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 < [email protected]> 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 [[email protected]] > Sent: Sunday, May 17, 2015 9:19 AM > To: [email protected] > 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 ??? >
