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Posted to commits@ctakes.apache.org by ma...@apache.org on 2013/01/18 22:12:56 UTC
svn commit: r1435343 - in
/incubator/ctakes/trunk/ctakes-clinical-pipeline/desc:
analysis_engine/assertion_training_steps/
collection_processing_engine/assertion_training_steps/
Author: mattcoarr
Date: Fri Jan 18 21:12:56 2013
New Revision: 1435343
URL: http://svn.apache.org/viewvc?rev=1435343&view=rev
Log:
added analysis engine and cpe descriptors to run xmi that only includes gold
entity/event mentions through the rest of ctakes (but not dictionary lookup or
assertion modules)
Added:
incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/assertion_training_steps/
incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/assertion_training_steps/AggregatePlaintextUMLSProcessor__no_dictionary_no_assertion.xml
- copied, changed from r1435232, incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml
incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/assertion_training_steps/
incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/assertion_training_steps/process_gold_assertion_data.xml
Copied: incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/assertion_training_steps/AggregatePlaintextUMLSProcessor__no_dictionary_no_assertion.xml (from r1435232, incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/assertion_training_steps/AggregatePlaintextUMLSProcessor__no_dictionary_no_assertion.xml?p2=incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/assertion_training_steps/AggregatePlaintextUMLSProcessor__no_dictionary_no_assertion.xml&p1=incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml&r1=1435232&r2=1435343&rev=1435343&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml (original)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/assertion_training_steps/AggregatePlaintextUMLSProcessor__no_dictionary_no_assertion.xml Fri Jan 18 21:12:56 2013
@@ -19,57 +19,68 @@
under the License.
-->
+<!--
+ comment: this is a version of the clinical document pipeline used for
+ pre-processing data before running through the assertion training+evaluation
+ process. The input files should be xmi files converted from knowtator xml.
+-->
<analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
<frameworkImplementation>org.apache.uima.java</frameworkImplementation>
<primitive>false</primitive>
<delegateAnalysisEngineSpecifiers>
<delegateAnalysisEngine key="Chunker">
- <import location="../../../ctakes-chunker/desc/Chunker.xml"/>
+ <import location="../../../../ctakes-chunker/desc/Chunker.xml"/>
</delegateAnalysisEngine>
<delegateAnalysisEngine key="TokenizerAnnotator">
- <import location="../../../ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml"/>
+ <import location="../../../../ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml"/>
</delegateAnalysisEngine>
<delegateAnalysisEngine key="ContextDependentTokenizerAnnotator">
- <import location="../../../ctakes-context-tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
+ <import location="../../../../ctakes-context-tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
</delegateAnalysisEngine>
+ <!--
<delegateAnalysisEngine key="DictionaryLookupAnnotatorDB">
- <import location="../../../ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml"/>
+ <import location="../../../../ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml"/>
</delegateAnalysisEngine>
+ -->
+ <!--
<delegateAnalysisEngine key="StatusAnnotator">
- <import location="../../../ctakes-ne-contexts/desc/StatusAnnotator.xml"/>
+ <import location="../../../../ctakes-ne-contexts/desc/StatusAnnotator.xml"/>
</delegateAnalysisEngine>
<delegateAnalysisEngine key="NegationAnnotator">
- <import location="../../../ctakes-ne-contexts/desc/NegationAnnotator.xml"/>
+ <import location="../../../../ctakes-ne-contexts/desc/NegationAnnotator.xml"/>
</delegateAnalysisEngine>
+ -->
<delegateAnalysisEngine key="ExtractionPrepAnnotator">
- <import location="ExtractionPrepAnnotator.xml"/>
+ <import location="../ExtractionPrepAnnotator.xml"/>
</delegateAnalysisEngine>
<delegateAnalysisEngine key="SentenceDetectorAnnotator">
- <import location="../../../ctakes-core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
+ <import location="../../../../ctakes-core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>
</delegateAnalysisEngine>
<delegateAnalysisEngine key="LookupWindowAnnotator">
