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From Damir Olejar <olejar.da...@gmail.com>
Subject Re: Problems with ExampleAggregatePipeline
Date Thu, 21 May 2015 15:14:31 GMT
Tim,
When can I expect the release to be available for a download?
In the meantime, would it be possible to do the NER with medical documents,
without the UIMA license, and to do it offline ?
Thank you.

Damir

On Sun, May 17, 2015 at 1:40 PM, Miller, Timothy <
Timothy.Miller@childrens.harvard.edu> wrote:

> The problem is probably related to the NLM recently changing the response
> their server gives to the license check. We have checked in a fix to trunk
> and there is a new release candidate being tested right now that should
> hopefully be released soon.
> Tim
>
> ________________________________________
> From: Damir Olejar [olejar.damir@gmail.com]
> Sent: Sunday, May 17, 2015 9:19 AM
> To: dev@ctakes.apache.org
> Subject: Problems with ExampleAggregatePipeline
>
> Hi, I am also new to cTakes and I would appretiate any help, since I want
> to begin using it programatically.
>
> I am trying to run the ExampleAggregatePipeline.
>
> Everything works fine with the line:
> builder.add(ClinicalPipelineFactory.getTokenProcessingPipeline());
>
>
> However, it fails when I change it to:
> builder.add(ClinicalPipelineFactory.getDefaultPipeline());
>
>
>
> 1. There is no "Failed to initilize. Invalid UMLS License” error (or at
> least, it is not visible)
> 2. ctakes.umlsuser and takes.umlspw are set in
> DictionaryLookupAnnotatorUMLS.xml
> 3. I am not using proxy and I am not behind a firewall
> 4. .../lookup/umls2011ab/umls does contain a data file
> 5. I am running the VM with the args: -Dctakes.umlsuser=MYUsername
> -Dctatkes.umlspw=ThePASSWORD
> 6. I can login to a
> https://urldefense.proofpoint.com/v2/url?u=https-3A__uts-2Dws.nlm.nih.gov_home.html&d=BQIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=AC19NW1kOknY5moWcOYwu7ieuHbMcB6prLhlziC2c-Y&s=68mMenrmbkyrDBboZoYsl8j7zvkJ3PbbFBpzopmkmQQ&e=
>
> The error I get is similar to:
>
> https://urldefense.proofpoint.com/v2/url?u=http-3A__t232398.apache-2Dctakes-2Ddevelopment.apachetalk.us_question-2Dabout-2Dcpe-2Ddescriptor-2Dand-2Dxml-2Dfile-2Dt232398.html&d=BQIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=AC19NW1kOknY5moWcOYwu7ieuHbMcB6prLhlziC2c-Y&s=LzwbORLndVm4vf6SJa3G4ekg-o3xkhYw9LNHui9pLcg&e=
>
>
>
> That is:
> Loading configuration.
> Loading feature templates.
> Loading lexica.
> Loading model:
>
> ........................................................................................
> 17 May 2015 08:11:15  INFO Chunker - Chunker model file:
> org/apache/ctakes/chunker/models/chunker-model.zip
> 17 May 2015 08:11:19  INFO JdbcConnectionResourceImpl - Connection
> established to:
> jdbc:hsqldb:res:/org/apache/ctakes/dictionary/lookup/umls2011ab/umls
> 17 May 2015 08:11:19  INFO JdbcConnectionResourceImpl - Connection
> established to:
> jdbc:hsqldb:res:/org/apache/ctakes/dictionary/lookup/rxnorm-hsqldb/umls
> 17 May 2015 08:11:19  INFO JdbcConnectionResourceImpl - Connection
> established to:
>
> jdbc:hsqldb:res:/org/apache/ctakes/dictionary/lookup/orange_book_hsqldb/umls
> 17 May 2015 08:11:19  INFO UmlsDictionaryLookupAnnotator - Parsing
> descriptor:
>
> /Users/damir/Documents/workspace/ctakes/ctakes-dictionary-lookup-res/target/classes/org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml
> 17 May 2015 08:11:19  INFO FirstTokenPermLookupInitializerImpl - Exclusion
> tagset loaded: [pp, pdt, prp$, vbn, vbp, wdt, ls, vbz, dt, pos, md, wp, cc,
> cd, in, pp$, wrb, vb, prp, ex, vbd, vbg, to, wps, rp]
> 17 May 2015 08:11:19  INFO FirstTokenPermLookupInitializerImpl - Exclusion
> tagset loaded: [cc, pp, cd, pdt, vbn, vbp, in, pp$, wdt, wrb, ls, vb, vbz,
> dt, ex, pos, md, vbd, wp, vbg, to, wps, rp]
> 17 May 2015 08:11:19  INFO UmlsDictionaryLookupAnnotator - Using
> ctakes.umlsaddr:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__uts-2Dws.nlm.nih.gov_restful_isValidUMLSUser-3A&d=BQIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=AC19NW1kOknY5moWcOYwu7ieuHbMcB6prLhlziC2c-Y&s=3N2BtvxOSjD9gfR3UvbeI-9A_S76P9syFP07E3JSm48&e=
> null
> Exception in thread "main"
> org.apache.uima.resource.ResourceInitializationException: Initialization of
> annotator class
> "org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator"
> failed.  (Descriptor: <unknown>)
>     at
>
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
>     at
>
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
>     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.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.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.fit.factory.AnalysisEngineFactory.createEngine(AnalysisEngineFactory.java:205)
>     at
>
> org.apache.uima.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:226)
>     at
>
> org.apache.uima.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:259)
>     at
>
> org.apache.ctakes.examples.pipelines.ExampleAggregatePipeline.main(ExampleAggregatePipeline.java:41)
> Caused by: org.apache.uima.resource.ResourceInitializationException
>     at
>
> org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.initialize(UmlsDictionaryLookupAnnotator.java:83)
>     at
>
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
>     ... 34 more
> Caused by: java.lang.NullPointerException
>     at java.net.URLEncoder.encode(URLEncoder.java:204)
>     at
>
> org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.isValidUMLSUser(UmlsDictionaryLookupAnnotator.java:92)
>     at
>
> org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator.initialize(UmlsDictionaryLookupAnnotator.java:74)
>     ... 35 more
>
> …..
>
> What am I doing wrong ???
>

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