[jira] [Commented] (CTAKES-370) Include smoking status in clinical pipeline
[ 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"/> -- This message was sent by Atlassian JIRA (v6.4.14#64029)
[jira] [Commented] (CTAKES-370) Include smoking status in clinical pipeline
[
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:
>
>
