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From seanfi...@apache.org
Subject svn commit: r1764965 - in /ctakes/trunk: ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/pipeline/ ctakes-clinical-pipeline-res/src/main/resources/org/apache/ctakes/clinical/pipeline/ ctakes-examples/src/main/resources/org/apache/ct...
Date Fri, 14 Oct 2016 21:21:56 GMT
Author: seanfinan
Date: Fri Oct 14 21:21:56 2016
New Revision: 1764965

URL: http://svn.apache.org/viewvc?rev=1764965&view=rev
Log:
Add AttributesCleartkSubPipe.piper
refactor other .piper files to use it

Added:
    ctakes/trunk/ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/pipeline/
    ctakes/trunk/ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/pipeline/AttributesCleartkSubPipe.piper
Modified:
    ctakes/trunk/ctakes-clinical-pipeline-res/src/main/resources/org/apache/ctakes/clinical/pipeline/DefaultFastPipeline.piper
    ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldCuiPipeline.piper
    ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldPipeline.piper
    ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldTkPropsPipeline.piper

Added: ctakes/trunk/ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/pipeline/AttributesCleartkSubPipe.piper
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/pipeline/AttributesCleartkSubPipe.piper?rev=1764965&view=auto
==============================================================================
--- ctakes/trunk/ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/pipeline/AttributesCleartkSubPipe.piper
(added)
+++ ctakes/trunk/ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/pipeline/AttributesCleartkSubPipe.piper
Fri Oct 14 21:21:56 2016
@@ -0,0 +1,14 @@
+// Commands and parameters to create a default entity attributes processing sub-pipeline.
 This is not a full pipeline.
+
+// Add the Dependency parser for use by cleartk
+addDescription ClearNLPDependencyParserAE
+
+// Add the cleartk package for cleartk class lookups
+addPackage org.apache.ctakes.assertion.medfacts.cleartk
+// Add the cleartk attribute engines
+addDescription PolarityCleartkAnalysisEngine
+addDescription UncertaintyCleartkAnalysisEngine
+addDescription HistoryCleartkAnalysisEngine
+addDescription ConditionalCleartkAnalysisEngine
+addDescription GenericCleartkAnalysisEngine
+addDescription SubjectCleartkAnalysisEngine

Modified: ctakes/trunk/ctakes-clinical-pipeline-res/src/main/resources/org/apache/ctakes/clinical/pipeline/DefaultFastPipeline.piper
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-clinical-pipeline-res/src/main/resources/org/apache/ctakes/clinical/pipeline/DefaultFastPipeline.piper?rev=1764965&r1=1764964&r2=1764965&view=diff
==============================================================================
--- ctakes/trunk/ctakes-clinical-pipeline-res/src/main/resources/org/apache/ctakes/clinical/pipeline/DefaultFastPipeline.piper
(original)
+++ ctakes/trunk/ctakes-clinical-pipeline-res/src/main/resources/org/apache/ctakes/clinical/pipeline/DefaultFastPipeline.piper
Fri Oct 14 21:21:56 2016
@@ -10,15 +10,5 @@ addDescription POSTagger
 // Default fast dictionary lookup
 add DefaultJCasTermAnnotator
 
-// Add the Dependency parser for use by cleartk
-addDescription ClearNLPDependencyParserAE
-
-// Add the cleartk package for cleartk class lookups
-addPackage org.apache.ctakes.assertion.medfacts.cleartk
-// Add the cleartk attribute engines
-addDescription PolarityCleartkAnalysisEngine
-addDescription UncertaintyCleartkAnalysisEngine
-addDescription HistoryCleartkAnalysisEngine
-addDescription ConditionalCleartkAnalysisEngine
-addDescription GenericCleartkAnalysisEngine
-addDescription SubjectCleartkAnalysisEngine
+// Add Cleartk Entity Attribute annotators
+load org/apache/ctakes/assertion/pipeline/AttributeCleartkSubPipe.piper

Modified: ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldCuiPipeline.piper
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldCuiPipeline.piper?rev=1764965&r1=1764964&r2=1764965&view=diff
==============================================================================
--- ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldCuiPipeline.piper
(original)
+++ ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldCuiPipeline.piper
Fri Oct 14 21:21:56 2016
@@ -1,10 +1,10 @@
 // This file contains commands and parameters to run the ctakes-examples "Hello World" pipeline
 // with UMLS Concept Unique Identifiers (CUI) output
 
-// Equivalent of ClinicalPipelineFactory.getTokenProcessingPipeline()
-add SimpleSegmentAnnotator
-add SentenceDetector
-add TokenizerAnnotatorPTB
+// Load a simple token processing pipeline from another pipeline file
+load org/apache/ctakes/core/pipeline/DefaultTokenizerPipeline.piper
+
+// Add non-core annotators
 add ContextDependentTokenizerAnnotator
 // The POSTagger has a -complex- startup, but it can create its own description to handle
it
 addDescription POSTagger

Modified: ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldPipeline.piper
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldPipeline.piper?rev=1764965&r1=1764964&r2=1764965&view=diff
==============================================================================
--- ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldPipeline.piper
(original)
+++ ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldPipeline.piper
Fri Oct 14 21:21:56 2016
@@ -1,9 +1,9 @@
 // This file contains commands and parameters to run the ctakes-examples "Hello World" pipeline
 
-// Equivalent of ClinicalPipelineFactory.getTokenProcessingPipeline()
-add SimpleSegmentAnnotator
-add SentenceDetector
-add TokenizerAnnotatorPTB
+// Load a simple token processing pipeline from another pipeline file
+load org/apache/ctakes/core/pipeline/DefaultTokenizerPipeline.piper
+
+// Add non-core annotators
 add ContextDependentTokenizerAnnotator
 // The POSTagger has a -complex- startup, but it can create its own description to handle
it
 addDescription POSTagger

Modified: ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldTkPropsPipeline.piper
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldTkPropsPipeline.piper?rev=1764965&r1=1764964&r2=1764965&view=diff
==============================================================================
--- ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldTkPropsPipeline.piper
(original)
+++ ctakes/trunk/ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldTkPropsPipeline.piper
Fri Oct 14 21:21:56 2016
@@ -4,20 +4,8 @@
 // Load a simple token processing pipeline from another file
 load org/apache/ctakes/examples/pipeline/HelloWorldPipeline.piper
 
-// I don't think that the chunker is strictly necessary, but here it is ...
-add Chunker
-addDescription adjuster.ChunkAdjuster NP,NP 1
-addDescription adjuster.ChunkAdjuster NP,PP,NP 2
-
-addDescription ClearNLPDependencyParserAE
-// Add the cleartk package for future class lookups
-addPackage org.apache.ctakes.assertion.medfacts.cleartk
-addDescription PolarityCleartkAnalysisEngine
-addDescription UncertaintyCleartkAnalysisEngine
-addDescription HistoryCleartkAnalysisEngine
-addDescription ConditionalCleartkAnalysisEngine
-addDescription GenericCleartkAnalysisEngine
-addDescription SubjectCleartkAnalysisEngine
+// Add Cleartk Entity Attribute annotators
+load org/apache/ctakes/assertion/pipeline/AttributeCleartkSubPipe.piper
 
 // Collect discovered Entity information for post-run access
 collectEntities



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