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From Saeed Hassanpour <saee...@stanford.edu>
Subject Re: cTAKES CPE Error: URI is not hierarchical
Date Wed, 08 Apr 2015 17:11:03 GMT
Hi Lance,

Thank you for the reply. I noticed the problem with the current
instructions for copying resources. However, I do not think that's the
problem. I used cp -R for copying the resources and as I mentioned
ctakesCVD works fine.

Best,
Saeed

On Wed, Apr 8, 2015 at 10:04 AM, Lance Eason <lance@iodinesoftware.com> wrote:
> The instructions should read:
>
> ditto /tmp/resources /usr/local/apache-ctakes-3.2.1/resources
>
> On Wed, Apr 8, 2015 at 11:47 AM, Lance Eason <lance@iodinesoftware.com>
> wrote:
>>
>> 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
>> .........................................................
>>
>
>
>
> --
> .........................................................
> Lance Eason
> Iodine Software
> Vice President of Engineering
> lance@iodinesoftware.com
> 512.785.5195 office | 801.203.8987 fax
> .........................................................
>

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