Hello Pei, It didn't work for me. If it works for you, please let me know.
Thank you, Harpreet On Wed, Jun 18, 2014 at 8:02 PM, Pei Chen <chen...@apache.org> wrote: > Harpreet, > looks like resources just made it to the maven central mirrors. But I > didn't not get a chance to try it out or fully test it yet. > If you would like to give it a whirl, you can update > ctakes-dictionary-lookup-res/pom.xml to use the latest. > If EclipseIDE doesn't unpack the resources automatically to target/classes, > you can force it to run mvn clean compile. > > <!-- cTAKES Resources --> > > <dependency> > > <groupId>net.sourceforge.ctakesresources</groupId> > > <artifactId>ctakes-resources-umls2011ab</artifactId> > > <version>3.1.3</version> > > </dependency> > > <dependency> > > <groupId>net.sourceforge.ctakesresources</groupId> > > <artifactId>ctakes-resources-rxnorm-hsqldb-2011ab</artifactId> > > <version>3.1.3</version> > > </dependency> > > <dependency> > > <groupId>net.sourceforge.ctakesresources</groupId> > > <artifactId>ctakes-resources-orangebook-hsqldb</artifactId> > > <version>3.1.3</version> > > </dependency> > > > On Wed, Jun 18, 2014 at 6:58 PM, Harpreet Khanduja <hsk5...@rit.edu> > wrote: > > > Hello Pei, > > Are you able to use trunk now? > > > > Thank you, > > Harpreet > > > > > > On Wed, Jun 18, 2014 at 12:47 PM, Harpreet Khanduja <hsk5...@g.rit.edu> > > wrote: > > > > > Hello Pei, > > > > > > Thank you so much for helping. > > > > > > > > > Harpreet > > > > > > > > > On Wed, Jun 18, 2014 at 11:08 AM, Pei Chen <chen...@apache.org> wrote: > > > > > >> Harpreet, > > >> I just did a fresh checkout of trunk and could recreate the error. I > > >> think > > >> I see the issue- the orangebook hsqldb resource is empty on maven > > central. > > >> I'm hoping to fix that up today. > > >> > > >> --Pei > > >> > > >> > > >> On Tue, Jun 17, 2014 at 6:22 PM, Harpreet Khanduja <hsk5...@rit.edu> > > >> wrote: > > >> > > >> > Hello Pei, > > >> > > > >> > I also ran from cmd line same exception > > >> > and I checked pom.xml file on this location. > > >> > https://svn.apache.org/repos/asf/ctakes/trunk > > >> > The version mentioned in the file is 3.1.1. > > >> > . > > >> > > > >> > Could you please tell me about the resources directory problem > which I > > >> > mentioned in the last email? > > >> > > > >> > Thank you so much for your time. > > >> > > > >> > Harpreet > > >> > > > >> > > > >> > > > >> > > > >> > On Tue, Jun 17, 2014 at 5:45 PM, Chen, Pei < > > >> pei.c...@childrens.harvard.edu > > >> > > > > >> > wrote: > > >> > > > >> > > If this is trunk, Can you do an 'svn update' to ensure you have > the > > >> > latest? > > >> > > If this is trunk you won't need to do a separate download- maven > > >> should > > >> > > download and unpack it automatically for you. > > >> > > Also try the command line alternative: > > >> > > 'mvn -PrunCVD compile' from the root dir. Let me know. > > >> > > > > >> > > > > >> > > Sent from my iPhone > > >> > > > > >> > > > On Jun 17, 2014, at 5:37 PM, "Harpreet Khanduja" < > hsk5...