Feat: Data Catalogue compliance for EJP-RD VP onboarding metadata lev…

…el 1 (#4796) * Fixes for FDP SHACL files * Correct casing for DCAT endpointURL * RDF API bugfix: prevent unintentional text to array * Compliance updates for Agent and Endpoint * Fix for EJP-RD resource SHACL file * Enable EJP-RD compliance for Data Catalogue * Sync back to shared to fix Beacon tests --------- Co-authored-by: K. Joeri van der Velde <[email protected]>
molgenis · Mar 5, 2025 · 25e112f · 25e112f
1 parent 5c8e735
commit 25e112f
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diff --git a/backend/molgenis-emx2-datamodels/src/test/java/org/molgenis/emx2/datamodels/TestLoaders.java b/backend/molgenis-emx2-datamodels/src/test/java/org/molgenis/emx2/datamodels/TestLoaders.java
@@ -94,7 +94,7 @@ void test06DataCatalogueLoader() throws Exception {
     testShaclCompliance(FAIR_DATA_POINT_SHACL_FILES, outputStream.toString());
     // testShaclCompliance(DCAT_AP_SHACL_FILES, outputStream.toString());
     testShaclCompliance(HEALTH_RI_SHACL_FILES, outputStream.toString());
-    // testShaclCompliance(EJP_RD_VP_SHACL_FILES, outputStream.toString());
+    testShaclCompliance(EJP_RD_VP_SHACL_FILES, outputStream.toString());
   }
 
   @Test

diff --git a/...enis-emx2-datamodels/src/test/resources/SHACL/EJP_RD_VP_Level_1/01-08-2024/resource.shacl b/...enis-emx2-datamodels/src/test/resources/SHACL/EJP_RD_VP_Level_1/01-08-2024/resource.shacl
@@ -57,7 +57,7 @@
     dash:editor dash:URIEditor ;
     dash:viewer dash:LabelViewer ;
   ],  [
-    sh:path dct:keyword ;
+    sh:path dcat:keyword ; # FIX: 'keyword' is a DCAT term (prefix: dcat), instead of a Dublin Core term (prefix: dct)
     sh:name "Keywords" ;
     sh:nodeKind sh:Literal ;
     sh:minCount 1 ;

diff --git a/backend/molgenis-emx2-rdf/src/main/java/org/molgenis/emx2/rdf/ColumnTypeRdfMapper.java b/backend/molgenis-emx2-rdf/src/main/java/org/molgenis/emx2/rdf/ColumnTypeRdfMapper.java
@@ -132,6 +132,12 @@ Set<Value> retrieveValues(String baseURL, Row row, Column column) {
         return basicRetrievalString(row.getStringArrayPreserveDelimiter(column), Values::literal);
       }
     },
+    TEXT(CoreDatatype.XSD.STRING) {
+      @Override
+      Set<Value> retrieveValues(String baseURL, Row row, Column column) {
+        return basicRetrievalString(row.getStringArrayPreserveDelimiter(column), Values::literal);
+      }
+    },
     INT(CoreDatatype.XSD.INT) {
       @Override
       Set<Value> retrieveValues(String baseURL, Row row, Column column) {

diff --git a/data/_demodata/applications/datacatalogue/Agent.csv b/data/_demodata/applications/datacatalogue/Agent.csv
@@ -1,3 +1,3 @@
-name,logo
-MOLGENIS,https://molgenis.org/assets/img/logo_green.png
-UMCG,https://www.umcg.nl/o/umcg-website-theme/images/desktop-umcg-logo.webp
+name,logo,url,mbox
+MOLGENIS,https://molgenis.org/assets/img/logo_green.png,https://molgenis.org,[email protected]
+UMCG,https://www.umcg.nl/o/umcg-website-theme/images/desktop-umcg-logo.webp,https://www.umcg.nl,[email protected]
diff --git a/data/_demodata/applications/datacatalogue/Endpoint.csv b/data/_demodata/applications/datacatalogue/Endpoint.csv
@@ -1,3 +1,3 @@
-id,type,name,version,description,publisher,language,license,conformsTo,rights,accessRights,contact,keyword,theme,endPointDescription,metadataCatalog.name,metadataCatalog.network,organisation,alternativeUrl,conformsToFdpSpec,EJP_RD_personalData,EJP_RD_vpConnection,issued,modified
