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From "Miller, Timothy" <Timothy.Mil...@childrens.harvard.edu>
Subject RE: Problems with ExampleAggregatePipeline
Date Sun, 17 May 2015 17:40:53 GMT
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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