Full synonym cross-products for TO eq template

* allow non-ASCII (i.e. Japanese) synonyms * see issue #80
geneontology · Nov 24, 2015 · dd904f0 · dd904f0
1 parent ade8886
commit dd904f0
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Showing 3 changed files with 17 additions and 10 deletions.
diff --git a/...eWebAppTO/src/main/java/org/bbop/termgenie/servlets/TermGenieWebAppTOContextListener.java b/...eWebAppTO/src/main/java/org/bbop/termgenie/servlets/TermGenieWebAppTOContextListener.java
@@ -67,7 +67,8 @@ protected IOCModule getCommitModule() {
 
 	@Override
 	protected IOCModule getRulesModule() {
-		return new XMLDynamicRulesModule("termgenie_rules_to.xml", false, true, true, applicationProperties);
+		boolean filterNonAsciiSynonyms = false; // allow japanese synonyms
+		return new XMLDynamicRulesModule("termgenie_rules_to.xml", false, true, filterNonAsciiSynonyms, applicationProperties);
 	}
 
 	@Override

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
@@ -8,9 +8,7 @@ function eq_simple() {
 	var definition = "A trait which is associated with the "
 			+ 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 synonyms = termgenie.synonyms(null, e, TO, " ", q, TO, "", null, label);
 
 	var mdef = createMDef("?Q and 'inheres in' some ?E");
 	mdef.addParameter('E', e, TO);

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 +1,11 @@
 package org.bbop.termgenie.rules;
 
-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 static org.junit.Assert.*;
 
 import java.io.File;
 import java.io.IOException;
 import java.util.Arrays;
+import java.util.Collection;
 import java.util.Collections;
 import java.util.List;
 
@@ -29,6 +27,8 @@
 import org.junit.BeforeClass;
 import org.junit.Test;
 import org.obolibrary.macro.ManchesterSyntaxTool;
+import org.obolibrary.oboformat.model.Clause;
+import org.obolibrary.oboformat.model.Frame;
 import org.obolibrary.oboformat.parser.OBOFormatConstants.OboFormatTag;
 import org.semanticweb.owlapi.model.OWLClassExpression;
 
@@ -55,8 +55,9 @@ private static IOCModule getOntologyModule() throws IOException {
 
 	@BeforeClass
 	public static void beforeClass() throws IOException {
+		boolean filterNonAsciiSynonyms = false; // allow japanese synonyms
 		IOCModule ontologyModule = getOntologyModule();
-		Injector injector = TermGenieGuice.createInjector(new XMLDynamicRulesModule("termgenie_rules_to.xml", false, true, true, null),
+		Injector injector = TermGenieGuice.createInjector(new XMLDynamicRulesModule("termgenie_rules_to.xml", false, true, filterNonAsciiSynonyms, null),
 				ontologyModule,
 				new ReasonerModule(null));
 
@@ -111,7 +112,14 @@ public void test_eq_simple_1() {
 		assertEquals(1, list.size());
 		TermGenerationOutput output = list.get(0);
 		assertNull(output.getError(), output.getError());
-		assertEquals("root cap permeability", output.getTerm().getTagValue(OboFormatTag.TAG_NAME));
+		Frame term = output.getTerm();
+		assertEquals("root cap permeability", term.getTagValue(OboFormatTag.TAG_NAME));
+		Collection<Clause> synonymClauses = term.getClauses(OboFormatTag.TAG_SYNONYM);
+		System.out.println(synonymClauses.size());
+		for (Clause clause : synonymClauses) {
+			System.out.println(clause);
+		}
+		assertFalse(synonymClauses.isEmpty());
 	}
 
 	private List<TermGenerationInput> createEQSimpleTask(String entity, String quality) {