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Posted to commits@ctakes.apache.org by se...@apache.org on 2013/01/09 19:57:20 UTC
svn commit: r1431008 - in /incubator/ctakes/trunk:
ctakes-clinical-pipeline/desc/collection_processing_engine/
ctakes-constituency-parser/desc/collection_processing_engine/
ctakes-smoking-status/desc/analysis_engine/
Author: seanfinan
Date: Wed Jan 9 18:57:19 2013
New Revision: 1431008
URL: http://svn.apache.org/viewvc?rev=1431008&view=rev
Log:
CTAKES-118 : updating urls to fit new directory structure
Modified:
incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/test_cda.xml
incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/test_plaintext.xml
incubator/ctakes/trunk/ctakes-constituency-parser/desc/collection_processing_engine/ParsingCPE.xml
incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml
incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ProductionPostSentenceAggregate_step2_libsvm.xml
Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/test_cda.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/test_cda.xml?rev=1431008&r1=1431007&r2=1431008&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/test_cda.xml (original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/test_cda.xml Wed Jan 9 18:57:19 2013
@@ -23,7 +23,7 @@
<collectionReader>
<collectionIterator>
<descriptor>
- <import location="../../coredesc/collection_reader/FilesInDirectoryCollectionReader.xml"/>
+ <import location="../../../ctakes-core/desc/collection_reader/FilesInDirectoryCollectionReader.xml"/>
</descriptor>
<configurationParameterSettings>
<nameValuePair>
@@ -50,7 +50,7 @@
</casProcessor>
<casProcessor deployment="integrated" name="Write CAS to XML file">
<descriptor>
- <import location="../../coredesc/cas_consumer/FileWriterCasConsumer.xml"/>
+ <import location="../../../ctakes-core/desc/cas_consumer/FileWriterCasConsumer.xml"/>
</descriptor>
<deploymentParameters/>
<errorHandling>
Modified: incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/test_plaintext.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/test_plaintext.xml?rev=1431008&r1=1431007&r2=1431008&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/test_plaintext.xml (original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/test_plaintext.xml Wed Jan 9 18:57:19 2013
@@ -23,7 +23,7 @@
<collectionReader>
<collectionIterator>
<descriptor>
- <import location="../../coredesc/collection_reader/FilesInDirectoryCollectionReader.xml"/>
+ <import location="../../../ctakes-core/desc/collection_reader/FilesInDirectoryCollectionReader.xml"/>
</descriptor>
<configurationParameterSettings>
<nameValuePair>
@@ -50,7 +50,7 @@
</casProcessor>
<casProcessor deployment="integrated" name="Write CAS to XML file">
<descriptor>
- <import location="../../coredesc/cas_consumer/FileWriterCasConsumer.xml"/>
+ <import location="../../../ctakes-core/desc/cas_consumer/FileWriterCasConsumer.xml"/>
</descriptor>
<deploymentParameters/>
<errorHandling>
Modified: incubator/ctakes/trunk/ctakes-constituency-parser/desc/collection_processing_engine/ParsingCPE.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-constituency-parser/desc/collection_processing_engine/ParsingCPE.xml?rev=1431008&r1=1431007&r2=1431008&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-constituency-parser/desc/collection_processing_engine/ParsingCPE.xml (original)
+++ incubator/ctakes/trunk/ctakes-constituency-parser/desc/collection_processing_engine/ParsingCPE.xml Wed Jan 9 18:57:19 2013
@@ -23,7 +23,7 @@
<collectionReader>
<collectionIterator>
<descriptor>
- <import location="../../coredesc/collection_reader/LinesFromFileCollectionReader.xml"/>
+ <import location="../../../ctakes-core/desc/collection_reader/LinesFromFileCollectionReader.xml"/>
</descriptor>
<configurationParameterSettings>
<nameValuePair>
Modified: incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml?rev=1431008&r1=1431007&r2=1431008&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.xml Wed Jan 9 18:57:19 2013
@@ -1,167 +1,167 @@
-<?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>true</primitive>
- <annotatorImplementationName>org.apache.ctakes.smokingstatus.ae.ClassifiableEntries</annotatorImplementationName>
- <analysisEngineMetaData>
- <name>ClassigiableEntriesAnnotator</name>
- <description>Converts Sentences to ClassifiableEntries (required by SmokingStatus pipeline) and ultimately to RecordSentence.
-
-Update 1/20: Removed param [String InputDirectory]</description>
- <version>1.0</version>
- <vendor>Mayo</vendor>
- <configurationParameters>
- <configurationParameter>
- <name>TruthFile</name>
- <description>Delimited Truth file. Delimiter is expected to be the TAB char.
