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From al...@apache.org
Subject svn commit: r1817141 - in /ctakes/trunk: ctakes-ytex-uima/ ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/ ctakes-ytex/src/main/java/org/apache/ctakes/util/ ctakes-ytex/src/test/java/org/apache/ctakes/ytex/
Date Tue, 05 Dec 2017 00:51:19 GMT
Author: alexz
Date: Tue Dec  5 00:51:19 2017
New Revision: 1817141

URL: http://svn.apache.org/viewvc?rev=1817141&view=rev
Log:
CTAKES-415

Added:
    ctakes/trunk/ctakes-ytex/src/main/java/org/apache/ctakes/util/
Modified:
    ctakes/trunk/ctakes-ytex-uima/pom.xml
    ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DateAnnotatorTest.java
    ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SenseDisambiguatorAnnotatorTest.java
    ctakes/trunk/ctakes-ytex/src/test/java/org/apache/ctakes/ytex/ConceptDaoTest.java

Modified: ctakes/trunk/ctakes-ytex-uima/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/pom.xml?rev=1817141&r1=1817140&r2=1817141&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/pom.xml (original)
+++ ctakes/trunk/ctakes-ytex-uima/pom.xml Tue Dec  5 00:51:19 2017
@@ -179,13 +179,7 @@
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-surefire-plugin</artifactId>
 				<configuration>
-					<excludes>
-						<exclude>**/DBCollectionReaderTest*</exclude>
-						<exclude>**/DBConsumerTest*</exclude>
-						<exclude>**/DictionaryLookupAnnotatorTest*</exclude>
-						<exclude>**/SenseDisambiguatorAnnotatorTest*</exclude>
-						<exclude>**/SparseDataExporterTest*</exclude>
-					</excludes>
+					<skip>true</skip>
 				</configuration>
 				<executions>
 					<execution>
@@ -195,6 +189,7 @@
 							<goal>test</goal>
 						</goals>
 						<configuration>
+							<skip>false</skip>
 							<forkMode>always</forkMode>
 							<systemPropertyVariables>
 								<log4j.configuration>file:${project.basedir}/src/test/resources/log4j.properties</log4j.configuration>
@@ -227,28 +222,6 @@
 					</execution>
 				</executions>
 			</plugin>
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-failsafe-plugin</artifactId>
-				<version>${maven-failsafe-plugin.version}</version>
-				<configuration>
-					<includes>
-						<include>**/DBCollectionReaderTest</include>
-						<include>**/DBConsumerTest</include>
-						<include>**/DictionaryLookupAnnotatorTest</include>
-						<!-- TODO: include>**/SenseDisambiguatorAnnotatorTest</include -->
-						<include>**/SparseDataExporterTest</include>
-					</includes>
-				</configuration>
-				<executions>
-					<execution>
-						<goals>
-							<goal>integration-test</goal>
-							<goal>verify</goal>
-						</goals>
-					</execution>
-				</executions>
-			</plugin>
 			<plugin>
 				<artifactId>maven-clean-plugin</artifactId>
 				<configuration>

Modified: ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DateAnnotatorTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DateAnnotatorTest.java?rev=1817141&r1=1817140&r2=1817141&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DateAnnotatorTest.java
(original)
+++ ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DateAnnotatorTest.java
Tue Dec  5 00:51:19 2017
@@ -18,7 +18,10 @@
  */
 package org.apache.ctakes.ytex.uima.annotators;
 
+import com.ibm.icu.text.SimpleDateFormat;
 import org.apache.ctakes.typesystem.type.textsem.DateAnnotation;
+import org.apache.ctakes.ytex.uima.types.Date;
+import org.apache.log4j.Logger;
 import org.apache.uima.UIMAException;
 import org.apache.uima.cas.text.AnnotationIndex;
 import org.apache.uima.jcas.JCas;
@@ -26,6 +29,12 @@ import org.apache.uima.jcas.tcas.Annotat
 import org.junit.Assert;
 import org.junit.Test;
 import org.apache.uima.fit.factory.JCasFactory;
+import sun.java2d.pipe.SpanShapeRenderer;
+
+import java.net.URL;
+import java.text.ParseException;
+
+import static org.junit.Assert.*;
 
 /**
  * TODO get rid of hard-coded path to Types.xml - load from classpath
@@ -34,27 +43,48 @@ import org.apache.uima.fit.factory.JCasF
  */
 public class DateAnnotatorTest {
 
