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 > >> >
