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 <[email protected]> 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 < > [email protected]> 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 < >> > [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 ??? >> >> >> >> >
