Excellent! Thanks -----Original Message----- From: Dligach, Dmitriy [mailto:ddlig...@luc.edu] Sent: Friday, April 14, 2017 11:11 AM To: dev@ctakes.apache.org Subject: Re: dictionary lookup error
Sean, thank you very much for your help. I just wanted to inform everybody that after I did an ‘svn up’ this morning, dictionary lookup started to work without doing the additional steps Sean describes below. Dima > On Apr 11, 2017, at 11:50, Finan, Sean <sean.fi...@childrens.harvard.edu> > wrote: > > Hi Dima, > > Great question. This is part of the change for v.4.0 > > You will need to pick up the new dictionary (sno_rx_16ab.zip) from > sourceforge: > https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_ctakesresources_files_&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=KmGEki1TU4BZLjRQjWCDwkDqhnTRLKVS3khDyoY-oDg&s=ZFumv_GSAUDMgrBdJQRHcgBV6WuUqOlErCxewLGAE6E&e= > > and unzip it in your resources/ directory. > > Sno_rx_16ab is a new database in hsqldb 2.3.4 format containing the standard > ctakes tuis, cuis, snomedct and rxnorm from the umls 2016ab release. > > The ctakes.apache.org website will have an updated dictionary-fast link when > we are ready to release 4.0. > The pom in trunk will be switched to automatically grab that resource when > you compile as soon as it is published from sourceforge (i.e. maven can find > it). > > I apologize for not sending out this information earlier. A few items have > fallen through the cracks wrt the 4.0 rc, trunk 4.0.1 updates, sourceforge > publication, etc. > > There are running edits on the instructions for future releases ... I hope > that we capture everything. > > Sean > > -----Original Message----- > From: Dligach, Dmitriy [mailto:ddlig...@luc.edu] > Sent: Tuesday, April 11, 2017 12:36 PM > To: cTAKES Developer list > Subject: dictionary lookup error > > Hello, > > > > After a recent ‘svn up’, a simple pipeline involving dictionary lookup > started to fail. It fails to locate a file: > org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml. > > > > The pipeline is here: > > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_dmitriydligach_ctakes-2Dmisc_blob_master_src_main_java_org_apache_ctakes_pipelines_BasicAnnotations.java&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=UlWU5Cj26g3v3pPKCjO8HMaLfwabkSR_pSDvc7er58A&s=DJO0GqRKzDgpx_rGUTN6yTFJX5xeB7B4oAiJoNRfNno&e= > > > > > Any thoughts on what might be going wrong? > > > > Thank you in advance. > > > > Here’s the full error message: > > > > Exception in thread "main" > org.apache.uima.resource.ResourceInitializationException: Initialization of > annotator class > "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed. > (Descriptor: <unknown>) > > at > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:271) > > at > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:170) > > 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:279) > > at > org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:407) > > at > org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:256) > > at > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:429) > > at > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:373) > > at > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:186) > > at > org.apache.uima.fit.factory.AnalysisEngineFactory.createEngine(AnalysisEngineFactory.java:711) > > at > org.apache.uima.fit.factory.AggregateBuilder.createAggregate(AggregateBuilder.java:207) > > at > org.apache.ctakes.pipelines.BasicAnnotations.main(BasicAnnotations.java:67) > > Caused by: org.apache.uima.resource.ResourceInitializationException > > at > org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:131) > > at > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:266) > > ... 12 more > > Caused by: java.io.FileNotFoundException: > org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml (No such file or > directory) > > at java.io.FileInputStream.open0(Native Method) > > at java.io.FileInputStream.open(FileInputStream.java:195) > > at java.io.FileInputStream.<init>(FileInputStream.java:138) > > at > org.apache.ctakes.core.resource.FileLocator.getAsStream(FileLocator.java:61) > > at > org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:128) > > ... 13 more > > > > > > Dima > > > > > > >
