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-resources > > > -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(JdbcCo > > > 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.initializeExternalR > > > esources(ResourceManager_impl.java:442) > > > > at > > > > > > > > > > > org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBas > > > e.java:153) > > > > at > > > > > > > > > > > org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize > > > (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(Analys > > > 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:375) > > > > at > > > > > > > > > > > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init > > > ialize(AggregateAnalysisEngine_impl.java:185) > > > > at > > > > > > > > > > > > > org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analys > > > 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:375) > > > > at > > > > > > > > > > > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init > > > ialize(AggregateAnalysisEngine_impl.java:185) > > > > at > > > > > > > > > > > > > org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analys > > > 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(AnalysisEngi > > > neFactory.java:424) > > > > at > > > org.uimafit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:16 > > > 5) > > > > at > > > org.uimafit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:19 > > > 0) > > > > at > > > > > > > > > > > org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory.main(Clinic > > > 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(JdbcCo > > > nnectionResourceImpl.java:109) > > > > ... 30 more > > > > > > > >
