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 > > > >> > > > > > >
