Merge branch 'master' into fix-ci-warning

edmcouncil · Jul 11, 2024 · e35e848 · e35e848
2 parents e96975d + 8e3c6e1
commit e35e848
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Showing 7 changed files with 24 additions and 31 deletions.
diff --git a/.github/workflows/unit_tests_run.yml b/.github/workflows/unit_tests_run.yml
@@ -34,7 +34,7 @@ jobs:
           ./etc/unit_tests/dependencies.sh
       - name: Run unit tests using Apache Jena
         run: |
-          java -Xmx5G -jar etc/unit_tests/target/unit-test-runner-1.0.jar \
+          java -Xmx8G -jar etc/unit_tests/target/unit-test-runner-1.0.jar \
             -ontology_location ./AboutIDMPDev-ReferenceIndividuals.ttl \
             -root_folder etc/unit_tests/ \
             -cq_source etc/CQ/Example/ \
@@ -52,7 +52,7 @@ jobs:
   GSRS:
     runs-on: ubuntu-latest
     env:
-      GSRS_VERSION: ${{ inputs.gsrs_version || '2022-12-15' }}
+      GSRS_VERSION: ${{ inputs.gsrs_version || '2023-12-14' }}
     steps:
       - uses: actions/checkout@v4
       - name: Set up Java 11
@@ -84,7 +84,7 @@ jobs:
           queries=(gsrs-public-data-identifiers gsrs-public-data-names gsrs-public-data-relationships gsrs-public-data-substances)
           for query in "${queries[@]}"; do
             echo "Transforming $query.rqg"
-            java -Xmx5G -jar sparql-generate.jar -l INFO -q etc/transformation/GSRS/$query.rqg -o $query.ttl
+            java -Xmx8G -jar sparql-generate.jar -l INFO -q etc/transformation/GSRS/$query.rqg -o $query.ttl
           done
           result=gsrs-transformed.ttl
           rm -rf $result
@@ -101,7 +101,7 @@ jobs:
           done
       - name: Run unit tests using Apache Jena
         run: |
-          java -Xmx5G -jar etc/unit_tests/target/unit-test-runner-1.0.jar \
+          java -Xmx8G -jar etc/unit_tests/target/unit-test-runner-1.0.jar \
             -ontology_location ./gsrs-final.ttl \
             -root_folder etc/unit_tests/ \
             -cq_source etc/CQ/Example/ \

diff --git a/etc/transformation/GSRS/gsrs-public-data-identifiers.rqg b/etc/transformation/GSRS/gsrs-public-data-identifiers.rqg
@@ -2,14 +2,12 @@ PREFIX iter: <http://w3id.org/sparql-generate/iter/>
 PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
-PREFIX cmns-id:   <https://www.omg.org/spec/Commons/Identifiers/>
+PREFIX cmns-id: <https://www.omg.org/spec/Commons/Identifiers/>
 PREFIX cmns-ra: <https://www.omg.org/spec/Commons/RegistrationAuthorities/>
 PREFIX idmp-nara: <https://spec.pistoiaalliance.org/idmp/ontology/ISO/NorthAmericanJurisdiction/NorthAmericanRegistrationAuthorities/>
-PREFIX cmns-txt:  <https://www.omg.org/spec/Commons/TextDatatype/>
+PREFIX cmns-txt: <https://www.omg.org/spec/Commons/TextDatatype/>
 PREFIX idmp-eura: <https://spec.pistoiaalliance.org/idmp/ontology/ISO/EuropeanJurisdiction/EuropeanRegistrationAuthorities/>
-PREFIX idmp-sub:  <https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/>
-PREFIX idmp-ra:  <https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/>
-PREFIX idmp-x: <https://spec.pistoiaalliance.org/idmp/ontology/ISO/ExtensionTBD/>
+PREFIX idmp-ra: <https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/>
 
 GENERATE {
     # Substance
@@ -83,7 +81,7 @@ BIND(
     IF(str(?CodeCodeSystem) = "USDA PLANTS", idmp-nara:PlantListOfAcceptedNomenclatureTaxonomyAndSymbols ,
     IF(str(?CodeCodeSystem) = "PUBCHEM", idmp-nara:PubChem ,
     IF(str(?CodeCodeSystem) = "USP-MC MONOGRAPH", idmp-nara:USPharmacopeiaMedicinesCompendium ,
-    IF(str(?CodeCodeSystem) = "USP-MC VALIDATION RPT", cmns-ra:USPharmacopeiaMedicinesCompendium ,
+    IF(str(?CodeCodeSystem) = "USP-MC VALIDATION RPT", idmp-nara:USPharmacopeiaMedicinesCompendium ,
     IF(str(?CodeCodeSystem) = "UNIPROT", idmp-eura:UniProt ,
     IF(str(?CodeCodeSystem) = "UCSF-FDA TRANSPORTAL", idmp-nara:UniversityOfCaliforniaSanFrancisoFederalDrugAdministrationTransport ,
     IF(str(?CodeCodeSystem) = "WHO INTERNATIONAL PHARMACOPOEIA", idmp-ra:WorldHealthOrganizationInternationalPharmacopoeia ,

