Merge pull request #73 from monarch-initiative/72-ontomatch-single-en…

…tity

[#72] added service for single entity

owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/classmatch/ClassMatcher.java

@@ -7,6 +7,7 @@
 import org.monarchinitiative.owlsim.kb.BMKnowledgeBase;
 import org.monarchinitiative.owlsim.kb.LabelMapper;
 
+import com.google.common.collect.Sets;
 import com.googlecode.javaewah.EWAHCompressedBitmap;
 
 /**
@@ -37,6 +38,18 @@ public ClassMatcher(BMKnowledgeBase kb) {
 		return matchClassSets(qids, tids);
 	}
 
+	/**
+	 * Find best match for one entity in a whole ontology
+	 * 
+	 * @param entity
+	 * @param tOnt
+	 * @return list of matches
+	 */
+	public List<SimpleClassMatch> matchEntity(String entity, String tOnt) {
+		Set<String> tids = kb.getClassIdsByOntology(tOnt);
+		return matchClassSets(Sets.newHashSet(kb.resolveIri(entity)), tids);
+	}
+
 	public List<SimpleClassMatch> matchClassSets(Set<String> qids, Set<String> tids) {
 		ArrayList<SimpleClassMatch> matches = new ArrayList<>();
 		for (String q : qids) {

owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/BMKnowledgeBase.java

@@ -351,11 +351,17 @@
 	public int getRootIndex();
 
 
+	/**
+	 * Resolves a CURIE into an IRI, if possible.
+	 * 
+	 * @return IRI version of a CURIE, or the string itself
+	 */
+	public String resolveIri(String entity);
+
+	
+	
 	public static OwlKnowledgeBase.Loader owlLoader() {
 		return OwlKnowledgeBase.loader();
 	}
 
-
-
-
 }

owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java

@@ -141,12 +141,8 @@ public void setKbMetdata(KBMetadata kbMetdata) {
 	}
 
 	private String getShortForm(IRI iri) {
-		if (curieUtil.getCurieMap().isEmpty()) {
-			return iri.toString();
-		} else {
-			String iriString = iri.toString();
-			return curieUtil.getCurie(iriString).orElse(iriString);
-		}
+		String iriString = iri.toString();
+		return curieUtil.getCurie(iriString).orElse(iriString);
 	}
 
 	private void populateLabelsFromOntology(LabelMapper labelMapper, OWLOntology ontology) {
@@ -1006,11 +1002,7 @@ protected String getIdentifier(OWLNamedObject obj) {
 	 */
 	private OWLClass getOWLClass(String id) {
 		Preconditions.checkNotNull(id);
-		if (curieUtil.getCurieMap().isEmpty()) {
-			return getOWLClass(IRI.create(id));
-		} else {
-			return getOWLClass(IRI.create(curieUtil.getIri(id).orElse(id)));
-		}
+		return getOWLClass(IRI.create(curieUtil.getIri(id).orElse(id)));
 	}
 
 	/**
@@ -1036,12 +1028,7 @@ private OWLNamedIndividual getOWLNamedIndividual(IRI iri) {
 	 */
 	private OWLNamedIndividual getOWLNamedIndividual(String id) {
 		Preconditions.checkNotNull(id);
-		//TODO: check - this is redundant code simply return getOWLNamedIndividual(IRI.create(curieUtil.getIri(id).orElse(id))); will suffice
-		if (curieUtil.getCurieMap().isEmpty()) {
-			return getOWLNamedIndividual(IRI.create(id));
-		} else {
-			return getOWLNamedIndividual(IRI.create(curieUtil.getIri(id).orElse(id)));
-		}
+		return getOWLNamedIndividual(IRI.create(curieUtil.getIri(id).orElse(id)));
 	}
 
 	public Attribute getAttribute(String id) {
@@ -1113,4 +1100,9 @@ public EWAHCompressedBitmap getFilteredDirectTypesBM(Set<String> classIds, Strin
 