-org.molgeniscloud.beaconv2,https://w3id.org/fdp/fdp-o#MetadataService,MOLGENIS EMX2 Beacon v2,v2,This MOLGENIS EMX2 Beacon v2 is based on the GA4GH Beacon v2.0 specification,MOLGENIS,,https://www.gnu.org/licenses/lgpl-3.0.html#license-text,https://github.com/ga4gh-beacon/beacon-v2/,,,[email protected],,https://www.wikidata.org/wiki/Q7321258,,testNetwork1,testNetwork1,UMCG,https://umcgresearch.org/w/gcc,https://github.com/ga4gh-beacon/beacon-v2/,,,1990-01-01 00:00:00.0,1990-01-01 00:00:00.0
-Example_FAIR_Data_Point,"https://w3id.org/fdp/fdp-o#MetadataService, http://www.w3.org/ns/dcat#Resource, http://www.w3.org/ns/dcat#DataService, https://w3id.org/fdp/fdp-o#FAIRDataPoint",Example MOLGENIS EMX2 FAIR Data Point,v1.2,"This example MOLGENIS EMX2 multi-interoperable FAIR Data Point is based on the FAIR Data Point 1.2 specification but includes extension points to support additional DCAT flavours including EJP RD Virtual Platform level 1 metadata, HealthRI core plateau 1 metadata, and so on.",MOLGENIS,https://www.loc.gov/standards/iso639-2/php/langcodes_name.php?iso_639_1=en,https://www.gnu.org/licenses/lgpl-3.0.html#license-text,https://specs.fairdatapoint.org/fdp-specs-v1.2.html,https://www.linktosomerightsstatement.org,https://www.linktosomeaccessrightsstatement.org,[email protected],"example, fdp, molgenis, emx2",https://www.wikidata.org/wiki/Q2352616,https://specs.fairdatapoint.org/fdp-specs-v1.2.html,"LifeCycle,ATHLETE","LifeCycle,ATHLETE",UMCG,https://alturl.org,https://specs.fairdatapoint.org/fdp-specs-v1.2.html,false,https://w3id.org/ejp-rd/vocabulary#VPDiscoverable,1990-01-01 00:00:00.0,1990-01-01 00:00:00.0
+id,type,name,version,description,publisher,language,license,conformsTo,rights,accessRights,contact,keyword,theme,endPointDescription,metadataCatalog.name,metadataCatalog.network,organisation,alternativeUrl,conformsToFdpSpec,EJP_RD_personalData,EJP_RD_vpConnection,issued,modified,url
+org.molgeniscloud.beaconv2,https://w3id.org/fdp/fdp-o#MetadataService,MOLGENIS EMX2 Beacon v2,v2,This MOLGENIS EMX2 Beacon v2 is based on the GA4GH Beacon v2.0 specification,MOLGENIS,,https://www.gnu.org/licenses/lgpl-3.0.html#license-text,https://github.com/ga4gh-beacon/beacon-v2/,,,MOLGENIS,"Example MOLGENIS EMX2 Beacon v2 endpoint",https://www.wikidata.org/wiki/Q7321258,,testNetwork1,testNetwork1,UMCG,https://umcgresearch.org/w/gcc,https://github.com/ga4gh-beacon/beacon-v2/,false,https://w3id.org/ejp-rd/vocabulary#VPDiscoverable,1990-01-01 00:00:00.0,1990-01-01 00:00:00.0,https://molgenis.org/
+Example_FAIR_Data_Point,"https://w3id.org/fdp/fdp-o#MetadataService, http://www.w3.org/ns/dcat#Resource, http://www.w3.org/ns/dcat#DataService, https://w3id.org/fdp/fdp-o#FAIRDataPoint","Example MOLGENIS EMX2 FAIR Data Point",v1.2,"This example MOLGENIS EMX2 multi-interoperable FAIR Data Point is based on the FAIR Data Point 1.2 specification but includes extension points to support additional DCAT flavours including EJP RD Virtual Platform level 1 metadata, HealthRI core plateau 1 metadata, and so on.",MOLGENIS,https://www.loc.gov/standards/iso639-2/php/langcodes_name.php?iso_639_1=en,https://www.gnu.org/licenses/lgpl-3.0.html#license-text,https://specs.fairdatapoint.org/fdp-specs-v1.2.html,https://www.linktosomerightsstatement.org,https://www.linktosomeaccessrightsstatement.org,MOLGENIS,"example, fdp, molgenis, emx2",https://www.wikidata.org/wiki/Q2352616,https://specs.fairdatapoint.org/fdp-specs-v1.2.html,"LifeCycle,ATHLETE","LifeCycle,ATHLETE",UMCG,https://alturl.org,https://specs.fairdatapoint.org/fdp-specs-v1.2.html,false,https://w3id.org/ejp-rd/vocabulary#VPDiscoverable,1990-01-01 00:00:00.0,1990-01-01 00:00:00.0,https://molgenis.org/
