Merge pull request #3279 from molgenis/feat/fdprootsettings

feat: FDP root now flexible through setting

backend/molgenis-emx2-fairdatapoint/src/main/java/org/molgenis/emx2/fairdatapoint/FAIRDataPoint.java

@@ -2,7 +2,6 @@
 
 import static org.eclipse.rdf4j.model.util.Values.iri;
 import static org.eclipse.rdf4j.model.util.Values.literal;
-import static org.molgenis.emx2.rdf.RDFService.*;
 import static org.molgenis.emx2.rdf.RDFUtils.*;
 
 import java.io.StringWriter;
@@ -12,7 +11,6 @@
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
-import org.eclipse.rdf4j.model.BNode;
 import org.eclipse.rdf4j.model.IRI;
 import org.eclipse.rdf4j.model.Model;
 import org.eclipse.rdf4j.model.ValueFactory;
@@ -29,7 +27,7 @@
 
 public class FAIRDataPoint {
 
-  // todo: double check cardinality
+  private static final String FDP_ROOT_METADATA = "FAIR Data Point root metadata";
 
   /**
    * Constructor
@@ -43,7 +41,7 @@ public FAIRDataPoint(Request request, Schema... schemas) {
     Date currentDateTime = new Date(System.currentTimeMillis());
     this.issued = formatter.format(currentDateTime);
     this.modified = formatter.format(currentDateTime);
-    this.version = Version.getVersion();
+    this.version = "MOLGENIS EMX2 " + Version.getVersion();
     this.request = request;
     this.schemas = schemas;
   }
@@ -125,7 +123,7 @@ public String getResult() throws Exception {
     String host = extractHost(requestURI);
     String apiFdp = host + "/api/fdp";
     String apiFdpCatalog = apiFdp + "/catalog";
-    String apiFdpProfile = apiFdp + "/catalog";
+    String apiFdpProfile = apiFdp + "/profile";
     String apiFdpIdentifier = apiFdp + "#identifier";
 
