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 >>
