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From "Murphy, Sean P." <Murphy.S...@mayo.edu>
Subject RE: Smoking Pipeline
Date Mon, 18 May 2015 14:58:42 GMT
Since the errors relate to the  location of resources during initialization it is likely that
there were changes in how the v3.2 version was being packaged or similar.

I have not yet downloaded and tested v3.2.  Can anyone else verify this is working or not
in the latest ctakes?

                Thanks,
                                ~Sean

From: Hegde, Harshad [mailto:hegde.harshad@marshfieldclinic.org]
Sent: Friday, May 15, 2015 11:30 AM
To: user@ctakes.apache.org
Subject: Smoking Pipeline

Hello,

I followed the step-by-step instruction in the Developer's Install Guide. I am using a Macbook
OSX 10.9.5 with Java ver 1.7.0_10.  The CVD and CPE worked perfectly for ctakes-clinical-pipeline.
I am trying to run the 'Smoking Pipeline'(ctakes-smoking-status) with the following parameters:

*         Descriptor: 'FilesInDirectoryCollectionReader.xml'

*         Input Directory: Folder containing test xml files which worked fine in v3.1

*         Analysis Engine: 'SimulatedProdSmokingTAE.xml'

This combination worked perfectly in v3.1.

But in v3.2, I am getting the following error:


descFile .../ctakes/ctakes-smoking-status-res/target/classes/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step2_libsvm.xml
org.apache.uima.resource.ResourceInitializationException: Initialization of CAS Processor
with name "SimulatedProdAggregateTAE" failed.
                at org.apache.uima.collection.impl.CollectionProcessingEngine_impl.initialize(CollectionProcessingEngine_impl.java:83)
                at org.apache.uima.impl.UIMAFramework_impl._produceCollectionProcessingEngine(UIMAFramework_impl.java:420)
                at org.apache.uima.UIMAFramework.produceCollectionProcessingEngine(UIMAFramework.java:864)
                at org.apache.uima.tools.cpm.CpmPanel.startProcessing(CpmPanel.java:573)
                at org.apache.uima.tools.cpm.CpmPanel.access$000(CpmPanel.java:105)
                at org.apache.uima.tools.cpm.CpmPanel$1.run(CpmPanel.java:713)
Caused by: org.apache.uima.resource.ResourceConfigurationException: Initialization of CAS
Processor with name "SimulatedProdAggregateTAE" failed.
                at org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1104)
                at org.apache.uima.collection.impl.cpm.container.CPEFactory.getCasProcessors(CPEFactory.java:550)
                at org.apache.uima.collection.impl.cpm.BaseCPMImpl.init(BaseCPMImpl.java:253)
                at org.apache.uima.collection.impl.cpm.BaseCPMImpl.<init>(BaseCPMImpl.java:127)
                at org.apache.uima.collection.impl.CollectionProcessingEngine_impl.initialize(CollectionProcessingEngine_impl.java:75)
                ... 5 more
Caused by: org.apache.uima.resource.ResourceInitializationException: Initialization of annotator
class "org.apache.ctakes.smokingstatus.ae.ClassifiableEntries" failed.  (Descriptor: file:.../ctakes/ctakes-smoking-status/desc/analysis_engine/ClassifiableEntriesAnnotator.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.produceResource(UIMAFramework.java:314)
                at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425)
                at org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1088)
                ... 9 more
Caused by: org.apache.uima.resource.ResourceInitializationException: An import could not be
resolved.  No .xml file with name "org.apache.ctakes.core.analysis_engine.TokenizerAnnotator"
was found in the class path or data path. (Descriptor: file:.../ctakes/ctakes-smoking-status-res/target/classes/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step1.xml)
                at org.apache.ctakes.smokingstatus.ae.ClassifiableEntries.initialize(ClassifiableEntries.java:178)
                at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
                ... 24 more
Caused by: org.apache.uima.resource.ResourceInitializationException: An import could not be
resolved.  No .xml file with name "org.apache.ctakes.core.analysis_engine.TokenizerAnnotator"
was found in the class path or data path. (Descriptor: file:.../ctakes/ctakes-smoking-status-res/target/classes/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step1.xml)
                at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:159)
                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.produceResource(UIMAFramework.java:314)
                at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425)
                at org.apache.ctakes.smokingstatus.ae.ClassifiableEntries.initialize(ClassifiableEntries.java:164)
                ... 25 more
Caused by: org.apache.uima.util.InvalidXMLException: An import could not be resolved.  No
.xml file with name "org.apache.ctakes.core.analysis_engine.TokenizerAnnotator" was found
in the class path or data path. (Descriptor: file:.../ctakes/ctakes-smoking-status-res/target/classes/org/apache/ctakes/smokingstatus/analysis_engine/ProductionPostSentenceAggregate_step1.xml)
                at org.apache.uima.resource.metadata.impl.Import_impl.findAbsoluteUrl(Import_impl.java:107)
                at org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveDelegateAnalysisEngineImports(AnalysisEngineDescription_impl.java:798)
                at org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveDelegateAnalysisEngineImports(AnalysisEngineDescription_impl.java:765)
                at org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.getDelegateAnalysisEngineSpecifiers(AnalysisEngineDescription_impl.java:193)
                at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:147)
                ... 31 more


Is there something I am missing??

Thanks,
Harshad.

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