From afe2cc0ba037e33a899ea9989f7dfcc69bc91ff2 Mon Sep 17 00:00:00 2001 From: Mallory Freeberg Date: Tue, 5 Dec 2017 15:52:28 +0000 Subject: [PATCH] Updated URLs to 4.2.0. --- json_schema/analysis.json | 272 ++++++++++++------------ json_schema/assay.json | 76 +++---- json_schema/assay_bundle.json | 40 ++-- json_schema/barcode.json | 62 +++--- json_schema/cell_suspension.json | 46 ++-- json_schema/contact.json | 214 +++++++++---------- json_schema/core.json | 44 ++-- json_schema/death.json | 60 +++--- json_schema/donor.json | 216 +++++++++---------- json_schema/enrichment.json | 58 ++--- json_schema/file.json | 48 ++--- json_schema/imaging.json | 96 ++++----- json_schema/immortalized_cell_line.json | 76 +++---- json_schema/ingest.json | 62 +++--- json_schema/ontology.json | 26 +-- json_schema/organoid.json | 18 +- json_schema/primary_cell_line.json | 46 ++-- json_schema/project.json | 172 +++++++-------- json_schema/project_bundle.json | 32 +-- json_schema/protocol.json | 80 +++---- json_schema/publication.json | 58 ++--- json_schema/rna.json | 114 +++++----- json_schema/sample.json | 178 ++++++++-------- json_schema/sample_bundle.json | 46 ++-- json_schema/seq.json | 192 ++++++++--------- json_schema/single_cell.json | 40 ++-- json_schema/specimen_from_organism.json | 38 ++-- json_schema/state_of_specimen.json | 88 ++++---- json_schema/submission.json | 138 ++++++------ json_schema/well.json | 52 ++--- 30 files changed, 1344 insertions(+), 1344 deletions(-) diff --git a/json_schema/analysis.json b/json_schema/analysis.json index 4df2273c0..65ed0a24a 100644 --- a/json_schema/analysis.json +++ b/json_schema/analysis.json @@ -1,155 +1,155 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", - "additionalProperties": true, + "title": "analysis", + "required": [ + "timestamp_start_utc", + "timestamp_stop_utc", + "computational_method", + "input_bundles", + "reference_bundle", + "analysis_id", + "analysis_run_type", + "metadata_schema", + "tasks", + "inputs", + "outputs" + ], + "additionalProperties": true, + "definitions": { + "task": { + "additionalProperties": false, + "required": [ + "name", + "start_time", + "stop_time", + "log", + "disk_size", + "docker_image", + "cpus", + "memory", + "zone" + ], + "type": "object", + "properties": { + "disk_size": "string", + "name": "string", + "zone": "string", + "log_err": "uri", + "start_time": "date-time", + "cpus": "int", + "log_out": "uri", + "stop_time": "date-time", + "memory": "string", + "docker_image": "string" + } + }, + "parameter": { + "additionalProperties": false, + "required": [ + "name", + "value" + ], + "type": "object", + "properties": { + "checksum": "string", + "name": "string", + "value": "string" + } + }, + "file": { + "additionalProperties": false, + "required": [ + "checksum", + "file_path", + "format" + ], + "type": "object", + "properties": { + "checksum": "string", + "file_path": "uri", + "format": "string" + } + } + }, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { - "tasks": { - "description": "Descriptions of tasks in the workflow.", - "type": "array", + "inputs": { "items": { "type": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/analysis.json#/definitions/task" + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/analysis.json#/definitions/parameter" } - } - }, - "analysis_id": { - "description": "A unique ID for this analysis.", - "type": "number" - }, - "name": { - "description": "A short, descriptive name for the analysis that need not be unique.", - "type": "string" - }, - "description": { - "description": "A general description of the analysis.", - "type": "string" - }, - "computational_method": { - "description": "A URI to a versioned workflow and versioned execution environment in a GA4GH-compliant repository.", - "type": "uri" - }, - "outputs": { + }, + "type": "array", + "description": "Input parameters used in the pipeline run, these can be files or string values (settings)." + }, + "reference_bundle": { + "type": "uri", + "description": "Bundle containing the reference used in running the pipeline." + }, + "tasks": { "items": { "type": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/analysis.json#/definitions/file" + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/analysis.json#/definitions/task" } - }, - "description": "Output generated by the pipeline run.", - "type": "array" - }, + }, + "type": "array", + "description": "Descriptions of tasks in the workflow." + }, + "description": { + "type": "string", + "description": "A general description of the analysis." + }, + "timestamp_stop_utc": { + "type": "date-time", + "description": "Terminal stop time of the full pipeline." + }, "input_bundles": { "items": { "type": "uri" - }, - "description": "The input bundles used in this analysis run.", - "type": "array" - }, - "timestamp_stop_utc": { - "type": "date-time", - "description": "Terminal stop time of the full pipeline." - }, - "metadata_schema": { - "description": "The version of the metadata schemas used for the json files.", - "type": "string" - }, - "timestamp_start_utc": { - "description": "Initial start time of the full pipeline.", - "type": "date-time" - }, - "inputs": { + }, + "type": "array", + "description": "The input bundles used in this analysis run." + }, + "outputs": { "items": { "type": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/analysis.json#/definitions/parameter" + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/analysis.json#/definitions/file" } - }, - "type": "array", - "description": "Input parameters used in the pipeline run, these can be files or string values (settings)." - }, + }, + "type": "array", + "description": "Output generated by the pipeline run." + }, + "name": { + "type": "string", + "description": "A short, descriptive name for the analysis that need not be unique." + }, + "computational_method": { + "type": "uri", + "description": "A URI to a versioned workflow and versioned execution environment in a GA4GH-compliant repository." + }, + "timestamp_start_utc": { + "type": "date-time", + "description": "Initial start time of the full pipeline." + }, + "core": { + "description": "Type and schema for this object.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/core.json" + }, "analysis_run_type": { "enum": [ - "run", + "run", "copy-forward" - ], - "description": "Indicator of whether the analysis actually ran or was just copied forward as an optimization.", - "type": "string" - }, - "reference_bundle": { - "description": "Bundle containing the reference used in running the pipeline.", - "type": "uri" - }, - "core": { - "description": "Type and schema for this object.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/core.json" - } - }, - "type": "object", - "definitions": { - "file": { - "additionalProperties": false, - "required": [ - "checksum", - "file_path", - "format" - ], - "properties": { - "format": "string", - "file_path": "uri", - "checksum": "string" - }, - "type": "object" - }, - "task": { - "properties": { - "start_time": "date-time", - "stop_time": "date-time", - "name": "string", - "log_err": "uri", - "log_out": "uri", - "disk_size": "string", - "docker_image": "string", - "cpus": "int", - "memory": "string", - "zone": "string" - }, - "required": [ - "name", - "start_time", - "stop_time", - "log", - "disk_size", - "docker_image", - "cpus", - "memory", - "zone" - ], - "additionalProperties": false, - "type": "object" - }, - "parameter": { - "additionalProperties": false, - "required": [ - "name", - "value" - ], - "properties": { - "checksum": "string", - "value": "string", - "name": "string" - }, - "type": "object" + ], + "type": "string", + "description": "Indicator of whether the analysis actually ran or was just copied forward as an optimization." + }, + "metadata_schema": { + "type": "string", + "description": "The version of the metadata schemas used for the json files." + }, + "analysis_id": { + "type": "number", + "description": "A unique ID for this analysis." } - }, - "title": "analysis", - "required": [ - "timestamp_start_utc", - "timestamp_stop_utc", - "computational_method", - "input_bundles", - "reference_bundle", - "analysis_id", - "analysis_run_type", - "metadata_schema", - "tasks", - "inputs", - "outputs" - ] + } } \ No newline at end of file diff --git a/json_schema/assay.json b/json_schema/assay.json index 4ea67bd7f..2281c083e 100644 --- a/json_schema/assay.json +++ b/json_schema/assay.json @@ -1,46 +1,46 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", - "additionalProperties": false, - "definitions": {}, - "description": "An assay contains information relevant to how a sample (in vitro) was converted into digital information (in silico).", + "description": "An assay contains information relevant to how a sample (in vitro) was converted into digital information (in silico).", + "title": "assay", + "required": [ + "core", + "assay_id" + ], + "additionalProperties": false, + "definitions": {}, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { "core": { - "description": "Type and schema for this object.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/core.json" - }, - "assay_id": { - "description": "A unique ID for this assay.", - "type": "string" - }, + "description": "Type and schema for this object.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/core.json" + }, "name": { - "description": "A short, descriptive name for the assay that need not be unique.", - "type": "string" - }, - "description": { - "description": "A general description of the assay.", - "type": "string" - }, - "imaging": { - "description": "Information on image based RNA quantification assays", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/imaging.json" - }, - "rna": { - "description": "Information about how RNA was converted to cDNA.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/rna.json" - }, + "type": "string", + "description": "A short, descriptive name for the assay that need not be unique." + }, "seq": { - "description": "Information about how a cDNA sample was sequenced.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/seq.json" - }, + "description": "Information about how a cDNA sample was sequenced.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/seq.json" + }, + "rna": { + "description": "Information about how RNA was converted to cDNA.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/rna.json" + }, "single_cell": { - "description": "Information on single-cell aspects of an assay.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/single_cell.json" + "description": "Information on single-cell aspects of an assay.