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Posted to commits@ctakes.apache.org by ch...@apache.org on 2014/11/25 17:42:34 UTC
svn commit: r1641650 - in /ctakes/branches/ctakes-3.2.1:
ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/
ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/
ctakes-dictionary-lookup-fast-re...
Author: chenpei
Date: Tue Nov 25 16:42:33 2014
New Revision: 1641650
URL: http://svn.apache.org/r1641650
Log:
CTAKES-335 - url typo in ctakessql.xml CTAKES-336 (FROM TRUNK)
Modified:
ctakes/branches/ctakes-3.2.1/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/MaxentParserWrapper.java
ctakes/branches/ctakes-3.2.1/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ConstituencyParser.java
ctakes/branches/ctakes-3.2.1/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/cTakesHsql.xml
ctakes/branches/ctakes-3.2.1/ctakes-dictionary-lookup-fast/desc/analysis_engine/SnomedLookupAnnotator.xml
ctakes/branches/ctakes-3.2.1/ctakes-dictionary-lookup-fast/desc/analysis_engine/SnomedOvLookupAnnotator.xml
ctakes/branches/ctakes-3.2.1/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml
ctakes/branches/ctakes-3.2.1/ctakes-side-effect/desc/analysis_engine/DictionaryLookupAnnotator_sideEffectUMLS.xml
Modified: ctakes/branches/ctakes-3.2.1/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/MaxentParserWrapper.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.2.1/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/MaxentParserWrapper.java?rev=1641650&r1=1641649&r2=1641650&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.2.1/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/MaxentParserWrapper.java (original)
+++ ctakes/branches/ctakes-3.2.1/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/MaxentParserWrapper.java Tue Nov 25 16:42:33 2014
@@ -18,48 +18,35 @@
*/
package org.apache.ctakes.constituency.parser;
-import java.io.File;
-import java.io.FileInputStream;
import java.io.IOException;
+import java.io.InputStream;
-import opennlp.tools.cmdline.parser.ParserTool;
import opennlp.tools.parser.AbstractBottomUpParser;
import opennlp.tools.parser.Parse;
import opennlp.tools.parser.ParserModel;
import opennlp.tools.parser.chunking.Parser;
-import opennlp.tools.util.Span;
import org.apache.ctakes.constituency.parser.util.TreeUtils;
import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
-import org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode;
import org.apache.ctakes.typesystem.type.syntax.TopTreebankNode;
-import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
import org.apache.log4j.Logger;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.cas.FSIterator;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.cas.FSArray;
-import org.apache.uima.jcas.cas.StringArray;
public class MaxentParserWrapper implements ParserWrapper {
Parser parser = null;
private String parseStr = "";
Logger logger = Logger.getLogger(this.getClass().getName());
- private boolean usePos;
-
- public MaxentParserWrapper(String dataDir) {
- this(dataDir, false);
- }
-
- public MaxentParserWrapper(String dataDir, boolean usePos){
+
+
+ public MaxentParserWrapper(InputStream is){
try {
- File d = new File(dataDir);
- this.usePos = usePos;
- if (!d.isDirectory()) {
- FileInputStream fis = new FileInputStream(d);
- ParserModel model = new ParserModel(fis);
+ if (is!=null) {
+ ParserModel model = new ParserModel(is);
parser = new Parser(model, AbstractBottomUpParser.defaultBeamSize, AbstractBottomUpParser.defaultAdvancePercentage);
}
} catch (IOException e) {
Modified: ctakes/branches/ctakes-3.2.1/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ConstituencyParser.java
