"]=this.minFractionDigits.serialize()),this.maxFractionDigits&&(t["max-fraction-digits"]=this.maxFractionDigits.serialize()),["number-format",this.number.serialize(),t]};var Nr=function(t){this.type=Ht,this.input=t};Nr.parse=function(t,e){if(2!==t.length)return e.error("Expected 1 argument, but found "+(t.length-1)+" instead.");var r=e.parse(t[1],1);return r?"array"!==r.type.kind&&"string"!==r.type.kind&&"value"!==r.type.kind?e.error("Expected argument of type string or array, but found "+Qt(r.type)+" instead."):new Nr(r):null},Nr.prototype.evaluate=function(t){var e=this.input.evaluate(t);if("string"==typeof e)return e.length;if(Array.isArray(e))return e.length;throw new ge("Expected value to be of type string or array, but found "+Qt(pe(e))+" instead.")},Nr.prototype.eachChild=function(t){t(this.input)},Nr.prototype.outputDefined=function(){return!1},Nr.prototype.serialize=function(){var t=["length"];return this.eachChild((function(e){t.push(e.serialize())})),t};var jr={"==":Or,"!=":Ir,">":zr,"<":Dr,">=":Fr,"<=":Rr,array:me,at:Tr,boolean:me,case:Sr,coalesce:_r,collator:Me,format:xe,image:be,in:kr,"index-of":Ar,interpolate:xr,"interpolate-hcl":xr,"interpolate-lab":xr,length:Nr,let:wr,literal:ve,match:Mr,number:me,"number-format":Br,object:me,slice:Er,step:Ke,string:me,"to-boolean":we,"to-color":we,"to-number":we,"to-string":we,var:Ye,within:He};function Ur(t,e){var r=e[0],n=e[1],i=e[2],a=e[3];r=r.evaluate(t),n=n.evaluate(t),i=i.evaluate(t);var o=a?a.evaluate(t):1,s=fe(r,n,i,o);if(s)throw new ge(s);return new oe(r/255*o,n/255*o,i/255*o,o)}function Vr(t,e){return t in e}function Hr(t,e){var r=e[t];return void 0===r?null:r}function qr(t){return{type:t}}function Gr(t){return{result:"success",value:t}}function Zr(t){return{result:"error",value:t}}function Yr(t){return"data-driven"===t["property-type"]||"cross-faded-data-driven"===t["property-type"]}function Wr(t){return!!t.expression&&t.expression.parameters.indexOf("zoom")>-1}function Xr(t){return!!t.expression&&t.expression.interpolated}function Jr(t){return t instanceof Number?"number":t instanceof String?"string":t instanceof Boolean?"boolean":Array.isArray(t)?"array":null===t?"null":typeof t}function Kr(t){return"object"==typeof t&&null!==t&&!Array.isArray(t)}function $r(t){return t}function Qr(t,e){var r,n,i,a="color"===e.type,o=t.stops&&"object"==typeof t.stops[0][0],s=o||void 0!==t.property,l=o||!s,u=t.type||(Xr(e)?"exponential":"interval");if(a&&((t=Ft({},t)).stops&&(t.stops=t.stops.map((function(t){return[t[0],oe.parse(t[1])]}))),t.default?t.default=oe.parse(t.default):t.default=oe.parse(e.default)),t.colorSpace&&"rgb"!==t.colorSpace&&!mr[t.colorSpace])throw new Error("Unknown color space: "+t.colorSpace);if("exponential"===u)r=nn;else if("interval"===u)r=rn;else if("categorical"===u){r=en,n=Object.create(null);for(var c=0,f=t.stops;c=t.stops[n-1][0])return t.stops[n-1][1];var i=Je(t.stops.map((function(t){return t[0]})),r);return t.stops[i][1]}function nn(t,e,r){var n=void 0!==t.base?t.base:1;if("number"!==Jr(r))return tn(t.default,e.default);var i=t.stops.length;if(1===i)return t.stops[0][1];if(r<=t.stops[0][0])return t.stops[0][1];if(r>=t.stops[i-1][0])return t.stops[i-1][1];var a=Je(t.stops.map((function(t){return t[0]})),r),o=function(t,e,r,n){var i=n-r,a=t-r;return 0===i?0:1===e?a/i:(Math.pow(e,a)-1)/(Math.pow(e,i)-1)}(r,n,t.stops[a][0],t.stops[a+1][0]),s=t.stops[a][1],l=t.stops[a+1][1],u=Qe[e.type]||$r;if(t.colorSpace&&"rgb"!==t.colorSpace){var c=mr[t.colorSpace];u=function(t,e){return c.reverse(c.interpolate(c.forward(t),c.forward(e),o))}}return"function"==typeof s.evaluate?{evaluate:function(){for(var t=[],e=arguments.length;e--;)t[e]=arguments[e];var r=s.evaluate.apply(void 0,t),n=l.evaluate.apply(void 0,t);if(void 0!==r&&void 0!==n)return u(r,n,o)}}:u(s,l,o)}function 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We(jr,[],e?function(t){var e={color:Zt,string:qt,number:Ht,enum:qt,boolean:Gt,formatted:Jt,resolvedImage:Kt};return"array"===t.type?$t(e[t.value]||Wt,t.length):e[t.type]}(e):void 0),n=r.parse(t,void 0,void 0,void 0,e&&"string"===e.type?{typeAnnotation:"coerce"}:void 0);return n?Gr(new on(n,e)):Zr(r.errors)}on.prototype.evaluateWithoutErrorHandling=function(t,e,r,n,i,a){return this._evaluator.globals=t,this._evaluator.feature=e,this._evaluator.featureState=r,this._evaluator.canonical=n,this._evaluator.availableImages=i||null,this._evaluator.formattedSection=a,this.expression.evaluate(this._evaluator)},on.prototype.evaluate=function(t,e,r,n,i,a){this._evaluator.globals=t,this._evaluator.feature=e||null,this._evaluator.featureState=r||null,this._evaluator.canonical=n,this._evaluator.availableImages=i||null,this._evaluator.formattedSection=a||null;try{var o=this.expression.evaluate(this._evaluator);if(null==o||"number"==typeof o&&o!=o)return this._defaultValue;if(this._enumValues&&!(o in this._enumValues))throw new ge("Expected value to be one of "+Object.keys(this._enumValues).map((function(t){return JSON.stringify(t)})).join(", ")+", but found "+JSON.stringify(o)+" instead.");return o}catch(t){return this._warningHistory[t.message]||(this._warningHistory[t.message]=!0,"undefined"!=typeof console&&console.warn(t.message)),this._defaultValue}};var un=function(t,e){this.kind=t,this._styleExpression=e,this.isStateDependent="constant"!==t&&!Ge(e.expression)};un.prototype.evaluateWithoutErrorHandling=function(t,e,r,n,i,a){return this._styleExpression.evaluateWithoutErrorHandling(t,e,r,n,i,a)},un.prototype.evaluate=function(t,e,r,n,i,a){return this._styleExpression.evaluate(t,e,r,n,i,a)};var cn=function(t,e,r,n){this.kind=t,this.zoomStops=r,this._styleExpression=e,this.isStateDependent="camera"!==t&&!Ge(e.expression),this.interpolationType=n};function fn(t,e){if("error"===(t=ln(t,e)).result)return t;var r=t.value.expression,n=qe(r);if(!n&&!Yr(e))return Zr([new jt("","data expressions not supported")]);var i=Ze(r,["zoom"]);if(!i&&!Wr(e))return Zr([new jt("","zoom expressions not supported")]);var a=pn(r);if(!a&&!i)return Zr([new jt("",'"zoom" expression may only be used as input to a top-level "step" or "interpolate" expression.')]);if(a instanceof jt)return Zr([a]);if(a instanceof xr&&!Xr(e))return Zr([new jt("",'"interpolate" expressions cannot be used with this property')]);if(!a)return Gr(new un(n?"constant":"source",t.value));var o=a instanceof xr?a.interpolation:void 0;return Gr(new cn(n?"camera":"composite",t.value,a.labels,o))}cn.prototype.evaluateWithoutErrorHandling=function(t,e,r,n,i,a){return this._styleExpression.evaluateWithoutErrorHandling(t,e,r,n,i,a)},cn.prototype.evaluate=function(t,e,r,n,i,a){return this._styleExpression.evaluate(t,e,r,n,i,a)},cn.prototype.interpolationFactor=function(t,e,r){return this.interpolationType?xr.interpolationFactor(this.interpolationType,t,e,r):0};var hn=function(t,e){this._parameters=t,this._specification=e,Ft(this,Qr(this._parameters,this._specification))};function pn(t){var e=null;if(t instanceof wr)e=pn(t.result);else if(t instanceof _r)for(var r=0,n=t.args;rn.maximum?[new zt(e,r,r+" is greater than the maximum value "+n.maximum)]:[]}function yn(t){var e,r,n,i=t.valueSpec,a=Bt(t.value.type),o={},s="categorical"!==a&&void 0===t.value.property,l=!s,u="array"===Jr(t.value.stops)&&"array"===Jr(t.value.stops[0])&&"object"===Jr(t.value.stops[0][0]),c=dn({key:t.key,value:t.value,valueSpec:t.styleSpec.function,style:t.style,styleSpec:t.styleSpec,objectElementValidators:{stops:function(t){if("identity"===a)return[new zt(t.key,t.value,'identity function may not have a "stops" property')];var e=[],r=t.value;return e=e.concat(vn({key:t.key,value:r,valueSpec:t.valueSpec,style:t.style,styleSpec:t.styleSpec,arrayElementValidator:f})),"array"===Jr(r)&&0===r.length&&e.push(new zt(t.key,r,"array must have at least one 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e=1;e"===r||"<="===r||">="===r?Mn(t[1],t[2],r):"any"===r?(e=t.slice(1),["any"].concat(e.map(An))):"all"===r?["all"].concat(t.slice(1).map(An)):"none"===r?["all"].concat(t.slice(1).map(An).map(Ln)):"in"===r?Sn(t[1],t.slice(2)):"!in"===r?Ln(Sn(t[1],t.slice(2))):"has"===r?En(t[1]):"!has"===r?Ln(En(t[1])):"within"!==r||t}function Mn(t,e,r){switch(t){case"$type":return["filter-type-"+r,e];case"$id":return["filter-id-"+r,e];default:return["filter-"+r,t,e]}}function Sn(t,e){if(0===e.length)return!1;switch(t){case"$type":return["filter-type-in",["literal",e]];case"$id":return["filter-id-in",["literal",e]];default:return e.length>200&&!e.some((function(t){return typeof t!=typeof e[0]}))?["filter-in-large",t,["literal",e.sort(Tn)]]:["filter-in-small",t,["literal",e]]}}function En(t){switch(t){case"$type":return!0;case"$id":return["filter-has-id"];default:return["filter-has",t]}}function Ln(t){return["!",t]}function Cn(t){return bn(Nt(t.value))?mn(Ft({},t,{expressionContext:"filter",valueSpec:{value:"boolean"}})):Pn(t)}function Pn(t){var e=t.value,r=t.key;if("array"!==Jr(e))return[new zt(r,e,"array expected, "+Jr(e)+" found")];var n,i=t.styleSpec,a=[];if(e.length<1)return[new zt(r,e,"filter array must have at least 1 element")];switch(a=a.concat(xn({key:r+"[0]",value:e[0],valueSpec:i.filter_operator,style:t.style,styleSpec:t.styleSpec})),Bt(e[0])){case"<":case"<=":case">":case">=":e.length>=2&&"$type"===Bt(e[1])&&a.push(new zt(r,e,'"$type" cannot be use with operator "'+e[0]+'"'));case"==":case"!=":3!==e.length&&a.push(new zt(r,e,'filter array for operator "'+e[0]+'" must have 3 elements'));case"in":case"!in":e.length>=2&&"string"!==(n=Jr(e[1]))&&a.push(new zt(r+"[1]",e[1],"string expected, "+n+" found"));for(var o=2;o=c[p+0]&&n>=c[p+1])?(o[h]=!0,a.push(u[h])):o[h]=!1}}},Qn.prototype._forEachCell=function(t,e,r,n,i,a,o,s){for(var l=this._convertToCellCoord(t),u=this._convertToCellCoord(e),c=this._convertToCellCoord(r),f=this._convertToCellCoord(n),h=l;h<=c;h++)for(var p=u;p<=f;p++){var d=this.d*p+h;if((!s||s(this._convertFromCellCoord(h),this._convertFromCellCoord(p),this._convertFromCellCoord(h+1),this._convertFromCellCoord(p+1)))&&i.call(this,t,e,r,n,d,a,o,s))return}},Qn.prototype._convertFromCellCoord=function(t){return(t-this.padding)/this.scale},Qn.prototype._convertToCellCoord=function(t){return Math.max(0,Math.min(this.d-1,Math.floor(t*this.scale)+this.padding))},Qn.prototype.toArrayBuffer=function(){if(this.arrayBuffer)return this.arrayBuffer;for(var t=this.cells,e=$n+this.cells.length+1+1,r=0,n=0;n=0)){var f=t[c];u[c]=ri[l].shallow.indexOf(c)>=0?f:si(f,e)}t instanceof Error&&(u.message=t.message)}if(u.$name)throw new Error("$name property is reserved for worker serialization logic.");return"Object"!==l&&(u.$name=l),u}throw new Error("can't serialize object of type "+typeof t)}function li(t){if(null==t||"boolean"==typeof t||"number"==typeof t||"string"==typeof t||t instanceof Boolean||t instanceof Number||t instanceof String||t instanceof Date||t instanceof RegExp||ai(t)||oi(t)||ArrayBuffer.isView(t)||t instanceof ti)return t;if(Array.isArray(t))return t.map(li);if("object"==typeof t){var e=t.$name||"Object",r=ri[e].klass;if(!r)throw new Error("can't deserialize unregistered class "+e);if(r.deserialize)return r.deserialize(t);for(var n=Object.create(r.prototype),i=0,a=Object.keys(t);i=0?s:li(s)}}return n}throw new Error("can't deserialize object of type "+typeof t)}var ui=function(){this.first=!0};ui.prototype.update=function(t,e){var r=Math.floor(t);return this.first?(this.first=!1,this.lastIntegerZoom=r,this.lastIntegerZoomTime=0,this.lastZoom=t,this.lastFloorZoom=r,!0):(this.lastFloorZoom>r?(this.lastIntegerZoom=r+1,this.lastIntegerZoomTime=e):this.lastFloorZoom=128&&t<=255},Arabic:function(t){return t>=1536&&t<=1791},"Arabic Supplement":function(t){return t>=1872&&t<=1919},"Arabic Extended-A":function(t){return t>=2208&&t<=2303},"Hangul Jamo":function(t){return t>=4352&&t<=4607},"Unified Canadian Aboriginal Syllabics":function(t){return t>=5120&&t<=5759},Khmer:function(t){return t>=6016&&t<=6143},"Unified Canadian Aboriginal Syllabics Extended":function(t){return t>=6320&&t<=6399},"General Punctuation":function(t){return t>=8192&&t<=8303},"Letterlike Symbols":function(t){return t>=8448&&t<=8527},"Number Forms":function(t){return t>=8528&&t<=8591},"Miscellaneous Technical":function(t){return t>=8960&&t<=9215},"Control Pictures":function(t){return t>=9216&&t<=9279},"Optical Character Recognition":function(t){return t>=9280&&t<=9311},"Enclosed Alphanumerics":function(t){return t>=9312&&t<=9471},"Geometric Shapes":function(t){return t>=9632&&t<=9727},"Miscellaneous Symbols":function(t){return t>=9728&&t<=9983},"Miscellaneous Symbols and Arrows":function(t){return t>=11008&&t<=11263},"CJK Radicals Supplement":function(t){return t>=11904&&t<=12031},"Kangxi Radicals":function(t){return t>=12032&&t<=12255},"Ideographic Description Characters":function(t){return t>=12272&&t<=12287},"CJK Symbols and Punctuation":function(t){return t>=12288&&t<=12351},Hiragana:function(t){return t>=12352&&t<=12447},Katakana:function(t){return t>=12448&&t<=12543},Bopomofo:function(t){return t>=12544&&t<=12591},"Hangul Compatibility Jamo":function(t){return t>=12592&&t<=12687},Kanbun:function(t){return t>=12688&&t<=12703},"Bopomofo Extended":function(t){return t>=12704&&t<=12735},"CJK Strokes":function(t){return t>=12736&&t<=12783},"Katakana Phonetic Extensions":function(t){return t>=12784&&t<=12799},"Enclosed CJK Letters and Months":function(t){return t>=12800&&t<=13055},"CJK Compatibility":function(t){return t>=13056&&t<=13311},"CJK Unified Ideographs Extension A":function(t){return t>=13312&&t<=19903},"Yijing Hexagram Symbols":function(t){return t>=19904&&t<=19967},"CJK Unified Ideographs":function(t){return 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this._transitionablePaint.setTransition(t.slice(0,-11),e||void 0),!1;var i=this._transitionablePaint._values[t],a="cross-faded-data-driven"===i.property.specification["property-type"],o=i.value.isDataDriven(),s=i.value;this._transitionablePaint.setValue(t,e),this._handleSpecialPaintPropertyUpdate(t);var l=this._transitionablePaint._values[t].value;return l.isDataDriven()||o||a||this._handleOverridablePaintPropertyUpdate(t,s,l)},e.prototype._handleSpecialPaintPropertyUpdate=function(t){},e.prototype._handleOverridablePaintPropertyUpdate=function(t,e,r){return!1},e.prototype.isHidden=function(t){return!!(this.minzoom&&t=this.maxzoom)||"none"===this.visibility},e.prototype.updateTransitions=function(t){this._transitioningPaint=this._transitionablePaint.transitioned(t,this._transitioningPaint)},e.prototype.hasTransition=function(){return this._transitioningPaint.hasTransition()},e.prototype.recalculate=function(t,e){t.getCrossfadeParameters&&(this._crossfadeParameters=t.getCrossfadeParameters()),this._unevaluatedLayout&&(this.layout=this._unevaluatedLayout.possiblyEvaluate(t,void 0,e)),this.paint=this._transitioningPaint.possiblyEvaluate(t,void 0,e)},e.prototype.serialize=function(){var t={id:this.id,type:this.type,source:this.source,"source-layer":this.sourceLayer,metadata:this.metadata,minzoom:this.minzoom,maxzoom:this.maxzoom,filter:this.filter,layout:this._unevaluatedLayout&&this._unevaluatedLayout.serialize(),paint:this._transitionablePaint&&this._transitionablePaint.serialize()};return this.visibility&&(t.layout=t.layout||{},t.layout.visibility=this.visibility),x(t,(function(t,e){return!(void 0===t||"layout"===e&&!Object.keys(t).length||"paint"===e&&!Object.keys(t).length)}))},e.prototype._validate=function(t,e,r,n,i){return void 0===i&&(i={}),(!i||!1!==i.validate)&&Jn(this,t.call(Zn,{key:e,layerType:this.type,objectKey:r,value:n,styleSpec:Dt,style:{glyphs:!0,sprite:!0}}))},e.prototype.is3D=function(){return!1},e.prototype.isTileClipped=function(){return!1},e.prototype.hasOffscreenPass=function(){return!1},e.prototype.resize=function(){},e.prototype.isStateDependent=function(){for(var t in this.paint._values){var e=this.paint.get(t);if(e instanceof Bi&&Yr(e.property.specification)&&("source"===e.value.kind||"composite"===e.value.kind)&&e.value.isStateDependent)return!0}return!1},e}(It),Wi={Int8:Int8Array,Uint8:Uint8Array,Int16:Int16Array,Uint16:Uint16Array,Int32:Int32Array,Uint32:Uint32Array,Float32:Float32Array},Xi=function(t,e){this._structArray=t,this._pos1=e*this.size,this._pos2=this._pos1/2,this._pos4=this._pos1/4,this._pos8=this._pos1/8},Ji=function(){this.isTransferred=!1,this.capacity=-1,this.resize(0)};function Ki(t,e){void 0===e&&(e=1);var r=0,n=0;return{members:t.map((function(t){var i,a=(i=t.type,Wi[i].BYTES_PER_ELEMENT),o=r=$i(r,Math.max(e,a)),s=t.components||1;return n=Math.max(n,a),r+=a*s,{name:t.name,type:t.type,components:s,offset:o}})),size:$i(r,Math.max(n,e)),alignment:e}}function $i(t,e){return Math.ceil(t/e)*e}Ji.serialize=function(t,e){return t._trim(),e&&(t.isTransferred=!0,e.push(t.arrayBuffer)),{length:t.length,arrayBuffer:t.arrayBuffer}},Ji.deserialize=function(t){var e=Object.create(this.prototype);return e.arrayBuffer=t.arrayBuffer,e.length=t.length,e.capacity=t.arrayBuffer.byteLength/e.bytesPerElement,e._refreshViews(),e},Ji.prototype._trim=function(){this.length!==this.capacity&&(this.capacity=this.length,this.arrayBuffer=this.arrayBuffer.slice(0,this.length*this.bytesPerElement),this._refreshViews())},Ji.prototype.clear=function(){this.length=0},Ji.prototype.resize=function(t){this.reserve(t),this.length=t},Ji.prototype.reserve=function(t){if(t>this.capacity){this.capacity=Math.max(t,Math.floor(5*this.capacity),128),this.arrayBuffer=new ArrayBuffer(this.capacity*this.bytesPerElement);var e=this.uint8;this._refreshViews(),e&&this.uint8.set(e)}},Ji.prototype._refreshViews=function(){throw new Error("_refreshViews() must be implemented by each concrete StructArray layout")};var Qi=function(t){function e(){t.apply(this,arguments)}return t&&(e.__proto__=t),e.prototype=Object.create(t&&t.prototype),e.prototype.constructor=e,e.prototype._refreshViews=function(){this.uint8=new Uint8Array(this.arrayBuffer),this.int16=new Int16Array(this.arrayBuffer)},e.prototype.emplaceBack=function(t,e){var r=this.length;return this.resize(r+1),this.emplace(r,t,e)},e.prototype.emplace=function(t,e,r){var n=2*t;return this.int16[n+0]=e,this.int16[n+1]=r,t},e}(Ji);Qi.prototype.bytesPerElement=4,ni("StructArrayLayout2i4",Qi);var ta=function(t){function e(){t.apply(this,arguments)}return t&&(e.__proto__=t),e.prototype=Object.create(t&&t.prototype),e.prototype.constructor=e,e.prototype._refreshViews=function(){this.uint8=new Uint8Array(this.arrayBuffer),this.int16=new Int16Array(this.arrayBuffer)},e.prototype.emplaceBack=function(t,e,r,n){var i=this.length;return this.resize(i+1),this.emplace(i,t,e,r,n)},e.prototype.emplace=function(t,e,r,n,i){var a=4*t;return this.int16[a+0]=e,this.int16[a+1]=r,this.int16[a+2]=n,this.int16[a+3]=i,t},e}(Ji);ta.prototype.bytesPerElement=8,ni("StructArrayLayout4i8",ta);var ea=function(t){function e(){t.apply(this,arguments)}return t&&(e.__proto__=t),e.prototype=Object.create(t&&t.prototype),e.prototype.constructor=e,e.prototype._refreshViews=function(){this.uint8=new Uint8Array(this.arrayBuffer),this.int16=new Int16Array(this.arrayBuffer)},e.prototype.emplaceBack=function(t,e,r,n,i,a){var o=this.length;return this.resize(o+1),this.emplace(o,t,e,r,n,i,a)},e.prototype.emplace=function(t,e,r,n,i,a,o){var s=6*t;return this.int16[s+0]=e,this.int16[s+1]=r,this.int16[s+2]=n,this.int16[s+3]=i,this.int16[s+4]=a,this.int16[s+5]=o,t},e}(Ji);ea.prototype.bytesPerElement=12,ni("StructArrayLayout2i4i12",ea);var ra=function(t){function e(){t.apply(this,arguments)}return t&&(e.__proto__=t),e.prototype=Object.create(t&&t.prototype),e.prototype.constructor=e,e.prototype._refreshViews=function(){this.uint8=new Uint8Array(this.arrayBuffer),this.int16=new Int16Array(this.arrayBuffer)},e.prototype.emplaceBack=function(t,e,r,n,i,a){var o=this.length;return this.resize(o+1),this.emplace(o,t,e,r,n,i,a)},e.prototype.emplace=function(t,e,r,n,i,a,o){var s=4*t,l=8*t;return this.int16[s+0]=e,this.int16[s+1]=r,this.uint8[l+4]=n,this.uint8[l+5]=i,this.uint8[l+6]=a,this.uint8[l+7]=o,t},e}(Ji);ra.prototype.bytesPerElement=8,ni("StructArrayLayout2i4ub8",ra);var na=function(t){function e(){t.apply(this,arguments)}return t&&(e.__proto__=t),e.prototype=Object.create(t&&t.prototype),e.prototype.constructor=e,e.prototype._refreshViews=function(){this.uint8=new Uint8Array(this.arrayBuffer),this.uint16=new Uint16Array(this.arrayBuffer)},e.prototype.emplaceBack=function(t,e,r,n,i,a,o,s,l,u){var c=this.length;return this.resize(c+1),this.emplace(c,t,e,r,n,i,a,o,s,l,u)},e.prototype.emplace=function(t,e,r,n,i,a,o,s,l,u,c){var f=9*t,h=18*t;return this.uint16[f+0]=e,this.uint16[f+1]=r,this.uint16[f+2]=n,this.uint16[f+3]=i,this.uint16[f+4]=a,this.uint16[f+5]=o,this.uint16[f+6]=s,this.uint16[f+7]=l,this.uint8[h+16]=u,this.uint8[h+17]=c,t},e}(Ji);na.prototype.bytesPerElement=18,ni("StructArrayLayout8ui2ub18",na);var ia=function(t){function e(){t.apply(this,arguments)}return t&&(e.__proto__=t),e.prototype=Object.create(t&&t.prototype),e.prototype.constructor=e,e.prototype._refreshViews=function(){this.uint8=new Uint8Array(this.arrayBuffer),this.int16=new Int16Array(this.arrayBuffer),this.uint16=new Uint16Array(this.arrayBuffer)},e.prototype.emplaceBack=function(t,e,r,n,i,a,o,s,l,u,c,f){var h=this.length;return this.resize(h+1),this.emplace(h,t,e,r,n,i,a,o,s,l,u,c,f)},e.prototype.emplace=function(t,e,r,n,i,a,o,s,l,u,c,f,h){var p=12*t;return this.int16[p+0]=e,this.int16[p+1]=r,this.int16[p+2]=n,this.int16[p+3]=i,this.uint16[p+4]=a,this.uint16[p+5]=o,this.uint16[p+6]=s,this.uint16[p+7]=l,this.int16[p+8]=u,this.int16[p+9]=c,this.int16[p+10]=f,this.int16[p+11]=h,t},e}(Ji);ia.prototype.bytesPerElement=24,ni("StructArrayLayout4i4ui4i24",ia);var aa=function(t){function e(){t.apply(this,arguments)}return t&&(e.__proto__=t),e.prototype=Object.create(t&&t.prototype),e.prototype.constructor=e,e.prototype._refreshViews=function(){this.uint8=new Uint8Array(this.arrayBuffer),this.float32=new Float32Array(this.arrayBuffer)},e.prototype.emplaceBack=function(t,e,r){var n=this.length;return this.resize(n+1),this.emplace(n,t,e,r)},e.prototype.emplace=function(t,e,r,n){var i=3*t;return this.float32[i+0]=e,this.float32[i+1]=r,this.float32[i+2]=n,t},e}(Ji);aa.prototype.bytesPerElement=12,ni("StructArrayLayout3f12",aa);var oa=function(t){function e(){t.apply(this,arguments)}return t&&(e.__proto__=t),e.prototype=Object.create(t&&t.prototype),e.prototype.constructor=e,e.prototype._refreshViews=function(){this.uint8=new Uint8Array(this.arrayBuffer),this.uint32=new Uint32Array(this.arrayBuffer)},e.prototype.emplaceBack=function(t){var e=this.length;return this.resize(e+1),this.emplace(e,t)},e.prototype.emplace=function(t,e){var r=1*t;return this.uint32[r+0]=e,t},e}(Ji);oa.prototype.bytesPerElement=4,ni("StructArrayLayout1ul4",oa);var sa=function(t){function e(){t.apply(this,arguments)}return t&&(e.__proto__=t),e.prototype=Object.create(t&&t.prototype),e.prototype.constructor=e,e.prototype._refreshViews=function(){this.uint8=new Uint8Array(this.arrayBuffer),this.int16=new Int16Array(this.arrayBuffer),this.uint32=new Uint32Array(this.arrayBuffer),this.uint16=new Uint16Array(this.arrayBuffer)},e.prototype.emplaceBack=function(t,e,r,n,i,a,o,s,l){var u=this.length;return this.resize(u+1),this.emplace(u,t,e,r,n,i,a,o,s,l)},e.prototype.emplace=function(t,e,r,n,i,a,o,s,l,u){var c=10*t,f=5*t;return this.int16[c+0]=e,this.int16[c+1]=r,this.int16[c+2]=n,this.int16[c+3]=i,this.int16[c+4]=a,this.int16[c+5]=o,this.uint32[f+3]=s,this.uint16[c+8]=l,this.uint16[c+9]=u,t},e}(Ji);sa.prototype.bytesPerElement=20,ni("StructArrayLayout6i1ul2ui20",sa);var la=function(t){function e(){t.apply(this,arguments)}return t&&(e.__proto__=t),e.prototype=Object.create(t&&t.prototype),e.prototype.constructor=e,e.prototype._refreshViews=function(){this.uint8=new Uint8Array(this.arrayBuffer),this.int16=new Int16Array(this.arrayBuffer)},e.prototype.emplaceBack=function(t,e,r,n,i,a){var o=this.length;return this.resize(o+1),this.emplace(o,t,e,r,n,i,a)},e.prototype.emplace=function(t,e,r,n,i,a,o){var s=6*t;return this.int16[s+0]=e,this.int16[s+1]=r,this.int16[s+2]=n,this.int16[s+3]=i,this.int16[s+4]=a,this.int16[s+5]=o,t},e}(Ji);la.prototype.bytesPerElement=12,ni("StructArrayLayout2i2i2i12",la);var ua=function(t){function e(){t.apply(this,arguments)}return t&&(e.__proto__=t),e.prototype=Object.create(t&&t.prototype),e.prototype.constructor=e,e.prototype._refreshViews=function(){this.uint8=new Uint8Array(this.arrayBuffer),this.float32=new Float32Array(this.arrayBuffer),this.int16=new Int16Array(this.arrayBuffer)},e.prototype.emplaceBack=function(t,e,r,n,i){var a=this.length;return this.resize(a+1),this.emplace(a,t,e,r,n,i)},e.prototype.emplace=function(t,e,r,n,i,a){var o=4*t,s=8*t;return this.float32[o+0]=e,this.float32[o+1]=r,this.float32[o+2]=n,this.int16[s+6]=i,this.int16[s+7]=a,t},e}(Ji);ua.prototype.bytesPerElement=16,ni("StructArrayLayout2f1f2i16",ua);var ca=function(t){function e(){t.apply(this,arguments)}return t&&(e.__proto__=t),e.prototype=Object.create(t&&t.prototype),e.prototype.constructor=e,e.prototype._refreshViews=function(){this.uint8=new Uint8Array(this.arrayBuffer),this.float32=new Float32Array(this.arrayBuffer)},e.prototype.emplaceBack=function(t,e,r,n){var i=this.length;return this.resize(i+1),this.emplace(i,t,e,r,n)},e.prototype.emplace=function(t,e,r,n,i){var a=12*t,o=3*t;return this.uint8[a+0]=e,this.uint8[a+1]=r,this.float32[o+1]=n,this.float32[o+2]=i,t},e}(Ji);ca.prototype.bytesPerElement=12,ni("StructArrayLayout2ub2f12",ca);var fa=function(t){function e(){t.apply(this,arguments)}return t&&(e.__proto__=t),e.prototype=Object.create(t&&t.prototype),e.prototype.constructor=e,e.prototype._refreshViews=function(){this.uint8=new Uint8Array(this.arrayBuffer),this.uint16=new Uint16Array(this.arrayBuffer)},e.prototype.emplaceBack=function(t,e,r){var n=this.length;return this.resize(n+1),this.emplace(n,t,e,r)},e.prototype.emplace=function(t,e,r,n){var i=3*t;return this.uint16[i+0]=e,this.uint16[i+1]=r,this.uint16[i+2]=n,t},e}(Ji);fa.prototype.bytesPerElement=6,ni("StructArrayLayout3ui6",fa);var ha=function(t){function e(){t.apply(this,arguments)}return t&&(e.__proto__=t),e.prototype=Object.create(t&&t.prototype),e.prototype.constructor=e,e.prototype._refreshViews=function(){this.uint8=new Uint8Array(this.arrayBuffer),this.int16=new Int16Array(this.arrayBuffer),this.uint16=new Uint16Array(this.arrayBuffer),this.uint32=new Uint32Array(this.arrayBuffer),this.float32=new Float32Array(this.arrayBuffer)},e.prototype.emplaceBack=function(t,e,r,n,i,a,o,s,l,u,c,f,h,p,d,v,g){var y=this.length;return this.resize(y+1),this.emplace(y,t,e,r,n,i,a,o,s,l,u,c,f,h,p,d,v,g)},e.prototype.emplace=function(t,e,r,n,i,a,o,s,l,u,c,f,h,p,d,v,g,y){var m=24*t,x=12*t,b=48*t;return this.int16[m+0]=e,this.int16[m+1]=r,this.uint16[m+2]=n,this.uint16[m+3]=i,this.uint32[x+2]=a,this.uint32[x+3]=o,this.uint32[x+4]=s,this.uint16[m+10]=l,this.uint16[m+11]=u,this.uint16[m+12]=c,this.float32[x+7]=f,this.float32[x+8]=h,this.uint8[b+36]=p,this.uint8[b+37]=d,this.uint8[b+38]=v,this.uint32[x+10]=g,this.int16[m+22]=y,t},e}(Ji);ha.prototype.bytesPerElement=48,ni("StructArrayLayout2i2ui3ul3ui2f3ub1ul1i48",ha);var pa=function(t){function e(){t.apply(this,arguments)}return t&&(e.__proto__=t),e.prototype=Object.create(t&&t.prototype),e.prototype.constructor=e,e.prototype._refreshViews=function(){this.uint8=new Uint8Array(this.arrayBuffer),this.int16=new Int16Array(this.arrayBuffer),this.uint16=new Uint16Array(this.arrayBuffer),this.uint32=new Uint32Array(this.arrayBuffer),this.float32=new Float32Array(this.arrayBuffer)},e.prototype.emplaceBack=function(t,e,r,n,i,a,o,s,l,u,c,f,h,p,d,v,g,y,m,x,b,_,w,T,k,A,M,S){var E=this.length;return this.resize(E+1),this.emplace(E,t,e,r,n,i,a,o,s,l,u,c,f,h,p,d,v,g,y,m,x,b,_,w,T,k,A,M,S)},e.prototype.emplace=function(t,e,r,n,i,a,o,s,l,u,c,f,h,p,d,v,g,y,m,x,b,_,w,T,k,A,M,S,E){var L=34*t,C=17*t;return this.int16[L+0]=e,this.int16[L+1]=r,this.int16[L+2]=n,this.int16[L+3]=i,this.int16[L+4]=a,this.int16[L+5]=o,this.int16[L+6]=s,this.int16[L+7]=l,this.uint16[L+8]=u,this.uint16[L+9]=c,this.uint16[L+10]=f,this.uint16[L+11]=h,this.uint16[L+12]=p,this.uint16[L+13]=d,this.uint16[L+14]=v,this.uint16[L+15]=g,this.uint16[L+16]=y,this.uint16[L+17]=m,this.uint16[L+18]=x,this.uint16[L+19]=b,this.uint16[L+20]=_,this.uint16[L+21]=w,this.uint16[L+22]=T,this.uint32[C+12]=k,this.float32[C+13]=A,this.float32[C+14]=M,this.float32[C+15]=S,this.float32[C+16]=E,t},e}(Ji);pa.prototype.bytesPerElement=68,ni("StructArrayLayout8i15ui1ul4f68",pa);var da=function(t){function e(){t.apply(this,arguments)}return t&&(e.__proto__=t),e.prototype=Object.create(t&&t.prototype),e.prototype.constructor=e,e.prototype._refreshViews=function(){this.uint8=new Uint8Array(this.arrayBuffer),this.float32=new Float32Array(this.arrayBuffer)},e.prototype.emplaceBack=function(t){var e=this.length;return this.resize(e+1),this.emplace(e,t)},e.prototype.emplace=function(t,e){var r=1*t;return this.float32[r+0]=e,t},e}(Ji);da.prototype.bytesPerElement=4,ni("StructArrayLayout1f4",da);var va=function(t){function e(){t.apply(this,arguments)}return t&&(e.__proto__=t),e.prototype=Object.create(t&&t.prototype),e.prototype.constructor=e,e.prototype._refreshViews=function(){this.uint8=new Uint8Array(this.arrayBuffer),this.int16=new Int16Array(this.arrayBuffer)},e.prototype.emplaceBack=function(t,e,r){var n=this.length;return this.resize(n+1),this.emplace(n,t,e,r)},e.prototype.emplace=function(t,e,r,n){var i=3*t;return this.int16[i+0]=e,this.int16[i+1]=r,this.int16[i+2]=n,t},e}(Ji);va.prototype.bytesPerElement=6,ni("StructArrayLayout3i6",va);var ga=function(t){function e(){t.apply(this,arguments)}return t&&(e.__proto__=t),e.prototype=Object.create(t&&t.prototype),e.prototype.constructor=e,e.prototype._refreshViews=function(){this.uint8=new Uint8Array(this.arrayBuffer),this.uint32=new Uint32Array(this.arrayBuffer),this.uint16=new Uint16Array(this.arrayBuffer)},e.prototype.emplaceBack=function(t,e,r){var n=this.length;return this.resize(n+1),this.emplace(n,t,e,r)},e.prototype.emplace=function(t,e,r,n){var i=2*t,a=4*t;return this.uint32[i+0]=e,this.uint16[a+2]=r,this.uint16[a+3]=n,t},e}(Ji);ga.prototype.bytesPerElement=8,ni("StructArrayLayout1ul2ui8",ga);var ya=function(t){function e(){t.apply(this,arguments)}return t&&(e.__proto__=t),e.prototype=Object.create(t&&t.prototype),e.prototype.constructor=e,e.prototype._refreshViews=function(){this.uint8=new Uint8Array(this.arrayBuffer),this.uint16=new 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t&&(e.__proto__=t),e.prototype=Object.create(t&&t.prototype),e.prototype.constructor=e,e.prototype._refreshViews=function(){this.uint8=new Uint8Array(this.arrayBuffer),this.float32=new Float32Array(this.arrayBuffer)},e.prototype.emplaceBack=function(t,e){var r=this.length;return this.resize(r+1),this.emplace(r,t,e)},e.prototype.emplace=function(t,e,r){var n=2*t;return this.float32[n+0]=e,this.float32[n+1]=r,t},e}(Ji);xa.prototype.bytesPerElement=8,ni("StructArrayLayout2f8",xa);var ba=function(t){function e(){t.apply(this,arguments)}return t&&(e.__proto__=t),e.prototype=Object.create(t&&t.prototype),e.prototype.constructor=e,e.prototype._refreshViews=function(){this.uint8=new Uint8Array(this.arrayBuffer),this.float32=new Float32Array(this.arrayBuffer)},e.prototype.emplaceBack=function(t,e,r,n){var i=this.length;return this.resize(i+1),this.emplace(i,t,e,r,n)},e.prototype.emplace=function(t,e,r,n,i){var a=4*t;return 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t.id}))};function el(t,e){return t.x===e.x&&(t.x<0||t.x>co)||t.y===e.y&&(t.y<0||t.y>co)}tl.prototype.populate=function(t,e,r){this.features=[],this.hasPattern=zs("fill-extrusion",this.layers,e);for(var n=0,i=t;nco}))||O.every((function(t){return t.y<0}))||O.every((function(t){return t.y>co}))))for(var v=0,g=0;g=1){var m=d[g-1];if(!el(y,m)){f.vertexLength+4>Oa.MAX_VERTEX_ARRAY_LENGTH&&(f=this.segments.prepareSegment(4,this.layoutVertexArray,this.indexArray));var x=y.sub(m)._perp()._unit(),b=m.dist(y);v+b>32768&&(v=0),Qs(this.layoutVertexArray,y.x,y.y,x.x,x.y,0,0,v),Qs(this.layoutVertexArray,y.x,y.y,x.x,x.y,0,1,v),v+=b,Qs(this.layoutVertexArray,m.x,m.y,x.x,x.y,0,0,v),Qs(this.layoutVertexArray,m.x,m.y,x.x,x.y,0,1,v);var 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i=t-1>>1,a=e[i];if(r(n,a)>=0)break;e[t]=a,t=i}e[t]=n},ju.prototype._down=function(t){for(var e=this.data,r=this.compare,n=this.length>>1,i=e[t];t=0)break;e[t]=o,t=a}e[t]=i};var Gu=7,Zu=Number.POSITIVE_INFINITY;function Yu(t,e){return e[1]!==Zu?function(t,e,r){var n=0,i=0;switch(e=Math.abs(e),r=Math.abs(r),t){case"top-right":case"top-left":case"top":i=r-Gu;break;case"bottom-right":case"bottom-left":case"bottom":i=-r+Gu}switch(t){case"top-right":case"bottom-right":case"right":n=-e;break;case"top-left":case"bottom-left":case"left":n=e}return[n,i]}(t,e[0],e[1]):function(t,e){var r=0,n=0;e<0&&(e=0);var i=e/Math.sqrt(2);switch(t){case"top-right":case"top-left":n=i-Gu;break;case"bottom-right":case"bottom-left":n=-i+Gu;break;case"bottom":n=-e+Gu;break;case"top":n=e-Gu}switch(t){case"top-right":case"bottom-right":r=-i;break;case"top-left":case"bottom-left":r=i;break;case"left":r=e;break;case"right":r=-e}return[r,n]}(t,e[0])}function Wu(t){switch(t){case"right":case"top-right":case"bottom-right":return"right";case"left":case"top-left":case"bottom-left":return"left"}return"center"}var Xu=255,Ju=Xu*bu;function Ku(t,e,r,n,i,o,s,l,u,c,f,h,p,d,v){var g=function(t,e,r,n,i,o,s,l){for(var u=n.layout.get("text-rotate").evaluate(o,{})*Math.PI/180,c=[],f=0,h=e.positionedLines;fJu&&w(t.layerIds[0]+': Value for "text-size" is >= '+Xu+'. 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this.hasDebugData()&&this.iconCollisionBox.segments.get().length>0},sc.prototype.addIndicesForPlacedSymbol=function(t,e){for(var r=t.placedSymbolArray.get(e),n=r.vertexStartIndex+4*r.numGlyphs,i=r.vertexStartIndex;i1||this.icon.segments.get().length>1)){this.symbolInstanceIndexes=this.getSortedSymbolIndexes(t),this.sortedAngle=t,this.text.indexArray.clear(),this.icon.indexArray.clear(),this.featureSortOrder=[];for(var r=0,n=this.symbolInstanceIndexes;r=0&&n.indexOf(t)===r&&e.addIndicesForPlacedSymbol(e.text,t)})),a.verticalPlacedTextSymbolIndex>=0&&this.addIndicesForPlacedSymbol(this.text,a.verticalPlacedTextSymbolIndex),a.placedIconSymbolIndex>=0&&this.addIndicesForPlacedSymbol(this.icon,a.placedIconSymbolIndex),a.verticalPlacedIconSymbolIndex>=0&&this.addIndicesForPlacedSymbol(this.icon,a.verticalPlacedIconSymbolIndex)}this.text.indexBuffer&&this.text.indexBuffer.updateData(this.text.indexArray),this.icon.indexBuffer&&this.icon.indexBuffer.updateData(this.icon.indexArray)}},ni("SymbolBucket",sc,{omit:["layers","collisionBoxArray","features","compareText"]}),sc.MAX_GLYPHS=65535,sc.addDynamicAttributes=nc;var lc=new Gi({"symbol-placement":new ji(Dt.layout_symbol["symbol-placement"]),"symbol-spacing":new ji(Dt.layout_symbol["symbol-spacing"]),"symbol-avoid-edges":new ji(Dt.layout_symbol["symbol-avoid-edges"]),"symbol-sort-key":new Ui(Dt.layout_symbol["symbol-sort-key"]),"symbol-z-order":new ji(Dt.layout_symbol["symbol-z-order"]),"icon-allow-overlap":new ji(Dt.layout_symbol["icon-allow-overlap"]),"icon-ignore-placement":new ji(Dt.layout_symbol["icon-ignore-placement"]),"icon-optional":new ji(Dt.layout_symbol["icon-optional"]),"icon-rotation-alignment":new ji(Dt.layout_symbol["icon-rotation-alignment"]),"icon-size":new Ui(Dt.layout_symbol["icon-size"]),"icon-text-fit":new ji(Dt.layout_symbol["icon-text-fit"]),"icon-text-fit-padding":new ji(Dt.layout_symbol["icon-text-fit-padding"]),"icon-image":new Ui(Dt.layout_symbol["icon-image"]),"icon-rotate":new Ui(Dt.layout_symbol["icon-rotate"]),"icon-padding":new ji(Dt.layout_symbol["icon-padding"]),"icon-keep-upright":new ji(Dt.layout_symbol["icon-keep-upright"]),"icon-offset":new Ui(Dt.layout_symbol["icon-offset"]),"icon-anchor":new Ui(Dt.layout_symbol["icon-anchor"]),"icon-pitch-alignment":new ji(Dt.layout_symbol["icon-pitch-alignment"]),"text-pitch-alignment":new ji(Dt.layout_symbol["text-pitch-alignment"]),"text-rotation-alignment":new ji(Dt.layout_symbol["text-rotation-alignment"]),"text-field":new Ui(Dt.layout_symbol["text-field"]),"text-font":new Ui(Dt.layout_symbol["text-font"]),"text-size":new Ui(Dt.layout_symbol["text-size"]),"text-max-width":new Ui(Dt.layout_symbol["text-max-width"]),"text-line-height":new ji(Dt.layout_symbol["text-line-height"]),"text-letter-spacing":new Ui(Dt.layout_symbol["text-letter-spacing"]),"text-justify":new Ui(Dt.layout_symbol["text-justify"]),"text-radial-offset":new Ui(Dt.layout_symbol["text-radial-offset"]),"text-variable-anchor":new ji(Dt.layout_symbol["text-variable-anchor"]),"text-anchor":new Ui(Dt.layout_symbol["text-anchor"]),"text-max-angle":new ji(Dt.layout_symbol["text-max-angle"]),"text-writing-mode":new ji(Dt.layout_symbol["text-writing-mode"]),"text-rotate":new Ui(Dt.layout_symbol["text-rotate"]),"text-padding":new ji(Dt.layout_symbol["text-padding"]),"text-keep-upright":new ji(Dt.layout_symbol["text-keep-upright"]),"text-transform":new Ui(Dt.layout_symbol["text-transform"]),"text-offset":new Ui(Dt.layout_symbol["text-offset"]),"text-allow-overlap":new ji(Dt.layout_symbol["text-allow-overlap"]),"text-ignore-placement":new ji(Dt.layout_symbol["text-ignore-placement"]),"text-optional":new ji(Dt.layout_symbol["text-optional"])}),uc={paint:new Gi({"icon-opacity":new Ui(Dt.paint_symbol["icon-opacity"]),"icon-color":new Ui(Dt.paint_symbol["icon-color"]),"icon-halo-color":new Ui(Dt.paint_symbol["icon-halo-color"]),"icon-halo-width":new Ui(Dt.paint_symbol["icon-halo-width"]),"icon-halo-blur":new Ui(Dt.paint_symbol["icon-halo-blur"]),"icon-translate":new ji(Dt.paint_symbol["icon-translate"]),"icon-translate-anchor":new ji(Dt.paint_symbol["icon-translate-anchor"]),"text-opacity":new Ui(Dt.paint_symbol["text-opacity"]),"text-color":new Ui(Dt.paint_symbol["text-color"],{runtimeType:Zt,getOverride:function(t){return t.textColor},hasOverride:function(t){return!!t.textColor}}),"text-halo-color":new Ui(Dt.paint_symbol["text-halo-color"]),"text-halo-width":new Ui(Dt.paint_symbol["text-halo-width"]),"text-halo-blur":new Ui(Dt.paint_symbol["text-halo-blur"]),"text-translate":new ji(Dt.paint_symbol["text-translate"]),"text-translate-anchor":new ji(Dt.paint_symbol["text-translate-anchor"])}),layout:lc},cc=function(t){this.type=t.property.overrides?t.property.overrides.runtimeType:Vt,this.defaultValue=t};cc.prototype.evaluate=function(t){if(t.formattedSection){var e=this.defaultValue.property.overrides;if(e&&e.hasOverride(t.formattedSection))return e.getOverride(t.formattedSection)}return t.feature&&t.featureState?this.defaultValue.evaluate(t.feature,t.featureState):this.defaultValue.property.specification.default},cc.prototype.eachChild=function(t){this.defaultValue.isConstant()||t(this.defaultValue.value._styleExpression.expression)},cc.prototype.outputDefined=function(){return!1},cc.prototype.serialize=function(){return null},ni("FormatSectionOverride",cc,{omit:["defaultValue"]});var fc=function(t){function e(e){t.call(this,e,uc)}return t&&(e.