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Posted to commits@ctakes.apache.org by sp...@apache.org on 2012/12/06 21:34:21 UTC
svn commit: r1418059 - in /incubator/ctakes/trunk/ctakes-pad-term-spotter:
./ desc/analysis_engine/ desc/collection_processing_engine/ launch/
Author: spmurphy50
Date: Thu Dec 6 20:34:20 2012
New Revision: 1418059
URL: http://svn.apache.org/viewvc?rev=1418059&view=rev
Log:
Fix CTAKES-101
Modified:
incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_DictionaryLookupCSVAnnotator.xml
incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_TermSpotterAnnotatorTAE.xml
incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/collection_processing_engine/Radiology_sample.xml
incubator/ctakes/trunk/ctakes-pad-term-spotter/launch/UIMA CAS Visual Debugger (PAD Term Spotter).launch
incubator/ctakes/trunk/ctakes-pad-term-spotter/pom.xml
Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_DictionaryLookupCSVAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_DictionaryLookupCSVAnnotator.xml?rev=1418059&r1=1418058&r2=1418059&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_DictionaryLookupCSVAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_DictionaryLookupCSVAnnotator.xml Thu Dec 6 20:34:20 2012
@@ -32,7 +32,7 @@
<configurationParameterSettings/>
<typeSystemDescription>
<imports>
-<import location="../type_system/PADSiteAndTerm.xml"/>
+<import name="org.apache.ctakes.padtermspotter.types.Typesystem"/>
</imports>
</typeSystemDescription>
<typePriorities/>
Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_TermSpotterAnnotatorTAE.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_TermSpotterAnnotatorTAE.xml?rev=1418059&r1=1418058&r2=1418059&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_TermSpotterAnnotatorTAE.xml (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/analysis_engine/Radiology_TermSpotterAnnotatorTAE.xml Thu Dec 6 20:34:20 2012
@@ -1,118 +1,98 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!--
-
- Licensed to the Apache Software Foundation (ASF) under one
- or more contributor license agreements. See the NOTICE file
- distributed with this work for additional information
- regarding copyright ownership. The ASF licenses this file
- to you under the Apache License, Version 2.0 (the
- "License"); you may not use this file except in compliance
- with the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing,
- software distributed under the License is distributed on an
- "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- KIND, either express or implied. See the License for the
- specific language governing permissions and limitations
- under the License.
-
--->
<taeDescription xmlns="http://uima.apache.org/resourceSpecifier">
-<frameworkImplementation>org.apache.uima.java</frameworkImplementation>
-<primitive>false</primitive>
-<delegateAnalysisEngineSpecifiers>
-<delegateAnalysisEngine key="PAD_Hit">
-<import location="PAD_Hit.xml"/>
-</delegateAnalysisEngine>
-<delegateAnalysisEngine key="DxStatusAnnotator">
-<import location="DxStatusAnnotator.xml"/>
-</delegateAnalysisEngine>
-<delegateAnalysisEngine key="SimpleSegmentAnnotator">
-<import location="../../../ctakes-core/desc/analysis_engine/SimpleSegmentAnnotator.xml"/>
-</delegateAnalysisEngine>
-<delegateAnalysisEngine key="SubSectionBoundaryAnnotator">
-<import location="SubSectionBoundaryAnnotator.xml"/>
-</delegateAnalysisEngine>
-<delegateAnalysisEngine key="Chunker">
-<import location="../../../ctakes-chunker/desc/Chunker.xml"/>
-</delegateAnalysisEngine>
-<delegateAnalysisEngine key="ContextDependentTokenizerAnnotator">
-<import location="../../../ctakes-context-tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
-</delegateAnalysisEngine>
