TTL flavor of the LinkedDataAPI is broken

[joerivandervelde]

Version: EMX2 8.195.0

The TTL flavor of the LinkedDataAPI in question runs at: <server>/<schema>/api/ttl. When calling this API, the original JSON-LD linked data string is converted into TTL format in LinkedDataService.java:

RDFParser rdfParser = Rio.createParser(RDFFormat.JSONLD);
Model model = new LinkedHashModel();
rdfParser.setRDFHandler(new StatementCollector(model));
rdfParser.parse(new StringReader(sw.toString()), "http://localhost/");
Rio.write(model, printWriter, RDFFormat.TURTLE);

But this fails when there are multiple ontology terms because apparently the JSON-LD notation cannot be parsed. For example [http://purl.obolibrary.org/obo/NCIT_C15607, http://semanticscience.org/resource/SIO_001003] throws the following exception:

org.molgenis.emx2.MolgenisException: generation of ttl failed: Could not parse JSONLD
	at org.molgenis.emx2.semantics.LinkedDataService.convertToTtl(LinkedDataService.java:235) ~[molgenis-emx2-semantics-8.195.1-fix-jsonldapi-SNAPSHOT.jar:a45b18b70]
	at org.molgenis.emx2.semantics.LinkedDataService.getTtlForSchema(LinkedDataService.java:218) ~[molgenis-emx2-semantics-8.195.1-fix-jsonldapi-SNAPSHOT.jar:a45b18b70]
	at org.molgenis.emx2.web.LinkedDataFragmentsApi.ttl(LinkedDataFragmentsApi.java:49) ~[molgenis-emx2-webapi-8.195.1-fix-jsonldapi-SNAPSHOT.jar:a45b18b70]
	at spark.RouteImpl$1.handle(RouteImpl.java:72) ~[spark-core-2.9.4.jar:?]
	at spark.http.matching.Routes.execute(Routes.java:61) ~[spark-core-2.9.4.jar:?]
	at spark.http.matching.MatcherFilter.doFilter(MatcherFilter.java:134) ~[spark-core-2.9.4.jar:?]
	at spark.embeddedserver.jetty.JettyHandler.doHandle(JettyHandler.java:50) ~[spark-core-2.9.4.jar:?]
	at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:1598) ~[jetty-server-9.4.48.v20220622.jar:9.4.48.v20220622]
	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141) ~[jetty-server-9.4.48.v20220622.jar:9.4.48.v20220622]
	at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:127) ~[jetty-server-9.4.48.v20220622.jar:9.4.48.v20220622]
	at org.eclipse.jetty.server.Server.handle(Server.java:516) ~[jetty-server-9.4.48.v20220622.jar:9.4.48.v20220622]
	at org.eclipse.jetty.server.HttpChannel.lambda$handle$1(HttpChannel.java:487) ~[jetty-server-9.4.48.v20220622.jar:9.4.48.v20220622]
	at org.eclipse.jetty.server.HttpChannel.dispatch(HttpChannel.java:732) [jetty-server-9.4.48.v20220622.jar:9.4.48.v20220622]
	at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:479) [jetty-server-9.4.48.v20220622.jar:9.4.48.v20220622]
	at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:277) [jetty-server-9.4.48.v20220622.jar:9.4.48.v20220622]
	at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:311) [jetty-io-9.4.48.v20220622.jar:9.4.48.v20220622]
	at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:105) [jetty-io-9.4.48.v20220622.jar:9.4.48.v20220622]
	at org.eclipse.jetty.io.ChannelEndPoint$1.run(ChannelEndPoint.java:104) [jetty-io-9.4.48.v20220622.jar:9.4.48.v20220622]
	at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:883) [jetty-util-9.4.48.v20220622.jar:9.4.48.v20220622]
	at org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run(QueuedThreadPool.java:1034) [jetty-util-9.4.48.v20220622.jar:9.4.48.v20220622]
	at java.lang.Thread.run(Thread.java:833) [?:?]
Caused by: org.eclipse.rdf4j.rio.RDFParseException: Could not parse JSONLD
	at org.eclipse.rdf4j.rio.jsonld.JSONLDParser.parse(JSONLDParser.java:136) ~[rdf4j-rio-jsonld-4.2.4.jar:4.2.4]
	at org.eclipse.rdf4j.rio.jsonld.JSONLDParser.parse(JSONLDParser.java:103) ~[rdf4j-rio-jsonld-4.2.4.jar:4.2.4]
	at org.molgenis.emx2.semantics.LinkedDataService.convertToTtl(LinkedDataService.java:232) ~[molgenis-emx2-semantics-8.195.1-fix-jsonldapi-SNAPSHOT.jar:a45b18b70]
	... 20 more
Caused by: com.github.jsonldjava.core.JsonLdError: invalid term definition: [http://purl.obolibrary.org/obo/NCIT_C15607, http://semanticscience.org/resource/SIO_001003]
	at com.github.jsonldjava.core.Context.createTermDefinition(Context.java:349) ~[jsonld-java-0.13.4.jar:?]
	at com.github.jsonldjava.core.Context.parse(Context.java:289) ~[jsonld-java-0.13.4.jar:?]
	at com.github.jsonldjava.core.Context.parse(Context.java:150) ~[jsonld-java-0.13.4.jar:?]
	at com.github.jsonldjava.core.Context.parse(Context.java:305) ~[jsonld-java-0.13.4.jar:?]
	at com.github.jsonldjava.core.JsonLdApi.expand(JsonLdApi.java:550) ~[jsonld-java-0.13.4.jar:?]
	at com.github.jsonldjava.core.JsonLdApi.expand(JsonLdApi.java:524) ~[jsonld-java-0.13.4.jar:?]
	at com.github.jsonldjava.core.JsonLdApi.expand(JsonLdApi.java:1027) ~[jsonld-java-0.13.4.jar:?]
	at com.github.jsonldjava.core.JsonLdProcessor.expand(JsonLdProcessor.java:139) ~[jsonld-java-0.13.4.jar:?]
	at com.github.jsonldjava.core.JsonLdProcessor.toRDF(JsonLdProcessor.java:528) ~[jsonld-java-0.13.4.jar:?]
	at org.eclipse.rdf4j.rio.jsonld.JSONLDParser.parse(JSONLDParser.java:134) ~[rdf4j-rio-jsonld-4.2.4.jar:4.2.4]
	at org.eclipse.rdf4j.rio.jsonld.JSONLDParser.parse(JSONLDParser.java:103) ~[rdf4j-rio-jsonld-4.2.4.jar:4.2.4]
	at org.molgenis.emx2.semantics.LinkedDataService.convertToTtl(LinkedDataService.java:232) ~[molgenis-emx2-semantics-8.195.1-fix-jsonldapi-SNAPSHOT.jar:a45b18b70]
	... 20 more
Caused by: org.eclipse.rdf4j.rio.RDFParseException: Could not parse JSONLD

Caused by: com.github.jsonldjava.core.JsonLdError: invalid term definition: [http://purl.obolibrary.org/obo/NCIT_C15607, http://semanticscience.org/resource/SIO_001003]

[esthervanenckevort]

Resolved in #2903