__proto__=t),e.prototype=Object.create(t&&t.prototype),e.prototype.constructor=e,e.prototype.recalculate=function(e,r){if(t.prototype.recalculate.call(this,e,r),"auto"===this.layout.get("icon-rotation-alignment")&&("point"!==this.layout.get("symbol-placement")?this.layout._values["icon-rotation-alignment"]="map":this.layout._values["icon-rotation-alignment"]="viewport"),"auto"===this.layout.get("text-rotation-alignment")&&("point"!==this.layout.get("symbol-placement")?this.layout._values["text-rotation-alignment"]="map":this.layout._values["text-rotation-alignment"]="viewport"),"auto"===this.layout.get("text-pitch-alignment")&&(this.layout._values["text-pitch-alignment"]=this.layout.get("text-rotation-alignment")),"auto"===this.layout.get("icon-pitch-alignment")&&(this.layout._values["icon-pitch-alignment"]=this.layout.get("icon-rotation-alignment")),"point"===this.layout.get("symbol-placement")){var n=this.layout.get("text-writing-mode");if(n){for(var i=[],a=0,o=n;a",targetMapId:n,sourceMapId:a.mapId})}}},Ac.prototype.receive=function(t){var e=t.data,r=e.id;if(r&&(!e.targetMapId||this.mapId===e.targetMapId))if(""===e.type){delete this.tasks[r];var n=this.cancelCallbacks[r];delete this.cancelCallbacks[r],n&&n()}else A()||e.mustQueue?(this.tasks[r]=e,this.taskQueue.push(r),this.invoker.trigger()):this.processTask(r,e)},Ac.prototype.process=function(){if(this.taskQueue.length){var t=this.taskQueue.shift(),e=this.tasks[t];delete this.tasks[t],this.taskQueue.length&&this.invoker.trigger(),e&&this.processTask(t,e)}},Ac.prototype.processTask=function(t,e){var r=this;if(""===e.type){var n=this.callbacks[t];delete this.callbacks[t],n&&(e.error?n(li(e.error)):n(null,li(e.data)))}else{var i=!1,a=E(this.globalScope)?void 0:[],o=e.hasCallback?function(e,n){i=!0,delete r.cancelCallbacks[t],r.target.postMessage({id:t,type:"",sourceMapId:r.mapId,error:e?si(e):null,data:si(n,a)},a)}:function(t){i=!0},s=null,l=li(e.data);if(this.parent[e.type])s=this.parent[e.type](e.sourceMapId,l,o);else if(this.parent.getWorkerSource){var u=e.type.split(".");s=this.parent.getWorkerSource(e.sourceMapId,u[0],l.source)[u[1]](l,o)}else o(new Error("Could not find function "+e.type));!i&&s&&s.cancel&&(this.cancelCallbacks[t]=s.cancel)}},Ac.prototype.remove=function(){this.invoker.remove(),this.target.removeEventListener("message",this.receive,!1)};var Sc=function(t,e){t&&(e?this.setSouthWest(t).setNorthEast(e):4===t.length?this.setSouthWest([t[0],t[1]]).setNorthEast([t[2],t[3]]):this.setSouthWest(t[0]).setNorthEast(t[1]))};Sc.prototype.setNorthEast=function(t){return this._ne=t instanceof Lc?new Lc(t.lng,t.lat):Lc.convert(t),this},Sc.prototype.setSouthWest=function(t){return this._sw=t instanceof Lc?new Lc(t.lng,t.lat):Lc.convert(t),this},Sc.prototype.extend=function(t){var e,r,n=this._sw,i=this._ne;if(t instanceof Lc)e=t,r=t;else{if(!(t instanceof Sc)){if(Array.isArray(t)){if(4===t.length||t.every(Array.isArray)){var a=t;return this.extend(Sc.convert(a))}var o=t;return this.extend(Lc.convert(o))}return this}if(e=t._sw,r=t._ne,!e||!r)return this}return n||i?(n.lng=Math.min(e.lng,n.lng),n.lat=Math.min(e.lat,n.lat),i.lng=Math.max(r.lng,i.lng),i.lat=Math.max(r.lat,i.lat)):(this._sw=new Lc(e.lng,e.lat),this._ne=new Lc(r.lng,r.lat)),this},Sc.prototype.getCenter=function(){return new Lc((this._sw.lng+this._ne.lng)/2,(this._sw.lat+this._ne.lat)/2)},Sc.prototype.getSouthWest=function(){return this._sw},Sc.prototype.getNorthEast=function(){return this._ne},Sc.prototype.getNorthWest=function(){return new Lc(this.getWest(),this.getNorth())},Sc.prototype.getSouthEast=function(){return new Lc(this.getEast(),this.getSouth())},Sc.prototype.getWest=function(){return this._sw.lng},Sc.prototype.getSouth=function(){return this._sw.lat},Sc.prototype.getEast=function(){return this._ne.lng},Sc.prototype.getNorth=function(){return this._ne.lat},Sc.prototype.toArray=function(){return[this._sw.toArray(),this._ne.toArray()]},Sc.prototype.toString=function(){return"LngLatBounds("+this._sw.toString()+", "+this._ne.toString()+")"},Sc.prototype.isEmpty=function(){return!(this._sw&&this._ne)},Sc.prototype.contains=function(t){var e=Lc.convert(t),r=e.lng,n=e.lat,i=this._sw.lat<=n&&n<=this._ne.lat,a=this._sw.lng<=r&&r<=this._ne.lng;return this._sw.lng>this._ne.lng&&(a=this._sw.lng>=r&&r>=this._ne.lng),i&&a},Sc.convert=function(t){return!t||t instanceof Sc?t:new Sc(t)};var Ec=6371008.8,Lc=function(t,e){if(isNaN(t)||isNaN(e))throw new Error("Invalid LngLat object: ("+t+", "+e+")");if(this.lng=+t,this.lat=+e,this.lat>90||this.lat<-90)throw new Error("Invalid LngLat latitude value: must be between -90 and 90")};Lc.prototype.wrap=function(){return new Lc(c(this.lng,-180,180),this.lat)},Lc.prototype.toArray=function(){return[this.lng,this.lat]},Lc.prototype.toString=function(){return"LngLat("+this.lng+", "+this.lat+")"},Lc.prototype.distanceTo=function(t){var e=Math.PI/180,r=this.lat*e,n=t.lat*e,i=Math.sin(r)*Math.sin(n)+Math.cos(r)*Math.cos(n)*Math.cos((t.lng-this.lng)*e);return Ec*Math.acos(Math.min(i,1))},Lc.prototype.toBounds=function(t){void 0===t&&(t=0);var e=360*t/40075017,r=e/Math.cos(Math.PI/180*this.lat);return new Sc(new Lc(this.lng-r,this.lat-e),new Lc(this.lng+r,this.lat+e))},Lc.convert=function(t){if(t instanceof Lc)return t;if(Array.isArray(t)&&(2===t.length||3===t.length))return new Lc(Number(t[0]),Number(t[1]));if(!Array.isArray(t)&&"object"==typeof t&&null!==t)return new Lc(Number("lng"in t?t.lng:t.lon),Number(t.lat));throw new Error("`LngLatLike` argument must be specified as a LngLat instance, an object {lng: , lat: }, an object {lon: , lat: }, or an array of [, ]")};var Cc=2*Math.PI*Ec;function Pc(t){return Cc*Math.cos(t*Math.PI/180)}function Oc(t){return(180+t)/360}function Ic(t){return(180-180/Math.PI*Math.log(Math.tan(Math.PI/4+t*Math.PI/360)))/360}function Dc(t,e){return t/Pc(e)}function zc(t){var e=180-360*t;return 360/Math.PI*Math.atan(Math.exp(e*Math.PI/180))-90}var Rc=function(t,e,r){void 0===r&&(r=0),this.x=+t,this.y=+e,this.z=+r};Rc.fromLngLat=function(t,e){void 0===e&&(e=0);var r=Lc.convert(t);return new Rc(Oc(r.lng),Ic(r.lat),Dc(e,r.lat))},Rc.prototype.toLngLat=function(){return new Lc(360*this.x-180,zc(this.y))},Rc.prototype.toAltitude=function(){return t=this.z,e=this.y,t*Pc(zc(e));var t,e},Rc.prototype.meterInMercatorCoordinateUnits=function(){return 1/Cc*(t=zc(this.y),1/Math.cos(t*Math.PI/180));var t};var Fc=function(t,e,r){this.z=t,this.x=e,this.y=r,this.key=jc(0,t,t,e,r)};Fc.prototype.equals=function(t){return this.z===t.z&&this.x===t.x&&this.y===t.y},Fc.prototype.url=function(t,e){var r,n,i,a,o,s=(r=this.x,n=this.y,i=this.z,a=Mc(256*r,256*(n=Math.pow(2,i)-n-1),i),o=Mc(256*(r+1),256*(n+1),i),a[0]+","+a[1]+","+o[0]+","+o[1]),l=function(t,e,r){for(var n,i="",a=t;a>0;a--)i+=(e&(n=1<this.canonical.z?new Nc(t,this.wrap,this.canonical.z,this.canonical.x,this.canonical.y):new Nc(t,this.wrap,t,this.canonical.x>>e,this.canonical.y>>e)},Nc.prototype.calculateScaledKey=function(t,e){var r=this.canonical.z-t;return t>this.canonical.z?jc(this.wrap*+e,t,this.canonical.z,this.canonical.x,this.canonical.y):jc(this.wrap*+e,t,t,this.canonical.x>>r,this.canonical.y>>r)},Nc.prototype.isChildOf=function(t){if(t.wrap!==this.wrap)return!1;var e=this.canonical.z-t.canonical.z;return 0===t.overscaledZ||t.overscaledZ>e&&t.canonical.y===this.canonical.y>>e},Nc.prototype.children=function(t){if(this.overscaledZ>=t)return[new Nc(this.overscaledZ+1,this.wrap,this.canonical.z,this.canonical.x,this.canonical.y)];var e=this.canonical.z+1,r=2*this.canonical.x,n=2*this.canonical.y;return[new Nc(e,this.wrap,e,r,n),new Nc(e,this.wrap,e,r+1,n),new Nc(e,this.wrap,e,r,n+1),new Nc(e,this.wrap,e,r+1,n+1)]},Nc.prototype.isLessThan=function(t){return this.wrapt.wrap)&&(this.overscaledZt.overscaledZ)&&(this.canonical.xt.canonical.x)&&this.canonical.y=this.dim+1||e<-1||e>=this.dim+1)throw new RangeError("out of range source coordinates for DEM data");return(e+1)*this.stride+(t+1)},Uc.prototype._unpackMapbox=function(t,e,r){return(256*t*256+256*e+r)/10-1e4},Uc.prototype._unpackTerrarium=function(t,e,r){return 256*t+e+r/256-32768},Uc.prototype.getPixels=function(){return new Wo({width:this.stride,height:this.stride},new Uint8Array(this.data.buffer))},Uc.prototype.backfillBorder=function(t,e,r){if(this.dim!==t.dim)throw new Error("dem dimension mismatch");var n=e*this.dim,i=e*this.dim+this.dim,a=r*this.dim,o=r*this.dim+this.dim;switch(e){case-1:n=i-1;break;case 1:i=n+1}switch(r){case-1:a=o-1;break;case 1:o=a+1}for(var s=-e*this.dim,l=-r*this.dim,u=a;u=0&&c[3]>=0&&s.insert(o,c[0],c[1],c[2],c[3])}},Zc.prototype.loadVTLayers=function(){return this.vtLayers||(this.vtLayers=new Js.VectorTile(new Sl(this.rawTileData)).layers,this.sourceLayerCoder=new Vc(this.vtLayers?Object.keys(this.vtLayers).sort():["_geojsonTileLayer"])),this.vtLayers},Zc.prototype.query=function(t,e,r,n){var i=this;this.loadVTLayers();for(var o=t.params||{},s=co/t.tileSize/t.scale,l=wn(o.filter),u=t.queryGeometry,c=t.queryPadding*s,f=Wc(u),h=this.grid.query(f.minX-c,f.minY-c,f.maxX+c,f.maxY+c),p=Wc(t.cameraQueryGeometry),d=0,v=this.grid3D.query(p.minX-c,p.minY-c,p.maxX+c,p.maxY+c,(function(e,r,n,i){return function(t,e,r,n,i){for(var o=0,s=t;o=l.x&&i>=l.y)return!0}var u=[new a(e,r),new a(e,i),new a(n,i),new a(n,r)];if(t.length>2)for(var c=0,f=u;c=0)return!0;return!1}(a,f)){var h=this.sourceLayerCoder.decode(r),p=this.vtLayers[h].feature(n);if(i.filter(new Pi(this.tileID.overscaledZ),p))for(var d=this.getId(p,h),v=0;vn)i=!1;else if(e)if(this.expirationTimect&&(t.getActor().send("enforceCacheSizeLimit",ut),yt=0)},t.clamp=u,t.clearTileCache=function(t){var e=self.caches.delete(lt);t&&e.catch(t).then((function(){return t()}))},t.clipLine=Ou,t.clone=function(t){var e=new Io(16);return e[0]=t[0],e[1]=t[1],e[2]=t[2],e[3]=t[3],e[4]=t[4],e[5]=t[5],e[6]=t[6],e[7]=t[7],e[8]=t[8],e[9]=t[9],e[10]=t[10],e[11]=t[11],e[12]=t[12],e[13]=t[13],e[14]=t[14],e[15]=t[15],e},t.clone$1=b,t.clone$2=function(t){var e=new Io(3);return e[0]=t[0],e[1]=t[1],e[2]=t[2],e},t.collisionCircleLayout=_l,t.config=B,t.create=function(){var t=new Io(16);return Io!=Float32Array&&(t[1]=0,t[2]=0,t[3]=0,t[4]=0,t[6]=0,t[7]=0,t[8]=0,t[9]=0,t[11]=0,t[12]=0,t[13]=0,t[14]=0),t[0]=1,t[5]=1,t[10]=1,t[15]=1,t},t.create$1=function(){var t=new Io(9);return Io!=Float32Array&&(t[1]=0,t[2]=0,t[3]=0,t[5]=0,t[6]=0,t[7]=0),t[0]=1,t[4]=1,t[8]=1,t},t.create$2=function(){var t=new Io(4);return Io!=Float32Array&&(t[1]=0,t[2]=0),t[0]=1,t[3]=1,t},t.createCommonjsModule=e,t.createExpression=ln,t.createLayout=Ki,t.createStyleLayer=function(t){return"custom"===t.type?new gc(t):new yc[t.type](t)},t.cross=function(t,e,r){var n=e[0],i=e[1],a=e[2],o=r[0],s=r[1],l=r[2];return t[0]=i*l-a*s,t[1]=a*o-n*l,t[2]=n*s-i*o,t},t.deepEqual=function t(e,r){if(Array.isArray(e)){if(!Array.isArray(r)||e.length!==r.length)return!1;for(var n=0;n0&&(a=1/Math.sqrt(a)),t[0]=e[0]*a,t[1]=e[1]*a,t[2]=e[2]*a,t},t.number=$e,t.offscreenCanvasSupported=mt,t.ortho=function(t,e,r,n,i,a,o){var s=1/(e-r),l=1/(n-i),u=1/(a-o);return t[0]=-2*s,t[1]=0,t[2]=0,t[3]=0,t[4]=0,t[5]=-2*l,t[6]=0,t[7]=0,t[8]=0,t[9]=0,t[10]=2*u,t[11]=0,t[12]=(e+r)*s,t[13]=(i+n)*l,t[14]=(o+a)*u,t[15]=1,t},t.parseGlyphPBF=function(t){return new Sl(t).readFields(Wl,[])},t.pbf=Sl,t.performSymbolLayout=function(t,e,r,n,i,a,o){t.createArrays();var s=512*t.overscaling;t.tilePixelRatio=co/s,t.compareText={},t.iconsNeedLinear=!1;var l=t.layers[0].layout,u=t.layers[0]._unevaluatedLayout._values,c={};if("composite"===t.textSizeData.kind){var f=t.textSizeData,h=f.minZoom,p=f.maxZoom;c.compositeTextSizes=[u["text-size"].possiblyEvaluate(new Pi(h),o),u["text-size"].possiblyEvaluate(new Pi(p),o)]}if("composite"===t.iconSizeData.kind){var d=t.iconSizeData,v=d.minZoom,g=d.maxZoom;c.compositeIconSizes=[u["icon-size"].possiblyEvaluate(new Pi(v),o),u["icon-size"].possiblyEvaluate(new Pi(g),o)]}c.layoutTextSize=u["text-size"].possiblyEvaluate(new Pi(t.zoom+1),o),c.layoutIconSize=u["icon-size"].possiblyEvaluate(new Pi(t.zoom+1),o),c.textMaxSize=u["text-size"].possiblyEvaluate(new Pi(18));for(var y=l.get("text-line-height")*kl,m="map"===l.get("text-rotation-alignment")&&"point"!==l.get("symbol-placement"),x=l.get("text-keep-upright"),b=l.get("text-size"),_=function(){var a=k[T],s=l.get("text-font").evaluate(a,{},o).join(","),u=b.evaluate(a,{},o),f=c.layoutTextSize.evaluate(a,{},o),h=c.layoutIconSize.evaluate(a,{},o),p={horizontal:{},vertical:void 0},d=a.text,v=[0,0];if(d){var g=d.toString(),_=l.get("text-letter-spacing").evaluate(a,{},o)*kl,A=function(t){for(var e=0,r=t;e=co||f.y<0||f.y>=co||function(t,e,r,n,i,a,o,s,l,u,c,f,h,p,d,v,g,y,m,x,b,_,T,k,A){var M,S,E,L,C,P=t.addToLineVertexArray(e,r),O=0,I=0,D=0,z=0,R=-1,F=-1,B={},N=Fa(""),j=0,U=0;if(void 0===s._unevaluatedLayout.getValue("text-radial-offset")?(j=(M=s.layout.get("text-offset").evaluate(b,{},k).map((function(t){return t*kl})))[0],U=M[1]):(j=s.layout.get("text-radial-offset").evaluate(b,{},k)*kl,U=Zu),t.allowVerticalPlacement&&n.vertical){var V=s.layout.get("text-rotate").evaluate(b,{},k)+90,H=n.vertical;L=new Nu(l,e,u,c,f,H,h,p,d,V),o&&(C=new Nu(l,e,u,c,f,o,g,y,d,V))}if(i){var q=s.layout.get("icon-rotate").evaluate(b,{}),G="none"!==s.layout.get("icon-text-fit"),Z=Du(i,q,T,G),Y=o?Du(o,q,T,G):void 0;E=new Nu(l,e,u,c,f,i,g,y,!1,q),O=4*Z.length;var W=t.iconSizeData,X=null;"source"===W.kind?(X=[bu*s.layout.get("icon-size").evaluate(b,{})])[0]>Ju&&w(t.layerIds[0]+': Value for "icon-size" is >= '+Xu+'. Reduce your "icon-size".'):"composite"===W.kind&&((X=[bu*_.compositeIconSizes[0].evaluate(b,{},k),bu*_.compositeIconSizes[1].evaluate(b,{},k)])[0]>Ju||X[1]>Ju)&&w(t.layerIds[0]+': Value for "icon-size" is >= '+Xu+'. Reduce your "icon-size".'),t.addSymbols(t.icon,Z,X,x,m,b,!1,e,P.lineStartIndex,P.lineLength,-1,k),R=t.icon.placedSymbolArray.length-1,Y&&(I=4*Y.length,t.addSymbols(t.icon,Y,X,x,m,b,nu.vertical,e,P.lineStartIndex,P.lineLength,-1,k),F=t.icon.placedSymbolArray.length-1)}for(var J in n.horizontal){var K=n.horizontal[J];if(!S){N=Fa(K.text);var $=s.layout.get("text-rotate").evaluate(b,{},k);S=new Nu(l,e,u,c,f,K,h,p,d,$)}var Q=1===K.positionedLines.length;if(D+=Ku(t,e,K,a,s,d,b,v,P,n.vertical?nu.horizontal:nu.horizontalOnly,Q?Object.keys(n.horizontal):[J],B,R,_,k),Q)break}n.vertical&&(z+=Ku(t,e,n.vertical,a,s,d,b,v,P,nu.vertical,["vertical"],B,F,_,k));var tt=S?S.boxStartIndex:t.collisionBoxArray.length,et=S?S.boxEndIndex:t.collisionBoxArray.length,rt=L?L.boxStartIndex:t.collisionBoxArray.length,nt=L?L.boxEndIndex:t.collisionBoxArray.length,it=E?E.boxStartIndex:t.collisionBoxArray.length,at=E?E.boxEndIndex:t.collisionBoxArray.length,ot=C?C.boxStartIndex:t.collisionBoxArray.length,st=C?C.boxEndIndex:t.collisionBoxArray.length,lt=-1,ut=function(t,e){return t&&t.circleDiameter?Math.max(t.circleDiameter,e):e};lt=ut(S,lt),lt=ut(L,lt),lt=ut(E,lt);var ct=(lt=ut(C,lt))>-1?1:0;ct&&(lt*=A/kl),t.glyphOffsetArray.length>=sc.MAX_GLYPHS&&w("Too many glyphs being rendered in a tile. See https://github.com/mapbox/mapbox-gl-js/issues/2907"),void 0!==b.sortKey&&t.addToSortKeyRanges(t.symbolInstances.length,b.sortKey),t.symbolInstances.emplaceBack(e.x,e.y,B.right>=0?B.right:-1,B.center>=0?B.center:-1,B.left>=0?B.left:-1,B.vertical||-1,R,F,N,tt,et,rt,nt,it,at,ot,st,u,D,z,O,I,ct,0,h,j,U,lt)}(t,f,s,r,n,i,h,t.layers[0],t.collisionBoxArray,e.index,e.sourceLayerIndex,t.index,m,T,M,l,b,k,S,d,e,a,u,c,o)};if("line"===E)for(var O=0,I=Ou(e.geometry,0,0,co,co);O1){var U=Lu(j,A,r.vertical||v,n,g,x);U&&P(j,U)}}else if("Polygon"===e.type)for(var V=0,H=Is(e.geometry,0);V=E.maxzoom||"none"!==E.visibility&&(o(S,this.zoom,n),(v[E.id]=E.createBucket({index:c.bucketLayerIDs.length,layers:S,zoom:this.zoom,pixelRatio:this.pixelRatio,overscaling:this.overscaling,collisionBoxArray:this.collisionBoxArray,sourceLayerIndex:b,sourceID:this.source})).populate(_,g,this.tileID.canonical),c.bucketLayerIDs.push(S.map((function(t){return t.id}))))}}}var L=t.mapObject(g.glyphDependencies,(function(t){return Object.keys(t).map(Number)}));Object.keys(L).length?a.send("getGlyphs",{uid:this.uid,stacks:L},(function(t,e){f||(f=t,h=e,O.call(l))})):h={};var C=Object.keys(g.iconDependencies);C.length?a.send("getImages",{icons:C,source:this.source,tileID:this.tileID,type:"icons"},(function(t,e){f||(f=t,p=e,O.call(l))})):p={};var P=Object.keys(g.patternDependencies);function O(){if(f)return s(f);if(h&&p&&d){var e=new i(h),r=new t.ImageAtlas(p,d);for(var a in v){var l=v[a];l instanceof t.SymbolBucket?(o(l.layers,this.zoom,n),t.performSymbolLayout(l,h,e.positions,p,r.iconPositions,this.showCollisionBoxes,this.tileID.canonical)):l.hasPattern&&(l instanceof t.LineBucket||l instanceof t.FillBucket||l instanceof t.FillExtrusionBucket)&&(o(l.layers,this.zoom,n),l.addFeatures(g,this.tileID.canonical,r.patternPositions))}this.status="done",s(null,{buckets:t.values(v).filter((function(t){return!t.isEmpty()})),featureIndex:c,collisionBoxArray:this.collisionBoxArray,glyphAtlasImage:e.image,imageAtlas:r,glyphMap:this.returnDependencies?h:null,iconMap:this.returnDependencies?p:null,glyphPositions:this.returnDependencies?e.positions:null})}}P.length?a.send("getImages",{icons:P,source:this.source,tileID:this.tileID,type:"patterns"},(function(t,e){f||(f=t,d=e,O.call(l))})):d={},O.call(this)};var l=function(t,e,r,n){this.actor=t,this.layerIndex=e,this.availableImages=r,this.loadVectorData=n||s,this.loading={},this.loaded={}};l.prototype.loadTile=function(e,r){var n=this,i=e.uid;this.loading||(this.loading={});var o=!!(e&&e.request&&e.request.collectResourceTiming)&&new t.RequestPerformance(e.request),s=this.loading[i]=new a(e);s.abort=this.loadVectorData(e,(function(e,a){if(delete n.loading[i],e||!a)return s.status="done",n.loaded[i]=s,r(e);var l=a.rawData,u={};a.expires&&(u.expires=a.expires),a.cacheControl&&(u.cacheControl=a.cacheControl);var c={};if(o){var f=o.finish();f&&(c.resourceTiming=JSON.parse(JSON.stringify(f)))}s.vectorTile=a.vectorTile,s.parse(a.vectorTile,n.layerIndex,n.availableImages,n.actor,(function(e,n){if(e||!n)return r(e);r(null,t.extend({rawTileData:l.slice(0)},n,u,c))})),n.loaded=n.loaded||{},n.loaded[i]=s}))},l.prototype.reloadTile=function(t,e){var r=this,n=this.loaded,i=t.uid,a=this;if(n&&n[i]){var o=n[i];o.showCollisionBoxes=t.showCollisionBoxes;var s=function(t,n){var i=o.reloadCallback;i&&(delete o.reloadCallback,o.parse(o.vectorTile,a.layerIndex,r.availableImages,a.actor,i)),e(t,n)};"parsing"===o.status?o.reloadCallback=s:"done"===o.status&&(o.vectorTile?o.parse(o.vectorTile,this.layerIndex,this.availableImages,this.actor,s):s())}},l.prototype.abortTile=function(t,e){var r=this.loading,n=t.uid;r&&r[n]&&r[n].abort&&(r[n].abort(),delete r[n]),e()},l.prototype.removeTile=function(t,e){var r=this.loaded,n=t.uid;r&&r[n]&&delete r[n],e()};var u=t.window.ImageBitmap,c=function(){this.loaded={}};c.prototype.loadTile=function(e,r){var n=e.uid,i=e.encoding,a=e.rawImageData,o=u&&a instanceof u?this.getImageData(a):a,s=new t.DEMData(n,o,i);this.loaded=this.loaded||{},this.loaded[n]=s,r(null,s)},c.prototype.getImageData=function(e){this.offscreenCanvas&&this.offscreenCanvasContext||(this.offscreenCanvas=new OffscreenCanvas(e.width,e.height),this.offscreenCanvasContext=this.offscreenCanvas.getContext("2d")),this.offscreenCanvas.width=e.width,this.offscreenCanvas.height=e.height,this.offscreenCanvasContext.drawImage(e,0,0,e.width,e.height);var r=this.offscreenCanvasContext.getImageData(-1,-1,e.width+2,e.height+2);return this.offscreenCanvasContext.clearRect(0,0,this.offscreenCanvas.width,this.offscreenCanvas.height),new t.RGBAImage({width:r.width,height:r.height},r.data)},c.prototype.removeTile=function(t){var e=this.loaded,r=t.uid;e&&e[r]&&delete e[r]};var f=function t(e,r){var n,i=e&&e.type;if("FeatureCollection"===i)for(n=0;n=0!=!!e&&t.reverse()}var d=t.vectorTile.VectorTileFeature.prototype.toGeoJSON,v=function(e){this._feature=e,this.extent=t.EXTENT,this.type=e.type,this.properties=e.tags,"id"in e&&!isNaN(e.id)&&(this.id=parseInt(e.id,10))};v.prototype.loadGeometry=function(){if(1===this._feature.type){for(var e=[],r=0,n=this._feature.geometry;r>31}function P(t,e){for(var r=t.loadGeometry(),n=t.type,i=0,a=0,o=r.length,s=0;s>1;D(t,e,o,n,i,a%2),I(t,e,r,n,o-1,a+1),I(t,e,r,o+1,i,a+1)}}function D(t,e,r,n,i,a){for(;i>n;){if(i-n>600){var o=i-n+1,s=r-n+1,l=Math.log(o),u=.5*Math.exp(2*l/3),c=.5*Math.sqrt(l*u*(o-u)/o)*(s-o/2<0?-1:1);D(t,e,r,Math.max(n,Math.floor(r-s*u/o+c)),Math.min(i,Math.floor(r+(o-s)*u/o+c)),a)}var f=e[2*r+a],h=n,p=i;for(z(t,e,n,r),e[2*i+a]>f&&z(t,e,n,i);hf;)p--}e[2*n+a]===f?z(t,e,n,p):z(t,e,++p,i),p<=r&&(n=p+1),r<=p&&(i=p-1)}}function z(t,e,r,n){R(t,r,n),R(e,2*r,2*n),R(e,2*r+1,2*n+1)}function R(t,e,r){var n=t[e];t[e]=t[r],t[r]=n}function F(t,e,r,n){var i=t-r,a=e-n;return i*i+a*a}_.fromVectorTileJs=w,_.fromGeojsonVt=T,_.GeoJSONWrapper=k;var B=function(t){return t[0]},N=function(t){return t[1]},j=function(t,e,r,n,i){void 0===e&&(e=B),void 0===r&&(r=N),void 0===n&&(n=64),void 0===i&&(i=Float64Array),this.nodeSize=n,this.points=t;for(var a=t.length<65536?Uint16Array:Uint32Array,o=this.ids=new a(t.length),s=this.coords=new i(2*t.length),l=0;l=r&&s<=i&&l>=n&&l<=a&&c.push(t[d]);else{var v=Math.floor((p+h)/2);s=e[2*v],l=e[2*v+1],s>=r&&s<=i&&l>=n&&l<=a&&c.push(t[v]);var g=(f+1)%2;(0===f?r<=s:n<=l)&&(u.push(p),u.push(v-1),u.push(g)),(0===f?i>=s:a>=l)&&(u.push(v+1),u.push(h),u.push(g))}}return c}(this.ids,this.coords,t,e,r,n,this.nodeSize)},j.prototype.within=function(t,e,r){return function(t,e,r,n,i,a){for(var o=[0,t.length-1,0],s=[],l=i*i;o.length;){var u=o.pop(),c=o.pop(),f=o.pop();if(c-f<=a)for(var h=f;h<=c;h++)F(e[2*h],e[2*h+1],r,n)<=l&&s.push(t[h]);else{var p=Math.floor((f+c)/2),d=e[2*p],v=e[2*p+1];F(d,v,r,n)<=l&&s.push(t[p]);var g=(u+1)%2;(0===u?r-i<=d:n-i<=v)&&(o.push(f),o.push(p-1),o.push(g)),(0===u?r+i>=d:n+i>=v)&&(o.push(p+1),o.push(c),o.push(g))}}return s}(this.ids,this.coords,t,e,r,this.nodeSize)};var U={minZoom:0,maxZoom:16,radius:40,extent:512,nodeSize:64,log:!1,generateId:!1,reduce:null,map:function(t){return t}},V=function(t){this.options=X(Object.create(U),t),this.trees=new Array(this.options.maxZoom+1)};function H(t,e,r,n,i){return{x:t,y:e,zoom:1/0,id:r,parentId:-1,numPoints:n,properties:i}}function q(t,e){var r=t.geometry.coordinates,n=r[0],i=r[1];return{x:Y(n),y:W(i),zoom:1/0,index:e,parentId:-1}}function G(t){return{type:"Feature",id:t.id,properties:Z(t),geometry:{type:"Point",coordinates:[(n=t.x,360*(n-.5)),(e=t.y,r=(180-360*e)*Math.PI/180,360*Math.atan(Math.exp(r))/Math.PI-90)]}};var e,r,n}function Z(t){var e=t.numPoints,r=e>=1e4?Math.round(e/1e3)+"k":e>=1e3?Math.round(e/100)/10+"k":e;return X(X({},t.properties),{cluster:!0,cluster_id:t.id,point_count:e,point_count_abbreviated:r})}function Y(t){return t/360+.5}function W(t){var e=Math.sin(t*Math.PI/180),r=.5-.25*Math.log((1+e)/(1-e))/Math.PI;return r<0?0:r>1?1:r}function X(t,e){for(var r in e)t[r]=e[r];return t}function J(t){return t.x}function K(t){return t.y}function $(t,e,r,n){for(var i,a=n,o=r-e>>1,s=r-e,l=t[e],u=t[e+1],c=t[r],f=t[r+1],h=e+3;ha)i=h,a=p;else if(p===a){var d=Math.abs(h-o);dn&&(i-e>3&&$(t,e,i,n),t[i+2]=a,r-i>3&&$(t,i,r,n))}function Q(t,e,r,n,i,a){var o=i-r,s=a-n;if(0!==o||0!==s){var l=((t-r)*o+(e-n)*s)/(o*o+s*s);l>1?(r=i,n=a):l>0&&(r+=o*l,n+=s*l)}return(o=t-r)*o+(s=e-n)*s}function tt(t,e,r,n){var i={id:void 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s,l,u=ft(t),c=0===i?dt:vt,f=t.start,h=0;hr&&(l=c(u,p,d,g,y,r),o&&(u.start=f+s*l)):m>n?x=r&&(l=c(u,p,d,g,y,r),b=!0),x>n&&m<=n&&(l=c(u,p,d,g,y,n),b=!0),!a&&b&&(o&&(u.end=f+s*l),e.push(u),u=ft(t)),o&&(f+=s)}var _=t.length-3;p=t[_],d=t[_+1],v=t[_+2],(m=0===i?p:d)>=r&&m<=n&&pt(u,p,d,v),_=u.length-3,a&&_>=3&&(u[_]!==u[0]||u[_+1]!==u[1])&&pt(u,u[0],u[1],u[2]),u.length&&e.push(u)}function ft(t){var e=[];return e.size=t.size,e.start=t.start,e.end=t.end,e}function ht(t,e,r,n,i,a){for(var o=0;oo.maxX&&(o.maxX=c),f>o.maxY&&(o.maxY=f)}return o}function _t(t,e,r,n){var i=e.geometry,a=e.type,o=[];if("Point"===a||"MultiPoint"===a)for(var s=0;s0&&e.size<(i?o:n))r.numPoints+=e.length/3;else{for(var s=[],l=0;lo)&&(r.numSimplified++,s.push(e[l]),s.push(e[l+1])),r.numPoints++;i&&function(t,e){for(var r=0,n=0,i=t.length,a=i-2;n0===e)for(n=0,i=t.length;n24)throw new Error("maxZoom should be in the 0-24 range");if(e.promoteId&&e.generateId)throw new Error("promoteId and generateId cannot be used together.");var n=function(t,e){var r=[];if("FeatureCollection"===t.type)for(var n=0;n=n;u--){var c=+Date.now();s=this._cluster(s,u),this.trees[u]=new j(s,J,K,a,Float32Array),r&&console.log("z%d: %d clusters in %dms",u,s.length,+Date.now()-c)}return r&&console.timeEnd("total time"),this},V.prototype.getClusters=function(t,e){var r=((t[0]+180)%360+360)%360-180,n=Math.max(-90,Math.min(90,t[1])),i=180===t[2]?180:((t[2]+180)%360+360)%360-180,a=Math.max(-90,Math.min(90,t[3]));if(t[2]-t[0]>=360)r=-180,i=180;else if(r>i){var o=this.getClusters([r,n,180,a],e),s=this.getClusters([-180,n,i,a],e);return o.concat(s)}for(var l=this.trees[this._limitZoom(e)],u=[],c=0,f=l.range(Y(r),W(a),Y(i),W(n));c1?this._map(u,!0):null,g=(l<<5)+(e+1)+this.points.length,y=0,m=f;y>5},V.prototype._getOriginZoom=function(t){return(t-this.points.length)%32},V.prototype._map=function(t,e){if(t.numPoints)return e?X({},t.properties):t.properties;var r=this.points[t.index].properties,n=this.options.map(r);return e&&n===r?X({},n):n},Tt.prototype.options={maxZoom:14,indexMaxZoom:5,indexMaxPoints:1e5,tolerance:3,extent:4096,buffer:64,lineMetrics:!1,promoteId:null,generateId:!1,debug:0},Tt.prototype.splitTile=function(t,e,r,n,i,a,o){for(var s=[t,e,r,n],l=this.options,u=l.debug;s.length;){n=s.pop(),r=s.pop(),e=s.pop(),t=s.pop();var c=1<1&&console.time("creation"),h=this.tiles[f]=bt(t,e,r,n,l),this.tileCoords.push({z:e,x:r,y:n}),u)){u>1&&(console.log("tile z%d-%d-%d (features: %d, points: %d, simplified: %d)",e,r,n,h.numFeatures,h.numPoints,h.numSimplified),console.timeEnd("creation"));var p="z"+e;this.stats[p]=(this.stats[p]||0)+1,this.total++}if(h.source=t,i){if(e===l.maxZoom||e===i)continue;var d=1<1&&console.time("clipping");var v,g,y,m,x,b,_=.5*l.buffer/l.extent,w=.5-_,T=.5+_,k=1+_;v=g=y=m=null,x=lt(t,c,r-_,r+T,0,h.minX,h.maxX,l),b=lt(t,c,r+w,r+k,0,h.minX,h.maxX,l),t=null,x&&(v=lt(x,c,n-_,n+T,1,h.minY,h.maxY,l),g=lt(x,c,n+w,n+k,1,h.minY,h.maxY,l),x=null),b&&(y=lt(b,c,n-_,n+T,1,h.minY,h.maxY,l),m=lt(b,c,n+w,n+k,1,h.minY,h.maxY,l),b=null),u>1&&console.timeEnd("clipping"),s.push(v||[],e+1,2*r,2*n),s.push(g||[],e+1,2*r,2*n+1),s.push(y||[],e+1,2*r+1,2*n),s.push(m||[],e+1,2*r+1,2*n+1)}}},Tt.prototype.getTile=function(t,e,r){var n=this.options,i=n.extent,a=n.debug;if(t<0||t>24)return null;var o=1<1&&console.log("drilling down to z%d-%d-%d",t,e,r);for(var l,u=t,c=e,f=r;!l&&u>0;)u--,c=Math.floor(c/2),f=Math.floor(f/2),l=this.tiles[kt(u,c,f)];return l&&l.source?(a>1&&console.log("found parent tile z%d-%d-%d",u,c,f),a>1&&console.time("drilling down"),this.splitTile(l.source,u,c,f,t,e,r),a>1&&console.timeEnd("drilling down"),this.tiles[s]?mt(this.tiles[s],i):null):null};var Mt=function(e){function r(t,r,n,i){e.call(this,t,r,n,At),i&&(this.loadGeoJSON=i)}return e&&(r.__proto__=e),r.prototype=Object.create(e&&e.prototype),r.prototype.constructor=r,r.prototype.loadData=function(t,e){this._pendingCallback&&this._pendingCallback(null,{abandoned:!0}),this._pendingCallback=e,this._pendingLoadDataParams=t,this._state&&"Idle"!==this._state?this._state="NeedsLoadData":(this._state="Coalescing",this._loadData())},r.prototype._loadData=function(){var e=this;if(this._pendingCallback&&this._pendingLoadDataParams){var r=this._pendingCallback,n=this._pendingLoadDataParams;delete this._pendingCallback,delete this._pendingLoadDataParams;var i=!!(n&&n.request&&n.request.collectResourceTiming)&&new t.RequestPerformance(n.request);this.loadGeoJSON(n,(function(a,o){if(a||!o)return r(a);if("object"!=typeof o)return r(new Error("Input data given to '"+n.source+"' is not a valid GeoJSON object."));f(o,!0);try{e._geoJSONIndex=n.cluster?new V(function(e){var r=e.superclusterOptions,n=e.clusterProperties;if(!n||!r)return r;for(var i={},a={},o={accumulated:null,zoom:0},s={properties:null},l=Object.keys(n),u=0,c=l;u=0?0:e.button},r.remove=function(t){t.parentNode&&t.parentNode.removeChild(t)};var h=function(e){function r(){e.call(this),this.images={},this.updatedImages={},this.callbackDispatchedThisFrame={},this.loaded=!1,this.requestors=[],this.patterns={},this.atlasImage=new t.RGBAImage({width:1,height:1}),this.dirty=!0}return e&&(r.__proto__=e),r.prototype=Object.create(e&&e.prototype),r.prototype.constructor=r,r.prototype.isLoaded=function(){return this.loaded},r.prototype.setLoaded=function(t){if(this.loaded!==t&&(this.loaded=t,t)){for(var e=0,r=this.requestors;e=0?1.2:1))}function y(t,e,r,n,i,a,o){for(var s=0;s65535)e(new Error("glyphs > 65535 not supported"));else if(a.ranges[s])e(null,{stack:r,id:i,glyph:o});else{var l=a.requests[s];l||(l=a.requests[s]=[],x.loadGlyphRange(r,s,n.url,n.requestManager,(function(t,e){if(e){for(var r in e)n._doesCharSupportLocalGlyph(+r)||(a.glyphs[+r]=e[+r]);a.ranges[s]=!0}for(var i=0,o=l;i1&&(l=t[++s]);var c=Math.abs(u-l.left),f=Math.abs(u-l.right),h=Math.min(c,f),p=void 0,d=i/r*(n+1);if(l.isDash){var v=n-Math.abs(d);p=Math.sqrt(h*h+v*v)}else p=n-Math.sqrt(h*h+d*d);this.data[o+u]=Math.max(0,Math.min(255,p+128))}},k.prototype.addRegularDash=function(t){for(var e=t.length-1;e>=0;--e){var r=t[e],n=t[e+1];r.zeroLength?t.splice(e,1):n&&n.isDash===r.isDash&&(n.left=r.left,t.splice(e,1))}var i=t[0],a=t[t.length-1];i.isDash===a.isDash&&(i.left=a.left-this.width,a.right=i.right+this.width);for(var o=this.width*this.nextRow,s=0,l=t[s],u=0;u1&&(l=t[++s]);var c=Math.abs(u-l.left),f=Math.abs(u-l.right),h=Math.min(c,f),p=l.isDash?h:-h;this.data[o+u]=Math.max(0,Math.min(255,p+128))}},k.prototype.addDash=function(e,r){var n=r?7:0,i=2*n+1;if(this.nextRow+i>this.height)return t.warnOnce("LineAtlas out of space"),null;for(var a=0,o=0;o=n&&e.x=i&&e.y0&&(l[new t.OverscaledTileID(e.overscaledZ,a,r.z,i,r.y-1).key]={backfilled:!1},l[new t.OverscaledTileID(e.overscaledZ,e.wrap,r.z,r.x,r.y-1).key]={backfilled:!1},l[new t.OverscaledTileID(e.overscaledZ,s,r.z,o,r.y-1).key]={backfilled:!1}),r.y+10&&(n.resourceTiming=e._resourceTiming,e._resourceTiming=[]),e.fire(new t.Event("data",n))}}))},r.prototype.onAdd=function(t){this.map=t,this.load()},r.prototype.setData=function(e){var r=this;return this._data=e,this.fire(new t.Event("dataloading",{dataType:"source"})),this._updateWorkerData((function(e){if(e)r.fire(new t.ErrorEvent(e));else{var n={dataType:"source",sourceDataType:"content"};r._collectResourceTiming&&r._resourceTiming&&r._resourceTiming.length>0&&(n.resourceTiming=r._resourceTiming,r._resourceTiming=[]),r.fire(new t.Event("data",n))}})),this},r.prototype.getClusterExpansionZoom=function(t,e){return this.actor.send("geojson.getClusterExpansionZoom",{clusterId:t,source:this.id},e),this},r.prototype.getClusterChildren=function(t,e){return this.actor.send("geojson.getClusterChildren",{clusterId:t,source:this.id},e),this},r.prototype.getClusterLeaves=function(t,e,r,n){return this.actor.send("geojson.getClusterLeaves",{source:this.id,clusterId:t,limit:e,offset:r},n),this},r.prototype._updateWorkerData=function(e){var r=this;this._loaded=!1;var n=t.extend({},this.workerOptions),i=this._data;"string"==typeof i?(n.request=this.map._requestManager.transformRequest(t.browser.resolveURL(i),t.ResourceType.Source),n.request.collectResourceTiming=this._collectResourceTiming):n.data=JSON.stringify(i),this.actor.send(this.type+".loadData",n,(function(t,i){r._removed||i&&i.abandoned||(r._loaded=!0,i&&i.resourceTiming&&i.resourceTiming[r.id]&&(r._resourceTiming=i.resourceTiming[r.id].slice(0)),r.actor.send(r.type+".coalesce",{source:n.source},null),e(t))}))},r.prototype.loaded=function(){return this._loaded},r.prototype.loadTile=function(e,r){var n=this,i=e.actor?"reloadTile":"loadTile";e.actor=this.actor;var a={type:this.type,uid:e.uid,tileID:e.tileID,zoom:e.tileID.overscaledZ,maxZoom:this.maxzoom,tileSize:this.tileSize,source:this.id,pixelRatio:t.browser.devicePixelRatio,showCollisionBoxes:this.map.showCollisionBoxes,promoteId:this.promoteId};e.request=this.actor.send(i,a,(function(t,a){return delete e.request,e.unloadVectorData(),e.aborted?r(null):t?r(t):(e.loadVectorData(a,n.map.painter,"reloadTile"===i),r(null))}))},r.prototype.abortTile=function(t){t.request&&(t.request.cancel(),delete t.request),t.aborted=!0},r.prototype.unloadTile=function(t){t.unloadVectorData(),this.actor.send("removeTile",{uid:t.uid,type:this.type,source:this.id})},r.prototype.onRemove=function(){this._removed=!0,this.actor.send("removeSource",{type:this.type,source:this.id})},r.prototype.serialize=function(){return t.extend({},this._options,{type:this.type,data:this._data})},r.prototype.hasTransition=function(){return!1},r}(t.Evented),O=t.createLayout([{name:"a_pos",type:"Int16",components:2},{name:"a_texture_pos",type:"Int16",components:2}]),I=function(e){function r(t,r,n,i){e.call(this),this.id=t,this.dispatcher=n,this.coordinates=r.coordinates,this.type="image",this.minzoom=0,this.maxzoom=22,this.tileSize=512,this.tiles={},this._loaded=!1,this.setEventedParent(i),this.options=r}return e&&(r.__proto__=e),r.prototype=Object.create(e&&e.prototype),r.prototype.constructor=r,r.prototype.load=function(e,r){var n=this;this._loaded=!1,this.fire(new t.Event("dataloading",{dataType:"source"})),this.url=this.options.url,t.getImage(this.map._requestManager.transformRequest(this.url,t.ResourceType.Image),(function(i,a){n._loaded=!0,i?n.fire(new t.ErrorEvent(i)):a&&(n.image=a,e&&(n.coordinates=e),r&&r(),n._finishLoading())}))},r.prototype.loaded=function(){return this._loaded},r.prototype.updateImage=function(t){var e=this;return this.image&&t.url?(this.options.url=t.url,this.load(t.coordinates,(function(){e.texture=null})),this):this},r.prototype._finishLoading=function(){this.map&&(this.setCoordinates(this.coordinates),this.fire(new t.Event("data",{dataType:"source",sourceDataType:"metadata"})))},r.prototype.onAdd=function(t){this.map=t,this.load()},r.prototype.setCoordinates=function(e){var r=this;this.coordinates=e;var n=e.map(t.MercatorCoordinate.fromLngLat);this.tileID=function(e){for(var r=1/0,n=1/0,i=-1/0,a=-1/0,o=0,s=e;or.end(0)?this.fire(new t.ErrorEvent(new t.ValidationError("sources."