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From "Miller, Timothy" <Timothy.Mil...@childrens.harvard.edu>
Subject Re: Problems with ExampleAggregatePipeline
Date Thu, 21 May 2015 15:25:38 GMT
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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