update test case for TO-eq template, issue #77

geneontology · Nov 13, 2015 · ade8886 · ade8886
1 parent aba359f
commit ade8886
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diff --git a/...eWebAppTO/src/main/java/org/bbop/termgenie/servlets/TermGenieWebAppTOContextListener.java b/...eWebAppTO/src/main/java/org/bbop/termgenie/servlets/TermGenieWebAppTOContextListener.java
@@ -4,23 +4,15 @@
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
 import java.util.List;
-import java.util.Map;
-import java.util.Set;
 
 import org.apache.commons.io.FileUtils;
-import org.apache.commons.lang3.StringUtils;
 import org.apache.log4j.Logger;
 import org.bbop.termgenie.core.ioc.IOCModule;
 import org.bbop.termgenie.mail.MailHandler;
 import org.bbop.termgenie.mail.SimpleMailHandler;
 import org.bbop.termgenie.mail.review.DefaultReviewMailHandlerModule;
 import org.bbop.termgenie.ontology.AdvancedPersistenceModule;
-import org.bbop.termgenie.ontology.git.CommitGitTokenModule;
-import org.bbop.termgenie.ontology.impl.FileCachingIgnoreFilter.IgnoresContainsDigits;
-import org.bbop.termgenie.ontology.impl.GitAwareOntologyModule;
 import org.bbop.termgenie.permissions.UserPermissionsModule;
 import org.bbop.termgenie.presistence.PersistenceBasicModule;
 import org.bbop.termgenie.rules.XMLDynamicRulesModule;
@@ -30,7 +22,6 @@
 import org.bbop.termgenie.services.freeform.FreeFormTermServiceModule;
 import org.bbop.termgenie.services.review.OboTermCommitReviewServiceImpl;
 import org.bbop.termgenie.services.review.TermCommitReviewServiceModule;
-import org.semanticweb.owlapi.model.IRI;
 
 
 public class TermGenieWebAppTOContextListener extends AbstractTermGenieContextListener {
@@ -64,48 +55,14 @@ public String getModuleName() {
 
 	@Override
 	protected IOCModule getOntologyModule() {
-		String configFile = "ontology-configuration_to.xml";
-		String repositoryURL = "https://github.com/Planteome/plant-trait-ontology.git";
 		String workFolder = null; // no default value
-
-		Map<IRI, String> mappedIRIs = new HashMap<IRI, String>();
-		mappedIRIs.put(IRI.create("http://purl.obolibrary.org/obo/to.owl"), "plant-trait-ontology.obo");
-
-		String catalogXML = null; //"src/ontology/catalog-v001.xml";
-
-		final Set<IRI> ignoreIRIs = new HashSet<IRI>();
-		ignoreIRIs.add(IRI.create("http://purl.obolibrary.org/obo/TEMP"));
-
-		GitAwareOntologyModule m = GitAwareOntologyModule.createAnonymousGitModule(configFile, applicationProperties);
-		m.setGitAwareRepositoryURL(repositoryURL);
-		m.setGitAwareMappedIRIs(mappedIRIs);
-		m.setGitAwareCatalogXML(catalogXML);
-		m.setGitAwareWorkFolder(workFolder);
-		m.setFileCacheFilter(new IgnoresContainsDigits(ignoreIRIs));
+		IOCModule m = ToOntologyHelper.createDefaultOntologyModule(workFolder, applicationProperties);
 		return m;
 	}
 
-	protected Map<IRI, File> getLocalMappings(String prefix) {
-		Map<IRI, File> localMappings = new HashMap<IRI, File>();
-		String localIRIMappings = IOCModule.getProperty(prefix, applicationProperties);
-		if (localIRIMappings != null) {
-			String[] localIRIMappingComponents = StringUtils.split(localIRIMappings, ','); // treat as comma separated list
-			for (String component : localIRIMappingComponents) {
-				String iri = IOCModule.getProperty(prefix+"."+component+".IRI", applicationProperties);
-				String file = IOCModule.getProperty(prefix+"."+component+".File", applicationProperties);
-				if (iri != null && file != null) {
-					localMappings.put(IRI.create(iri), new File(file).getAbsoluteFile());
-				}
-			}
-		}
-		return localMappings;
-	}
-
 	@Override
 	protected IOCModule getCommitModule() {
-		String repositoryURL = "https://github.com/Planteome/plant-trait-ontology.git";
-		String remoteTargetFile = "plant-trait-ontology.obo";
-		return CommitGitTokenModule.createOboModule(repositoryURL, remoteTargetFile, applicationProperties);
+		return ToOntologyHelper.getCommitModule(applicationProperties);
 	}
 
