tests

owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/enrich/impl/EnrichmentAllByAll.java

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+package org.monarchinitiative.owlsim.compute.enrich.impl;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.monarchinitiative.owlsim.compute.enrich.EnrichmentEngine;
+import org.monarchinitiative.owlsim.compute.enrich.EnrichmentQuery;
+import org.monarchinitiative.owlsim.compute.enrich.EnrichmentResultSet;
+import org.monarchinitiative.owlsim.kb.BMKnowledgeBase;
+
+import com.googlecode.javaewah.EWAHCompressedBitmap;
+
+public class EnrichmentAllByAll {
+
+    private Logger LOG = Logger.getLogger(EnrichmentAllByAll.class);
+
+    /**
+     * @param engine
+     * @param rootCls1
+     * @param rootCls2
+     * @return list of resultsets
+     */
+    public List<EnrichmentResultSet> getAllByAll(EnrichmentEngine engine,
+            String rootCls1, String rootCls2) {
+
+        BMKnowledgeBase kb = engine.getKnowledgeBase();
+
+        EWAHCompressedBitmap bm1 = kb.getSubClasses(kb.getClassIndex(rootCls1));
+        EWAHCompressedBitmap bm2 = kb.getSubClasses(kb.getClassIndex(rootCls2));
+        Set<String> targetClassIds = kb.getClassIds(bm2);
+
+        List<EnrichmentResultSet> resultSets = new ArrayList<>();
+        for (Integer c1ix : bm1.getPositions()) {
+            String c1 = kb.getClassId(c1ix);
+            LOG.info("Performing enrichment for individual set:" +c1);
+            EnrichmentQuery query = new EnrichmentQueryImpl(c1);
+            EnrichmentResultSet rs = engine.calculateEnrichmentAgainstKb(query, targetClassIds);
+            if (rs.getResults().size() > 0)
+                resultSets.add(rs);
+        }
+
+        return resultSets;
+    }
+
+}
+
+

owlsim-core/src/test/java/org/monarchinitiative/owlsim/compute/enrich/impl/AbstractEnrichmentTest.java

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+package org.monarchinitiative.owlsim.compute.enrich.impl;
+
+import java.net.URL;
+
+import org.monarchinitiative.owlsim.io.OWLLoader;
+import org.monarchinitiative.owlsim.kb.BMKnowledgeBase;
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+
+public class AbstractEnrichmentTest {
+
+    protected BMKnowledgeBase kb;
+
+    /**
+     * Load an ontology from resources folder
+     * 
+     * @param fn
+     * @throws OWLOntologyCreationException
+     */
+    protected void load(String fn) throws OWLOntologyCreationException {
+        OWLLoader loader = new OWLLoader();
+        loader.load("src/test/resources/"+fn);
+        kb = loader.createKnowledgeBaseInterface();
+    }
+
+    /**
+     * Load ontology plus data ontologies
+     * 
+     * @param fn
+     * @param ontfns
+     * @throws OWLOntologyCreationException
+     */
+    protected void load(String fn, String... ontfns) throws OWLOntologyCreationException {
+        OWLLoader loader = new OWLLoader();
+        loader.load(getClass().getResource(fn).getFile());
+        for (String ontfn : ontfns) {
+            URL res = getClass().getResource(ontfn);
+            loader.loadOntologies(res.getFile());
+        }
+        kb = loader.createKnowledgeBaseInterface();
+    }
+
+
+}

owlsim-core/src/test/java/org/monarchinitiative/owlsim/compute/enrich/impl/EnrichmentAllByAllTest.java

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+package org.monarchinitiative.owlsim.compute.enrich.impl;
+
+import static org.junit.Assert.*;
+
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.junit.Test;
+import org.monarchinitiative.owlsim.compute.enrich.EnrichmentEngine;
+import org.monarchinitiative.owlsim.compute.enrich.EnrichmentQuery;
+import org.monarchinitiative.owlsim.compute.enrich.EnrichmentResult;
+import org.monarchinitiative.owlsim.compute.enrich.EnrichmentResultSet;
+import org.monarchinitiative.owlsim.kb.BMKnowledgeBase;
+import org.semanticweb.owlapi.model.OWLOntologyCreationException;
+
+public class EnrichmentAllByAllTest extends AbstractEnrichmentTest {
+
+    private Logger LOG = Logger.getLogger(EnrichmentAllByAllTest.class);
+
+
+    @Test
+    public void test() throws OWLOntologyCreationException {
+        load("simple-pheno-with-negation.owl");
+        EnrichmentEngine ee = HypergeometricEnrichmentEngine.create(kb);
+
+        String root = "http://x.org/phenotype";
+        EnrichmentAllByAll axa = new EnrichmentAllByAll();
+        List<EnrichmentResultSet> rsl = axa.getAllByAll(ee, root, root);
+        for (EnrichmentResultSet rs : rsl) {
+            LOG.info("RS="+rs);
+        }
+
+
+    }
+
+    @Test
+    public void testMP() throws OWLOntologyCreationException {
+        load("mp-subset.ttl");
+        EnrichmentEngine ee = HypergeometricEnrichmentEngine.create(kb);
+
+        String root = "http://purl.obolibrary.org/obo/MP_0000001";
+        EnrichmentAllByAll axa = new EnrichmentAllByAll();
+        List<EnrichmentResultSet> rsl = axa.getAllByAll(ee, root, root);
+        for (EnrichmentResultSet rs : rsl) {
+            LOG.info("RS="+rs);
+        }
+
+
+    }
+
+}