-<delegateAnalysisEngine key="NegationAnnotator">
-<import location="../../../ctakes-ne-contexts/desc/NegationAnnotator.xml"/>
-</delegateAnalysisEngine>
-<delegateAnalysisEngine key="SentenceDetectorAnnotator">
-<import location="../../../ctakes-core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
-</delegateAnalysisEngine>
-<delegateAnalysisEngine key="TokenizerAnnotator">
-<import location="../../../ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml"/>
-</delegateAnalysisEngine>
-<delegateAnalysisEngine key="NegationDxAnnotator">
-<import location="NegationDxAnnotator.xml"/>
-</delegateAnalysisEngine>
-<delegateAnalysisEngine key="POSTagger">
-<import location="../../../ctakes-pos-tagger/desc/POSTagger.xml"/>
-</delegateAnalysisEngine>
-<delegateAnalysisEngine key="Radiology_DictionaryLookupCSVAnnotator">
-<import location="Radiology_DictionaryLookupCSVAnnotator.xml"/>
-</delegateAnalysisEngine>
-</delegateAnalysisEngineSpecifiers>
-<analysisEngineMetaData>
-<name>PAD_term_spotter</name>
-<description>Term spotter for Peripheral Artery Disease (PAD) </description>
-<version>1.0</version>
-<vendor>Mayo Clinic</vendor>
-<configurationParameters searchStrategy="language_fallback">
-<configurationParameter>
-<name>ChunkCreatorClass</name>
-<type>String</type>
-<multiValued>false</multiValued>
-<mandatory>true</mandatory>
-<overrides>
-<parameter>Chunker/ChunkCreatorClass</parameter>
-</overrides>
-</configurationParameter>
-</configurationParameters>
-<configurationParameterSettings>
-<nameValuePair>
-<name>ChunkCreatorClass</name>
-<value>
-<string>edu.mayo.bmi.uima.chunker.PhraseTypeChunkCreator</string>
-</value>
-</nameValuePair>
-</configurationParameterSettings>
-<flowConstraints>
-<fixedFlow>
-<node>SimpleSegmentAnnotator</node>
-<node>TokenizerAnnotator</node>
-<node>SentenceDetectorAnnotator</node>
-<node>SubSectionBoundaryAnnotator</node>
-<node>ContextDependentTokenizerAnnotator</node>
-<node>POSTagger</node>
-<node>Chunker</node>
-<node>Radiology_DictionaryLookupCSVAnnotator</node>
-<node>NegationAnnotator</node>
-<node>PAD_Hit</node>
-<node>DxStatusAnnotator</node>
-<node>NegationDxAnnotator</node>
-</fixedFlow>
-</flowConstraints>
-<fsIndexCollection/>
-<capabilities>
-<capability>
-<inputs/>
-<outputs/>
-<languagesSupported/>
-</capability>
-</capabilities>
-<operationalProperties>
-<modifiesCas>true</modifiesCas>
-<multipleDeploymentAllowed>true</multipleDeploymentAllowed>
-<outputsNewCASes>false</outputsNewCASes>
-</operationalProperties>
-</analysisEngineMetaData>
-<resourceManagerConfiguration/>
+ <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+ <primitive>false</primitive>
+ <delegateAnalysisEngineSpecifiers>
+ <delegateAnalysisEngine key="SubSectionBoundaryAnnotator">
+ <import location="SubSectionBoundaryAnnotator.xml"/>
+ </delegateAnalysisEngine>
+ <delegateAnalysisEngine key="Chunker">
+ <import location="../../../ctakes-chunker/desc/Chunker.xml"/>
+ </delegateAnalysisEngine>
+ <delegateAnalysisEngine key="TokenizerAnnotator">
+ <import location="../../../ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml"/>
+ </delegateAnalysisEngine>
+ <delegateAnalysisEngine key="ContextDependentTokenizerAnnotator">
+ <import location="../../../ctakes-context-tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
+ </delegateAnalysisEngine>
+ <delegateAnalysisEngine key="NegationDxAnnotator">
+ <import location="NegationDxAnnotator.xml"/>
+ </delegateAnalysisEngine>
+ <delegateAnalysisEngine key="NegationAnnotator">
+ <import location="../../../ctakes-ne-contexts/desc/NegationAnnotator.xml"/>
+ </delegateAnalysisEngine>
+ <delegateAnalysisEngine key="SentenceDetectorAnnotator">
+ <import location="../../../ctakes-core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