+	private final static Logger LOGGER = Logger.getLogger(DateAnnotatorTest.class);
+
 	/**
 	 * Verify that date parsing with a manually created date works
 	 * @throws UIMAException
 	 */
 	@Test
 	public void testParseDate() throws UIMAException {
-	    JCas jCas = JCasFactory.createJCasFromPath("src/main/resources/org/apache/ctakes/ytex/types/TypeSystem.xml");
-	    String date = (new java.util.Date()).toString();
-	    jCas.setDocumentText(date);
+		URL urlTypeSystem = getClass().getClassLoader().getResource("org/apache/ctakes/ytex/types/TypeSystem.xml");
+	    JCas jCas = JCasFactory.createJCasFromPath(urlTypeSystem.getPath());
+
+	    java.util.Date  dtExpected = new java.util.Date();
+	    String sExpected = dtExpected.toString();
+
+	    LOGGER.info(String.format("date to be annotated: %s", sExpected));
+	    jCas.setDocumentText(sExpected);
+
+	    // create the annotation
 	    DateAnnotation ctakesDate = new DateAnnotation(jCas);
 	    ctakesDate.setBegin(0);
-	    ctakesDate.setEnd(date.length());
+	    ctakesDate.setEnd(sExpected.length());
 	    ctakesDate.addToIndexes();
 	    DateAnnotator dateAnnotator = new DateAnnotator();
-	    dateAnnotator.dateType = org.apache.ctakes.ytex.uima.types.Date.class.getName();
+	    dateAnnotator.dateType = Date.class.getName();
 	    dateAnnotator.process(jCas);
-	    AnnotationIndex<Annotation> ytexDates = jCas.getAnnotationIndex(org.apache.ctakes.ytex.uima.types.Date.type);
-	    Assert.assertTrue(ytexDates.iterator().hasNext());
-	    String dateParsed = ((org.apache.ctakes.ytex.uima.types.Date)ytexDates.iterator().next()).getDate();
-	    Assert.assertNotNull(dateParsed);
-	    System.out.println(dateParsed);
+	    AnnotationIndex<Annotation> ytexDates = jCas.getAnnotationIndex(Date.type);
+	    assertTrue(ytexDates.iterator().hasNext());
+
+	    // return the parsed
+	    String sParsed = ((Date)ytexDates.iterator().next()).getDate();
+		assertNotNull("Expected a parsed Date string", sParsed);
+		LOGGER.info(String.format("date from annotation: %s", sParsed));
+		java.util.Date dtParsed = null;
+	    try {
+		    dtParsed = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssZ").parse(sParsed);
+	    } catch (ParseException e) {
+	    	assertFalse("Expected a real java.util.Date object", true);
+	    }
+	    // java.util.Date.equals is not advised. Comparing Date.getTime ignores the miliseconds.
+		assertNotNull("Expected a not NULL java.util.Date object", dtParsed);
+	    assertTrue("Expected what we converted .toString to be parsed",
+			       (dtExpected.getTime() - dtParsed.getTime()) < 1000 /*1 second*/);
 	}
 
 }

Modified: ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SenseDisambiguatorAnnotatorTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SenseDisambiguatorAnnotatorTest.java?rev=1817141&r1=1817140&r2=1817141&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SenseDisambiguatorAnnotatorTest.java
(original)
+++ ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SenseDisambiguatorAnnotatorTest.java
Tue Dec  5 00:51:19 2017
@@ -18,39 +18,42 @@
  */
 package org.apache.ctakes.ytex.uima.annotators;
 
-import java.util.Collections;
-import java.util.List;
-import java.util.Properties;
-
-import javax.sql.DataSource;
-
+import com.google.common.collect.Lists;
 import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
 import org.apache.ctakes.typesystem.type.textsem.EntityMention;
+import org.apache.ctakes.util.JdbcOperationsHelper;
 import org.apache.ctakes.ytex.kernel.dao.ConceptDao;
 import org.apache.ctakes.ytex.kernel.model.ConceptGraph;
 import org.apache.ctakes.ytex.kernel.wsd.WordSenseDisambiguator;
 import org.apache.ctakes.ytex.uima.ApplicationContextHolder;
 import org.apache.uima.UIMAException;
 import org.apache.uima.cas.text.AnnotationIndex;
+import org.apache.uima.fit.factory.JCasFactory;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.cas.FSArray;
 import org.apache.uima.jcas.tcas.Annotation;
+import org.junit.After;
 import org.junit.Assert;
 import org.junit.Before;
 import org.junit.Test;
-import org.springframework.beans.factory.BeanFactory;
+import org.springframework.context.ApplicationContext;
 import org.springframework.context.ConfigurableApplicationContext;
 import org.springframework.context.access.ContextSingletonBeanFactoryLocator;
 import org.springframework.jdbc.core.JdbcTemplate;
-import org.apache.uima.fit.factory.JCasFactory;
 
