[jira] [Commented] (CTAKES-370) Include smoking status in clinical pipeline

[Jeff Headley (JIRA)]

[ 
https://issues.apache.org/jira/browse/CTAKES-370?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16070983#comment-16070983
 ] 

Jeff Headley commented on CTAKES-370:
-

In case it might help save someone else days of frustration, the advice 
mentioned in CTAKES-363 seems to have solved my problem. I extracted the files 
out of ctakes-smoking-status-res-3.2.2.jar and placed them in ctakes/desc and 
then edited the import lines as mentioned above and the errors went away.

> Include smoking status in clinical pipeline
> ---
>
> Key: CTAKES-370
> URL: https://issues.apache.org/jira/browse/CTAKES-370
> Project: cTAKES
>  Issue Type: Improvement
>  Components: ctakes-clinical-pipeline, ctakes-smoking-status
>Affects Versions: 3.2.2
> Environment: Linux
>Reporter: Tomasz Oliwa
>Priority: Minor
> Attachments: AggregatePlaintextFastUMLSProcessor.xml
>
>
> The smoking status detection can be included in the clinical pipeline. 
> Attached is a AggregatePlaintextFastUMLSProcessor.xml that has the clinical 
> pipeline + the smoking status detection integrated.
> Currently cTAKES has smoking status resources that need to have 
> their imports adjusted for any smoking status detection to work. As a 
> workaround, in:
> ProductionPostSentenceAggregate_step1.xml
> change:
> 
>  name="org.apache.ctakes.core.analysis_engine.SentenceDetectorAnnotator"/>
> to the absolute or relative path (depends on the installed system, on my 
> machine it is) of these annotators:
>  location="../../../../../../desc/ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml"/>
>  location="../../../../../../desc/ctakes-core/desc/analysis_engine/SentenceDetectorAnnotator.xml"/>



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[jira] [Comment Edited] (CTAKES-370) Include smoking status in clinical pipeline

[Jeff Headley (JIRA)]

[ 
https://issues.apache.org/jira/browse/CTAKES-370?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16070968#comment-16070968
 ] 

Jeff Headley edited comment on CTAKES-370 at 7/1/17 3:02 AM:
-

I'm using version 3.2.2 and trying to do this in my application. It was 
previously working with the AggregatePlaintextFastUMLSProcessor. I tried using 
the one attached to this issue and made the import changes as mentioned in the 
description, but I am getting the below error:


{code:java}
org.apache.uima.resource.ResourceInitializationException: Initialization of 
annotator class 
"org.apache.ctakes.smokingstatus.ae.KuRuleBasedClassifierAnnotator" failed.  
(Descriptor: 
file:/D:/Software/project/cTAKES/desc/ctakes-smoking-status/desc/analysis_engine/KuRuleBasedClassifierAnnotator.xml)
at 
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at 
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
at 
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at 
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at 
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at 
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at 
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at 
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at 
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at 
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at 
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at 
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
.
.
Caused by: org.apache.uima.resource.ResourceInitializationException
at 
org.apache.ctakes.smokingstatus.ae.KuRuleBasedClassifierAnnotator.initialize(KuRuleBasedClassifierAnnotator.java:74)
at 
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
... 19 more
Caused by: java.lang.IllegalArgumentException: URI is not hierarchical
at java.io.File.(File.java:418)
at 
org.apache.ctakes.core.resource.FileLocator.locateOnClasspath(FileLocator.java:182)
at 
org.apache.ctakes.core.resource.FileLocator.getFullPath(FileLocator.java:125)
at 
org.apache.ctakes.core.resource.FileLocator.locateFile(FileLocator.java:70)
at 
org.apache.ctakes.smokingstatus.ae.KuRuleBasedClassifierAnnotator.initialize(KuRuleBasedClassifierAnnotator.java:67)
... 20 more
{code}

The error happens in {{FileLocator}} at method {{private static File 
locateOnClasspath( final String relativePath )}} and the passed in parameter 
is: org/apache/ctakes/smokingstatus/data/KU/keywords.txt



was (Author: jheadley):
I'm using version 3.2.2 and trying to do this in my application. It was 
previously working with the AggregatePlaintextFastUMLSProcessor. I tried using 
the one attached to this issue and made the import changes as mentioned in the 
description, but I am getting the below error:


{code:java}
org.apache.uima.resource.ResourceInitializationException: Initialization of 
annotator class 
"org.apache.ctakes.smokingstatus.ae.KuRuleBasedClassifierAnnotator" failed.  
(Descriptor: 
file:/D:/Software/Epividian/cTAKES/desc/ctakes-smoking-status/desc/analysis_engine/KuRuleBasedClassifierAnnotator.xml)
at 
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at 
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
at 
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at 
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at 
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at 
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at 

