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From seanfi...@apache.org
Subject 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/
Date Wed, 09 Jan 2013 18:57:20 GMT
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>



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