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/single_cell.json" + }, + "imaging": { + "description": "Information on image based RNA quantification assays", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/imaging.json" + }, + "assay_id": { + "type": "string", + "description": "A unique ID for this assay." + }, + "description": { + "type": "string", + "description": "A general description of the assay." } - }, - "required": [ - "core", - "assay_id" - ], - "title": "assay", - "type": "object" + } } \ No newline at end of file diff --git a/json_schema/assay_bundle.json b/json_schema/assay_bundle.json index 09531b4f3..789ca6fe8 100644 --- a/json_schema/assay_bundle.json +++ b/json_schema/assay_bundle.json @@ -1,36 +1,36 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", - "description": "A schema for an assay bundle", - "type": "array", "definitions": { "assay_ingest": { - "type": "object", "required": [ - "hca_ingest", + "hca_ingest", "content" - ], + ], + "type": "object", "properties": { - "hca_ingest": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/ingest.json", - "description": "core fields added by HCA ingest service", - "type": "object" - }, "content": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/assay.json", - "description": "Assay content", - "type": "object" - }, + "type": "object", + "description": "Assay content", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/assay.json" + }, "derivation_protocols": { "items": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/protocol.json", - "description": "An array of protocols used in derivation of this sample." - }, + "description": "An array of protocols used in derivation of this sample.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/protocol.json" + }, "type": "array" + }, + "hca_ingest": { + "type": "object", + "description": "core fields added by HCA ingest service", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ingest.json" } } } - }, + }, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "array", + "description": "A schema for an assay bundle", "items": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/assay_bundle.json#/definitions/assay_ingest" + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/assay_bundle.json#/definitions/assay_ingest" } } \ No newline at end of file diff --git a/json_schema/barcode.json b/json_schema/barcode.json index 37ee70394..96fb99d5a 100644 --- a/json_schema/barcode.json +++ b/json_schema/barcode.json @@ -1,39 +1,39 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", - "additionalProperties": false, - "description": "This object describes where a particular type of barcode is in a read.", + "description": "This object describes where a particular type of barcode is in a read.", + "title": "barcode", + "required": [ + "offset", + "size", + "read" + ], + "additionalProperties": false, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { - "offset": { - "description": "Offset in read of barcode. 0 for beginning of read.", - "maximum": 50, - "minimum": 0, - "type": "integer" - }, - "size": { - "description": "Size of barcode in nucleotides.", - "maximum": 50, - "minimum": 0, - "type": "integer" - }, "read": { - "description": "The read that the barcode is found in. Should be one of Read 1, Read 2, i7 Index, or i5 Index.", "enum": [ - "Read 1", - "Read 2", - "i7 Index", + "Read 1", + "Read 2", + "i7 Index", "i5 Index" - ] - }, + ], + "description": "The read that the barcode is found in. Should be one of Read 1, Read 2, i7 Index, or i5 Index." + }, + "size": { + "minimum": 0, + "type": "integer", + "description": "Size of barcode in nucleotides.", + "maximum": 50 + }, "white_list_file": { - "description": "Name of file containing legitimate barcode sequences. Unused for randomly generated barcodes.", - "type": "string" + "type": "string", + "description": "Name of file containing legitimate barcode sequences. Unused for randomly generated barcodes." + }, + "offset": { + "minimum": 0, + "type": "integer", + "description": "Offset in read of barcode. 0 for beginning of read.", + "maximum": 50 } - }, - "required": [ - "offset", - "size", - "read" - ], - "title": "barcode", - "type": "object" + } } \ No newline at end of file diff --git a/json_schema/cell_suspension.json b/json_schema/cell_suspension.json index 3ac76971a..b8dae1f87 100644 --- a/json_schema/cell_suspension.json +++ b/json_schema/cell_suspension.json @@ -1,31 +1,31 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", - "description": "Information about the cell suspension derived from the collected or cultured specimen", + "$schema": "http://json-schema.org/draft-04/schema#", + "title": "cell_suspension", + "description": "Information about the cell suspension derived from the collected or cultured specimen", "properties": { + "well": { + "description": "Information about wells in a plate or chip used for single-cell isolation.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/well.json" + }, "target_cell_type": { - "description": "Cell types present in the suspension.", - "type": "array", "items": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/ontology_json/cell_type_ontology.json" - } - }, + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology_json/cell_type_ontology.json" + }, + "type": "array", + "description": "Cell types present in the suspension." + }, + "total_estimated_cells": { + "minimum": 0.1, + "type": "number", + "description": "Total estimated number of cells in sample. May be 1 for well-based assays.", + "maximum": 1000000000.0 + }, "enrichment": { - "description": "How sample was enriched for specific cell type(s).", - "type": "array", "items": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/enrichment.json" - } - }, - "total_estimated_cells": { - "description": "Total estimated number of cells in sample. May be 1 for well-based assays.", - "maximum": 1000000000.0, - "minimum": 0.1, - "type": "number" - }, - "well": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/well.json", - "description": "Information about wells in a plate or chip used for single-cell isolation." + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/enrichment.json" + }, + "type": "array", + "description": "How sample was enriched for specific cell type(s)." } - }, - "title": "cell_suspension" + } } \ No newline at end of file diff --git a/json_schema/contact.json b/json_schema/contact.json index b873fd7cf..53f2b7029 100644 --- a/json_schema/contact.json +++ b/json_schema/contact.json @@ -1,117 +1,117 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", - "additionalProperties": false, - "definitions": {}, - "description": "contact schema generate by tagSchemaToJson from contact", + "description": "contact schema generate by tagSchemaToJson from contact", + "title": "contact", + "required": [ + "name", + "email" + ], + "additionalProperties": false, + "definitions": {}, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { - "address": { - "description": "Full mailing address where contact works. Should include street name and number, city, state, postal code, country.", - "type": "string" - }, + "country_division": { + "enum": [ + "AL", + "AK", + "AR", + "AZ", + "CA", + "CO", + "CT", + "DE", + "FL", + "GA", + "HI", + "ID", + "IA", + "IL", + "IN", + "KS", + "KY", + "LA", + "MA", + "MD", + "ME", + "MI", + "MN", + "MO", + "MS", + "MT", + "NC", + "ND", + "NE", + "NH", + "NJ", + "NM", + "NV", + "NY", + "OH", + "OK", + "OR", + "PA", + "RI", + "SC", + "SD", + "TN", + "TX", + "UT", + "VT", + "VA", + "WA", + "WV", + "WI", + "XY", + "FU", + "PR", + "VI" + ], + "description": "Name of state, province, canton, or other country subdivision." + }, "city": { - "description": "Name of city where contact works.", - "type": "string" - }, + "type": "string", + "description": "Name of city where contact works." + }, + "name": { + "type": "string", + "description": "The contact's name. Should be in the format first, middle, last name. Middle can be initial or left blank. e.g. John,D,Doe or Jane,,Smith" + }, "country": { - "description": "Name of country where contact works. Please spell out (except for USA or UK).", "enum": [ - "Austria", - "Canada", - "China", - "France", - "Germany", - "Israel", - "Japan", - "Sweden", - "Switzerland", - "UK", + "Austria", + "Canada", + "China", + "France", + "Germany", + "Israel", + "Japan", + "Sweden", + "Switzerland", + "UK", "USA" - ] - }, - "country_division": { - "description": "Name of state, province, canton, or other country subdivision.", - "enum": [ - "AL", - "AK", - "AR", - "AZ", - "CA", - "CO", - "CT", - "DE", - "FL", - "GA", - "HI", - "ID", - "IA", - "IL", - "IN", - "KS", - "KY", - "LA", - "MA", - "MD", - "ME", - "MI", - "MN", - "MO", - "MS", - "MT", - "NC", - "ND", - "NE", - "NH", - "NJ", - "NM", - "NV", - "NY", - "OH", - "OK", - "OR", - "PA", - "RI", - "SC", - "SD", - "TN", - "TX", - "UT", - "VT", - "VA", - "WA", - "WV", - "WI", - "XY", - "FU", - "PR", - "VI" - ] - }, - "email": { - "description": "An email address for the contact.", - "pattern": "^.*@.*..*$", - "type": "string" - }, + ], + "description": "Name of country where contact works. Please spell out (except for USA or UK)." + }, "institution": { - "description": "Name of primary institute where contact works.", - "type": "string" - }, - "laboratory": { - "description": "Name of lab (often the PI name) within institute where contact works.", - "type": "string" - }, - "name": { - "description": "The contact's name. Should be in the format first, middle, last name. Middle can be initial or left blank. e.g. John,D,Doe or Jane,,Smith", - "type": "string" - }, + "type": "string", + "description": "Name of primary institute where contact works." + }, "phone": { - "description": "Phone number (including country code) of contact or contact's lab.", - "type": "string" + "type": "string", + "description": "Phone number (including country code) of contact or contact's lab." + }, + "address": { + "type": "string", + "description": "Full mailing address where contact works. Should include street name and number, city, state, postal code, country." + }, + "laboratory": { + "type": "string", + "description": "Name of lab (often the PI name) within institute where contact works." + }, + "email": { + "pattern": "^.*@.*..*$", + "type": "string", + "description": "An email address for the contact." } - }, - "required": [ - "name", - "email" - ], - "title": "contact", - "type": "object" + } } \ No newline at end of file diff --git a/json_schema/core.json b/json_schema/core.json index 7e3f1da8b..86519a63e 100644 --- a/json_schema/core.json +++ b/json_schema/core.json @@ -1,29 +1,29 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", - "description": "Core object found in all modules.", + "$schema": "http://json-schema.org/draft-04/schema#", + "required": [ + "type" + ], + "description": "Core object found in all modules.", "properties": { - "schema_url": { - "description": "URL of JSON schema document that validates this version of this module.", - "type": "string" - }, - "schema_version": { - "description": "Version number in major.minor.patch format. e.g. 3.2.4. Major version changes likely require changes to software. Minor version changes should not require software changes. Patches are just documentation changes.", - "pattern": "^...*..*$", - "type": "string" - }, "type": { - "description": "The name of the core metadata entity type.", "enum": [ - "assay", - "project", - "protocol", - "sample", - "file", + "assay", + "project", + "protocol", + "sample", + "file", "analysis" - ] + ], + "description": "The name of the core metadata entity type." + }, + "schema_url": { + "type": "string", + "description": "URL of JSON schema document that validates this version of this module." + }, + "schema_version": { + "pattern": "^...*..