[jira] [Commented] (CTAKES-370) Include smoking status in clinical pipeline

[Jeff Headley (JIRA)]

[ 
https://issues.apache.org/jira/browse/CTAKES-370?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16070968#comment-16070968
 ] 

Jeff Headley commented on CTAKES-370:
-

I'm using version 3.2.2 and trying to do this in my application. It was 
previously working with the AggregatePlaintextFastUMLSProcessor. I tried using 
the one attached to this issue and made the import changes as mentioned in the 
description, but I am getting the below error:


{code:java}
org.apache.uima.resource.ResourceInitializationException: Initialization of 
annotator class 
"org.apache.ctakes.smokingstatus.ae.KuRuleBasedClassifierAnnotator" failed.  
(Descriptor: 
file:/D:/Software/Epividian/cTAKES/desc/ctakes-smoking-status/desc/analysis_engine/KuRuleBasedClassifierAnnotator.xml)
at 
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at 
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
at 
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at 
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at 
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at 
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at 
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at 
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at 
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at 
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at 
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at 
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
at 
com.epividian.ctakes.utils.CTAKESUtils.getAnalysisEngine(CTAKESUtils.java:143)
at 
com.epividian.ctakes.processors.CommandLineProcessor.processLine(CommandLineProcessor.java:144)
at 
java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1374)
at 
java.util.stream.ReferencePipeline$Head.forEach(ReferencePipeline.java:580)
at 
com.epividian.ctakes.processors.CommandLineProcessor.run(CommandLineProcessor.java:112)
at com.epividian.ctakes.App.main(App.java:109)
Caused by: org.apache.uima.resource.ResourceInitializationException
at 
org.apache.ctakes.smokingstatus.ae.KuRuleBasedClassifierAnnotator.initialize(KuRuleBasedClassifierAnnotator.java:74)
at 
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
... 19 more
Caused by: java.lang.IllegalArgumentException: URI is not hierarchical
at java.io.File.(File.java:418)
at 
org.apache.ctakes.core.resource.FileLocator.locateOnClasspath(FileLocator.java:182)
at 
org.apache.ctakes.core.resource.FileLocator.getFullPath(FileLocator.java:125)
at 
org.apache.ctakes.core.resource.FileLocator.locateFile(FileLocator.java:70)
at 
org.apache.ctakes.smokingstatus.ae.KuRuleBasedClassifierAnnotator.initialize(KuRuleBasedClassifierAnnotator.java:67)
... 20 more
{code}

The error happens in {{FileLocator}} at method {{private static File 
locateOnClasspath( final String relativePath )}} and the passed in parameter 
is: org/apache/ctakes/smokingstatus/data/KU/keywords.txt


> Include smoking status in clinical pipeline
> ---
>
> Key: CTAKES-370
> URL: https://issues.apache.org/jira/browse/CTAKES-370
> Project: cTAKES
>  Issue Type: Improvement
>  Components: ctakes-clinical-pipeline, ctakes-smoking-status
>Affects Versions: 3.2.2
> Environment: Linux
>Reporter: Tomasz Oliwa
>Priority: Minor
> Attachments: AggregatePlaintextFastUMLSProcessor.xml
>
>
> The smoking status detection can be included in the clinical pipeline. 
> Attached is a AggregatePlaintextFastUMLSProcessor.xml that has the clinical 
> pipeline + the smoking status detection integrated.
> Currently cTAKES has smoking status resources that need to have 
> their imports adjusted for any smoking status detection to work. As a 
> workaround, in:
> ProductionPostSentenceAggregate_step1.xml
> change:
> 
>  

[jira] [Created] (CTAKES-449) PolarityCleartkAnalysisEngine slow for large documents

[Dmitriy Dligach (JIRA)]

Dmitriy Dligach created CTAKES-449:
--

 Summary: PolarityCleartkAnalysisEngine slow for large documents
 Key: CTAKES-449
 URL: https://issues.apache.org/jira/browse/CTAKES-449
 Project: cTAKES
  Issue Type: Improvement
  Components: ctakes-assertion
Reporter: Dmitriy Dligach


As soon as I add at the end of my pipeline the negation AE:
aggregateBuilder.add( 
PolarityCleartkAnalysisEngine.createAnnotatorDescription() );

The pipeline becomes 50-100 times slower. This likely has to do with the line:
List sents = new ArrayList<>(JCasUtil.selectCovering(jCas, 
Sentence.class, entityOrEventMention.getBegin(), 
entityOrEventMention.getEnd()));

in AssertionCleartkAnalysisEngine. I am running the pipeline on large files 
(i.e. having a large number of sentences). The slowdown is caused by the code's 
obtaining all sentences in a document for each identified annotation.

The full pipeline is here:
https://github.com/dmitriydligach/ctakes-misc/blob/master/src/main/java/org/apache/ctakes/pipelines/UmlsLookupPipeline.java



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