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 > > >> > > >