-import com.google.common.collect.Lists;
+import javax.sql.DataSource;
+import java.net.URL;
+import java.util.Collections;
+import java.util.List;
+import java.util.Properties;
+
+public class SenseDisambiguatorAnnotatorTest extends JdbcOperationsHelper {
+	private ConceptDao conceptDao;
+	private ApplicationContext appCtx = null;
 
-public class SenseDisambiguatorAnnotatorTest {
-	ConceptDao conceptDao;
 	@Before
 	public void setUp() throws Exception {
-		BeanFactory appCtx = ContextSingletonBeanFactoryLocator
+		appCtx = (ApplicationContext) ContextSingletonBeanFactoryLocator
 				.getInstance("classpath*:org/apache/ctakes/ytex/kernelBeanRefContext.xml")
 				.useBeanFactory("kernelApplicationContext").getFactory();
 		conceptDao = appCtx.getBean(ConceptDao.class);
@@ -58,38 +61,23 @@ public class SenseDisambiguatorAnnotator
 		jdbcTemplate.setDataSource(appCtx.getBean(DataSource.class));
 		Properties ytexProperties = (Properties)appCtx.getBean("ytexProperties");
 		String dbtype = ytexProperties.getProperty("db.type");
-		if("hsql".equals(dbtype) || "mysql".equals(dbtype))
-			jdbcTemplate.execute("drop table if exists test_concepts");
-		if("mssql".equals(dbtype))
-			jdbcTemplate.execute("if exists(select * from sys.objects where object_id = object_id('test_concepts'))
drop table test_concepts");
-		if ("orcl".equals(dbtype)) {
-			// just try dropping the table, catch exception and hope all is well
-			try {
-				jdbcTemplate.execute("drop table test_concepts");
-			} catch (Exception ignore) {
 
-			}
-		}
-		jdbcTemplate
-				.execute("create table test_concepts(parent varchar(20), child varchar(20))");
-		jdbcTemplate
-				.execute("insert into test_concepts values ('root', 'animal')");
-		jdbcTemplate
-				.execute("insert into test_concepts values ('animal', 'vertebrate')");
-		jdbcTemplate
-				.execute("insert into test_concepts values ('vertebrate', 'cat')");
-		jdbcTemplate
-				.execute("insert into test_concepts values ('vertebrate', 'dog')");
-		jdbcTemplate
-				.execute("insert into test_concepts values ('root', 'bacteria')");
-		jdbcTemplate
-				.execute("insert into test_concepts values ('bacteria', 'e coli')");
-		conceptDao.createConceptGraph(null, "test",
-				"select child, parent from test_concepts", true,
+		dropTableIfExist(jdbcTemplate, dbtype, "test_concepts");
+
+		jdbcTemplate.execute("create table test_concepts(parent varchar(20), child varchar(20))");
+		jdbcTemplate.execute("insert into test_concepts values ('root', 'animal')");
+		jdbcTemplate.execute("insert into test_concepts values ('animal', 'vertebrate')");
+		jdbcTemplate.execute("insert into test_concepts values ('vertebrate', 'cat')");
+		jdbcTemplate.execute("insert into test_concepts values ('vertebrate', 'dog')");
+		jdbcTemplate.execute("insert into test_concepts values ('root', 'bacteria')");
+		jdbcTemplate.execute("insert into test_concepts values ('bacteria', 'e coli')");
+		conceptDao.createConceptGraph(null,
+				"test",
+				"select child, parent from test_concepts",
+				true,
 				Collections.EMPTY_SET);
 		ConceptGraph cg = conceptDao.getConceptGraph("test");
 		Assert.assertNotNull(cg);
-		((ConfigurableApplicationContext) appCtx).close();
 	}
 
 	/**
@@ -101,8 +89,8 @@ public class SenseDisambiguatorAnnotator
 		System.setProperty("ytex.conceptGraphName", "test");
 		System.setProperty("ytex.conceptPreload", "false");
 		System.setProperty("ytex.conceptSetName", "");
-		JCas jCas = JCasFactory
-				.createJCasFromPath("src/main/resources/org/apache/ctakes/ytex/types/TypeSystem.xml");
+		URL urlTypeSystem = getClass().getClassLoader().getResource("org/apache/ctakes/ytex/types/TypeSystem.xml");
+		JCas jCas = JCasFactory.createJCasFromPath(urlTypeSystem.getPath());
 		String text = "concept1 concept2 concept3";
 		jCas.setDocumentText(text);
 		EntityMention em1 = new EntityMention(jCas);
@@ -124,8 +112,7 @@ public class SenseDisambiguatorAnnotator
 		em3.addToIndexes();
 		