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.2.1/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ConstituencyParser.java?rev=1641650&r1=1641649&r2=1641650&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.2.1/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ConstituencyParser.java (original)
+++ ctakes/branches/ctakes-3.2.1/ctakes-constituency-parser/src/main/java/org/apache/ctakes/constituency/parser/ae/ConstituencyParser.java Tue Nov 25 16:42:33 2014
@@ -25,16 +25,17 @@ import org.apache.ctakes.constituency.pa
import org.apache.ctakes.core.resource.FileLocator;
import org.apache.log4j.Logger;
import org.apache.uima.UimaContext;
+import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
-import org.apache.uima.jcas.JCas;
-import org.apache.uima.resource.ResourceInitializationException;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
import org.apache.uima.fit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.resource.ResourceInitializationException;
public class ConstituencyParser extends JCasAnnotator_ImplBase {
public static final String PARAM_MODEL_FILENAME = "MODEL_FILENAME";
- public static final String PARAM_USE_POS = "USE_POS";
@ConfigurationParameter(
name = PARAM_MODEL_FILENAME,
@@ -43,12 +44,6 @@ public class ConstituencyParser extends
defaultValue = "org/apache/ctakes/constituency/parser/models/sharpacq-3.1.bin"
) private String modelFilename;
- @ConfigurationParameter(
- name = PARAM_USE_POS,
- description = "Whether to use the POS tags generated by cTAKES pos tagger or generate our own",
- mandatory = false,
- defaultValue = "false"
- ) private boolean usePos;
private ParserWrapper parser = null;
private Logger logger = Logger.getLogger(this.getClass());
@@ -59,7 +54,7 @@ public class ConstituencyParser extends
super.initialize(aContext);
try {
logger.info("Initializing parser...");
- parser = new MaxentParserWrapper(FileLocator.locateFile(modelFilename).getAbsolutePath(), usePos);
+ parser = new MaxentParserWrapper(FileLocator.getAsStream(modelFilename));
} catch (FileNotFoundException e) {
e.printStackTrace();
logger.error("Error reading parser model file/directory: " + e.getMessage());
@@ -72,4 +67,17 @@ public class ConstituencyParser extends
public void process(JCas jcas) throws AnalysisEngineProcessException {
parser.createAnnotations(jcas);
}
+
+ public static AnalysisEngineDescription createAnnotatorDescription(
+ String modelPath) throws ResourceInitializationException {
+ return AnalysisEngineFactory.createEngineDescription(
+ ConstituencyParser.class,
+ ConstituencyParser.PARAM_MODEL_FILENAME,
+ modelPath);
+ }
+ public static AnalysisEngineDescription createAnnotatorDescription()
+ throws ResourceInitializationException {
+ return AnalysisEngineFactory.createEngineDescription(
+ ConstituencyParser.class);
+ }
}
Modified: ctakes/branches/ctakes-3.2.1/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/cTakesHsql.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.2.1/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/cTakesHsql.xml?rev=1641650&r1=1641649&r2=1641650&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.2.1/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/cTakesHsql.xml (original)
+++ ctakes/branches/ctakes-3.2.1/ctakes-dictionary-lookup-fast-res/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/cTakesHsql.xml Tue Nov 25 16:42:33 2014
@@ -38,7 +38,7 @@
<property key="jdbcUser" value="sa"/>
<property key="jdbcPass" value=""/>
<property key="rareWordTable" value="cui_terms"/>
- <property key="umlsUrl" value="https://uts-ws.nlm.nih.gov/restful/isValidctakes.umlsuser"/>
+ <property key="umlsUrl" value="https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser"/>
<property key="umlsVendor" value="NLM-6515182895"/>
<property key="umlsUser" value="CHANGEME"/>
<property key="umlsPass" value="CHANGEME"/>
@@ -65,7 +65,7 @@
<!--<property key="rxNormTable" value="rxnorm"/>-->