*$", + "type": "string", + "description": "Version number in major.minor.patch format. e.g. 3.2.4. Major version changes likely require changes to software. Minor version changes should not require software changes. Patches are just documentation changes." } - }, - "required": [ - "type" - ] + } } \ No newline at end of file diff --git a/json_schema/death.json b/json_schema/death.json index 6e77ef120..a6d408e1f 100644 --- a/json_schema/death.json +++ b/json_schema/death.json @@ -1,38 +1,38 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", - "additionalProperties": false, - "definitions": {}, - "description": "Information relating to the death of the donor", + "description": "Information relating to the death of the donor", + "title": "death", + "required": [ + "cause_of_death" + ], + "additionalProperties": false, + "definitions": {}, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { "cause_of_death": { - "description": "Cause of death from death report for human donor, from research lab for mouse.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/ontology.json" - }, + "description": "Cause of death from death report for human donor, from research lab for mouse.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology.json" + }, + "hardy_scale": { + "minimum": 0, + "type": "integer", + "description": "Should be integer representing: (0) ventilator case, (1) violent and fast death, (2) fast death of natural causes, (3) intermediate death, or (4) slow death.", + "maximum": 4 + }, "cold_perfused": { - "description": "Yes if perfused with cold fluid to help preserve tissues before heart stopped. No otherwise.", - "type": "boolean" - }, + "type": "boolean", + "description": "Yes if perfused with cold fluid to help preserve tissues before heart stopped. No otherwise." + }, "days_on_ventilator": { - "description": "Days on ventilator before dying.", - "maximum": 10000, - "minimum": 0, - "type": "number" - }, - "hardy_scale": { - "description": "Should be integer representing: (0) ventilator case, (1) violent and fast death, (2) fast death of natural causes, (3) intermediate death, or (4) slow death.", - "maximum": 4, - "minimum": 0, - "type": "integer" - }, + "minimum": 0, + "type": "number", + "description": "Days on ventilator before dying.", + "maximum": 10000 + }, "time_of_death": { - "description": "Date and time of death on death certificate for deceased donor.", - "format": "date-time", - "type": "string" + "type": "string", + "description": "Date and time of death on death certificate for deceased donor.", + "format": "date-time" } - }, - "required": [ - "cause_of_death" - ], - "title": "death", - "type": "object" + } } \ No newline at end of file diff --git a/json_schema/donor.json b/json_schema/donor.json index 049dea82d..0ee07a2a5 100644 --- a/json_schema/donor.json +++ b/json_schema/donor.json @@ -1,124 +1,124 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", - "description": "Information about the donor from which a specimen was collected", - "additionalProperties": false, + "description": "Information about the donor from which a specimen was collected", + "title": "donor", + "required": [ + "is_living" + ], + "additionalProperties": false, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { - "age": { - "description": "Age in age_units. For embryos, measured since fertilization. For all others, measured since birth.", - "pattern": "^[0-9]+\\.?[0-9]*-?[0-9]*\\.?[0-9]*$", - "type": "string" - }, - "age_unit": { - "description": "The unit in which age is expressed. Must be one of day, week, month, or year.", + "nutritional_state": { "enum": [ - "hour", - "day", - "week", - "year", - "hours", - "days", - "weeks", - "years" - ] - }, - "alcohol_history": { - "description": "Number of drinks consumed on a typical day.", - "type": "string" - }, - "ancestry": { - "description": "An array of ontology terms from EMBL-EBI's Ancestry Ontology describing ancestral groups, uncategorised ancestral groups, and population isolates.", - "type": "array", - "items": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/ontology.json" - } - }, - "body_mass_index": { - "description": "The body mass index of the donor.", - "maximum": 100, - "minimum": 5, - "type": "number" - }, + "normal", + "fasting", + "feeding tube removed" + ], + "description": "Should be one of normal, fasting, or feeding tube removed." + }, + "is_living": { + "type": "boolean", + "description": "Should be yes if donor is living at time of sample donation. Otherwise, should be no." + }, "death": { - "description": "Information about conditions of death (or info that donor was living at time of collection).", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/death.json" - }, - "development_stage": { - "description": "More detailed (especially for embryos) version of life_stage. e.g. \"E9\" or \"P17\" for mouse.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/ontology.json" - }, - "disease": { - "description": "Short description of disease status of individual.", - "type": "array", - "items": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/ontology_json/disease_ontology.json" - } - }, + "description": "Information about conditions of death (or info that donor was living at time of collection).", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/death.json" + }, "genotype": { - "description": "Genotype of donor including strain, cross, and genetic modification information. Must be in MGI format for mice.", - "type": "string" - }, - "height": { - "description": "Height of donor, in meters. Can be a range separated by a hyphen.", - "pattern": "^[0-9]+\\.?[0-9]*-?[0-9]*\\.?[0-9]*$", - "type": "string" - }, - "is_living": { - "description": "Should be yes if donor is living at time of sample donation. Otherwise, should be no.", - "type": "boolean" - }, + "type": "string", + "description": "Genotype of donor including strain, cross, and genetic modification information. Must be in MGI format for mice." + }, + "weight": { + "pattern": "^[0-9]+\\.?[0-9]*-?[0-9]*\\.?[0-9]*$", + "type": "string", + "description": "Weight of donor, in kilograms. Can be a range separated by a hyphen." + }, + "strain": { + "items": { + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology.json" + }, + "type": "array", + "description": "The name of th mouse inbred strain. e.g. C57BL/6." + }, + "alcohol_history": { + "type": "string", + "description": "Number of drinks consumed on a typical day." + }, + "age": { + "pattern": "^[0-9]+\\.?[0-9]*-?[0-9]*\\.?[0-9]*$", + "type": "string", + "description": "Age in age_units. For embryos, measured since fertilization. For all others, measured since birth." + }, "life_stage": { - "description": "Should be one of adult, child, embryo, or postpartum.", "enum": [ - "adult", - "child", - "embryo", + "adult", + "child", + "embryo", "postpartum" - ] - }, - "medication": { - "description": "List of medications the donor was currently taking at time of sample donation.", - "type": "array", + ], + "description": "Should be one of adult, child, embryo, or postpartum." + }, + "disease": { "items": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/ontology.json" - } - }, - "nutritional_state": { - "description": "Should be one of normal, fasting, or feeding tube removed.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology_json/disease_ontology.json" + }, + "type": "array", + "description": "Short description of disease status of individual." + }, + "age_unit": { "enum": [ - "normal", - "fasting", - "feeding tube removed" - ] - }, + "hour", + "day", + "week", + "year", + "hours", + "days", + "weeks", + "years" + ], + "description": "The unit in which age is expressed. Must be one of day, week, month, or year." + }, + "height": { + "pattern": "^[0-9]+\\.?[0-9]*-?[0-9]*\\.?[0-9]*$", + "type": "string", + "description": "Height of donor, in meters. Can be a range separated by a hyphen." + }, + "body_mass_index": { + "minimum": 5, + "type": "number", + "description": "The body mass index of the donor.", + "maximum": 100 + }, + "ancestry": { + "items": { + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology.json" + }, + "type": "array", + "description": "An array of ontology terms from EMBL-EBI's Ancestry Ontology describing ancestral groups, uncategorised ancestral groups, and population isolates." + }, + "smoking_history": { + "type": "string", + "description": "Estimated number of cigarettes smoked per day and for how many years." + }, "sex": { - "description": "Sex of donor. Should be one of male, female, mixed, or unknown.", "enum": [ - "female", - "male", - "mixed", + "female", + "male", + "mixed", "unknown" - ] - }, - "smoking_history": { - "description": "Estimated number of cigarettes smoked per day and for how many years.", - "type": "string" - }, - "strain": { - "description": "The name of th mouse inbred strain. e.g. C57BL/6.", - "type": "array", + ], + "description": "Sex of donor. Should be one of male, female, mixed, or unknown." + }, + "medication": { "items": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/ontology.json" - } - }, - "weight": { - "description": "Weight of donor, in kilograms. Can be a range separated by a hyphen.", - "pattern": "^[0-9]+\\.?[0-9]*-?[0-9]*\\.?[0-9]*$", - "type": "string" + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology.json" + }, + "type": "array", + "description": "List of medications the donor was currently taking at time of sample donation." + }, + "development_stage": { + "description": "More detailed (especially for embryos) version of life_stage. e.g. \"E9\" or \"P17\" for mouse.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology.json" } - }, - "required": [ - "is_living" - ], - "title": "donor", - "type": "object" + } } \ No newline at end of file diff --git a/json_schema/enrichment.json b/json_schema/enrichment.json index 9e39fe9bd..db4989b1b 100644 --- a/json_schema/enrichment.json +++ b/json_schema/enrichment.json @@ -1,36 +1,36 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", - "description": "enrichment schema generate by tagSchemaToJson from enrichment", - "additionalProperties": false, + "description": "enrichment schema generate by tagSchemaToJson from enrichment", + "title": "enrichment", + "required": [ + "type" + ], + "additionalProperties": false, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { - "markers": { - "description": "Space-delimited list of markers (with +/-) used for enrichment. e.g. CD4+ CD8-", - "type": "string" - }, - "size_max": { - "description": "Maximum size passing selection, in microns.", - "maximum": 10000, - "minimum": 0.01, - "type": "number" - }, - "size_min": { - "description": "Minimum size passing selection, in microns.", - "maximum": 10000, - "minimum": 0.01, - "type": "number" - }, "type": { - "description": "The method by which enrichment was achieved. e.g. MACS, FACS, Ficoli gradient", "enum": [ - "FACS", - "MACS", + "FACS", + "MACS", "Ficoll gradient" - ] + ], + "description": "The method by which enrichment was achieved. e.g. MACS, FACS, Ficoli gradient" + }, + "size_min": { + "minimum": 0.01, + "type": "number", + "description": "Minimum size passing selection, in microns.", + "maximum": 10000 + }, + "size_max": { + "minimum": 0.01, + "type": "number", + "description": "Maximum size passing selection, in microns.", + "maximum": 10000 + }, + "markers": { + "type": "string", + "description": "Space-delimited list of markers (with +/-) used for enrichment. e.g. CD4+ CD8-" } - }, - "required": [ - "type" - ], - "title": "enrichment", - "type": "object" + } } \ No newline at end of file diff --git a/json_schema/file.json b/json_schema/file.json index 42f10a41d..78be06329 100644 --- a/json_schema/file.json +++ b/json_schema/file.json @@ -1,31 +1,31 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", - "additionalProperties": false, - "description": "Information about the data files produced from single cells.", - "title": "file", - "type": "object", + "description": "Information about the data files produced from single cells.", + "title": "file", + "required": [ + "filename" + ], + "additionalProperties": false, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { - "filename": { - "description": "A filename for a data file. Must have a valid extension.", - "pattern": "^.