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From Lance Eason <la...@iodinesoftware.com>
Subject Re: cTAKES CPE Error: URI is not hierarchical
Date Wed, 08 Apr 2015 17:28:08 GMT
Okay.  The exception message is entirely cryptic and non-specific, but in
general what I've found it means is that one of the HSQL databases
referenced in whichever pipeline file you're using isn't found on the file
system at the named location.  So I'd suggest looking at the pipeline file
(and any files it includes) and validating the various HSQLDB URLs.

For example DictionaryLookupAnnotatorUMLS.xml contains:

<name>URL</name>
<value>

<string>jdbc:hsqldb:res:org/apache/ctakes/dictionary/lookup/umls2011ab/umls</string>
</value>


If that component is in your pipeline and it doesn't find an unpacked HSQL
database (as opposed to finding it in one of the jar files) at <ctakes
home>/resources/org/apache/ctakes/ditctionary/lookup/umls2011ab/umls then
you'll get the "URI is not hierarchical" exception.

On Wed, Apr 8, 2015 at 12:11 PM, Saeed Hassanpour <saeedhp@stanford.edu>
wrote:

> 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
> > .........................................................
> >
>



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

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