-
-This param is optional. If not specified, then the classification feature of the RecordSentence object will not be set.</description>
- <type>String</type>
- <multiValued>false</multiValued>
- <mandatory>false</mandatory>
- </configurationParameter>
- <configurationParameter>
- <name>AllowedClassifications</name>
- <description>See org.apache.ctakes.smokingstatus.Const.java for permitted string values.</description>
- <type>String</type>
- <multiValued>true</multiValued>
- <mandatory>false</mandatory>
- </configurationParameter>
- <configurationParameter>
- <name>SectionsToIgnore</name>
- <description>sections to ignore for ClassifiableEntries - Family History (20109)</description>
- <type>String</type>
- <multiValued>true</multiValued>
- <mandatory>false</mandatory>
- </configurationParameter>
- </configurationParameters>
- <configurationParameterSettings>
- <nameValuePair>
- <name>TruthFile</name>
- <value>
- <string/>
- </value>
- </nameValuePair>
- <nameValuePair>
- <name>AllowedClassifications</name>
- <value>
- <array>
- <string>SMOKER</string>
- <string>CURRENT_SMOKER</string>
- <string>NON_SMOKER</string>
- <string>PAST_SMOKER</string>
- <string>UNKNOWN</string>
- </array>
- </value>
- </nameValuePair>
- <nameValuePair>
- <name>SectionsToIgnore</name>
- <value>
- <array>
- <string>20109</string>
- <string>20138</string>
- </array>
- </value>
- </nameValuePair>
- </configurationParameterSettings>
- <typeSystemDescription>
- <imports>
- <import name="org.apache.ctakes.smokingstatus.types.TypeSystem"/>
- </imports>
- </typeSystemDescription>
- <capabilities>
- <capability>
- <inputs/>
- <outputs/>
- <languagesSupported/>
- </capability>
- </capabilities>
- <operationalProperties>
- <modifiesCas>true</modifiesCas>
- <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
- <outputsNewCASes>false</outputsNewCASes>
- </operationalProperties>
- </analysisEngineMetaData>
- <externalResourceDependencies>
- <externalResourceDependency>
- <key>UimaDescriptorStep1Key</key>
- <description/>
- <interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
- <optional>false</optional>
- </externalResourceDependency>
- <externalResourceDependency>
- <key>UimaDescriptorStep2Key</key>
- <description/>
- <interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
- <optional>false</optional>
- </externalResourceDependency>
- <externalResourceDependency>
- <key>negationContradictionWordsKey</key>
- <description/>
- <interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
- <optional>false</optional>
- </externalResourceDependency>
- </externalResourceDependencies>
- <resourceManagerConfiguration>
- <externalResources>
- <externalResource>
- <name>UimaDescriptorStep1</name>
- <description/>
- <fileResourceSpecifier>
- <fileUrl>file:org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step1.xml</fileUrl>
- </fileResourceSpecifier>
- <implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
- </externalResource>
- <externalResource>
- <name>UimaDescriptorStep2</name>
- <description/>
- <fileResourceSpecifier>
- <fileUrl>file:org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step2_libsvm.xml</fileUrl>
- </fileResourceSpecifier>
- <implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
- </externalResource>
- <externalResource>
- <name>negationContradictionWords</name>
- <description/>
- <fileResourceSpecifier>
- <fileUrl>file:org/apache/ctakes/smokingstatus/data/context/negationContradictionWords.txt</fileUrl>
- </fileResourceSpecifier>
- <implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
- </externalResource>
- </externalResources>
- <externalResourceBindings>
- <externalResourceBinding>
- <key>UimaDescriptorStep1Key</key>
- <resourceName>UimaDescriptorStep1</resourceName>
- </externalResourceBinding>
- <externalResourceBinding>
- <key>UimaDescriptorStep2Key</key>
- <resourceName>UimaDescriptorStep2</resourceName>
- </externalResourceBinding>
- <externalResourceBinding>
- <key>negationContradictionWordsKey</key>
- <resourceName>negationContradictionWords</resourceName>
- </externalResourceBinding>
- </externalResourceBindings>
- </resourceManagerConfiguration>
-</taeDescription>
+<?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>true</primitive>
+ <annotatorImplementationName>org.apache.ctakes.smokingstatus.ae.ClassifiableEntries</annotatorImplementationName>
+ <analysisEngineMetaData>
+ <name>ClassifiableEntriesAnnotator</name>
+ <description>Converts Sentences to ClassifiableEntries (required by SmokingStatus pipeline) and ultimately to RecordSentence.
+
+Update 1/20: Removed param [String InputDirectory]</description>
+ <version>1.0</version>
+ <vendor>Mayo</vendor>
+ <configurationParameters>
+ <configurationParameter>
+ <name>TruthFile</name>
+ <description>Delimited Truth file. Delimiter is expected to be the TAB char.