 	@Override

diff --git a/...cations/TermGenieWebAppTO/src/main/java/org/bbop/termgenie/servlets/ToOntologyHelper.java b/...cations/TermGenieWebAppTO/src/main/java/org/bbop/termgenie/servlets/ToOntologyHelper.java
@@ -0,0 +1,43 @@
+package org.bbop.termgenie.servlets;
+
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Properties;
+import java.util.Set;
+
+import org.bbop.termgenie.core.ioc.IOCModule;
+import org.bbop.termgenie.ontology.git.CommitGitTokenModule;
+import org.bbop.termgenie.ontology.impl.GitAwareOntologyModule;
+import org.bbop.termgenie.ontology.impl.FileCachingIgnoreFilter.IgnoresContainsDigits;
+import org.semanticweb.owlapi.model.IRI;
+
+public class ToOntologyHelper {
+
+	public static IOCModule createDefaultOntologyModule(String workFolder, Properties applicationProperties) {
+		String configFile = "ontology-configuration_to.xml";
+		String repositoryURL = "https://github.com/Planteome/plant-trait-ontology.git";
+
+		Map<IRI, String> mappedIRIs = new HashMap<IRI, String>();
+		mappedIRIs.put(IRI.create("http://purl.obolibrary.org/obo/to.owl"), "plant-trait-ontology.obo");
+
+		String catalogXML = "catalog-v001.xml";
+
+		final Set<IRI> ignoreIRIs = new HashSet<IRI>();
+		ignoreIRIs.add(IRI.create("http://purl.obolibrary.org/obo/TEMP"));
+
+		GitAwareOntologyModule m = GitAwareOntologyModule.createAnonymousGitModule(configFile, applicationProperties);
+		m.setGitAwareRepositoryURL(repositoryURL);
+		m.setGitAwareMappedIRIs(mappedIRIs);
+		m.setGitAwareCatalogXML(catalogXML);
+		m.setGitAwareWorkFolder(workFolder);
+		m.setFileCacheFilter(new IgnoresContainsDigits(ignoreIRIs));
+		return m;
+	}
+
+	static IOCModule getCommitModule(Properties applicationProperties) {
+		String repositoryURL = "https://github.com/Planteome/plant-trait-ontology.git";
+		String remoteTargetFile = "plant-trait-ontology.obo";
+		return CommitGitTokenModule.createOboModule(repositoryURL, remoteTargetFile, applicationProperties);
+	}
+}
diff --git a/TermGenie/WebApplications/TermGenieWebAppTO/src/main/resources/rules/to/eq_simple.js b/TermGenie/WebApplications/TermGenieWebAppTO/src/main/resources/rules/to/eq_simple.js
@@ -6,13 +6,13 @@ function eq_simple() {
 
 	var label = termname(e, TO) + ' ' + termname(q, TO);
 	var definition = "A trait which is associated with the "
-			+ termname(q, TO) + " of a " + refname(e, TO) + ".";
+			+ termname(q, TO) + " of " + refname(e, TO) + ".";
 
 	var synonyms = null;
 	// String label, List<ISynonym> results, String prefix, String infix, String suffix, String scope
 	synonyms = termgenie.addSynonym(label, synonyms, null, label, ' trait', 'EXACT');
 
-	var mdef = createMDef("?Q and inheres_in some ?E");
+	var mdef = createMDef("?Q and 'inheres in' some ?E");
 	mdef.addParameter('E', e, TO);
 	mdef.addParameter('Q', q, TO);
 	createTerm(label, definition, synonyms, mdef);

diff --git a/...mGenieWebAppTO/src/test/java/org/bbop/termgenie/rules/SimpleEntityQualityPatternTest.java b/...mGenieWebAppTO/src/test/java/org/bbop/termgenie/rules/SimpleEntityQualityPatternTest.java
@@ -1,13 +1,20 @@
 package org.bbop.termgenie.rules;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.fail;
 
+import java.io.File;
+import java.io.IOException;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
 
