Thanks Bruce for the help. I think I’m experiencing something similar. Even though I’m using <scope>provided</scope>, the cTAKES jars are ending up in my jar. I think I need to start over and maybe not use Maven and/or Spring Boot. Nothing I’m trying is keeping the cTAKES jars out of my jar’s lib folder.
> On Jun 29, 2015, at 10:17 AM, Bruce Tietjen > <[email protected]> wrote: > > If you can run your process in a debugger like eclipse, then you can suspend > execution during that 12 minutes and check the stack to see what is > happening. > > When I experienced similar behavior, the Dictionary Lookup was reading the > database files from a .JAR file that was in my .m2 (maven) repository. The > easiest way I found to avoid this happening was to delete or rename the file > from my .m2 directory. This is very annoying because rebuilding will > re-download the files and I have to do it again. (If there is a better way, I > would love to hear about it.) > > > > > <http://imatsolutions.com/> Bruce Tietjen > Senior Software Engineer > 801.634.1547 > [email protected] <mailto:[email protected]> > > On Sat, Jun 27, 2015 at 9:08 PM, Jeff Headley <[email protected] > <mailto:[email protected]>> wrote: > I was able to get by the error by modifying my installation's > DictionaryLookupAnnotatorUMLS.xml file. I changed: > <fileUrl>file:org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml</fileUrl> > > to > <fileUrl>file:resources/org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml</fileUrl> > > and that seemed to work. > > I saw only a slight performance improvement however. Would anyone be able to > tell me what is going on between these two log statements that takes about 12 > minutes? > > 2015-06-27 22:45:02.374 INFO 8972 --- [ main] > .a.c.d.l.a.UmlsDictionaryLookupAnnotator : process(JCas) > 2015-06-27 22:57:39.385 INFO 8972 --- [ main] > o.a.c.c.parser.MaxentParserWrapper : Started processing: null > > On Sat, Jun 27, 2015 at 12:45 PM, Jeff Headley <[email protected] > <mailto:[email protected]>> wrote: > I have changed my cTAKES dependencies in my pom back to > <scope>provided</scope> and I think I have the classpath set correctly as it > seems to start out ok but eventually gets this new error. I'm hoping maybe > someone has seen this before and can help me out. I believe my cTAKES is > installed correctly. I followed the guide and can use the CVD. The analysis > engine I'm attempting to load is > desc/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml. > > 2015-06-27 12:36:07.425 DEBUG 10332 --- [ main] > o.a.ctakes.core.ae.OverlapAnnotator : Overlap bitset: {3} > 2015-06-27 12:36:07.453 INFO 10332 --- [ main] > o.a.c.d.p.ae.ClearNLPDependencyParserAE : using Morphy analysis? true > Loading configuration. > Loading feature templates. > Loading lexica. > Loading model: > ........................................................................................ > 2015-06-27 12:36:16.930 INFO 10332 --- [ main] > org.apache.ctakes.chunker.ae.Chunker : Chunker model file: > org/apache/ctakes/chunker/models/chunker-model.zip > 2015-06-27 12:36:17.952 INFO 10332 --- [ main] > c.c.a.ContextDependentTokenizerAnnotator : Finite state machines loaded. > 2015-06-27 12:36:17.959 INFO 10332 --- [ main] > o.a.c.c.parser.ae.ConstituencyParser : Initializing parser... > 2015-06-27 12:36:20.616 INFO 10332 --- [ main] > o.a.ctakes.necontexts.ContextAnnotator : SCOPE ORDER: [1, 3] > 2015-06-27 12:36:20.619 INFO 10332 --- [ main] > o.a.c.n.n.NegationContextAnalyzer : initBoundaryData() called for > ContextInitializer > 2015-06-27 12:36:20.758 INFO 10332 --- [ main] > org.apache.ctakes.postagger.POSTagger : POS tagger model file: > org/apache/ctakes/postagger/models/mayo-pos.zip > 2015-06-27 12:36:21.061 ERROR 10332 --- [ main] > c.e.c.processors.CommandLineProcessor : ResourceInitializationException: > > org.apache.uima.resource.ResourceInitializationException: Error initializing > "org.apache.uima.resource.impl.DataResource_impl" from descriptor > file:/D:/java/apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml. > at > org.apache.uima.util.SimpleResourceFactory.produceResource(SimpleResourceFactory.java:144) > 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:243) > at > org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:565) > at > org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442) > at > org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153) > at > org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.java:157) > at > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:123) > 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 > . > . > . > Caused by: org.apache.uima.resource.ResourceInitializationException: Could > not access the resource data at > file:org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml. > at > org.apache.uima.resource.impl.DataResource_impl.initialize(DataResource_impl.java:127) > at > org.apache.uima.util.SimpleResourceFactory.produceResource(SimpleResourceFactory.java:123) > ... 35 common frames omitted > > On Fri, Jun 26, 2015 at 9:46 AM, Bruce Tietjen > <[email protected] > <mailto:[email protected]>> wrote: > I'm sorry I don't have any current numbers for running that pipeline because > we need more than just entity recognition. We also need polarity, certainty, > etc. > > We have done a lot of optimization work in the more expensive parts of the > pipeline and have made modifications to some areas to make them thread safe > to enable running multiple pipelines concurrently within the same process. We > have also made changes so most of the models that are loaded can be shared > across multiple pipelines. > > We have not had time and resources to share these changes with the community > yet, but intend to make our changes available to the community as soon as we > feel they are ready. > > > <http://imatsolutions.com/> Bruce Tietjen > Senior Software Engineer > 801.634.1547 <tel:801.634.1547> > [email protected] <mailto:[email protected]> > > On Thu, Jun 25, 2015 at 11:43 PM, Sai Anuroop <[email protected] > <mailto:[email protected]>> wrote: > Hi All, > I am presently working with developer version of cTAKES in Windows through > eclipse. > @Jeff:Thanks for your reply. > @Lance:I am new to cTAKES and Java.So please Can you give me the code which > runs cTAKES CPE in background without opening the CUI and produces XML > output.If the code given does the same then can you please tell where to > create above java class(in which project). > @Bruce:Thanks for your posts.Can you tell What is the average and best time > of cTAKES analyzing say a 20 line discharge report using > AggregatePlaintextFastUMLSProcessor. > > Regards, > Vetsa Sai Anuroop > > > > >