diff --git a/etc/transformation/GSRS/gsrs-public-data-names.rqg b/etc/transformation/GSRS/gsrs-public-data-names.rqg
@@ -1,24 +1,24 @@
 PREFIX iter: <http://w3id.org/sparql-generate/iter/>
 PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
-PREFIX cmns-dsg:  <https://www.omg.org/spec/Commons/Designators/>
-PREFIX cmns-txt:  <https://www.omg.org/spec/Commons/TextDatatype/>
-PREFIX idmp-sub:  <https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/>
+PREFIX cmns-dsg: <https://www.omg.org/spec/Commons/Designators/>
+PREFIX cmns-cxtdsg: <https://www.omg.org/spec/Commons/ContextualDesignators/>
+PREFIX cmns-txt: <https://www.omg.org/spec/Commons/TextDatatype/>
+PREFIX idmp-sub: <https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/>
 
 GENERATE {
-
     # Substance
     ?Substance ?labelProperty ?OfficialSubstanceName ;
         rdfs:label ?OfficialSubstanceName ;
         cmns-dsg:hasName ?SubstanceName ;
     .
 
     # Names
-    ?SubstanceName a cmns-dsg:ContextualName ;
+    ?SubstanceName a cmns-cxtdsg:ContextualName ;
         cmns-txt:hasTextValue ?SubstanceNameValue ;
         cmns-dsg:isNameOf ?Substance ;
         idmp-sub:hasSubstanceNameType ?SubstanceNameType ;
-        .
+    .
 }
 
 ITERATOR iter:JSONSurfer(<public_data.json>,

diff --git a/etc/transformation/GSRS/gsrs-public-data-relationships.rqg b/etc/transformation/GSRS/gsrs-public-data-relationships.rqg
@@ -2,11 +2,8 @@ PREFIX iter: <http://w3id.org/sparql-generate/iter/>
 PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
 PREFIX cmns-cxtdsg: <https://www.omg.org/spec/Commons/ContextualDesignators/>
 PREFIX cmns-rlcmp: <https://www.omg.org/spec/Commons/RolesAndCompositions/>
-PREFIX cmns-pts: <https://www.omg.org/spec/Commons/PartiesAndSituations/>
-PREFIX idmp-ra:  <https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/>
-PREFIX idmp-nara: <https://spec.pistoiaalliance.org/idmp/ontology/ISO/NorthAmericanJurisdiction/NorthAmericanRegistrationAuthorities/>
 PREFIX idmp-narga: <https://spec.pistoiaalliance.org/idmp/ontology/ISO/NorthAmericanJurisdiction/NorthAmericanRegulatoryAgencies/>
-PREFIX idmp-sub:  <https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/>
+PREFIX idmp-sub: <https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/>
 
 GENERATE {
 

diff --git a/etc/transformation/GSRS/gsrs-public-data-substances.rqg b/etc/transformation/GSRS/gsrs-public-data-substances.rqg
@@ -1,12 +1,9 @@
 PREFIX iter: <http://w3id.org/sparql-generate/iter/>
-PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 PREFIX owl: <http://www.w3.org/2002/07/owl#>
-PREFIX idmp: <https://purl.iso.org/idmp/>
 PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
-PREFIX idmp-sub:  <https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/>
-PREFIX idmp-ra:  <https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-RegistrationAuthorities/>
-PREFIX cmns-txt:  <https://www.omg.org/spec/Commons/TextDatatype/>
+PREFIX idmp-sub: <https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/>
+PREFIX cmns-txt: <https://www.omg.org/spec/Commons/TextDatatype/>
 PREFIX cmns-dsg: <https://www.omg.org/spec/Commons/Designators/>
 