diff --git a/data/_demodata/shared-examples/Agent.csv b/data/_demodata/shared-examples/Agent.csv
@@ -1,3 +1,3 @@
-name,logo
-MOLGENIS,https://molgenis.org/assets/img/logo_green.png
-UMCG,https://www.umcg.nl/o/umcg-website-theme/images/desktop-umcg-logo.webp
+name,logo,url,mbox
+MOLGENIS,https://molgenis.org/assets/img/logo_green.png,https://molgenis.org,[email protected]
+UMCG,https://www.umcg.nl/o/umcg-website-theme/images/desktop-umcg-logo.webp,https://www.umcg.nl,[email protected]
diff --git a/data/_demodata/shared-examples/Endpoint.csv b/data/_demodata/shared-examples/Endpoint.csv
@@ -1,3 +1,3 @@
-id,type,name,description,publisher,language,license,conformsTo,rights,accessRights,contact,keyword,theme,url,endPointDescription,metadataIdentifier,metadataCatalog,organisation,alternativeUrl,EJP_RD_personalData,EJP_RD_vpConnection
-org.molgeniscloud.beaconv2,https://w3id.org/fdp/fdp-o#MetadataService,MOLGENIS EMX2 Beacon v2,This MOLGENIS EMX2 Beacon v2 is based on the GA4GH Beacon v2.0 specification,MOLGENIS,,https://www.gnu.org/licenses/lgpl-3.0.html#license-text,https://github.com/ga4gh-beacon/beacon-v2/,,,[email protected],,https://www.wikidata.org/wiki/Q7321258,https://molgenis.org/,,,,UMCG,https://umcgresearch.org/w/gcc,,
-Example_FAIR_Data_Point,"https://w3id.org/fdp/fdp-o#MetadataService, http://www.w3.org/ns/dcat#Resource, http://www.w3.org/ns/dcat#DataService, https://w3id.org/fdp/fdp-o#FAIRDataPoint",Example MOLGENIS EMX2 FAIR Data Point,"This example MOLGENIS EMX2 multi-interoperable FAIR Data Point is based on the FAIR Data Point 1.2 specification but includes extension points to support additional DCAT flavours including EJP RD Virtual Platform level 1 metadata, HealthRI core plateau 1 metadata, and so on.",MOLGENIS,https://www.loc.gov/standards/iso639-2/php/langcodes_name.php?iso_639_1=en,https://www.gnu.org/licenses/lgpl-3.0.html#license-text,https://specs.fairdatapoint.org/fdp-specs-v1.2.html,https://www.linktosomerightsstatement.org,https://www.linktosomeaccessrightsstatement.org,[email protected],"example, fdp, molgenis, emx2",https://www.wikidata.org/wiki/Q2352616,https://www.MyMOLGENISServer.org/myFDPschema/api/rdf,https://specs.fairdatapoint.org/fdp-specs-v1.2.html,https://www.MyMOLGENISServer.org/myFDPschema/api/rdf,"catalogId01,catalogId02",UMCG,https://alturl.org,false,https://w3id.org/ejp-rd/vocabulary#VPDiscoverable
+id,type,name,version,description,publisher,language,license,conformsTo,rights,accessRights,contact,keyword,theme,endPointDescription,metadataCatalog.name,metadataCatalog.network,organisation,alternativeUrl,conformsToFdpSpec,EJP_RD_personalData,EJP_RD_vpConnection,issued,modified,url
+org.molgeniscloud.beaconv2,https://w3id.org/fdp/fdp-o#MetadataService,MOLGENIS EMX2 Beacon v2,v2,This MOLGENIS EMX2 Beacon v2 is based on the GA4GH Beacon v2.0 specification,MOLGENIS,,https://www.gnu.org/licenses/lgpl-3.0.html#license-text,https://github.com/ga4gh-beacon/beacon-v2/,,,MOLGENIS,"Example MOLGENIS EMX2 Beacon v2 endpoint",https://www.wikidata.org/wiki/Q7321258,,testNetwork1,testNetwork1,UMCG,https://umcgresearch.org/w/gcc,https://github.com/ga4gh-beacon/beacon-v2/,false,https://w3id.org/ejp-rd/vocabulary#VPDiscoverable,1990-01-01 00:00:00.0,1990-01-01 00:00:00.0,https://molgenis.org/