     IRI apiFdpEnc = encodedIRI(apiFdp);
@@ -137,13 +135,6 @@ public String getResult() throws Exception {
     Required by FDP specification (https://specs.fairdatapoint.org/)
      */
     builder.add(apiFdpEnc, RDF.TYPE, iri("https://w3id.org/fdp/fdp-o#MetadataService"));
-    builder.add(
-        apiFdpEnc, DCTERMS.TITLE, "FAIR Data Point hosted by MOLGENIS-EMX2 at " + apiFdpEnc);
-    BNode publisher = vf.createBNode();
-    builder.add(apiFdpEnc, DCTERMS.PUBLISHER, publisher);
-    builder.add(publisher, RDF.TYPE, FOAF.AGENT);
-    builder.add(publisher, FOAF.NAME, "MOLGENIS-EMX2 FAIR Data Point API");
-    builder.add(apiFdpEnc, DCTERMS.LICENSE, iri("https://www.gnu.org/licenses/lgpl-3.0.rdf"));
     builder.add(apiFdpEnc, DCTERMS.CONFORMS_TO, apiFdpProfileEnc);
     builder.add(apiFdpEnc, DCAT.ENDPOINT_URL, apiFdpEnc);
     builder.add(
@@ -182,37 +173,11 @@ Required by FDP specification (https://specs.fairdatapoint.org/)
     /*
     Optional in FDP specification (https://specs.fairdatapoint.org/)
      */
-    builder.add(
-        apiFdpEnc,
-        DCTERMS.DESCRIPTION,
-        "FAIR Data Point hosted by MOLGENIS-EMX2 at "
-            + apiFdpEnc
-            + ". This implementation follows the FAIR Data Point Working Draft, 23 August 2021 at https://specs.fairdatapoint.org/.");
-    builder.add(apiFdpEnc, DCTERMS.LANGUAGE, iri("http://lexvo.org/id/iso639-3/eng"));
-    BNode rights = vf.createBNode();
-    builder.add(apiFdpEnc, DCTERMS.RIGHTS, rights);
-    builder.add(rights, RDF.TYPE, DCTERMS.RIGHTS_STATEMENT);
-    builder.add(rights, DCTERMS.DESCRIPTION, "Rights are provided on a per-dataset basis.");
-    BNode accessRights = vf.createBNode();
-    builder.add(apiFdpEnc, DCTERMS.ACCESS_RIGHTS, accessRights);
-    builder.add(accessRights, RDF.TYPE, DCTERMS.RIGHTS_STATEMENT);
-    builder.add(
-        accessRights, DCTERMS.DESCRIPTION, "Access rights are provided on a per-dataset basis.");
-    BNode vcard = vf.createBNode();
-    builder.add(apiFdpEnc, DCAT.CONTACT_POINT, vcard);
-    builder.add(vcard, RDF.TYPE, VCARD4.KIND);
-    builder.add(vcard, VCARD4.INDIVIDUAL, "MOLGENIS support desk");
-    builder.add(vcard, VCARD4.HAS_EMAIL, "[email protected]");
-    builder.add(vcard, VCARD4.HAS_URL, "https://molgenis.org/");
     builder.add(apiFdpEnc, DCAT.ENDPOINT_DESCRIPTION, encodedIRI(host + "/api/openapi"));
     builder.add(
         apiFdpEnc, iri("https://w3id.org/fdp/fdp-o#startDate"), literal(issued, XSD.DATETIME));
     builder.add(
         apiFdpEnc, iri("https://w3id.org/fdp/fdp-o#endDate"), literal(modified, XSD.DATETIME));
-    builder.add(
-        apiFdpEnc,
-        iri("https://w3id.org/fdp/fdp-o#uiLanguage"),
-        iri("http://lexvo.org/id/iso639-3/eng"));
     builder.add(apiFdpEnc, iri("https://w3id.org/fdp/fdp-o#hasSoftwareVersion"), this.version);
     builder.add(
         apiFdpEnc,
@@ -225,7 +190,6 @@ Not part of FDP specification but good practice (https://specs.fairdatapoint.org
     builder.add(apiFdpEnc, RDF.TYPE, DCAT.RESOURCE);
     builder.add(apiFdpEnc, RDF.TYPE, DCAT.DATA_SERVICE);
     builder.add(apiFdpEnc, RDF.TYPE, iri("https://w3id.org/fdp/fdp-o#FAIRDataPoint"));
-    builder.add(apiFdpEnc, RDFS.LABEL, "FAIR Data Point hosted by MOLGENIS-EMX2 at " + apiFdpEnc);
     builder.add(apiFdpEnc, DCTERMS.HAS_VERSION, this.version);
     builder.add(
         apiFdpEnc,
@@ -240,6 +204,50 @@ Not part of FDP specification but good practice (https://specs.fairdatapoint.org
     Model model = builder.build();
     StringWriter stringWriter = new StringWriter();
     Rio.write(model, stringWriter, applicationOntologyFormat, config);
+    stringWriter.append(getFDPRootMetadata(apiFdpEnc.toString()));
     return stringWriter.toString();
   }
+
+  private String getFDPRootMetadata(String apiFdpEnc) {
+    for (Schema schema : schemas) {
+      if (schema.hasSetting(FDP_ROOT_METADATA)) {
+        return schema.getSettingValue(FDP_ROOT_METADATA);
+      }
+    }
+    Schema schema = addFDPRootMetadataIfMissing(apiFdpEnc);
+    return schema.getSettingValue(FDP_ROOT_METADATA);
+  }
+
+  private Schema addFDPRootMetadataIfMissing(String apiFdpEnc) {
+    schemas[0]
+        .getMetadata()
+        .setSetting(
+            FDP_ROOT_METADATA,
+            """
+            %s
+            <%s>
+              dcterms:title "FAIR Data Point hosted by MOLGENIS-EMX2";
+              dcterms:publisher [ a foaf:Agent;
+                  foaf:name "MOLGENIS-EMX2 FAIR Data Point API"
+                ];
+              dcterms:license <https://www.gnu.org/licenses/lgpl-3.0.rdf>;
+              dcterms:description "FAIR Data Point hosted by MOLGENIS-EMX2. This implementation follows the FAIR Data Point Working Draft, 23 August 2021 at https://specs.fairdatapoint.org/.";
+              dcterms:language lang:eng;
+              dcterms:rights [ a dcterms:RightsStatement;
+                  dcterms:description "Rights are provided on a per-dataset basis."
+                ];
+              dcterms:accessRights [ a dcterms:RightsStatement;
+                  dcterms:description "Access rights are provided on a per-dataset basis."
+                ];
+              dcat:contactPoint [ a vc:Kind;
+                  vc:Individual "MOLGENIS support desk";
+                  vc:hasEmail "[email protected]";
+                  vc:hasURL "https://molgenis.org/"
+                ];
+              fdp-o:uiLanguage lang:eng;
+              rdfs:label "FAIR Data Point hosted by MOLGENIS-EMX2" .
+              """
+                .formatted(System.lineSeparator(), apiFdpEnc));
+    return schemas[0];
+  }
 }