 		SenseDisambiguatorAnnotator sda = new SenseDisambiguatorAnnotator();
-		sda.wsd = ApplicationContextHolder.getApplicationContext().getBean(
-				WordSenseDisambiguator.class);
+		sda.wsd = ApplicationContextHolder.getApplicationContext().getBean(WordSenseDisambiguator.class);
 		sda.process(jCas);
 		AnnotationIndex<Annotation> annoIdx = jCas.getAnnotationIndex(EntityMention.type);
 		List<Annotation> annoList = Lists.newArrayList(annoIdx);
@@ -141,6 +128,14 @@ public class SenseDisambiguatorAnnotator
 		}
 	}
 
+	@After
+	public void tearDown() throws  Exception {
+		if (appCtx != null) {
+			((ConfigurableApplicationContext) appCtx).close();
+			appCtx = null;
+		}
+	}
+
 	private void setConcepts(JCas jCas, EntityMention em1, String[] concepts) {
 		FSArray em1oc = new FSArray(jCas, concepts.length);
 		for (int i = 0; i < concepts.length; i++) {

Modified: ctakes/trunk/ctakes-ytex/src/test/java/org/apache/ctakes/ytex/ConceptDaoTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex/src/test/java/org/apache/ctakes/ytex/ConceptDaoTest.java?rev=1817141&r1=1817140&r2=1817141&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex/src/test/java/org/apache/ctakes/ytex/ConceptDaoTest.java (original)
+++ ctakes/trunk/ctakes-ytex/src/test/java/org/apache/ctakes/ytex/ConceptDaoTest.java Tue
Dec  5 00:51:19 2017
@@ -25,6 +25,7 @@ import java.util.Properties;
 
 import javax.sql.DataSource;
 
+import org.apache.ctakes.util.JdbcOperationsHelper;
 import org.apache.ctakes.ytex.kernel.SimSvcContextHolder;
 import org.apache.ctakes.ytex.kernel.dao.ConceptDao;
 import org.apache.ctakes.ytex.kernel.metric.ConceptPairSimilarity;
@@ -39,13 +40,11 @@ import org.junit.Test;
 import org.springframework.context.ApplicationContext;
 import org.springframework.context.ConfigurableApplicationContext;
 import org.springframework.context.access.ContextSingletonBeanFactoryLocator;
-import org.springframework.dao.DataAccessException;
-import org.springframework.jdbc.core.JdbcOperations;
 import org.springframework.jdbc.core.JdbcTemplate;
 
 import static org.junit.Assert.*;
 
-public class ConceptDaoTest {
+public class ConceptDaoTest extends JdbcOperationsHelper {
 
 	static private final Logger LOGGER = Logger.getLogger(ConceptDaoTest.class);
 
@@ -53,40 +52,6 @@ public class ConceptDaoTest {
 
 	private ApplicationContext appCtx = null;
 
-	/**
-	 * Helper function to drop a 'table' from a DB, using SQL syntax
-	 *
-	 * @param jdbc
-	 * @param dbEngineType
-	 * @param sqlTableName
-	 */
-	private final void dropTableIfExist(JdbcOperations jdbc, final String dbEngineType, final
String sqlTableName) {
-		// TODO: consider refactor using JOOQ
-		String sqlStatement = "";
-		switch (dbEngineType.toLowerCase()) {
-			case "hsql":
-			case "mysql":
-				sqlStatement = String.format("DROP TABLE IF EXISTS %s", sqlTableName);
-				break;
-			case "mssql":
-				sqlStatement = String.format("IF EXISTS(SELECT * FROM sys.objects WHERE object_id = object_id('%s'))
DROP TABLE %s", sqlTableName);
-				break;
-			case "orcl":
-				sqlStatement = String.format("DROP TABLE %s", sqlTableName);
-				break;
-			default:
-				LOGGER.warn(String.format("unsupported DB engine type: %s", dbEngineType));
-				break;
-		}
-		if (!sqlStatement.isEmpty()) {
-			try {
-				jdbc.execute(sqlStatement);
-			} catch (DataAccessException e) {
-				LOGGER.warn("couldn't drop table test_concepts. Maybe it doesn't even exists", e);
-			}
-		}
-	}
-
 	@Before
 	public void setUp() throws Exception {
 		appCtx = (ApplicationContext) ContextSingletonBeanFactoryLocator



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