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 > >> > > >> > >> > > > >> > > >> > > > > >
