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Add back annotation extension filtering based on evidence. #147

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merged 4 commits into from
Oct 5, 2017
Merged

Add back annotation extension filtering based on evidence. #147

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f04e9dc
Added back annotation extension filtering based on evidence. Fixes #140.
balhoff Oct 5, 2017
ad65137
Fixed missed refactoring.
balhoff Oct 5, 2017
5e2e17e
Added RO file needed for tests.
balhoff Oct 5, 2017
b0088e5
Merge branch 'master' into issue-140
balhoff Oct 5, 2017
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2 changes: 1 addition & 1 deletion minerva-cli/src/main/java/org/geneontology/minerva/cli/MinervaCommandRunner.java
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Original file line number Diff line number Diff line change
Expand Up @@ -438,7 +438,7 @@ else if (opts.nextEq("--ontology")) {
CurieMappings localMappings = new CurieMappings.SimpleCurieMappings(Collections.singletonMap(modelIdcurie, modelIdPrefix));
CurieHandler curieHandler = new MappedCurieHandler(DefaultCurieHandler.loadDefaultMappings(), localMappings);
for (IRI modelIRI : m3.getAvailableModelIds()) {
String gpad = new GPADSPARQLExport(curieHandler, null, m3.getLegacyRelationShorthandIndex()).exportGPAD(m3.createInferredModel(modelIRI));
String gpad = new GPADSPARQLExport(curieHandler, m3.getLegacyRelationShorthandIndex()).exportGPAD(m3.createInferredModel(modelIRI));
String fileName = StringUtils.replaceOnce(modelIRI.toString(), modelIdPrefix, "") + ".gpad";
Writer writer = new OutputStreamWriter(new FileOutputStream(Paths.get(gpadOutputFolder, fileName).toFile()), StandardCharsets.UTF_8);
writer.write(gpad);
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5 changes: 1 addition & 4 deletions minerva-converter/src/main/java/org/geneontology/minerva/legacy/sparql/GPADRenderer.java
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Expand Up @@ -10,21 +10,18 @@

import org.geneontology.minerva.curie.CurieHandler;
import org.geneontology.minerva.legacy.sparql.GPADData.ConjunctiveExpression;
import org.geneontology.minerva.lookup.ExternalLookupService;
import org.semanticweb.owlapi.model.IRI;

public class GPADRenderer {

private final CurieHandler curieHandler;
private final Map<IRI, String> relationShorthandIndex;
//private final ExternalLookupService lookupService;

public static final String HEADER = "!gpa-version: 1.2";

public GPADRenderer(CurieHandler handler, ExternalLookupService lookup, Map<IRI, String> shorthandIndex) {
public GPADRenderer(CurieHandler handler, Map<IRI, String> shorthandIndex) {
this.curieHandler = handler;
this.relationShorthandIndex = shorthandIndex;
//this.lookupService = lookup;
}

public String renderAll(Collection<GPADData> data) {
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18 changes: 11 additions & 7 deletions minerva-converter/src/main/java/org/geneontology/minerva/legacy/sparql/GPADSPARQLExport.java
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,6 @@
import org.apache.log4j.Logger;
import org.geneontology.minerva.curie.CurieHandler;
import org.geneontology.minerva.legacy.sparql.GPADData.ConjunctiveExpression;
import org.geneontology.minerva.lookup.ExternalLookupService;
import org.geneontology.rules.engine.Explanation;
import org.geneontology.rules.engine.WorkingMemory;
import org.geneontology.rules.util.Bridge;
Expand All @@ -53,7 +52,7 @@ public class GPADSPARQLExport {
private static final String BP = "http://purl.obolibrary.org/obo/GO_0008150";
private static final String CC = "http://purl.obolibrary.org/obo/GO_0005575";
private static final Set<String> rootTerms = new HashSet<>(Arrays.asList(MF, BP, CC));

private static String mainQuery;
static {
try {
Expand All @@ -80,12 +79,10 @@ public class GPADSPARQLExport {
}
private final CurieHandler curieHandler;
private final Map<IRI, String> relationShorthandIndex;
private final ExternalLookupService lookupService;

public GPADSPARQLExport(CurieHandler handler, ExternalLookupService lookup, Map<IRI, String> shorthandIndex) {
public GPADSPARQLExport(CurieHandler handler, Map<IRI, String> shorthandIndex) {
this.curieHandler = handler;
this.relationShorthandIndex = shorthandIndex;
this.lookupService = lookup;
}