*.fastq$|^.*.fastq.gz$|^.*.jpg$|^.*.jpeg$|^.*.tiff$|^.*.png$", - "type": "string" - }, + "core": { + "description": "Type and schema for this object.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/core.json" + }, "file_format": { - "description": "The format that the data file is in. Must be one of: fastq, fastq.gz, tiff, jpg, png.", "enum": [ - "fastq", - "fastq.gz", - "tiff", - "jpg", + "fastq", + "fastq.gz", + "tiff", + "jpg", "png" - ] - }, - "core": { - "description": "Type and schema for this object.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/core.json" + ], + "description": "The format that the data file is in. Must be one of: fastq, fastq.gz, tiff, jpg, png." + }, + "filename": { + "pattern": "^.*.fastq$|^.*.fastq.gz$|^.*.jpg$|^.*.jpeg$|^.*.tiff$|^.*.png$", + "type": "string", + "description": "A filename for a data file. Must have a valid extension." } - }, - "required": [ - "filename" - ] + } } \ No newline at end of file diff --git a/json_schema/imaging.json b/json_schema/imaging.json index 9269f11f2..4e4f1b1ef 100644 --- a/json_schema/imaging.json +++ b/json_schema/imaging.json @@ -1,61 +1,61 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", - "additionalProperties": false, - "definitions": {}, - "description": "imaging schema generate by tagSchemaToJson from imaging", + "description": "imaging schema generate by tagSchemaToJson from imaging", + "title": "imaging", + "required": [ + "field_counts", + "field_resolution", + "probes" + ], + "additionalProperties": false, + "definitions": {}, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { - "embedding": { - "description": "Description of embedding conditions", - "type": "string" - }, "exposure_time": { - "description": "Exposure time as a floating point number in units of seconds", - "maximum": 1000, - "minimum": 1e-09, - "type": "number" - }, - "field_counts": { - "description": "number of fields in x and y dimensions", - "items": { - "type": "integer" - }, - "type": "array" - }, + "minimum": 1e-09, + "type": "number", + "description": "Exposure time as a floating point number in units of seconds", + "maximum": 1000 + }, "field_microns": { - "description": "microns covered by a field in x,y, and z. Z includes all focal planes in a single file", - "items": { - "type": "integer" - }, - "type": "array" - }, - "field_resolution": { - "description": "x, y, and z (number of focal planes) resolution of an individual field", "items": { "type": "integer" - }, - "type": "array" - }, + }, + "type": "array", + "description": "microns covered by a field in x,y, and z. Z includes all focal planes in a single file" + }, "fixation": { - "description": "Description of fixation conditions", - "type": "string" - }, + "type": "string", + "description": "Description of fixation conditions" + }, "microscope": { - "description": "Microscope used for imaging", "enum": [ - "generic confocal", + "generic confocal", "generic two photon" - ] - }, + ], + "description": "Microscope used for imaging" + }, + "embedding": { + "type": "string", + "description": "Description of embedding conditions" + }, + "field_resolution": { + "items": { + "type": "integer" + }, + "type": "array", + "description": "x, y, and z (number of focal planes) resolution of an individual field" + }, "probes": { - "description": "A file containing information on probe sequence, genes they cover, and colors", - "type": "string" + "type": "string", + "description": "A file containing information on probe sequence, genes they cover, and colors" + }, + "field_counts": { + "items": { + "type": "integer" + }, + "type": "array", + "description": "number of fields in x and y dimensions" } - }, - "required": [ - "field_counts", - "field_resolution", - "probes" - ], - "title": "imaging", - "type": "object" + } } \ No newline at end of file diff --git a/json_schema/immortalized_cell_line.json b/json_schema/immortalized_cell_line.json index b34a5f436..da13b900b 100644 --- a/json_schema/immortalized_cell_line.json +++ b/json_schema/immortalized_cell_line.json @@ -1,48 +1,48 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", - "additionalProperties": false, - "description": "Information about the immortalized cell line used in the sample", + "description": "Information about the immortalized cell line used in the sample", + "title": "immortalized_cell_line", + "additionalProperties": false, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { - "catalog_number": { - "description": "The supplier catalogue number for the cell line.", - "type": "string" - }, "catalog_url": { - "description": "The supplier catalogue URL for the cell line.", - "type": "string" - }, + "type": "string", + "description": "The supplier catalogue URL for the cell line." + }, "cell_type": { - "description": "What cell type the line was derived from. CLO ontology.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/ontology_json/cell_type_ontology.json" - }, + "description": "What cell type the line was derived from. CLO ontology.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology_json/cell_type_ontology.json" + }, "date_established": { - "description": "When the cell line was established.", - "format": "date-time", - "type": "string" - }, + "type": "string", + "description": "When the cell line was established.", + "format": "date-time" + }, + "catalog_number": { + "type": "string", + "description": "The supplier catalogue number for the cell line." + }, "disease": { - "description": "A disease associated with the cell line. EFO ontology.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/ontology_json/disease_ontology.json" - }, - "karyotype": { - "description": "The karyotype of the cell line.", - "type": "string" - }, + "description": "A disease associated with the cell line. EFO ontology.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology_json/disease_ontology.json" + }, "passage_number": { - "description": "The number of passages the cell line as been through.", - "maximum": 1000, - "minimum": 0, - "type": "integer" - }, - "publication": { - "description": "The publication in which the cell line creation was cited.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/publication.json" - }, + "minimum": 0, + "type": "integer", + "description": "The number of passages the cell line as been through.", + "maximum": 1000 + }, "cell_cycle": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/ontology.json", - "description": "The cell cycle phase, if known." + "description": "The cell cycle phase, if known.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology.json" + }, + "karyotype": { + "type": "string", + "description": "The karyotype of the cell line." + }, + "publication": { + "description": "The publication in which the cell line creation was cited.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/publication.json" } - }, - "title": "immortalized_cell_line", - "type": "object" + } } \ No newline at end of file diff --git a/json_schema/ingest.json b/json_schema/ingest.json index 2a41ccad4..24f571287 100644 --- a/json_schema/ingest.json +++ b/json_schema/ingest.json @@ -1,39 +1,39 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", - "additionalProperties": false, - "description": "Information added or generated at ingest time.", + "additionalProperties": false, + "$schema": "http://json-schema.org/draft-04/schema#", + "required": [ + "document_id", + "submissionDate" + ], + "description": "Information added or generated at ingest time.", "properties": { + "accession": { + "type": "string", + "description": "A unique accession for this entity, provided by the broker." + }, "submissionDate": { - "description": "When project was first submitted to database.", - "format": "date-time", - "type": "string" - }, + "type": "string", + "description": "When project was first submitted to database.", + "format": "date-time" + }, "submitter_id": { - "description": "ID of contact who first submitted project", - "type": "string" - }, + "type": "string", + "description": "ID of contact who first submitted project" + }, "updateDate": { - "description": "When project was last updated", - "format": "date-time", - "type": "string" - }, - "updater_id": { - "description": "ID of contact who last updated project", - "type": "string" - }, + "type": "string", + "description": "When project was last updated", + "format": "date-time" + }, "document_id": { - "description": "Identifier for document.", - "comment": "This structure supports the current ingest API. It may change in future.", - "type": "string", - "pattern": ".{8}-.{4}-.{4}-.{4}-.{12}" - }, - "accession": { - "description": "A unique accession for this entity, provided by the broker.", - "type": "string" + "comment": "This structure supports the current ingest API. It may change in future.", + "pattern": ".{8}-.{4}-.{4}-.{4}-.{12}", + "type": "string", + "description": "Identifier for document." + }, + "updater_id": { + "type": "string", + "description": "ID of contact who last updated project" } - }, - "required": [ - "document_id", - "submissionDate" - ] + } } \ No newline at end of file diff --git a/json_schema/ontology.json b/json_schema/ontology.json index b25986af3..71513c541 100644 --- a/json_schema/ontology.json +++ b/json_schema/ontology.json @@ -1,19 +1,19 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", - "description": "A term that may be associated with an ontology term", + "description": "A term that may be associated with an ontology term", + "title": "ontology", + "required": [ + "text" + ], + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { "text": { - "description": "The text for the term as the user provides it.", - "type": "string" - }, + "type": "string", + "description": "The text for the term as the user provides it." + }, "ontology": { - "description": "An optional ontology reference in format where prefix_ indicates which ontology", - "type": "string" + "type": "string", + "description": "An optional ontology reference in format where prefix_ indicates which ontology" } - }, - "required": [ - "text" - ], - "title": "ontology", - "type": "object" + } } \ No newline at end of file diff --git a/json_schema/organoid.json b/json_schema/organoid.json index 5c2ea626a..310e49341 100644 --- a/json_schema/organoid.json +++ b/json_schema/organoid.json @@ -1,14 +1,14 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", - "description": "A description of an organoid sample.", + "required": [ + "model_for_organ" + ], + "$schema": "http://json-schema.org/draft-04/schema#", + "title": "organoid", + "description": "A description of an organoid sample.", "properties": { "model_for_organ": { - "description": "Organ that this organoid is a model system for.