@rit.edu > > > > > >> > > wrote: > > >> > > > > > >> > > > Pei, > > >> > > > > > >> > > > Thank you for the quick reply. > > >> > > > I am using CVD GUI within eclipse which is under > > >> > > >> ctakes-clinical-pipeline project.. > > >> > > >> resources > > >> > > >> launch > > >> > > > UIMA_CVD---clinical_documents_pipeline.launch. > > >> > > > > > >> > > > I am using ctakes 3.1.1 and resouces also 3.1 > > >> > > > > > >> > > > I used this link for svn : > > >> > https://svn.apache.org/repos/asf/ctakes/trunk > > >> > > > when I downloaded ctakes using Eclipse. > > >> > > > > > >> > > > isn't this svn for ctakes 3.1.1? > > >> > > > > > >> > > > Thank you, > > >> > > > > > >> > > > Harpreet > > >> > > > > > >> > > > > > >> > > >> On Tue, Jun 17, 2014 at 5:29 PM, Pei Chen <chen...@apache.org> > > >> wrote: > > >> > > >> > > >> > > >> Harpreet, > > >> > > >> Are you using the CVD GUI? or within Eclipse IDE? > > >> > > >> Also which version cTAKES are you using? trunk? > > >> > > >> --Pei > > >> > > >> > > >> > > >> > > >> > > >> On Tue, Jun 17, 2014 at 5:13 PM, Harpreet Khanduja < > > >> hsk5...@rit.edu> > > >> > > >> wrote: > > >> > > >> > > >> > > >>> Hello Pei, > > >> > > >>> I would really appreciate if you could help me again. > > >> > > >>> After talking to you and reading other email archives. I have > > >> done > > >> > > >> almost > > >> > > >>> everything I could, but I am not able to use > > >> > > >>> AggregatePlainTextUMLSProcessor.xml using > > >> > > >>> UIMA_CVD----clinical-pipeline.launch. > > >> > > >>> > > >> > > >>> Just to be sure. > > >> > > >>> The resources folder that from < > > >> > > >> > > >> > > > > >> > > > >> > > > http://sourceforge.net/projects/ctakesresources/files/ctakes-resources-3.1.0.zip/download > > >> > > >>> url > > >> > > >>> is used to replace the resources folder which is already > inside > > >> > > >>> ctakes/ctakes-dictionary-lookup/ -- directory or > > >> > > >>> ctakes/ctakes-dictionary-lookup-res/source/main/ -- > > >> > directory. > > >> > > >>> > > >> > > >>> And then which directory is used as a classpath to > > >> > > >>> ctakes-clinical-pipeline project. > > >> > > >>> > > >> > > >>> I still get the same exception that I was getting earlier. I > > >> looked > > >> > > into > > >> > > >>> the exception deeply and I found that the exception is thrown > > >> > > >>> while creating a connection object ( iv_conn ) in > > >> > > >>> JdbcConnectionResourceImpl.java ( line 109 or 110 ) which is > > >> inside > > >> > > >>> ctakes- core/ > > >> > > >>>> src/main/java > > >> > > >>>> org.apache.ctakes.core.resource > > >> > > >>> package. > > >> > > >>> > > >> > > >>> Thank you very much. > > >> > > >>> Harpreet > > >> > > >>> > > >> > > >>> > > >> > > >>> On Wed, Jun 11, 2014 at 4:33 PM, Chen, Pei < > > >> > > >> pei.c...