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Posted to commits@ctakes.apache.org by al...@apache.org on 2017/12/04 17:39:43 UTC
svn commit: r1817108 - in /ctakes/trunk: ctakes-ytex-uima/pom.xml
ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/tools/SetupAuiFirstWord.java
ctakes-ytex/pom.xml pom.xml
Author: alexz
Date: Mon Dec 4 17:39:43 2017
New Revision: 1817108
URL: http://svn.apache.org/viewvc?rev=1817108&view=rev
Log:
CTAKES-488: fix ytex-uima integration-tests except SenseDisambiguatorAnnotatorTest"
Modified:
ctakes/trunk/ctakes-ytex-uima/pom.xml
ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/tools/SetupAuiFirstWord.java
ctakes/trunk/ctakes-ytex/pom.xml
ctakes/trunk/pom.xml
Modified: ctakes/trunk/ctakes-ytex-uima/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/pom.xml?rev=1817108&r1=1817107&r2=1817108&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/pom.xml (original)
+++ ctakes/trunk/ctakes-ytex-uima/pom.xml Mon Dec 4 17:39:43 2017
@@ -179,7 +179,13 @@
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
- <skip>true</skip>
+ <excludes>
+ <exclude>**/DBCollectionReaderTest*</exclude>
+ <exclude>**/DBConsumerTest*</exclude>
+ <exclude>**/DictionaryLookupAnnotatorTest*</exclude>
+ <exclude>**/SenseDisambiguatorAnnotatorTest*</exclude>
+ <exclude>**/SparseDataExporterTest*</exclude>
+ </excludes>
</configuration>
<executions>
<execution>
@@ -189,7 +195,6 @@
<goal>test</goal>
</goals>
<configuration>
- <skip>false</skip>
<forkMode>always</forkMode>
<systemPropertyVariables>
<log4j.configuration>file:${project.basedir}/src/test/resources/log4j.properties</log4j.configuration>
@@ -199,7 +204,7 @@
<forkCount>1</forkCount>
<reuseForks>false</reuseForks>
<forkedProcessTimeoutInSeconds>900</forkedProcessTimeoutInSeconds>
- <additionalClasspathElements>
+ <!-- additionalClasspathElements>
<additionalClasspathElement>${project.basedir}/../ctakes-assertion-res/src/main/resources</additionalClasspathElement>
<additionalClasspathElement>${project.basedir}/../ctakes-assertion-zoner-res/src/main/resources</additionalClasspathElement>
<additionalClasspathElement>${project.basedir}/../ctakes-chunker-res/src/main/resources</additionalClasspathElement>
@@ -217,11 +222,33 @@
<additionalClasspathElement>${project.basedir}/../ctakes-smoking-status-res/src/main/resources</additionalClasspathElement>
<additionalClasspathElement>${project.basedir}/../ctakes-temporal-res/src/main/resources</additionalClasspathElement>
<additionalClasspathElement>${project.basedir}/../ctakes-ytex-res/src/main/resources</additionalClasspathElement>
- </additionalClasspathElements>
+ </additionalClasspathElements -->
</configuration>
</execution>
</executions>
</plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-failsafe-plugin</artifactId>
+ <version>${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/main/java/org/apache/ctakes/ytex/tools/SetupAuiFirstWord.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/tools/SetupAuiFirstWord.java?rev=1817108&r1=1817107&r2=1817108&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/tools/SetupAuiFirstWord.java (original)
+++ ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/tools/SetupAuiFirstWord.java Mon Dec 4 17:39:43 2017
@@ -18,39 +18,26 @@
*/
package org.apache.ctakes.ytex.tools;
-import java.io.BufferedInputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Locale;
-import java.util.Set;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.ParserConfigurationException;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
+import gov.nih.nlm.nls.lvg.Api.LvgCmdApi;
+import org.apache.ctakes.core.nlp.tokenizer.Token;
+import org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB;
+import org.apache.ctakes.ytex.kernel.KernelContextHolder;
+import org.apache.ctakes.ytex.umls.dao.UMLSDao;
+import org.apache.ctakes.ytex.umls.model.UmlsAuiFirstWord;
+import org.apache.log4j.Logger;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.support.TransactionTemplate;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.NodeList;
import org.xml.sax.SAXException;
-import org.apache.ctakes.core.nlp.tokenizer.Token;
-import org.apache.ctakes.core.nlp.tokenizer.TokenizerPTB;
-import org.apache.ctakes.ytex.kernel.KernelContextHolder;
-import org.apache.ctakes.ytex.umls.dao.UMLSDao;
-import org.apache.ctakes.ytex.umls.model.UmlsAuiFirstWord;
-import gov.nih.nlm.nls.lvg.Api.LvgCmdApi;
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+import java.io.*;
+import java.net.URL;
+import java.util.*;
/**
* setup umls_aui_fword table
@@ -59,7 +46,9 @@ import gov.nih.nlm.nls.lvg.Api.LvgCmdApi
*
*/
public class SetupAuiFirstWord {
- private static final Log log = LogFactory.getLog(SetupAuiFirstWord.class);
+