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/ontology.json" + "description": "Organ that this organoid is a model system for.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology.json" } - }, - "title": "organoid", - "required": [ - "model_for_organ" - ] + } } \ No newline at end of file diff --git a/json_schema/primary_cell_line.json b/json_schema/primary_cell_line.json index c8a32fb30..1c52b7ee2 100644 --- a/json_schema/primary_cell_line.json +++ b/json_schema/primary_cell_line.json @@ -1,32 +1,32 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", - "additionalProperties": false, - "description": "Information about the primary cell line used in the sample", + "description": "Information about the primary cell line used in the sample", + "title": "primary_cell_line", + "additionalProperties": false, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { "cell_type": { - "description": "The cell type that the cell line was derived from. Should be a CLO ontology.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/ontology_json/cell_type_ontology.json" - }, + "description": "The cell type that the cell line was derived from. Should be a CLO ontology.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology_json/cell_type_ontology.json" + }, "date_established": { - "description": "When the cell line was established, in date-time format.", - "format": "date-time", - "type": "string" - }, + "type": "string", + "description": "When the cell line was established, in date-time format.", + "format": "date-time" + }, "disease": { - "description": "Free text describing any disease association to the cell type. Should be found in EFO ontology.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/ontology_json/disease_ontology.json" - }, + "description": "Free text describing any disease association to the cell type. Should be found in EFO ontology.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology_json/disease_ontology.json" + }, "passage_number": { - "description": "The number of passages the cell line has been through.", - "maximum": 1000, - "minimum": 0, - "type": "integer" - }, + "minimum": 0, + "type": "integer", + "description": "The number of passages the cell line has been through.", + "maximum": 1000 + }, "cell_cycle": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/ontology.json", - "description": "The cell cycle phase if the cell line is synchronized growing cells or the phase is known." + "description": "The cell cycle phase if the cell line is synchronized growing cells or the phase is known.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology.json" } - }, - "title": "primary_cell_line", - "type": "object" + } } \ No newline at end of file diff --git a/json_schema/project.json b/json_schema/project.json index 98a05e538..18e817a06 100644 --- a/json_schema/project.json +++ b/json_schema/project.json @@ -1,106 +1,106 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", - "additionalProperties": false, - "definitions": {}, - "description": "project schema generate by tagSchemaToJson from project", + "description": "project schema generate by tagSchemaToJson from project", + "title": "project", + "required": [ + "core", + "contributors", + "project_id" + ], "patternProperties": { "^characteristics_.*$": { - "description": "Fields that begin with characteristics_ can contain any value, and the field name can be anything after the prefix", - "type": "string" + "type": "string", + "description": "Fields that begin with characteristics_ can contain any value, and the field name can be anything after the prefix" } - }, + }, + "additionalProperties": false, + "definitions": {}, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { - "project_id": { - "description": "A unique ID for this project.", - "type": "string" - }, + "core": { + "description": "type and schema for this object", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/core.json" + }, + "related_projects": { + "items": { + "type": "string" + }, + "type": "array", + "description": "A list of other projects that may be logically grouped with this one." + }, "name": { - "description": "A short, descriptive name for the project that need not be unique.", - "type": "string" - }, - "description": { - "description": "A general description of the project.", - "type": "string" - }, - "array_express_investigation": { - "description": "An EBI ArrayExpress investigation accession.", - "pattern": "^E-....-.*$", - "type": "string" - }, + "type": "string", + "description": "A short, descriptive name for the project that need not be unique." + }, "contributors": { - "description": "List of people contributing to the project.", "items": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/contact.json" - }, - "type": "array" - }, - "core": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/core.json", - "description": "type and schema for this object" - }, - "experimental_design": { - "items": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/ontology.json", - "description": "A short description of overall experiment type. e.g. \"single cell RNA sequencing.\"" - }, - "type": "array" - }, + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/contact.json" + }, + "type": "array", + "description": "List of people contributing to the project." + }, "experimental_factor_name": { - "description": "A list of the factors that vary between samples in the experiment. e.g. \"time since collection\", \"preservation method\"", "items": { "type": "string" - }, - "type": "array" - }, - "geo_series": { - "description": "An NCBI GEO series accession.", - "pattern": "^GSE.*$", - "type": "string" - }, - "insdc_project": { - "description": "An INSDC (International Nucleotide Sequence Database Collaboration) project accession. Can be from the DDBJ, EMBL-EBI, or NCBI. Accession must start with DRP, ERP, or SRP.", - "pattern": "^[D|E|S]RP[0-9]+$", - "type": "string" - }, - "insdc_study": { - "description": "An INSDC (International Nucleotide Sequence Database Collaboration) study accession. Can be from the DDBJ, EMBL-EBI, or NCBI. Accession must start with PRJE, PRJN, or PRJD", - "pattern": "^PRJ[E|N|D][a-zA-Z][0-9]+$", - "type": "string" - }, - "publications": { + }, + "type": "array", + "description": "A list of the factors that vary between samples in the experiment. e.g. \"time since collection\", \"preservation method\"" + }, + "submitters": { "items": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/publication.json", - "description": "An array of publication modules." - }, - "type": "array" - }, - "related_projects": { - "description": "A list of other projects that may be logically grouped with this one.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/contact.json" + }, + "type": "array", + "description": "List of people submitting data to the project." + }, + "insdc_project": { + "pattern": "^[D|E|S]RP[0-9]+$", + "type": "string", + "description": "An INSDC (International Nucleotide Sequence Database Collaboration) project accession. Can be from the DDBJ, EMBL-EBI, or NCBI. Accession must start with DRP, ERP, or SRP." + }, + "supplementary_files": { "items": { "type": "string" - }, - "type": "array" - }, - "submitters": { - "description": "List of people submitting data to the project.", + }, + "type": "array", + "description": "Project-level supplementary files. e.g. experimental design documents, lab spreadsheets, manuscripts in preparation." + }, + "geo_series": { + "pattern": "^GSE.*$", + "type": "string", + "description": "An NCBI GEO series accession." + }, + "experimental_design": { "items": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/contact.json" - }, + "description": "A short description of overall experiment type. e.g. \"single cell RNA sequencing.\"", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology.json" + }, "type": "array" - }, - "supplementary_files": { - "description": "Project-level supplementary files. e.g. experimental design documents, lab spreadsheets, manuscripts in preparation.", + }, + "publications": { "items": { - "type": "string" - }, + "description": "An array of publication modules.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/publication.json" + }, "type": "array" + }, + "array_express_investigation": { + "pattern": "^E-....-.*$", + "type": "string", + "description": "An EBI ArrayExpress investigation accession." + }, + "project_id": { + "type": "string", + "description": "A unique ID for this project." + }, + "insdc_study": { + "pattern": "^PRJ[E|N|D][a-zA-Z][0-9]+$", + "type": "string", + "description": "An INSDC (International Nucleotide Sequence Database Collaboration) study accession. Can be from the DDBJ, EMBL-EBI, or NCBI. Accession must start with PRJE, PRJN, or PRJD" + }, + "description": { + "type": "string", + "description": "A general description of the project." } - }, - "required": [ - "core", - "contributors", - "project_id" - ], - "title": "project", - "type": "object" + } } \ No newline at end of file diff --git a/json_schema/project_bundle.json b/json_schema/project_bundle.json index faa2aa2ba..0dc483c05 100644 --- a/json_schema/project_bundle.json +++ b/json_schema/project_bundle.json @@ -1,29 +1,29 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", - "description": "A schema for a project bundle", - "type": "array", "definitions": { "project_ingest": { - "type": "object", "required": [ - "hca_ingest", + "hca_ingest", "content" - ], + ], + "type": "object", "properties": { - "hca_ingest": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/ingest.json", - "description": "core fields added by HCA ingest service", - "type": "object" - }, "content": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/project.json", - "description": "Project content", - "type": "object" + "type": "object", + "description": "Project content", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/project.json" + }, + "hca_ingest": { + "type": "object", + "description": "core fields added by HCA ingest service", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ingest.json" } } } - }, + }, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "array", + "description": "A schema for a project bundle", "items": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/project_bundle.json#/definitions/project_ingest" + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/project_bundle.json#/definitions/project_ingest" } } \ No newline at end of file diff --git a/json_schema/protocol.json b/json_schema/protocol.json index dd1d0c498..271037e87 100644 --- a/json_schema/protocol.json +++ b/json_schema/protocol.json @@ -1,48 +1,48 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", - "additionalProperties": false, - "definitions": {}, - "description": "protocol schema generate by tagSchemaToJson from protocol", + "description": "protocol schema generate by tagSchemaToJson from protocol", + "title": "protocol", + "required": [ + "core", + "protocol_id", + "type" + ], + "additionalProperties": false, + "definitions": {}, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { - "protocol_id": { - "description": "A unique ID for this protocol.", - "type": "string" - }, - "name": { - "description": "A short, descriptive name for the protocol that need not be unique.", - "type": "string" - }, + "core": { + "description": "type and schema for this object", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/core.json" + }, + "retail_name": { + "type": "string", + "description": "The retail name of the kit used. e.g SureCell WTA 3' Library Prep Kit" + }, "description": { - "description": "A general description of the protocol.", - "type": "string" - }, + "type": "string", + "description": "A general description of the protocol." + }, + "protocol_id": { + "type": "string", + "description": "A unique ID for this protocol." + }, "batch_number": { - "description": "The batch of kit used.", - "type": "string" - }, - "core": { - "description": "type and schema for this object", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/core.json" - }, + "type": "string", + "description": "The batch of kit used." + }, "pdf": { - "description": "A filename of a PDF containing the details of the protocol.", - "pattern": "^.