+ </delegateAnalysisEngine>
+ <delegateAnalysisEngine key="Radiology_DictionaryLookupCSVAnnotator">
+ <import location="Radiology_DictionaryLookupCSVAnnotator.xml"/>
+ </delegateAnalysisEngine>
+ <delegateAnalysisEngine key="PAD_Hit">
+ <import location="PAD_Hit.xml"/>
+ </delegateAnalysisEngine>
+ <delegateAnalysisEngine key="DxStatusAnnotator">
+ <import location="DxStatusAnnotator.xml"/>
+ </delegateAnalysisEngine>
+ <delegateAnalysisEngine key="SimpleSegmentAnnotator">
+ <import location="../../../ctakes-core/desc/analysis_engine/SimpleSegmentAnnotator.xml"/>
+ </delegateAnalysisEngine>
+ <delegateAnalysisEngine key="POSTagger">
+ <import location="../../../ctakes-pos-tagger/desc/POSTagger.xml"/>
+ </delegateAnalysisEngine>
+ </delegateAnalysisEngineSpecifiers>
+ <analysisEngineMetaData>
+ <name>PAD_term_spotter</name>
+ <description>Term spotter for Peripheral Artery Disease (PAD)</description>
+ <version>1.0</version>
+ <vendor>Mayo Clinic</vendor>
+ <configurationParameters searchStrategy="language_fallback">
+ <configurationParameter>
+ <name>ChunkCreatorClass</name>
+ <type>String</type>
+ <multiValued>false</multiValued>
+ <mandatory>true</mandatory>
+ <overrides>
+ <parameter>Chunker/ChunkCreatorClass</parameter>
+ </overrides>
+ </configurationParameter>
+ </configurationParameters>
+ <configurationParameterSettings>
+ <nameValuePair>
+ <name>ChunkCreatorClass</name>
+ <value>
+ <string>org.apache.ctakes.chunker.ae.PhraseTypeChunkCreator</string>
+ </value>
+ </nameValuePair>
+ </configurationParameterSettings>
+ <flowConstraints>
+ <fixedFlow>
+ <node>SimpleSegmentAnnotator</node>
+ <node>SentenceDetectorAnnotator</node>
+ <node>TokenizerAnnotator</node>
+ <node>SubSectionBoundaryAnnotator</node>
+ <node>ContextDependentTokenizerAnnotator</node>
+ <node>POSTagger</node>
+ <node>Chunker</node>
+ <node>Radiology_DictionaryLookupCSVAnnotator</node>
+ <node>NegationAnnotator</node>
+ <node>PAD_Hit</node>
+ <node>DxStatusAnnotator</node>
+ <node>NegationDxAnnotator</node>
+ </fixedFlow>
+ </flowConstraints>
+ <fsIndexCollection/>
+ <capabilities>
+ <capability>
+ <inputs/>
+ <outputs/>
+ <languagesSupported/>
+ </capability>
+ </capabilities>
+ <operationalProperties>
+ <modifiesCas>true</modifiesCas>
+ <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+ <outputsNewCASes>false</outputsNewCASes>
+ </operationalProperties>
+ </analysisEngineMetaData>
+ <resourceManagerConfiguration/>
</taeDescription>
Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/collection_processing_engine/Radiology_sample.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/collection_processing_engine/Radiology_sample.xml?rev=1418059&r1=1418058&r2=1418059&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/collection_processing_engine/Radiology_sample.xml (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/desc/collection_processing_engine/Radiology_sample.xml Thu Dec 6 20:34:20 2012
@@ -1,108 +1,88 @@
<?xml version="1.0" encoding="UTF-8"?>
-<!--
-
- Licensed to the Apache Software Foundation (ASF) under one
- or more contributor license agreements. See the NOTICE file
- distributed with this work for additional information
- regarding copyright ownership. The ASF licenses this file
- to you under the Apache License, Version 2.0 (the
- "License"); you may not use this file except in compliance
- with the License. You may obtain a copy of the License at
-
- http://www.apache.org/licenses/LICENSE-2.0
-
- Unless required by applicable law or agreed to in writing,
- software distributed under the License is distributed on an
- "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- KIND, either express or implied. See the License for the
- specific language governing permissions and limitations
- under the License.
