Merge pull request #340 from geneontology/add-root-types-for-partial-…

…response adding root types for partial model responses
geneontology · Jul 23, 2020 · 7304c44 · 7304c44
2 parents 567d6a0 + e7ededc
commit 7304c44
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diff --git a/minerva-core/src/main/java/org/geneontology/minerva/json/MolecularModelJsonRenderer.java b/minerva-core/src/main/java/org/geneontology/minerva/json/MolecularModelJsonRenderer.java
@@ -208,6 +208,23 @@ private static JsonAnnotation[] renderAnnotations(Set<OWLAnnotation> annotations
  }
 
  public Pair<JsonOwlIndividual[], JsonOwlFact[]> renderIndividuals(Collection<OWLNamedIndividual> individuals) {
+
+ //add root types in case these are new to the model
+ if(go_lego_repo!=null) {
+ try {
+ if(type_roots==null) {
+ type_roots = new HashMap<OWLNamedIndividual, Set<String>>();
+ }
+ Map<OWLNamedIndividual, Set<String>> t_r = go_lego_repo.getSuperCategoryMapForIndividuals(new HashSet<OWLNamedIndividual>(individuals), ont);
+ if(t_r!=null) {
+ type_roots.putAll(t_r); 
+ }
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+
  List<JsonOwlIndividual> iObjs = new ArrayList<JsonOwlIndividual>();
  Set<OWLNamedIndividual> individualIds = new HashSet<OWLNamedIndividual>();
  final Set<OWLObjectPropertyAssertionAxiom> opAxioms = new HashSet<OWLObjectPropertyAssertionAxiom>();
@@ -218,6 +235,7 @@ public Pair<JsonOwlIndividual[], JsonOwlFact[]> renderIndividuals(Collection<OWL
  individualIds.add(named);
  }
  }
+
  // filter object property axioms. Only retain axioms which use individuals from the given subset
  for (OWLNamedIndividual i : individualIds) {
  Set<OWLObjectPropertyAssertionAxiom> axioms = ont.getObjectPropertyAssertionAxioms(i);

diff --git a/minerva-core/src/test/java/org/geneontology/minerva/BlazegraphOntologyManagerTest.java b/minerva-core/src/test/java/org/geneontology/minerva/BlazegraphOntologyManagerTest.java
@@ -255,4 +255,27 @@ public void testGetUpperTypes() throws IOException {
  assertTrue("WBGene00000275 not subclass of CHEBI_36695 information biomacromolecule", supers.contains("http://purl.obolibrary.org/obo/CHEBI_33695"));
  assertTrue("WBGene00000275 not subclass of CHEBI_24431 chemical entity", supers.contains("http://purl.obolibrary.org/obo/CHEBI_24431"));
  }
+
+ @Test 
+ public void testGetComplexPortalTypes() throws IOException {
+ //make sure its possible to get from leaf to root for the key classes
+ Set<String> uris = new HashSet<String>();
+ String cp1 = "http://purl.obolibrary.org/obo/ComplexPortal_CPX-9";
+ String cp2 = "http://purl.obolibrary.org/obo/ComplexPortal_CPX-4082";
+//this doesn't work now. It should work while the ones above do not. this is problem with the neo ontology. 
+// String cp3 = "https://www.ebi.ac.uk/complexportal/complex/CPX-9";
+ uris.add(cp1);
+ uris.add(cp2);
+// uris.add(cp3);
+
+ Map<String, Set<String>> uri_roots = onto_repo.getSuperCategoryMap(uris);
+ Set<String> supers = uri_roots.get(cp1);
+ assertTrue("ComplexPortal_CPX-9 not an information biomacromolecule", supers.contains("http://purl.obolibrary.org/obo/CHEBI_33695"));
+ supers = uri_roots.get(cp2);
+ assertTrue("ComplexPortal_CPX-4082 not an information biomacromolecule", supers.contains("http://purl.obolibrary.org/obo/CHEBI_33695"));
+// supers = uri_roots.get(cp3);
+// assertTrue("ComplexPortal_CPX-9 as https://www.ebi.ac.uk/complexportal/complex/CPX-9 is not an information biomacromolecule", supers.contains("http://purl.obolibrary.org/obo/CHEBI_33695"));
+
+
+ }
 }