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From spmurph...@apache.org
Subject svn commit: r1418059 - in /incubator/ctakes/trunk/ctakes-pad-term-spotter: ./ desc/analysis_engine/ desc/collection_processing_engine/ launch/
Date Thu, 06 Dec 2012 20:34:21 GMT
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="&quot;-Djava.util.logging.config.file=${env_var:UIMA_HOME}/Logger.properties&quot;
 -Xms700M -Xmx700M"/>
-<stringAttribute key="org.eclipse.jdt.launching.WORKING_DIRECTORY" value="${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>



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