-
--->
<cpeDescription xmlns="http://uima.apache.org/resourceSpecifier">
-<collectionReader>
-<collectionIterator>
-<descriptor>
-<import location="../collection_reader/RadiologyRecordsCollectionReader.xml"/>
-</descriptor>
-<configurationParameterSettings>
-<nameValuePair>
-<name>InputFileName</name>
-<value>
-<string>{inst-root-dir}/PAD term spotter/data/SampleInputRadiologyNotes.txt</string>
-</value>
-</nameValuePair>
-<nameValuePair>
-<name>CommentString</name>
-<value>
-<string>CLINIC</string>
-</value>
-</nameValuePair>
-<nameValuePair>
-<name>IdDelimeter</name>
-<value>
-<string>`</string>
-</value>
-</nameValuePair>
-<nameValuePair>
-<name>ColumnCount</name>
-<value>
-<integer>15</integer>
-</value>
-</nameValuePair>
-<nameValuePair>
-<name>FilterExamTypes</name>
-<value>
-<string>{inst-root-dir}/PAD term spotter/resources/lookup/radiology/examsForPAD.csv</string>
-</value>
-</nameValuePair>
-<nameValuePair>
-<name>FilterExamColumnNumber</name>
-<value>
-<integer>11</integer>
-</value>
-</nameValuePair>
-</configurationParameterSettings>
-</collectionIterator>
-</collectionReader>
-<casProcessors casPoolSize="3" processingUnitThreadCount="1">
-<casProcessor deployment="integrated" name="PAD_term_spotter">
-<descriptor>
-<import location="../analysis_engine/Radiology_TermSpotterAnnotatorTAE.xml"/>
-</descriptor>
-<deploymentParameters/>
-<errorHandling>
-<errorRateThreshold action="terminate" value="0/1000"/>
-<maxConsecutiveRestarts action="terminate" value="30"/>
-<timeout max="100000" default="-1"/>
-</errorHandling>
-<checkpoint batch="10000" time="1000ms"/>
-</casProcessor>
-<casProcessor deployment="integrated" name="PADOffSetRecord">
-<descriptor>
-<import location="../cas_consumer/PADOffsetsRecordConsumer.xml"/>
-</descriptor>
-<deploymentParameters/>
-<errorHandling>
-<errorRateThreshold action="terminate" value="0/1000"/>
-<maxConsecutiveRestarts action="terminate" value="30"/>
-<timeout max="100000" default="-1"/>
-</errorHandling>
-<checkpoint batch="10000" time="1000ms"/>
-<configurationParameterSettings>
-<nameValuePair>
-<name>outputFileName</name>
-<value>
-<string>{inst-root-dir}/PAD term spotter/output/Sample_PAD_record_level.txt</string>
-</value>
-</nameValuePair>
-</configurationParameterSettings>
-</casProcessor>
-</casProcessors>
-<cpeConfig>
-<numToProcess>-1</numToProcess>
-<deployAs>immediate</deployAs>
-<checkpoint batch="0" time="300000ms"/>
-<timerImpl></timerImpl>
-</cpeConfig>
+ <collectionReader>
+ <collectionIterator>
+ <descriptor>
+ <import location="../collection_reader/RadiologyRecordsCollectionReader.xml"/>
+ </descriptor>
+ <configurationParameterSettings>
+ <nameValuePair>
+ <name>InputFileName</name>
+ <value>
+ <string>data/SampleInputRadiologyNotes.txt</string>
+ </value>
+ </nameValuePair>
+ <nameValuePair>
+ <name>CommentString</name>
+ <value>
+ <string>CLINIC</string>
+ </value>
+ </nameValuePair>
+ <nameValuePair>
+ <name>IdDelimeter</name>
+ <value>
+ <string>`</string>
+ </value>
+ </nameValuePair>
+ <nameValuePair>
+ <name>ColumnCount</name>
+ <value>
+ <integer>15</integer>
+ </value>
+ </nameValuePair>
+ <nameValuePair>
+ <name>FilterExamTypes</name>
+ <value>
+ <string>src/main/resources/org/apache/ctakes/padtermspotter/lookup/radiology/examsForPAD.csv</string>
+ </value>
+ </nameValuePair>
+ <nameValuePair>
+ <name>FilterExamColumnNumber</name>
+ <value>
+ <integer>11</integer>
+ </value>
+ </nameValuePair>
+ </configurationParameterSettings>
+ </collectionIterator>
+ </collectionReader>
+ <casProcessors casPoolSize="3" processingUnitThreadCount="1">
