From e7ededcb39fb85d21cb5069eab1497d9c6bb86e8 Mon Sep 17 00:00:00 2001
From: goodb <ben.mcgee.good@gmail.com>
Date: Thu, 23 Jul 2020 12:24:51 -0700
Subject: [PATCH] adding root types for partial responses.

---
 .../json/MolecularModelJsonRenderer.java      | 18 +++++++++++++++
 .../BlazegraphOntologyManagerTest.java        | 23 +++++++++++++++++++
 2 files changed, 41 insertions(+)

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
index 194e098b..07c8bad5 100644
--- 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
index e80ba029..3835b4ad 100644
--- 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"));
+		
+
+	}
 }