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Merge 8b0a01a into 84ce6cb
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@jnguyenx
jnguyenx authored Mar 16, 2017
2 parents 84ce6cb + 8b0a01a commit d4b1fd2
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Showing 3 changed files with 95 additions and 56 deletions.
13 changes: 13 additions & 0 deletions owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/classmatch/ClassMatcher.java
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Expand Up @@ -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;

/**
Expand Down Expand Up @@ -37,6 +38,18 @@ public List<SimpleClassMatch> matchOntologies(String qOnt, String tOnt) {
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(entity), tids);
}

public List<SimpleClassMatch> matchClassSets(Set<String> qids, Set<String> tids) {
ArrayList<SimpleClassMatch> matches = new ArrayList<>();
for (String q : qids) {
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95 changes: 54 additions & 41 deletions ...-core/src/test/java/org/monarchinitiative/owlsim/compute/classmatch/ClassMatcherTest.java
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Expand Up @@ -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());
}

}
43 changes: 28 additions & 15 deletions .../src/main/java/org/monarchinitiative/owlsim/services/resources/OntologyMatchResource.java
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@@ -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}")
Expand All @@ -61,6 +52,28 @@ public List<SimpleClassMatch> getOntoMatches(
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 {

// TODO it's weird to resolve the curie here
String resolveEntity = curieUtil.getIri(entity).orElse(entity);

List<SimpleClassMatch> matches =
classMatcher.matchEntity(resolveEntity, ontology);
return matches;
}

}

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