+ <casProcessor deployment="integrated" name="PAD_term_spotter">
+ <descriptor>
+ <import location="../analysis_engine/Radiology_TermSpotterAnnotatorTAE.xml"/>
+ </descriptor>
+ <deploymentParameters/>
+ <errorHandling>
+ <errorRateThreshold action="terminate" value="0/1000"/>
+ <maxConsecutiveRestarts action="terminate" value="30"/>
+ <timeout max="100000" default="-1"/>
+ </errorHandling>
+ <checkpoint batch="10000" time="1000ms"/>
+ </casProcessor>
+ <casProcessor deployment="integrated" name="PADOffSetRecord">
+ <descriptor>
+ <import location="../cas_consumer/PADOffsetsRecordConsumer.xml"/>
+ </descriptor>
+ <deploymentParameters/>
+ <errorHandling>
+ <errorRateThreshold action="terminate" value="0/1000"/>
+ <maxConsecutiveRestarts action="terminate" value="30"/>
+ <timeout max="100000" default="-1"/>
+ </errorHandling>
+ <checkpoint batch="10000" time="1000ms"/>
+ <configurationParameterSettings>
+ <nameValuePair>
+ <name>outputFileName</name>
+ <value>
+ <string>output\PAD_output.txt</string>
+ </value>
+ </nameValuePair>
+ </configurationParameterSettings>
+ </casProcessor>
+ </casProcessors>
+ <cpeConfig>
+ <numToProcess>-1</numToProcess>
+ <deployAs>immediate</deployAs>
+ <checkpoint batch="0" time="300000ms"/>
+ <timerImpl/>
+ </cpeConfig>
</cpeDescription>
Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/launch/UIMA CAS Visual Debugger (PAD Term Spotter).launch
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/launch/UIMA%20CAS%20Visual%20Debugger%20%28PAD%20Term%20Spotter%29.launch?rev=1418059&r1=1418058&r2=1418059&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/launch/UIMA CAS Visual Debugger (PAD Term Spotter).launch (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/launch/UIMA CAS Visual Debugger (PAD Term Spotter).launch Thu Dec 6 20:34:20 2012
@@ -10,9 +10,9 @@
<stringAttribute key="org.eclipse.debug.ui.target_debug_perspective" value="perspective_default"/>
<stringAttribute key="org.eclipse.debug.ui.target_run_perspective" value="perspective_default"/>
<stringAttribute key="org.eclipse.jdt.launching.CLASSPATH_PROVIDER" value="org.eclipse.m2e.launchconfig.classpathProvider"/>
-<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="com.ibm.uima.annot_view.Gladis"/>
+<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.apache.uima.tools.cvd.CVD"/>
<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="ctakes-pad-term-spotter"/>
<stringAttribute key="org.eclipse.jdt.launching.SOURCE_PATH_PROVIDER" value="org.eclipse.m2e.launchconfig.sourcepathProvider"/>
<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value=""-Djava.util.logging.config.file=${env_var:UIMA_HOME}/Logger.properties" -Xms700M -Xmx700M"/>
-<stringAttribute key="org.eclipse.jdt.launching.WORKING_DIRECTORY" value="${workspace_loc:core}"/>
+<stringAttribute key="org.eclipse.jdt.launching.WORKING_DIRECTORY" value="${workspace_loc:ctakes-core}"/>
</launchConfiguration>
Modified: incubator/ctakes/trunk/ctakes-pad-term-spotter/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-pad-term-spotter/pom.xml?rev=1418059&r1=1418058&r2=1418059&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-pad-term-spotter/pom.xml (original)
+++ incubator/ctakes/trunk/ctakes-pad-term-spotter/pom.xml Thu Dec 6 20:34:20 2012
@@ -58,6 +58,14 @@
<groupId>junit</groupId>
<artifactId>junit</artifactId>
</dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-chunker</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-context-tokenizer</artifactId>
+ </dependency>
</dependencies>
<build>