@childrens.harvard.edu > > >> > > >>> wrote: > > >> > > >>> > > >> > > >>>> Harpreet, > > >> > > >>>> Just curious- is maven able to connect to the internet (maven > > >> > central > > >> > > >>>> repositories)? i.e. did you have to set your > ~/.m2/settings.xml > > >> with > > >> > > >>> proxy > > >> > > >>>> info if behind a firewall? > > >> > > >>>> If it was an intermittent issue, you can try clearing out the > > >> local > > >> > > >>>> ~/.m2/repository? > > >> > > >>>> --Pei > > >> > > >>>> > > >> > > >>>>> -----Original Message----- > > >> > > >>>>> From: Harpreet Khanduja [mailto:hsk5...@rit.edu] > > >> > > >>>>> Sent: Wednesday, June 11, 2014 3:54 PM > > >> > > >>>>> To: dev@ctakes.apache.org > > >> > > >>>>> Subject: Re: query > > >> > > >>>>> > > >> > > >>>>> Pei, > > >> > > >>>>> I had provided the classpath = > > >> ctakes-dictionay-look-up/resources > > >> > > >> to > > >> > > >>>> all the > > >> > > >>>>> projects in ctakes. > > >> > > >>>>> as it says in the documentation but there was nothing > inside > > >> my > > >> > > >>> target > > >> > > >>>>> folder in ctakes-clinical-pipeline directory. > > >> > > >>>>> So, then I ran maven compile and I got following error. > > >> > > >>>>> > > >> > > >>>>> > > >> > > >>>>> [ERROR] Failed to execute goal on project > > >> ctakes-clinical-pipeline: > > >> > > >>>> Could not > > >> > > >>>>> resolve dependencies for project > > >> > > >>>>> > org.apache.ctakes:ctakes-clinical-pipeline:jar:3.1.2-SNAPSHOT: > > >> > Failed > > >> > > >>> to > > >> > > >>>>> collect dependencies for > > >> > > >>> [org.apache.ctakes:ctakes-type-system:jar:3.1.2- > > >> > > >>>>> SNAPSHOT (compile), > > >> > org.apache.ctakes:ctakes-core:jar:3.1.2-SNAPSHOT > > >> > > >>>>> (compile), org.apache.ctakes:ctakes-utils:jar:3.1.2-SNAPSHOT > > >> > > >> (compile), > > >> > > >>>>> jdom:jdom:jar:1.0 (compile), junit:junit:jar:4.10 (test), > > >> > > >>>>> > org.apache.ctakes:ctakes-context-tokenizer:jar:3.1.2-SNAPSHOT > > >> > > >>> (compile), > > >> > > >>>>> > org.apache.ctakes:ctakes-dictionary-lookup:jar:3.1.2-SNAPSHOT > > >> > > >>> (compile), > > >> > > >>>>> org.apache.ctakes:ctakes-preprocessor:jar:3.1.2-SNAPSHOT > > >> (compile), > > >> > > >>>>> org.apache.ctakes:ctakes-lvg:jar:3.1.2-SNAPSHOT (compile), > > >> > > >>>>> org.apache.ctakes:ctakes-chunker:jar:3.1.2-SNAPSHOT > (compile), > > >> > > >>>>> org.apache.ctakes:ctakes-ne-contexts:jar:3.1.2-SNAPSHOT > > >> (compile), > > >> > > >>>>> org.apache.ctakes:ctakes-pos-tagger:jar:3.1.2-SNAPSHOT > > >> (compile), > > >> > > >>>>> org.apache.ctakes:ctakes-assertion:jar:3.1.2-SNAPSHOT > > (compile), > > >> > > >>>>> > org.apache.ctakes:ctakes-dependency-parser:jar:3.1.2-SNAPSHOT > > >> > > >>> (compile), > > >> > > >>>>> > > >> org.apache.ctakes:ctakes-dependency-parser-res:jar:3.1.2-SNAPSHOT > > >> > > >>>>> (compile), org.apache.ctakes:ctakes-ytex:jar:3.1.2-SNAPSHOT > > >> > > >> (compile), > > >> > > >>>>> org.apache.ctakes:ctakes-ytex-res:jar:3.1.2-SNAPSHOT > > (compile), > > >> > > >>>>> org.apache.ctakes:ctakes-ytex-uima:jar:3.1.2-SNAPSHOT > > >> (compile)]: > > >> > > >>> Failed > > >> > > >>>>> to read artifact descriptor for > > >> > > >>>>> org.apache.ctakes:ctakes-type-system:jar:3.1.2-SNAPSHOT: > > >> Failure to > > >> > > >>> find > > >> > > >>>>> org.apache.ctakes:ctakes:pom:3.1.2-SNAPSHOT in > > >> > > >>>>> http://repository.apache.org/snapshots was cached in the > > local > > >> > > >>>> repository, > > >> > > >>>>> resolution will not be reattempted until the update interval > > of > > >> > > >>>>> apache.snapshots has elapsed or updates are forced -> [Help > 1] > > >> > > >> [ERROR] > > >> > > >>>>> > > >> > > >>>>> > > >> > > >>>>> > > >> > > >>>>> On Wed, Jun 11, 2014 at 2:17 PM, Chen, Pei > > >> > > >>>>> <pei.c...@childrens.harvard.edu> > > >> > > >>>>> wrote: > > >> > > >>>>> > > >> > > >>>>>> Harpreet, > > >> > > >>>>>> I had a closer look at your log file and it looks like you > > were > > >> > > >>>>>> actually trying to run it from Eclipse IDE? > > >> > > >>>>>> If so, just ensure that the resources do exist in the > > >> classpath. > > >> > > >>>>>> If it's within eclipse ide, the plugin should download and > > >> unpack > > >> > > >> the > > >> > > >>>>>> umls dictionaries automatically actually. (you can check > the > > >> below > > >> > > >> to > > >> > > >>>>>> ensure it exists > > >> > > >>>>>> > > target/classes/org/apache/ctakes/dictionary/lookup/umls2011ab/) > > >> > > >>>>>> You can also try running 'mvn clean compile' from the > command > > >> line > > >> > > >> as > > >> > > >>>>> well. > > >> > > >>>>>> > > >> > > >>>>>> > > >> > > >>>>>> > > >> > > >>>>>>> -----Original Message----- > > >> > > >>>>>>> From: Harpreet Khanduja [mailto:hsk5...@rit.edu] > > >> > > >>>>>>> Sent: Wednesday, June 11, 2014 2:09 PM > > >> > > >>>>>>> To: dev@ctakes.apache.org > > >> > > >>>>>>> Subject: Re: query > > >> > > >>>>>>> > > >> > > >>>>>>> Hello, > > >> > > >>>>>>> Thanks for the reply, but I have already done that and I > > >> made > > >> > > >>>>>>> sure > > >> > > >>>>>> that > > >> > > >>>>>>> these resources are there all over again. > > >> > > >>>>>>> > > >> > > >>>>>>> Harpreet > > >> > > >>>>>>> > > >> > > >>>>>>> > > >> > > >>>>>>> > > >> > > >>>>>>> On Wed, Jun 11, 2014 at 1:49 PM, Pei Chen < > > chen...@apache.org > > >> > > > >> > > >>>>> wrote: > > >> > > >>>>>>> > > >> > > >>>>>>>> Harpreet, > > >> > > >>>>>>>> Ensure that you have downloaded the dictionaries (umls) > per > > >> > > >>>>>>>> download > > >> > > >>>>>>> page: > > >> > > >>>>>>>> http://ctakes.apache.org/downloads.cgi > > >> > > >>>>>>>> Resources > > >> > > >>>>>>>> > > >> > > >>>>>>>> Resources are required to run most of cTAKES. They are > > >> > > >> available > > >> > > >>>>>>>> for download from SourceForge: > ctakes-resources-3.1.0.zip < > > >> > > >>> > > >> http://sourceforge.net/projects/ctakesresources/files/ctakes-resou > > >> > > >>>>>>>> rces > > >> > > >>>>>>>> -3.1.0.zip/download > > >> > > >>>>>>>> . > > >> > > >>>>>>>> > > >> > > >>>>>>>> Please download, unzip and add/merge the contents to the > > >> > > >> existing > > >> > > >>>>>>>> resources directory. Follow the User > > >> > > >>>>>>>> <https://cwiki.apache.org/confluence/x/oxAHAg> > > >> > > >>>>>>>> or Developer < > https://cwiki.apache.org/confluence/x/nxAHAg > > > > > >> > > >>>>>>>> Install Guide to direct you through the installation > > process. > > >> > > >>>>>>>> > > >> > > >>>>>>>> > > >> > > >>>>>>>> On Wed, Jun 11, 2014 at 1:45 PM, Harpreet Khanduja > > >> > > >>>>>>>> <hsk5...