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Date: Tue, 11 Sep 2012 06:20:07 +1100 (NCT)
From: "Pei Chen (JIRA)" <jira@apache.org>
To: ctakes-dev@incubator.apache.org
Message-ID: <1007546223.59336.1347304807665.JavaMail.jiratomcat@arcas>
In-Reply-To: <964943725.2511.1345669842445.JavaMail.jiratomcat@arcas>
Subject: [jira] [Updated] (CTAKES-43) Spaces in directory names STILL cause
 problems for UIMA
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     [ https://issues.apache.org/jira/browse/CTAKES-43?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]

Pei Chen updated CTAKES-43:
---------------------------

    Affects Version/s: 2.6-incubating
    
> Spaces in directory names STILL cause problems for UIMA
> -------------------------------------------------------
>
>                 Key: CTAKES-43
>                 URL: https://issues.apache.org/jira/browse/CTAKES-43
>             Project: cTAKES
>          Issue Type: Improvement
>    Affects Versions: 2.6-incubating
>            Reporter: Pei Chen
>            Assignee: Pei Chen
>             Fix For: 3.0-incubating
>
>
> The following command works just fine for me:
> ~/bin/apache-uima-as-2.3.1/bin/runAE.sh -l en ~/bin/apache-uima-as-2.3.1/examples/descriptors/analysis_engine/NamesAndPersonTitles_TAE.xml ../test_data/ozborn/ ./
> The following fails due to spaces:
> ~/bin/apache-uima-as-2.3.1/bin/runAE.sh -l en "../ctakes_pipeline_root/clinical documents pipeline/desc/analysis_engine/AggregatePlaintextProcessor.xml" ../test_data/ozborn/ ./
> This is with bash 3.2.39 on Suse linux, but it also fails on my Ubuntu box as well. It doesn't work any better with single quotes.
> Also it should be pointed out that runAE.sh (the UIMA script which isn't handle spaces well) contains the $@ as shown below but still fails:
> "$UIMA_HOME/bin/runUimaClass.sh" org.apache.uima.tools.RunAE $@
> "~/bin/apache-uima-as-2.3.1/bin/runAE.sh"
> The way I have worked around this is to create a symbolic link using underscores to replace the spaces. However when I run this:
> ~/bin/apache-uima-as-2.3.1/bin/runAE.sh -l en ../ctakes_pipeline_root/clinical_documents_pipeline/desc/analysis_engine/AggregatePlaintextProcessor.xml ../test_data/ozborn/ ./
> I know get this error message:
> org.apache.uima.resource.ResourceInitializationException: Initialization of CAS Processor with name "UserAE" 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:821)
> at org.apache.uima.tools.RunAE.<init>(RunAE.java:216)
> at org.apache.uima.tools.RunAE.main(RunAE.java:419)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> at java.lang.reflect.Method.invoke(Method.java:592)
> at org.apache.uima.bootstrap.UimaBootstrap.main(UimaBootstrap.java:98)
> Caused by: org.apache.uima.resource.ResourceConfigurationException: Initialization of CAS Processor with name "UserAE" 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)
> ... 9 more
> Caused by: org.apache.uima.resource.ResourceInitializationException: Annotator class "edu.mayo.bmi.uima.core.ae.OverlapAnnotator" was not found. (Descriptor: file:/home/AD/josborne/nlp/ctakes_pipeline_root/clinical_documents_pipeline/desc/analysis_engine/MaxLookupWindows.xml)
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:206)
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:155)
> 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:267)
> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:361)
> 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:267)
> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:361)
> 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:267)
> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:312)
> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:392)
> at org.apache.uima.collection.impl.cpm.container.CPEFactory.produceIntegratedCasProcessor(CPEFactory.java:1088)
> ... 13 more
> Caused by: java.lang.ClassNotFoundException: edu.mayo.bmi.uima.core.ae.OverlapAnnotator
> at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
> at java.security.AccessController.doPrivileged(Native Method)
> at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:268)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:252)
> at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:320)
> at java.lang.Class.forName0(Native Method)
> at java.lang.Class.forName(Class.java:164)
> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:203)
> ... 36 more
> If I pass runAE.sh a different parameter set like this:
> ~/bin/apache-uima-as-2.3.1/bin/runAE.sh -l en ~/bin/apache-uima-as-2.3.1/examples/descriptors/analysis_engine/NamesAndPersonTitles_TAE.xml ../test_data/ozborn/ ./
> Then everything works fine, and it pulls titles out of my trial document.
> Any help would be greatly appreciated,
> -John
> --------------------------------------------------------------------------------

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