+Example_FAIR_Data_Point,"https://w3id.org/fdp/fdp-o#MetadataService, http://www.w3.org/ns/dcat#Resource, http://www.w3.org/ns/dcat#DataService, https://w3id.org/fdp/fdp-o#FAIRDataPoint","Example MOLGENIS EMX2 FAIR Data Point",v1.2,"This example MOLGENIS EMX2 multi-interoperable FAIR Data Point is based on the FAIR Data Point 1.2 specification but includes extension points to support additional DCAT flavours including EJP RD Virtual Platform level 1 metadata, HealthRI core plateau 1 metadata, and so on.",MOLGENIS,https://www.loc.gov/standards/iso639-2/php/langcodes_name.php?iso_639_1=en,https://www.gnu.org/licenses/lgpl-3.0.html#license-text,https://specs.fairdatapoint.org/fdp-specs-v1.2.html,https://www.linktosomerightsstatement.org,https://www.linktosomeaccessrightsstatement.org,MOLGENIS,"example, fdp, molgenis, emx2",https://www.wikidata.org/wiki/Q2352616,https://specs.fairdatapoint.org/fdp-specs-v1.2.html,"LifeCycle,ATHLETE","LifeCycle,ATHLETE",UMCG,https://alturl.org,https://specs.fairdatapoint.org/fdp-specs-v1.2.html,false,https://w3id.org/ejp-rd/vocabulary#VPDiscoverable,1990-01-01 00:00:00.0,1990-01-01 00:00:00.0,https://molgenis.org/
diff --git a/data/_models/shared/Agent.csv b/data/_models/shared/Agent.csv
@@ -1,4 +1,6 @@
 tableName,tableExtends,columnName,columnType,key,required,refSchema,refTable,refLink,refBack,validation,semantics,description,profiles
-Agent,,,,,,,,,,,"http://xmlns.com/foaf/0.1/Agent","An agent (eg. person, group, software or physical artifact).","DCAT,Beacon v2,DataCatalogueFlat"
+Agent,,,,,,,,,,,"http://xmlns.com/foaf/0.1/Agent,http://www.w3.org/2006/vcard/ns#Agent","An agent (eg. person, group, software or physical artifact).","DCAT,Beacon v2,DataCatalogueFlat"
 Agent,,name,string,1,TRUE,,,,,,"http://xmlns.com/foaf/0.1/name,http://purl.org/dc/terms/identifier",A name and identifier for this agent.,"DCAT,Beacon v2,DataCatalogueFlat"
 Agent,,logo,hyperlink,,,,,,,,"http://xmlns.com/foaf/0.1/logo",A logo representing some thing.,"DCAT,Beacon v2,DataCatalogueFlat"
+Agent,,url,hyperlink,,,,,,,,"http://www.w3.org/2006/vcard/ns#url",An URL representing some thing.,"Beacon v2,DataCatalogueFlat"
+Agent,,mbox,email,,,,,,,,"http://www.w3.org/2006/vcard/ns#hasEmail,http://xmlns.com/foaf/0.1/mbox","An email address is an identifier to send mail to particular electronic mailbox of a contact person or organization.","Beacon v2,DataCatalogueFlat"
diff --git a/data/_models/shared/Endpoint.csv b/data/_models/shared/Endpoint.csv
@@ -4,14 +4,14 @@ Endpoint,,id,string,1,TRUE,,,,,,"http://schema.org/identifier","A unique proper
 Endpoint,,type,hyperlink_array,,TRUE,,,,,,http://www.w3.org/1999/02/22-rdf-syntax-ns#type,This row is an instance of one or more of these class(es) other than the Endpoint table.,"FAIRDataPoint,DataCatalogueFlat"
 Endpoint,,name,string_array,,TRUE,,,,,,http://purl.org/dc/terms/title,A name given to the resource.,"Beacon v2,FAIRDataPoint,DataCatalogueFlat"
 Endpoint,,version,text,,,,,,,,http://purl.org/dc/terms/hasVersion,An account of the resource version.,"DataCatalogueFlat"
-Endpoint,,description,text_array,,,,,,,,http://purl.org/dc/terms/description,An account of the resource.,"Beacon v2,FAIRDataPoint,DataCatalogueFlat"
+Endpoint,,description,text,,,,,,,,http://purl.org/dc/terms/description,An account of the resource.,"Beacon v2,FAIRDataPoint,DataCatalogueFlat"
 Endpoint,,publisher,ref_array,,TRUE,,Agent,,,,http://purl.org/dc/terms/publisher,An entity responsible for making the resource available.,"Beacon v2,FAIRDataPoint,DataCatalogueFlat"
 Endpoint,,language,hyperlink_array,,,,,,,,http://purl.org/dc/terms/language,A language of the resource.,"FAIRDataPoint,DataCatalogueFlat"
