Merge pull request #249 from geneontology/issue-126-source-url-comment

Add contributor_link comment for #126
geneontology · May 10, 2023 · 700b047 · 700b047
2 parents be540fc + a7143b1
commit 700b047
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diff --git a/exchange/src/main/java/org/geneontology/gocam/exchange/BioPaxtoGO.java b/exchange/src/main/java/org/geneontology/gocam/exchange/BioPaxtoGO.java
@@ -278,13 +278,15 @@ void convert(
 				go_cam.path2bgjournal = blazegraph_output_journal;
 				go_cam.blazegraphdb = blaze;
 				go_cam.name = getBioPaxName(currentPathway);
+				go_cam.contributor_link = contributor_link;
 			}
 			//make the OWL individual representing the pathway so it can be used below
 			OWLNamedIndividual p = go_cam.makeAnnotatedIndividual(GoCAM.makeGoCamifiedIRI(null, model_id));
 			//annotate it with any provenance comments
 			for(String comment : pathway_source_comments) {
 				go_cam.addComment(p, comment);
 			}
+			go_cam.addComment(p, go_cam.contributor_link);
 			//define it (add types etc)
 			definePathwayEntity(go_cam, currentPathway, model_id, expand_subpathways, add_pathway_components);	
 			//get and set parent pathways

diff --git a/exchange/src/main/java/org/geneontology/gocam/exchange/GoCAM.java b/exchange/src/main/java/org/geneontology/gocam/exchange/GoCAM.java
@@ -153,6 +153,7 @@ public class GoCAM {
 	//for convenience
 	String name;
 	String default_namespace_prefix;
+	String contributor_link;
 
 	public GoCAM() throws OWLOntologyCreationException {
 		ontman = OWLManager.createOWLOntologyManager();				
@@ -488,6 +489,7 @@ Set<OWLAnnotation> getDefaultAnnotations(){
 		annos.add(df.getOWLAnnotation(contributor_prop, df.getOWLLiteral(this.base_contributor)));
 		annos.add(df.getOWLAnnotation(date_prop, df.getOWLLiteral(this.base_date)));
 		annos.add(df.getOWLAnnotation(provided_by_prop, df.getOWLLiteral(this.base_provider)));
+		annos.add(df.getOWLAnnotation(rdfs_comment, df.getOWLLiteral(this.contributor_link)));
 		return annos;
 	}