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 ??? > >> > >