+this.id,null,"Playback for this video can be set only between the "+r.start(0)+" and "+r.end(0)+"-second mark."))):this.video.currentTime=e}},r.prototype.getVideo=function(){return this.video},r.prototype.onAdd=function(t){this.map||(this.map=t,this.load(),this.video&&(this.video.play(),this.setCoordinates(this.coordinates)))},r.prototype.prepare=function(){if(!(0===Object.keys(this.tiles).length||this.video.readyState<2)){var e=this.map.painter.context,r=e.gl;for(var n in this.boundsBuffer||(this.boundsBuffer=e.createVertexBuffer(this._boundsArray,O.members)),this.boundsSegments||(this.boundsSegments=t.SegmentVector.simpleSegment(0,0,4,2)),this.texture?this.video.paused||(this.texture.bind(r.LINEAR,r.CLAMP_TO_EDGE),r.texSubImage2D(r.TEXTURE_2D,0,0,0,r.RGBA,r.UNSIGNED_BYTE,this.video)):(this.texture=new t.Texture(e,this.video,r.RGBA),this.texture.bind(r.LINEAR,r.CLAMP_TO_EDGE)),this.tiles){var i=this.tiles[n];"loaded"!==i.state&&(i.state="loaded",i.texture=this.texture)}}},r.prototype.serialize=function(){return{type:"video",urls:this.urls,coordinates:this.coordinates}},r.prototype.hasTransition=function(){return this.video&&!this.video.paused},r}(I),z=function(e){function r(r,n,i,a){e.call(this,r,n,i,a),n.coordinates?Array.isArray(n.coordinates)&&4===n.coordinates.length&&!n.coordinates.some((function(t){return!Array.isArray(t)||2!==t.length||t.some((function(t){return"number"!=typeof t}))}))||this.fire(new t.ErrorEvent(new t.ValidationError("sources."+r,null,'"coordinates" property must be an array of 4 longitude/latitude array pairs'))):this.fire(new t.ErrorEvent(new t.ValidationError("sources."+r,null,'missing required property "coordinates"'))),n.animate&&"boolean"!=typeof n.animate&&this.fire(new t.ErrorEvent(new t.ValidationError("sources."+r,null,'optional "animate" property must be a boolean value'))),n.canvas?"string"==typeof n.canvas||n.canvas instanceof t.window.HTMLCanvasElement||this.fire(new t.ErrorEvent(new t.ValidationError("sources."+r,null,'"canvas" must be either a string representing the ID of the canvas element from which to read, or an HTMLCanvasElement instance'))):this.fire(new t.ErrorEvent(new t.ValidationError("sources."+r,null,'missing required property "canvas"'))),this.options=n,this.animate=void 0===n.animate||n.animate}return e&&(r.__proto__=e),r.prototype=Object.create(e&&e.prototype),r.prototype.constructor=r,r.prototype.load=function(){this._loaded=!0,this.canvas||(this.canvas=this.options.canvas instanceof t.window.HTMLCanvasElement?this.options.canvas:t.window.document.getElementById(this.options.canvas)),this.width=this.canvas.width,this.height=this.canvas.height,this._hasInvalidDimensions()?this.fire(new t.ErrorEvent(new Error("Canvas dimensions cannot be less than or equal to zero."))):(this.play=function(){this._playing=!0,this.map.triggerRepaint()},this.pause=function(){this._playing&&(this.prepare(),this._playing=!1)},this._finishLoading())},r.prototype.getCanvas=function(){return this.canvas},r.prototype.onAdd=function(t){this.map=t,this.load(),this.canvas&&this.animate&&this.play()},r.prototype.onRemove=function(){this.pause()},r.prototype.prepare=function(){var e=!1;if(this.canvas.width!==this.width&&(this.width=this.canvas.width,e=!0),this.canvas.height!==this.height&&(this.height=this.canvas.height,e=!0),!this._hasInvalidDimensions()&&0!==Object.keys(this.tiles).length){var r=this.map.painter.context,n=r.gl;for(var i in this.boundsBuffer||(this.boundsBuffer=r.createVertexBuffer(this._boundsArray,O.members)),this.boundsSegments||(this.boundsSegments=t.SegmentVector.simpleSegment(0,0,4,2)),this.texture?(e||this._playing)&&this.texture.update(this.canvas,{premultiply:!0}):this.texture=new t.Texture(r,this.canvas,n.RGBA,{premultiply:!0}),this.tiles){var a=this.tiles[i];"loaded"!==a.state&&(a.state="loaded",a.texture=this.texture)}}},r.prototype.serialize=function(){return{type:"canvas",coordinates:this.coordinates}},r.prototype.hasTransition=function(){return this._playing},r.prototype._hasInvalidDimensions=function(){for(var t=0,e=[this.canvas.width,this.canvas.height];tthis.max){var o=this._getAndRemoveByKey(this.order[0]);o&&this.onRemove(o)}return this},j.prototype.has=function(t){return t.wrapped().key in this.data},j.prototype.getAndRemove=function(t){return this.has(t)?this._getAndRemoveByKey(t.wrapped().key):null},j.prototype._getAndRemoveByKey=function(t){var e=this.data[t].shift();return e.timeout&&clearTimeout(e.timeout),0===this.data[t].length&&delete this.data[t],this.order.splice(this.order.indexOf(t),1),e.value},j.prototype.getByKey=function(t){var e=this.data[t];return e?e[0].value:null},j.prototype.get=function(t){return this.has(t)?this.data[t.wrapped().key][0].value:null},j.prototype.remove=function(t,e){if(!this.has(t))return this;var r=t.wrapped().key,n=void 0===e?0:this.data[r].indexOf(e),i=this.data[r][n];return this.data[r].splice(n,1),i.timeout&&clearTimeout(i.timeout),0===this.data[r].length&&delete this.data[r],this.onRemove(i.value),this.order.splice(this.order.indexOf(r),1),this},j.prototype.setMaxSize=function(t){for(this.max=t;this.order.length>this.max;){var e=this._getAndRemoveByKey(this.order[0]);e&&this.onRemove(e)}return this},j.prototype.filter=function(t){var e=[];for(var r in this.data)for(var n=0,i=this.data[r];n1||(Math.abs(r)>1&&(1===Math.abs(r+i)?r+=i:1===Math.abs(r-i)&&(r-=i)),e.dem&&t.dem&&(t.dem.backfillBorder(e.dem,r,n),t.neighboringTiles&&t.neighboringTiles[a]&&(t.neighboringTiles[a].backfilled=!0)))}},r.prototype.getTile=function(t){return this.getTileByID(t.key)},r.prototype.getTileByID=function(t){return this._tiles[t]},r.prototype._retainLoadedChildren=function(t,e,r,n){for(var i in this._tiles){var a=this._tiles[i];if(!(n[i]||!a.hasData()||a.tileID.overscaledZ<=e||a.tileID.overscaledZ>r)){for(var o=a.tileID;a&&a.tileID.overscaledZ>e+1;){var s=a.tileID.scaledTo(a.tileID.overscaledZ-1);(a=this._tiles[s.key])&&a.hasData()&&(o=s)}for(var l=o;l.overscaledZ>e;)if(t[(l=l.scaledTo(l.overscaledZ-1)).key]){n[o.key]=o;break}}}},r.prototype.findLoadedParent=function(t,e){if(t.key in this._loadedParentTiles){var r=this._loadedParentTiles[t.key];return r&&r.tileID.overscaledZ>=e?r:null}for(var n=t.overscaledZ-1;n>=e;n--){var i=t.scaledTo(n),a=this._getLoadedTile(i);if(a)return a}},r.prototype._getLoadedTile=function(t){var e=this._tiles[t.key];return e&&e.hasData()?e:this._cache.getByKey(t.wrapped().key)},r.prototype.updateCacheSize=function(t){var e=(Math.ceil(t.width/this._source.tileSize)+1)*(Math.ceil(t.height/this._source.tileSize)+1),r=Math.floor(5*e),n="number"==typeof this._maxTileCacheSize?Math.min(this._maxTileCacheSize,r):r;this._cache.setMaxSize(n)},r.prototype.handleWrapJump=function(t){var e=(t-(void 0===this._prevLng?t:this._prevLng))/360,r=Math.round(e);if(this._prevLng=t,r){var n={};for(var i in this._tiles){var a=this._tiles[i];a.tileID=a.tileID.unwrapTo(a.tileID.wrap+r),n[a.tileID.key]=a}for(var o in this._tiles=n,this._timers)clearTimeout(this._timers[o]),delete this._timers[o];for(var s in this._tiles){var l=this._tiles[s];this._setTileReloadTimer(s,l)}}},r.prototype.update=function(e){var n=this;if(this.transform=e,this._sourceLoaded&&!this._paused){var i;this.updateCacheSize(e),this.handleWrapJump(this.transform.center.lng),this._coveredTiles={},this.used?this._source.tileID?i=e.getVisibleUnwrappedCoordinates(this._source.tileID).map((function(e){return new t.OverscaledTileID(e.canonical.z,e.wrap,e.canonical.z,e.canonical.x,e.canonical.y)})):(i=e.coveringTiles({tileSize:this._source.tileSize,minzoom:this._source.minzoom,maxzoom:this._source.maxzoom,roundZoom:this._source.roundZoom,reparseOverscaled:this._source.reparseOverscaled}),this._source.hasTile&&(i=i.filter((function(t){return n._source.hasTile(t)})))):i=[];var a=e.coveringZoomLevel(this._source),o=Math.max(a-r.maxOverzooming,this._source.minzoom),s=Math.max(a+r.maxUnderzooming,this._source.minzoom),l=this._updateRetainedTiles(i,a);if(Dt(this._source.type)){for(var u={},c={},f=0,h=Object.keys(l);fthis._source.maxzoom){var g=d.children(this._source.maxzoom)[0],y=this.getTile(g);if(y&&y.hasData()){n[g.key]=g;continue}}else{var m=d.children(this._source.maxzoom);if(n[m[0].key]&&n[m[1].key]&&n[m[2].key]&&n[m[3].key])continue}for(var x=v.wasRequested(),b=d.overscaledZ-1;b>=a;--b){var _=d.scaledTo(b);if(i[_.key])break;if(i[_.key]=!0,!(v=this.getTile(_))&&x&&(v=this._addTile(_)),v&&(n[_.key]=_,x=v.wasRequested(),v.hasData()))break}}}return n},r.prototype._updateLoadedParentTileCache=function(){for(var t in this._loadedParentTiles={},this._tiles){for(var e=[],r=void 0,n=this._tiles[t].tileID;n.overscaledZ>0;){if(n.key in this._loadedParentTiles){r=this._loadedParentTiles[n.key];break}e.push(n.key);var i=n.scaledTo(n.overscaledZ-1);if(r=this._getLoadedTile(i))break;n=i}for(var a=0,o=e;a0||(e.hasData()&&"reloading"!==e.state?this._cache.add(e.tileID,e,e.getExpiryTimeout()):(e.aborted=!0,this._abortTile(e),this._unloadTile(e))))},r.prototype.clearTiles=function(){for(var t in this._shouldReloadOnResume=!1,this._paused=!1,this._tiles)this._removeTile(t);this._cache.reset()},r.prototype.tilesIn=function(e,r,n){var i=this,a=[],o=this.transform;if(!o)return a;for(var s=n?o.getCameraQueryGeometry(e):e,l=e.map((function(t){return o.pointCoordinate(t)})),u=s.map((function(t){return o.pointCoordinate(t)})),c=this.getIds(),f=1/0,h=1/0,p=-1/0,d=-1/0,v=0,g=u;v=0&&y[1].y+g>=0){var m=l.map((function(t){return s.getTilePoint(t)})),x=u.map((function(t){return s.getTilePoint(t)}));a.push({tile:n,tileID:s,queryGeometry:m,cameraQueryGeometry:x,scale:v})}}},x=0;x=t.browser.now())return!0}return!1},r.prototype.setFeatureState=function(t,e,r){t=t||"_geojsonTileLayer",this._state.updateState(t,e,r)},r.prototype.removeFeatureState=function(t,e,r){t=t||"_geojsonTileLayer",this._state.removeFeatureState(t,e,r)},r.prototype.getFeatureState=function(t,e){return t=t||"_geojsonTileLayer",this._state.getState(t,e)},r.prototype.setDependencies=function(t,e,r){var n=this._tiles[t];n&&n.setDependencies(e,r)},r.prototype.reloadTilesForDependencies=function(t,e){for(var r in this._tiles)this._tiles[r].hasDependency(t,e)&&this._reloadTile(r,"reloading");this._cache.filter((function(r){return!r.hasDependency(t,e)}))},r}(t.Evented);function It(t,e){var r=Math.abs(2*t.wrap)-+(t.wrap<0),n=Math.abs(2*e.wrap)-+(e.wrap<0);return t.overscaledZ-e.overscaledZ||n-r||e.canonical.y-t.canonical.y||e.canonical.x-t.canonical.x}function Dt(t){return"raster"===t||"image"===t||"video"===t}function zt(){return new t.window.Worker(na.workerUrl)}Ot.maxOverzooming=10,Ot.maxUnderzooming=3;var Rt="mapboxgl_preloaded_worker_pool",Ft=function(){this.active={}};Ft.prototype.acquire=function(t){if(!this.workers)for(this.workers=[];this.workers.length0?(i-o)/s:0;return this.points[a].mult(1-l).add(this.points[r].mult(l))};var Qt=function(t,e,r){var n=this.boxCells=[],i=this.circleCells=[];this.xCellCount=Math.ceil(t/r),this.yCellCount=Math.ceil(e/r);for(var a=0;a=-e[0]&&r<=e[0]&&n>=-e[1]&&n<=e[1]}function ae(e,r,n,i,a,o,s,l){var u=i?e.textSizeData:e.iconSizeData,c=t.evaluateSizeForZoom(u,n.transform.zoom),f=[256/n.width*2+1,256/n.height*2+1],h=i?e.text.dynamicLayoutVertexArray:e.icon.dynamicLayoutVertexArray;h.clear();for(var p=e.lineVertexArray,d=i?e.text.placedSymbolArray:e.icon.placedSymbolArray,v=n.transform.width/n.transform.height,g=!1,y=0;yMath.abs(n.x-r.x)*i?{useVertical:!0}:(e===t.WritingMode.vertical?r.yn.x)?{needsFlipping:!0}:null}function le(e,r,n,i,a,o,s,l,u,c,f,h,p,d){var v,g=r/24,y=e.lineOffsetX*g,m=e.lineOffsetY*g;if(e.numGlyphs>1){var x=e.glyphStartIndex+e.numGlyphs,b=e.lineStartIndex,_=e.lineStartIndex+e.lineLength,w=oe(g,l,y,m,n,f,h,e,u,o,p);if(!w)return{notEnoughRoom:!0};var T=re(w.first.point,s).point,k=re(w.last.point,s).point;if(i&&!n){var A=se(e.writingMode,T,k,d);if(A)return A}v=[w.first];for(var M=e.glyphStartIndex+1;M0?C.point:ue(h,L,S,1,a),O=se(e.writingMode,S,P,d);if(O)return O}var I=ce(g*l.getoffsetX(e.glyphStartIndex),y,m,n,f,h,e.segment,e.lineStartIndex,e.lineStartIndex+e.lineLength,u,o,p);if(!I)return{notEnoughRoom:!0};v=[I]}for(var D=0,z=v;D0?1:-1,v=0;i&&(d*=-1,v=Math.PI),d<0&&(v+=Math.PI);for(var g=d>0?l+s:l+s+1,y=a,m=a,x=0,b=0,_=Math.abs(p),w=[];x+b<=_;){if((g+=d)=u)return null;if(m=y,w.push(y),void 0===(y=h[g])){var T=new t.Point(c.getx(g),c.gety(g)),k=re(T,f);if(k.signedDistanceFromCamera>0)y=h[g]=k.point;else{var A=g-d;y=ue(0===x?o:new t.Point(c.getx(A),c.gety(A)),T,m,_-x+1,f)}}x+=b,b=m.dist(y)}var M=(_-x)/b,S=y.sub(m),E=S.mult(M)._add(m);E._add(S._unit()._perp()._mult(n*d));var L=v+Math.atan2(y.y-m.y,y.x-m.x);return w.push(E),{point:E,angle:L,path:w}}Qt.prototype.keysLength=function(){return this.boxKeys.length+this.circleKeys.length},Qt.prototype.insert=function(t,e,r,n,i){this._forEachCell(e,r,n,i,this._insertBoxCell,this.boxUid++),this.boxKeys.push(t),this.bboxes.push(e),this.bboxes.push(r),this.bboxes.push(n),this.bboxes.push(i)},Qt.prototype.insertCircle=function(t,e,r,n){this._forEachCell(e-n,r-n,e+n,r+n,this._insertCircleCell,this.circleUid++),this.circleKeys.push(t),this.circles.push(e),this.circles.push(r),this.circles.push(n)},Qt.prototype._insertBoxCell=function(t,e,r,n,i,a){this.boxCells[i].push(a)},Qt.prototype._insertCircleCell=function(t,e,r,n,i,a){this.circleCells[i].push(a)},Qt.prototype._query=function(t,e,r,n,i,a){if(r<0||t>this.width||n<0||e>this.height)return!i&&[];var o=[];if(t<=0&&e<=0&&this.width<=r&&this.height<=n){if(i)return!0;for(var s=0;s0:o},Qt.prototype._queryCircle=function(t,e,r,n,i){var a=t-r,o=t+r,s=e-r,l=e+r;if(o<0||a>this.width||l<0||s>this.height)return!n&&[];var u=[],c={hitTest:n,circle:{x:t,y:e,radius:r},seenUids:{box:{},circle:{}}};return this._forEachCell(a,s,o,l,this._queryCellCircle,u,c,i),n?u.length>0:u},Qt.prototype.query=function(t,e,r,n,i){return this._query(t,e,r,n,!1,i)},Qt.prototype.hitTest=function(t,e,r,n,i){return this._query(t,e,r,n,!0,i)},Qt.prototype.hitTestCircle=function(t,e,r,n){return this._queryCircle(t,e,r,!0,n)},Qt.prototype._queryCell=function(t,e,r,n,i,a,o,s){var l=o.seenUids,u=this.boxCells[i];if(null!==u)for(var c=this.bboxes,f=0,h=u;f=c[d+0]&&n>=c[d+1]&&(!s||s(this.boxKeys[p]))){if(o.hitTest)return a.push(!0),!0;a.push({key:this.boxKeys[p],x1:c[d],y1:c[d+1],x2:c[d+2],y2:c[d+3]})}}}var v=this.circleCells[i];if(null!==v)for(var g=this.circles,y=0,m=v;yo*o+s*s},Qt.prototype._circleAndRectCollide=function(t,e,r,n,i,a,o){var s=(a-n)/2,l=Math.abs(t-(n+s));if(l>s+r)return!1;var u=(o-i)/2,c=Math.abs(e-(i+u));if(c>u+r)return!1;if(l<=s||c<=u)return!0;var f=l-s,h=c-u;return f*f+h*h<=r*r};var fe=new Float32Array([-1/0,-1/0,0,-1/0,-1/0,0,-1/0,-1/0,0,-1/0,-1/0,0]);function he(t,e){for(var r=0;r=1;P--)C.push(E.path[P]);for(var O=1;O0){for(var R=C[0].clone(),F=C[0].clone(),B=1;B=A.x&&F.x<=M.x&&R.y>=A.y&&F.y<=M.y?[C]:F.xM.x||F.yM.y?[]:t.clipLine([C],A.x,A.y,M.x,M.y)}for(var N=0,j=z;N=this.screenRightBoundary||nthis.screenBottomBoundary},ve.prototype.isInsideGrid=function(t,e,r,n){return r>=0&&t=0&&e0?(this.prevPlacement&&this.prevPlacement.variableOffsets[f.crossTileID]&&this.prevPlacement.placements[f.crossTileID]&&this.prevPlacement.placements[f.crossTileID].text&&(v=this.prevPlacement.variableOffsets[f.crossTileID].anchor),this.variableOffsets[f.crossTileID]={textOffset:g,width:r,height:n,anchor:t,textBoxScale:i,prevAnchor:v},this.markUsedJustification(h,t,f,p),h.allowVerticalPlacement&&(this.markUsedOrientation(h,p,f),this.placedOrientations[f.crossTileID]=p),{shift:y,placedGlyphBoxes:m}):void 0},Ae.prototype.placeLayerBucketPart=function(e,r,n){var i=this,a=e.parameters,o=a.bucket,s=a.layout,l=a.posMatrix,u=a.textLabelPlaneMatrix,c=a.labelToScreenMatrix,f=a.textPixelRatio,h=a.holdingForFade,p=a.collisionBoxArray,d=a.partiallyEvaluatedTextSize,v=a.collisionGroup,g=s.get("text-optional"),y=s.get("icon-optional"),m=s.get("text-allow-overlap"),x=s.get("icon-allow-overlap"),b="map"===s.get("text-rotation-alignment"),_="map"===s.get("text-pitch-alignment"),w="none"!==s.get("icon-text-fit"),T="viewport-y"===s.get("symbol-z-order"),k=m&&(x||!o.hasIconData()||y),A=x&&(m||!o.hasTextData()||g);!o.collisionArrays&&p&&o.deserializeCollisionBoxes(p);var M=function(e,a){if(!r[e.crossTileID])if(h)i.placements[e.crossTileID]=new xe(!1,!1,!1);else{var p,T=!1,M=!1,S=!0,E=null,L={box:null,offscreen:null},C={box:null,offscreen:null},P=null,O=null,I=0,D=0,z=0;a.textFeatureIndex?I=a.textFeatureIndex:e.useRuntimeCollisionCircles&&(I=e.featureIndex),a.verticalTextFeatureIndex&&(D=a.verticalTextFeatureIndex);var R=a.textBox;if(R){var F=function(r){var n=t.WritingMode.horizontal;if(o.allowVerticalPlacement&&!r&&i.prevPlacement){var a=i.prevPlacement.placedOrientations[e.crossTileID];a&&(i.placedOrientations[e.crossTileID]=a,n=a,i.markUsedOrientation(o,n,e))}return n},B=function(r,n){if(o.allowVerticalPlacement&&e.numVerticalGlyphVertices>0&&a.verticalTextBox)for(var i=0,s=o.writingModes;i0&&(N=N.filter((function(t){return t!==j.anchor}))).unshift(j.anchor)}var U=function(t,r,n){for(var a=t.x2-t.x1,s=t.y2-t.y1,u=e.textBoxScale,c=w&&!x?r:null,h={box:[],offscreen:!1},p=m?2*N.length:N.length,d=0;d=N.length,k=i.attemptAnchorPlacement(g,t,a,s,u,b,_,f,l,v,y,e,o,n,c);if(k&&(h=k.placedGlyphBoxes)&&h.box&&h.box.length){T=!0,E=k.shift;break}}return h};B((function(){return U(R,a.iconBox,t.WritingMode.horizontal)}),(function(){var r=a.verticalTextBox,n=L&&L.box&&L.box.length;return o.allowVerticalPlacement&&!n&&e.numVerticalGlyphVertices>0&&r?U(r,a.verticalIconBox,t.WritingMode.vertical):{box:null,offscreen:null}})),L&&(T=L.box,S=L.offscreen);var V=F(L&&L.box);if(!T&&i.prevPlacement){var H=i.prevPlacement.variableOffsets[e.crossTileID];H&&(i.variableOffsets[e.crossTileID]=H,i.markUsedJustification(o,H.anchor,e,V))}}else{var q=function(t,r){var n=i.collisionIndex.placeCollisionBox(t,m,f,l,v.predicate);return n&&n.box&&n.box.length&&(i.markUsedOrientation(o,r,e),i.placedOrientations[e.crossTileID]=r),n};B((function(){return q(R,t.WritingMode.horizontal)}),(function(){var r=a.verticalTextBox;return o.allowVerticalPlacement&&e.numVerticalGlyphVertices>0&&r?q(r,t.WritingMode.vertical):{box:null,offscreen:null}})),F(L&&L.box&&L.box.length)}}if(T=(p=L)&&p.box&&p.box.length>0,S=p&&p.offscreen,e.useRuntimeCollisionCircles){var G=o.text.placedSymbolArray.get(e.centerJustifiedTextSymbolIndex),Z=t.evaluateSizeForFeature(o.textSizeData,d,G),Y=s.get("text-padding"),W=e.collisionCircleDiameter;P=i.collisionIndex.placeCollisionCircles(m,G,o.lineVertexArray,o.glyphOffsetArray,Z,l,u,c,n,_,v.predicate,W,Y),T=m||P.circles.length>0&&!P.collisionDetected,S=S&&P.offscreen}if(a.iconFeatureIndex&&(z=a.iconFeatureIndex),a.iconBox){var X=function(t){var e=w&&E?ke(t,E.x,E.y,b,_,i.transform.angle):t;return i.collisionIndex.placeCollisionBox(e,x,f,l,v.predicate)};M=C&&C.box&&C.box.length&&a.verticalIconBox?(O=X(a.verticalIconBox)).box.length>0:(O=X(a.iconBox)).box.length>0,S=S&&O.offscreen}var J=g||0===e.numHorizontalGlyphVertices&&0===e.numVerticalGlyphVertices,K=y||0===e.numIconVertices;if(J||K?K?J||(M=M&&T):T=M&&T:M=T=M&&T,T&&p&&p.box&&(C&&C.box&&D?i.collisionIndex.insertCollisionBox(p.box,s.get("text-ignore-placement"),o.bucketInstanceId,D,v.ID):i.collisionIndex.insertCollisionBox(p.box,s.get("text-ignore-placement"),o.bucketInstanceId,I,v.ID)),M&&O&&i.collisionIndex.insertCollisionBox(O.box,s.get("icon-ignore-placement"),o.bucketInstanceId,z,v.ID),P&&(T&&i.collisionIndex.insertCollisionCircles(P.circles,s.get("text-ignore-placement"),o.bucketInstanceId,I,v.ID),n)){var $=o.bucketInstanceId,Q=i.collisionCircleArrays[$];void 0===Q&&(Q=i.collisionCircleArrays[$]=new be);for(var tt=0;tt=0;--E){var L=S[E];M(o.symbolInstances.get(L),o.collisionArrays[L])}else for(var C=e.symbolInstanceStart;C=0&&(e.text.placedSymbolArray.get(u).crossTileID=a>=0&&u!==a?0:n.crossTileID)}},Ae.prototype.markUsedOrientation=function(e,r,n){for(var i=r===t.WritingMode.horizontal||r===t.WritingMode.horizontalOnly?r:0,a=r===t.WritingMode.vertical?r:0,o=0,s=[n.leftJustifiedTextSymbolIndex,n.centerJustifiedTextSymbolIndex,n.rightJustifiedTextSymbolIndex];o0||l>0,x=a.numIconVertices>0,b=i.placedOrientations[a.crossTileID],_=b===t.WritingMode.vertical,w=b===t.WritingMode.horizontal||b===t.WritingMode.horizontalOnly;if(m){var T=De(y.text),k=_?ze:T;d(e.text,s,k);var A=w?ze:T;d(e.text,l,A);var M=y.text.isHidden();[a.rightJustifiedTextSymbolIndex,a.centerJustifiedTextSymbolIndex,a.leftJustifiedTextSymbolIndex].forEach((function(t){t>=0&&(e.text.placedSymbolArray.get(t).hidden=M||_?1:0)})),a.verticalPlacedTextSymbolIndex>=0&&(e.text.placedSymbolArray.get(a.verticalPlacedTextSymbolIndex).hidden=M||w?1:0);var S=i.variableOffsets[a.crossTileID];S&&i.markUsedJustification(e,S.anchor,a,b);var E=i.placedOrientations[a.crossTileID];E&&(i.markUsedJustification(e,"left",a,E),i.markUsedOrientation(e,E,a))}if(x){var L=De(y.icon),C=!(h&&a.verticalPlacedIconSymbolIndex&&_);if(a.placedIconSymbolIndex>=0){var P=C?L:ze;d(e.icon,a.numIconVertices,P),e.icon.placedSymbolArray.get(a.placedIconSymbolIndex).hidden=y.icon.isHidden()}if(a.verticalPlacedIconSymbolIndex>=0){var O=C?ze:L;d(e.icon,a.numVerticalIconVertices,O),e.icon.placedSymbolArray.get(a.verticalPlacedIconSymbolIndex).hidden=y.icon.isHidden()}}if(e.hasIconCollisionBoxData()||e.hasTextCollisionBoxData()){var I=e.collisionArrays[n];if(I){var D=new t.Point(0,0);if(I.textBox||I.verticalTextBox){var z=!0;if(u){var R=i.variableOffsets[v];R?(D=Te(R.anchor,R.width,R.height,R.textOffset,R.textBoxScale),c&&D._rotate(f?i.transform.angle:-i.transform.angle)):z=!1}I.textBox&&Me(e.textCollisionBox.collisionVertexArray,y.text.placed,!z||_,D.x,D.y),I.verticalTextBox&&Me(e.textCollisionBox.collisionVertexArray,y.text.placed,!z||w,D.x,D.y)}var F=Boolean(!w&&I.verticalIconBox);I.iconBox&&Me(e.iconCollisionBox.collisionVertexArray,y.icon.placed,F,h?D.x:0,h?D.y:0),I.verticalIconBox&&Me(e.iconCollisionBox.collisionVertexArray,y.icon.placed,!F,h?D.x:0,h?D.y:0)}}},g=0;gt},Ae.prototype.setStale=function(){this.stale=!0};var Se=Math.pow(2,25),Ee=Math.pow(2,24),Le=Math.pow(2,17),Ce=Math.pow(2,16),Pe=Math.pow(2,9),Oe=Math.pow(2,8),Ie=Math.pow(2,1);function De(t){if(0===t.opacity&&!t.placed)return 0;if(1===t.opacity&&t.placed)return 4294967295;var e=t.placed?1:0,r=Math.floor(127*t.opacity);return r*Se+e*Ee+r*Le+e*Ce+r*Pe+e*Oe+r*Ie+e}var ze=0,Re=function(t){this._sortAcrossTiles="viewport-y"!==t.layout.get("symbol-z-order")&&void 0!==t.layout.get("symbol-sort-key").constantOr(1),this._currentTileIndex=0,this._currentPartIndex=0,this._seenCrossTileIDs={},this._bucketParts=[]};Re.prototype.continuePlacement=function(t,e,r,n,i){for(var a=this._bucketParts;this._currentTileIndex2};this._currentPlacementIndex>=0;){var s=r[e[this._currentPlacementIndex]],l=this.placement.collisionIndex.transform.zoom;if("symbol"===s.type&&(!s.minzoom||s.minzoom<=l)&&(!s.maxzoom||s.maxzoom>l)){if(this._inProgressLayer||(this._inProgressLayer=new Re(s)),this._inProgressLayer.continuePlacement(n[s.source],this.placement,this._showCollisionBoxes,s,o))return;delete this._inProgressLayer}this._currentPlacementIndex--}this._done=!0},Fe.prototype.commit=function(t){return this.placement.commit(t),this.placement};var Be=512/t.EXTENT/2,Ne=function(t,e,r){this.tileID=t,this.indexedSymbolInstances={},this.bucketInstanceId=r;for(var n=0;nt.overscaledZ)for(var s in o){var l=o[s];l.tileID.isChildOf(t)&&l.findMatches(e.symbolInstances,t,i)}else{var u=o[t.scaledTo(Number(a)).key];u&&u.findMatches(e.symbolInstances,t,i)}}for(var c=0;c1?"@2x":"",l=t.getJSON(r.transformRequest(r.normalizeSpriteURL(e,s,".json"),t.ResourceType.SpriteJSON),(function(t,e){l=null,o||(o=t,i=e,c())})),u=t.getImage(r.transformRequest(r.normalizeSpriteURL(e,s,".png"),t.ResourceType.SpriteImage),(function(t,e){u=null,o||(o=t,a=e,c())}));function c(){if(o)n(o);else if(i&&a){var e=t.browser.getImageData(a),r={};for(var s in i){var l=i[s],u=l.width,c=l.height,f=l.x,h=l.y,p=l.sdf,d=l.pixelRatio,v=l.stretchX,g=l.stretchY,y=l.content,m=new t.RGBAImage({width:u,height:c});t.RGBAImage.copy(e,m,{x:f,y:h},{x:0,y:0},{width:u,height:c}),r[s]={data:m,pixelRatio:d,sdf:p,stretchX:v,stretchY:g,content:y}}n(null,r)}}return{cancel:function(){l&&(l.cancel(),l=null),u&&(u.cancel(),u=null)}}}(e,this.map._requestManager,(function(e,n){if(r._spriteRequest=null,e)r.fire(new t.ErrorEvent(e));else if(n)for(var i in n)r.imageManager.addImage(i,n[i]);r.imageManager.setLoaded(!0),r._availableImages=r.imageManager.listImages(),r.dispatcher.broadcast("setImages",r._availableImages),r.fire(new t.Event("data",{dataType:"style"}))}))},r.prototype._validateLayer=function(e){var r=this.sourceCaches[e.source];if(r){var n=e.sourceLayer;if(n){var i=r.getSource();("geojson"===i.type||i.vectorLayerIds&&-1===i.vectorLayerIds.indexOf(n))&&this.fire(new t.ErrorEvent(new Error('Source layer "'+n+'" does not exist on source "'+i.id+'" as specified by style layer "'+e.id+'"')))}}},r.prototype.loaded=function(){if(!this._loaded)return!1;if(Object.keys(this._updatedSources).length)return!1;for(var t in this.sourceCaches)if(!this.sourceCaches[t].loaded())return!1;return!!this.imageManager.isLoaded()},r.prototype._serializeLayers=function(t){for(var e=[],r=0,n=t;r0)throw new Error("Unimplemented: "+i.map((function(t){return t.command})).join(", ")+".");return n.forEach((function(t){"setTransition"!==t.command&&r[t.command].apply(r,t.args)})),this.stylesheet=e,!0},r.prototype.addImage=function(e,r){if(this.getImage(e))return this.fire(new t.ErrorEvent(new Error("An image with this name already exists.")));this.imageManager.addImage(e,r),this._availableImages=this.imageManager.listImages(),this._changedImages[e]=!0,this._changed=!0,this.fire(new t.Event("data",{dataType:"style"}))},r.prototype.updateImage=function(t,e){this.imageManager.updateImage(t,e)},r.prototype.getImage=function(t){return this.imageManager.getImage(t)},r.prototype.removeImage=function(e){if(!this.getImage(e))return this.fire(new t.ErrorEvent(new Error("No image with this name exists.")));this.imageManager.removeImage(e),this._availableImages=this.imageManager.listImages(),this._changedImages[e]=!0,this._changed=!0,this.fire(new t.Event("data",{dataType:"style"}))},r.prototype.listImages=function(){return this._checkLoaded(),this.imageManager.listImages()},r.prototype.addSource=function(e,r,n){var i=this;if(void 0===n&&(n={}),this._checkLoaded(),void 0!==this.sourceCaches[e])throw new Error("There is already a source with this ID");if(!r.type)throw new Error("The type property must be defined, but the only the following properties were given: "+Object.keys(r).join(", ")+".");if(!(["vector","raster","geojson","video","image"].indexOf(r.type)>=0&&this._validate(t.validateStyle.source,"sources."+e,r,null,n))){this.map&&this.map._collectResourceTiming&&(r.collectResourceTiming=!0);var a=this.sourceCaches[e]=new Ot(e,r,this.dispatcher);a.style=this,a.setEventedParent(this,(function(){return{isSourceLoaded:i.loaded(),source:a.serialize(),sourceId:e}})),a.onAdd(this.map),this._changed=!0}},r.prototype.removeSource=function(e){if(this._checkLoaded(),void 0===this.sourceCaches[e])throw new Error("There is no source with this ID");for(var r in this._layers)if(this._layers[r].source===e)return this.fire(new t.ErrorEvent(new Error('Source "'+e+'" cannot be removed while layer "'+r+'" is using it.')));var n=this.sourceCaches[e];delete this.sourceCaches[e],delete this._updatedSources[e],n.fire(new t.Event("data",{sourceDataType:"metadata",dataType:"source",sourceId:e})),n.setEventedParent(null),n.clearTiles(),n.onRemove&&n.onRemove(this.map),this._changed=!0},r.prototype.setGeoJSONSourceData=function(t,e){this._checkLoaded(),this.sourceCaches[t].getSource().setData(e),this._changed=!0},r.prototype.getSource=function(t){return this.sourceCaches[t]&&this.sourceCaches[t].getSource()},r.prototype.addLayer=function(e,r,n){void 0===n&&(n={}),this._checkLoaded();var i=e.id;if(this.getLayer(i))this.fire(new t.ErrorEvent(new Error('Layer with id "'+i+'" already exists on this map')));else{var a;if("custom"===e.type){if(He(this,t.validateCustomStyleLayer(e)))return;a=t.createStyleLayer(e)}else{if("object"==typeof e.source&&(this.addSource(i,e.source),e=t.clone$1(e),e=t.extend(e,{source:i})),this._validate(t.validateStyle.layer,"layers."+i,e,{arrayIndex:-1},n))return;a=t.createStyleLayer(e),this._validateLayer(a),a.setEventedParent(this,{layer:{id:i}}),this._serializedLayers[a.id]=a.serialize()}var o=r?this._order.indexOf(r):this._order.length;if(r&&-1===o)this.fire(new t.ErrorEvent(new Error('Layer with id "'+r+'" does not exist on this map.')));else{if(this._order.splice(o,0,i),this._layerOrderChanged=!0,this._layers[i]=a,this._removedLayers[i]&&a.source&&"custom"!==a.type){var s=this._removedLayers[i];delete this._removedLayers[i],s.type!==a.type?this._updatedSources[a.source]="clear":(this._updatedSources[a.source]="reload",this.sourceCaches[a.source].pause())}this._updateLayer(a),a.onAdd&&a.onAdd(this.map)}}},r.prototype.moveLayer=function(e,r){if(this._checkLoaded(),this._changed=!0,this._layers[e]){if(e!==r){var n=this._order.indexOf(e);this._order.splice(n,1);var i=r?this._order.indexOf(r):this._order.length;r&&-1===i?this.fire(new t.ErrorEvent(new Error('Layer with id "'+r+'" does not exist on this map.'))):(this._order.splice(i,0,e),this._layerOrderChanged=!0)}}else this.fire(new t.ErrorEvent(new Error("The layer '"+e+"' does not exist in the map's style and cannot be moved.")))},r.prototype.removeLayer=function(e){this._checkLoaded();var r=this._layers[e];if(r){r.setEventedParent(null);var n=this._order.indexOf(e);this._order.splice(n,1),this._layerOrderChanged=!0,this._changed=!0,this._removedLayers[e]=r,delete this._layers[e],delete this._serializedLayers[e],delete this._updatedLayers[e],delete this._updatedPaintProps[e],r.onRemove&&r.onRemove(this.map)}else this.fire(new t.ErrorEvent(new Error("The layer '"+e+"' does not exist in the map's style and cannot be removed.")))},r.prototype.getLayer=function(t){return this._layers[t]},r.prototype.hasLayer=function(t){return t in this._layers},r.prototype.setLayerZoomRange=function(e,r,n){this._checkLoaded();var i=this.getLayer(e);i?i.minzoom===r&&i.maxzoom===n||(null!=r&&(i.minzoom=r),null!=n&&(i.maxzoom=n),this._updateLayer(i)):this.fire(new t.ErrorEvent(new Error("The layer '"+e+"' does not exist in the map's style and cannot have zoom extent.")))},r.prototype.setFilter=function(e,r,n){void 0===n&&(n={}),this._checkLoaded();var i=this.getLayer(e);if(i){if(!t.deepEqual(i.filter,r))return null==r?(i.filter=void 0,void this._updateLayer(i)):void(this._validate(t.validateStyle.filter,"layers."+i.id+".filter",r,null,n)||(i.filter=t.clone$1(r),this._updateLayer(i)))}else this.fire(new t.ErrorEvent(new Error("The layer '"+e+"' does not exist in the map's style and cannot be filtered.")))},r.prototype.getFilter=function(e){return t.clone$1(this.getLayer(e).filter)},r.prototype.setLayoutProperty=function(e,r,n,i){void 0===i&&(i={}),this._checkLoaded();var a=this.getLayer(e);a?t.deepEqual(a.getLayoutProperty(r),n)||(a.setLayoutProperty(r,n,i),this._updateLayer(a)):this.fire(new t.ErrorEvent(new Error("The layer '"+e+"' does not exist in the map's style and cannot be styled.")))},r.prototype.getLayoutProperty=function(e,r){var n=this.getLayer(e);if(n)return n.getLayoutProperty(r);this.fire(new t.ErrorEvent(new Error("The layer '"+e+"' does not exist in the map's style.")))},r.prototype.setPaintProperty=function(e,r,n,i){void 0===i&&(i={}),this._checkLoaded();var a=this.getLayer(e);a?t.deepEqual(a.getPaintProperty(r),n)||(a.setPaintProperty(r,n,i)&&this._updateLayer(a),this._changed=!0,this._updatedPaintProps[e]=!0):this.fire(new t.ErrorEvent(new Error("The layer '"+e+"' does not exist in the map's style and cannot be styled.")))},r.prototype.getPaintProperty=function(t,e){return this.getLayer(t).getPaintProperty(e)},r.prototype.setFeatureState=function(e,r){this._checkLoaded();var n=e.source,i=e.sourceLayer,a=this.sourceCaches[n];if(void 0!==a){var o=a.getSource().type;"geojson"===o&&i?this.fire(new t.ErrorEvent(new Error("GeoJSON sources cannot have a sourceLayer parameter."))):"vector"!==o||i?(void 0===e.id&&this.fire(new t.ErrorEvent(new Error("The feature id parameter must be provided."))),a.setFeatureState(i,e.id,r)):this.fire(new t.ErrorEvent(new Error("The sourceLayer parameter must be provided for vector source types.")))}else this.fire(new t.ErrorEvent(new Error("The source '"+n+"' does not exist in the map's style.")))},r.prototype.removeFeatureState=function(e,r){this._checkLoaded();var n=e.source,i=this.sourceCaches[n];if(void 0!==i){var a=i.getSource().type,o="vector"===a?e.sourceLayer:void 0;"vector"!==a||o?r&&"string"!=typeof e.id&&"number"!=typeof e.id?this.fire(new t.ErrorEvent(new Error("A feature id is requred to remove its specific state property."))):i.removeFeatureState(o,e.id,r):this.fire(new t.ErrorEvent(new Error("The sourceLayer parameter must be provided for vector source types.")))}else this.fire(new t.ErrorEvent(new Error("The source '"+n+"' does not exist in the map's style.")))},r.prototype.getFeatureState=function(e){this._checkLoaded();var r=e.source,n=e.sourceLayer,i=this.sourceCaches[r];if(void 0!==i){if("vector"!==i.getSource().type||n)return void 0===e.id&&this.fire(new t.ErrorEvent(new Error("The feature id parameter must be provided."))),i.getFeatureState(n,e.id);this.fire(new t.ErrorEvent(new Error("The sourceLayer parameter must be provided for vector source types.")))}else this.fire(new t.ErrorEvent(new Error("The source '"+r+"' does not exist in the map's style.")))},r.prototype.getTransition=function(){return t.extend({duration:300,delay:0},this.stylesheet&&this.stylesheet.transition)},r.prototype.serialize=function(){return t.filterObject({version:this.stylesheet.version,name:this.stylesheet.name,metadata:this.stylesheet.metadata,light:this.stylesheet.light,center:this.stylesheet.center,zoom:this.stylesheet.zoom,bearing:this.stylesheet.bearing,pitch:this.stylesheet.pitch,sprite:this.stylesheet.sprite,glyphs:this.stylesheet.glyphs,transition:this.stylesheet.transition,sources:t.mapObject(this.sourceCaches,(function(t){return t.serialize()})),layers:this._serializeLayers(this._order)},(function(t){return void 0!==t}))},r.prototype._updateLayer=function(t){this._updatedLayers[t.id]=!0,t.source&&!this._updatedSources[t.source]&&"raster"!