+
+This param is optional. If not specified, then the classification feature of the RecordSentence object will not be set.</description>
+ <type>String</type>
+ <multiValued>false</multiValued>
+ <mandatory>false</mandatory>
+ </configurationParameter>
+ <configurationParameter>
+ <name>AllowedClassifications</name>
+ <description>See org.apache.ctakes.smokingstatus.Const.java for permitted string values.</description>
+ <type>String</type>
+ <multiValued>true</multiValued>
+ <mandatory>false</mandatory>
+ </configurationParameter>
+ <configurationParameter>
+ <name>SectionsToIgnore</name>
+ <description>sections to ignore for ClassifiableEntries - Family History (20109)</description>
+ <type>String</type>
+ <multiValued>true</multiValued>
+ <mandatory>false</mandatory>
+ </configurationParameter>
+ </configurationParameters>
+ <configurationParameterSettings>
+ <nameValuePair>
+ <name>TruthFile</name>
+ <value>
+ <string/>
+ </value>
+ </nameValuePair>
+ <nameValuePair>
+ <name>AllowedClassifications</name>
+ <value>
+ <array>
+ <string>SMOKER</string>
+ <string>CURRENT_SMOKER</string>
+ <string>NON_SMOKER</string>
+ <string>PAST_SMOKER</string>
+ <string>UNKNOWN</string>
+ </array>
+ </value>
+ </nameValuePair>
+ <nameValuePair>
+ <name>SectionsToIgnore</name>
+ <value>
+ <array>
+ <string>20109</string>
+ <string>20138</string>
+ </array>
+ </value>
+ </nameValuePair>
+ </configurationParameterSettings>
+ <typeSystemDescription>
+ <imports>
+ <import name="org.apache.ctakes.smokingstatus.types.TypeSystem"/>
+ </imports>
+ </typeSystemDescription>
+ <capabilities>
+ <capability>
+ <inputs/>
+ <outputs/>
+ <languagesSupported/>
+ </capability>
+ </capabilities>
+ <operationalProperties>
+ <modifiesCas>true</modifiesCas>
+ <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+ <outputsNewCASes>false</outputsNewCASes>
+ </operationalProperties>
+ </analysisEngineMetaData>
+ <externalResourceDependencies>
+ <externalResourceDependency>
+ <key>UimaDescriptorStep1Key</key>
+ <description/>
+ <interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
+ <optional>false</optional>
+ </externalResourceDependency>
+ <externalResourceDependency>
+ <key>UimaDescriptorStep2Key</key>
+ <description/>
+ <interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
+ <optional>false</optional>
+ </externalResourceDependency>
+ <externalResourceDependency>
+ <key>negationContradictionWordsKey</key>
+ <description/>
+ <interfaceName>org.apache.ctakes.core.resource.FileResource</interfaceName>
+ <optional>false</optional>
+ </externalResourceDependency>
+ </externalResourceDependencies>
+ <resourceManagerConfiguration>
+ <externalResources>
+ <externalResource>
+ <name>UimaDescriptorStep1</name>
+ <description/>
+ <fileResourceSpecifier>
+ <fileUrl>file:ctakes-smoking-status/desc/analysis_engine/ProductionPostSentenceAggregate_step1.xml</fileUrl>
+ </fileResourceSpecifier>
+ <implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
+ </externalResource>
+ <externalResource>
+ <name>UimaDescriptorStep2</name>
+ <description/>
+ <fileResourceSpecifier>
+ <fileUrl>file:ctakes-smoking-status/desc/analysis_engine/ProductionPostSentenceAggregate_step2_libsvm.xml</fileUrl>
+ </fileResourceSpecifier>
+ <implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
+ </externalResource>
+ <externalResource>
+ <name>negationContradictionWords</name>
+ <description/>
+ <fileResourceSpecifier>
+ <fileUrl>file:org/apache/ctakes/smokingstatus/data/context/negationContradictionWords.txt</fileUrl>
+ </fileResourceSpecifier>
+ <implementationName>org.apache.ctakes.core.resource.FileResourceImpl</implementationName>
+ </externalResource>
+ </externalResources>
+ <externalResourceBindings>
+ <externalResourceBinding>
+ <key>UimaDescriptorStep1Key</key>
+ <resourceName>UimaDescriptorStep1</resourceName>
+ </externalResourceBinding>
+ <externalResourceBinding>
+ <key>UimaDescriptorStep2Key</key>
+ <resourceName>UimaDescriptorStep2</resourceName>
+ </externalResourceBinding>
+ <externalResourceBinding>
+ <key>negationContradictionWordsKey</key>
+ <resourceName>negationContradictionWords</resourceName>
+ </externalResourceBinding>
+ </externalResourceBindings>
+ </resourceManagerConfiguration>
+</taeDescription>
Modified: incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ProductionPostSentenceAggregate_step2_libsvm.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ProductionPostSentenceAggregate_step2_libsvm.xml?rev=1431008&r1=1431007&r2=1431008&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ProductionPostSentenceAggregate_step2_libsvm.xml (original)
+++ incubator/ctakes/trunk/ctakes-smoking-status/desc/analysis_engine/ProductionPostSentenceAggregate_step2_libsvm.xml Wed Jan 9 18:57:19 2013
@@ -36,7 +36,7 @@
<import location="PcsClassifierAnnotator_libsvm.xml"/>
</delegateAnalysisEngine>
<delegateAnalysisEngine key="NegationAnnotator">
-<import location="file:NegationAnnotator.xml"/>
+<import location="../../../ctakes-ne-contexts/desc/NegationAnnotator.xml"/>
</delegateAnalysisEngine>
</delegateAnalysisEngineSpecifiers>
<analysisEngineMetaData>