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From Damir Olejar <olejar.da...@gmail.com>
Subject Re: Problems with ExampleAggregatePipeline
Date Fri, 22 May 2015 22:02:35 GMT
Tim (and others interested), I have done a dirty-fix which is to
hard-code/override the variables, username and password under the
class: UmlsDictionaryLookupAnnotator
method: isValidUMLSUser( String umlsaddr, String vendor, String username,
String password )

This means that server and everything else is fine, except that for some
reason the password is passed as a "null"  (prior to hard-coding) and that
is what is causing the error to appear (somewhere the values are being
lost).  I will let you know if I get enough time to debug it, where the
error is exactly located.

Damir Olejar

On Fri, May 22, 2015 at 4:44 PM, Damir Olejar <olejar.damir@gmail.com>
wrote:

>
> 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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