 Endpoint,,license,hyperlink,,TRUE,,,,,,http://purl.org/dc/terms/license,A legal document giving official permission to do something with the resource.,"FAIRDataPoint,DataCatalogueFlat"
 Endpoint,,conformsTo,hyperlink,,TRUE,,,,,,http://purl.org/dc/terms/conformsTo,An established standard to which the described resource conforms.,"FAIRDataPoint,DataCatalogueFlat"
 Endpoint,,rights,hyperlink_array,,,,,,,,http://purl.org/dc/terms/rights,Information about rights held in and over the resource.,"FAIRDataPoint,DataCatalogueFlat"
 Endpoint,,accessRights,hyperlink_array,,,,,,,,http://purl.org/dc/terms/accessRights,Information about who access the resource or an indication of its security status.,"FAIRDataPoint,DataCatalogueFlat"
-Endpoint,,contact,string,,,,,,,,http://www.w3.org/ns/dcat#contactPoint,Relevant contact information for the catalogued resource. Use of vCard is recommended.,"Beacon v2,FAIRDataPoint,DataCatalogueFlat"
+Endpoint,,contact,ref,,,,Agent,,,,http://www.w3.org/ns/dcat#contactPoint,"Relevant contact information for the cataloged resource. Use of vCard is recommended [VCARD-RDF].","Beacon v2,FAIRDataPoint,DataCatalogueFlat"
 Endpoint,,keyword,string_array,,,,,,,,http://www.w3.org/ns/dcat#keyword,A keyword or tag describing a resource.,"FAIRDataPoint,DataCatalogueFlat"
 Endpoint,,theme,hyperlink_array,,,,,,,,http://www.w3.org/ns/dcat#theme,A main category of the resource. A resource can have multiple themes.,"FAIRDataPoint,DataCatalogueFlat"
 Endpoint,,url,hyperlink,,,,,,,,http://www.w3.org/ns/dcat#endpointURL,"The root location or primary endpoint of the service (a web-resolvable IRI). For Beacon v2 only, in other cases we want to autogenerate this information.","Beacon v2"
@@ -21,7 +21,7 @@ Endpoint,,metadataCatalog,ref_array,,,,Catalog,,,,https://w3id.org/fdp/fdp-o#met
 Endpoint,,organisation,ontology,,,,Organisations,,,,http://purl.obolibrary.org/obo/NCIT_C25412,Name of the organisation. E.g. University Medical Center Groningen,Beacon v2
 Endpoint,,alternativeUrl,,,,,,,,,"http://purl.org/dc/terms/alternative, http://schema.org/url",Alternative endpoint URL.,Beacon v2
 Endpoint,,conformsToFdpSpec,hyperlink,,TRUE,,,,,,https://w3id.org/fdp/fdp-o#conformsToFdpSpec,The relation should point to an URI that contains the version of the FDP specifications for which this instance of the FDP conforms to,"DataCatalogueFlat"
-Endpoint,,EJP_RD_personalData,bool,,,,,,,,https://w3id.org/ejp-rd/vocabulary#personalData,"Set to true if the resource onboarded to the EJP-RD Virtual Platform contains personal data, personal data meaning data related to identified or identifiable persons (as per GDPR definition), otherwise false.","FAIRDataPoint,DataCatalogueFlat"
+Endpoint,,EJP_RD_personalData,string,,,,,,,,https://w3id.org/ejp-rd/vocabulary#personalData,"Set to true if the resource onboarded to the EJP-RD Virtual Platform contains personal data, personal data meaning data related to identified or identifiable persons (as per GDPR definition), otherwise false. Must be String as workaround for current FDP reference implementation limitations.","FAIRDataPoint,DataCatalogueFlat"
 Endpoint,,EJP_RD_vpConnection,hyperlink,,,,,,,,https://w3id.org/ejp-rd/vocabulary#vpConnection,"This property must be attached to every entity that you wish the EJP-RD Virtual Platform to explore.","FAIRDataPoint,DataCatalogueFlat"
 Endpoint,,issued,datetime,,,,,,,,"http://purl.org/dc/terms/issued,https://w3id.org/fdp/fdp-o#metadataIssued",,DataCatalogueFlat,
 Endpoint,,modified,datetime,,,,,,,,"http://purl.org/dc/terms/modified,https://w3id.org/fdp/fdp-o#metadataModified",,DataCatalogueFlat,