Hello Pei, No problem. It was my pleasure.
Now, umls part is working. Thank you so much for your help. I really appreciate it. Harpreet On Thu, Jun 19, 2014 at 10:22 AM, Pei Chen <chen...@apache.org> wrote: > Harpreet, > There was a typo/incorrect path in one of the xml descriptors. > Fixed in r1603885. > Thanks again for testing out trunk... > --Pei > > > On Wed, Jun 18, 2014 at 8:31 PM, Harpreet Khanduja <hsk5...@rit.edu> > wrote: > > > 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 > > > > >> > > >> > > > > >> > > > > > > >> > > > > > >> > > > > > > > > > > > > > > > > > > > >