 	}
 
+	@Override
+	public String resolveIri(String entity) {
+		return curieUtil.getIri(entity).orElse(entity);
+	}
+
 }

owlsim-core/src/test/java/org/monarchinitiative/owlsim/compute/classmatch/ClassMatcherTest.java

@@ -14,49 +14,62 @@
 import java.util.List;
 import java.util.stream.Collectors;
 
-import static org.junit.Assert.assertEquals;
+import javax.swing.plaf.synth.SynthSplitPaneUI;
+
+import static org.junit.Assert.*;
 
 public class ClassMatcherTest {
 
-    protected BMKnowledgeBase kb;
-    protected ClassMatcher classMatcher;
-    private Logger LOG = Logger.getLogger(ClassMatcherTest.class);
-
-    protected void load(String fn, String... ontfns) throws OWLOntologyCreationException, URISyntaxException, NoRootException {
-//        OWLLoader loader = new OWLLoader();
-//        LOG.info("Loading: "+fn);
-//        loader.load(IRI.create(Resources.getResource(fn)));
-//        for (String ontfn : ontfns) {
-//            URL res = getClass().getResource(ontfn);
-//            LOG.info("RES="+res);
-//            loader.ontologies(res.getFile());
-//        }
-//        kb = loader.createKnowledgeBaseInterface();
-        kb = OwlKnowledgeBase.loader()
-                .loadOntology(filePath(fn))
-                .loadOntologies(Arrays.stream(ontfns).map(ontfn -> filePath(ontfn)).collect(Collectors.toList()))
-                .createKnowledgeBase();
-        classMatcher = new ClassMatcher(kb);
-    }
-
-    private String filePath(String filename) {
-        return Paths.get("src/test/resources/", filename).toString();
-    }
-
-    @Test
-    public void selfTest() throws OWLOntologyCreationException, URISyntaxException, NoRootException {
-        load("mp-subset.ttl");
-        LabelMapper lm = kb.getLabelMapper();
-        
-        List<SimpleClassMatch> matches = classMatcher.matchOntologies("MP", "MP");
-        
-        int numNonSelfMatches = 0;
-        for (SimpleClassMatch m : matches) {
-            if (!m.getQueryClassId().equals(m.getMatchClassId())) {
-                numNonSelfMatches++;
-            }
-        }
-        assertEquals(0, numNonSelfMatches);
-    }
+	protected BMKnowledgeBase kb;
+	private Logger LOG = Logger.getLogger(ClassMatcherTest.class);
+
+	protected ClassMatcher load(String fn, String... ontfns)
+			throws OWLOntologyCreationException, URISyntaxException, NoRootException {
+		// OWLLoader loader = new OWLLoader();
+		// LOG.info("Loading: "+fn);
+		// loader.load(IRI.create(Resources.getResource(fn)));
+		// for (String ontfn : ontfns) {
+		// URL res = getClass().getResource(ontfn);
+		// LOG.info("RES="+res);
+		// loader.ontologies(res.getFile());
+		// }
+		// kb = loader.createKnowledgeBaseInterface();
+		kb = OwlKnowledgeBase.loader().loadOntology(filePath(fn))
+				.loadOntologies(Arrays.stream(ontfns).map(ontfn -> filePath(ontfn)).collect(Collectors.toList()))
+				.createKnowledgeBase();
+		return new ClassMatcher(kb);
+	}
+
+	private String filePath(String filename) {
+		return Paths.get("src/test/resources/", filename).toString();
+	}
+
+	@Test
+	public void selfTest() throws OWLOntologyCreationException, URISyntaxException, NoRootException {
+		ClassMatcher classMatcher = load("mp-subset.ttl");
+		LabelMapper lm = kb.getLabelMapper();
+
+		List<SimpleClassMatch> matches = classMatcher.matchOntologies("MP", "MP");
+
+		int numNonSelfMatches = 0;
+		for (SimpleClassMatch m : matches) {
+			if (!m.getQueryClassId().equals(m.getMatchClassId())) {
+				numNonSelfMatches++;
+			}
+		}
+		assertEquals(0, numNonSelfMatches);
+	}
+
+	@Test
+	public void entityMatchTest() throws OWLOntologyCreationException, URISyntaxException, NoRootException {
+		ClassMatcher classMatcher = load("mp-subset.ttl");
+
+		String testEntity = "http://purl.obolibrary.org/obo/MP_0001951";
+
+		List<SimpleClassMatch> matches = classMatcher.matchEntity(testEntity, "MP");
+
+		assertFalse(matches.isEmpty());
+		assertEquals(testEntity, matches.get(0).getMatchClassId());
+	}
 