*.pdf$", - "type": "string" - }, - "retail_name": { - "description": "The retail name of the kit used. e.g SureCell WTA 3' Library Prep Kit", - "type": "string" - }, + "pattern": "^.*.pdf$", + "type": "string", + "description": "A filename of a PDF containing the details of the protocol." + }, "type": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/ontology.json", - "description": "The type of protocol. Ideally an EFO term." + "description": "The type of protocol. Ideally an EFO term.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology.json" + }, + "name": { + "type": "string", + "description": "A short, descriptive name for the protocol that need not be unique." } - }, - "required": [ - "core", - "protocol_id", - "type" - ], - "title": "protocol", - "type": "object" + } } \ No newline at end of file diff --git a/json_schema/publication.json b/json_schema/publication.json index 87ea18210..fa0b252cb 100644 --- a/json_schema/publication.json +++ b/json_schema/publication.json @@ -1,36 +1,36 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", - "additionalProperties": false, - "description": "A publication contains information about a journal article, book, web page or other external available documentation on a project", + "description": "A publication contains information about a journal article, book, web page or other external available documentation on a project", + "title": "publication", + "required": [ + "authors", + "title" + ], + "additionalProperties": false, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { + "url": { + "type": "string", + "description": "A URL, preferably not behind a paywall, for the publication." + }, + "title": { + "type": "string", + "description": "The full title of the publication." + }, + "pmid": { + "type": "integer", + "description": "A PubMed ID of the publication, if available. e.g. 27565351" + }, + "doi": { + "type": "string", + "description": "The publication digital object identifier (doi), if available. e.g. \"10.1016/j.cell.2016.07.054\"" + }, "authors": { - "description": "A list of authors associated with the publication. Should be in \"surname initials\" format. e.g. \"Tran NM\", \"Kowalczyk M\", \"de Silva-Schmidt CKJ\"", "items": { "type": "string" - }, - "type": "array" - }, - "doi": { - "description": "The publication digital object identifier (doi), if available. e.g. \"10.1016/j.cell.2016.07.054\"", - "type": "string" - }, - "pmid": { - "description": "A PubMed ID of the publication, if available. e.g. 27565351", - "type": "integer" - }, - "title": { - "description": "The full title of the publication.", - "type": "string" - }, - "url": { - "description": "A URL, preferably not behind a paywall, for the publication.", - "type": "string" + }, + "type": "array", + "description": "A list of authors associated with the publication. Should be in \"surname initials\" format. e.g. \"Tran NM\", \"Kowalczyk M\", \"de Silva-Schmidt CKJ\"" } - }, - "required": [ - "authors", - "title" - ], - "title": "publication", - "type": "object" + } } \ No newline at end of file diff --git a/json_schema/rna.json b/json_schema/rna.json index 2124c6265..3181e26f2 100644 --- a/json_schema/rna.json +++ b/json_schema/rna.json @@ -1,70 +1,70 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", - "additionalProperties": false, - "definitions": {}, - "description": "Information about how RNA was converted to cDNA for sequencing.", + "description": "Information about how RNA was converted to cDNA for sequencing.", + "title": "rna", + "required": [ + "end_bias", + "library_construction", + "strand" + ], + "additionalProperties": false, + "definitions": {}, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { + "spike_in_dilution": { + "minimum": 1, + "type": "integer", + "description": "Dilution of RNA spike-in.", + "maximum": 1000000 + }, + "library_protocol": { + "pattern": "^P-....-.*$", + "type": "string", + "description": "RNA preparation protocol" + }, + "spike_in": { + "enum": [ + "ERCC" + ], + "description": "Name of RNA spike-in kit. e.g. ERCC." + }, "end_bias": { - "description": "The type of end bias the library has. Must be one of 3' bias, 5' bias, 3' end, 5' end, or none.", "enum": [ - "three_prime_end", - "three_prime_bias", - "five_prime_end", - "five_prime_bias", + "three_prime_end", + "three_prime_bias", + "five_prime_end", + "five_prime_bias", "none" - ] - }, - "library_construction": { - "description": "The general approach for sequencing library construction. e.g. Smart-seq, Drop-seq, 10x.", - "enum": [ - "unknown", - "CEL-seq", - "SMARTer Ultra Low RNA Kit", - "modified smart-seq2", - "smart-seq2", - "QUARTZ-Seq", - "10x_v2", - "drop-seq", - "inDrop" - ] - }, - "library_protocol": { - "description": "RNA preparation protocol", - "pattern": "^P-....-.*$", - "type": "string" - }, + ], + "description": "The type of end bias the library has. Must be one of 3' bias, 5' bias, 3' end, 5' end, or none." + }, "primer": { - "description": "Primer used for cDNA synthesis from RNA. Must be either poly-dT or random.", "enum": [ - "poly-dT", + "poly-dT", "random" - ] - }, - "spike_in": { - "description": "Name of RNA spike-in kit. e.g. ERCC.", - "enum": [ - "ERCC" - ] - }, - "spike_in_dilution": { - "description": "Dilution of RNA spike-in.", - "maximum": 1000000, - "minimum": 1, - "type": "integer" - }, + ], + "description": "Primer used for cDNA synthesis from RNA. Must be either poly-dT or random." + }, "strand": { - "description": "Single stranded?", "enum": [ - "both", + "both", "first" - ] + ], + "description": "Single stranded?" + }, + "library_construction": { + "enum": [ + "unknown", + "CEL-seq", + "SMARTer Ultra Low RNA Kit", + "modified smart-seq2", + "smart-seq2", + "QUARTZ-Seq", + "10x_v2", + "drop-seq", + "inDrop" + ], + "description": "The general approach for sequencing library construction. e.g. Smart-seq, Drop-seq, 10x." } - }, - "required": [ - "end_bias", - "library_construction", - "strand" - ], - "title": "rna", - "type": "object" + } } \ No newline at end of file diff --git a/json_schema/sample.json b/json_schema/sample.json index a41b70c67..4a83d92f9 100644 --- a/json_schema/sample.json +++ b/json_schema/sample.json @@ -1,126 +1,126 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", - "description": "A sample contains information on the biosample that was sequenced or imaged. This includes donor, body part, and anything that comes between removing the sample from a donor and the assay.", - "additionalProperties": false, - "patternProperties": { - "^characteristics_.*$": { - "description": "Fields that begin with characteristics_ can contain any value, and the field name can be anything after the prefix.", - "type": "string" - } - }, - "allOf": [ - { - "required": [ - "sample_id", - "core", - "ncbi_taxon_id" - ] - } - ], "oneOf": [ { "required": [ "donor" ] - }, + }, { "required": [ "immortalized_cell_line" ] - }, + }, { "required": [ "cell_suspension" ] - }, + }, { "required": [ "organoid" ] - }, + }, { "required": [ "primary_cell_line" ] - }, + }, { "required": [ "specimen_from_organism" ] } - ], + ], + "description": "A sample contains information on the biosample that was sequenced or imaged. This includes donor, body part, and anything that comes between removing the sample from a donor and the assay.", + "allOf": [ + { + "required": [ + "sample_id", + "core", + "ncbi_taxon_id" + ] + } + ], + "title": "sample", + "patternProperties": { + "^characteristics_.*$": { + "type": "string", + "description": "Fields that begin with characteristics_ can contain any value, and the field name can be anything after the prefix." + } + }, + "additionalProperties": false, + "$schema": "http://json-schema.org/draft-04/schema#", "properties": { "core": { - "description": "Type and schema for this object.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/core.json" - }, - "sample_id": { - "description": "A unique ID for this sample.", - "type": "string" - }, - "name": { - "description": "A short, descriptive name for the sample that need not be unique.", - "type": "string" - }, - "description": { - "description": "A general description of the sample.", - "type": "string" - }, - "donor": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/donor.json" - }, - "specimen_from_organism": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/specimen_from_organism.json" - }, + "description": "Type and schema for this object.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/core.json" + }, + "sample_accessions": { + "additionalProperties": false, + "type": "object", + "description": "One or more accession numbers from a standard archive.", + "properties": { + "insdc_sample": { + "pattern": "^[D|E|S]RS[0-9]+$", + "type": "string", + "description": "An INSDC (International Nucleotide Sequence Database Collaboration) sample accession. Can be from the DDBJ, EMBL-EBI, or NCBI. Accession must start with DRS, ERS, or SRS." + }, + "biosd_sample": { + "pattern": "^SAM[E|N|D][A|G]?[0-9]+$", + "type": "string", + "description": "A DDBJ, NCBI, or EBI BioSample ID. Accessions must start with SAMD, SAMN, or SAME." + } + } + }, "immortalized_cell_line": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/immortalized_cell_line.json" - }, - "primary_cell_line": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/primary_cell_line.json" - }, - "organoid": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/organoid.json" - }, + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/immortalized_cell_line.json" + }, + "description": { + "type": "string", + "description": "A general description of the sample." + }, "cell_suspension": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/cell_suspension.json" - }, - "ncbi_taxon_id": { - "description": "A taxonomy ID (taxonID) from NCBI.", - "type": "integer" - }, + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/cell_suspension.json" + }, + "specimen_from_organism": { + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/specimen_from_organism.json" + }, "genus_species": { - "description": "Scientific binomial name of donor species. e.g. Homo sapiens.