 GENERATE {
@@ -187,7 +184,11 @@ BIND(IF(str(?substanceClass) = "chemical", idmp-sub:ChemicalSubstance ,
     IF(str(?substanceClass) = "polymer", idmp-sub:PolymerSubstance ,
     IF(str(?substanceClass) = "structurallyDiverse", idmp-sub:StructurallyDiverseSubstance ,
     IF(str(?substanceClass) = "specifiedSubstance", idmp-sub:SpecifiedSubstance ,
-    idmp-sub:Substance )))))))
+    IF(str(?substanceClass) = "specifiedSubstanceG1", idmp-sub:SpecifiedSubstanceGroup1 ,
+    IF(str(?substanceClass) = "specifiedSubstanceG2", idmp-sub:SpecifiedSubstanceGroup2 ,
+    IF(str(?substanceClass) = "specifiedSubstanceG3", idmp-sub:SpecifiedSubstanceGroup3 ,
+    IF(str(?substanceClass) = "specifiedSubstanceG4", idmp-sub:SpecifiedSubstanceGroup4 ,
+    idmp-sub:Substance )))))))))))
     AS ?SubstanceType)
 
 BIND(IF(str(?structureStereochemistry) = "ABSOLUTE", idmp-sub:Stereochemistry-Absolute ,

diff --git a/etc/transformation/SPOR/referentials/spor-referentials.rqg b/etc/transformation/SPOR/referentials/spor-referentials.rqg
@@ -8,8 +8,6 @@ PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 PREFIX owl: <http://www.w3.org/2002/07/owl#>
 PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
 PREFIX cmns-cls: <https://www.omg.org/spec/Commons/Classifiers/>
-PREFIX cmns-dsg: <https://www.omg.org/spec/Commons/Designators/>
-PREFIX idmp-spor: <https://spec.pistoiaalliance.org/idmp/ontology/ISO/EuropeanJurisdiction/SubstancesProductsOrganisationsReferentials/>
 
 GENERATE {
     <https://spor.ema.europa.eu/v1/lists/{ ?Identifier }/terms>

diff --git a/etc/transformation/SPOR/substances/spor-substances.rqg b/etc/transformation/SPOR/substances/spor-substances.rqg
@@ -11,7 +11,6 @@ PREFIX idmp-ra: <https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Reg
 PREFIX idmp-eura: <https://spec.pistoiaalliance.org/idmp/ontology/ISO/EuropeanJurisdiction/EuropeanRegistrationAuthorities/>
 PREFIX idmp-eureg: <https://spec.pistoiaalliance.org/idmp/ontology/ISO/EuropeanJurisdiction/EuropeanRegulatoryAgencies/>
 PREFIX idmp-nara: <https://spec.pistoiaalliance.org/idmp/ontology/ISO/NorthAmericanJurisdiction/NorthAmericanRegistrationAuthorities/>
-PREFIX cmns-ra: <https://www.omg.org/spec/Commons/RegistrationAuthorities/>
 PREFIX spor-st: <https://spor.ema.europa.eu/v1/lists/100000075826/terms/>
 
 GENERATE {
@@ -37,7 +36,7 @@ GENERATE {
     a idmp-eura:EudraVigilanceCode, cmns-ra:RegisteredIdentifier ;
     cmns-id:identifies <https://spor.ema.europa.eu/v1/lists/SubstanceDefinition/terms/{ ?SMS_ID }> ;
     cmns-txt:hasTextValue ?External_Code_XEVMPD ;
-    cmns-ra:registeredIn idmp-eura:ExtendedEudraVigilanceMedicinalProductDictionary;
+    cmns-ra:isRegisteredIn idmp-eura:ExtendedEudraVigilanceMedicinalProductDictionary ;
     .
 }
 ITERATOR iter:CSV(<sms-substances-list.csv>) AS
@@ -147,7 +146,7 @@ WHERE {
     IF(?Name_Source = "FDA SUBSTANCE REGISTRATION SYSTEM", idmp-nara:FoodAndDrugAdministrationRegistrationAuthority, # valid
     IF(?Name_Source = "INN", idmp-ra:InternationalNonproprietaryName, # valid
     IF(?Name_Source = "ITIS (INTEGRATED TAXONOMIC INFORMATION SYSTEM)", idmp-nara:IntegratedTaxonomicInformationSystem, # valid
-    IF(?Name_Source = "PUBCHEM", cmns-ra:PubChem, # valid
+    IF(?Name_Source = "PUBCHEM", idmp-nara:PubChem, # valid
     IF(?Name_Source = "THE MERCK INDEX 20TH EDITION", idmp-ra:MerckIndexOnline, # valid
     IF(?Name_Source = "USP", idmp-nara:USPharmacopeiaMedicinesCompendium, # valid
     IF(?Name_Source = "WHO", idmp-ra:WorldHealthOrganization, # valid