- <import location="LookupWindowAnnotator.xml"/>
+ <import location="../LookupWindowAnnotator.xml"/>
</delegateAnalysisEngine>
<delegateAnalysisEngine key="AdjustNounPhraseToIncludeFollowingNP">
- <import location="../../../ctakes-chunker/desc/AdjustNounPhraseToIncludeFollowingNP.xml"/>
+ <import location="../../../../ctakes-chunker/desc/AdjustNounPhraseToIncludeFollowingNP.xml"/>
</delegateAnalysisEngine>
<delegateAnalysisEngine key="AdjustNounPhraseToIncludeFollowingPPNP">
- <import location="../../../ctakes-chunker/desc/AdjustNounPhraseToIncludeFollowingPPNP.xml"/>
+ <import location="../../../../ctakes-chunker/desc/AdjustNounPhraseToIncludeFollowingPPNP.xml"/>
</delegateAnalysisEngine>
<delegateAnalysisEngine key="SimpleSegmentAnnotator">
- <import location="SimpleSegmentAnnotator.xml"/>
+ <import location="../SimpleSegmentAnnotator.xml"/>
</delegateAnalysisEngine>
<delegateAnalysisEngine key="POSTagger">
- <import location="../../../ctakes-pos-tagger/desc/POSTagger.xml"/>
+ <import location="../../../../ctakes-pos-tagger/desc/POSTagger.xml"/>
</delegateAnalysisEngine>
<delegateAnalysisEngine key="LvgAnnotator">
- <import location="../../../ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml"/>
+ <import location="../../../../ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml"/>
</delegateAnalysisEngine>
+ <!--
<delegateAnalysisEngine key="AssertionAnnotator">
- <import location="../../../ctakes-assertion/desc/AssertionMiniPipelineAnalysisEngine.xml"/>
+ <import location="../../../../ctakes-assertion/desc/AssertionMiniPipelineAnalysisEngine.xml"/>
</delegateAnalysisEngine>
+ -->
<delegateAnalysisEngine key="DependencyParser">
- <import location="../../../ctakes-dependency-parser/desc/analysis_engine/ClearParserDependencyParserAE.xml"/>
+ <import location="../../../../ctakes-dependency-parser/desc/analysis_engine/ClearParserDependencyParserAE.xml"/>
</delegateAnalysisEngine>
</delegateAnalysisEngineSpecifiers>
<analysisEngineMetaData>
@@ -120,9 +131,9 @@ and requires an UMLS license. Please up
<node>AdjustNounPhraseToIncludeFollowingNP</node>
<node>AdjustNounPhraseToIncludeFollowingPPNP</node>
<node>LookupWindowAnnotator</node>
- <node>DictionaryLookupAnnotatorDB</node>
+ <!-- <node>DictionaryLookupAnnotatorDB</node> -->
<node>DependencyParser</node>
- <node>AssertionAnnotator</node>
+ <!-- <node>AssertionAnnotator</node> -->
<!--
<node>StatusAnnotator</node>
<node>NegationAnnotator</node>
Added: incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/assertion_training_steps/process_gold_assertion_data.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/assertion_training_steps/process_gold_assertion_data.xml?rev=1435343&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/assertion_training_steps/process_gold_assertion_data.xml (added)
+++ incubator/ctakes/trunk/ctakes-clinical-pipeline/desc/collection_processing_engine/assertion_training_steps/process_gold_assertion_data.xml Fri Jan 18 21:12:56 2013
@@ -0,0 +1,58 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<cpeDescription xmlns="http://uima.apache.org/resourceSpecifier">
+ <collectionReader>
+ <collectionIterator>
+ <descriptor>
+ <import location="../../../../ctakes-core/desc/collection_reader/XmiCollectionReaderCtakes.xml"/>
+ </descriptor>
+ <configurationParameterSettings>
+ <nameValuePair>
+ <name>InputDirectory</name>
+ <value>
+ <string>/tmp/assertion_data/input</string>
+ </value>
+ </nameValuePair>
+ </configurationParameterSettings>
+ </collectionIterator>
+ </collectionReader>
+ <casProcessors casPoolSize="3" processingUnitThreadCount="1">
+ <casProcessor deployment="integrated" name="AggregatePlaintextUMLSProcessor">
+ <descriptor>
+ <import location="../../analysis_engine/assertion_training_steps/AggregatePlaintextUMLSProcessor__no_dictionary_no_assertion.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="XMI Writer CAS Consumer">
+ <descriptor>
+ <import location="../../../../ctakes-core/desc/cas_consumer/__XmiWriterCasConsumer.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>OutputDirectory</name>
+ <value>
+ <string>/tmp/assertion_data/output</string>
+ </value>
+ </nameValuePair>
+ </configurationParameterSettings>
+ </casProcessor>
+ </casProcessors>
+ <cpeConfig>
+ <numToProcess>-1</numToProcess>
+ <deployAs>immediate</deployAs>
+ <checkpoint batch="0" time="300000ms"/>
+ <timerImpl/>
+ </cpeConfig>
+</cpeDescription>