backend/molgenis-emx2-fairdatapoint/src/test/java/org/molgenis/emx2/fairdatapoint/FAIRDataPointTest.java

@@ -6,7 +6,6 @@
 import static org.molgenis.emx2.fairdatapoint.FormatMimeTypes.formatToMediaType;
 
 import org.junit.jupiter.api.BeforeAll;
-import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Tag;
 import org.junit.jupiter.api.Test;
 import org.molgenis.emx2.Database;
@@ -40,7 +39,6 @@ public static void setup() {
   }
 
   @Test
-  @Disabled
   public void FDPMetadataSchemaService() throws Exception {
     Request request = mock(Request.class);
     when(request.url()).thenReturn("http://localhost:8080/api/fdp");
@@ -50,9 +48,7 @@ public void FDPMetadataSchemaService() throws Exception {
     assertTrue(
         result.contains(
             "<http://localhost:8080/api/fdp> a fdp-o:MetadataService, dcat:Resource, dcat:DataService,"));
-    assertTrue(
-        result.contains(
-            "dcterms:title \"FAIR Data Point hosted by MOLGENIS-EMX2 at http://localhost:8080/api/fdp\";"));
+    assertTrue(result.contains("dcterms:title \"FAIR Data Point hosted by MOLGENIS-EMX2\";"));
     assertTrue(result.contains("dcterms:publisher [ a foaf:Agent;"));
     assertTrue(result.contains("foaf:name \"MOLGENIS-EMX2 FAIR Data Point API\""));
     assertTrue(

docs/molgenis/dev_fairdatapoint.md

@@ -11,7 +11,14 @@ The easiest way to enable FDP in MOLGENIS EMX2 is by choosing 'FAIR_DATA_HUB' as
 This will add three tables that will define the content of your FAIR Data Point:
 [Catalog](https://github.com/molgenis/molgenis-emx2/blob/master/data/fairdatahub/fairdatapoint/demodata/Catalog.csv), [Dataset](https://github.com/molgenis/molgenis-emx2/blob/master/data/fairdatahub/fairdatapoint/demodata/Dataset.csv) and [Distribution](https://github.com/molgenis/molgenis-emx2/blob/master/data/fairdatahub/fairdatapoint/demodata/Distribution.csv).
 Loading the 'FAIR_DATA_HUB' template including the example data will result in a fully operational FAIR Data Point.
-The example data can be used as a reference on how to enter data into the system, but can be safely removed or replaced.
+The example data can be used as a reference on how to enter data into the system.
+It can be safely removed or replaced.
+
+Before the FDP can be used, log in as the `admin` user and visit your FDP at `<server>/api/fdp`.
+This will add a database setting called _FAIR Data Point root metadata_ to the schema that enables your FDP.
+This setting contains a piece of RDF/TTL that is part of your FDP root endpoint which is fully customizable.
+Here, you can change the information about your FDP such as title, publisher, contact point and language.
+To make changes, go to your FDP-enabling schema, go to Settings, Advanced settings, and click the Edit button for  _FAIR Data Point root metadata_.
 
 After setting up these tables, this is how its contents are translated to the FDP structure:
 - Each Dataset contains a reference to one or multiple Catalogs via the `belongsToCatalog` field.