==this.sourceCaches[t.source].getSource().type&&(this._updatedSources[t.source]="reload",this.sourceCaches[t.source].pause()),this._changed=!0},r.prototype._flattenAndSortRenderedFeatures=function(t){for(var e=this,r=function(t){return"fill-extrusion"===e._layers[t].type},n={},i=[],a=this._order.length-1;a>=0;a--){var o=this._order[a];if(r(o)){n[o]=a;for(var s=0,l=t;s=0;d--){var v=this._order[d];if(r(v))for(var g=i.length-1;g>=0;g--){var y=i[g].feature;if(n[y.layer.id] 0.5) {gl_FragColor=vec4(0.0,0.0,1.0,0.5)*alpha;}if (v_notUsed > 0.5) {gl_FragColor*=.1;}}","attribute vec2 a_pos;attribute vec2 a_anchor_pos;attribute vec2 a_extrude;attribute vec2 a_placed;attribute vec2 a_shift;uniform mat4 u_matrix;uniform vec2 u_extrude_scale;uniform float u_camera_to_center_distance;varying float v_placed;varying float v_notUsed;void main() {vec4 projectedPoint=u_matrix*vec4(a_anchor_pos,0,1);highp float camera_to_anchor_distance=projectedPoint.w;highp float collision_perspective_ratio=clamp(0.5+0.5*(u_camera_to_center_distance/camera_to_anchor_distance),0.0,4.0);gl_Position=u_matrix*vec4(a_pos,0.0,1.0);gl_Position.xy+=(a_extrude+a_shift)*u_extrude_scale*gl_Position.w*collision_perspective_ratio;v_placed=a_placed.x;v_notUsed=a_placed.y;}"),nr=_r("varying float v_radius;varying vec2 v_extrude;varying float v_perspective_ratio;varying float v_collision;void main() {float alpha=0.5*min(v_perspective_ratio,1.0);float stroke_radius=0.9*max(v_perspective_ratio,1.0);float distance_to_center=length(v_extrude);float distance_to_edge=abs(distance_to_center-v_radius);float opacity_t=smoothstep(-stroke_radius,0.0,-distance_to_edge);vec4 color=mix(vec4(0.0,0.0,1.0,0.5),vec4(1.0,0.0,0.0,1.0),v_collision);gl_FragColor=color*alpha*opacity_t;}","attribute vec2 a_pos;attribute float a_radius;attribute vec2 a_flags;uniform mat4 u_matrix;uniform mat4 u_inv_matrix;uniform vec2 u_viewport_size;uniform float u_camera_to_center_distance;varying float v_radius;varying vec2 v_extrude;varying float v_perspective_ratio;varying float v_collision;vec3 toTilePosition(vec2 screenPos) {vec4 rayStart=u_inv_matrix*vec4(screenPos,-1.0,1.0);vec4 rayEnd =u_inv_matrix*vec4(screenPos, 1.0,1.0);rayStart.xyz/=rayStart.w;rayEnd.xyz /=rayEnd.w;highp float t=(0.0-rayStart.z)/(rayEnd.z-rayStart.z);return mix(rayStart.xyz,rayEnd.xyz,t);}void main() {vec2 quadCenterPos=a_pos;float radius=a_radius;float collision=a_flags.x;float vertexIdx=a_flags.y;vec2 quadVertexOffset=vec2(mix(-1.0,1.0,float(vertexIdx >=2.0)),mix(-1.0,1.0,float(vertexIdx >=1.0 && vertexIdx <=2.0)));vec2 quadVertexExtent=quadVertexOffset*radius;vec3 tilePos=toTilePosition(quadCenterPos);vec4 clipPos=u_matrix*vec4(tilePos,1.0);highp float camera_to_anchor_distance=clipPos.w;highp float collision_perspective_ratio=clamp(0.5+0.5*(u_camera_to_center_distance/camera_to_anchor_distance),0.0,4.0);float padding_factor=1.2;v_radius=radius;v_extrude=quadVertexExtent*padding_factor;v_perspective_ratio=collision_perspective_ratio;v_collision=collision;gl_Position=vec4(clipPos.xyz/clipPos.w,1.0)+vec4(quadVertexExtent*padding_factor/u_viewport_size*2.0,0.0,0.0);}"),ir=_r("uniform highp vec4 u_color;uniform sampler2D u_overlay;varying vec2 v_uv;void main() {vec4 overlay_color=texture2D(u_overlay,v_uv);gl_FragColor=mix(u_color,overlay_color,overlay_color.a);}","attribute vec2 a_pos;varying vec2 v_uv;uniform mat4 u_matrix;uniform float u_overlay_scale;void main() {v_uv=a_pos/8192.0;gl_Position=u_matrix*vec4(a_pos*u_overlay_scale,0,1);}"),ar=_r("#pragma mapbox: define highp vec4 color\n#pragma mapbox: define lowp float opacity\nvoid main() {\n#pragma mapbox: initialize highp vec4 color\n#pragma mapbox: initialize lowp float opacity\ngl_FragColor=color*opacity;\n#ifdef OVERDRAW_INSPECTOR\ngl_FragColor=vec4(1.0);\n#endif\n}","attribute vec2 a_pos;uniform mat4 u_matrix;\n#pragma mapbox: define highp vec4 color\n#pragma mapbox: define lowp float opacity\nvoid main() {\n#pragma mapbox: initialize highp vec4 color\n#pragma mapbox: initialize lowp float opacity\ngl_Position=u_matrix*vec4(a_pos,0,1);}"),or=_r("varying vec2 v_pos;\n#pragma mapbox: define highp vec4 outline_color\n#pragma mapbox: define lowp float opacity\nvoid main() {\n#pragma mapbox: initialize highp vec4 outline_color\n#pragma mapbox: initialize lowp float opacity\nfloat dist=length(v_pos-gl_FragCoord.xy);float alpha=1.0-smoothstep(0.0,1.0,dist);gl_FragColor=outline_color*(alpha*opacity);\n#ifdef OVERDRAW_INSPECTOR\ngl_FragColor=vec4(1.0);\n#endif\n}","attribute vec2 a_pos;uniform mat4 u_matrix;uniform vec2 u_world;varying vec2 v_pos;\n#pragma mapbox: define highp vec4 outline_color\n#pragma mapbox: define lowp float opacity\nvoid main() {\n#pragma mapbox: initialize highp vec4 outline_color\n#pragma mapbox: initialize lowp float opacity\ngl_Position=u_matrix*vec4(a_pos,0,1);v_pos=(gl_Position.xy/gl_Position.w+1.0)/2.0*u_world;}"),sr=_r("uniform vec2 u_texsize;uniform sampler2D u_image;uniform float u_fade;varying vec2 v_pos_a;varying vec2 v_pos_b;varying vec2 v_pos;\n#pragma mapbox: define lowp float opacity\n#pragma mapbox: define lowp vec4 pattern_from\n#pragma mapbox: define lowp vec4 pattern_to\nvoid main() {\n#pragma mapbox: initialize lowp float opacity\n#pragma mapbox: initialize mediump vec4 pattern_from\n#pragma mapbox: initialize mediump vec4 pattern_to\nvec2 pattern_tl_a=pattern_from.xy;vec2 pattern_br_a=pattern_from.zw;vec2 pattern_tl_b=pattern_to.xy;vec2 pattern_br_b=pattern_to.zw;vec2 imagecoord=mod(v_pos_a,1.0);vec2 pos=mix(pattern_tl_a/u_texsize,pattern_br_a/u_texsize,imagecoord);vec4 color1=texture2D(u_image,pos);vec2 imagecoord_b=mod(v_pos_b,1.0);vec2 pos2=mix(pattern_tl_b/u_texsize,pattern_br_b/u_texsize,imagecoord_b);vec4 color2=texture2D(u_image,pos2);float dist=length(v_pos-gl_FragCoord.xy);float alpha=1.0-smoothstep(0.0,1.0,dist);gl_FragColor=mix(color1,color2,u_fade)*alpha*opacity;\n#ifdef OVERDRAW_INSPECTOR\ngl_FragColor=vec4(1.0);\n#endif\n}","uniform mat4 u_matrix;uniform vec2 u_world;uniform vec2 u_pixel_coord_upper;uniform vec2 u_pixel_coord_lower;uniform vec3 u_scale;attribute vec2 a_pos;varying vec2 v_pos_a;varying vec2 v_pos_b;varying vec2 v_pos;\n#pragma mapbox: define lowp float opacity\n#pragma mapbox: define lowp vec4 pattern_from\n#pragma mapbox: define lowp vec4 pattern_to\n#pragma mapbox: define lowp float pixel_ratio_from\n#pragma mapbox: define lowp float pixel_ratio_to\nvoid main() {\n#pragma mapbox: initialize lowp float opacity\n#pragma mapbox: initialize mediump vec4 pattern_from\n#pragma mapbox: initialize mediump vec4 pattern_to\n#pragma mapbox: initialize lowp float pixel_ratio_from\n#pragma mapbox: initialize lowp float pixel_ratio_to\nvec2 pattern_tl_a=pattern_from.xy;vec2 pattern_br_a=pattern_from.zw;vec2 pattern_tl_b=pattern_to.xy;vec2 pattern_br_b=pattern_to.zw;float tileRatio=u_scale.x;float fromScale=u_scale.y;float toScale=u_scale.z;gl_Position=u_matrix*vec4(a_pos,0,1);vec2 display_size_a=(pattern_br_a-pattern_tl_a)/pixel_ratio_from;vec2 display_size_b=(pattern_br_b-pattern_tl_b)/pixel_ratio_to;v_pos_a=get_pattern_pos(u_pixel_coord_upper,u_pixel_coord_lower,fromScale*display_size_a,tileRatio,a_pos);v_pos_b=get_pattern_pos(u_pixel_coord_upper,u_pixel_coord_lower,toScale*display_size_b,tileRatio,a_pos);v_pos=(gl_Position.xy/gl_Position.w+1.0)/2.0*u_world;}"),lr=_r("uniform vec2 u_texsize;uniform float u_fade;uniform sampler2D u_image;varying vec2 v_pos_a;varying vec2 v_pos_b;\n#pragma mapbox: define lowp float opacity\n#pragma mapbox: define lowp vec4 pattern_from\n#pragma mapbox: define lowp vec4 pattern_to\nvoid main() {\n#pragma mapbox: initialize lowp float opacity\n#pragma mapbox: initialize mediump vec4 pattern_from\n#pragma mapbox: initialize mediump vec4 pattern_to\nvec2 pattern_tl_a=pattern_from.xy;vec2 pattern_br_a=pattern_from.zw;vec2 pattern_tl_b=pattern_to.xy;vec2 pattern_br_b=pattern_to.zw;vec2 imagecoord=mod(v_pos_a,1.0);vec2 pos=mix(pattern_tl_a/u_texsize,pattern_br_a/u_texsize,imagecoord);vec4 color1=texture2D(u_image,pos);vec2 imagecoord_b=mod(v_pos_b,1.0);vec2 pos2=mix(pattern_tl_b/u_texsize,pattern_br_b/u_texsize,imagecoord_b);vec4 color2=texture2D(u_image,pos2);gl_FragColor=mix(color1,color2,u_fade)*opacity;\n#ifdef OVERDRAW_INSPECTOR\ngl_FragColor=vec4(1.0);\n#endif\n}","uniform mat4 u_matrix;uniform vec2 u_pixel_coord_upper;uniform vec2 u_pixel_coord_lower;uniform vec3 u_scale;attribute vec2 a_pos;varying vec2 v_pos_a;varying vec2 v_pos_b;\n#pragma mapbox: define lowp float opacity\n#pragma mapbox: define lowp vec4 pattern_from\n#pragma mapbox: define lowp vec4 pattern_to\n#pragma mapbox: define lowp float pixel_ratio_from\n#pragma mapbox: define lowp float pixel_ratio_to\nvoid main() {\n#pragma mapbox: initialize lowp float opacity\n#pragma mapbox: initialize mediump vec4 pattern_from\n#pragma mapbox: initialize mediump vec4 pattern_to\n#pragma mapbox: initialize lowp float pixel_ratio_from\n#pragma mapbox: initialize lowp float pixel_ratio_to\nvec2 pattern_tl_a=pattern_from.xy;vec2 pattern_br_a=pattern_from.zw;vec2 pattern_tl_b=pattern_to.xy;vec2 pattern_br_b=pattern_to.zw;float tileZoomRatio=u_scale.x;float fromScale=u_scale.y;float toScale=u_scale.z;vec2 display_size_a=(pattern_br_a-pattern_tl_a)/pixel_ratio_from;vec2 display_size_b=(pattern_br_b-pattern_tl_b)/pixel_ratio_to;gl_Position=u_matrix*vec4(a_pos,0,1);v_pos_a=get_pattern_pos(u_pixel_coord_upper,u_pixel_coord_lower,fromScale*display_size_a,tileZoomRatio,a_pos);v_pos_b=get_pattern_pos(u_pixel_coord_upper,u_pixel_coord_lower,toScale*display_size_b,tileZoomRatio,a_pos);}"),ur=_r("varying vec4 v_color;void main() {gl_FragColor=v_color;\n#ifdef OVERDRAW_INSPECTOR\ngl_FragColor=vec4(1.0);\n#endif\n}","uniform mat4 u_matrix;uniform vec3 u_lightcolor;uniform lowp vec3 u_lightpos;uniform lowp float u_lightintensity;uniform float u_vertical_gradient;uniform lowp float u_opacity;attribute vec2 a_pos;attribute vec4 a_normal_ed;varying vec4 v_color;\n#pragma mapbox: define highp float base\n#pragma mapbox: define highp float height\n#pragma mapbox: define highp vec4 color\nvoid main() {\n#pragma mapbox: initialize highp float base\n#pragma mapbox: initialize highp float height\n#pragma mapbox: initialize highp vec4 color\nvec3 normal=a_normal_ed.xyz;base=max(0.0,base);height=max(0.0,height);float t=mod(normal.x,2.0);gl_Position=u_matrix*vec4(a_pos,t > 0.0 ? height : base,1);float colorvalue=color.r*0.2126+color.g*0.7152+color.b*0.0722;v_color=vec4(0.0,0.0,0.0,1.0);vec4 ambientlight=vec4(0.03,0.03,0.03,1.0);color+=ambientlight;float directional=clamp(dot(normal/16384.0,u_lightpos),0.0,1.0);directional=mix((1.0-u_lightintensity),max((1.0-colorvalue+u_lightintensity),1.0),directional);if (normal.y !=0.0) {directional*=((1.0-u_vertical_gradient)+(u_vertical_gradient*clamp((t+base)*pow(height/150.0,0.5),mix(0.7,0.98,1.0-u_lightintensity),1.0)));}v_color.r+=clamp(color.r*directional*u_lightcolor.r,mix(0.0,0.3,1.0-u_lightcolor.r),1.0);v_color.g+=clamp(color.g*directional*u_lightcolor.g,mix(0.0,0.3,1.0-u_lightcolor.g),1.0);v_color.b+=clamp(color.b*directional*u_lightcolor.b,mix(0.0,0.3,1.0-u_lightcolor.b),1.0);v_color*=u_opacity;}"),cr=_r("uniform vec2 u_texsize;uniform float u_fade;uniform sampler2D u_image;varying vec2 v_pos_a;varying vec2 v_pos_b;varying vec4 v_lighting;\n#pragma mapbox: define lowp float base\n#pragma mapbox: define lowp float height\n#pragma mapbox: define lowp vec4 pattern_from\n#pragma mapbox: define lowp vec4 pattern_to\n#pragma mapbox: define lowp float pixel_ratio_from\n#pragma mapbox: define lowp float pixel_ratio_to\nvoid main() {\n#pragma mapbox: initialize lowp float base\n#pragma mapbox: initialize lowp float height\n#pragma mapbox: initialize mediump vec4 pattern_from\n#pragma mapbox: initialize mediump vec4 pattern_to\n#pragma mapbox: initialize lowp float pixel_ratio_from\n#pragma mapbox: initialize lowp float pixel_ratio_to\nvec2 pattern_tl_a=pattern_from.xy;vec2 pattern_br_a=pattern_from.zw;vec2 pattern_tl_b=pattern_to.xy;vec2 pattern_br_b=pattern_to.zw;vec2 imagecoord=mod(v_pos_a,1.0);vec2 pos=mix(pattern_tl_a/u_texsize,pattern_br_a/u_texsize,imagecoord);vec4 color1=texture2D(u_image,pos);vec2 imagecoord_b=mod(v_pos_b,1.0);vec2 pos2=mix(pattern_tl_b/u_texsize,pattern_br_b/u_texsize,imagecoord_b);vec4 color2=texture2D(u_image,pos2);vec4 mixedColor=mix(color1,color2,u_fade);gl_FragColor=mixedColor*v_lighting;\n#ifdef OVERDRAW_INSPECTOR\ngl_FragColor=vec4(1.0);\n#endif\n}","uniform mat4 u_matrix;uniform vec2 u_pixel_coord_upper;uniform vec2 u_pixel_coord_lower;uniform float u_height_factor;uniform vec3 u_scale;uniform float u_vertical_gradient;uniform lowp float u_opacity;uniform vec3 u_lightcolor;uniform lowp vec3 u_lightpos;uniform lowp float u_lightintensity;attribute vec2 a_pos;attribute vec4 a_normal_ed;varying vec2 v_pos_a;varying vec2 v_pos_b;varying vec4 v_lighting;\n#pragma mapbox: define lowp float base\n#pragma mapbox: define lowp float height\n#pragma mapbox: define lowp vec4 pattern_from\n#pragma mapbox: define lowp vec4 pattern_to\n#pragma mapbox: define lowp float pixel_ratio_from\n#pragma mapbox: define lowp float pixel_ratio_to\nvoid main() {\n#pragma mapbox: initialize lowp float base\n#pragma mapbox: initialize lowp float height\n#pragma mapbox: initialize mediump vec4 pattern_from\n#pragma mapbox: initialize mediump vec4 pattern_to\n#pragma mapbox: initialize lowp float pixel_ratio_from\n#pragma mapbox: initialize lowp float pixel_ratio_to\nvec2 pattern_tl_a=pattern_from.xy;vec2 pattern_br_a=pattern_from.zw;vec2 pattern_tl_b=pattern_to.xy;vec2 pattern_br_b=pattern_to.zw;float tileRatio=u_scale.x;float fromScale=u_scale.y;float toScale=u_scale.z;vec3 normal=a_normal_ed.xyz;float edgedistance=a_normal_ed.w;vec2 display_size_a=(pattern_br_a-pattern_tl_a)/pixel_ratio_from;vec2 display_size_b=(pattern_br_b-pattern_tl_b)/pixel_ratio_to;base=max(0.0,base);height=max(0.0,height);float t=mod(normal.x,2.0);float z=t > 0.0 ? height : base;gl_Position=u_matrix*vec4(a_pos,z,1);vec2 pos=normal.x==1.0 && normal.y==0.0 && normal.z==16384.0\n? a_pos\n: vec2(edgedistance,z*u_height_factor);v_pos_a=get_pattern_pos(u_pixel_coord_upper,u_pixel_coord_lower,fromScale*display_size_a,tileRatio,pos);v_pos_b=get_pattern_pos(u_pixel_coord_upper,u_pixel_coord_lower,toScale*display_size_b,tileRatio,pos);v_lighting=vec4(0.0,0.0,0.0,1.0);float directional=clamp(dot(normal/16383.0,u_lightpos),0.0,1.0);directional=mix((1.0-u_lightintensity),max((0.5+u_lightintensity),1.0),directional);if (normal.y !=0.0) {directional*=((1.0-u_vertical_gradient)+(u_vertical_gradient*clamp((t+base)*pow(height/150.0,0.5),mix(0.7,0.98,1.0-u_lightintensity),1.0)));}v_lighting.rgb+=clamp(directional*u_lightcolor,mix(vec3(0.0),vec3(0.3),1.0-u_lightcolor),vec3(1.0));v_lighting*=u_opacity;}"),fr=_r("#ifdef GL_ES\nprecision highp float;\n#endif\nuniform sampler2D u_image;varying vec2 v_pos;uniform vec2 u_dimension;uniform float u_zoom;uniform float u_maxzoom;uniform vec4 u_unpack;float getElevation(vec2 coord,float bias) {vec4 data=texture2D(u_image,coord)*255.0;data.a=-1.0;return dot(data,u_unpack)/4.0;}void main() {vec2 epsilon=1.0/u_dimension;float a=getElevation(v_pos+vec2(-epsilon.x,-epsilon.y),0.0);float b=getElevation(v_pos+vec2(0,-epsilon.y),0.0);float c=getElevation(v_pos+vec2(epsilon.x,-epsilon.y),0.0);float d=getElevation(v_pos+vec2(-epsilon.x,0),0.0);float e=getElevation(v_pos,0.0);float f=getElevation(v_pos+vec2(epsilon.x,0),0.0);float g=getElevation(v_pos+vec2(-epsilon.x,epsilon.y),0.0);float h=getElevation(v_pos+vec2(0,epsilon.y),0.0);float i=getElevation(v_pos+vec2(epsilon.x,epsilon.y),0.0);float exaggeration=u_zoom < 2.0 ? 0.4 : u_zoom < 4.5 ? 0.35 : 0.3;vec2 deriv=vec2((c+f+f+i)-(a+d+d+g),(g+h+h+i)-(a+b+b+c))/ pow(2.0,(u_zoom-u_maxzoom)*exaggeration+19.2562-u_zoom);gl_FragColor=clamp(vec4(deriv.x/2.0+0.5,deriv.y/2.0+0.5,1.0,1.0),0.0,1.0);\n#ifdef OVERDRAW_INSPECTOR\ngl_FragColor=vec4(1.0);\n#endif\n}","uniform mat4 u_matrix;uniform vec2 u_dimension;attribute vec2 a_pos;attribute vec2 a_texture_pos;varying vec2 v_pos;void main() {gl_Position=u_matrix*vec4(a_pos,0,1);highp vec2 epsilon=1.0/u_dimension;float scale=(u_dimension.x-2.0)/u_dimension.x;v_pos=(a_texture_pos/8192.0)*scale+epsilon;}"),hr=_r("uniform sampler2D u_image;varying vec2 v_pos;uniform vec2 u_latrange;uniform vec2 u_light;uniform vec4 u_shadow;uniform vec4 u_highlight;uniform vec4 u_accent;\n#define PI 3.141592653589793\nvoid main() {vec4 pixel=texture2D(u_image,v_pos);vec2 deriv=((pixel.rg*2.0)-1.0);float scaleFactor=cos(radians((u_latrange[0]-u_latrange[1])*(1.0-v_pos.y)+u_latrange[1]));float slope=atan(1.25*length(deriv)/scaleFactor);float aspect=deriv.x !=0.0 ? atan(deriv.y,-deriv.x) : PI/2.0*(deriv.y > 0.0 ? 1.0 :-1.0);float intensity=u_light.x;float azimuth=u_light.y+PI;float base=1.875-intensity*1.75;float maxValue=0.5*PI;float scaledSlope=intensity !=0.5 ? ((pow(base,slope)-1.0)/(pow(base,maxValue)-1.0))*maxValue : slope;float accent=cos(scaledSlope);vec4 accent_color=(1.0-accent)*u_accent*clamp(intensity*2.0,0.0,1.0);float shade=abs(mod((aspect+azimuth)/PI+0.5,2.0)-1.0);vec4 shade_color=mix(u_shadow,u_highlight,shade)*sin(scaledSlope)*clamp(intensity*2.0,0.0,1.0);gl_FragColor=accent_color*(1.0-shade_color.a)+shade_color;\n#ifdef OVERDRAW_INSPECTOR\ngl_FragColor=vec4(1.0);\n#endif\n}","uniform mat4 u_matrix;attribute vec2 a_pos;attribute vec2 a_texture_pos;varying vec2 v_pos;void main() {gl_Position=u_matrix*vec4(a_pos,0,1);v_pos=a_texture_pos/8192.0;}"),pr=_r("uniform lowp float u_device_pixel_ratio;varying vec2 v_width2;varying vec2 v_normal;varying float v_gamma_scale;\n#pragma mapbox: define highp vec4 color\n#pragma mapbox: define lowp float blur\n#pragma mapbox: define lowp float opacity\nvoid main() {\n#pragma mapbox: initialize highp vec4 color\n#pragma mapbox: initialize lowp float blur\n#pragma mapbox: initialize lowp float opacity\nfloat dist=length(v_normal)*v_width2.s;float blur2=(blur+1.0/u_device_pixel_ratio)*v_gamma_scale;float alpha=clamp(min(dist-(v_width2.t-blur2),v_width2.s-dist)/blur2,0.0,1.0);gl_FragColor=color*(alpha*opacity);\n#ifdef OVERDRAW_INSPECTOR\ngl_FragColor=vec4(1.0);\n#endif\n}","\n#define scale 0.015873016\nattribute vec2 a_pos_normal;attribute vec4 a_data;uniform mat4 u_matrix;uniform mediump float u_ratio;uniform vec2 u_units_to_pixels;uniform lowp float u_device_pixel_ratio;varying vec2 v_normal;varying vec2 v_width2;varying float v_gamma_scale;varying highp float v_linesofar;\n#pragma mapbox: define highp vec4 color\n#pragma mapbox: define lowp float blur\n#pragma mapbox: define lowp float opacity\n#pragma mapbox: define mediump float gapwidth\n#pragma mapbox: define lowp float offset\n#pragma mapbox: define mediump float width\nvoid main() {\n#pragma mapbox: initialize highp vec4 color\n#pragma mapbox: initialize lowp float blur\n#pragma mapbox: initialize lowp float opacity\n#pragma mapbox: initialize mediump float gapwidth\n#pragma mapbox: initialize lowp float offset\n#pragma mapbox: initialize mediump float width\nfloat ANTIALIASING=1.0/u_device_pixel_ratio/2.0;vec2 a_extrude=a_data.xy-128.0;float a_direction=mod(a_data.z,4.0)-1.0;v_linesofar=(floor(a_data.z/4.0)+a_data.w*64.0)*2.0;vec2 pos=floor(a_pos_normal*0.5);mediump vec2 normal=a_pos_normal-2.0*pos;normal.y=normal.y*2.0-1.0;v_normal=normal;gapwidth=gapwidth/2.0;float halfwidth=width/2.0;offset=-1.0*offset;float inset=gapwidth+(gapwidth > 0.0 ? ANTIALIASING : 0.0);float outset=gapwidth+halfwidth*(gapwidth > 0.0 ? 2.0 : 1.0)+(halfwidth==0.0 ? 0.0 : ANTIALIASING);mediump vec2 dist=outset*a_extrude*scale;mediump float u=0.5*a_direction;mediump float t=1.0-abs(u);mediump vec2 offset2=offset*a_extrude*scale*normal.y*mat2(t,-u,u,t);vec4 projected_extrude=u_matrix*vec4(dist/u_ratio,0.0,0.0);gl_Position=u_matrix*vec4(pos+offset2/u_ratio,0.0,1.0)+projected_extrude;float extrude_length_without_perspective=length(dist);float extrude_length_with_perspective=length(projected_extrude.xy/gl_Position.w*u_units_to_pixels);v_gamma_scale=extrude_length_without_perspective/extrude_length_with_perspective;v_width2=vec2(outset,inset);}"),dr=_r("uniform lowp float u_device_pixel_ratio;uniform sampler2D u_image;varying vec2 v_width2;varying vec2 v_normal;varying float v_gamma_scale;varying highp float v_lineprogress;\n#pragma mapbox: define lowp float blur\n#pragma mapbox: define lowp float opacity\nvoid main() {\n#pragma mapbox: initialize lowp float blur\n#pragma mapbox: initialize lowp float opacity\nfloat dist=length(v_normal)*v_width2.s;float blur2=(blur+1.0/u_device_pixel_ratio)*v_gamma_scale;float alpha=clamp(min(dist-(v_width2.t-blur2),v_width2.s-dist)/blur2,0.0,1.0);vec4 color=texture2D(u_image,vec2(v_lineprogress,0.5));gl_FragColor=color*(alpha*opacity);\n#ifdef OVERDRAW_INSPECTOR\ngl_FragColor=vec4(1.0);\n#endif\n}","\n#define MAX_LINE_DISTANCE 32767.0\n#define scale 0.015873016\nattribute vec2 a_pos_normal;attribute vec4 a_data;uniform mat4 u_matrix;uniform mediump float u_ratio;uniform lowp float u_device_pixel_ratio;uniform vec2 u_units_to_pixels;varying vec2 v_normal;varying vec2 v_width2;varying float v_gamma_scale;varying highp float v_lineprogress;\n#pragma mapbox: define lowp float blur\n#pragma mapbox: define lowp float opacity\n#pragma mapbox: define mediump float gapwidth\n#pragma mapbox: define lowp float offset\n#pragma mapbox: define mediump float width\nvoid main() {\n#pragma mapbox: initialize lowp float blur\n#pragma mapbox: initialize lowp float opacity\n#pragma mapbox: initialize mediump float gapwidth\n#pragma mapbox: initialize lowp float offset\n#pragma mapbox: initialize mediump float width\nfloat ANTIALIASING=1.0/u_device_pixel_ratio/2.0;vec2 a_extrude=a_data.xy-128.0;float a_direction=mod(a_data.z,4.0)-1.0;v_lineprogress=(floor(a_data.z/4.0)+a_data.w*64.0)*2.0/MAX_LINE_DISTANCE;vec2 pos=floor(a_pos_normal*0.5);mediump vec2 normal=a_pos_normal-2.0*pos;normal.y=normal.y*2.0-1.0;v_normal=normal;gapwidth=gapwidth/2.0;float halfwidth=width/2.0;offset=-1.0*offset;float inset=gapwidth+(gapwidth > 0.0 ? ANTIALIASING : 0.0);float outset=gapwidth+halfwidth*(gapwidth > 0.0 ? 2.0 : 1.0)+(halfwidth==0.0 ? 0.0 : ANTIALIASING);mediump vec2 dist=outset*a_extrude*scale;mediump float u=0.5*a_direction;mediump float t=1.0-abs(u);mediump vec2 offset2=offset*a_extrude*scale*normal.y*mat2(t,-u,u,t);vec4 projected_extrude=u_matrix*vec4(dist/u_ratio,0.0,0.0);gl_Position=u_matrix*vec4(pos+offset2/u_ratio,0.0,1.0)+projected_extrude;float extrude_length_without_perspective=length(dist);float extrude_length_with_perspective=length(projected_extrude.xy/gl_Position.w*u_units_to_pixels);v_gamma_scale=extrude_length_without_perspective/extrude_length_with_perspective;v_width2=vec2(outset,inset);}"),vr=_r("uniform lowp float u_device_pixel_ratio;uniform vec2 u_texsize;uniform float u_fade;uniform mediump vec3 u_scale;uniform sampler2D u_image;varying vec2 v_normal;varying vec2 v_width2;varying float v_linesofar;varying float v_gamma_scale;varying float v_width;\n#pragma mapbox: define lowp vec4 pattern_from\n#pragma mapbox: define lowp vec4 pattern_to\n#pragma mapbox: define lowp float pixel_ratio_from\n#pragma mapbox: define lowp float pixel_ratio_to\n#pragma mapbox: define lowp float blur\n#pragma mapbox: define lowp float opacity\nvoid main() {\n#pragma mapbox: initialize mediump vec4 pattern_from\n#pragma mapbox: initialize mediump vec4 pattern_to\n#pragma mapbox: initialize lowp float pixel_ratio_from\n#pragma mapbox: initialize lowp float pixel_ratio_to\n#pragma mapbox: initialize lowp float blur\n#pragma mapbox: initialize lowp float opacity\nvec2 pattern_tl_a=pattern_from.xy;vec2 pattern_br_a=pattern_from.zw;vec2 pattern_tl_b=pattern_to.xy;vec2 pattern_br_b=pattern_to.zw;float tileZoomRatio=u_scale.x;float fromScale=u_scale.y;float toScale=u_scale.z;vec2 display_size_a=(pattern_br_a-pattern_tl_a)/pixel_ratio_from;vec2 display_size_b=(pattern_br_b-pattern_tl_b)/pixel_ratio_to;vec2 pattern_size_a=vec2(display_size_a.x*fromScale/tileZoomRatio,display_size_a.y);vec2 pattern_size_b=vec2(display_size_b.x*toScale/tileZoomRatio,display_size_b.y);float aspect_a=display_size_a.y/v_width;float aspect_b=display_size_b.y/v_width;float dist=length(v_normal)*v_width2.s;float blur2=(blur+1.0/u_device_pixel_ratio)*v_gamma_scale;float alpha=clamp(min(dist-(v_width2.t-blur2),v_width2.s-dist)/blur2,0.0,1.0);float x_a=mod(v_linesofar/pattern_size_a.x*aspect_a,1.0);float x_b=mod(v_linesofar/pattern_size_b.x*aspect_b,1.0);float y=0.5*v_normal.y+0.5;vec2 texel_size=1.0/u_texsize;vec2 pos_a=mix(pattern_tl_a*texel_size-texel_size,pattern_br_a*texel_size+texel_size,vec2(x_a,y));vec2 pos_b=mix(pattern_tl_b*texel_size-texel_size,pattern_br_b*texel_size+texel_size,vec2(x_b,y));vec4 color=mix(texture2D(u_image,pos_a),texture2D(u_image,pos_b),u_fade);gl_FragColor=color*alpha*opacity;\n#ifdef OVERDRAW_INSPECTOR\ngl_FragColor=vec4(1.0);\n#endif\n}","\n#define scale 0.015873016\n#define LINE_DISTANCE_SCALE 2.0\nattribute vec2 a_pos_normal;attribute vec4 a_data;uniform mat4 u_matrix;uniform vec2 u_units_to_pixels;uniform mediump float u_ratio;uniform lowp float u_device_pixel_ratio;varying vec2 v_normal;varying vec2 v_width2;varying float v_linesofar;varying float v_gamma_scale;varying float v_width;\n#pragma mapbox: define lowp float blur\n#pragma mapbox: define lowp float opacity\n#pragma mapbox: define lowp float offset\n#pragma mapbox: define mediump float gapwidth\n#pragma mapbox: define mediump float width\n#pragma mapbox: define lowp float floorwidth\n#pragma mapbox: define lowp vec4 pattern_from\n#pragma mapbox: define lowp vec4 pattern_to\n#pragma mapbox: define lowp float pixel_ratio_from\n#pragma mapbox: define lowp float pixel_ratio_to\nvoid main() {\n#pragma mapbox: initialize lowp float blur\n#pragma mapbox: initialize lowp float opacity\n#pragma mapbox: initialize lowp float offset\n#pragma mapbox: initialize mediump float gapwidth\n#pragma mapbox: initialize mediump float width\n#pragma mapbox: initialize lowp float floorwidth\n#pragma mapbox: initialize mediump vec4 pattern_from\n#pragma mapbox: initialize mediump vec4 pattern_to\n#pragma mapbox: initialize lowp float pixel_ratio_from\n#pragma mapbox: initialize lowp float pixel_ratio_to\nfloat ANTIALIASING=1.0/u_device_pixel_ratio/2.0;vec2 a_extrude=a_data.xy-128.0;float a_direction=mod(a_data.z,4.0)-1.0;float a_linesofar=(floor(a_data.z/4.0)+a_data.w*64.0)*LINE_DISTANCE_SCALE;vec2 pos=floor(a_pos_normal*0.5);mediump vec2 normal=a_pos_normal-2.0*pos;normal.y=normal.y*2.0-1.0;v_normal=normal;gapwidth=gapwidth/2.0;float halfwidth=width/2.0;offset=-1.0*offset;float inset=gapwidth+(gapwidth > 0.0 ? ANTIALIASING : 0.0);float outset=gapwidth+halfwidth*(gapwidth > 0.0 ? 2.0 : 1.0)+(halfwidth==0.0 ? 0.0 : ANTIALIASING);mediump vec2 dist=outset*a_extrude*scale;mediump float u=0.5*a_direction;mediump float t=1.0-abs(u);mediump vec2 offset2=offset*a_extrude*scale*normal.y*mat2(t,-u,u,t);vec4 projected_extrude=u_matrix*vec4(dist/u_ratio,0.0,0.0);gl_Position=u_matrix*vec4(pos+offset2/u_ratio,0.0,1.0)+projected_extrude;float extrude_length_without_perspective=length(dist);float extrude_length_with_perspective=length(projected_extrude.xy/gl_Position.w*u_units_to_pixels);v_gamma_scale=extrude_length_without_perspective/extrude_length_with_perspective;v_linesofar=a_linesofar;v_width2=vec2(outset,inset);v_width=floorwidth;}"),gr=_r("uniform lowp float u_device_pixel_ratio;uniform sampler2D u_image;uniform float u_sdfgamma;uniform float u_mix;varying vec2 v_normal;varying vec2 v_width2;varying vec2 v_tex_a;varying vec2 v_tex_b;varying float v_gamma_scale;\n#pragma mapbox: define highp vec4 color\n#pragma mapbox: define lowp float blur\n#pragma mapbox: define lowp float opacity\n#pragma mapbox: define mediump float width\n#pragma mapbox: define lowp float floorwidth\nvoid main() {\n#pragma mapbox: initialize highp vec4 color\n#pragma mapbox: initialize lowp float blur\n#pragma mapbox: initialize lowp float opacity\n#pragma mapbox: initialize mediump float width\n#pragma mapbox: initialize lowp float floorwidth\nfloat dist=length(v_normal)*v_width2.s;float blur2=(blur+1.0/u_device_pixel_ratio)*v_gamma_scale;float alpha=clamp(min(dist-(v_width2.t-blur2),v_width2.s-dist)/blur2,0.0,1.0);float sdfdist_a=texture2D(u_image,v_tex_a).a;float sdfdist_b=texture2D(u_image,v_tex_b).a;float sdfdist=mix(sdfdist_a,sdfdist_b,u_mix);alpha*=smoothstep(0.5-u_sdfgamma/floorwidth,0.5+u_sdfgamma/floorwidth,sdfdist);gl_FragColor=color*(alpha*opacity);\n#ifdef OVERDRAW_INSPECTOR\ngl_FragColor=vec4(1.0);\n#endif\n}","\n#define scale 0.015873016\n#define LINE_DISTANCE_SCALE 2.0\nattribute vec2 a_pos_normal;attribute vec4 a_data;uniform mat4 u_matrix;uniform mediump float u_ratio;uniform lowp float u_device_pixel_ratio;uniform vec2 u_patternscale_a;uniform float u_tex_y_a;uniform vec2 u_patternscale_b;uniform float u_tex_y_b;uniform vec2 u_units_to_pixels;varying vec2 v_normal;varying vec2 v_width2;varying vec2 v_tex_a;varying vec2 v_tex_b;varying float v_gamma_scale;\n#pragma mapbox: define highp vec4 color\n#pragma mapbox: define lowp float blur\n#pragma mapbox: define lowp float opacity\n#pragma mapbox: define mediump float gapwidth\n#pragma mapbox: define lowp float offset\n#pragma mapbox: define mediump float width\n#pragma mapbox: define lowp float floorwidth\nvoid main() {\n#pragma mapbox: initialize highp vec4 color\n#pragma mapbox: initialize lowp float blur\n#pragma mapbox: initialize lowp float opacity\n#pragma mapbox: initialize mediump float gapwidth\n#pragma mapbox: initialize lowp float offset\n#pragma mapbox: initialize mediump float width\n#pragma mapbox: initialize lowp float floorwidth\nfloat ANTIALIASING=1.0/u_device_pixel_ratio/2.0;vec2 a_extrude=a_data.xy-128.0;float a_direction=mod(a_data.z,4.0)-1.0;float a_linesofar=(floor(a_data.z/4.0)+a_data.w*64.0)*LINE_DISTANCE_SCALE;vec2 pos=floor(a_pos_normal*0.5);mediump vec2 normal=a_pos_normal-2.0*pos;normal.y=normal.y*2.0-1.0;v_normal=normal;gapwidth=gapwidth/2.0;float halfwidth=width/2.0;offset=-1.0*offset;float inset=gapwidth+(gapwidth > 0.0 ? ANTIALIASING : 0.0);float outset=gapwidth+halfwidth*(gapwidth > 0.0 ? 2.0 : 1.0)+(halfwidth==0.0 ? 0.0 : ANTIALIASING);mediump vec2 dist=outset*a_extrude*scale;mediump float u=0.5*a_direction;mediump float t=1.0-abs(u);mediump vec2 offset2=offset*a_extrude*scale*normal.y*mat2(t,-u,u,t);vec4 projected_extrude=u_matrix*vec4(dist/u_ratio,0.0,0.0);gl_Position=u_matrix*vec4(pos+offset2/u_ratio,0.0,1.0)+projected_extrude;float extrude_length_without_perspective=length(dist);float extrude_length_with_perspective=length(projected_extrude.xy/gl_Position.w*u_units_to_pixels);v_gamma_scale=extrude_length_without_perspective/extrude_length_with_perspective;v_tex_a=vec2(a_linesofar*u_patternscale_a.x/floorwidth,normal.y*u_patternscale_a.y+u_tex_y_a);v_tex_b=vec2(a_linesofar*u_patternscale_b.x/floorwidth,normal.y*u_patternscale_b.y+u_tex_y_b);v_width2=vec2(outset,inset);}"),yr=_r("uniform float u_fade_t;uniform float u_opacity;uniform sampler2D u_image0;uniform sampler2D u_image1;varying vec2 v_pos0;varying vec2 v_pos1;uniform float u_brightness_low;uniform float u_brightness_high;uniform float u_saturation_factor;uniform float u_contrast_factor;uniform vec3 u_spin_weights;void main() {vec4 color0=texture2D(u_image0,v_pos0);vec4 color1=texture2D(u_image1,v_pos1);if (color0.a > 0.0) {color0.rgb=color0.rgb/color0.a;}if (color1.a > 0.0) {color1.rgb=color1.rgb/color1.a;}vec4 color=mix(color0,color1,u_fade_t);color.a*=u_opacity;vec3 rgb=color.rgb;rgb=vec3(dot(rgb,u_spin_weights.xyz),dot(rgb,u_spin_weights.zxy),dot(rgb,u_spin_weights.yzx));float average=(color.r+color.g+color.b)/3.0;rgb+=(average-rgb)*u_saturation_factor;rgb=(rgb-0.5)*u_contrast_factor+0.5;vec3 u_high_vec=vec3(u_brightness_low,u_brightness_low,u_brightness_low);vec3 u_low_vec=vec3(u_brightness_high,u_brightness_high,u_brightness_high);gl_FragColor=vec4(mix(u_high_vec,u_low_vec,rgb)*color.a,color.a);\n#ifdef OVERDRAW_INSPECTOR\ngl_FragColor=vec4(1.0);\n#endif\n}","uniform mat4 u_matrix;uniform vec2 u_tl_parent;uniform float u_scale_parent;uniform float u_buffer_scale;attribute vec2 a_pos;attribute vec2 a_texture_pos;varying vec2 v_pos0;varying vec2 v_pos1;void main() {gl_Position=u_matrix*vec4(a_pos,0,1);v_pos0=(((a_texture_pos/8192.0)-0.5)/u_buffer_scale )+0.5;v_pos1=(v_pos0*u_scale_parent)+u_tl_parent;}"),mr=_r("uniform sampler2D u_texture;varying vec2 v_tex;varying float v_fade_opacity;\n#pragma mapbox: define lowp float opacity\nvoid main() {\n#pragma mapbox: initialize lowp float opacity\nlowp float alpha=opacity*v_fade_opacity;gl_FragColor=texture2D(u_texture,v_tex)*alpha;\n#ifdef OVERDRAW_INSPECTOR\ngl_FragColor=vec4(1.0);\n#endif\n}","const float PI=3.141592653589793;attribute vec4 a_pos_offset;attribute vec4 a_data;attribute vec4 a_pixeloffset;attribute vec3 a_projected_pos;attribute float a_fade_opacity;uniform bool u_is_size_zoom_constant;uniform bool u_is_size_feature_constant;uniform highp float u_size_t;uniform highp float u_size;uniform highp float u_camera_to_center_distance;uniform highp float u_pitch;uniform bool u_rotate_symbol;uniform highp float u_aspect_ratio;uniform float u_fade_change;uniform mat4 u_matrix;uniform mat4 u_label_plane_matrix;uniform mat4 u_coord_matrix;uniform bool u_is_text;uniform bool u_pitch_with_map;uniform vec2 u_texsize;varying vec2 v_tex;varying float v_fade_opacity;\n#pragma mapbox: define lowp float opacity\nvoid main() {\n#pragma mapbox: initialize lowp float opacity\nvec2 a_pos=a_pos_offset.xy;vec2 a_offset=a_pos_offset.zw;vec2 a_tex=a_data.xy;vec2 a_size=a_data.zw;float a_size_min=floor(a_size[0]*0.5);vec2 a_pxoffset=a_pixeloffset.xy;vec2 a_minFontScale=a_pixeloffset.zw/256.0;highp float segment_angle=-a_projected_pos[2];float size;if (!u_is_size_zoom_constant && !u_is_size_feature_constant) {size=mix(a_size_min,a_size[1],u_size_t)/128.0;} else if (u_is_size_zoom_constant && !u_is_size_feature_constant) {size=a_size_min/128.0;} else {size=u_size;}vec4 projectedPoint=u_matrix*vec4(a_pos,0,1);highp float camera_to_anchor_distance=projectedPoint.w;highp float distance_ratio=u_pitch_with_map ?\ncamera_to_anchor_distance/u_camera_to_center_distance :\nu_camera_to_center_distance/camera_to_anchor_distance;highp float perspective_ratio=clamp(0.5+0.5*distance_ratio,0.0,4.0);size*=perspective_ratio;float fontScale=u_is_text ? size/24.0 : size;highp float symbol_rotation=0.0;if (u_rotate_symbol) {vec4 offsetProjectedPoint=u_matrix*vec4(a_pos+vec2(1,0),0,1);vec2 a=projectedPoint.xy/projectedPoint.w;vec2 b=offsetProjectedPoint.xy/offsetProjectedPoint.w;symbol_rotation=atan((b.y-a.y)/u_aspect_ratio,b.x-a.x);}highp float angle_sin=sin(segment_angle+symbol_rotation);highp float angle_cos=cos(segment_angle+symbol_rotation);mat2 rotation_matrix=mat2(angle_cos,-1.0*angle_sin,angle_sin,angle_cos);vec4 projected_pos=u_label_plane_matrix*vec4(a_projected_pos.xy,0.0,1.0);gl_Position=u_coord_matrix*vec4(projected_pos.xy/projected_pos.w+rotation_matrix*(a_offset/32.0*max(a_minFontScale,fontScale)+a_pxoffset/16.0),0.0,1.0);v_tex=a_tex/u_texsize;vec2 fade_opacity=unpack_opacity(a_fade_opacity);float fade_change=fade_opacity[1] > 0.5 ? u_fade_change :-u_fade_change;v_fade_opacity=max(0.0,min(1.0,fade_opacity[0]+fade_change));}"),xr=_r("#define SDF_PX 8.0\nuniform bool u_is_halo;uniform sampler2D u_texture;uniform highp float u_gamma_scale;uniform lowp float u_device_pixel_ratio;uniform bool u_is_text;varying vec2 v_data0;varying vec3 v_data1;\n#pragma mapbox: define highp vec4 fill_color\n#pragma mapbox: define highp vec4 halo_color\n#pragma mapbox: define lowp float opacity\n#pragma mapbox: define lowp float halo_width\n#pragma mapbox: define lowp float halo_blur\nvoid main() {\n#pragma mapbox: initialize highp vec4 fill_color\n#pragma mapbox: initialize highp vec4 halo_color\n#pragma mapbox: initialize lowp float opacity\n#pragma mapbox: initialize lowp float halo_width\n#pragma mapbox: initialize lowp float halo_blur\nfloat EDGE_GAMMA=0.105/u_device_pixel_ratio;vec2 tex=v_data0.xy;float gamma_scale=v_data1.x;float size=v_data1.y;float fade_opacity=v_data1[2];float fontScale=u_is_text ? size/24.0 : size;lowp vec4 color=fill_color;highp float gamma=EDGE_GAMMA/(fontScale*u_gamma_scale);lowp float buff=(256.0-64.0)/256.0;if (u_is_halo) {color=halo_color;gamma=(halo_blur*1.19/SDF_PX+EDGE_GAMMA)/(fontScale*u_gamma_scale);buff=(6.0-halo_width/fontScale)/SDF_PX;}lowp float dist=texture2D(u_texture,tex).a;highp float gamma_scaled=gamma*gamma_scale;highp float alpha=smoothstep(buff-gamma_scaled,buff+gamma_scaled,dist);gl_FragColor=color*(alpha*opacity*fade_opacity);\n#ifdef OVERDRAW_INSPECTOR\ngl_FragColor=vec4(1.0);\n#endif\n}","const float PI=3.141592653589793;attribute vec4 a_pos_offset;attribute vec4 a_data;attribute vec4 a_pixeloffset;attribute vec3 a_projected_pos;attribute float a_fade_opacity;uniform bool u_is_size_zoom_constant;uniform bool u_is_size_feature_constant;uniform highp float u_size_t;uniform highp float u_size;uniform mat4 u_matrix;uniform mat4 u_label_plane_matrix;uniform mat4 u_coord_matrix;uniform bool u_is_text;uniform bool u_pitch_with_map;uniform highp float u_pitch;uniform bool u_rotate_symbol;uniform highp float u_aspect_ratio;uniform highp float u_camera_to_center_distance;uniform float u_fade_change;uniform vec2 u_texsize;varying vec2 v_data0;varying vec3 v_data1;\n#pragma mapbox: define highp vec4 fill_color\n#pragma mapbox: define highp vec4 halo_color\n#pragma mapbox: define lowp float opacity\n#pragma mapbox: define lowp float halo_width\n#pragma mapbox: define lowp float halo_blur\nvoid main() {\n#pragma mapbox: initialize highp vec4 fill_color\n#pragma mapbox: initialize highp vec4 halo_color\n#pragma mapbox: initialize lowp float opacity\n#pragma mapbox: initialize lowp float halo_width\n#pragma mapbox: initialize lowp float halo_blur\nvec2 a_pos=a_pos_offset.xy;vec2 a_offset=a_pos_offset.zw;vec2 a_tex=a_data.xy;vec2 a_size=a_data.zw;float a_size_min=floor(a_size[0]*0.5);vec2 a_pxoffset=a_pixeloffset.xy;highp float segment_angle=-a_projected_pos[2];float size;if (!u_is_size_zoom_constant && !u_is_size_feature_constant) {size=mix(a_size_min,a_size[1],u_size_t)/128.0;} else if (u_is_size_zoom_constant && !u_is_size_feature_constant) {size=a_size_min/128.0;} else {size=u_size;}vec4 projectedPoint=u_matrix*vec4(a_pos,0,1);highp float camera_to_anchor_distance=projectedPoint.w;highp float distance_ratio=u_pitch_with_map ?