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Posted to commits@ctakes.apache.org by se...@apache.org on 2016/10/14 21:21:56 UTC
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...
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