 }

owlsim-services/src/main/java/org/monarchinitiative/owlsim/services/resources/OntologyMatchResource.java

@@ -1,48 +1,39 @@
 package org.monarchinitiative.owlsim.services.resources;
 
-import java.util.Collection;
-import java.util.HashMap;
 import java.util.List;
-import java.util.Map;
-import java.util.Set;
 import java.util.concurrent.TimeUnit;
 
 import javax.inject.Inject;
 import javax.ws.rs.GET;
 import javax.ws.rs.Path;
 import javax.ws.rs.PathParam;
 import javax.ws.rs.Produces;
-import javax.ws.rs.QueryParam;
 import javax.ws.rs.core.MediaType;
 
 import org.monarchinitiative.owlsim.compute.classmatch.ClassMatcher;
 import org.monarchinitiative.owlsim.compute.classmatch.SimpleClassMatch;
 import org.monarchinitiative.owlsim.compute.cpt.IncoherentStateException;
-import org.monarchinitiative.owlsim.compute.matcher.NegationAwareProfileMatcher;
-import org.monarchinitiative.owlsim.compute.matcher.ProfileMatcher;
-import org.monarchinitiative.owlsim.kb.filter.AnonIndividualFilter;
-import org.monarchinitiative.owlsim.kb.filter.TypeFilter;
 import org.monarchinitiative.owlsim.kb.filter.UnknownFilterException;
 import org.monarchinitiative.owlsim.model.match.MatchSet;
-import org.monarchinitiative.owlsim.model.match.ProfileQuery;
-import org.monarchinitiative.owlsim.model.match.ProfileQueryFactory;
-import org.monarchinitiative.owlsim.services.exceptions.NonNegatedMatcherException;
-import org.monarchinitiative.owlsim.services.exceptions.UnknownMatcherException;
+import org.prefixcommons.CurieUtil;
 
 import com.codahale.metrics.annotation.Timed;
+
+import io.dropwizard.jersey.caching.CacheControl;
 import io.swagger.annotations.Api;
 import io.swagger.annotations.ApiOperation;
 import io.swagger.annotations.ApiParam;
 
-import io.dropwizard.jersey.caching.CacheControl;
-
 @Path("/ontomatch")
 @Api(value = "/ontomatch", description = "ontology match services")
 @Produces({MediaType.APPLICATION_JSON})
 public class OntologyMatchResource {
 
     @Inject
     ClassMatcher classMatcher;
+    
+    @Inject
+    CurieUtil curieUtil;
 
     @GET
     @Path("/{queryOntology}/{targetOntology}")
@@ -61,6 +52,24 @@
         return matches;
     }
 
+    
     // TODO - API for comparing two entities
 
+    @GET
+    @Path("/{entity}/{ontology}")
+    @Timed
+    @CacheControl(maxAge = 2, maxAgeUnit = TimeUnit.HOURS)
+    @ApiOperation(value = "Match", response = MatchSet.class,
+    notes = "Additional notes on the match resource.")
+    public List<SimpleClassMatch> getEntityMatches(
+            @ApiParam(value = "entity, e.g. MP:0001951",
+            required = true) @PathParam("entity") String entity,
+            @ApiParam(value = "ontology to be matched, e.g. HP",
+            required = true) @PathParam("ontology") String ontology)
+                    throws UnknownFilterException, IncoherentStateException {
+        List<SimpleClassMatch> matches = 
+                classMatcher.matchEntity(entity, ontology);
+		return matches;
+	}
+
 }