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/ontology.json" - }, - "derived_from": { - "type": "string", - "description": "If this sample is derived from another sample e.g. a tissue or donor, enter the sample_id for the sample this was derived from", - "comment": "This field is primarily required for spreadsheet based submissions" - }, + "description": "Scientific binomial name of donor species. e.g. Homo sapiens.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology.json" + }, "supplementary_files": { - "description": "A list of filenames of sample-level supplementary files.", "items": { "type": "string" - }, - "type": "array" - }, - "sample_accessions": { - "type": "object", - "description": "One or more accession numbers from a standard archive.", - "additionalProperties": false, - "properties": { - "biosd_sample": { - "description": "A DDBJ, NCBI, or EBI BioSample ID. Accessions must start with SAMD, SAMN, or SAME.", - "pattern": "^SAM[E|N|D][A|G]?[0-9]+$", - "type": "string" - }, - "insdc_sample": { - "description": "An INSDC (International Nucleotide Sequence Database Collaboration) sample accession. Can be from the DDBJ, EMBL-EBI, or NCBI. Accession must start with DRS, ERS, or SRS.", - "pattern": "^[D|E|S]RS[0-9]+$", - "type": "string" - } - } + }, + "type": "array", + "description": "A list of filenames of sample-level supplementary files." + }, + "ncbi_taxon_id": { + "type": "integer", + "description": "A taxonomy ID (taxonID) from NCBI." + }, + "derived_from": { + "comment": "This field is primarily required for spreadsheet based submissions", + "type": "string", + "description": "If this sample is derived from another sample e.g. a tissue or donor, enter the sample_id for the sample this was derived from" + }, + "sample_id": { + "type": "string", + "description": "A unique ID for this sample." + }, + "donor": { + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/donor.json" + }, + "primary_cell_line": { + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/primary_cell_line.json" + }, + "organoid": { + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/organoid.json" + }, + "name": { + "type": "string", + "description": "A short, descriptive name for the sample that need not be unique." } - }, - "title": "sample" + } } \ No newline at end of file diff --git a/json_schema/sample_bundle.json b/json_schema/sample_bundle.json index de5daf521..7c0a7ba32 100644 --- a/json_schema/sample_bundle.json +++ b/json_schema/sample_bundle.json @@ -1,39 +1,39 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", - "description": "A schema for a sample bundle", - "type": "array", "definitions": { "sample_ingest": { - "type": "object", "required": [ - "hca_ingest", + "hca_ingest", "content" - ], + ], + "type": "object", "properties": { - "hca_ingest": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/ingest.json", - "description": "core fields added by HCA ingest service", - "type": "object" - }, "content": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/sample.json", - "description": "Sample content", - "type": "object" - }, - "derived_from": { - "type": "string" - }, + "type": "object", + "description": "Sample content", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/sample.json" + }, "derivation_protocols": { "items": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/protocol.json", - "description": "An array of protocols used in derivation of this sample." - }, + "description": "An array of protocols used in derivation of this sample.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/protocol.json" + }, "type": "array" + }, + "hca_ingest": { + "type": "object", + "description": "core fields added by HCA ingest service", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ingest.json" + }, + "derived_from": { + "type": "string" } } } - }, + }, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "array", + "description": "A schema for a sample bundle", "items": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/sample_bundle.json#/definitions/sample_ingest" + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/sample_bundle.json#/definitions/sample_ingest" } } \ No newline at end of file diff --git a/json_schema/seq.json b/json_schema/seq.json index c2ca24794..613cba4ce 100644 --- a/json_schema/seq.json +++ b/json_schema/seq.json @@ -1,120 +1,120 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", - "additionalProperties": false, + "description": "Information about how a sample was sequenced.", + "title": "seq", + "required": [ + "instrument_model", + "instrument_platform", + "lanes", + "molecule", + "paired_ends" + ], + "additionalProperties": false, "definitions": { "lanes": { "items": { - "additionalProperties": false, + "additionalProperties": false, + "required": [ + "r1" + ], + "type": "object", "properties": { - "number": { - "description": "Which lane number", - "type": "number" - }, - "r1": { - "description": "File name of first read in paired-end read sequencing assay, or only read for unpaired.", - "type": "string" - }, - "r2": { - "description": "File name of second read in paired-end read assay.", - "type": "string" - }, "i1": { - "description": "A barcode index file. Often index off of first read.", - "type": "string" - }, + "type": "string", + "description": "A barcode index file. Often index off of first read." + }, "i2": { - "description": "A barcode index file. Often index off of second read.", - "type": "string" + "type": "string", + "description": "A barcode index file. Often index off of second read." + }, + "number": { + "type": "number", + "description": "Which lane number" + }, + "r2": { + "type": "string", + "description": "File name of second read in paired-end read assay." + }, + "r1": { + "type": "string", + "description": "File name of first read in paired-end read sequencing assay, or only read for unpaired." } - }, - "required": [ - "r1" - ], - "title": "A sequencing lane.", - "type": "object" - }, - "title": "lane array", - "type": "array" + }, + "title": "A sequencing lane." + }, + "type": "array", + "title": "lane array" } - }, - "description": "Information about how a sample was sequenced.", + }, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { - "insdc_experiment": { - "description": "An INSDC (International Nucleotide Sequence Database Collaboration) experiment accession. Accession must start with DRX, ERX, or SRX.", - "pattern": "^[D|E|S]RX[0-9]+$", - "type": "string" - }, + "paired_ends": { + "type": "boolean", + "description": "Was a paired-end sequencing strategy used? Must be either yes or no." + }, + "lanes": { + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/seq.json#/definitions/lanes" + }, + "umi_barcode": { + "description": "Information about unique molecular identifier (UMI) barcode sequences.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/barcode.json" + }, "insdc_run": { - "description": "An INSDC (International Nucleotide Sequence Database Collaboration) run accession. Accession must start with DRR, ERR, or SRR.", "items": { - "pattern": "^[D|E|S]RR[0-9]+$", + "pattern": "^[D|E|S]RR[0-9]+$", "type": "string" - }, - "type": "array" - }, + }, + "type": "array", + "description": "An INSDC (International Nucleotide Sequence Database Collaboration) run accession. Accession must start with DRR, ERR, or SRR." + }, + "local_machine_name": { + "type": "string", + "description": "Local name for the particular machine on which the sample was sequenced." + }, + "molecule": { + "enum": [ + "polyA RNA", + "total RNA", + "genomic DNA" + ], + "description": "Specific type of molecule sequenced. e.g. total RNA, genomic DNA, polyA RNA." + }, "instrument_model": { - "description": "The model of the sequencer used. e.g. HiSeq 2000, Sequel.", "enum": [ - "HiSeq 2000", - "HiSeq 2500", - "HiSeq 4000", - "MiSeq", - "NextSeq 500", + "HiSeq 2000", + "HiSeq 2500", + "HiSeq 4000", + "MiSeq", + "NextSeq 500", "Sequel" - ] - }, + ], + "description": "The model of the sequencer used. e.g. HiSeq 2000, Sequel." + }, "instrument_platform": { - "description": "The sequencing platform used. e.g. Illumina, Ion Torrent, Pacific Biosciences.", "enum": [ - "Illumina", - "Ion Torrent", + "Illumina", + "Ion Torrent", "Pacific Biosciences" - ] - }, - "lanes": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/seq.json#/definitions/lanes" - }, + ], + "description": "The sequencing platform used. e.g. Illumina, Ion Torrent, Pacific Biosciences." + }, + "library_protocol": { + "pattern": "^P-....-.*$", + "type": "string", + "description": "DNA sequencing library preparation protocol." + }, + "insdc_experiment": { + "pattern": "^[D|E|S]RX[0-9]+$", + "type": "string", + "description": "An INSDC (International Nucleotide Sequence Database Collaboration) experiment accession. Accession must start with DRX, ERX, or SRX." + }, "library_construction": { - "description": "How the DNA sequencing library was prepared. e.g. Nextera XT, TrueSeq.", "enum": [ - "Nextera XT", - "TruSeq", + "Nextera XT", + "TruSeq", "modified Nextera XT" - ] - }, - "library_protocol": { - "description": "DNA sequencing library preparation protocol.", - "pattern": "^P-....-.*$", - "type": "string" - }, - "local_machine_name": { - "description": "Local name for the particular machine on which the sample was sequenced.", - "type": "string" - }, - "molecule": { - "description": "Specific type of molecule sequenced. e.g. total RNA, genomic DNA, polyA RNA.", - "enum": [ - "polyA RNA", - "total RNA", - "genomic DNA" - ] - }, - "paired_ends": { - "description": "Was a paired-end sequencing strategy used? Must be either yes or no.", - "type": "boolean" - }, - "umi_barcode": { - "description": "Information about unique molecular identifier (UMI) barcode sequences.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/barcode.json" + ], + "description": "How the DNA sequencing library was prepared. e.g. Nextera XT, TrueSeq." } - }, - "required": [ - "instrument_model", - "instrument_platform", - "lanes", - "molecule", - "paired_ends" - ], - "title": "seq", - "type": "object" + } } \ No newline at end of file diff --git a/json_schema/single_cell.json b/json_schema/single_cell.json index 51ad41682..a2500be55 100644 --- a/json_schema/single_cell.json +++ b/json_schema/single_cell.json @@ -1,28 +1,28 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", - "additionalProperties": false, - "description": "Contains information on single cell aspects of an assay.", + "description": "Contains information on single cell aspects of an assay.", + "title": "single_cell", + "required": [ + "cell_handling" + ], + "additionalProperties": false, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { "cell_barcode": { - "description": "Information about cell identifier barcode.", - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/barcode.json" - }, + "description": "Information about cell identifier barcode.