\ncamera_to_anchor_distance/u_camera_to_center_distance :\nu_camera_to_center_distance/camera_to_anchor_distance;highp float perspective_ratio=clamp(0.5+0.5*distance_ratio,0.0,4.0);size*=perspective_ratio;float fontScale=u_is_text ? size/24.0 : size;highp float symbol_rotation=0.0;if (u_rotate_symbol) {vec4 offsetProjectedPoint=u_matrix*vec4(a_pos+vec2(1,0),0,1);vec2 a=projectedPoint.xy/projectedPoint.w;vec2 b=offsetProjectedPoint.xy/offsetProjectedPoint.w;symbol_rotation=atan((b.y-a.y)/u_aspect_ratio,b.x-a.x);}highp float angle_sin=sin(segment_angle+symbol_rotation);highp float angle_cos=cos(segment_angle+symbol_rotation);mat2 rotation_matrix=mat2(angle_cos,-1.0*angle_sin,angle_sin,angle_cos);vec4 projected_pos=u_label_plane_matrix*vec4(a_projected_pos.xy,0.0,1.0);gl_Position=u_coord_matrix*vec4(projected_pos.xy/projected_pos.w+rotation_matrix*(a_offset/32.0*fontScale+a_pxoffset),0.0,1.0);float gamma_scale=gl_Position.w;vec2 fade_opacity=unpack_opacity(a_fade_opacity);float fade_change=fade_opacity[1] > 0.5 ? u_fade_change :-u_fade_change;float interpolated_fade_opacity=max(0.0,min(1.0,fade_opacity[0]+fade_change));v_data0=a_tex/u_texsize;v_data1=vec3(gamma_scale,size,interpolated_fade_opacity);}"),br=_r("#define SDF_PX 8.0\n#define SDF 1.0\n#define ICON 0.0\nuniform bool u_is_halo;uniform sampler2D u_texture;uniform sampler2D u_texture_icon;uniform highp float u_gamma_scale;uniform lowp float u_device_pixel_ratio;varying vec4 v_data0;varying vec4 v_data1;\n#pragma mapbox: define highp vec4 fill_color\n#pragma mapbox: define highp vec4 halo_color\n#pragma mapbox: define lowp float opacity\n#pragma mapbox: define lowp float halo_width\n#pragma mapbox: define lowp float halo_blur\nvoid main() {\n#pragma mapbox: initialize highp vec4 fill_color\n#pragma mapbox: initialize highp vec4 halo_color\n#pragma mapbox: initialize lowp float opacity\n#pragma mapbox: initialize lowp float halo_width\n#pragma mapbox: initialize lowp float halo_blur\nfloat fade_opacity=v_data1[2];if (v_data1.w==ICON) {vec2 tex_icon=v_data0.zw;lowp float alpha=opacity*fade_opacity;gl_FragColor=texture2D(u_texture_icon,tex_icon)*alpha;\n#ifdef OVERDRAW_INSPECTOR\ngl_FragColor=vec4(1.0);\n#endif\nreturn;}vec2 tex=v_data0.xy;float EDGE_GAMMA=0.105/u_device_pixel_ratio;float gamma_scale=v_data1.x;float size=v_data1.y;float fontScale=size/24.0;lowp vec4 color=fill_color;highp float gamma=EDGE_GAMMA/(fontScale*u_gamma_scale);lowp float buff=(256.0-64.0)/256.0;if (u_is_halo) {color=halo_color;gamma=(halo_blur*1.19/SDF_PX+EDGE_GAMMA)/(fontScale*u_gamma_scale);buff=(6.0-halo_width/fontScale)/SDF_PX;}lowp float dist=texture2D(u_texture,tex).a;highp float gamma_scaled=gamma*gamma_scale;highp float alpha=smoothstep(buff-gamma_scaled,buff+gamma_scaled,dist);gl_FragColor=color*(alpha*opacity*fade_opacity);\n#ifdef OVERDRAW_INSPECTOR\ngl_FragColor=vec4(1.0);\n#endif\n}","const float PI=3.141592653589793;attribute vec4 a_pos_offset;attribute vec4 a_data;attribute vec3 a_projected_pos;attribute float a_fade_opacity;uniform bool u_is_size_zoom_constant;uniform bool u_is_size_feature_constant;uniform highp float u_size_t;uniform highp float u_size;uniform mat4 u_matrix;uniform mat4 u_label_plane_matrix;uniform mat4 u_coord_matrix;uniform bool u_is_text;uniform bool u_pitch_with_map;uniform highp float u_pitch;uniform bool u_rotate_symbol;uniform highp float u_aspect_ratio;uniform highp float u_camera_to_center_distance;uniform float u_fade_change;uniform vec2 u_texsize;uniform vec2 u_texsize_icon;varying vec4 v_data0;varying vec4 v_data1;\n#pragma mapbox: define highp vec4 fill_color\n#pragma mapbox: define highp vec4 halo_color\n#pragma mapbox: define lowp float opacity\n#pragma mapbox: define lowp float halo_width\n#pragma mapbox: define lowp float halo_blur\nvoid main() {\n#pragma mapbox: initialize highp vec4 fill_color\n#pragma mapbox: initialize highp vec4 halo_color\n#pragma mapbox: initialize lowp float opacity\n#pragma mapbox: initialize lowp float halo_width\n#pragma mapbox: initialize lowp float halo_blur\nvec2 a_pos=a_pos_offset.xy;vec2 a_offset=a_pos_offset.zw;vec2 a_tex=a_data.xy;vec2 a_size=a_data.zw;float a_size_min=floor(a_size[0]*0.5);float is_sdf=a_size[0]-2.0*a_size_min;highp float segment_angle=-a_projected_pos[2];float size;if (!u_is_size_zoom_constant && !u_is_size_feature_constant) {size=mix(a_size_min,a_size[1],u_size_t)/128.0;} else if (u_is_size_zoom_constant && !u_is_size_feature_constant) {size=a_size_min/128.0;} else {size=u_size;}vec4 projectedPoint=u_matrix*vec4(a_pos,0,1);highp float camera_to_anchor_distance=projectedPoint.w;highp float distance_ratio=u_pitch_with_map ?\ncamera_to_anchor_distance/u_camera_to_center_distance :\nu_camera_to_center_distance/camera_to_anchor_distance;highp float perspective_ratio=clamp(0.5+0.5*distance_ratio,0.0,4.0);size*=perspective_ratio;float fontScale=size/24.0;highp float symbol_rotation=0.0;if (u_rotate_symbol) {vec4 offsetProjectedPoint=u_matrix*vec4(a_pos+vec2(1,0),0,1);vec2 a=projectedPoint.xy/projectedPoint.w;vec2 b=offsetProjectedPoint.xy/offsetProjectedPoint.w;symbol_rotation=atan((b.y-a.y)/u_aspect_ratio,b.x-a.x);}highp float angle_sin=sin(segment_angle+symbol_rotation);highp float angle_cos=cos(segment_angle+symbol_rotation);mat2 rotation_matrix=mat2(angle_cos,-1.0*angle_sin,angle_sin,angle_cos);vec4 projected_pos=u_label_plane_matrix*vec4(a_projected_pos.xy,0.0,1.0);gl_Position=u_coord_matrix*vec4(projected_pos.xy/projected_pos.w+rotation_matrix*(a_offset/32.0*fontScale),0.0,1.0);float gamma_scale=gl_Position.w;vec2 fade_opacity=unpack_opacity(a_fade_opacity);float fade_change=fade_opacity[1] > 0.5 ? u_fade_change :-u_fade_change;float interpolated_fade_opacity=max(0.0,min(1.0,fade_opacity[0]+fade_change));v_data0.xy=a_tex/u_texsize;v_data0.zw=a_tex/u_texsize_icon;v_data1=vec4(gamma_scale,size,interpolated_fade_opacity,is_sdf);}");function _r(t,e){var r=/#pragma mapbox: ([\w]+) ([\w]+) ([\w]+) ([\w]+)/g,n={};return{fragmentSource:t=t.replace(r,(function(t,e,r,i,a){return n[a]=!0,"define"===e?"\n#ifndef HAS_UNIFORM_u_"+a+"\nvarying "+r+" "+i+" "+a+";\n#else\nuniform "+r+" "+i+" u_"+a+";\n#endif\n":"\n#ifdef HAS_UNIFORM_u_"+a+"\n "+r+" "+i+" "+a+" = u_"+a+";\n#endif\n"})),vertexSource:e=e.replace(r,(function(t,e,r,i,a){var o="float"===i?"vec2":"vec4",s=a.match(/color/)?"color":o;return n[a]?"define"===e?"\n#ifndef HAS_UNIFORM_u_"+a+"\nuniform lowp float u_"+a+"_t;\nattribute "+r+" "+o+" a_"+a+";\nvarying "+r+" "+i+" "+a+";\n#else\nuniform "+r+" "+i+" u_"+a+";\n#endif\n":"vec4"===s?"\n#ifndef HAS_UNIFORM_u_"+a+"\n "+a+" = a_"+a+";\n#else\n "+r+" "+i+" "+a+" = u_"+a+";\n#endif\n":"\n#ifndef HAS_UNIFORM_u_"+a+"\n "+a+" = unpack_mix_"+s+"(a_"+a+", u_"+a+"_t);\n#else\n "+r+" "+i+" "+a+" = u_"+a+";\n#endif\n":"define"===e?"\n#ifndef HAS_UNIFORM_u_"+a+"\nuniform lowp float u_"+a+"_t;\nattribute "+r+" "+o+" a_"+a+";\n#else\nuniform "+r+" "+i+" u_"+a+";\n#endif\n":"vec4"===s?"\n#ifndef HAS_UNIFORM_u_"+a+"\n "+r+" "+i+" "+a+" = a_"+a+";\n#else\n "+r+" "+i+" "+a+" = u_"+a+";\n#endif\n":"\n#ifndef HAS_UNIFORM_u_"+a+"\n "+r+" "+i+" "+a+" = unpack_mix_"+s+"(a_"+a+", u_"+a+"_t);\n#else\n "+r+" "+i+" "+a+" = u_"+a+";\n#endif\n"}))}}var wr=Object.freeze({__proto__:null,prelude:Xe,background:Je,backgroundPattern:Ke,circle:$e,clippingMask:Qe,heatmap:tr,heatmapTexture:er,collisionBox:rr,collisionCircle:nr,debug:ir,fill:ar,fillOutline:or,fillOutlinePattern:sr,fillPattern:lr,fillExtrusion:ur,fillExtrusionPattern:cr,hillshadePrepare:fr,hillshade:hr,line:pr,lineGradient:dr,linePattern:vr,lineSDF:gr,raster:yr,symbolIcon:mr,symbolSDF:xr,symbolTextAndIcon:br}),Tr=function(){this.boundProgram=null,this.boundLayoutVertexBuffer=null,this.boundPaintVertexBuffers=[],this.boundIndexBuffer=null,this.boundVertexOffset=null,this.boundDynamicVertexBuffer=null,this.vao=null};Tr.prototype.bind=function(t,e,r,n,i,a,o,s){this.context=t;for(var l=this.boundPaintVertexBuffers.length!==n.length,u=0;!l&&u>16,s>>16],u_pixel_coord_lower:[65535&o,65535&s]}}kr.prototype.draw=function(t,e,r,n,i,a,o,s,l,u,c,f,h,p,d,v){var g,y=t.gl;if(!this.failedToCreate){for(var m in t.program.set(this.program),t.setDepthMode(r),t.setStencilMode(n),t.setColorMode(i),t.setCullFace(a),this.fixedUniforms)this.fixedUniforms[m].set(o[m]);p&&p.setUniforms(t,this.binderUniforms,f,{zoom:h});for(var x=(g={},g[y.LINES]=2,g[y.TRIANGLES]=3,g[y.LINE_STRIP]=1,g)[e],b=0,_=c.get();b<_.length;b+=1){var w=_[b],T=w.vaos||(w.vaos={});(T[s]||(T[s]=new Tr)).bind(t,this,l,p?p.getPaintVertexBuffers():[],u,w.vertexOffset,d,v),y.drawElements(e,w.primitiveLength*x,y.UNSIGNED_SHORT,w.primitiveOffset*x*2)}}};var Mr=function(e,r,n,i){var a=r.style.light,o=a.properties.get("position"),s=[o.x,o.y,o.z],l=t.create$1();"viewport"===a.properties.get("anchor")&&t.fromRotation(l,-r.transform.angle),t.transformMat3(s,s,l);var u=a.properties.get("color");return{u_matrix:e,u_lightpos:s,u_lightintensity:a.properties.get("intensity"),u_lightcolor:[u.r,u.g,u.b],u_vertical_gradient:+n,u_opacity:i}},Sr=function(e,r,n,i,a,o,s){return t.extend(Mr(e,r,n,i),Ar(o,r,s),{u_height_factor:-Math.pow(2,a.overscaledZ)/s.tileSize/8})},Er=function(t){return{u_matrix:t}},Lr=function(e,r,n,i){return t.extend(Er(e),Ar(n,r,i))},Cr=function(t,e){return{u_matrix:t,u_world:e}},Pr=function(e,r,n,i,a){return t.extend(Lr(e,r,n,i),{u_world:a})},Or=function(e,r,n,i){var a,o,s=e.transform;if("map"===i.paint.get("circle-pitch-alignment")){var l=ge(n,1,s.zoom);a=!0,o=[l,l]}else a=!1,o=s.pixelsToGLUnits;return{u_camera_to_center_distance:s.cameraToCenterDistance,u_scale_with_map:+("map"===i.paint.get("circle-pitch-scale")),u_matrix:e.translatePosMatrix(r.posMatrix,n,i.paint.get("circle-translate"),i.paint.get("circle-translate-anchor")),u_pitch_with_map:+a,u_device_pixel_ratio:t.browser.devicePixelRatio,u_extrude_scale:o}},Ir=function(t,e,r){var n=ge(r,1,e.zoom),i=Math.pow(2,e.zoom-r.tileID.overscaledZ),a=r.tileID.overscaleFactor();return{u_matrix:t,u_camera_to_center_distance:e.cameraToCenterDistance,u_pixels_to_tile_units:n,u_extrude_scale:[e.pixelsToGLUnits[0]/(n*i),e.pixelsToGLUnits[1]/(n*i)],u_overscale_factor:a}},Dr=function(t,e,r){return{u_matrix:t,u_inv_matrix:e,u_camera_to_center_distance:r.cameraToCenterDistance,u_viewport_size:[r.width,r.height]}},zr=function(t,e,r){return void 0===r&&(r=1),{u_matrix:t,u_color:e,u_overlay:0,u_overlay_scale:r}},Rr=function(t){return{u_matrix:t}},Fr=function(t,e,r,n){return{u_matrix:t,u_extrude_scale:ge(e,1,r),u_intensity:n}},Br=function(e,r,n,i){var a=t.create();t.ortho(a,0,e.width,e.height,0,0,1);var o=e.context.gl;return{u_matrix:a,u_world:[o.drawingBufferWidth,o.drawingBufferHeight],u_image:n,u_color_ramp:i,u_opacity:r.paint.get("heatmap-opacity")}},Nr=function(e,r,n){var i=n.paint.get("hillshade-shadow-color"),a=n.paint.get("hillshade-highlight-color"),o=n.paint.get("hillshade-accent-color"),s=n.paint.get("hillshade-illumination-direction")*(Math.PI/180);"viewport"===n.paint.get("hillshade-illumination-anchor")&&(s-=e.transform.angle);var l,u,c,f=!e.options.moving;return{u_matrix:e.transform.calculatePosMatrix(r.tileID.toUnwrapped(),f),u_image:0,u_latrange:(l=r.tileID,u=Math.pow(2,l.canonical.z),c=l.canonical.y,[new t.MercatorCoordinate(0,c/u).toLngLat().lat,new t.MercatorCoordinate(0,(c+1)/u).toLngLat().lat]),u_light:[n.paint.get("hillshade-exaggeration"),s],u_shadow:i,u_highlight:a,u_accent:o}},jr=function(e,r,n){var i=r.stride,a=t.create();return t.ortho(a,0,t.EXTENT,-t.EXTENT,0,0,1),t.translate(a,a,[0,-t.EXTENT,0]),{u_matrix:a,u_image:1,u_dimension:[i,i],u_zoom:e.overscaledZ,u_maxzoom:n,u_unpack:r.getUnpackVector()}};var Ur=function(e,r,n){var i=e.transform;return{u_matrix:Zr(e,r,n),u_ratio:1/ge(r,1,i.zoom),u_device_pixel_ratio:t.browser.devicePixelRatio,u_units_to_pixels:[1/i.pixelsToGLUnits[0],1/i.pixelsToGLUnits[1]]}},Vr=function(e,r,n){return t.extend(Ur(e,r,n),{u_image:0})},Hr=function(e,r,n,i){var a=e.transform,o=Gr(r,a);return{u_matrix:Zr(e,r,n),u_texsize:r.imageAtlasTexture.size,u_ratio:1/ge(r,1,a.zoom),u_device_pixel_ratio:t.browser.devicePixelRatio,u_image:0,u_scale:[o,i.fromScale,i.toScale],u_fade:i.t,u_units_to_pixels:[1/a.pixelsToGLUnits[0],1/a.pixelsToGLUnits[1]]}},qr=function(e,r,n,i,a){var o=e.transform,s=e.lineAtlas,l=Gr(r,o),u="round"===n.layout.get("line-cap"),c=s.getDash(i.from,u),f=s.getDash(i.to,u),h=c.width*a.fromScale,p=f.width*a.toScale;return t.extend(Ur(e,r,n),{u_patternscale_a:[l/h,-c.height/2],u_patternscale_b:[l/p,-f.height/2],u_sdfgamma:s.width/(256*Math.min(h,p)*t.browser.devicePixelRatio)/2,u_image:0,u_tex_y_a:c.y,u_tex_y_b:f.y,u_mix:a.t})};function Gr(t,e){return 1/ge(t,1,e.tileZoom)}function Zr(t,e,r){return t.translatePosMatrix(e.tileID.posMatrix,e,r.paint.get("line-translate"),r.paint.get("line-translate-anchor"))}var Yr=function(t,e,r,n,i){return{u_matrix:t,u_tl_parent:e,u_scale_parent:r,u_buffer_scale:1,u_fade_t:n.mix,u_opacity:n.opacity*i.paint.get("raster-opacity"),u_image0:0,u_image1:1,u_brightness_low:i.paint.get("raster-brightness-min"),u_brightness_high:i.paint.get("raster-brightness-max"),u_saturation_factor:(o=i.paint.get("raster-saturation"),o>0?1-1/(1.001-o):-o),u_contrast_factor:(a=i.paint.get("raster-contrast"),a>0?1/(1-a):1+a),u_spin_weights:Wr(i.paint.get("raster-hue-rotate"))};var a,o};function Wr(t){t*=Math.PI/180;var e=Math.sin(t),r=Math.cos(t);return[(2*r+1)/3,(-Math.sqrt(3)*e-r+1)/3,(Math.sqrt(3)*e-r+1)/3]}var Xr,Jr=function(t,e,r,n,i,a,o,s,l,u){var c=i.transform;return{u_is_size_zoom_constant:+("constant"===t||"source"===t),u_is_size_feature_constant:+("constant"===t||"camera"===t),u_size_t:e?e.uSizeT:0,u_size:e?e.uSize:0,u_camera_to_center_distance:c.cameraToCenterDistance,u_pitch:c.pitch/360*2*Math.PI,u_rotate_symbol:+r,u_aspect_ratio:c.width/c.height,u_fade_change:i.options.fadeDuration?i.symbolFadeChange:1,u_matrix:a,u_label_plane_matrix:o,u_coord_matrix:s,u_is_text:+l,u_pitch_with_map:+n,u_texsize:u,u_texture:0}},Kr=function(e,r,n,i,a,o,s,l,u,c,f){var h=a.transform;return t.extend(Jr(e,r,n,i,a,o,s,l,u,c),{u_gamma_scale:i?Math.cos(h._pitch)*h.cameraToCenterDistance:1,u_device_pixel_ratio:t.browser.devicePixelRatio,u_is_halo:+f})},$r=function(e,r,n,i,a,o,s,l,u,c){return t.extend(Kr(e,r,n,i,a,o,s,l,!0,u,!0),{u_texsize_icon:c,u_texture_icon:1})},Qr=function(t,e,r){return{u_matrix:t,u_opacity:e,u_color:r}},tn=function(e,r,n,i,a,o){return t.extend(function(t,e,r,n){var i=r.imageManager.getPattern(t.from.toString()),a=r.imageManager.getPattern(t.to.toString()),o=r.imageManager.getPixelSize(),s=o.width,l=o.height,u=Math.pow(2,n.tileID.overscaledZ),c=n.tileSize*Math.pow(2,r.transform.tileZoom)/u,f=c*(n.tileID.canonical.x+n.tileID.wrap*u),h=c*n.tileID.canonical.y;return{u_image:0,u_pattern_tl_a:i.tl,u_pattern_br_a:i.br,u_pattern_tl_b:a.tl,u_pattern_br_b:a.br,u_texsize:[s,l],u_mix:e.t,u_pattern_size_a:i.displaySize,u_pattern_size_b:a.displaySize,u_scale_a:e.fromScale,u_scale_b:e.toScale,u_tile_units_to_pixels:1/ge(n,1,r.transform.tileZoom),u_pixel_coord_upper:[f>>16,h>>16],u_pixel_coord_lower:[65535&f,65535&h]}}(i,o,n,a),{u_matrix:e,u_opacity:r})},en={fillExtrusion:function(e,r){return{u_matrix:new t.UniformMatrix4f(e,r.u_matrix),u_lightpos:new t.Uniform3f(e,r.u_lightpos),u_lightintensity:new t.Uniform1f(e,r.u_lightintensity),u_lightcolor:new t.Uniform3f(e,r.u_lightcolor),u_vertical_gradient:new t.Uniform1f(e,r.u_vertical_gradient),u_opacity:new t.Uniform1f(e,r.u_opacity)}},fillExtrusionPattern:function(e,r){return{u_matrix:new t.UniformMatrix4f(e,r.u_matrix),u_lightpos:new t.Uniform3f(e,r.u_lightpos),u_lightintensity:new t.Uniform1f(e,r.u_lightintensity),u_lightcolor:new t.Uniform3f(e,r.u_lightcolor),u_vertical_gradient:new t.Uniform1f(e,r.u_vertical_gradient),u_height_factor:new t.Uniform1f(e,r.u_height_factor),u_image:new t.Uniform1i(e,r.u_image),u_texsize:new t.Uniform2f(e,r.u_texsize),u_pixel_coord_upper:new t.Uniform2f(e,r.u_pixel_coord_upper),u_pixel_coord_lower:new t.Uniform2f(e,r.u_pixel_coord_lower),u_scale:new t.Uniform3f(e,r.u_scale),u_fade:new t.Uniform1f(e,r.u_fade),u_opacity:new t.Uniform1f(e,r.u_opacity)}},fill:function(e,r){return{u_matrix:new t.UniformMatrix4f(e,r.u_matrix)}},fillPattern:function(e,r){return{u_matrix:new t.UniformMatrix4f(e,r.u_matrix),u_image:new t.Uniform1i(e,r.u_image),u_texsize:new t.Uniform2f(e,r.u_texsize),u_pixel_coord_upper:new t.Uniform2f(e,r.u_pixel_coord_upper),u_pixel_coord_lower:new t.Uniform2f(e,r.u_pixel_coord_lower),u_scale:new t.Uniform3f(e,r.u_scale),u_fade:new t.Uniform1f(e,r.u_fade)}},fillOutline:function(e,r){return{u_matrix:new t.UniformMatrix4f(e,r.u_matrix),u_world:new t.Uniform2f(e,r.u_world)}},fillOutlinePattern:function(e,r){return{u_matrix:new t.UniformMatrix4f(e,r.u_matrix),u_world:new t.Uniform2f(e,r.u_world),u_image:new t.Uniform1i(e,r.u_image),u_texsize:new t.Uniform2f(e,r.u_texsize),u_pixel_coord_upper:new t.Uniform2f(e,r.u_pixel_coord_upper),u_pixel_coord_lower:new t.Uniform2f(e,r.u_pixel_coord_lower),u_scale:new t.Uniform3f(e,r.u_scale),u_fade:new t.Uniform1f(e,r.u_fade)}},circle:function(e,r){return{u_camera_to_center_distance:new t.Uniform1f(e,r.u_camera_to_center_distance),u_scale_with_map:new t.Uniform1i(e,r.u_scale_with_map),u_pitch_with_map:new t.Uniform1i(e,r.u_pitch_with_map),u_extrude_scale:new t.Uniform2f(e,r.u_extrude_scale),u_device_pixel_ratio:new t.Uniform1f(e,r.u_device_pixel_ratio),u_matrix:new t.UniformMatrix4f(e,r.u_matrix)}},collisionBox:function(e,r){return{u_matrix:new t.UniformMatrix4f(e,r.u_matrix),u_camera_to_center_distance:new t.Uniform1f(e,r.u_camera_to_center_distance),u_pixels_to_tile_units:new t.Uniform1f(e,r.u_pixels_to_tile_units),u_extrude_scale:new t.Uniform2f(e,r.u_extrude_scale),u_overscale_factor:new t.Uniform1f(e,r.u_overscale_factor)}},collisionCircle:function(e,r){return{u_matrix:new t.UniformMatrix4f(e,r.u_matrix),u_inv_matrix:new t.UniformMatrix4f(e,r.u_inv_matrix),u_camera_to_center_distance:new t.Uniform1f(e,r.u_camera_to_center_distance),u_viewport_size:new t.Uniform2f(e,r.u_viewport_size)}},debug:function(e,r){return{u_color:new t.UniformColor(e,r.u_color),u_matrix:new t.UniformMatrix4f(e,r.u_matrix),u_overlay:new t.Uniform1i(e,r.u_overlay),u_overlay_scale:new t.Uniform1f(e,r.u_overlay_scale)}},clippingMask:function(e,r){return{u_matrix:new t.UniformMatrix4f(e,r.u_matrix)}},heatmap:function(e,r){return{u_extrude_scale:new t.Uniform1f(e,r.u_extrude_scale),u_intensity:new t.Uniform1f(e,r.u_intensity),u_matrix:new t.UniformMatrix4f(e,r.u_matrix)}},heatmapTexture:function(e,r){return{u_matrix:new t.UniformMatrix4f(e,r.u_matrix),u_world:new t.Uniform2f(e,r.u_world),u_image:new t.Uniform1i(e,r.u_image),u_color_ramp:new t.Uniform1i(e,r.u_color_ramp),u_opacity:new t.Uniform1f(e,r.u_opacity)}},hillshade:function(e,r){return{u_matrix:new t.UniformMatrix4f(e,r.u_matrix),u_image:new t.Uniform1i(e,r.u_image),u_latrange:new t.Uniform2f(e,r.u_latrange),u_light:new t.Uniform2f(e,r.u_light),u_shadow:new t.UniformColor(e,r.u_shadow),u_highlight:new t.UniformColor(e,r.u_highlight),u_accent:new t.UniformColor(e,r.u_accent)}},hillshadePrepare:function(e,r){return{u_matrix:new t.UniformMatrix4f(e,r.u_matrix),u_image:new t.Uniform1i(e,r.u_image),u_dimension:new t.Uniform2f(e,r.u_dimension),u_zoom:new t.Uniform1f(e,r.u_zoom),u_maxzoom:new t.Uniform1f(e,r.u_maxzoom),u_unpack:new t.Uniform4f(e,r.u_unpack)}},line:function(e,r){return{u_matrix:new t.UniformMatrix4f(e,r.u_matrix),u_ratio:new t.Uniform1f(e,r.u_ratio),u_device_pixel_ratio:new t.Uniform1f(e,r.u_device_pixel_ratio),u_units_to_pixels:new t.Uniform2f(e,r.u_units_to_pixels)}},lineGradient:function(e,r){return{u_matrix:new t.UniformMatrix4f(e,r.u_matrix),u_ratio:new t.Uniform1f(e,r.u_ratio),u_device_pixel_ratio:new t.Uniform1f(e,r.u_device_pixel_ratio),u_units_to_pixels:new t.Uniform2f(e,r.u_units_to_pixels),u_image:new t.Uniform1i(e,r.u_image)}},linePattern:function(e,r){return{u_matrix:new t.UniformMatrix4f(e,r.u_matrix),u_texsize:new t.Uniform2f(e,r.u_texsize),u_ratio:new t.Uniform1f(e,r.u_ratio),u_device_pixel_ratio:new t.Uniform1f(e,r.u_device_pixel_ratio),u_image:new t.Uniform1i(e,r.u_image),u_units_to_pixels:new t.Uniform2f(e,r.u_units_to_pixels),u_scale:new t.Uniform3f(e,r.u_scale),u_fade:new t.Uniform1f(e,r.u_fade)}},lineSDF:function(e,r){return{u_matrix:new t.UniformMatrix4f(e,r.u_matrix),u_ratio:new t.Uniform1f(e,r.u_ratio),u_device_pixel_ratio:new t.Uniform1f(e,r.u_device_pixel_ratio),u_units_to_pixels:new t.Uniform2f(e,r.u_units_to_pixels),u_patternscale_a:new t.Uniform2f(e,r.u_patternscale_a),u_patternscale_b:new t.Uniform2f(e,r.u_patternscale_b),u_sdfgamma:new t.Uniform1f(e,r.u_sdfgamma),u_image:new t.Uniform1i(e,r.u_image),u_tex_y_a:new t.Uniform1f(e,r.u_tex_y_a),u_tex_y_b:new t.Uniform1f(e,r.u_tex_y_b),u_mix:new t.Uniform1f(e,r.u_mix)}},raster:function(e,r){return{u_matrix:new t.UniformMatrix4f(e,r.u_matrix),u_tl_parent:new t.Uniform2f(e,r.u_tl_parent),u_scale_parent:new t.Uniform1f(e,r.u_scale_parent),u_buffer_scale:new t.Uniform1f(e,r.u_buffer_scale),u_fade_t:new t.Uniform1f(e,r.u_fade_t),u_opacity:new t.Uniform1f(e,r.u_opacity),u_image0:new t.Uniform1i(e,r.u_image0),u_image1:new t.Uniform1i(e,r.u_image1),u_brightness_low:new t.Uniform1f(e,r.u_brightness_low),u_brightness_high:new t.Uniform1f(e,r.u_brightness_high),u_saturation_factor:new t.Uniform1f(e,r.u_saturation_factor),u_contrast_factor:new t.Uniform1f(e,r.u_contrast_factor),u_spin_weights:new t.Uniform3f(e,r.u_spin_weights)}},symbolIcon:function(e,r){return{u_is_size_zoom_constant:new t.Uniform1i(e,r.u_is_size_zoom_constant),u_is_size_feature_constant:new t.Uniform1i(e,r.u_is_size_feature_constant),u_size_t:new t.Uniform1f(e,r.u_size_t),u_size:new t.Uniform1f(e,r.u_size),u_camera_to_center_distance:new t.Uniform1f(e,r.u_camera_to_center_distance),u_pitch:new t.Uniform1f(e,r.u_pitch),u_rotate_symbol:new t.Uniform1i(e,r.u_rotate_symbol),u_aspect_ratio:new t.Uniform1f(e,r.u_aspect_ratio),u_fade_change:new t.Uniform1f(e,r.u_fade_change),u_matrix:new t.UniformMatrix4f(e,r.u_matrix),u_label_plane_matrix:new t.UniformMatrix4f(e,r.u_label_plane_matrix),u_coord_matrix:new t.UniformMatrix4f(e,r.u_coord_matrix),u_is_text:new t.Uniform1i(e,r.u_is_text),u_pitch_with_map:new t.Uniform1i(e,r.u_pitch_with_map),u_texsize:new t.Uniform2f(e,r.u_texsize),u_texture:new t.Uniform1i(e,r.u_texture)}},symbolSDF:function(e,r){return{u_is_size_zoom_constant:new t.Uniform1i(e,r.u_is_size_zoom_constant),u_is_size_feature_constant:new t.Uniform1i(e,r.u_is_size_feature_constant),u_size_t:new t.Uniform1f(e,r.u_size_t),u_size:new t.Uniform1f(e,r.u_size),u_camera_to_center_distance:new t.Uniform1f(e,r.u_camera_to_center_distance),u_pitch:new t.Uniform1f(e,r.u_pitch),u_rotate_symbol:new t.Uniform1i(e,r.u_rotate_symbol),u_aspect_ratio:new t.Uniform1f(e,r.u_aspect_ratio),u_fade_change:new t.Uniform1f(e,r.u_fade_change),u_matrix:new t.UniformMatrix4f(e,r.u_matrix),u_label_plane_matrix:new t.UniformMatrix4f(e,r.u_label_plane_matrix),u_coord_matrix:new t.UniformMatrix4f(e,r.u_coord_matrix),u_is_text:new t.Uniform1i(e,r.u_is_text),u_pitch_with_map:new t.Uniform1i(e,r.u_pitch_with_map),u_texsize:new t.Uniform2f(e,r.u_texsize),u_texture:new t.Uniform1i(e,r.u_texture),u_gamma_scale:new t.Uniform1f(e,r.u_gamma_scale),u_device_pixel_ratio:new t.Uniform1f(e,r.u_device_pixel_ratio),u_is_halo:new t.Uniform1i(e,r.u_is_halo)}},symbolTextAndIcon:function(e,r){return{u_is_size_zoom_constant:new t.Uniform1i(e,r.u_is_size_zoom_constant),u_is_size_feature_constant:new t.Uniform1i(e,r.u_is_size_feature_constant),u_size_t:new t.Uniform1f(e,r.u_size_t),u_size:new t.Uniform1f(e,r.u_size),u_camera_to_center_distance:new t.Uniform1f(e,r.u_camera_to_center_distance),u_pitch:new t.Uniform1f(e,r.u_pitch),u_rotate_symbol:new t.Uniform1i(e,r.u_rotate_symbol),u_aspect_ratio:new t.Uniform1f(e,r.u_aspect_ratio),u_fade_change:new t.Uniform1f(e,r.u_fade_change),u_matrix:new t.UniformMatrix4f(e,r.u_matrix),u_label_plane_matrix:new t.UniformMatrix4f(e,r.u_label_plane_matrix),u_coord_matrix:new t.UniformMatrix4f(e,r.u_coord_matrix),u_is_text:new t.Uniform1i(e,r.u_is_text),u_pitch_with_map:new t.Uniform1i(e,r.u_pitch_with_map),u_texsize:new t.Uniform2f(e,r.u_texsize),u_texsize_icon:new t.Uniform2f(e,r.u_texsize_icon),u_texture:new t.Uniform1i(e,r.u_texture),u_texture_icon:new t.Uniform1i(e,r.u_texture_icon),u_gamma_scale:new t.Uniform1f(e,r.u_gamma_scale),u_device_pixel_ratio:new t.Uniform1f(e,r.u_device_pixel_ratio),u_is_halo:new t.Uniform1i(e,r.u_is_halo)}},background:function(e,r){return{u_matrix:new t.UniformMatrix4f(e,r.u_matrix),u_opacity:new t.Uniform1f(e,r.u_opacity),u_color:new t.UniformColor(e,r.u_color)}},backgroundPattern:function(e,r){return{u_matrix:new t.UniformMatrix4f(e,r.u_matrix),u_opacity:new t.Uniform1f(e,r.u_opacity),u_image:new t.Uniform1i(e,r.u_image),u_pattern_tl_a:new t.Uniform2f(e,r.u_pattern_tl_a),u_pattern_br_a:new t.Uniform2f(e,r.u_pattern_br_a),u_pattern_tl_b:new t.Uniform2f(e,r.u_pattern_tl_b),u_pattern_br_b:new t.Uniform2f(e,r.u_pattern_br_b),u_texsize:new t.Uniform2f(e,r.u_texsize),u_mix:new t.Uniform1f(e,r.u_mix),u_pattern_size_a:new t.Uniform2f(e,r.u_pattern_size_a),u_pattern_size_b:new t.Uniform2f(e,r.u_pattern_size_b),u_scale_a:new t.Uniform1f(e,r.u_scale_a),u_scale_b:new t.Uniform1f(e,r.u_scale_b),u_pixel_coord_upper:new t.Uniform2f(e,r.u_pixel_coord_upper),u_pixel_coord_lower:new t.Uniform2f(e,r.u_pixel_coord_lower),u_tile_units_to_pixels:new t.Uniform1f(e,r.u_tile_units_to_pixels)}}};function rn(e,r,n,i,a,o,s){for(var l=e.context,u=l.gl,c=e.useProgram("collisionBox"),f=[],h=0,p=0,d=0;d0){var _=t.create(),w=m;t.mul(_,y.placementInvProjMatrix,e.transform.glCoordMatrix),t.mul(_,_,y.placementViewportMatrix),f.push({circleArray:b,circleOffset:p,transform:w,invTransform:_}),p=h+=b.length/4}x&&c.draw(l,u.LINES,Mt.disabled,Et.disabled,e.colorModeForRenderPass(),Ct.disabled,Ir(m,e.transform,g),n.id,x.layoutVertexBuffer,x.indexBuffer,x.segments,null,e.transform.zoom,null,null,x.collisionVertexBuffer)}}if(s&&f.length){var T=e.useProgram("collisionCircle"),k=new t.StructArrayLayout2f1f2i16;k.resize(4*h),k._trim();for(var A=0,M=0,S=f;M=0&&(v[y.associatedIconIndex]={shiftedAnchor:S,angle:E})}else he(y.numGlyphs,p)}if(f){d.clear();for(var C=e.icon.placedSymbolArray,P=0;P0){var s=t.browser.now(),l=(s-e.timeAdded)/o,u=r?(s-r.timeAdded)/o:-1,c=n.getSource(),f=a.coveringZoomLevel({tileSize:c.tileSize,roundZoom:c.roundZoom}),h=!r||Math.abs(r.tileID.overscaledZ-f)>Math.abs(e.tileID.overscaledZ-f),p=h&&e.refreshedUponExpiration?1:t.clamp(h?l:1-u,0,1);return e.refreshedUponExpiration&&l>=1&&(e.refreshedUponExpiration=!1),r?{opacity:1,mix:1-p}:{opacity:p,mix:0}}return{opacity:1,mix:0}}var vn=new t.Color(1,0,0,1),gn=new t.Color(0,1,0,1),yn=new t.Color(0,0,1,1),mn=new t.Color(1,0,1,1),xn=new t.Color(0,1,1,1);function bn(t){var e=t.transform.padding;_n(t,t.transform.height-(e.top||0),3,vn),_n(t,e.bottom||0,3,gn),wn(t,e.left||0,3,yn),wn(t,t.transform.width-(e.right||0),3,mn);var r=t.transform.centerPoint;!function(t,e,r,n){var i=20,a=2;Tn(t,e-a/2,r-i/2,a,i,n),Tn(t,e-i/2,r-a/2,i,a,n)}(t,r.x,t.transform.height-r.y,xn)}function _n(t,e,r,n){Tn(t,0,e+r/2,t.transform.width,r,n)}function wn(t,e,r,n){Tn(t,e-r/2,0,r,t.transform.height,n)}function Tn(e,r,n,i,a,o){var s=e.context,l=s.gl;l.enable(l.SCISSOR_TEST),l.scissor(r*t.browser.devicePixelRatio,n*t.browser.devicePixelRatio,i*t.browser.devicePixelRatio,a*t.browser.devicePixelRatio),s.clear({color:o}),l.disable(l.SCISSOR_TEST)}function kn(e,r,n){var i=e.context,a=i.gl,o=n.posMatrix,s=e.useProgram("debug"),l=Mt.disabled,u=Et.disabled,c=e.colorModeForRenderPass(),f="$debug";i.activeTexture.set(a.TEXTURE0),e.emptyTexture.bind(a.LINEAR,a.CLAMP_TO_EDGE),s.draw(i,a.LINE_STRIP,l,u,c,Ct.disabled,zr(o,t.Color.red),f,e.debugBuffer,e.tileBorderIndexBuffer,e.debugSegments);var h=r.getTileByID(n.key).latestRawTileData,p=h&&h.byteLength||0,d=Math.floor(p/1024),v=r.getTile(n).tileSize,g=512/Math.min(v,512)*(n.overscaledZ/e.transform.zoom)*.5,y=n.canonical.toString();n.overscaledZ!==n.canonical.z&&(y+=" => "+n.overscaledZ),function(t,e){t.initDebugOverlayCanvas();var r=t.debugOverlayCanvas,n=t.context.gl,i=t.debugOverlayCanvas.getContext("2d");i.clearRect(0,0,r.width,r.height),i.shadowColor="white",i.shadowBlur=2,i.lineWidth=1.5,i.strokeStyle="white",i.textBaseline="top",i.font="bold 36px Open Sans, sans-serif",i.fillText(e,5,5),i.strokeText(e,5,5),t.debugOverlayTexture.update(r),t.debugOverlayTexture.bind(n.LINEAR,n.CLAMP_TO_EDGE)}(e,y+" "+d+"kb"),s.draw(i,a.TRIANGLES,l,u,Lt.alphaBlended,Ct.disabled,zr(o,t.Color.transparent,g),f,e.debugBuffer,e.quadTriangleIndexBuffer,e.debugSegments)}var An={symbol:function(e,r,n,i,a){if("translucent"===e.renderPass){var o=Et.disabled,s=e.colorModeForRenderPass();n.layout.get("text-variable-anchor")&&function(e,r,n,i,a,o,s){for(var l=r.transform,u="map"===a,c="map"===o,f=0,h=e;f256&&this.clearStencil(),r.setColorMode(Lt.disabled),r.setDepthMode(Mt.disabled);var i=this.useProgram("clippingMask");this._tileClippingMaskIDs={};for(var a=0,o=e;a256&&this.clearStencil();var t=this.nextStencilID++,e=this.context.gl;return new Et({func:e.NOTEQUAL,mask:255},t,255,e.KEEP,e.KEEP,e.REPLACE)},Mn.prototype.stencilModeForClipping=function(t){var e=this.context.gl;return new Et({func:e.EQUAL,mask:255},this._tileClippingMaskIDs[t.key],0,e.KEEP,e.KEEP,e.REPLACE)},Mn.prototype.stencilConfigForOverlap=function(t){var e,r=this.context.gl,n=t.sort((function(t,e){return e.overscaledZ-t.overscaledZ})),i=n[n.length-1].overscaledZ,a=n[0].overscaledZ-i+1;if(a>1){this.currentStencilSource=void 0,this.nextStencilID+a>256&&this.clearStencil();for(var o={},s=0;s=0;this.currentLayer--){var w=this.style._layers[i[this.currentLayer]],T=a[w.source],k=c[w.source];this._renderTileClippingMasks(w,k),this.renderLayer(this,T,w,k)}for(this.renderPass="translucent",this.currentLayer=0;this.currentLayer0?e.pop():null},Mn.prototype.isPatternMissing=function(t){if(!t)return!1;if(!t.from||!t.to)return!0;var e=this.imageManager.getPattern(t.from.toString()),r=this.imageManager.getPattern(t.to.toString());return!e||!r},Mn.prototype.useProgram=function(t,e){this.cache=this.cache||{};var r=""+t+(e?e.cacheKey:"")+(this._showOverdrawInspector?"/overdraw":"");return this.cache[r]||(this.cache[r]=new kr(this.context,wr[t],e,en[t],this._showOverdrawInspector)),this.cache[r]},Mn.prototype.setCustomLayerDefaults=function(){this.context.unbindVAO(),this.context.cullFace.setDefault(),this.context.activeTexture.setDefault(),this.context.pixelStoreUnpack.setDefault(),this.context.pixelStoreUnpackPremultiplyAlpha.setDefault(),this.context.pixelStoreUnpackFlipY.setDefault()},Mn.prototype.setBaseState=function(){var t=this.context.gl;this.context.cullFace.set(!1),this.context.viewport.set([0,0,this.width,this.height]),this.context.blendEquation.set(t.FUNC_ADD)},Mn.prototype.initDebugOverlayCanvas=function(){if(null==this.debugOverlayCanvas){this.debugOverlayCanvas=t.window.document.createElement("canvas"),this.debugOverlayCanvas.width=512,this.debugOverlayCanvas.height=512;var e=this.context.gl;this.debugOverlayTexture=new t.Texture(this.context,this.debugOverlayCanvas,e.RGBA)}},Mn.prototype.destroy=function(){this.emptyTexture.destroy(),this.debugOverlayTexture&&this.debugOverlayTexture.destroy()};var Sn=function(t,e){this.points=t,this.planes=e};Sn.fromInvProjectionMatrix=function(e,r,n){var i=Math.pow(2,n),a=[[-1,1,-1,1],[1,1,-1,1],[1,-1,-1,1],[-1,-1,-1,1],[-1,1,1,1],[1,1,1,1],[1,-1,1,1],[-1,-1,1,1]].map((function(r){return t.transformMat4([],r,e)})).map((function(e){return t.scale$1([],e,1/e[3]/r*i)})),o=[[0,1,2],[6,5,4],[0,3,7],[2,1,5],[3,2,6],[0,4,5]].map((function(e){var r=t.sub([],a[e[0]],a[e[1]]),n=t.sub([],a[e[2]],a[e[1]]),i=t.normalize([],t.cross([],r,n)),o=-t.dot(i,a[e[1]]);return i.concat(o)}));return new Sn(a,o)};var En=function(e,r){this.min=e,this.max=r,this.center=t.scale$2([],t.add([],this.min,this.max),.5)};En.prototype.quadrant=function(e){for(var r=[e%2==0,e<2],n=t.clone$2(this.min),i=t.clone$2(this.max),a=0;a=0;if(0===o)return 0;o!==r.length&&(n=!1)}if(n)return 2;for(var l=0;l<3;l++){for(var u=Number.MAX_VALUE,c=-Number.MAX_VALUE,f=0;fthis.max[l]-this.min[l])return 0}return 1};var Ln=function(t,e,r,n){if(void 0===t&&(t=0),void 0===e&&(e=0),void 0===r&&(r=0),void 0===n&&(n=0),isNaN(t)||t<0||isNaN(e)||e<0||isNaN(r)||r<0||isNaN(n)||n<0)throw new Error("Invalid value for edge-insets, top, bottom, left and right must all be numbers");this.top=t,this.bottom=e,this.left=r,this.right=n};Ln.prototype.interpolate=function(e,r,n){return null!=r.top&&null!=e.top&&(this.top=t.number(e.top,r.top,n)),null!=r.bottom&&null!=e.bottom&&(this.bottom=t.number(e.bottom,r.bottom,n)),null!=r.left&&null!=e.left&&(this.left=t.number(e.left,r.left,n)),null!=r.right&&null!=e.right&&(this.right=t.number(e.right,r.right,n)),this},Ln.prototype.getCenter=function(e,r){var n=t.clamp((this.left+e-this.right)/2,0,e),i=t.clamp((this.top+r-this.bottom)/2,0,r);return new t.Point(n,i)},Ln.prototype.equals=function(t){return this.top===t.top&&this.bottom===t.bottom&&this.left===t.left&&this.right===t.right},Ln.prototype.clone=function(){return new Ln(this.top,this.bottom,this.left,this.right)},Ln.prototype.toJSON=function(){return{top:this.top,bottom:this.bottom,left:this.left,right:this.right}};var Cn=function(e,r,n,i,a){this.tileSize=512,this.maxValidLatitude=85.051129,this._renderWorldCopies=void 0===a||a,this._minZoom=e||0,this._maxZoom=r||22,this._minPitch=null==n?0:n,this._maxPitch=null==i?60:i,this.setMaxBounds(),this.width=0,this.height=0,this._center=new t.LngLat(0,0),this.zoom=0,this.angle=0,this._fov=.6435011087932844,this._pitch=0,this._unmodified=!0,this._edgeInsets=new Ln,this._posMatrixCache={},this._alignedPosMatrixCache={}},Pn={minZoom:{configurable:!0},maxZoom:{configurable:!0},minPitch:{configurable:!0},maxPitch:{configurable:!0},renderWorldCopies:{configurable:!0},worldSize:{configurable:!0},centerOffset:{configurable:!0},size:{configurable:!0},bearing:{configurable:!0},pitch:{configurable:!0},fov:{configurable:!0},zoom:{configurable:!0},center:{configurable:!0},padding:{configurable:!0},centerPoint:{configurable:!0},unmodified:{configurable:!0},point:{configurable:!0}};Cn.prototype.clone=function(){var t=new Cn(this._minZoom,this._maxZoom,this._minPitch,this.maxPitch,this._renderWorldCopies);return t.tileSize=this.tileSize,t.latRange=this.latRange,t.width=this.width,t.height=this.height,t._center=this._center,t.zoom=this.zoom,t.angle=this.angle,t._fov=this._fov,t._pitch=this._pitch,t._unmodified=this._unmodified,t._edgeInsets=this._edgeInsets.clone(),t._calcMatrices(),t},Pn.minZoom.get=function(){return this._minZoom},Pn.minZoom.set=function(t){this._minZoom!==t&&(this._minZoom=t,this.zoom=Math.max(this.zoom,t))},Pn.maxZoom.get=function(){return this._maxZoom},Pn.maxZoom.set=function(t){this._maxZoom!==t&&(this._maxZoom=t,this.zoom=Math.min(this.zoom,t))},Pn.minPitch.get=function(){return this._minPitch},Pn.minPitch.set=function(t){this._minPitch!==t&&(this._minPitch=t,this.pitch=Math.max(this.pitch,t))},Pn.maxPitch.get=function(){return this._maxPitch},Pn.maxPitch.set=function(t){this._maxPitch!==t&&(this._maxPitch=t,this.pitch=Math.min(this.pitch,t))},Pn.renderWorldCopies.get=function(){return this._renderWorldCopies},Pn.renderWorldCopies.set=function(t){void 0===t?t=!0:null===t&&(t=!1),this._renderWorldCopies=t},Pn.worldSize.get=function(){return this.tileSize*this.scale},Pn.centerOffset.get=function(){return this.centerPoint._sub(this.size._div(2))},Pn.size.get=function(){return new t.Point(this.width,this.height)},Pn.bearing.get=function(){return-this.angle/Math.PI*180},Pn.bearing.set=function(e){var r=-t.wrap(e,-180,180)*Math.PI/180;this.angle!==r&&(this._unmodified=!1,this.angle=r,this._calcMatrices(),this.rotationMatrix=t.create$2(),t.rotate(this.rotationMatrix,this.rotationMatrix,this.angle))},Pn.pitch.get=function(){return this._pitch/Math.PI*180},Pn.pitch.set=function(e){var r=t.clamp(e,this.minPitch,this.maxPitch)/180*Math.PI;this._pitch!==r&&(this._unmodified=!1,this._pitch=r,this._calcMatrices())},Pn.fov.get=function(){return this._fov/Math.PI*180},Pn.fov.set=function(t){t=Math.max(.01,Math.min(60,t)),this._fov!==t&&(this._unmodified=!1,this._fov=t/180*Math.PI,this._calcMatrices())},Pn.zoom.get=function(){return this._zoom},Pn.zoom.set=function(t){var e=Math.min(Math.max(t,this.minZoom),this.maxZoom);this._zoom!==e&&(this._unmodified=!1,this._zoom=e,this.scale=this.zoomScale(e),this.tileZoom=Math.floor(e),this.zoomFraction=e-this.tileZoom,this._constrain(),this._calcMatrices())},Pn.center.get=function(){return this._center},Pn.center.set=function(t){t.lat===this._center.lat&&t.lng===this._center.lng||(this._unmodified=!1,this._center=t,this._constrain(),this._calcMatrices())},Pn.padding.get=function(){return this._edgeInsets.toJSON()},Pn.padding.set=function(t){this._edgeInsets.equals(t)||(this._unmodified=!1,this._edgeInsets.interpolate(this._edgeInsets,t,1),this._calcMatrices())},Pn.centerPoint.get=function(){return this._edgeInsets.getCenter(this.width,this.height)},Cn.prototype.isPaddingEqual=function(t){return this._edgeInsets.equals(t)},Cn.prototype.interpolatePadding=function(t,e,r){this._unmodified=!1,this._edgeInsets.interpolate(t,e,r),this._constrain(),this._calcMatrices()},Cn.prototype.coveringZoomLevel=function(t){var e=(t.roundZoom?Math.round:Math.floor)(this.zoom+this.scaleZoom(this.tileSize/t.tileSize));return Math.max(0,e)},Cn.prototype.getVisibleUnwrappedCoordinates=function(e){var r=[new t.UnwrappedTileID(0,e)];if(this._renderWorldCopies)for(var n=this.pointCoordinate(new t.Point(0,0)),i=this.pointCoordinate(new t.Point(this.width,0)),a=this.pointCoordinate(new t.Point(this.width,this.height)),o=this.pointCoordinate(new t.Point(0,this.height)),s=Math.floor(Math.min(n.x,i.x,a.x,o.x)),l=Math.floor(Math.max(n.x,i.x,a.x,o.x)),u=s-1;u<=l+1;u++)0!