/*
Expand All @@ -107,6 +104,7 @@ public String exportGPAD(WorkingMemory wm) {
Set<AnnotationExtension> possibleExtensions = possibleExtensions(basicAnnotations, model);
Set<Triple> statementsToExplain = new HashSet<>();
basicAnnotations.forEach(ba -> statementsToExplain.add(Triple.create(ba.getObjectNode(), NodeFactory.createURI(ba.getQualifier().toString()), ba.getOntologyClassNode())));
possibleExtensions.forEach(ae -> statementsToExplain.add(ae.getTriple()));
Map<Triple, Set<Explanation>> allExplanations = statementsToExplain.stream().collect(Collectors.toMap(Function.identity(), s -> toJava(wm.explain(Bridge.tripleFromJena(s)))));
Map<Triple, Set<GPADEvidence>> allEvidences = evidencesForFacts(allExplanations.values().stream().flatMap(es -> es.stream()).flatMap(e -> toJava(e.facts()).stream().map(t -> Bridge.jenaFromTriple(t))).collect(Collectors.toSet()), model, modelID);
for (BasicGPADData annotation : basicAnnotations) {
Expand All @@ -124,7 +122,13 @@ public String exportGPAD(WorkingMemory wm) {
for (AnnotationExtension extension : possibleExtensions) {
if (extension.getTriple().getSubject().equals(annotation.getOntologyClassNode()) &&
!(extension.getTriple().getObject().equals(annotation.getObjectNode()))) {
goodExtensions.add(new DefaultConjunctiveExpression(IRI.create(extension.getTriple().getPredicate().getURI()), extension.getValueType()));
for (Explanation expl : allExplanations.get(extension.getTriple())) {
boolean allFactsOfExplanationHaveRefMatchingAnnotation = toJava(expl.facts()).stream().map(fact -> allEvidences.getOrDefault(Bridge.jenaFromTriple(fact), Collections.emptySet())).allMatch(evidenceSet ->
evidenceSet.stream().anyMatch(ev -> ev.getReference().equals(reference)));
if (allFactsOfExplanationHaveRefMatchingAnnotation) {
goodExtensions.add(new DefaultConjunctiveExpression(IRI.create(extension.getTriple().getPredicate().getURI()), extension.getValueType()));
}
}
}
}
final boolean rootViolation;
Expand All @@ -139,7 +143,7 @@ public String exportGPAD(WorkingMemory wm) {
}
}
}
return new GPADRenderer(curieHandler, lookupService, relationShorthandIndex).renderAll(annotations);
return new GPADRenderer(curieHandler, relationShorthandIndex).renderAll(annotations);
}

private Map<Triple, Set<GPADEvidence>> evidencesForFacts(Set<Triple> facts, Model model, String modelID) {
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63 changes: 63 additions & 0 deletions minerva-converter/src/test/java/org/geneontology/minerva/legacy/sparql/GPADSPARQLTest.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,63 @@
package org.geneontology.minerva.legacy.sparql;

import java.util.HashMap;
import java.util.HashSet;
import java.util.Set;
import java.util.stream.Collectors;

import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.ModelFactory;
import org.apache.jena.reasoner.rulesys.Rule;
import org.apache.jena.system.JenaSystem;
import org.geneontology.jena.OWLtoRules;
import org.geneontology.minerva.curie.DefaultCurieHandler;
import org.geneontology.rules.engine.RuleEngine;
import org.geneontology.rules.engine.Triple;
import org.geneontology.rules.engine.WorkingMemory;
import org.geneontology.rules.util.Bridge;
import org.junit.Assert;
import org.junit.BeforeClass;
import org.junit.Test;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.model.parameters.Imports;

import scala.collection.JavaConverters;

public class GPADSPARQLTest {

private static RuleEngine arachne;
private static GPADSPARQLExport exporter;

@BeforeClass
public static void setupRules() throws OWLOntologyCreationException {
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
OWLOntology ont = manager.loadOntologyFromOntologyDocument(GPADSPARQLTest.class.getResourceAsStream("/ro-merged-2017-10-02.ofn"));
Set<Rule> rules = new HashSet<>();
rules.addAll(JavaConverters.setAsJavaSetConverter(OWLtoRules.translate(ont, Imports.INCLUDED, true, true, true, true)).asJava());
rules.addAll(JavaConverters.setAsJavaSetConverter(OWLtoRules.indirectRules(ont)).asJava());
arachne = new RuleEngine(Bridge.rulesFromJena(JavaConverters.asScalaSetConverter(rules).asScala()), true);
}

@BeforeClass
public static void setupExporter() {
JenaSystem.init();
exporter = new GPADSPARQLExport(DefaultCurieHandler.getDefaultHandler(), new HashMap<IRI, String>());
}

@Test
public void testGPADOutput() throws Exception {
Model model = ModelFactory.createDefaultModel();
model.read(this.getClass().getResourceAsStream("/581e072c00000473.ttl"), "", "ttl");
Set<Triple> triples = model.listStatements().toList().stream().map(s -> Bridge.tripleFromJena(s.asTriple())).collect(Collectors.toSet());
WorkingMemory mem = arachne.processTriples(JavaConverters.asScalaSetConverter(triples).asScala());
String gpad = exporter.exportGPAD(mem);
int lines = gpad.split("\n", -1).length;
//TODO test contents of annotations; dumb test for now
Assert.assertTrue("Should produce annotations", lines > 2);
}

}
722 changes: 722 additions & 0 deletions minerva-converter/src/test/resources/581e072c00000473.ttl
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