+import org.apache.commons.io.FileUtils;
 import org.bbop.termgenie.core.TemplateField;
 import org.bbop.termgenie.core.TermTemplate;
+import org.bbop.termgenie.core.ioc.IOCModule;
 import org.bbop.termgenie.core.ioc.TermGenieGuice;
 import org.bbop.termgenie.core.rules.ReasonerModule;
 import org.bbop.termgenie.core.rules.TermGenerationEngine;
@@ -17,11 +24,12 @@
 import org.bbop.termgenie.ontology.OntologyLoader;
 import org.bbop.termgenie.ontology.OntologyTaskManager;
 import org.bbop.termgenie.ontology.OntologyTaskManager.OntologyTask;
-import org.bbop.termgenie.ontology.impl.OntologyModule;
+import org.bbop.termgenie.servlets.ToOntologyHelper;
+import org.junit.AfterClass;
 import org.junit.BeforeClass;
-import org.junit.Ignore;
 import org.junit.Test;
 import org.obolibrary.macro.ManchesterSyntaxTool;
+import org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag;
 import org.semanticweb.owlapi.model.OWLClassExpression;
 
 import owltools.graph.OWLGraphWrapper;
@@ -33,10 +41,21 @@ public class SimpleEntityQualityPatternTest {
 
 	private static TermGenerationEngine generationEngine;
 	private static OntologyLoader loader;
+
+	private static File workFolder;
+
+	private static IOCModule getOntologyModule() throws IOException {
+		File tempFile = File.createTempFile("junit", "", FileUtils.getTempDirectory()).getCanonicalFile();
+		FileUtils.deleteQuietly(tempFile);
+		workFolder = new File(tempFile.getParentFile(), tempFile.getName()+"-folder");
+		workFolder.mkdirs();
+		IOCModule m = ToOntologyHelper.createDefaultOntologyModule(workFolder.getAbsolutePath(), null);
+		return m;
+	}
 
 	@BeforeClass
-	public static void beforeClass() {
-		OntologyModule ontologyModule = new OntologyModule("ontology-configuration_to.xml");
+	public static void beforeClass() throws IOException {
+		IOCModule ontologyModule = getOntologyModule();
 		Injector injector = TermGenieGuice.createInjector(new XMLDynamicRulesModule("termgenie_rules_to.xml", false, true, true, null),
 				ontologyModule,
 				new ReasonerModule(null));
@@ -45,7 +64,11 @@ public static void beforeClass() {
 		loader = injector.getInstance(OntologyLoader.class);
 	}
 
-	@Ignore("Ontology is missing the imports")
+	@AfterClass
+	public static void afterClass() throws Exception {
+		FileUtils.deleteDirectory(workFolder);
+	}
+
 	@Test
 	public void testManchesterSyntaxTool() throws Exception {
 		OntologyTaskManager ontologyManager = loader.getOntologyManager();
@@ -56,6 +79,7 @@ protected void runCatching(OWLGraphWrapper managed) throws TaskException, Except
 				ManchesterSyntaxTool tool = new ManchesterSyntaxTool(managed.getSourceOntology(), managed.getSupportOntologySet());
 
 				assertNotNull(managed.getOWLObjectByLabel("inheres in"));
+				assertNotNull(managed.getOWLObjectByIdentifier("inheres_in"));
 				assertNotNull(managed.getOWLObjectByIdentifier("RO:0000052"));
 
 				assertNotNull(tool.parseManchesterExpression("'plant trait'"));
@@ -65,7 +89,7 @@ protected void runCatching(OWLGraphWrapper managed) throws TaskException, Except
 				OWLClassExpression expression = tool.parseManchesterExpression("PATO_0000970 and 'inheres in' some PO_0020123");
 				assertNotNull(expression);
 
-				expression = tool.parseManchesterExpression("PATO_0000970 and 'inheres in' some PO_0020123");
+				expression = tool.parseManchesterExpression("PATO_0000970 and RO_0000052 some PO_0020123");
 				assertNotNull(expression);
 
 			}
@@ -78,7 +102,6 @@ protected void runCatching(OWLGraphWrapper managed) throws TaskException, Except
 
 	}
 
-	@Ignore("Ontology is missing the imports")
 	@Test
 	public void test_eq_simple_1() {
 
@@ -88,7 +111,7 @@ public void test_eq_simple_1() {
 		assertEquals(1, list.size());
 		TermGenerationOutput output = list.get(0);
 		assertNull(output.getError(), output.getError());
-		// TODO verify output
+		assertEquals("root cap permeability", output.getTerm().getTagValue(OboFormatTag.TAG_NAME));
 	}
 
 	private List<TermGenerationInput> createEQSimpleTask(String entity, String quality) {