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
