cleaning up physical entity builder

geneontology · Jan 27, 2020 · 3af3372 · 3af3372
1 parent 24a5826
commit 3af3372
Showing 1 changed file with 11 additions and 19 deletions.
diff --git a/exchange/src/main/java/org/geneontology/gocam/exchange/PhysicalEntityOntologyBuilder.java b/exchange/src/main/java/org/geneontology/gocam/exchange/PhysicalEntityOntologyBuilder.java
@@ -216,7 +216,7 @@ public static void main(String[] args) throws OWLOntologyCreationException, IOEx
 		for (PhysicalEntity entity : biopax_model.getObjects(PhysicalEntity.class)){		
 			String model_id = entity.hashCode()+"";
 			n++;
-			System.out.println(n+" defining "+entity.getDisplayName()+" "+entity.getModelInterface()+" "+entity.getUri());
+			//System.out.println(n+" defining "+entity.getDisplayName()+" "+entity.getModelInterface()+" "+entity.getUri());
 			converter.definePhysicalEntity(go_cam, entity, null, model_id);
 		}
 
@@ -258,10 +258,10 @@ public static void main(String[] args) throws OWLOntologyCreationException, IOEx
 
 		go_cam.writeGoCAM_jena(outfilename, false, outputformat);
 
-		int n_objects = 0;
-		for(String id : converter.id_class_map.keySet()) {
-			System.out.println(id+" "+(n_objects++)+" "+converter.id_class_map.get(id));
-		}
+//		int n_objects = 0;
+//		for(String id : converter.id_class_map.keySet()) {
+//			System.out.println(id+" "+(n_objects++)+" "+converter.id_class_map.get(id));
+//		}
 	}
 
 
@@ -277,10 +277,6 @@ private OWLClassExpression definePhysicalEntity(GoCAM go_cam, PhysicalEntity ent
 			this_iri = GoCAM.makeGoCamifiedIRI(model_id, entity_id);
 		}
 
-		if(this_iri.toString().contains("R-HSA-9663470")) {
-			System.out.println("Checking R-HSA-9663470 "+entity.getDisplayName());
-		}
-
 		//add entity to ontology as a class, whatever it is
 		OWLClass e = go_cam.df.getOWLClass(this_iri); 	
 		if(entity_id!=null) {
@@ -508,9 +504,8 @@ else if(entity.getModelInterface().equals(Protein.class)||entity.getModelInterfa
 					}
 				}else if(entity.getModelInterface().equals(Protein.class)) {
 					go_cam.addSubclassAssertion(e, GoCAM.chebi_protein, null);	
-					System.out.println("non uniprot protein detected: "+entity.getDisplayName());
+					//System.out.println("non uniprot protein detected: "+entity.getDisplayName());
 				}else { //entity is just PhysicalEntity.class
-					System.out.println("ambiguous physical entity detected: "+entity.getDisplayName());
 					Set<Xref> e_xrefs = entity.getXref();
 					boolean entity_type_set = false;
 					if(e_xrefs!=null) {
@@ -544,6 +539,7 @@ else if(entity.getModelInterface().equals(Protein.class)||entity.getModelInterfa
 						//everything is at least a continuant...
 						go_cam.addSubclassAssertion(e, GoCAM.continuant_class, null);	
 						go_cam.addUriAnnotations2Individual(e.getIRI(), GoCAM.canonical_record, GoCAM.continuant_class.getIRI());					
+						System.out.println("unclassified entity\t"+e+"\t"+entity.getDisplayName());
 					}
 				}
 			}
@@ -832,7 +828,7 @@ public static String getDrugReferenceId(Entity bp_entity) {
 			}else if(bp_entity.getModelInterface().equals(DnaRegion.class)){
 				r = ((DnaRegion) bp_entity).getEntityReference();
 			}else if(bp_entity.getModelInterface().equals(PhysicalEntity.class)) {
-				System.err.println("Can not access EntityReference for untyped physical entity: "+bp_entity.getDisplayName());
+				//System.err.println("Can not access EntityReference for untyped physical entity: "+bp_entity.getDisplayName());
 			}
 			if(r!=null) {
 				Set<Xref> erefs = r.getXref();
@@ -845,9 +841,9 @@ public static String getDrugReferenceId(Entity bp_entity) {
 		}catch(Exception e) {
 			return null;
 		}
-		if(id!=null) {
-			System.out.println("found drug id "+id+" "+bp_entity.getDisplayName());
-		}
+//		if(id!=null) {
+//			System.out.println("found drug id "+id+" "+bp_entity.getDisplayName());
+//		}
 		return id;
 	}
 
@@ -873,10 +869,6 @@ public static void countPhysical(Model biopax_model) throws IOException {
 				n_all_pro++;
 				in_pro = true;
 			}
-			if(e.getDisplayName()!=null&&e.getDisplayName().equals("pertuzumab")) {
-				String testdrug_id = getDrugReferenceId(e);
-				System.out.println("hello pertuzumab "+testdrug_id);
-			}
 			String drug_id = getDrugReferenceId(e);
 			if(drug_id==null) {
 				drug_id = "no_IUPHAR";