ctakes-user mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From Lance Eason <la...@iodinesoftware.com>
Subject Re: cTAKES CPE Error: URI is not hierarchical
Date Wed, 08 Apr 2015 17:04:24 GMT
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
.........................................................

Mime
View raw message