@rit.edu> > > >> > > >>>>>>>> wrote: > > >> > > >>>>>>>> > > >> > > >>>>>>>>> Hello, > > >> > > >>>>>>>>> I am trying to use ctakes as a developer. I am not able > > to > > >> > > >>> use > > >> > > >>>>>>>>> UMLS resources when I run > > >> > > >>>>>>>>> the AEs which use UMLS Dictionary. > > >> > > >>>>>>>>> I have signed up on the UMLS website and I am using the > > >> > > >>>>>>>>> correct email > > >> > > >>>>>>>> and > > >> > > >>>>>>>>> password. > > >> > > >>>>>>>>> I have specified username and password in > > >> > > >>>>>>>>> > > >> > > >>>>>>>>> Dictionary Lookup: > <cTAKES_HOME>/desc/ctakes-dictionary- > > >> > > >>>>> > lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml* > > >> > > >>>>>>>>> > > >> > > >>>>>>>>> > > >> > > >>>>>>>>> But I keep getting the exception. I would really > > appreciate > > >> > > >>>>>>>>> any help on this. > > >> > > >>>>>>>>> > > >> > > >>>>>>>>> OUTPUT THAT I GET on running > > >> > > >>>>> AggregatePlaintextUMLSProcessor.xml : > > >> > > >>>>>>>>> > > >> > > >>>>>>>>> > > >> > > >>>>>>>>> log4j: reset attribute= "false". > > >> > > >>>>>>>>> log4j: Threshold ="null". > > >> > > >>>>>>>>> log4j: Level value for root is [INFO]. > > >> > > >>>>>>>>> log4j: root level set to INFO > > >> > > >>>>>>>>> log4j: Class name: [org.apache.log4j.ConsoleAppender] > > >> > > >>>>>>>>> log4j: Parsing layout of class: > > >> > > >>> "org.apache.log4j.PatternLayout" > > >> > > >>>>>>>>> log4j: Setting property [conversionPattern] to [%d{dd > MMM > > >> > > >> yyyy > > >> > > >>>>>>>>> HH:mm:ss} %5p %c{1} - %m%n]. > > >> > > >>>>>>>>> log4j: Adding appender named [consoleAppender] to > category > > >> > > >>>> [root]. > > >> > > >>>>>>>>> 11 Jun 2014 13:07:01 INFO TokenizerAnnotatorPTB - > > >> > > >> Initializing > > >> > > >>>>>>>>> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB > > >> > > >>>>>>>>> 11 Jun 2014 13:07:01 INFO POSTagger - POS tagger model > > >> file: > > >> > > >>>>>>>>> org/apache/ctakes/postagger/models/mayo-pos.zip > > >> > > >>>>>>>>> 11 Jun 2014 13:07:01 INFO > > >> > > >> ContextDependentTokenizerAnnotator - > > >> > > >>>>>>>>> Finite state machines loaded. > > >> > > >>>>>>>>> 11 Jun 2014 13:07:01 INFO Chunker - Chunker model file: > > >> > > >>>>>>>>> org/apache/ctakes/chunker/models/chunker-model.zip > > >> > > >>>>>>>>> 11 Jun 2014 13:07:03 INFO SentenceDetector - Sentence > > >> > > >> detector > > >> > > >>>>>>>>> model > > >> > > >>>>>>>> file: > > >> > > >>>>>>>>> org/apache/ctakes/core/sentdetect/sd-med-model.zip > > >> > > >>>>>>>>> 11 Jun 2014 13:07:03 INFO LvgCmdApiResourceImpl - > Loading > > >> > > >> NLM > > >> > > >>>>>>>>> Norm and > > >> > > >>>>>>>> Lvg > > >> > > >>>>>>>>> with config file = > > >> > > >>>>>>>> D:\workspaces\workspace_cTakes\ctakes\ctakes-dictionary- > > >> > > >>>>>>> lookup\resourc > > >> > > >>>>>>>> es\org\apache\ctakes\lvg\data\config\lvg.properties > > >> > > >>>>>>>>> 11 Jun 2014 13:07:03 INFO LvgCmdApiResourceImpl - > > config > > >> > > >>> file > > >> > > >>>>>> absolute > > >> > > >>>>>>>>> path = > > >> > > >>>>>>>> D:\workspaces\workspace_cTakes\ctakes\ctakes-dictionary- > > >> > > >>>>>>> lookup\resourc > > >> > > >>>>>>>> es\org\apache\ctakes\lvg\data\config\lvg.properties > > >> > > >>>>>>>>> 11 Jun 2014 13:07:03 INFO LvgCmdApiResourceImpl - cwd = > > >> > > >> D:\workspaces\workspace_cTakes\ctakes\ctakes-clinical-pipeline > > >> > > >>>>>>>>> 11 Jun 2014 13:07:03 INFO LvgCmdApiResourceImpl - cd > > >> > > >>>>>>>> D:\workspaces\workspace_cTakes\ctakes\ctakes-dictionary- > > >> > > >>>>>>> lookup\resourc > > >> > > >>>>>>>> es\org\apache\ctakes\lvg\ > > >> > > >>>>>>>>> 11 Jun 2014 13:07:03 INFO LvgCmdApiResourceImpl - cd > > >> > > >> D:\workspaces\workspace_cTakes\ctakes\ctakes-clinical-pipeline > > >> > > >>>>>>>>> 11 Jun 2014 13:07:04 INFO JdbcConnectionResourceImpl - > > >> > > >>>>>>>>> Connection established to: > > >> > > >>> > jdbc:hsqldb:res:/org/apache/ctakes/dictionary/lookup/umls2011ab/ > > >> > > >>>>>>>>> umls > > >> > > >>>>>>>>> Exception in thread "main" > > >> > > >>>>>>>>> org.apache.uima.resource.ResourceInitializationException > > >> > > >>>>>>>>> at > > >> > > >>> > > >> org.apache.ctakes.core.resource.JdbcConnectionResourceImpl.load(Jdbc > > >> > > >>>>>>> Co > > >> > > >>>>>>>> nnectionResourceImpl.java:130) > > >> > > >>>>>>>>> at > > >> > > >>>>> > > >> > org.apache.uima.resource.impl.ResourceManager_impl.registerResource( > > >> > > >>>>>>> Re > > >> > > >>>>>>>> sourceManager_impl.java:603) > > >> > > >>>>>>>>> at > > >> > > >>> > > org.apache.uima.resource.impl.ResourceManager_impl.initializeExter > > >> > > >>>>>>>> nalR > > >> > > >>>>>>>> esources(ResourceManager_impl.java:442) > > >> > > >>>>>>>>> at > > >> > > >>> > > org.apache.uima.resource.Resource_ImplBase.initialize(Resource_Imp > > >> > > >>>>>>>> lBas > > >> > > >>>>>>>> e.java:153) > > >> > > >>>>>>>>> at > > >> > > >>> > > org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initia > > >> > > >>>>>>>> lize > > >> > > >>>>>>>> (AnalysisEngineImplBase.java:157) > > >> > > >>>>>>>>> at > > >> > > >>> > > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl. > > >> > > >>>>>>>> init > > >> > > >>>>>>>> ialize(PrimitiveAnalysisEngine_impl.java:123) > > >> > > >>>>>>>>> at > > >> > > >>>>> > > >> > org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Anal > > >> > > >>>>>>> ys > > >> > > >>>>>>>> isEngineFactory_impl.java:94) > > >> > > >>>>>>>>> at > > >> > > >>>>> > > >> > org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(C > > >> > > >>>>>>> om > > >> > > >>>>>>>> positeResourceFactory_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. > > >> > > >>>>>>>> init > > >> > > >>>>>>>> ASB(AggregateAnalysisEngine_impl.java:431) > > >> > > >>>>>>>>> at > > >> > > >>> > > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl. > > >> > > >>>>>>>> init > > >> > > >>> > > ializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:37 > > >> > > >>>>>>>> 5) > > >> > > >>>>>>>>> at > > >> > > >>> > > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl. > > >> > > >>>>>>>> init > > >> > > >>>>>>>> ialize(AggregateAnalysisEngine_impl.java:185) > > >> > > >>>>>>>>> at > > >> > > >>>>> > > >> > org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Anal > > >> > > >>>>>>> ys > > >> > > >>>>>>>> isEngineFactory_impl.java:94) > > >> > > >>>>>>>>> at > > >> > > >>>>> > > >> > org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(C > > >> > > >>>>>>> om > > >> > > >>>>>>>> positeResourceFactory_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. > > >> > > >>>>>>>> init > > >> > > >>>>>>>> ASB(AggregateAnalysisEngine_impl.java:431) > > >> > > >>>>>>>>> at > > >> > > >>> > > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl. > > >> > > >>>>>>>> init > > >> > > >>> > > ializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:37 > > >> > > >>>>>>>> 5) > > >> > > >>>>>>>>> at > > >> > > >>> > > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl. > > >> > > >>>>>>>> init > > >> > > >>>>>>>> ialize(AggregateAnalysisEngine_impl.java:185) > > >> > > >>>>>>>>> at > > >> > > >>>>> > > >> > org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Anal > > >> > > >>>>>>> ys > > >> > > >>>>>>>> isEngineFactory_impl.java:94) > > >> > > >>>>>>>>> at > > >> > > >>>>> > > >> > org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(C > > >> > > >>>>>>> om > > >> > > >>>>>>>> positeResourceFactory_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.uimafit.factory.AnalysisEngineFactory.createAggregate(Analysis > > >> > > >>>>>>>> Engi > > >> > > >>>>>>>> neFactory.java:424) > > >> > > >>>>>>>>> at > > >> > > >>> > > org.uimafit.pipeline.SimplePipeline.runPipeline(SimplePipeline.jav > > >> > > >>>>>>>> a:16 > > >> > > >>>>>>>> 5) > > >> > > >>>>>>>>> at > > >> > > >>> > > org.uimafit.pipeline.SimplePipeline.runPipeline(SimplePipeline.jav > > >> > > >>>>>>>> a:19 > > >> > > >>>>>>>> 0) > > >> > > >>>>>>>>> at > > >> > > >>> > > org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory.main(Cl > > >> > > >>>>>>>> inic > > >> > > >>>>>>>> alPipelineFactory.java:116) > > >> > > >>>>>>>>> Caused by: java.sql.SQLException: File input/output > error: > > >> > > >>>>>>>>> java.io.IOException: Stream closed at > > >> > > >>>>>>>>> org.hsqldb.jdbc.Util.sqlException(Unknown Source) at > > >> > > >>>>>>>>> org.hsqldb.jdbc.jdbcConnection.<init>(Unknown Source) at > > >> > > >>>>>>>>> org.hsqldb.jdbcDriver.getConnection(Unknown Source) at > > >> > > >>>>>>>>> org.hsqldb.jdbcDriver.connect(Unknown Source) at > > >> > > >>>>>>>>> java.sql.DriverManager.getConnection(Unknown Source) at > > >> > > >>>>>>>>> java.sql.DriverManager.getConnection(Unknown Source) at > > >> > > >>> > > >> org.apache.ctakes.core.resource.JdbcConnectionResourceImpl.load(Jdbc > > >> > > >>>>>>> Co > > >> > > >>>>>>>> nnectionResourceImpl.java:109) > > >> > > >>>>>>>>> ... 30 more > > >> > > >> > > >> > > > > >> > > > >> > > > > > > > > >