<!--<property key="icd9Table" value="icd9cm"/>-->
<!--<property key="icd10Table" value="icd10pcs"/>-->
- <property key="umlsUrl" value="https://uts-ws.nlm.nih.gov/restful/isValidctakes.umlsuser"/>
+ <property key="umlsUrl" value="https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser"/>
<property key="umlsVendor" value="NLM-6515182895"/>
<property key="umlsUser" value="CHANGEME"/>
<property key="umlsPass" value="CHANGEME"/>
Modified: ctakes/branches/ctakes-3.2.1/ctakes-dictionary-lookup-fast/desc/analysis_engine/SnomedLookupAnnotator.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.2.1/ctakes-dictionary-lookup-fast/desc/analysis_engine/SnomedLookupAnnotator.xml?rev=1641650&r1=1641649&r2=1641650&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.2.1/ctakes-dictionary-lookup-fast/desc/analysis_engine/SnomedLookupAnnotator.xml (original)
+++ ctakes/branches/ctakes-3.2.1/ctakes-dictionary-lookup-fast/desc/analysis_engine/SnomedLookupAnnotator.xml Tue Nov 25 16:42:33 2014
@@ -113,7 +113,7 @@
<!--<nameValuePair>-->
<!--<name>ctakes.umlsaddr</name>-->
<!--<value>-->
- <!--<string>https://uts-ws.nlm.nih.gov/restful/isValidctakes.umlsuser</string>-->
+ <!--<string>https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser</string>-->
<!--</value>-->
<!--</nameValuePair>-->
<!--<nameValuePair>-->
Modified: ctakes/branches/ctakes-3.2.1/ctakes-dictionary-lookup-fast/desc/analysis_engine/SnomedOvLookupAnnotator.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.2.1/ctakes-dictionary-lookup-fast/desc/analysis_engine/SnomedOvLookupAnnotator.xml?rev=1641650&r1=1641649&r2=1641650&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.2.1/ctakes-dictionary-lookup-fast/desc/analysis_engine/SnomedOvLookupAnnotator.xml (original)
+++ ctakes/branches/ctakes-3.2.1/ctakes-dictionary-lookup-fast/desc/analysis_engine/SnomedOvLookupAnnotator.xml Tue Nov 25 16:42:33 2014
@@ -139,7 +139,7 @@
<nameValuePair>
<name>ctakes.umlsaddr</name>
<value>
- <string>https://uts-ws.nlm.nih.gov/restful/isValidctakes.umlsuser</string>
+ <string>https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser</string>
</value>
</nameValuePair>
<nameValuePair>
Modified: ctakes/branches/ctakes-3.2.1/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.2.1/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml?rev=1641650&r1=1641649&r2=1641650&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.2.1/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml (original)
+++ ctakes/branches/ctakes-3.2.1/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml Tue Nov 25 16:42:33 2014
@@ -80,7 +80,7 @@
<nameValuePair>
<name>ctakes.umlsaddr</name>
<value>
- <string>https://uts-ws.nlm.nih.gov/restful/isValidctakes.umlsuser</string>
+ <string>https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser</string>
</value>
</nameValuePair>
<nameValuePair>
Modified: ctakes/branches/ctakes-3.2.1/ctakes-side-effect/desc/analysis_engine/DictionaryLookupAnnotator_sideEffectUMLS.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ctakes-3.2.1/ctakes-side-effect/desc/analysis_engine/DictionaryLookupAnnotator_sideEffectUMLS.xml?rev=1641650&r1=1641649&r2=1641650&view=diff
==============================================================================
--- ctakes/branches/ctakes-3.2.1/ctakes-side-effect/desc/analysis_engine/DictionaryLookupAnnotator_sideEffectUMLS.xml (original)
+++ ctakes/branches/ctakes-3.2.1/ctakes-side-effect/desc/analysis_engine/DictionaryLookupAnnotator_sideEffectUMLS.xml Tue Nov 25 16:42:33 2014
@@ -80,7 +80,7 @@
<nameValuePair>
<name>ctakes.umlsaddr</name>
<value>
- <string>https://uts-ws.nlm.nih.gov/restful/isValidctakes.umlsuser</string>
+ <string>https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser</string>
</value>
</nameValuePair>
<nameValuePair>