You are viewing a plain text version of this content. The canonical link for it is here.
Posted to dev@ctakes.apache.org by "Pei Chen (JIRA)" <ji...@apache.org> on 2012/08/22 23:10:42 UTC
[jira] [Created] (CTAKES-43) Spaces in directory names STILL cause
problems for UIMA
Pei Chen created CTAKES-43:
------------------------------
Summary: 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
Reporter: Pei Chen
Assignee: Pei Chen
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
--------------------------------------------------------------------------------
--
This message is automatically generated by JIRA.
If you think it was sent incorrectly, please contact your JIRA administrators: https://issues.apache.org/jira/secure/ContactAdministrators!default.jspa
For more information on JIRA, see: http://www.atlassian.com/software/jira
[jira] [Resolved] (CTAKES-43) Spaces in directory names STILL cause
problems for UIMA
Posted by "Pei Chen (JIRA)" <ji...@apache.org>.
[ https://issues.apache.org/jira/browse/CTAKES-43?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]
Pei Chen resolved CTAKES-43.
----------------------------
Resolution: Fixed
All projects names has been replaced with dashes (-) and all lowered cased.
> 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
> --------------------------------------------------------------------------------
--
This message is automatically generated by JIRA.
If you think it was sent incorrectly, please contact your JIRA administrators
For more information on JIRA, see: http://www.atlassian.com/software/jira
[jira] [Updated] (CTAKES-43) Spaces in directory names STILL cause
problems for UIMA
Posted by "Pei Chen (JIRA)" <ji...@apache.org>.
[ 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
> --------------------------------------------------------------------------------
--
This message is automatically generated by JIRA.
If you think it was sent incorrectly, please contact your JIRA administrators
For more information on JIRA, see: http://www.atlassian.com/software/jira
[jira] [Updated] (CTAKES-43) Spaces in directory names STILL cause
problems for UIMA
Posted by "Pei Chen (JIRA)" <ji...@apache.org>.
[ https://issues.apache.org/jira/browse/CTAKES-43?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]
Pei Chen updated CTAKES-43:
---------------------------
Fix Version/s: 3.0-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
> --------------------------------------------------------------------------------
--
This message is automatically generated by JIRA.
If you think it was sent incorrectly, please contact your JIRA administrators
For more information on JIRA, see: http://www.atlassian.com/software/jira