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 < > [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 ??? >>