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/barcode.json" + }, "cell_handling": { - "description": "How cells are separated. e.g. FACS, drop-seq, 10X_v2, Fluidigm C1.", "enum": [ - "10x_v2", - "FACS", - "Fluidigm C1", - "drop-seq", - "inDrop", - "mouth pipette", + "10x_v2", + "FACS", + "Fluidigm C1", + "drop-seq", + "inDrop", + "mouth pipette", "bulk" - ] + ], + "description": "How cells are separated. e.g. FACS, drop-seq, 10X_v2, Fluidigm C1." } - }, - "required": [ - "cell_handling" - ], - "title": "single_cell", - "type": "object" + } } \ No newline at end of file diff --git a/json_schema/specimen_from_organism.json b/json_schema/specimen_from_organism.json index e45176eca..687c7d280 100644 --- a/json_schema/specimen_from_organism.json +++ b/json_schema/specimen_from_organism.json @@ -1,25 +1,25 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", - "additionalProperties": false, - "description": "Information about the specimen that was extracted from the donor organism.", - "title": "specimen_from_organism", - "type": "object", + "description": "Information about the specimen that was extracted from the donor organism.", + "title": "specimen_from_organism", + "required": [ + "body_part", + "organ" + ], + "additionalProperties": false, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { "body_part": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/ontology_json/body_part_ontology.json", - "description": "A more detailed position within the body than the term given in the organ field." - }, - "organ": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/ontology.json", - "description": "The organ that the sample came from. e.g. liver, spleen. Blood and connective tissue count as organs." - }, + "description": "A more detailed position within the body than the term given in the organ field.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology_json/body_part_ontology.json" + }, "state_of_specimen": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/state_of_specimen.json", - "description": "State of body_part at collection and how it was preserved after removal." + "description": "State of body_part at collection and how it was preserved after removal.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/state_of_specimen.json" + }, + "organ": { + "description": "The organ that the sample came from. e.g. liver, spleen. Blood and connective tissue count as organs.", + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology.json" } - }, - "required": [ - "body_part", - "organ" - ] + } } \ No newline at end of file diff --git a/json_schema/state_of_specimen.json b/json_schema/state_of_specimen.json index 4867f0cb4..06991787e 100644 --- a/json_schema/state_of_specimen.json +++ b/json_schema/state_of_specimen.json @@ -1,54 +1,54 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", - "additionalProperties": false, - "definitions": {}, - "description": "State of body part at collection and how it was preserved after removal and/or cell enrichment", + "description": "State of body part at collection and how it was preserved after removal and/or cell enrichment", + "title": "state_of_specimen", + "additionalProperties": false, + "definitions": {}, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { - "autolysis_score": { - "description": "State of tissue breakdown due to self-digestion. Must be one of: none, mild, moderate.", - "enum": [ - "none", - "mild", - "moderate" - ] - }, - "gross_description": { - "description": "Color, size, and other aspects of specimen as visible to naked eye.", - "type": "string" - }, + "ischemic_time": { + "minimum": 0, + "type": "integer", + "description": "Duration of time, in seconds, that the body part had insufficient blood supply.", + "maximum": 100000 + }, "gross_image": { - "description": "List of filenames of photographs of body part without magnification. Must be of format JPEG, TIFF, or PNG.", "items": { - "pattern": "^.*.jpg$|^.*.jpeg$|^.*.tiff$|^.*.png$", + "pattern": "^.*.jpg$|^.*.jpeg$|^.*.tiff$|^.*.png$", "type": "string" - }, - "type": "array" - }, - "ischemic_time": { - "description": "Duration of time, in seconds, that the body part had insufficient blood supply.", - "maximum": 100000, - "minimum": 0, - "type": "integer" - }, - "microscopic_description": { - "description": "How the sample looks under the microscope and how it compares with normal cells.", - "type": "string" - }, + }, + "type": "array", + "description": "List of filenames of photographs of body part without magnification. Must be of format JPEG, TIFF, or PNG." + }, + "postmortem_interval": { + "minimum": 0, + "type": "integer", + "description": "Duration of time, in seconds, between when death is declared and when the tissue is preserved or processed.", + "maximum": 100000 + }, + "gross_description": { + "type": "string", + "description": "Color, size, and other aspects of specimen as visible to naked eye." + }, + "autolysis_score": { + "enum": [ + "none", + "mild", + "moderate" + ], + "description": "State of tissue breakdown due to self-digestion. Must be one of: none, mild, moderate." + }, "microscopic_image": { - "description": "List of filenames of photographs of body part under microscope. Must be of format JPEG, TIFF, or PNG.", "items": { - "pattern": "^.*.jpg$|^.*.jpeg$|^.*.tiff$|^.*.png$", + "pattern": "^.*.jpg$|^.*.jpeg$|^.*.tiff$|^.*.png$", "type": "string" - }, - "type": "array" - }, - "postmortem_interval": { - "description": "Duration of time, in seconds, between when death is declared and when the tissue is preserved or processed.", - "maximum": 100000, - "minimum": 0, - "type": "integer" + }, + "type": "array", + "description": "List of filenames of photographs of body part under microscope. Must be of format JPEG, TIFF, or PNG." + }, + "microscopic_description": { + "type": "string", + "description": "How the sample looks under the microscope and how it compares with normal cells." } - }, - "title": "state_of_specimen", - "type": "object" + } } \ No newline at end of file diff --git a/json_schema/submission.json b/json_schema/submission.json index 627c43c0e..cf142b35c 100644 --- a/json_schema/submission.json +++ b/json_schema/submission.json @@ -1,87 +1,87 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", - "additionalProperties": false, + "title": "submission", + "required": [ + "transfer_service_version", + "submitted_files" + ], + "additionalProperties": false, "definitions": { - "transfer_service_version": { - "additionalProperties": false, - "type": "string" - }, "submitted_files": { - "additionalProperties": false, - "type": "array", + "additionalProperties": false, "items": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/submission.json#/definitions/file" - } - }, + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/submission.json#/definitions/file" + }, + "type": "array" + }, + "transfer_service_version": { + "additionalProperties": false, + "type": "string" + }, "file": { - "type": "object", - "additionalProperties": false, + "additionalProperties": false, + "required": [ + "name", + "content_type", + "size", + "id", + "checksums" + ], + "type": "object", "properties": { - "name": { - "description": "Name of the file", - "type": "string" - }, - "content_type": { - "description": "type of file e.g hca-sample-json, hca-assay-json, hca-rnaseq-fastq-gz", - "type": "string" - }, - "size": { - "description": "Length of file in bytes", - "type": "integer" - }, "id": { - "description": "URI of the Data Storage System file resource that describes this file", - "type": "string" - }, + "type": "string", + "description": "URI of the Data Storage System file resource that describes this file" + }, "checksums": { - "type": "object", + "required": [ + "s3etag", + "sha1", + "sha256", + "crc32" + ], + "type": "object", "properties": { + "crc32": { + "type": "string", + "description": "CRC-32 checksum of this file" + }, + "sha256": { + "type": "string", + "description": "SHA-256 checksum of this file" + }, "s3etag": { - "description": "S3 ETAG checksum of this file", - "type": "string" - }, + "type": "string", + "description": "S3 ETAG checksum of this file" + }, "sha1": { - "description": "SHA-1 checksum of this file", - "type": "string" - }, - "sha256": { - "description": "SHA-256 checksum of this file", - "type": "string" - }, - "crc32": { - "description": "CRC-32 checksum of this file", - "type": "string" + "type": "string", + "description": "SHA-1 checksum of this file" } - }, - "required": [ - "s3etag", - "sha1", - "sha256", - "crc32" - ] + } + }, + "name": { + "type": "string", + "description": "Name of the file" + }, + "content_type": { + "type": "string", + "description": "type of file e.g hca-sample-json, hca-assay-json, hca-rnaseq-fastq-gz" + }, + "size": { + "type": "integer", + "description": "Length of file in bytes" } - }, - "required": [ - "name", - "content_type", - "size", - "id", - "checksums" - ] + } } - }, + }, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { - "transfer_service_version": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/submission.json#/definitions/transfer_service_version" - }, "submitted_files": { - "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.1.0/json_schema/submission.json#/definitions/submitted_files" + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/submission.json#/definitions/submitted_files" + }, + "transfer_service_version": { + "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/submission.json#/definitions/transfer_service_version" } - }, - "required": [ - "transfer_service_version", - "submitted_files" - ], - "title": "submission", - "type": "object" + } } \ No newline at end of file diff --git a/json_schema/well.json b/json_schema/well.json index 03eed4fdb..c97f57ae0 100644 --- a/json_schema/well.json +++ b/json_schema/well.json @@ -1,34 +1,34 @@ { - "$schema": "http://json-schema.org/draft-04/schema#", - "additionalProperties": false, - "description": "This describes the well inside the plate or fluidics chip where sample came from.", + "description": "This describes the well inside the plate or fluidics chip where sample came from.", + "title": "well", + "additionalProperties": false, + "$schema": "http://json-schema.org/draft-04/schema#", + "type": "object", "properties": { - "col": { - "description": "Well column in plate.", - "type": "string" - }, - "name": { - "description": "A name for the well. Should be unique for the plate", - "type": "string" - }, "plate": { - "description": "An ID for the plate that the well is located on.", - "type": "string" - }, + "type": "string", + "description": "An ID for the plate that the well is located on." + }, + "row": { + "type": "string", + "description": "Well row in plate." + }, "quality": { - "description": "Note on how good cell looks if imaged in well before sequencing.", "enum": [ - "OK", - "control, 2-cell well", - "control, empty well", + "OK", + "control, 2-cell well", + "control, empty well", "low quality cell" - ] - }, - "row": { - "description": "Well row in plate.", - "type": "string" + ], + "description": "Note on how good cell looks if imaged in well before sequencing." + }, + "col": { + "type": "string", + "description": "Well column in plate." + }, + "name": { + "type": "string", + "description": "A name for the well. Should be unique for the plate" } - }, - "title": "well", - "type": "object" + } } \ No newline at end of file