+ static private final Logger LOGGER = Logger.getLogger(SetupAuiFirstWord.class);
+
// private static final Pattern nonWord = Pattern.compile("\\W");
private TokenizerPTB tokenizer;
private LvgCmdApi lvgCmd;
@@ -102,18 +91,16 @@ public class SetupAuiFirstWord {
try {
URL uri = this.getClass().getClassLoader()
.getResource("org/apache/ctakes/lvg/data/config/lvg.properties");
- if (log.isInfoEnabled())
- log.info("loading lvg.properties from:" + uri.getPath());
+ LOGGER.info("loading lvg.properties from:" + uri.getPath());
File f = new File(uri.getPath());
+ LOGGER.info(f.getAbsolutePath());
String configDir = f.getParentFile().getAbsolutePath();
String lvgDir = configDir.substring(0, configDir.length()
- "data/config".length());
System.setProperty("user.dir", lvgDir);
lvgCmd = new LvgCmdApi("-f:l:b", f.getAbsolutePath());
} catch (Exception e) {
- log.warn(
- "could not initialize lvg - will not create a stemmed dictionary.",
- e);
+ LOGGER.warn("could not initialize lvg - will not create a stemmed dictionary.", e);
}
}
@@ -135,13 +122,13 @@ public class SetupAuiFirstWord {
.getResourceAsStream(
"ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml");
if(isLvgAnno == null) {
- log.warn("classpath:ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml not available, attempting to load from file system");
+ LOGGER.warn("classpath:ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml not available, attempting to load from file system");
File f = new File("../ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml");
if(f.exists())
isLvgAnno = new BufferedInputStream(new FileInputStream(f));
}
if (isLvgAnno == null) {
- log.warn("ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml not available, using empty exclusion set");
+ LOGGER.warn("ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml not available, using empty exclusion set");
} else {
DocumentBuilderFactory dbFactory = DocumentBuilderFactory
.newInstance();
@@ -215,32 +202,29 @@ public class SetupAuiFirstWord {
try {
UmlsAuiFirstWord fw = this.tokenizeStr(aui, str);
if (fw == null)
- log.error("Error tokenizing aui=" + aui + ", str="
+ LOGGER.error("Error tokenizing aui=" + aui + ", str="
+ str);
else if (fw.getFword().length() > 70)
- log.debug("fword too long: aui=" + aui + ", str="
+ LOGGER.debug("fword too long: aui=" + aui + ", str="
+ fw.getFword());
else if (fw.getTokenizedStr().length() > 250)
- log.debug("string too long: aui=" + aui + ", str="
+ LOGGER.debug("string too long: aui=" + aui + ", str="
+ str);
else {
- if (log.isDebugEnabled())
- log.debug("aui=" + aui + ", fw=" + fw);
+ LOGGER.debug("aui=" + aui + ", fw=" + fw);
listFword.add(fw);
}
} catch (Exception e) {
- log.error("Error tokenizing aui=" + aui + ", str="
- + str, e);
+ LOGGER.error("Error tokenizing aui=" + aui + ", str=" + str, e);
}
} else {
- log.debug("Skipping aui because str to long: aui=" + aui
- + ", str=" + str);
+ LOGGER.debug("Skipping aui because str to long: aui=" + aui + ", str=" + str);
}
}
// batch insert
if (listFword.size() > 0) {
umlsDao.insertAuiFirstWord(listFword);
- log.info("inserted " + listFword.size() + " rows");
+ LOGGER.info("inserted " + listFword.size() + " rows");
}
} while (listAuiStr.size() > 0);
}
@@ -334,7 +318,7 @@ public class SetupAuiFirstWord {
if (out != null)
output = out.split("\\|");
else {
- log.warn("mutateToString returned null for: " + word);
+ LOGGER.warn("mutateToString returned null for: " + word);
}
if ((output != null) && (output.length >= 2)
Modified: ctakes/trunk/ctakes-ytex/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex/pom.xml?rev=1817108&r1=1817107&r2=1817108&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex/pom.xml (original)
+++ ctakes/trunk/ctakes-ytex/pom.xml Mon Dec 4 17:39:43 2017
@@ -331,7 +331,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-failsafe-plugin</artifactId>
- <version>2.20.1</version>
+ <version>${maven-failsafe-plugin.version}</version>
<configuration>
<includes>
<include>**/ConceptDaoTest</include>
Modified: ctakes/trunk/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/pom.xml?rev=1817108&r1=1817107&r2=1817108&view=diff
==============================================================================
--- ctakes/trunk/pom.xml (original)
+++ ctakes/trunk/pom.xml Mon Dec 4 17:39:43 2017
@@ -122,6 +122,7 @@
<mastif.version>1.4</mastif.version>
<maven-antrun-plugin.version>1.6</maven-antrun-plugin.version>
<maven-assembly-plugin.version>2.4</maven-assembly-plugin.version>
+ <maven-failsafe-plugin.version>2.20.1</maven-failsafe-plugin.version>
<maven-surefire-plugin.version>2.12.1</maven-surefire-plugin.version>
<maven-war-plugin.version>2.4</maven-war-plugin.version>
<mysql-connector.version>5.1.26</mysql-connector.version>