==u&&r.push(new t.UnwrappedTileID(u,e));return r},Cn.prototype.coveringTiles=function(e){var r=this.coveringZoomLevel(e),n=r;if(void 0!==e.minzoom&&re.maxzoom&&(r=e.maxzoom);var i=t.MercatorCoordinate.fromLngLat(this.center),a=Math.pow(2,r),o=[a*i.x,a*i.y,0],s=Sn.fromInvProjectionMatrix(this.invProjMatrix,this.worldSize,r),l=e.minzoom||0;this.pitch<=60&&this._edgeInsets.top<.1&&(l=r);var u=function(t){return{aabb:new En([t*a,0,0],[(t+1)*a,a,0]),zoom:0,x:0,y:0,wrap:t,fullyVisible:!1}},c=[],f=[],h=r,p=e.reparseOverscaled?n:r;if(this._renderWorldCopies)for(var d=1;d<=3;d++)c.push(u(-d)),c.push(u(d));for(c.push(u(0));c.length>0;){var v=c.pop(),g=v.x,y=v.y,m=v.fullyVisible;if(!m){var x=v.aabb.intersects(s);if(0===x)continue;m=2===x}var b=v.aabb.distanceX(o),_=v.aabb.distanceY(o),w=Math.max(Math.abs(b),Math.abs(_)),T=3+(1<T&&v.zoom>=l)f.push({tileID:new t.OverscaledTileID(v.zoom===h?p:v.zoom,v.wrap,v.zoom,g,y),distanceSq:t.sqrLen([o[0]-.5-g,o[1]-.5-y])});else for(var k=0;k<4;k++){var A=(g<<1)+k%2,M=(y<<1)+(k>>1);c.push({aabb:v.aabb.quadrant(k),zoom:v.zoom+1,x:A,y:M,wrap:v.wrap,fullyVisible:m})}}return f.sort((function(t,e){return t.distanceSq-e.distanceSq})).map((function(t){return t.tileID}))},Cn.prototype.resize=function(t,e){this.width=t,this.height=e,this.pixelsToGLUnits=[2/t,-2/e],this._constrain(),this._calcMatrices()},Pn.unmodified.get=function(){return this._unmodified},Cn.prototype.zoomScale=function(t){return Math.pow(2,t)},Cn.prototype.scaleZoom=function(t){return Math.log(t)/Math.LN2},Cn.prototype.project=function(e){var r=t.clamp(e.lat,-this.maxValidLatitude,this.maxValidLatitude);return new t.Point(t.mercatorXfromLng(e.lng)*this.worldSize,t.mercatorYfromLat(r)*this.worldSize)},Cn.prototype.unproject=function(e){return new t.MercatorCoordinate(e.x/this.worldSize,e.y/this.worldSize).toLngLat()},Pn.point.get=function(){return this.project(this.center)},Cn.prototype.setLocationAtPoint=function(e,r){var n=this.pointCoordinate(r),i=this.pointCoordinate(this.centerPoint),a=this.locationCoordinate(e),o=new t.MercatorCoordinate(a.x-(n.x-i.x),a.y-(n.y-i.y));this.center=this.coordinateLocation(o),this._renderWorldCopies&&(this.center=this.center.wrap())},Cn.prototype.locationPoint=function(t){return this.coordinatePoint(this.locationCoordinate(t))},Cn.prototype.pointLocation=function(t){return this.coordinateLocation(this.pointCoordinate(t))},Cn.prototype.locationCoordinate=function(e){return t.MercatorCoordinate.fromLngLat(e)},Cn.prototype.coordinateLocation=function(t){return t.toLngLat()},Cn.prototype.pointCoordinate=function(e){var r=[e.x,e.y,0,1],n=[e.x,e.y,1,1];t.transformMat4(r,r,this.pixelMatrixInverse),t.transformMat4(n,n,this.pixelMatrixInverse);var i=r[3],a=n[3],o=r[0]/i,s=n[0]/a,l=r[1]/i,u=n[1]/a,c=r[2]/i,f=n[2]/a,h=c===f?0:(0-c)/(f-c);return new t.MercatorCoordinate(t.number(o,s,h)/this.worldSize,t.number(l,u,h)/this.worldSize)},Cn.prototype.coordinatePoint=function(e){var r=[e.x*this.worldSize,e.y*this.worldSize,0,1];return t.transformMat4(r,r,this.pixelMatrix),new t.Point(r[0]/r[3],r[1]/r[3])},Cn.prototype.getBounds=function(){return(new t.LngLatBounds).extend(this.pointLocation(new t.Point(0,0))).extend(this.pointLocation(new t.Point(this.width,0))).extend(this.pointLocation(new t.Point(this.width,this.height))).extend(this.pointLocation(new t.Point(0,this.height)))},Cn.prototype.getMaxBounds=function(){return this.latRange&&2===this.latRange.length&&this.lngRange&&2===this.lngRange.length?new t.LngLatBounds([this.lngRange[0],this.latRange[0]],[this.lngRange[1],this.latRange[1]]):null},Cn.prototype.setMaxBounds=function(t){t?(this.lngRange=[t.getWest(),t.getEast()],this.latRange=[t.getSouth(),t.getNorth()],this._constrain()):(this.lngRange=null,this.latRange=[-this.maxValidLatitude,this.maxValidLatitude])},Cn.prototype.calculatePosMatrix=function(e,r){void 0===r&&(r=!1);var n=e.key,i=r?this._alignedPosMatrixCache:this._posMatrixCache;if(i[n])return i[n];var a=e.canonical,o=this.worldSize/this.zoomScale(a.z),s=a.x+Math.pow(2,a.z)*e.wrap,l=t.identity(new Float64Array(16));return t.translate(l,l,[s*o,a.y*o,0]),t.scale(l,l,[o/t.EXTENT,o/t.EXTENT,1]),t.multiply(l,r?this.alignedProjMatrix:this.projMatrix,l),i[n]=new Float32Array(l),i[n]},Cn.prototype.customLayerMatrix=function(){return this.mercatorMatrix.slice()},Cn.prototype._constrain=function(){if(this.center&&this.width&&this.height&&!this._constraining){this._constraining=!0;var e,r,n,i,a=-90,o=90,s=-180,l=180,u=this.size,c=this._unmodified;if(this.latRange){var f=this.latRange;a=t.mercatorYfromLat(f[1])*this.worldSize,e=(o=t.mercatorYfromLat(f[0])*this.worldSize)-ao&&(i=o-g)}if(this.lngRange){var y=p.x,m=u.x/2;y-ml&&(n=l-m)}void 0===n&&void 0===i||(this.center=this.unproject(new t.Point(void 0!==n?n:p.x,void 0!==i?i:p.y))),this._unmodified=c,this._constraining=!1}},Cn.prototype._calcMatrices=function(){if(this.height){var e=this._fov/2,r=this.centerOffset;this.cameraToCenterDistance=.5/Math.tan(e)*this.height;var n=Math.PI/2+this._pitch,i=this._fov*(.5+r.y/this.height),a=Math.sin(i)*this.cameraToCenterDistance/Math.sin(t.clamp(Math.PI-n-i,.01,Math.PI-.01)),o=this.point,s=o.x,l=o.y,u=1.01*(Math.cos(Math.PI/2-this._pitch)*a+this.cameraToCenterDistance),c=this.height/50,f=new Float64Array(16);t.perspective(f,this._fov,this.width/this.height,c,u),f[8]=2*-r.x/this.width,f[9]=2*r.y/this.height,t.scale(f,f,[1,-1,1]),t.translate(f,f,[0,0,-this.cameraToCenterDistance]),t.rotateX(f,f,this._pitch),t.rotateZ(f,f,this.angle),t.translate(f,f,[-s,-l,0]),this.mercatorMatrix=t.scale([],f,[this.worldSize,this.worldSize,this.worldSize]),t.scale(f,f,[1,1,t.mercatorZfromAltitude(1,this.center.lat)*this.worldSize,1]),this.projMatrix=f,this.invProjMatrix=t.invert([],this.projMatrix);var h=this.width%2/2,p=this.height%2/2,d=Math.cos(this.angle),v=Math.sin(this.angle),g=s-Math.round(s)+d*h+v*p,y=l-Math.round(l)+d*p+v*h,m=new Float64Array(f);if(t.translate(m,m,[g>.5?g-1:g,y>.5?y-1:y,0]),this.alignedProjMatrix=m,f=t.create(),t.scale(f,f,[this.width/2,-this.height/2,1]),t.translate(f,f,[1,-1,0]),this.labelPlaneMatrix=f,f=t.create(),t.scale(f,f,[1,-1,1]),t.translate(f,f,[-1,-1,0]),t.scale(f,f,[2/this.width,2/this.height,1]),this.glCoordMatrix=f,this.pixelMatrix=t.multiply(new Float64Array(16),this.labelPlaneMatrix,this.projMatrix),!(f=t.invert(new Float64Array(16),this.pixelMatrix)))throw new Error("failed to invert matrix");this.pixelMatrixInverse=f,this._posMatrixCache={},this._alignedPosMatrixCache={}}},Cn.prototype.maxPitchScaleFactor=function(){if(!this.pixelMatrixInverse)return 1;var e=this.pointCoordinate(new t.Point(0,0)),r=[e.x*this.worldSize,e.y*this.worldSize,0,1];return t.transformMat4(r,r,this.pixelMatrix)[3]/this.cameraToCenterDistance},Cn.prototype.getCameraPoint=function(){var e=this._pitch,r=Math.tan(e)*(this.cameraToCenterDistance||1);return this.centerPoint.add(new t.Point(0,r))},Cn.prototype.getCameraQueryGeometry=function(e){var r=this.getCameraPoint();if(1===e.length)return[e[0],r];for(var n=r.x,i=r.y,a=r.x,o=r.y,s=0,l=e;s=3&&!t.some((function(t){return isNaN(t)}))){var e=this._map.dragRotate.isEnabled()&&this._map.touchZoomRotate.isEnabled()?+(t[3]||0):this._map.getBearing();return this._map.jumpTo({center:[+t[2],+t[1]],zoom:+t[0],bearing:e,pitch:+(t[4]||0)}),!0}return!1},On.prototype._updateHashUnthrottled=function(){var e=this.getHashString();try{t.window.history.replaceState(t.window.history.state,"",e)}catch(t){}};var In={linearity:.3,easing:t.bezier(0,0,.3,1)},Dn=t.extend({deceleration:2500,maxSpeed:1400},In),zn=t.extend({deceleration:20,maxSpeed:1400},In),Rn=t.extend({deceleration:1e3,maxSpeed:360},In),Fn=t.extend({deceleration:1e3,maxSpeed:90},In),Bn=function(t){this._map=t,this.clear()};function Nn(t,e){(!t.duration||t.duration0&&r-e[0].time>160;)e.shift()},Bn.prototype._onMoveEnd=function(e){if(this._drainInertiaBuffer(),!(this._inertiaBuffer.length<2)){for(var r={zoom:0,bearing:0,pitch:0,pan:new t.Point(0,0),pinchAround:void 0,around:void 0},n=0,i=this._inertiaBuffer;n=this._clickTolerance||this._map.fire(new Un(t.type,this._map,t))},qn.prototype.dblclick=function(t){return this._firePreventable(new Un(t.type,this._map,t))},qn.prototype.mouseover=function(t){this._map.fire(new Un(t.type,this._map,t))},qn.prototype.mouseout=function(t){this._map.fire(new Un(t.type,this._map,t))},qn.prototype.touchstart=function(t){return this._firePreventable(new Vn(t.type,this._map,t))},qn.prototype.touchmove=function(t){this._map.fire(new Vn(t.type,this._map,t))},qn.prototype.touchend=function(t){this._map.fire(new Vn(t.type,this._map,t))},qn.prototype.touchcancel=function(t){this._map.fire(new Vn(t.type,this._map,t))},qn.prototype._firePreventable=function(t){if(this._map.fire(t),t.defaultPrevented)return{}},qn.prototype.isEnabled=function(){return!0},qn.prototype.isActive=function(){return!1},qn.prototype.enable=function(){},qn.prototype.disable=function(){};var Gn=function(t){this._map=t};Gn.prototype.reset=function(){this._delayContextMenu=!1,delete this._contextMenuEvent},Gn.prototype.mousemove=function(t){this._map.fire(new Un(t.type,this._map,t))},Gn.prototype.mousedown=function(){this._delayContextMenu=!0},Gn.prototype.mouseup=function(){this._delayContextMenu=!1,this._contextMenuEvent&&(this._map.fire(new Un("contextmenu",this._map,this._contextMenuEvent)),delete this._contextMenuEvent)},Gn.prototype.contextmenu=function(t){this._delayContextMenu?this._contextMenuEvent=t:this._map.fire(new Un(t.type,this._map,t)),this._map.listens("contextmenu")&&t.preventDefault()},Gn.prototype.isEnabled=function(){return!0},Gn.prototype.isActive=function(){return!1},Gn.prototype.enable=function(){},Gn.prototype.disable=function(){};var Zn=function(t,e){this._map=t,this._el=t.getCanvasContainer(),this._container=t.getContainer(),this._clickTolerance=e.clickTolerance||1};function Yn(t,e){for(var r={},n=0;nthis.numTouches)&&(this.aborted=!0),this.aborted||(void 0===this.startTime&&(this.startTime=e.timeStamp),n.length===this.numTouches&&(this.centroid=function(e){for(var r=new t.Point(0,0),n=0,i=e;n30)&&(this.aborted=!0)}}},Wn.prototype.touchend=function(t,e,r){if((!this.centroid||t.timeStamp-this.startTime>500)&&(this.aborted=!0),0===r.length){var n=!this.aborted&&this.centroid;if(this.reset(),n)return n}};var Xn=function(t){this.singleTap=new Wn(t),this.numTaps=t.numTaps,this.reset()};Xn.prototype.reset=function(){this.lastTime=1/0,delete this.lastTap,this.count=0,this.singleTap.reset()},Xn.prototype.touchstart=function(t,e,r){this.singleTap.touchstart(t,e,r)},Xn.prototype.touchmove=function(t,e,r){this.singleTap.touchmove(t,e,r)},Xn.prototype.touchend=function(t,e,r){var n=this.singleTap.touchend(t,e,r);if(n){var i=t.timeStamp-this.lastTime<500,a=!this.lastTap||this.lastTap.dist(n)<30;if(i&&a||this.reset(),this.count++,this.lastTime=t.timeStamp,this.lastTap=n,this.count===this.numTaps)return this.reset(),n}};var Jn=function(){this._zoomIn=new Xn({numTouches:1,numTaps:2}),this._zoomOut=new Xn({numTouches:2,numTaps:1}),this.reset()};Jn.prototype.reset=function(){this._active=!1,this._zoomIn.reset(),this._zoomOut.reset()},Jn.prototype.touchstart=function(t,e,r){this._zoomIn.touchstart(t,e,r),this._zoomOut.touchstart(t,e,r)},Jn.prototype.touchmove=function(t,e,r){this._zoomIn.touchmove(t,e,r),this._zoomOut.touchmove(t,e,r)},Jn.prototype.touchend=function(t,e,r){var n=this,i=this._zoomIn.touchend(t,e,r),a=this._zoomOut.touchend(t,e,r);return i?(this._active=!0,t.preventDefault(),setTimeout((function(){return n.reset()}),0),{cameraAnimation:function(e){return e.easeTo({duration:300,zoom:e.getZoom()+1,around:e.unproject(i)},{originalEvent:t})}}):a?(this._active=!0,t.preventDefault(),setTimeout((function(){return n.reset()}),0),{cameraAnimation:function(e){return e.easeTo({duration:300,zoom:e.getZoom()-1,around:e.unproject(a)},{originalEvent:t})}}):void 0},Jn.prototype.touchcancel=function(){this.reset()},Jn.prototype.enable=function(){this._enabled=!0},Jn.prototype.disable=function(){this._enabled=!1,this.reset()},Jn.prototype.isEnabled=function(){return this._enabled},Jn.prototype.isActive=function(){return this._active};var Kn=function(t){this.reset(),this._clickTolerance=t.clickTolerance||1};Kn.prototype.reset=function(){this._active=!1,this._moved=!1,delete this._lastPoint,delete this._eventButton},Kn.prototype._correctButton=function(t,e){return!1},Kn.prototype._move=function(t,e){return{}},Kn.prototype.mousedown=function(t,e){if(!this._lastPoint){var n=r.mouseButton(t);this._correctButton(t,n)&&(this._lastPoint=e,this._eventButton=n)}},Kn.prototype.mousemoveWindow=function(t,e){var r=this._lastPoint;if(r&&(t.preventDefault(),this._moved||!(e.dist(r)0&&(this._active=!0);var i=Yn(n,r),a=new t.Point(0,0),o=new t.Point(0,0),s=0;for(var l in i){var u=i[l],c=this._touches[l];c&&(a._add(u),o._add(u.sub(c)),s++,i[l]=u)}if(this._touches=i,!(sMath.abs(t.x)}var ui=function(t){function e(){t.apply(this,arguments)}return t&&(e.__proto__=t),e.prototype=Object.create(t&&t.prototype),e.prototype.constructor=e,e.prototype.reset=function(){t.prototype.reset.call(this),this._valid=void 0,delete this._firstMove,delete this._lastPoints},e.prototype._start=function(t){this._lastPoints=t,li(t[0].sub(t[1]))&&(this._valid=!1)},e.prototype._move=function(t,e,r){var n=t[0].sub(this._lastPoints[0]),i=t[1].sub(this._lastPoints[1]);if(this._valid=this.gestureBeginsVertically(n,i,r.timeStamp),this._valid)return this._lastPoints=t,this._active=!0,{pitchDelta:(n.y+i.y)/2*-.5}},e.prototype.gestureBeginsVertically=function(t,e,r){if(void 0!==this._valid)return this._valid;var n=t.mag()>=2,i=e.mag()>=2;if(n||i){if(!n||!i)return void 0===this._firstMove&&(this._firstMove=r),r-this._firstMove<100&&void 0;var a=t.y>0==e.y>0;return li(t)&&li(e)&&a}},e}(ri),ci={panStep:100,bearingStep:15,pitchStep:10},fi=function(){var t=ci;this._panStep=t.panStep,this._bearingStep=t.bearingStep,this._pitchStep=t.pitchStep};function hi(t){return t*(2-t)}fi.prototype.reset=function(){this._active=!1},fi.prototype.keydown=function(t){var e=this;if(!(t.altKey||t.ctrlKey||t.metaKey)){var r=0,n=0,i=0,a=0,o=0;switch(t.keyCode){case 61:case 107:case 171:case 187:r=1;break;case 189:case 109:case 173:r=-1;break;case 37:t.shiftKey?n=-1:(t.preventDefault(),a=-1);break;case 39:t.shiftKey?n=1:(t.preventDefault(),a=1);break;case 38:t.shiftKey?i=1:(t.preventDefault(),o=-1);break;case 40:t.shiftKey?i=-1:(t.preventDefault(),o=1);break;default:return}return{cameraAnimation:function(s){var l=s.getZoom();s.easeTo({duration:300,easeId:"keyboardHandler",easing:hi,zoom:r?Math.round(l)+r*(t.shiftKey?2:1):l,bearing:s.getBearing()+n*e._bearingStep,pitch:s.getPitch()+i*e._pitchStep,offset:[-a*e._panStep,-o*e._panStep],center:s.getCenter()},{originalEvent:t})}}}},fi.prototype.enable=function(){this._enabled=!0},fi.prototype.disable=function(){this._enabled=!1,this.reset()},fi.prototype.isEnabled=function(){return this._enabled},fi.prototype.isActive=function(){return this._active};var pi=4.000244140625,di=function(e,r){this._map=e,this._el=e.getCanvasContainer(),this._handler=r,this._delta=0,this._defaultZoomRate=.01,this._wheelZoomRate=.0022222222222222222,t.bindAll(["_onWheel","_onTimeout","_onScrollFrame","_onScrollFinished"],this)};di.prototype.setZoomRate=function(t){this._defaultZoomRate=t},di.prototype.setWheelZoomRate=function(t){this._wheelZoomRate=t},di.prototype.isEnabled=function(){return!!this._enabled},di.prototype.isActive=function(){return!!this._active||void 0!==this._finishTimeout},di.prototype.isZooming=function(){return!!this._zooming},di.prototype.enable=function(t){this.isEnabled()||(this._enabled=!0,this._aroundCenter=t&&"center"===t.around)},di.prototype.disable=function(){this.isEnabled()&&(this._enabled=!1)},di.prototype.wheel=function(e){if(this.isEnabled()){var r=e.deltaMode===t.window.WheelEvent.DOM_DELTA_LINE?40*e.deltaY:e.deltaY,n=t.browser.now(),i=n-(this._lastWheelEventTime||0);this._lastWheelEventTime=n,0!==r&&r%pi==0?this._type="wheel":0!==r&&Math.abs(r)<4?this._type="trackpad":i>400?(this._type=null,this._lastValue=r,this._timeout=setTimeout(this._onTimeout,40,e)):this._type||(this._type=Math.abs(i*r)<200?"trackpad":"wheel",this._timeout&&(clearTimeout(this._timeout),this._timeout=null,r+=this._lastValue)),e.shiftKey&&r&&(r/=4),this._type&&(this._lastWheelEvent=e,this._delta-=r,this._active||this._start(e)),e.preventDefault()}},di.prototype._onTimeout=function(t){this._type="wheel",this._delta-=this._lastValue,this._active||this._start(t)},di.prototype._start=function(e){if(this._delta){this._frameId&&(this._frameId=null),this._active=!0,this.isZooming()||(this._zooming=!0),this._finishTimeout&&(clearTimeout(this._finishTimeout),delete this._finishTimeout);var n=r.mousePos(this._el,e);this._around=t.LngLat.convert(this._aroundCenter?this._map.getCenter():this._map.unproject(n)),this._aroundPoint=this._map.transform.locationPoint(this._around),this._frameId||(this._frameId=!0,this._handler._triggerRenderFrame())}},di.prototype.renderFrame=function(){return this._onScrollFrame()},di.prototype._onScrollFrame=function(){var e=this;if(this._frameId&&(this._frameId=null,this.isActive())){var r=this._map.transform;if(0!==this._delta){var n="wheel"===this._type&&Math.abs(this._delta)>pi?this._wheelZoomRate:this._defaultZoomRate,i=2/(1+Math.exp(-Math.abs(this._delta*n)));this._delta<0&&0!==i&&(i=1/i);var a="number"==typeof this._targetZoom?r.zoomScale(this._targetZoom):r.scale;this._targetZoom=Math.min(r.maxZoom,Math.max(r.minZoom,r.scaleZoom(a*i))),"wheel"===this._type&&(this._startZoom=r.zoom,this._easing=this._smoothOutEasing(200)),this._delta=0}var o,s="number"==typeof this._targetZoom?this._targetZoom:r.zoom,l=this._startZoom,u=this._easing,c=!1;if("wheel"===this._type&&l&&u){var f=Math.min((t.browser.now()-this._lastWheelEventTime)/200,1),h=u(f);o=t.number(l,s,h),f<1?this._frameId||(this._frameId=!0):c=!0}else o=s,c=!0;return this._active=!0,c&&(this._active=!1,this._finishTimeout=setTimeout((function(){e._zooming=!1,e._handler._triggerRenderFrame(),delete e._targetZoom,delete e._finishTimeout}),200)),{noInertia:!0,needsRenderFrame:!c,zoomDelta:o-r.zoom,around:this._aroundPoint,originalEvent:this._lastWheelEvent}}},di.prototype._smoothOutEasing=function(e){var r=t.ease;if(this._prevEase){var n=this._prevEase,i=(t.browser.now()-n.start)/n.duration,a=n.easing(i+.01)-n.easing(i),o=.27/Math.sqrt(a*a+1e-4)*.01,s=Math.sqrt(.0729-o*o);r=t.bezier(o,s,.25,1)}return this._prevEase={start:t.browser.now(),duration:e,easing:r},r},di.prototype.reset=function(){this._active=!1};var vi=function(t,e){this._clickZoom=t,this._tapZoom=e};vi.prototype.enable=function(){this._clickZoom.enable(),this._tapZoom.enable()},vi.prototype.disable=function(){this._clickZoom.disable(),this._tapZoom.disable()},vi.prototype.isEnabled=function(){return this._clickZoom.isEnabled()&&this._tapZoom.isEnabled()},vi.prototype.isActive=function(){return this._clickZoom.isActive()||this._tapZoom.isActive()};var gi=function(){this.reset()};gi.prototype.reset=function(){this._active=!1},gi.prototype.dblclick=function(t,e){return t.preventDefault(),{cameraAnimation:function(r){r.easeTo({duration:300,zoom:r.getZoom()+(t.shiftKey?-1:1),around:r.unproject(e)},{originalEvent:t})}}},gi.prototype.enable=function(){this._enabled=!0},gi.prototype.disable=function(){this._enabled=!1,this.reset()},gi.prototype.isEnabled=function(){return this._enabled},gi.prototype.isActive=function(){return this._active};var yi=function(){this._tap=new Xn({numTouches:1,numTaps:1}),this.reset()};yi.prototype.reset=function(){this._active=!1,delete this._swipePoint,delete this._swipeTouch,delete this._tapTime,this._tap.reset()},yi.prototype.touchstart=function(t,e,r){this._swipePoint||(this._tapTime&&t.timeStamp-this._tapTime>500&&this.reset(),this._tapTime?r.length>0&&(this._swipePoint=e[0],this._swipeTouch=r[0].identifier):this._tap.touchstart(t,e,r))},yi.prototype.touchmove=function(t,e,r){if(this._tapTime){if(this._swipePoint){if(r[0].identifier!==this._swipeTouch)return;var n=e[0],i=n.y-this._swipePoint.y;return this._swipePoint=n,t.preventDefault(),this._active=!0,{zoomDelta:i/128}}}else this._tap.touchmove(t,e,r)},yi.prototype.touchend=function(t,e,r){this._tapTime?this._swipePoint&&0===r.length&&this.reset():this._tap.touchend(t,e,r)&&(this._tapTime=t.timeStamp)},yi.prototype.touchcancel=function(){this.reset()},yi.prototype.enable=function(){this._enabled=!0},yi.prototype.disable=function(){this._enabled=!1,this.reset()},yi.prototype.isEnabled=function(){return this._enabled},yi.prototype.isActive=function(){return this._active};var mi=function(t,e,r){this._el=t,this._mousePan=e,this._touchPan=r};mi.prototype.enable=function(t){this._inertiaOptions=t||{},this._mousePan.enable(),this._touchPan.enable(),this._el.classList.add("mapboxgl-touch-drag-pan")},mi.prototype.disable=function(){this._mousePan.disable(),this._touchPan.disable(),this._el.classList.remove("mapboxgl-touch-drag-pan")},mi.prototype.isEnabled=function(){return this._mousePan.isEnabled()&&this._touchPan.isEnabled()},mi.prototype.isActive=function(){return this._mousePan.isActive()||this._touchPan.isActive()};var xi=function(t,e,r){this._pitchWithRotate=t.pitchWithRotate,this._mouseRotate=e,this._mousePitch=r};xi.prototype.enable=function(){this._mouseRotate.enable(),this._pitchWithRotate&&this._mousePitch.enable()},xi.prototype.disable=function(){this._mouseRotate.disable(),this._mousePitch.disable()},xi.prototype.isEnabled=function(){return this._mouseRotate.isEnabled()&&(!this._pitchWithRotate||this._mousePitch.isEnabled())},xi.prototype.isActive=function(){return this._mouseRotate.isActive()||this._mousePitch.isActive()};var bi=function(t,e,r,n){this._el=t,this._touchZoom=e,this._touchRotate=r,this._tapDragZoom=n,this._rotationDisabled=!1,this._enabled=!0};bi.prototype.enable=function(t){this._touchZoom.enable(t),this._rotationDisabled||this._touchRotate.enable(t),this._tapDragZoom.enable(),this._el.classList.add("mapboxgl-touch-zoom-rotate")},bi.prototype.disable=function(){this._touchZoom.disable(),this._touchRotate.disable(),this._tapDragZoom.disable(),this._el.classList.remove("mapboxgl-touch-zoom-rotate")},bi.prototype.isEnabled=function(){return this._touchZoom.isEnabled()&&(this._rotationDisabled||this._touchRotate.isEnabled())&&this._tapDragZoom.isEnabled()},bi.prototype.isActive=function(){return this._touchZoom.isActive()||this._touchRotate.isActive()||this._tapDragZoom.isActive()},bi.prototype.disableRotation=function(){this._rotationDisabled=!0,this._touchRotate.disable()},bi.prototype.enableRotation=function(){this._rotationDisabled=!1,this._touchZoom.isEnabled()&&this._touchRotate.enable()};var _i=function(t){return t.zoom||t.drag||t.pitch||t.rotate},wi=function(t){function e(){t.apply(this,arguments)}return t&&(e.__proto__=t),e.prototype=Object.create(t&&t.prototype),e.prototype.constructor=e,e}(t.Event);function Ti(t){return t.panDelta&&t.panDelta.mag()||t.zoomDelta||t.bearingDelta||t.pitchDelta}var ki=function(e,n){this._map=e,this._el=this._map.getCanvasContainer(),this._handlers=[],this._handlersById={},this._changes=[],this._inertia=new Bn(e),this._bearingSnap=n.bearingSnap,this._previousActiveHandlers={},this._eventsInProgress={},this._addDefaultHandlers(n),t.bindAll(["handleEvent","handleWindowEvent"],this);var i=this._el;this._listeners=[[i,"touchstart",{passive:!1}],[i,"touchmove",{passive:!1}],[i,"touchend",void 0],[i,"touchcancel",void 0],[i,"mousedown",void 0],[i,"mousemove",void 0],[i,"mouseup",void 0],[t.window.document,"mousemove",{capture:!0}],[t.window.document,"mouseup",void 0],[i,"mouseover",void 0],[i,"mouseout",void 0],[i,"dblclick",void 0],[i,"click",void 0],[i,"keydown",{capture:!1}],[i,"keyup",void 0],[i,"wheel",{passive:!1}],[i,"contextmenu",void 0],[t.window,"blur",void 0]];for(var a=0,o=this._listeners;aa?Math.min(2,_):Math.max(.5,_),w=Math.pow(g,1-e),T=i.unproject(x.add(b.mult(e*w)).mult(v));i.setLocationAtPoint(i.renderWorldCopies?T.wrap():T,d)}n._fireMoveEvents(r)}),(function(t){n._afterEase(r,t)}),e),this},r.prototype._prepareEase=function(e,r,n){void 0===n&&(n={}),this._moving=!0,r||n.moving||this.fire(new t.Event("movestart",e)),this._zooming&&!n.zooming&&this.fire(new t.Event("zoomstart",e)),this._rotating&&!n.rotating&&this.fire(new t.Event("rotatestart",e)),this._pitching&&!n.pitching&&this.fire(new t.Event("pitchstart",e))},r.prototype._fireMoveEvents=function(e){this.fire(new t.Event("move",e)),this._zooming&&this.fire(new t.Event("zoom",e)),this._rotating&&this.fire(new t.Event("rotate",e)),this._pitching&&this.fire(new t.Event("pitch",e))},r.prototype._afterEase=function(e,r){if(!this._easeId||!r||this._easeId!==r){delete this._easeId;var n=this._zooming,i=this._rotating,a=this._pitching;this._moving=!1,this._zooming=!1,this._rotating=!1,this._pitching=!1,this._padding=!1,n&&this.fire(new t.Event("zoomend",e)),i&&this.fire(new t.Event("rotateend",e)),a&&this.fire(new t.Event("pitchend",e)),this.fire(new t.Event("moveend",e))}},r.prototype.flyTo=function(e,r){var n=this;if(!e.essential&&t.browser.prefersReducedMotion){var i=t.pick(e,["center","zoom","bearing","pitch","around"]);return this.jumpTo(i,r)}this.stop(),e=t.extend({offset:[0,0],speed:1.2,curve:1.42,easing:t.ease},e);var a=this.transform,o=this.getZoom(),s=this.getBearing(),l=this.getPitch(),u=this.getPadding(),c="zoom"in e?t.clamp(+e.zoom,a.minZoom,a.maxZoom):o,f="bearing"in e?this._normalizeBearing(e.bearing,s):s,h="pitch"in e?+e.pitch:l,p="padding"in e?e.padding:a.padding,d=a.zoomScale(c-o),v=t.Point.convert(e.offset),g=a.centerPoint.add(v),y=a.pointLocation(g),m=t.LngLat.convert(e.center||y);this._normalizeCenter(m);var x=a.project(y),b=a.project(m).sub(x),_=e.curve,w=Math.max(a.width,a.height),T=w/d,k=b.mag();if("minZoom"in e){var A=t.clamp(Math.min(e.minZoom,o,c),a.minZoom,a.maxZoom),M=w/a.zoomScale(A-o);_=Math.sqrt(M/k*2)}var S=_*_;function E(t){var e=(T*T-w*w+(t?-1:1)*S*S*k*k)/(2*(t?T:w)*S*k);return Math.log(Math.sqrt(e*e+1)-e)}function L(t){return(Math.exp(t)-Math.exp(-t))/2}function C(t){return(Math.exp(t)+Math.exp(-t))/2}var P=E(0),O=function(t){return C(P)/C(P+_*t)},I=function(t){return w*((C(P)*(L(e=P+_*t)/C(e))-L(P))/S)/k;var e},D=(E(1)-P)/_;if(Math.abs(k)<1e-6||!isFinite(D)){if(Math.abs(w-T)<1e-6)return this.easeTo(e,r);var z=Te.maxDuration&&(e.duration=0),this._zooming=!0,this._rotating=s!==f,this._pitching=h!==l,this._padding=!a.isPaddingEqual(p),this._prepareEase(r,!1),this._ease((function(e){var i=e*D,d=1/O(i);a.zoom=1===e?c:o+a.scaleZoom(d),n._rotating&&(a.bearing=t.number(s,f,e)),n._pitching&&(a.pitch=t.number(l,h,e)),n._padding&&(a.interpolatePadding(u,p,e),g=a.centerPoint.add(v));var y=1===e?m:a.unproject(x.add(b.mult(I(i))).mult(d));a.setLocationAtPoint(a.renderWorldCopies?y.wrap():y,g),n._fireMoveEvents(r)}),(function(){return n._afterEase(r)}),e),this},r.prototype.isEasing=function(){return!!this._easeFrameId},r.prototype.stop=function(){return this._stop()},r.prototype._stop=function(t,e){if(this._easeFrameId&&(this._cancelRenderFrame(this._easeFrameId),delete this._easeFrameId,delete this._onEaseFrame),this._onEaseEnd){var r=this._onEaseEnd;delete this._onEaseEnd,r.call(this,e)}if(!t){var n=this.handlers;n&&n.stop()}return this},r.prototype._ease=function(e,r,n){!1===n.animate||0===n.duration?(e(1),r()):(this._easeStart=t.browser.now(),this._easeOptions=n,this._onEaseFrame=e,this._onEaseEnd=r,this._easeFrameId=this._requestRenderFrame(this._renderFrameCallback))},r.prototype._renderFrameCallback=function(){var e=Math.min((t.browser.now()-this._easeStart)/this._easeOptions.duration,1);this._onEaseFrame(this._easeOptions.easing(e)),e<1?this._easeFrameId=this._requestRenderFrame(this._renderFrameCallback):this.stop()},r.prototype._normalizeBearing=function(e,r){e=t.wrap(e,-180,180);var n=Math.abs(e-r);return Math.abs(e-360-r)180?-360:r<-180?360:0}},r}(t.Evented),Mi=function(e){void 0===e&&(e={}),this.options=e,t.bindAll(["_updateEditLink","_updateData","_updateCompact"],this)};Mi.prototype.getDefaultPosition=function(){return"bottom-right"},Mi.prototype.onAdd=function(t){var e=this.options&&this.options.compact;return this._map=t,this._container=r.create("div","mapboxgl-ctrl mapboxgl-ctrl-attrib"),this._innerContainer=r.create("div","mapboxgl-ctrl-attrib-inner",this._container),e&&this._container.classList.add("mapboxgl-compact"),this._updateAttributions(),this._updateEditLink(),this._map.on("styledata",this._updateData),this._map.on("sourcedata",this._updateData),this._map.on("moveend",this._updateEditLink),void 0===e&&(this._map.on("resize",this._updateCompact),this._updateCompact()),this._container},Mi.prototype.onRemove=function(){r.remove(this._container),this._map.off("styledata",this._updateData),this._map.off("sourcedata",this._updateData),this._map.off("moveend",this._updateEditLink),this._map.off("resize",this._updateCompact),this._map=void 0,this._attribHTML=void 0},Mi.prototype._updateEditLink=function(){var e=this._editLink;e||(e=this._editLink=this._container.querySelector(".mapbox-improve-map"));var r=[{key:"owner",value:this.styleOwner},{key:"id",value:this.styleId},{key:"access_token",value:this._map._requestManager._customAccessToken||t.config.ACCESS_TOKEN}];if(e){var n=r.reduce((function(t,e,n){return e.value&&(t+=e.key+"="+e.value+(n=0)return!1;return!0}))).join(" | ");o!==this._attribHTML&&(this._attribHTML=o,t.length?(this._innerContainer.innerHTML=o,this._container.classList.remove("mapboxgl-attrib-empty")):this._container.classList.add("mapboxgl-attrib-empty"),this._editLink=null)}},Mi.prototype._updateCompact=function(){this._map.getCanvasContainer().offsetWidth<=640?this._container.classList.add("mapboxgl-compact"):this._container.classList.remove("mapboxgl-compact")};var Si=function(){t.bindAll(["_updateLogo"],this),t.bindAll(["_updateCompact"],this)};Si.prototype.onAdd=function(t){this._map=t,this._container=r.create("div","mapboxgl-ctrl");var e=r.create("a","mapboxgl-ctrl-logo");return e.target="_blank",e.rel="noopener nofollow",e.href="https://www.mapbox.com/",e.setAttribute("aria-label",this._map._getUIString("LogoControl.Title")),e.setAttribute("rel","noopener nofollow"),this._container.appendChild(e),this._container.style.display="none",this._map.on("sourcedata",this._updateLogo),this._updateLogo(),this._map.on("resize",this._updateCompact),this._updateCompact(),this._container},Si.prototype.onRemove=function(){r.remove(this._container),this._map.off("sourcedata",this._updateLogo),this._map.off("resize",this._updateCompact)},Si.prototype.getDefaultPosition=function(){return"bottom-left"},Si.prototype._updateLogo=function(t){t&&"metadata"!==t.sourceDataType||(this._container.style.display=this._logoRequired()?"block":"none")},Si.prototype._logoRequired=function(){if(this._map.style){var t=this._map.style.sourceCaches;for(var e in t)if(t[e].getSource().mapbox_logo)return!0;return!1}},Si.prototype._updateCompact=function(){var t=this._container.children;if(t.length){var e=t[0];this._map.getCanvasContainer().offsetWidth<250?e.classList.add("mapboxgl-compact"):e.classList.remove("mapboxgl-compact")}};var Ei=function(){this._queue=[],this._id=0,this._cleared=!1,this._currentlyRunning=!1};Ei.prototype.add=function(t){var e=++this._id;return this._queue.push({callback:t,id:e,cancelled:!1}),e},Ei.prototype.remove=function(t){for(var e=this._currentlyRunning,r=0,n=e?this._queue.concat(e):this._queue;re.maxZoom)throw new Error("maxZoom must be greater than or equal to minZoom");if(null!=e.minPitch&&null!=e.maxPitch&&e.minPitch>e.maxPitch)throw new Error("maxPitch must be greater than or equal to minPitch");if(null!=e.minPitch&&e.minPitch<0)throw new Error("minPitch must be greater than or equal to 0");if(null!=e.maxPitch&&e.maxPitch>Ii)throw new Error("maxPitch must be less than or equal to 60");var i=new Cn(e.minZoom,e.maxZoom,e.minPitch,e.maxPitch,e.renderWorldCopies);if(n.call(this,i,e),this._interactive=e.interactive,this._maxTileCacheSize=e.maxTileCacheSize,this._failIfMajorPerformanceCaveat=e.failIfMajorPerformanceCaveat,this._preserveDrawingBuffer=e.preserveDrawingBuffer,this._antialias=e.antialias,this._trackResize=e.trackResize,this._bearingSnap=e.bearingSnap,this._refreshExpiredTiles=e.refreshExpiredTiles,this._fadeDuration=e.fadeDuration,this._crossSourceCollisions=e.crossSourceCollisions,this._crossFadingFactor=1,this._collectResourceTiming=e.collectResourceTiming,this._renderTaskQueue=new Ei,this._controls=[],this._mapId=t.uniqueId(),this._locale=t.extend({},Li,e.locale),this._requestManager=new t.RequestManager(e.transformRequest,e.accessToken),"string"==typeof e.container){if(this._container=t.window.document.getElementById(e.container),!this._container)throw new Error("Container '"+e.container+"' not found.")}else{if(!(e.container instanceof Pi))throw new Error("Invalid type: 'container' must be a String or HTMLElement.");this._container=e.container}if(e.maxBounds&&this.setMaxBounds(e.maxBounds),t.bindAll(["_onWindowOnline","_onWindowResize","_contextLost","_contextRestored"],this),this._setupContainer(),this._setupPainter(),void 0===this.painter)throw new Error("Failed to initialize WebGL.");this.on("move",(function(){return r._update(!1)})),this.on("moveend",(function(){return r._update(!1)})),this.on("zoom",(function(){return r._update(!0)})),void 0!==t.window&&(t.window.addEventListener("online",this._onWindowOnline,!1),t.window.addEventListener("resize",this._onWindowResize,!1)),this.handlers=new ki(this,e);var a="string"==typeof e.hash&&e.hash||void 0;this._hash=e.hash&&new On(a).addTo(this),this._hash&&this._hash._onHashChange()||(this.jumpTo({center:e.center,zoom:e.zoom,bearing:e.bearing,pitch:e.pitch}),e.bounds&&(this.resize(),this.fitBounds(e.bounds,t.extend({},e.fitBoundsOptions,{duration:0})))),this.resize(),this._localIdeographFontFamily=e.localIdeographFontFamily,e.style&&this.setStyle(e.style,{localIdeographFontFamily:e.localIdeographFontFamily}),e.attributionControl&&this.addControl(new Mi({customAttribution:e.customAttribution})),this.addControl(new Si,e.logoPosition),this.on("style.load",(function(){r.transform.unmodified&&r.jumpTo(r.style.stylesheet)})),this.on("data",(function(e){r._update("style"===e.dataType),r.fire(new t.Event(e.dataType+"data",e))})),this.on("dataloading",(function(e){r.fire(new t.Event(e.dataType+"dataloading",e))}))}n&&(i.__proto__=n),i.prototype=Object.create(n&&n.prototype),i.prototype.constructor=i;var a={showTileBoundaries:{configurable:!0},showPadding:{configurable:!0},showCollisionBoxes:{configurable:!0},showOverdrawInspector:{configurable:!0},repaint:{configurable:!0},vertices:{configurable:!0},version:{configurable:!0}};return i.prototype._getMapId=function(){return this._mapId},i.prototype.addControl=function(e,r){if(void 0===r&&e.getDefaultPosition&&(r=e.getDefaultPosition()),void 0===r&&(r="top-right"),!e||!e.onAdd)return this.fire(new t.ErrorEvent(new Error("Invalid argument to map.addControl(). Argument must be a control with onAdd and onRemove methods.")));var n=e.onAdd(this);this._controls.push(e);var i=this._controlPositions[r];return-1!==r.indexOf("bottom")?i.insertBefore(n,i.firstChild):i.appendChild(n),this},i.prototype.removeControl=function(e){if(!e||!e.onRemove)return this.fire(new t.ErrorEvent(new Error("Invalid argument to map.removeControl(). Argument must be a control with onAdd and onRemove methods.")));var r=this._controls.indexOf(e);return r>-1&&this._controls.splice(r,1),e.onRemove(this),this},i.prototype.resize=function(e){var r=this._containerDimensions(),n=r[0],i=r[1];this._resizeCanvas(n,i),this.transform.resize(n,i),this.painter.resize(n,i);var a=!this._moving;return a&&(this.stop(),this.fire(new t.Event("movestart",e)).fire(new t.Event("move",e))),this.fire(new t.Event("resize",e)),a&&this.fire(new t.Event("moveend",e)),this},i.prototype.getBounds=function(){return this.transform.getBounds()},i.prototype.getMaxBounds=function(){return this.transform.getMaxBounds()},i.prototype.setMaxBounds=function(e){return this.transform.setMaxBounds(t.LngLatBounds.convert(e)),this._update()},i.prototype.setMinZoom=function(t){if((t=null==t?