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From Lance Eason <la...@iodinesoftware.com>
Subject Re: cTAKES CPE Error: URI is not hierarchical
Date Wed, 08 Apr 2015 16:47:16 GMT
Saeed,

The install instructions for Mac tell you to merge in the resources using:

ditto /tmp/resources/* /usr/local/apache-ctakes-3.2.1/resources

This places the files at the wrong location and leads to the error above.
I ended up copying the resources into the appropriate location by hand.

- Lance

On Wed, Apr 8, 2015 at 11:24 AM, Saeed Hassanpour <saeedhp@stanford.edu>
wrote:

> Hi,
>
> I am running ctakes 3.2.1 on my mac and I went through user install
> guide step by step
> (
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2+User+Install+Guide
> ).
> I successfully ran ctakesCVD with UMLS and
> AggregatePlaintextFastUMLSProcessor.xml. However, when I tested
> bin/runctakesCPE.sh with test1.xml as it is described in the tutorial,
> I am getting the following error in the terminal:
>
> org.apache.uima.resource.ResourceInitializationException:
> Initialization of CAS Processor with name "AggregateCdaProcessor"
> 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 "AggregateCdaProcessor"
> 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: java.lang.IllegalArgumentException: URI is not hierarchical
> at java.io.File.<init>(File.java:418)
> at
> org.apache.ctakes.core.resource.FileResourceImpl.load(FileResourceImpl.java:44)
> at
> org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:603)
> at
> org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442)
> at
> org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153)
> at
> org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.java:157)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:123)
> 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
>
> Could you please help me to resolve this error?
>
> Best,
> Saeed
>



-- 
.........................................................
*Lance Eason*
Iodine Software
Vice President of Engineering
lance@iodinesoftware.com
512.785.5195 office | 801.203.8987 fax
.........................................................

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