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From Damir Olejar <olejar.da...@gmail.com>
Subject Re: Problems with ExampleAggregatePipeline
Date Fri, 22 May 2015 20:44:08 GMT
Tim, I would like to ask which patch you are referring to, since I have
partially solved it by doing the following (in Eclipse) ?

1. Import as Maven, by svn, the:
https://svn.apache.org/repos/asf/ctakes/branches/ctakes-3.2.2/

2. (exit eclipse) download and merge with the workspace the -src:
https://dist.apache.org/repos/dist/dev/ctakes/ctakes-3.2.2-rc2/

3. (load eclipse again) Do everything that needs to be done as described
here:
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+Developer+Install+Guide

4. Run the UIMA_CVD--clinical_documents_pipeline.launch with the configured
run settings with the UMLS username and a password


5. The gui will work, but the ExampleAggregatePipeline will not (error with
IdentifiedAnnotation)

6. Comment-out the code in ExampleAggregatePipeline with an error, then run
as a Java application (having the username and password configured for the
run).

7. Comment-in the code, and run the application again

-it worked all until this point

8. change ClinicalPipelineFactory.getTokenProcessingPipeline() to
ClinicalPipelineFactory.getDefaultPipeline()... and... Same error appears
!?!?!?

Thanks.

Damir



On Thu, May 21, 2015 at 11:25 AM, Miller, Timothy <
Timothy.Miller@childrens.harvard.edu> wrote:

> If you are running -src you can modify the source with the patch
> discussed on the list and recompile (the change will be in the
> dictionary sub-modules).
>
> If you are running -bin you can drop in updated jars from the lib/
> directory of the -bin release candidate:
> https://dist.apache.org/repos/dist/dev/ctakes/ctakes-3.2.2-rc2/
>
> Tim
>
> On 05/21/2015 11:15 AM, Damir Olejar wrote:
> > 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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