-2:t)>=-2&&t<=this.transform.maxZoom)return this.transform.minZoom=t,this._update(),this.getZoom()=this.transform.minZoom)return this.transform.maxZoom=t,this._update(),this.getZoom()>t&&this.setZoom(t),this;throw new Error("maxZoom must be greater than the current minZoom")},i.prototype.getMaxZoom=function(){return this.transform.maxZoom},i.prototype.setMinPitch=function(t){if((t=null==t?0:t)<0)throw new Error("minPitch must be greater than or equal to 0");if(t>=0&&t<=this.transform.maxPitch)return this.transform.minPitch=t,this._update(),this.getPitch()Ii)throw new Error("maxPitch must be less than or equal to 60");if(t>=this.transform.minPitch)return this.transform.maxPitch=t,this._update(),this.getPitch()>t&&this.setPitch(t),this;throw new Error("maxPitch must be greater than the current minPitch")},i.prototype.getMaxPitch=function(){return this.transform.maxPitch},i.prototype.getRenderWorldCopies=function(){return this.transform.renderWorldCopies},i.prototype.setRenderWorldCopies=function(t){return this.transform.renderWorldCopies=t,this._update()},i.prototype.project=function(e){return this.transform.locationPoint(t.LngLat.convert(e))},i.prototype.unproject=function(e){return this.transform.pointLocation(t.Point.convert(e))},i.prototype.isMoving=function(){return this._moving||this.handlers.isMoving()},i.prototype.isZooming=function(){return this._zooming||this.handlers.isZooming()},i.prototype.isRotating=function(){return this._rotating||this.handlers.isRotating()},i.prototype._createDelegatedListener=function(t,e,r){var n,i=this;if("mouseenter"===t||"mouseover"===t){var a=!1;return{layer:e,listener:r,delegates:{mousemove:function(n){var o=i.getLayer(e)?i.queryRenderedFeatures(n.point,{layers:[e]}):[];o.length?a||(a=!0,r.call(i,new Un(t,i,n.originalEvent,{features:o}))):a=!1},mouseout:function(){a=!1}}}}if("mouseleave"===t||"mouseout"===t){var o=!1;return{layer:e,listener:r,delegates:{mousemove:function(n){(i.getLayer(e)?i.queryRenderedFeatures(n.point,{layers:[e]}):[]).length?o=!0:o&&(o=!1,r.call(i,new Un(t,i,n.originalEvent)))},mouseout:function(e){o&&(o=!1,r.call(i,new Un(t,i,e.originalEvent)))}}}}return{layer:e,listener:r,delegates:(n={},n[t]=function(t){var n=i.getLayer(e)?i.queryRenderedFeatures(t.point,{layers:[e]}):[];n.length&&(t.features=n,r.call(i,t),delete t.features)},n)}},i.prototype.on=function(t,e,r){if(void 0===r)return n.prototype.on.call(this,t,e);var i=this._createDelegatedListener(t,e,r);for(var a in this._delegatedListeners=this._delegatedListeners||{},this._delegatedListeners[t]=this._delegatedListeners[t]||[],this._delegatedListeners[t].push(i),i.delegates)this.on(a,i.delegates[a]);return this},i.prototype.once=function(t,e,r){if(void 0===r)return n.prototype.once.call(this,t,e);var i=this._createDelegatedListener(t,e,r);for(var a in i.delegates)this.once(a,i.delegates[a]);return this},i.prototype.off=function(t,e,r){var i=this;if(void 0===r)return n.prototype.off.call(this,t,e);return this._delegatedListeners&&this._delegatedListeners[t]&&function(n){for(var a=n[t],o=0;o180;){var s=n.locationPoint(e);if(s.x>=0&&s.y>=0&&s.x<=n.width&&s.y<=n.height)break;e.lng>n.center.lng?e.lng-=360:e.lng+=360}return e}Ni.prototype.down=function(t,e){this.mouseRotate.mousedown(t,e),this.mousePitch&&this.mousePitch.mousedown(t,e),r.disableDrag()},Ni.prototype.move=function(t,e){var r=this.map,n=this.mouseRotate.mousemoveWindow(t,e);if(n&&n.bearingDelta&&r.setBearing(r.getBearing()+n.bearingDelta),this.mousePitch){var i=this.mousePitch.mousemoveWindow(t,e);i&&i.pitchDelta&&r.setPitch(r.getPitch()+i.pitchDelta)}},Ni.prototype.off=function(){var t=this.element;r.removeEventListener(t,"mousedown",this.mousedown),r.removeEventListener(t,"touchstart",this.touchstart,{passive:!1}),r.removeEventListener(t,"touchmove",this.touchmove),r.removeEventListener(t,"touchend",this.touchend),r.removeEventListener(t,"touchcancel",this.reset),this.offTemp()},Ni.prototype.offTemp=function(){r.enableDrag(),r.removeEventListener(t.window,"mousemove",this.mousemove),r.removeEventListener(t.window,"mouseup",this.mouseup)},Ni.prototype.mousedown=function(e){this.down(t.extend({},e,{ctrlKey:!0,preventDefault:function(){return e.preventDefault()}}),r.mousePos(this.element,e)),r.addEventListener(t.window,"mousemove",this.mousemove),r.addEventListener(t.window,"mouseup",this.mouseup)},Ni.prototype.mousemove=function(t){this.move(t,r.mousePos(this.element,t))},Ni.prototype.mouseup=function(t){this.mouseRotate.mouseupWindow(t),this.mousePitch&&this.mousePitch.mouseupWindow(t),this.offTemp()},Ni.prototype.touchstart=function(t){1!==t.targetTouches.length?this.reset():(this._startPos=this._lastPos=r.touchPos(this.element,t.targetTouches)[0],this.down({type:"mousedown",button:0,ctrlKey:!0,preventDefault:function(){return t.preventDefault()}},this._startPos))},Ni.prototype.touchmove=function(t){1!==t.targetTouches.length?this.reset():(this._lastPos=r.touchPos(this.element,t.targetTouches)[0],this.move({preventDefault:function(){return t.preventDefault()}},this._lastPos))},Ni.prototype.touchend=function(t){0===t.targetTouches.length&&this._startPos&&this._lastPos&&this._startPos.dist(this._lastPos)e.getEast()||r.latitudee.getNorth())},n.prototype._setErrorState=function(){switch(this._watchState){case"WAITING_ACTIVE":this._watchState="ACTIVE_ERROR",this._geolocateButton.classList.remove("mapboxgl-ctrl-geolocate-active"),this._geolocateButton.classList.add("mapboxgl-ctrl-geolocate-active-error");break;case"ACTIVE_LOCK":this._watchState="ACTIVE_ERROR",this._geolocateButton.classList.remove("mapboxgl-ctrl-geolocate-active"),this._geolocateButton.classList.add("mapboxgl-ctrl-geolocate-active-error"),this._geolocateButton.classList.add("mapboxgl-ctrl-geolocate-waiting");break;case"BACKGROUND":this._watchState="BACKGROUND_ERROR",this._geolocateButton.classList.remove("mapboxgl-ctrl-geolocate-background"),this._geolocateButton.classList.add("mapboxgl-ctrl-geolocate-background-error"),this._geolocateButton.classList.add("mapboxgl-ctrl-geolocate-waiting")}},n.prototype._onSuccess=function(e){if(this._map){if(this._isOutOfMapMaxBounds(e))return this._setErrorState(),this.fire(new t.Event("outofmaxbounds",e)),this._updateMarker(),void this._finish();if(this.options.trackUserLocation)switch(this._lastKnownPosition=e,this._watchState){case"WAITING_ACTIVE":case"ACTIVE_LOCK":case"ACTIVE_ERROR":this._watchState="ACTIVE_LOCK",this._geolocateButton.classList.remove("mapboxgl-ctrl-geolocate-waiting"),this._geolocateButton.classList.remove("mapboxgl-ctrl-geolocate-active-error"),this._geolocateButton.classList.add("mapboxgl-ctrl-geolocate-active");break;case"BACKGROUND":case"BACKGROUND_ERROR":this._watchState="BACKGROUND",this._geolocateButton.classList.remove("mapboxgl-ctrl-geolocate-waiting"),this._geolocateButton.classList.remove("mapboxgl-ctrl-geolocate-background-error"),this._geolocateButton.classList.add("mapboxgl-ctrl-geolocate-background")}this.options.showUserLocation&&"OFF"!==this._watchState&&this._updateMarker(e),this.options.trackUserLocation&&"ACTIVE_LOCK"!==this._watchState||this._updateCamera(e),this.options.showUserLocation&&this._dotElement.classList.remove("mapboxgl-user-location-dot-stale"),this.fire(new t.Event("geolocate",e)),this._finish()}},n.prototype._updateCamera=function(e){var r=new t.LngLat(e.coords.longitude,e.coords.latitude),n=e.coords.accuracy,i=this._map.getBearing(),a=t.extend({bearing:i},this.options.fitBoundsOptions);this._map.fitBounds(r.toBounds(n),a,{geolocateSource:!0})},n.prototype._updateMarker=function(e){if(e){var r=new t.LngLat(e.coords.longitude,e.coords.latitude);this._accuracyCircleMarker.setLngLat(r).addTo(this._map),this._userLocationDotMarker.setLngLat(r).addTo(this._map),this._accuracy=e.coords.accuracy,this.options.showUserLocation&&this.options.showAccuracyCircle&&this._updateCircleRadius()}else this._userLocationDotMarker.remove(),this._accuracyCircleMarker.remove()},n.prototype._updateCircleRadius=function(){var t=this._map._container.clientHeight/2,e=this._map.unproject([0,t]),r=this._map.unproject([1,t]),n=e.distanceTo(r),i=Math.ceil(2*this._accuracy/n);this._circleElement.style.width=i+"px",this._circleElement.style.height=i+"px"},n.prototype._onZoom=function(){this.options.showUserLocation&&this.options.showAccuracyCircle&&this._updateCircleRadius()},n.prototype._onError=function(e){if(this._map){if(this.options.trackUserLocation)if(1===e.code){this._watchState="OFF",this._geolocateButton.classList.remove("mapboxgl-ctrl-geolocate-waiting"),this._geolocateButton.classList.remove("mapboxgl-ctrl-geolocate-active"),this._geolocateButton.classList.remove("mapboxgl-ctrl-geolocate-active-error"),this._geolocateButton.classList.remove("mapboxgl-ctrl-geolocate-background"),this._geolocateButton.classList.remove("mapboxgl-ctrl-geolocate-background-error"),this._geolocateButton.disabled=!0;var r=this._map._getUIString("GeolocateControl.LocationNotAvailable");this._geolocateButton.title=r,this._geolocateButton.setAttribute("aria-label",r),void 0!==this._geolocationWatchID&&this._clearWatch()}else{if(3===e.code&&Yi)return;this._setErrorState()}"OFF"!==this._watchState&&this.options.showUserLocation&&this._dotElement.classList.add("mapboxgl-user-location-dot-stale"),this.fire(new t.Event("error",e)),this._finish()}},n.prototype._finish=function(){this._timeoutId&&clearTimeout(this._timeoutId),this._timeoutId=void 0},n.prototype._setupUI=function(e){var n=this;if(this._container.addEventListener("contextmenu",(function(t){return t.preventDefault()})),this._geolocateButton=r.create("button","mapboxgl-ctrl-geolocate",this._container),r.create("span","mapboxgl-ctrl-icon",this._geolocateButton).setAttribute("aria-hidden",!0),this._geolocateButton.type="button",!1===e){t.warnOnce("Geolocation support is not available so the GeolocateControl will be disabled.");var i=this._map._getUIString("GeolocateControl.LocationNotAvailable");this._geolocateButton.disabled=!0,this._geolocateButton.title=i,this._geolocateButton.setAttribute("aria-label",i)}else{var a=this._map._getUIString("GeolocateControl.FindMyLocation");this._geolocateButton.title=a,this._geolocateButton.setAttribute("aria-label",a)}this.options.trackUserLocation&&(this._geolocateButton.setAttribute("aria-pressed","false"),this._watchState="OFF"),this.options.showUserLocation&&(this._dotElement=r.create("div","mapboxgl-user-location-dot"),this._userLocationDotMarker=new qi(this._dotElement),this._circleElement=r.create("div","mapboxgl-user-location-accuracy-circle"),this._accuracyCircleMarker=new qi({element:this._circleElement,pitchAlignment:"map"}),this.options.trackUserLocation&&(this._watchState="OFF"),this._map.on("zoom",this._onZoom)),this._geolocateButton.addEventListener("click",this.trigger.bind(this)),this._setup=!0,this.options.trackUserLocation&&this._map.on("movestart",(function(e){var r=e.originalEvent&&"resize"===e.originalEvent.type;e.geolocateSource||"ACTIVE_LOCK"!==n._watchState||r||(n._watchState="BACKGROUND",n._geolocateButton.classList.add("mapboxgl-ctrl-geolocate-background"),n._geolocateButton.classList.remove("mapboxgl-ctrl-geolocate-active"),n.fire(new t.Event("trackuserlocationend")))}))},n.prototype.trigger=function(){if(!this._setup)return t.warnOnce("Geolocate control triggered before added to a map"),!1;if(this.options.trackUserLocation){switch(this._watchState){case"OFF":this._watchState="WAITING_ACTIVE",this.fire(new t.Event("trackuserlocationstart"));break;case"WAITING_ACTIVE":case"ACTIVE_LOCK":case"ACTIVE_ERROR":case"BACKGROUND_ERROR":Zi--,Yi=!1,this._watchState="OFF",this._geolocateButton.classList.remove("mapboxgl-ctrl-geolocate-waiting"),this._geolocateButton.classList.remove("mapboxgl-ctrl-geolocate-active"),this._geolocateButton.classList.remove("mapboxgl-ctrl-geolocate-active-error"),this._geolocateButton.classList.remove("mapboxgl-ctrl-geolocate-background"),this._geolocateButton.classList.remove("mapboxgl-ctrl-geolocate-background-error"),this.fire(new t.Event("trackuserlocationend"));break;case"BACKGROUND":this._watchState="ACTIVE_LOCK",this._geolocateButton.classList.remove("mapboxgl-ctrl-geolocate-background"),this._lastKnownPosition&&this._updateCamera(this._lastKnownPosition),this.fire(new t.Event("trackuserlocationstart"))}switch(this._watchState){case"WAITING_ACTIVE":this._geolocateButton.classList.add("mapboxgl-ctrl-geolocate-waiting"),this._geolocateButton.classList.add("mapboxgl-ctrl-geolocate-active");break;case"ACTIVE_LOCK":this._geolocateButton.classList.add("mapboxgl-ctrl-geolocate-active");break;case"ACTIVE_ERROR":this._geolocateButton.classList.add("mapboxgl-ctrl-geolocate-waiting"),this._geolocateButton.classList.add("mapboxgl-ctrl-geolocate-active-error");break;case"BACKGROUND":this._geolocateButton.classList.add("mapboxgl-ctrl-geolocate-background");break;case"BACKGROUND_ERROR":this._geolocateButton.classList.add("mapboxgl-ctrl-geolocate-waiting"),this._geolocateButton.classList.add("mapboxgl-ctrl-geolocate-background-error")}if("OFF"===this._watchState&&void 0!==this._geolocationWatchID)this._clearWatch();else if(void 0===this._geolocationWatchID){var e;this._geolocateButton.classList.add("mapboxgl-ctrl-geolocate-waiting"),this._geolocateButton.setAttribute("aria-pressed","true"),++Zi>1?(e={maximumAge:6e5,timeout:0},Yi=!0):(e=this.options.positionOptions,Yi=!1),this._geolocationWatchID=t.window.navigator.geolocation.watchPosition(this._onSuccess,this._onError,e)}}else t.window.navigator.geolocation.getCurrentPosition(this._onSuccess,this._onError,this.options.positionOptions),this._timeoutId=setTimeout(this._finish,1e4);return!0},n.prototype._clearWatch=function(){t.window.navigator.geolocation.clearWatch(this._geolocationWatchID),this._geolocationWatchID=void 0,this._geolocateButton.classList.remove("mapboxgl-ctrl-geolocate-waiting"),this._geolocateButton.setAttribute("aria-pressed","false"),this.options.showUserLocation&&this._updateMarker(null)},n}(t.Evented),Xi={maxWidth:100,unit:"metric"},Ji=function(e){this.options=t.extend({},Xi,e),t.bindAll(["_onMove","setUnit"],this)};function Ki(t,e,r){var n=r&&r.maxWidth||100,i=t._container.clientHeight/2,a=t.unproject([0,i]),o=t.unproject([n,i]),s=a.distanceTo(o);if(r&&"imperial"===r.unit){var l=3.2808*s;l>5280?$i(e,n,l/5280,t._getUIString("ScaleControl.Miles")):$i(e,n,l,t._getUIString("ScaleControl.Feet"))}else r&&"nautical"===r.unit?$i(e,n,s/1852,t._getUIString("ScaleControl.NauticalMiles")):s>=1e3?$i(e,n,s/1e3,t._getUIString("ScaleControl.Kilometers")):$i(e,n,s,t._getUIString("ScaleControl.Meters"))}function $i(t,e,r,n){var i,a,o,s=(i=r,(a=Math.pow(10,(""+Math.floor(i)).length-1))*((o=i/a)>=10?10:o>=5?5:o>=3?3:o>=2?2:o>=1?1:function(t){var e=Math.pow(10,Math.ceil(-Math.log(t)/Math.LN10));return Math.round(t*e)/e}(o))),l=s/r;t.style.width=e*l+"px",t.innerHTML=s+" "+n}Ji.prototype.getDefaultPosition=function(){return"bottom-left"},Ji.prototype._onMove=function(){Ki(this._map,this._container,this.options)},Ji.prototype.onAdd=function(t){return this._map=t,this._container=r.create("div","mapboxgl-ctrl 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this._map=e,this._container||(this._container=this._map.getContainer()),this._controlContainer=r.create("div","mapboxgl-ctrl mapboxgl-ctrl-group"),this._checkFullscreenSupport()?this._setupUI():(this._controlContainer.style.display="none",t.warnOnce("This device does not support fullscreen mode.")),this._controlContainer},Qi.prototype.onRemove=function(){r.remove(this._controlContainer),this._map=null,t.window.document.removeEventListener(this._fullscreenchange,this._changeIcon)},Qi.prototype._checkFullscreenSupport=function(){return!!(t.window.document.fullscreenEnabled||t.window.document.mozFullScreenEnabled||t.window.document.msFullscreenEnabled||t.window.document.webkitFullscreenEnabled)},Qi.prototype._setupUI=function(){var e=this._fullscreenButton=r.create("button","mapboxgl-ctrl-fullscreen",this._controlContainer);r.create("span","mapboxgl-ctrl-icon",e).setAttribute("aria-hidden",!0),e.type="button",this._updateTitle(),this._fullscreenButton.addEventListener("click",this._onClickFullscreen),t.window.document.addEventListener(this._fullscreenchange,this._changeIcon)},Qi.prototype._updateTitle=function(){var t=this._getTitle();this._fullscreenButton.setAttribute("aria-label",t),this._fullscreenButton.title=t},Qi.prototype._getTitle=function(){return this._map._getUIString(this._isFullscreen()?"FullscreenControl.Exit":"FullscreenControl.Enter")},Qi.prototype._isFullscreen=function(){return this._fullscreen},Qi.prototype._changeIcon=function(){(t.window.document.fullscreenElement||t.window.document.mozFullScreenElement||t.window.document.webkitFullscreenElement||t.window.document.msFullscreenElement)===this._container!==this._fullscreen&&(this._fullscreen=!this._fullscreen,this._fullscreenButton.classList.toggle("mapboxgl-ctrl-shrink"),this._fullscreenButton.classList.toggle("mapboxgl-ctrl-fullscreen"),this._updateTitle())},Qi.prototype._onClickFullscreen=function(){this._isFullscreen()?t.window.document.exitFullscreen?t.window.document.exitFullscreen():t.window.document.mozCancelFullScreen?t.window.document.mozCancelFullScreen():t.window.document.msExitFullscreen?t.window.document.msExitFullscreen():t.window.document.webkitCancelFullScreen&&t.window.document.webkitCancelFullScreen():this._container.requestFullscreen?this._container.requestFullscreen():this._container.mozRequestFullScreen?this._container.mozRequestFullScreen():this._container.msRequestFullscreen?this._container.msRequestFullscreen():this._container.webkitRequestFullscreen&&this._container.webkitRequestFullscreen()};var ta={closeButton:!0,closeOnClick:!0,className:"",maxWidth:"240px"},ea=function(e){function n(r){e.call(this),this.options=t.extend(Object.create(ta),r),t.bindAll(["_update","_onClose","remove","_onMouseMove","_onMouseUp","_onDrag"],this)}return e&&(n.__proto__=e),n.prototype=Object.create(e&&e.prototype),n.prototype.constructor=n,n.prototype.addTo=function(e){return this._map&&this.remove(),this._map=e,this.options.closeOnClick&&this._map.on("click",this._onClose),this.options.closeOnMove&&this._map.on("move",this._onClose),this._map.on("remove",this.remove),this._update(),this._trackPointer?(this._map.on("mousemove",this._onMouseMove),this._map.on("mouseup",this._onMouseUp),this._container&&this._container.classList.add("mapboxgl-popup-track-pointer"),this._map._canvasContainer.classList.add("mapboxgl-track-pointer")):this._map.on("move",this._update),this.fire(new t.Event("open")),this},n.prototype.isOpen=function(){return!!this._map},n.prototype.remove=function(){return 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this._trackPointer=!0,this._pos=null,this._update(),this._map&&(this._map.off("move",this._update),this._map.on("mousemove",this._onMouseMove),this._map.on("drag",this._onDrag),this._container&&this._container.classList.add("mapboxgl-popup-track-pointer"),this._map._canvasContainer.classList.add("mapboxgl-track-pointer")),this},n.prototype.getElement=function(){return this._container},n.prototype.setText=function(e){return this.setDOMContent(t.window.document.createTextNode(e))},n.prototype.setHTML=function(e){var r,n=t.window.document.createDocumentFragment(),i=t.window.document.createElement("body");for(i.innerHTML=e;r=i.firstChild;)n.appendChild(r);return this.setDOMContent(n)},n.prototype.getMaxWidth=function(){return this._container&&this._container.style.maxWidth},n.prototype.setMaxWidth=function(t){return this.options.maxWidth=t,this._update(),this},n.prototype.setDOMContent=function(t){return this._createContent(),this._content.appendChild(t),this._update(),this},n.prototype.addClassName=function(t){this._container&&this._container.classList.add(t)},n.prototype.removeClassName=function(t){this._container&&this._container.classList.remove(t)},n.prototype.toggleClassName=function(t){if(this._container)return this._container.classList.toggle(t)},n.prototype._createContent=function(){this._content&&r.remove(this._content),this._content=r.create("div","mapboxgl-popup-content",this._container),this.options.closeButton&&(this._closeButton=r.create("button","mapboxgl-popup-close-button",this._content),this._closeButton.type="button",this._closeButton.setAttribute("aria-label","Close 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r=Math.round(Math.sqrt(.5*Math.pow(e,2)));return{center:new t.Point(0,0),top:new t.Point(0,e),"top-left":new t.Point(r,r),"top-right":new t.Point(-r,r),bottom:new t.Point(0,-e),"bottom-left":new t.Point(r,-r),"bottom-right":new t.Point(-r,-r),left:new t.Point(e,0),right:new t.Point(-e,0)}}if(e instanceof t.Point||Array.isArray(e)){var n=t.Point.convert(e);return{center:n,top:n,"top-left":n,"top-right":n,bottom:n,"bottom-left":n,"bottom-right":n,left:n,right:n}}return{center:t.Point.convert(e.center||[0,0]),top:t.Point.convert(e.top||[0,0]),"top-left":t.Point.convert(e["top-left"]||[0,0]),"top-right":t.Point.convert(e["top-right"]||[0,0]),bottom:t.Point.convert(e.bottom||[0,0]),"bottom-left":t.Point.convert(e["bottom-left"]||[0,0]),"bottom-right":t.Point.convert(e["bottom-right"]||[0,0]),left:t.Point.convert(e.left||[0,0]),right:t.Point.convert(e.right||[0,0])}}return ra(new t.Point(0,0))}var 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n=r(56131);function i(){this.regionalOptions=[],this.regionalOptions[""]={invalidCalendar:"Calendar {0} not found",invalidDate:"Invalid {0} date",invalidMonth:"Invalid {0} month",invalidYear:"Invalid {0} year",differentCalendars:"Cannot mix {0} and {1} dates"},this.local=this.regionalOptions[""],this.calendars={},this._localCals={}}function a(t,e,r,n){if(this._calendar=t,this._year=e,this._month=r,this._day=n,0===this._calendar._validateLevel&&!this._calendar.isValid(this._year,this._month,this._day))throw(u.local.invalidDate||u.regionalOptions[""].invalidDate).replace(/\{0\}/,this._calendar.local.name)}function o(t,e){return"000000".substring(0,e-(t=""+t).length)+t}function s(){this.shortYearCutoff="+10"}function l(t){this.local=this.regionalOptions[t]||this.regionalOptions[""]}n(i.prototype,{instance:function(t,e){t=(t||"gregorian").toLowerCase(),e=e||"";var r=this._localCals[t+"-"+e];if(!r&&this.calendars[t]&&(r=new 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0===arguments.length?this._day:this.set(t,"d")},date:function(t,e,r){if(!this._calendar.isValid(t,e,r))throw(u.local.invalidDate||u.regionalOptions[""].invalidDate).replace(/\{0\}/,this._calendar.local.name);return this._year=t,this._month=e,this._day=r,this},leapYear:function(){return this._calendar.leapYear(this)},epoch:function(){return this._calendar.epoch(this)},formatYear:function(){return this._calendar.formatYear(this)},monthOfYear:function(){return this._calendar.monthOfYear(this)},weekOfYear:function(){return this._calendar.weekOfYear(this)},daysInYear:function(){return this._calendar.daysInYear(this)},dayOfYear:function(){return this._calendar.dayOfYear(this)},daysInMonth:function(){return this._calendar.daysInMonth(this)},dayOfWeek:function(){return this._calendar.dayOfWeek(this)},weekDay:function(){return this._calendar.weekDay(this)},extraInfo:function(){return this._calendar.extraInfo(this)},add:function(t,e){return this._calendar.add(this,t,e)},set:function(t,e){return this._calendar.set(this,t,e)},compareTo:function(t){if(this._calendar.name!==t._calendar.name)throw(u.local.differentCalendars||u.regionalOptions[""].differentCalendars).replace(/\{0\}/,this._calendar.local.name).replace(/\{1\}/,t._calendar.local.name);var e=this._year!==t._year?this._year-t._year:this._month!==t._month?this.monthOfYear()-t.monthOfYear():this._day-t._day;return 0===e?0:e<0?-1:1},calendar:function(){return this._calendar},toJD:function(){return this._calendar.toJD(this)},fromJD:function(t){return this._calendar.fromJD(t)},toJSDate:function(){return this._calendar.toJSDate(this)},fromJSDate:function(t){return this._calendar.fromJSDate(t)},toString:function(){return(this.year()<0?"-":"")+o(Math.abs(this.year()),4)+"-"+o(this.month(),2)+"-"+o(this.day(),2)}}),n(s.prototype,{_validateLevel:0,newDate:function(t,e,r){return null==t?this.today():(t.year&&(this._validate(t,e,r,u.local.invalidDate||u.regionalOptions[""].invalidDate),r=t.day(),e=t.month(),t=t.year()),new a(this,t,e,r))},today:function(){return this.fromJSDate(new Date)},epoch:function(t){return this._validate(t,this.minMonth,this.minDay,u.local.invalidYear||u.regionalOptions[""].invalidYear).year()<0?this.local.epochs[0]:this.local.epochs[1]},formatYear:function(t){var e=this._validate(t,this.minMonth,this.minDay,u.local.invalidYear||u.regionalOptions[""].invalidYear);return(e.year()<0?"-":"")+o(Math.abs(e.year()),4)},monthsInYear:function(t){return this._validate(t,this.minMonth,this.minDay,u.local.invalidYear||u.regionalOptions[""].invalidYear),12},monthOfYear:function(t,e){var r=this._validate(t,e,this.minDay,u.local.invalidMonth||u.regionalOptions[""].invalidMonth);return(r.month()+this.monthsInYear(r)-this.firstMonth)%this.monthsInYear(r)+this.minMonth},fromMonthOfYear:function(t,e){var r=(e+this.firstMonth-2*this.minMonth)%this.monthsInYear(t)+this.minMonth;return 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Array(i),o=new Array(i),s=new Array(i);for(r=0;r=1?(r=1,e-1):Math.floor(r*e),i=t[n],a=t[n+1],o=n>0?t[n-1]:2*i-a,s=na&&(i=e.slice(a,i),s[o]?s[o]+=i:s[++o]=i),(r=r[0])===(n=n[0])?s[o]?s[o]+=n:s[++o]=n:(s[++o]=null,l.push({i:o,x:q(r,n)})),a=W.lastIndex;return a "general/item_title",:locals=>{:item=>@model,:title_postfix=>" - Copasi #{t('model')} Simulation"} %> <% blob = (File.read(@display_model.content_blobs.first.filepath)).html_safe %> - - <%= open_with_copasi_js_button @display_model %> <%= open_with_copasi_ui_button @display_model %>
    + diff --git a/lib/seek/copasi/simulator.rb b/lib/seek/copasi/simulator.rb index 070ae70641..f2e0c49342 100644 --- a/lib/seek/copasi/simulator.rb +++ b/lib/seek/copasi/simulator.rb @@ -4,7 +4,7 @@ module Simulator extend ActiveSupport::Concern included do - before_action :find_display_asset_for_copasi, only: [:copasi_simulate] + before_action :find_display_asset_for_copasi, :find_model_file, only: [:copasi_simulate] end def copasi_simulate @@ -13,12 +13,40 @@ def copasi_simulate render 'copasi_simulate' end - def select_copasi_content_blob + def find_model_file + + @blob = nil + + content_blob = @display_model.content_blobs.first + + if content_blob.file_exists? + @blob = (File.read(content_blob.file)).html_safe + else + blob_url = content_blob.url + begin + handler = ContentBlob.remote_content_handler_for(blob_url) + data = handler.fetch + @blob = (File.read(data)).html_safe + true + rescue Seek::DownloadHandling::BadResponseCodeException => e + flash.now[:error] = "URL could not be accessed: #{e.message}" + false + rescue StandardError => e + flash.now[:error] = 'There is a problem to load the model file.' + false + end + end + + if @blob.nil? + flash.now[:error] = 'There is a problem to load the model file.' + end + end def find_display_asset_for_copasi find_display_asset Model.find_by_id(params[:id]) end + end end end From a2c309c28bd7e51f55af2bb94a4cb6e11b958af7 Mon Sep 17 00:00:00 2001 From: whomingbird Date: Thu, 20 Jun 2024 21:39:44 +0200 Subject: [PATCH 104/548] Load the first COPASI-compatible item when multiple items are associated with a model. --- lib/seek/copasi/simulator.rb | 7 ++++++- lib/seek/models/model_type_handling.rb | 4 ++++ 2 files changed, 10 insertions(+), 1 deletion(-) diff --git a/lib/seek/copasi/simulator.rb b/lib/seek/copasi/simulator.rb index f2e0c49342..1f01a6f301 100644 --- a/lib/seek/copasi/simulator.rb +++ b/lib/seek/copasi/simulator.rb @@ -17,7 +17,7 @@ def find_model_file @blob = nil - content_blob = @display_model.content_blobs.first + content_blob = select_copasi_content_blob if content_blob.file_exists? @blob = (File.read(content_blob.file)).html_safe @@ -40,7 +40,12 @@ def find_model_file if @blob.nil? flash.now[:error] = 'There is a problem to load the model file.' end + end + def select_copasi_content_blob + blob = @display_model.copasi_supported_content_blobs.first + raise 'Unable to find file to support Copasi Online' unless blob + blob end def find_display_asset_for_copasi diff --git a/lib/seek/models/model_type_handling.rb b/lib/seek/models/model_type_handling.rb index 155073bf0d..d18a58ccde 100644 --- a/lib/seek/models/model_type_handling.rb +++ b/lib/seek/models/model_type_handling.rb @@ -30,6 +30,10 @@ def jws_supported_content_blobs(model = self) model.content_blobs.select { |cb| cb.is_jws_dat? || cb.is_sbml? } end + def copasi_supported_content_blobs(model = self) + model.content_blobs.select { |cb| cb.is_copasi? || cb.is_sbml? } + end + def is_jws_supported?(model = self) !model.content_blobs.detect { |cb| cb.is_jws_dat? || cb.is_sbml? }.nil? end From ace41da62208677596a8da168074c94168cb9967 Mon Sep 17 00:00:00 2001 From: whomingbird Date: Fri, 21 Jun 2024 12:44:01 +0200 Subject: [PATCH 105/548] bug fix: Load the first COPASI-compatible item to CopasiUI (the desk application) when multiple items are associated with a model. --- app/helpers/assets_helper.rb | 7 ++++--- app/views/models/copasi_simulate.html.erb | 2 +- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/app/helpers/assets_helper.rb b/app/helpers/assets_helper.rb index 6fef246a95..899b5294ae 100644 --- a/app/helpers/assets_helper.rb +++ b/app/helpers/assets_helper.rb @@ -214,7 +214,7 @@ def download_or_link_button(asset, download_path, link_url, _human_name = nil, o end end - def open_with_copasi_js_button (asset) + def open_with_copasi_js_button tooltip_text = "Simulate model in the browser with javascript library" button_link_to 'Simulate Online', 'copasi', '#', class: '', onclick: 'simulate()', disabled: @blob.nil?, 'data-tooltip' => tooltip(tooltip_text) @@ -223,8 +223,9 @@ def open_with_copasi_js_button (asset) def open_with_copasi_ui_button (asset) - files = asset.content_blobs - download_path = polymorphic_path([files.first.asset, files.first], action: :download, code: params[:code]) + file = asset.copasi_supported_content_blobs.first + download_path = polymorphic_path([file.asset, file], action: :download, code: params[:code]) + copasi_download_path = "copasi://process?downloadUrl=http://"+request.host_with_port+download_path+"&activate=Time%20Course&createPlot=Concentrations%2C%20Volumes%2C%20and%20Global%20Quantity%20Values&runTask=Time-Course" tooltip_text_copasi_button = "Simulate the publicly accessible model in your local installed Copasi. " diff --git a/app/views/models/copasi_simulate.html.erb b/app/views/models/copasi_simulate.html.erb index a7771548d2..af7c026485 100644 --- a/app/views/models/copasi_simulate.html.erb +++ b/app/views/models/copasi_simulate.html.erb @@ -108,7 +108,7 @@ - <%= open_with_copasi_js_button @display_model %> + <%= open_with_copasi_js_button %> <%= open_with_copasi_ui_button @display_model %> From a37cac077b8b86d27c0e27e514d77741b83b8855 Mon Sep 17 00:00:00 2001 From: whomingbird Date: Fri, 21 Jun 2024 13:11:10 +0200 Subject: [PATCH 106/548] make sure a non-public model can be loaded to Copasi with a temporary access link. --- app/views/models/_buttons.html.erb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/app/views/models/_buttons.html.erb b/app/views/models/_buttons.html.erb index 27e3fdf4d7..892fa39dd5 100644 --- a/app/views/models/_buttons.html.erb +++ b/app/views/models/_buttons.html.erb @@ -1,5 +1,5 @@ <% if show_copasi_button? %> - <%= button_link_to("Simulate #{t('model')} on Copasi", 'copasi', copasi_simulate_model_path(:model => @model, :version => @display_model.version),:method=>:post) %> + <%= button_link_to("Simulate #{t('model')} on Copasi", 'copasi', copasi_simulate_model_path(:model => @model, :version => @display_model.version, :code => params[:code] ),:method=>:post) %> <% end %> <% if show_jws_simulate? %> From 4b847531a0811c61100de874994e98d217ace807 Mon Sep 17 00:00:00 2001 From: whomingbird Date: Fri, 21 Jun 2024 16:07:01 +0200 Subject: [PATCH 107/548] Show the "Simulate Model on Copasi" button on the model page if the user has the right to download the asset. --- app/helpers/models_helper.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/app/helpers/models_helper.rb b/app/helpers/models_helper.rb index 997cf9ac3a..2d66fad0d0 100644 --- a/app/helpers/models_helper.rb +++ b/app/helpers/models_helper.rb @@ -40,6 +40,6 @@ def jws_online_logo end def show_copasi_button? - Seek::Config.copasi_enabled && (@display_model.policy.access_type == Policy::ALL_USERS) && @display_model.is_copasi_supported? + Seek::Config.copasi_enabled && @display_model.is_copasi_supported? && can_download_asset?(@model, params[:code]) end end From f88e99ecc37e38db52ae96cbebce28c5e3f6b65f Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Wed, 26 Jun 2024 09:35:43 +0200 Subject: [PATCH 108/548] Add function to propagate the assay stream's permission to the child assays. --- app/controllers/assays_controller.rb | 25 +++++++++++++++++++++++-- 1 file changed, 23 insertions(+), 2 deletions(-) diff --git a/app/controllers/assays_controller.rb b/app/controllers/assays_controller.rb index 4aa210b8b5..e2ae7d747a 100644 --- a/app/controllers/assays_controller.rb +++ b/app/controllers/assays_controller.rb @@ -19,6 +19,8 @@ class AssaysController < ApplicationController # => Rearrange positions after_action :rearrange_assay_positions_at_destroy, only: :destroy + before_action :propagate_permissions_to_children, only: :manage_update + include Seek::Publishing::PublishingCommon include Seek::IsaGraphExtensions @@ -160,6 +162,26 @@ def show private + def propagate_permissions_to_children + return unless params[:propagate_permissions] + + # flash[:error] = 'You do not have the necessary permissions to propagate permissions to children' + + errors = [] + @assay.child_assays.map do |assay| + unless assay.can_manage? + msg = "
  • You do not have the necessary permissions to propagate permissions to #{t('assay').downcase} [#{assay.id}]: '#{assay.title}'
    • " + errors.append(msg) + next + end + + assay.update(assay_params) + update_sharing_policies assay + end + # Add an error message to the flash + flash[:error] = "
      #{errors.join('')}
    ".html_safe unless errors.empty? + end + def delete_linked_sample_types return unless @assay.is_isa_json_compliant? return if @assay.sample_type.nil? @@ -191,8 +213,7 @@ def assay_params { placeholders_attributes: %i[asset_id direction relationship_type_id] }, { publication_ids: [] }, { extended_metadata_attributes: determine_extended_metadata_keys }, - { discussion_links_attributes:[:id, :url, :label, :_destroy] } - ).tap do |assay_params| + { discussion_links_attributes: %i[id url label _destroy] }).tap do |assay_params| assay_params[:document_ids].select! { |id| Document.find_by_id(id).try(:can_view?) } if assay_params.key?(:document_ids) assay_params[:sop_ids].select! { |id| Sop.find_by_id(id).try(:can_view?) } if assay_params.key?(:sop_ids) assay_params[:model_ids].select! { |id| Model.find_by_id(id).try(:can_view?) } if assay_params.key?(:model_ids) From c8b37c32ae9b44c3632767da50b6f42c81856ce7 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Wed, 26 Jun 2024 09:36:44 +0200 Subject: [PATCH 109/548] Add a checkbox to the form --- app/views/sharing/_form.html.erb | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/app/views/sharing/_form.html.erb b/app/views/sharing/_form.html.erb index 803abae2cd..7fb86e342b 100644 --- a/app/views/sharing/_form.html.erb +++ b/app/views/sharing/_form.html.erb @@ -9,6 +9,7 @@ else projects = [] end + is_assay_stream = object.respond_to?("is_assay_stream?") ? object.is_assay_stream? : false %> <%= folding_panel('Sharing', false, id: 'sharing_form', @@ -52,4 +53,12 @@ <% end %> <%= render partial: 'sharing/permissions_table', locals: { object: object, policy: policy, projects: projects } %> + <% if is_assay_stream %> +
    + <%= check_box_tag 'propagate_permissions' %> + +
    + <% end %> <% end %> From 0c6ce362d4b4d5210888d18cf50f71172348d833 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Wed, 26 Jun 2024 09:36:58 +0200 Subject: [PATCH 110/548] Create a test --- test/functional/assays_controller_test.rb | 28 +++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/test/functional/assays_controller_test.rb b/test/functional/assays_controller_test.rb index 3102f4a868..1c8ab2fb27 100644 --- a/test/functional/assays_controller_test.rb +++ b/test/functional/assays_controller_test.rb @@ -2159,4 +2159,32 @@ def check_fixtures_for_authorization_of_sops_and_datafiles_links assert_equal end_assay.position, 1 end end + + test 'assay stream permissions propagation' do + with_config_value(:isa_json_compliance_enabled, true) do + person = FactoryBot.create(:person) + other_person = FactoryBot.create(:person) + project = person.projects.first + investigation = FactoryBot.create(:investigation, is_isa_json_compliant: true, contributor: person) + study = FactoryBot.create(:isa_json_compliant_study, investigation: ) + assay_stream = FactoryBot.create(:assay_stream, study: , contributor: person, position: 0) + + authorized_child_assay = FactoryBot.create(:assay, contributor: person, study: , assay_stream:, position: 0) + unauthorized_child_assay = FactoryBot.create(:assay, contributor: other_person, study: , assay_stream:, position: 1) + + login_as(person) + refute unauthorized_child_assay.can_manage? + refute authorized_child_assay.can_manage?(other_person) + patch :manage_update, params: { id: assay_stream, propagate_permissions: '1', assay: {creator_ids: [other_person.id]}, policy_attributes: {access_type: Policy::VISIBLE, permissions_attributes: {'1' => {contributor_type: 'Person', contributor_id: other_person.id, access_type: Policy::MANAGING}}}} + + # assert the flash[:error] text. The permissions of the unauthorized assay should not be propagated + assert flash[:error], "
    • You do not have the necessary permissions to propagate permissions to #{t('assay').downcase} [#{unauthorized_child_assay.id}]: '#{unauthorized_child_assay.title}'
    " + assert_redirected_to assay_path(assay_stream) + + # assert that the permissions of the authorized assay were propagated + authorized_child_assay.reload + assert authorized_child_assay.can_manage?(other_person) + end + end + end From 8843ffa0ce7daa9c36d4f2c87e7b7640e08a9f70 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Wed, 26 Jun 2024 16:37:31 +0200 Subject: [PATCH 111/548] Change to after_action --- app/controllers/assays_controller.rb | 10 +++++++--- test/functional/assays_controller_test.rb | 4 ++-- 2 files changed, 9 insertions(+), 5 deletions(-) diff --git a/app/controllers/assays_controller.rb b/app/controllers/assays_controller.rb index e2ae7d747a..de8dcd4488 100644 --- a/app/controllers/assays_controller.rb +++ b/app/controllers/assays_controller.rb @@ -19,7 +19,7 @@ class AssaysController < ApplicationController # => Rearrange positions after_action :rearrange_assay_positions_at_destroy, only: :destroy - before_action :propagate_permissions_to_children, only: :manage_update + after_action :propagate_permissions_to_children, only: :manage_update include Seek::Publishing::PublishingCommon @@ -165,7 +165,8 @@ def show def propagate_permissions_to_children return unless params[:propagate_permissions] - # flash[:error] = 'You do not have the necessary permissions to propagate permissions to children' + # Should only propagate permissions to child assays if the assay is an assay stream + return unless @assay.is_assay_stream? errors = [] @assay.child_assays.map do |assay| @@ -175,7 +176,10 @@ def propagate_permissions_to_children next end - assay.update(assay_params) + current_assay_policy = assay.policy + # Clone the policy from the parent assay + assay.update(policy: @assay.policy.deep_copy) + current_assay_policy.destroy if current_assay_policy update_sharing_policies assay end # Add an error message to the flash diff --git a/test/functional/assays_controller_test.rb b/test/functional/assays_controller_test.rb index 1c8ab2fb27..971367c3f0 100644 --- a/test/functional/assays_controller_test.rb +++ b/test/functional/assays_controller_test.rb @@ -2160,7 +2160,7 @@ def check_fixtures_for_authorization_of_sops_and_datafiles_links end end - test 'assay stream permissions propagation' do + test 'Should propagate assay stream permissions' do with_config_value(:isa_json_compliance_enabled, true) do person = FactoryBot.create(:person) other_person = FactoryBot.create(:person) @@ -2175,7 +2175,7 @@ def check_fixtures_for_authorization_of_sops_and_datafiles_links login_as(person) refute unauthorized_child_assay.can_manage? refute authorized_child_assay.can_manage?(other_person) - patch :manage_update, params: { id: assay_stream, propagate_permissions: '1', assay: {creator_ids: [other_person.id]}, policy_attributes: {access_type: Policy::VISIBLE, permissions_attributes: {'1' => {contributor_type: 'Person', contributor_id: other_person.id, access_type: Policy::MANAGING}}}} + patch :manage_update, params: { id: assay_stream, propagate_permissions: '1', assay: {creator_ids: [other_person.id]}, policy_attributes: {access_type: Policy::NO_ACCESS, permissions_attributes: {'1' => {contributor_type: 'Person', contributor_id: other_person.id, access_type: Policy::MANAGING}}}} # assert the flash[:error] text. The permissions of the unauthorized assay should not be propagated assert flash[:error], "
    • You do not have the necessary permissions to propagate permissions to #{t('assay').downcase} [#{unauthorized_child_assay.id}]: '#{unauthorized_child_assay.title}'
    " From 4b6080ee7403a89302c130f2307cbd0063bd603d Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Wed, 26 Jun 2024 16:50:40 +0200 Subject: [PATCH 112/548] Add test for the visibility of the propagate permissions checkbox --- test/functional/assays_controller_test.rb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/test/functional/assays_controller_test.rb b/test/functional/assays_controller_test.rb index 971367c3f0..55be9db459 100644 --- a/test/functional/assays_controller_test.rb +++ b/test/functional/assays_controller_test.rb @@ -2160,6 +2160,25 @@ def check_fixtures_for_authorization_of_sops_and_datafiles_links end end + test 'visibility of the propagate permissions button' do + with_config_value(:isa_json_compliance_enabled, true) do + person = FactoryBot.create(:person) + login_as(person) + investigation = FactoryBot.create(:investigation, is_isa_json_compliant: true, contributor: person) + study = FactoryBot.create(:isa_json_compliant_study, investigation: ) + assay_stream = FactoryBot.create(:assay_stream, study: , contributor: person, position: 0) + experimental_assay = FactoryBot.create(:assay, contributor: person, study: , assay_stream:, position: 0) + + get :manage, params: { id: assay_stream } + assert_response :success + assert_select 'input[type=checkbox][name=propagate_permissions]', count: 1 + + get :manage, params: { id: experimental_assay } + assert_response :success + assert_select 'input[type=checkbox][name=propagate_permissions]', count: 0 + end + end + test 'Should propagate assay stream permissions' do with_config_value(:isa_json_compliance_enabled, true) do person = FactoryBot.create(:person) From 4c533bad5e9b2425c5ab7f789404ea51a4ba2578 Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Wed, 26 Jun 2024 17:08:19 +0200 Subject: [PATCH 113/548] Add test for non-authorized samples --- test/functional/assays_controller_test.rb | 35 +++++++++++++++++++---- 1 file changed, 29 insertions(+), 6 deletions(-) diff --git a/test/functional/assays_controller_test.rb b/test/functional/assays_controller_test.rb index 55be9db459..fd2b4177ba 100644 --- a/test/functional/assays_controller_test.rb +++ b/test/functional/assays_controller_test.rb @@ -2183,26 +2183,49 @@ def check_fixtures_for_authorization_of_sops_and_datafiles_links with_config_value(:isa_json_compliance_enabled, true) do person = FactoryBot.create(:person) other_person = FactoryBot.create(:person) - project = person.projects.first investigation = FactoryBot.create(:investigation, is_isa_json_compliant: true, contributor: person) study = FactoryBot.create(:isa_json_compliant_study, investigation: ) assay_stream = FactoryBot.create(:assay_stream, study: , contributor: person, position: 0) authorized_child_assay = FactoryBot.create(:assay, contributor: person, study: , assay_stream:, position: 0) - unauthorized_child_assay = FactoryBot.create(:assay, contributor: other_person, study: , assay_stream:, position: 1) login_as(person) - refute unauthorized_child_assay.can_manage? refute authorized_child_assay.can_manage?(other_person) patch :manage_update, params: { id: assay_stream, propagate_permissions: '1', assay: {creator_ids: [other_person.id]}, policy_attributes: {access_type: Policy::NO_ACCESS, permissions_attributes: {'1' => {contributor_type: 'Person', contributor_id: other_person.id, access_type: Policy::MANAGING}}}} + # assert that the permissions of the authorized assay were propagated + # other_person should see the assay stream and the authorized assay + assay_stream.reload + assert assay_stream.can_manage?(other_person) + authorized_child_assay.reload + assert authorized_child_assay.can_manage?(other_person) + end + end + + test 'should not propagate assay stream permissions when not authorized' do + with_config_value(:isa_json_compliance_enabled, true) do + person = FactoryBot.create(:person) + second_person = FactoryBot.create(:person) + third_person = FactoryBot.create(:person) + + investigation = FactoryBot.create(:investigation, is_isa_json_compliant: true, contributor: person) + study = FactoryBot.create(:isa_json_compliant_study, investigation: ) + assay_stream = FactoryBot.create(:assay_stream, study: , contributor: person, position: 0) + unauthorized_child_assay = FactoryBot.create(:assay, contributor: second_person, study: , assay_stream:, position: 0) + + login_as(person) + patch :manage_update, params: { id: assay_stream, propagate_permissions: '1', assay: {creator_ids: [third_person.id]}, policy_attributes: {access_type: Policy::NO_ACCESS, permissions_attributes: {'1' => {contributor_type: 'Person', contributor_id: third_person.id, access_type: Policy::MANAGING}}}} + # assert the flash[:error] text. The permissions of the unauthorized assay should not be propagated assert flash[:error], "
    • You do not have the necessary permissions to propagate permissions to #{t('assay').downcase} [#{unauthorized_child_assay.id}]: '#{unauthorized_child_assay.title}'
    " assert_redirected_to assay_path(assay_stream) - # assert that the permissions of the authorized assay were propagated - authorized_child_assay.reload - assert authorized_child_assay.can_manage?(other_person) + # assert that the permissions of the unauthorized assay were not propagated + # third_person should not see the unauthorized assay but still see the assay stream + assay_stream.reload + assert assay_stream.can_manage?(third_person) + unauthorized_child_assay.reload + refute unauthorized_child_assay.can_manage?(third_person) end end From c6915004382ad0ae58360fb3941974c437e16bed Mon Sep 17 00:00:00 2001 From: Kevin De Pelseneer Date: Wed, 26 Jun 2024 17:19:56 +0200 Subject: [PATCH 114/548] Add test for when checkbox is not checked --- app/controllers/assays_controller.rb | 2 +- test/functional/assays_controller_test.rb | 68 +++++++++++++++++------ 2 files changed, 51 insertions(+), 19 deletions(-) diff --git a/app/controllers/assays_controller.rb b/app/controllers/assays_controller.rb index de8dcd4488..a6ba0721cb 100644 --- a/app/controllers/assays_controller.rb +++ b/app/controllers/assays_controller.rb @@ -163,7 +163,7 @@ def show private def propagate_permissions_to_children - return unless params[:propagate_permissions] + return unless params[:propagate_permissions] == '1' # Should only propagate permissions to child assays if the assay is an assay stream return unless @assay.is_assay_stream? diff --git a/test/functional/assays_controller_test.rb b/test/functional/assays_controller_test.rb index fd2b4177ba..53041d3239 100644 --- a/test/functional/assays_controller_test.rb +++ b/test/functional/assays_controller_test.rb @@ -1929,15 +1929,15 @@ def check_fixtures_for_authorization_of_sops_and_datafiles_links sample_collection_st = FactoryBot.create(:isa_sample_collection_sample_type, contributor: person, projects: [project], linked_sample_type: source_st) - study = FactoryBot.create(:study, investigation: , contributor: person, + study = FactoryBot.create(:study, investigation:, contributor: person, policy: FactoryBot.create(:private_policy, permissions: [FactoryBot.create(:permission, contributor: person, access_type: Policy::MANAGING)]), sops: [FactoryBot.create(:sop, policy: FactoryBot.create(:public_policy))], sample_types: [source_st, sample_collection_st]) - assay_stream = FactoryBot.create(:assay_stream, study: , contributor: person) + assay_stream = FactoryBot.create(:assay_stream, study:, contributor: person) assay_sample_type = FactoryBot.create :isa_assay_material_sample_type, linked_sample_type: sample_collection_st, contributor: person, isa_template: FactoryBot.build(:isa_assay_material_template) assay = FactoryBot.create(:assay, - study: , + study:, policy: FactoryBot.create(:private_policy, permissions:[FactoryBot.create(:permission,contributor: person, access_type:Policy::EDITING)]), sample_type: assay_sample_type, contributor: person, @@ -1983,8 +1983,8 @@ def check_fixtures_for_authorization_of_sops_and_datafiles_links sops: [FactoryBot.create(:sop, policy: FactoryBot.create(:public_policy))], sample_types: [source_st, sample_collection_st]) - assay_stream = FactoryBot.create(:assay_stream, study: , contributor: person) - assay1 = FactoryBot.create(:assay, study: , contributor: person, sample_type: assay_st1, + assay_stream = FactoryBot.create(:assay_stream, study:, contributor: person) + assay1 = FactoryBot.create(:assay, study:, contributor: person, sample_type: assay_st1, policy: FactoryBot.create(:private_policy, permissions: [FactoryBot.create(:permission, contributor: person, access_type: Policy::MANAGING)]), position: 0, assay_stream: ) assay2 = FactoryBot.create(:assay, study: study, contributor: person, sample_type: assay_st2, @@ -2036,7 +2036,7 @@ def check_fixtures_for_authorization_of_sops_and_datafiles_links login_as(current_user) investigation = FactoryBot.create(:investigation, is_isa_json_compliant: true, contributor: current_user.person) study = FactoryBot.create(:isa_json_compliant_study, investigation: ) - assay_stream = FactoryBot.create(:assay_stream, study: , contributor: current_user.person) + assay_stream = FactoryBot.create(:assay_stream, study:, contributor: current_user.person) get :show, params: { id: assay_stream } assert_response :success @@ -2044,7 +2044,7 @@ def check_fixtures_for_authorization_of_sops_and_datafiles_links assert_select 'a', text: /Design #{I18n.t('assay')}/i, count: 1 assay_sample_type1 = FactoryBot.create(:isa_assay_material_sample_type, linked_sample_type: study.sample_types.second) - assay1 = FactoryBot.create(:assay, contributor: current_user.person, study: , assay_stream:, sample_type: assay_sample_type1) + assay1 = FactoryBot.create(:assay, contributor: current_user.person, study:, assay_stream:, sample_type: assay_sample_type1) assert_equal assay_stream.study, assay1.study @@ -2061,7 +2061,7 @@ def check_fixtures_for_authorization_of_sops_and_datafiles_links assert_select 'a', text: /Design the next #{I18n.t('assay')}/i, count: 1 assay_sample_type2 = FactoryBot.create(:isa_assay_material_sample_type, linked_sample_type: assay_sample_type1) - assay2 = FactoryBot.create(:assay, contributor: current_user.person, study: , assay_stream:, sample_type: assay_sample_type2) + assay2 = FactoryBot.create(:assay, contributor: current_user.person, study:, assay_stream:, sample_type: assay_sample_type2) get :show, params: { id: assay1 } assert_response :success @@ -2137,16 +2137,16 @@ def check_fixtures_for_authorization_of_sops_and_datafiles_links login_as(person) investigation = FactoryBot.create(:investigation, is_isa_json_compliant: true, contributor: person) study = FactoryBot.create(:isa_json_compliant_study, investigation: ) - assay_stream = FactoryBot.create(:assay_stream, study: , contributor: person, position: 0) + assay_stream = FactoryBot.create(:assay_stream, study:, contributor: person, position: 0) begin_assay_sample_type = FactoryBot.create(:isa_assay_material_sample_type, linked_sample_type: study.sample_types.second, projects: [project], contributor: person) - begin_assay = FactoryBot.create(:assay, contributor: person, study: , assay_stream:, sample_type: begin_assay_sample_type, position: 0) + begin_assay = FactoryBot.create(:assay, contributor: person, study:, assay_stream:, sample_type: begin_assay_sample_type, position: 0) middle_assay_sample_type = FactoryBot.create(:isa_assay_material_sample_type, linked_sample_type: begin_assay_sample_type, projects: [project], contributor: person) - middle_assay = FactoryBot.create(:assay, contributor: person, study: , assay_stream:, sample_type: middle_assay_sample_type, position: 1) + middle_assay = FactoryBot.create(:assay, contributor: person, study:, assay_stream:, sample_type: middle_assay_sample_type, position: 1) end_assay_sample_type = FactoryBot.create(:isa_assay_data_file_sample_type, linked_sample_type: middle_assay_sample_type, projects: [project], contributor: person) - end_assay = FactoryBot.create(:assay, contributor: person, study: , assay_stream:, sample_type: end_assay_sample_type, position: 2) + end_assay = FactoryBot.create(:assay, contributor: person, study:, assay_stream:, sample_type: end_assay_sample_type, position: 2) assert_difference('Assay.count', -1) do assert_difference('SampleType.count', -1) do @@ -2166,8 +2166,8 @@ def check_fixtures_for_authorization_of_sops_and_datafiles_links login_as(person) investigation = FactoryBot.create(:investigation, is_isa_json_compliant: true, contributor: person) study = FactoryBot.create(:isa_json_compliant_study, investigation: ) - assay_stream = FactoryBot.create(:assay_stream, study: , contributor: person, position: 0) - experimental_assay = FactoryBot.create(:assay, contributor: person, study: , assay_stream:, position: 0) + assay_stream = FactoryBot.create(:assay_stream, study:, contributor: person, position: 0) + experimental_assay = FactoryBot.create(:assay, contributor: person, study:, assay_stream:, position: 0) get :manage, params: { id: assay_stream } assert_response :success @@ -2185,9 +2185,9 @@ def check_fixtures_for_authorization_of_sops_and_datafiles_links other_person = FactoryBot.create(:person) investigation = FactoryBot.create(:investigation, is_isa_json_compliant: true, contributor: person) study = FactoryBot.create(:isa_json_compliant_study, investigation: ) - assay_stream = FactoryBot.create(:assay_stream, study: , contributor: person, position: 0) + assay_stream = FactoryBot.create(:assay_stream, study:, contributor: person, position: 0) - authorized_child_assay = FactoryBot.create(:assay, contributor: person, study: , assay_stream:, position: 0) + authorized_child_assay = FactoryBot.create(:assay, contributor: person, study:, assay_stream:, position: 0) login_as(person) refute authorized_child_assay.can_manage?(other_person) @@ -2210,8 +2210,8 @@ def check_fixtures_for_authorization_of_sops_and_datafiles_links investigation = FactoryBot.create(:investigation, is_isa_json_compliant: true, contributor: person) study = FactoryBot.create(:isa_json_compliant_study, investigation: ) - assay_stream = FactoryBot.create(:assay_stream, study: , contributor: person, position: 0) - unauthorized_child_assay = FactoryBot.create(:assay, contributor: second_person, study: , assay_stream:, position: 0) + assay_stream = FactoryBot.create(:assay_stream, study:, contributor: person, position: 0) + unauthorized_child_assay = FactoryBot.create(:assay, contributor: second_person, study:, assay_stream:, position: 0) login_as(person) patch :manage_update, params: { id: assay_stream, propagate_permissions: '1', assay: {creator_ids: [third_person.id]}, policy_attributes: {access_type: Policy::NO_ACCESS, permissions_attributes: {'1' => {contributor_type: 'Person', contributor_id: third_person.id, access_type: Policy::MANAGING}}}} @@ -2228,5 +2228,37 @@ def check_fixtures_for_authorization_of_sops_and_datafiles_links refute unauthorized_child_assay.can_manage?(third_person) end end + + test 'Should not propagate assay stream permissions when propagate_permissions param is not true' do + with_config_value(:isa_json_compliance_enabled, true) do + person = FactoryBot.create(:person) + other_person = FactoryBot.create(:person) + investigation = FactoryBot.create(:investigation, is_isa_json_compliant: true, contributor: person) + study = FactoryBot.create(:isa_json_compliant_study, investigation: ) + assay_stream = FactoryBot.create(:assay_stream, study:, contributor: person, position: 0) + authorized_child_assay = FactoryBot.create(:assay, contributor: person, study:, assay_stream:, position: 0) + + login_as(person) + refute authorized_child_assay.can_manage?(other_person) + patch :manage_update, params: { id: assay_stream, assay: {creator_ids: [other_person.id] }, policy_attributes: {access_type: Policy::NO_ACCESS, permissions_attributes: {'1' => {contributor_type: 'Person', contributor_id: other_person.id, access_type: Policy::MANAGING}}}} + + assert flash[:error].nil? + + # assert that the permissions of the authorized assay were not propagated + # other_person should not see the authorized assay + authorized_child_assay.reload + refute authorized_child_assay.can_manage?(other_person) + + patch :manage_update, params: { id: assay_stream, propagate_permissions: '0', assay: {creator_ids: [other_person.id] }, policy_attributes: {access_type: Policy::NO_ACCESS, permissions_attributes: {'1' => {contributor_type: 'Person', contributor_id: other_person.id, access_type: Policy::MANAGING}}}} + + assert flash[:error].nil? + + # assert that the permissions of the authorized assay were not propagated + # other_person should not see the authorized assay + authorized_child_assay.reload + refute authorized_child_assay.can_manage?(other_person) + + end + end end From 5ea08e750cacb2cc0d73ba042e6d909108786cd3 Mon Sep 17 00:00:00 2001 From: Finn Bacall Date: Wed, 26 Jun 2024 17:08:43 +0100 Subject: [PATCH 115/548] Associate creator based on ORCiD before save --- app/models/assets_creator.rb | 8 ++++++ lib/seek/workflow_extractors/base.rb | 5 +--- test/unit/assets_creators_test.rb | 28 +++++++++++++++++++ .../ro_crate_extraction_test.rb | 7 +---- 4 files changed, 38 insertions(+), 10 deletions(-) diff --git a/app/models/assets_creator.rb b/app/models/assets_creator.rb index d2b7db74f9..2f8fa268e3 100644 --- a/app/models/assets_creator.rb +++ b/app/models/assets_creator.rb @@ -11,6 +11,8 @@ class AssetsCreator < ApplicationRecord include Seek::OrcidSupport include Seek::BioSchema::Support + before_validation :associate_creator_from_orcid + update_rdf_on_change :asset default_scope { order(:pos) } @@ -74,4 +76,10 @@ def rdf_resource end end + private + + def associate_creator_from_orcid + return if orcid.blank? || creator.present? + self.creator = Person.find_by_orcid(orcid) + end end diff --git a/lib/seek/workflow_extractors/base.rb b/lib/seek/workflow_extractors/base.rb index fccfcd088b..7d0b14fc91 100644 --- a/lib/seek/workflow_extractors/base.rb +++ b/lib/seek/workflow_extractors/base.rb @@ -83,10 +83,7 @@ def extract_author(obj) end end orcid = obj['identifier'] || obj['@id'] - if orcid.present? && orcid.include?('orcid.org') - author[:orcid] = orcid - author[:creator_id] = Person.select(:id).find_by_orcid(author[:orcid])&.id - end + author[:orcid] = orcid if orcid.present? && orcid.include?('orcid.org') author[:given_name] = given_name if given_name.present? author[:family_name] = family_name if family_name.present? end diff --git a/test/unit/assets_creators_test.rb b/test/unit/assets_creators_test.rb index f47501b5b4..11ec3db3bf 100644 --- a/test/unit/assets_creators_test.rb +++ b/test/unit/assets_creators_test.rb @@ -173,4 +173,32 @@ def teardown end end end + + test 'automatically links to creator based on orcid' do + explicitly_linked_person = FactoryBot.create(:person, first_name: 'Link', orcid: 'https://orcid.org/0000-0002-5111-7263') + orcid_linked_person = FactoryBot.create(:person_not_in_project, first_name: 'Orc', orcid: 'https://orcid.org/0000-0002-1825-0097') + should_not_be_linked = FactoryBot.create(:person_not_in_project, orcid: 'https://orcid.org/0000-0001-9842-9718') + + sop = FactoryBot.create(:sop) + + disable_authorization_checks do + assert_difference('AssetsCreator.count', 2) do + sop.update(assets_creators_attributes: { + '4634' => { + orcid: 'https://orcid.org/0000-0001-9842-9718', + creator_id: explicitly_linked_person.id + }, + '123' => { + orcid: 'https://orcid.org/0000-0002-1825-0097' + } + }) + + ac = sop.reload.assets_creators.to_a + assert_equal 2, ac.length + assert_equal orcid_linked_person, ac.detect { |a| a.given_name == 'Orc' }.creator + assert_equal explicitly_linked_person, ac.detect { |a| a.given_name == 'Link' }.creator, + 'If creator is explicitly set, it should not attempt to link a different creator via orcid' + end + end + end end diff --git a/test/unit/workflow_extraction/ro_crate_extraction_test.rb b/test/unit/workflow_extraction/ro_crate_extraction_test.rb index 918e78b7d1..e4112dce29 100644 --- a/test/unit/workflow_extraction/ro_crate_extraction_test.rb +++ b/test/unit/workflow_extraction/ro_crate_extraction_test.rb @@ -38,7 +38,6 @@ class RoCrateExtractionTest < ActiveSupport::TestCase end test 'extracts both authors and creators from ro-crate' do - existing_person = FactoryBot.create(:person_not_in_project, orcid: 'https://orcid.org/0000-0002-1825-0097') wf = open_fixture_file('workflows/author_and_creator_test.crate.zip') extractor = Seek::WorkflowExtractors::ROCrate.new(wf) metadata = extractor.metadata @@ -53,15 +52,13 @@ class RoCrateExtractionTest < ActiveSupport::TestCase assert_equal 'Smith', first[:family_name] assert_nil first[:affiliation] assert_nil first[:orcid] - assert_nil first[:creator_id] assert_equal 0, first[:pos] second = author_meta.detect { |a| a[:given_name] == 'Josiah' } assert second assert_equal 'Carberry', second[:family_name] assert_equal 'Cool University', second[:affiliation] - assert_equal 'https://orcid.org/0000-0002-1825-0097', second[:orcid] - assert_equal existing_person.id, second[:creator_id] + assert 'https://orcid.org/0000-0002-1825-0097', second[:orcid] assert_equal 1, second[:pos] third = author_meta.detect { |a| a[:given_name] == 'Bert' } @@ -69,7 +66,6 @@ class RoCrateExtractionTest < ActiveSupport::TestCase assert_equal 'Droesbeke', third[:family_name] assert_nil third[:affiliation] assert_equal 'https://orcid.org/0000-0003-0522-5674', third[:orcid] - assert_nil third[:creator_id] assert_equal 2, third[:pos] fourth = author_meta.detect { |a| a[:given_name] == 'Mittens' } @@ -77,7 +73,6 @@ class RoCrateExtractionTest < ActiveSupport::TestCase assert_equal 'Smith', fourth[:family_name] assert_nil fourth[:affiliation] assert_nil fourth[:orcid] - assert_nil fourth[:creator_id] assert_equal 3, fourth[:pos] end From 32ff6ad2f01dd105e93fbf0fca6784252d86740f Mon Sep 17 00:00:00 2001 From: whomingbird Date: Thu, 27 Jun 2024 11:07:59 +0200 Subject: [PATCH 116/548] When the model is not publicly accessible but can be downloaded by the current user, use SpecialAuthCode to enable loading the model into CopasiUI (desktop application) --- app/helpers/assets_helper.rb | 9 +++-- app/views/models/copasi_simulate.html.erb | 4 +-- lib/seek/copasi/simulator.rb | 43 ++++++++++++++++++++--- 3 files changed, 46 insertions(+), 10 deletions(-) diff --git a/app/helpers/assets_helper.rb b/app/helpers/assets_helper.rb index 899b5294ae..ca7ea03a5f 100644 --- a/app/helpers/assets_helper.rb +++ b/app/helpers/assets_helper.rb @@ -221,10 +221,13 @@ def open_with_copasi_js_button end - def open_with_copasi_ui_button (asset) + def open_with_copasi_ui_button - file = asset.copasi_supported_content_blobs.first - download_path = polymorphic_path([file.asset, file], action: :download, code: params[:code]) + blob = @display_model.copasi_supported_content_blobs.first + + auth_code = @model.special_auth_codes.where('code LIKE ?', 'copasi_%').first.code + + download_path = polymorphic_path([@model, blob], action: :download, code:auth_code) copasi_download_path = "copasi://process?downloadUrl=http://"+request.host_with_port+download_path+"&activate=Time%20Course&createPlot=Concentrations%2C%20Volumes%2C%20and%20Global%20Quantity%20Values&runTask=Time-Course" diff --git a/app/views/models/copasi_simulate.html.erb b/app/views/models/copasi_simulate.html.erb index af7c026485..266b17d7e8 100644 --- a/app/views/models/copasi_simulate.html.erb +++ b/app/views/models/copasi_simulate.html.erb @@ -1,4 +1,4 @@ -<% content_for(:buttons) { button_link_to("Back to #{t('model')}", 'back', model_path(@model,:version=>@display_model.version)) } %> +<% content_for(:buttons) { button_link_to("Back to #{t('model')}", 'back', model_path(@model,:version=>@display_model.version, :code=>params[:code])) } %> <%= render :partial => "general/item_title",:locals=>{:item=>@model,:title_postfix=>" - Copasi #{t('model')} Simulation"} %> @@ -109,7 +109,7 @@ <%= open_with_copasi_js_button %> - <%= open_with_copasi_ui_button @display_model %> + <%= open_with_copasi_ui_button %>
    diff --git a/lib/seek/copasi/simulator.rb b/lib/seek/copasi/simulator.rb index 1f01a6f301..5ecc69365a 100644 --- a/lib/seek/copasi/simulator.rb +++ b/lib/seek/copasi/simulator.rb @@ -4,16 +4,21 @@ module Simulator extend ActiveSupport::Concern included do - before_action :find_display_asset_for_copasi, :find_model_file, only: [:copasi_simulate] + before_action :find_model, :find_display_asset_for_copasi, :select_model_file_for_simulation, only: [:copasi_simulate] + before_action :fetch_special_auth_code, if: -> { is_special_auth_code_required? }, only: [:copasi_simulate] + end def copasi_simulate - @model = Model.find_by_id(params[:id]) - @content_blob = @model.content_blobs.first render 'copasi_simulate' end - def find_model_file + def find_model + @model = Model.find_by_id(params[:id]) + end + + # # If the content blob is not available locally, fetch a copy from the remote URL + def select_model_file_for_simulation @blob = nil @@ -42,6 +47,7 @@ def find_model_file end end + # select the first COPASI-compatible content_blob when multiple items are associated with the display model. def select_copasi_content_blob blob = @display_model.copasi_supported_content_blobs.first raise 'Unable to find file to support Copasi Online' unless blob @@ -49,7 +55,34 @@ def select_copasi_content_blob end def find_display_asset_for_copasi - find_display_asset Model.find_by_id(params[:id]) + find_display_asset + end + + + # fetches or generates a special auth code with a "copasi_" prefix, which is used by COPASI desk application to load the non public model + def fetch_special_auth_code + copasi_codes = special_auth_codes_with_copasi_prefix + + if copasi_codes.empty? + # Generate a special auth code for a day + auth_code = SpecialAuthCode.new(expiration_date: Time.now + 1.day) + auth_code.update(code: "copasi_#{auth_code.code}") + @model.special_auth_codes << auth_code + auth_code # Ensure the new auth code is returned + else + copasi_codes.first + end + end + + private + + def special_auth_codes_with_copasi_prefix + @model.special_auth_codes.where('code LIKE ?', 'copasi_%') + end + + def is_special_auth_code_required? + # If the model is not publicly accessible but can be downloaded by the current user, the special auth code will be required. + Seek::Config.copasi_enabled && @display_model.is_copasi_supported? && @display_model.model.can_download? && !@model.public? end end From 79da9d33370205afd3cefaf31c7cc6979c33c8ea Mon Sep 17 00:00:00 2001 From: whomingbird Date: Fri, 28 Jun 2024 09:51:50 +0200 Subject: [PATCH 117/548] minor tweak --- app/helpers/assets_helper.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/app/helpers/assets_helper.rb b/app/helpers/assets_helper.rb index ca7ea03a5f..6b70962232 100644 --- a/app/helpers/assets_helper.rb +++ b/app/helpers/assets_helper.rb @@ -225,7 +225,7 @@ def open_with_copasi_ui_button blob = @display_model.copasi_supported_content_blobs.first - auth_code = @model.special_auth_codes.where('code LIKE ?', 'copasi_%').first.code + auth_code = @model.special_auth_codes.where('code LIKE ?', 'copasi_%').first.code unless @model.public? download_path = polymorphic_path([@model, blob], action: :download, code:auth_code) From 8715db6b462c2223822b1cc584de5875dfd7539a Mon Sep 17 00:00:00 2001 From: whomingbird Date: Fri, 28 Jun 2024 11:49:10 +0200 Subject: [PATCH 118/548] add tests for 'Simulate Model on Copasi button visibility' --- app/views/models/_buttons.html.erb | 2 +- app/views/models/copasi_simulate.html.erb | 2 +- lib/seek/copasi/simulator.rb | 2 +- test/factories/content_blobs.rb | 6 + test/factories/models.rb | 7 + test/fixtures/files/brusselator.cps | 929 ++++++++++++++++++++++ test/functional/copasi_test.rb | 54 ++ 7 files changed, 999 insertions(+), 3 deletions(-) create mode 100644 test/fixtures/files/brusselator.cps create mode 100644 test/functional/copasi_test.rb diff --git a/app/views/models/_buttons.html.erb b/app/views/models/_buttons.html.erb index 892fa39dd5..256438255b 100644 --- a/app/views/models/_buttons.html.erb +++ b/app/views/models/_buttons.html.erb @@ -1,5 +1,5 @@ <% if show_copasi_button? %> - <%= button_link_to("Simulate #{t('model')} on Copasi", 'copasi', copasi_simulate_model_path(:model => @model, :version => @display_model.version, :code => params[:code] ),:method=>:post) %> + <%= button_link_to("Simulate #{t('model')} on Copasi", 'copasi', copasi_simulate_model_path(:version => @display_model.version, :code => params[:code] ),:method=>:post) %> <% end %> <% if show_jws_simulate? %> diff --git a/app/views/models/copasi_simulate.html.erb b/app/views/models/copasi_simulate.html.erb index 266b17d7e8..e4f03fbe73 100644 --- a/app/views/models/copasi_simulate.html.erb +++ b/app/views/models/copasi_simulate.html.erb @@ -1,4 +1,4 @@ -<% content_for(:buttons) { button_link_to("Back to #{t('model')}", 'back', model_path(@model,:version=>@display_model.version, :code=>params[:code])) } %> +<% content_for(:buttons) { button_link_to("Back to #{t('model')}", 'back', model_path(:version=>@display_model.version, :code=>params[:code])) } %> <%= render :partial => "general/item_title",:locals=>{:item=>@model,:title_postfix=>" - Copasi #{t('model')} Simulation"} %> diff --git a/lib/seek/copasi/simulator.rb b/lib/seek/copasi/simulator.rb index 5ecc69365a..39942aef21 100644 --- a/lib/seek/copasi/simulator.rb +++ b/lib/seek/copasi/simulator.rb @@ -82,7 +82,7 @@ def special_auth_codes_with_copasi_prefix def is_special_auth_code_required? # If the model is not publicly accessible but can be downloaded by the current user, the special auth code will be required. - Seek::Config.copasi_enabled && @display_model.is_copasi_supported? && @display_model.model.can_download? && !@model.public? + Seek::Config.copasi_enabled && @display_model.is_copasi_supported? && @model.can_download? && !@model.public? end end diff --git a/test/factories/content_blobs.rb b/test/factories/content_blobs.rb index 392295c3fe..47c25d3480 100644 --- a/test/factories/content_blobs.rb +++ b/test/factories/content_blobs.rb @@ -477,4 +477,10 @@ original_filename { 'transparent-fairdom-logo-square.svg' } data { File.new("#{Rails.root}/test/fixtures/files/transparent-fairdom-logo-square.svg", 'rb').read } end + + factory(:copasi_content_blob, parent: :content_blob) do + content_type { 'application/xml' } + original_filename { 'brusselator.cps' } + data { File.new("#{Rails.root}/test/fixtures/files/brusselator.cps", 'rb').read } + end end diff --git a/test/factories/models.rb b/test/factories/models.rb index ef7d76326d..3b87877f07 100644 --- a/test/factories/models.rb +++ b/test/factories/models.rb @@ -154,6 +154,13 @@ ] end end + + + factory(:copasi_model, parent: :model) do + after(:create) do |model| + model.content_blobs = [FactoryBot.create(:copasi_content_blob, asset: model, asset_version: model.version)] + end + end # Model::Version factory(:model_version, class: Model::Version) do diff --git a/test/fixtures/files/brusselator.cps b/test/fixtures/files/brusselator.cps new file mode 100644 index 0000000000..4a8a3d8487 --- /dev/null +++ b/test/fixtures/files/brusselator.cps @@ -0,0 +1,929 @@ + + + + + + + + + + + + + + + +Mass action rate law for first order irreversible reactions +

    +Reaction scheme where the products are created from the reactants and the change of a product quantity is proportional to the product of reactant activities. The reaction scheme does not include any reverse process that creates the reactants from the products. The change of a product quantity is proportional to the quantity of one reactant. +

    + +     + + k1*PRODUCT<substrate_i> + + + + + +     +     + + + + + + + 2014-04-15T09:23:42Z + + + + + + + + +

    The famous Brusselator model in which a chemical species X catalyses its own formation. In a certain region of parameter space the Brusselator can function in a limit cycle regime around an unstable steady state. Run this simulation and then check the report file to see how Gepasi can find an unstable steady state, and calculate the eigenvalues of the Jacobian matrix.

    + +     + + + + + + + + + + + + + + 2014-04-15T09:23:51Z + + + + + + + + + + + + + + 2014-04-15T09:23:50Z + + + + + + + + + + + + + + + + 2014-04-15T09:23:50Z + + + + + + + + + + + + + + + + + + 2014-04-15T09:23:51Z + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 0 1.80664e+021 1.80664e+021 3.01107e+020 1.80664e+021 0 0 1 + +     + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Automatically generated report. + + +
    -

    -

    -
    -

    + + +
    + aria-controls="cps_form">show model file
    -
    @@ -128,13 +108,13 @@