Sean, thanks for getting back to me on this. I am now trying to run PiperFileRunner in Eclipse (ultimately I want to run it from command line), so I believe the working directory now is ctakes-core.
I am specifying the full path to DefaultFastPipeline.piper because I couldn’t get it to work any other way. Dima > On Apr 26, 2017, at 11:27, Finan, Sean <sean.fi...@childrens.harvard.edu> > wrote: > > Hi Dima, > > The error messages is telling you that ContextDependentTokenizerAnnotator is > not found. That is the first ae outside of core. It is in > ctakes-contexttokenizer. > > It also looks like you are specifying a full path to > DefaultFastPipeline.piper. > > So I have to ask: what is your working directory and what is your classpath? > > Thanks, > Sean > > -----Original Message----- > From: Dligach, Dmitriy [mailto:ddlig...@luc.edu] > Sent: Wednesday, April 26, 2017 12:16 PM > To: dev@ctakes.apache.org > Subject: Re: URI is not hierarchical > > Hi Sean, > > > > Thanks again for providing this information — the piper approach looks very > promising. > > > > So I gave it a try, but it didn’t quite work. As you suggested, I am trying > to run the PiperFileRunner class in core.pipelines. I give it the following > parameters: > > > > -p > /Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-clinical-pipeline-res/src/main/resources/org/apache/ctakes/clinical/pipeline/DefaultFastPipeline.piper > > -i > /Users/Dima/Loyola/Workspaces/cTakes/ctakes/ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/ > > --xmiOut /Users/Dima/Temp/ > > --user <my login> > > --pass <my password> > > > > I get this error: > > > > 26 Apr 2017 11:11:40 ERROR PiperFileRunner - MESSAGE LOCALIZATION FAILED: > Can't find resource for bundle java.util.PropertyResourceBundle, key No > Analysis Component found for ContextDependentTokenizerAnnotator > > > > Any thoughts? > > > > Best, > > > > Dima > > > > > > > >> On Apr 14, 2017, at 11:35, Finan, Sean <sean.fi...@childrens.harvard.edu> >> wrote: > >> > >> Hi Dima, > >> > >> Where did you get that class? I don't have UmlsLookupPipeline or the >> package org.apache.ctakes.pipelines. > >> > >> If you want to run from command-line I highly recommend that you use the >> PiperFileRunner class in core.pipeline. > >> > >> To run the clinical pipeline use cli parameters: > >> -p DefaultFastPipeline.piper > >> -i {inputDir} > >> --xmiOut {outputDir} > >> --user {umlsUsername} > >> --pass {umlsPassword} > >> > >> If you have the binary installation there is a runClinicalPipeline script in >> bin/ > >> > >> PiperFileRunner can run other piper files and take other parameters > >> # Runs the pipeline in the piper file specified by -p (piperfile) > >> # with any other provided parameters. Standard parameters are: > >> # -i , --inputDir {inputDirectory} > >> # -o , --outputDir {outputDirectory} > >> # -s , --subDir {subDirectory} (for i/o) > >> # --xmiOut {xmiOutputDirectory} (if different from -o) > >> # -l , --lookupXml {dictionaryConfigFile} (fast only) > >> # --user {umlsUsername} > >> # --pass {umlsPassword} > >> # -? , --help > >> # > >> # Other parameters may be declared in the piper file using the cli command: > >> # cli {parameterName}={singleCharacter} > >> # For instance, for declaration of ParagraphAnnotator path to regex file >> optional parameter PARAGRAPH_TYPES_PATH, > >> # in the custom piper file add the line: > >> # cli PARAGRAPH_TYPES_PATH=t > >> # and when executing this script use: > >> # runPiperFile -p path/to/my/custom.piper -t path/to/my/custom.bsv ... > >> > >> > >> The above is a snippet from the runPiperFile script in the bin/ directory. > >> > >> I am in the process of writing documentation on piper files in the wiki. > >> > >> https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_Piper-2BFiles&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=QvJHfwMRwE-eH8zLpe6-qM3SFrDndefi0oRgnOIDowI&s=jfzeOzImM6Wyvbi7yAj5D6CfSaqoIspmc0NCbrt4Fcs&e= >> > >> > >> > >> -----Original Message----- > >> From: Dligach, Dmitriy [mailto:ddlig...@luc.edu] > >> Sent: Friday, April 14, 2017 12:17 PM > >> To: cTAKES Developer list > >> Subject: URI is not hierarchical > >> > >> Dear cTAKES developers, > >> > >> > >> > >> I am trying to run a simple pipeline that involves dictionary lookup: > >> > >> > >> > >> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_dmitriydligach_ctakes-2Dmisc_blob_master_src_main_java_org_apache_ctakes_pipelines_UmlsLookupPipeline.java&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q303b0Q&s=NWoDwPNChJkDhFseM3j8Gi7KNDdVqzi1BFt0onalf9I&e= >> > >> > >> > >> > >> from command line as follows: > >> > >> > >> > >> mvn exec:java >> -Dexec.mainClass=“org.apache.ctakes.pipelines.UmlsLookupPipeline” > >> > >> > >> > >> It runs fine if the dictionary lookup related fragmented is commented out, >> but it fails with “URI is not hierarchical” when the dictionary lookup is >> enabled. > >> > >> > >> > >> I believe this is an old issue, so are there any plans for fixing it in the >> new release? In the meantime, are there any workarounds? > >> > >> > >> > >> Many thanks! > >> > >> > >> > >> The full error is below. > >> > >> > >> > >> Dima > >> > >> > >> > >> > >> > >> > >> > >> 14 Apr 2017 11:04:24 INFO LvgAnnotator - URL for lvg.properties >> =file:/home/dima/.m2/repository/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties > >> > >> 14 Apr 2017 11:04:24 INFO SentenceDetector - Sentence detector model file: >> org/apache/ctakes/core/sentdetect/sd-med-model.zip > >> > >> 14 Apr 2017 11:04:24 INFO TokenizerAnnotatorPTB - Initializing >> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB > >> > >> 14 Apr 2017 11:04:24 INFO ContextDependentTokenizerAnnotator - Finite state >> machines loaded. > >> > >> 14 Apr 2017 11:04:24 INFO POSTagger - POS tagger model file: >> org/apache/ctakes/postagger/models/mayo-pos.zip > >> > >> 14 Apr 2017 11:04:24 INFO Chunker - Chunker model file: >> /home/dima/cTakes/trunk/ctakes-chunker-res/src/main/resources/org/apache/ctakes/chunker/models/chunker-model.zip > >> > >> 14 Apr 2017 11:04:26 INFO AbstractJCasTermAnnotator - Using dictionary >> lookup window type: org.apache.ctakes.typesystem.type.textspan.Sentence > >> > >> 14 Apr 2017 11:04:26 INFO AbstractJCasTermAnnotator - Exclusion tagset >> loaded: CC CD DT EX IN LS MD PDT POS PP PP$ PRP PRP$ RP TO VB VBD VBG VBN >> VBP VBZ WDT WP WPS WRB > >> > >> 14 Apr 2017 11:04:26 INFO AbstractJCasTermAnnotator - Using minimum term >> text span: 3 > >> > >> 14 Apr 2017 11:04:26 INFO AbstractJCasTermAnnotator - Using Dictionary >> Descriptor: org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml > >> > >> 14 Apr 2017 11:04:26 INFO DictionaryDescriptorParser - Parsing dictionary >> specifications: > >> > >> 14 Apr 2017 11:04:26 INFO UmlsUserApprover - Checking UMLS Account at >> https://urldefense.proofpoint.com/v2/url?u=https-3A__uts-2Dws.nlm.nih.gov_restful_isValidUMLSUser&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q303b0Q&s=k4vvKW_sfiLO__5LyOVbw7jMlmz2h1urVXde-7hEzg8&e= >> for user dmitriydligach: > >> > >> .14 Apr 2017 11:04:26 INFO UmlsUserApprover - UMLS Account at >> https://urldefense.proofpoint.com/v2/url?u=https-3A__uts-2Dws.nlm.nih.gov_restful_isValidUMLSUser&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q303b0Q&s=k4vvKW_sfiLO__5LyOVbw7jMlmz2h1urVXde-7hEzg8&e= >> for user dmitriydligach has been validated > >> > >> > >> > >> 14 Apr 2017 11:04:26 INFO JdbcConnectionFactory - Connecting to >> jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab: > >> > >> 14 Apr 2017 11:04:26 INFO ENGINE - open start - state not modified > >> > >> ................. > >> > >> 14 Apr 2017 11:04:32 INFO JdbcConnectionFactory - Database connected > >> > >> 14 Apr 2017 11:04:32 INFO JdbcRareWordDictionary - Connected to cui and >> term table CUI_TERMS > >> > >> 14 Apr 2017 11:04:32 INFO JdbcConceptFactory - Connected to concept table >> TUI with class TUI > >> > >> 14 Apr 2017 11:04:32 INFO JdbcConceptFactory - Connected to concept table >> RXNORM with class LONG > >> > >> 14 Apr 2017 11:04:32 INFO JdbcConceptFactory - Connected to concept table >> PREFTERM with class PREFTERM > >> > >> 14 Apr 2017 11:04:32 INFO JdbcConceptFactory - Connected to concept table >> SNOMEDCT_US with class LONG > >> > >> [WARNING] > >> > >> java.lang.IllegalArgumentException: URI is not hierarchical > >> > >> at java.io.File.<init>(File.java:418) > >> > >> at >> org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl.load(LvgCmdApiResourceImpl.java:65) > >> > >> at >> org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:628) > >> > >> at >> org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:464) > >> > >> at >> org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:193) > >> > >> at >> org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.java:157) > >> > >> at >> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:131) > >> > >> at >> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) > >> > >> at >> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62) > >> > >> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:279) > >> > >> at >> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:407) > >> > >> at >> org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:256) > >> > >> at >> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:429) > >> > >> at >> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:373) > >> > >> at >> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:186) > >> > >> at >> org.apache.uima.fit.factory.AnalysisEngineFactory.createEngine(AnalysisEngineFactory.java:711) > >> > >> at >> org.apache.uima.fit.factory.AggregateBuilder.createAggregate(AggregateBuilder.java:207) > >> > >> at >> org.apache.ctakes.pipelines.UmlsLookupPipeline.main(UmlsLookupPipeline.java:66) > >> > >> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > >> > >> at >> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) > >> > >> at >> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) > >> > >> at java.lang.reflect.Method.invoke(Method.java:498) > >> > >> at org.codehaus.mojo.exec.ExecJavaMojo$1.run(ExecJavaMojo.java:282) > >> > >> at java.lang.Thread.run(Thread.java:745) > >> > >> [INFO] >> ------------------------------------------------------------------------ > >> > >> [INFO] BUILD FAILURE > >> > >> [INFO] >> ------------------------------------------------------------------------ > >> > >> [INFO] Total time: 9.900 s > >> > >> [INFO] Finished at: 2017-04-14T11:04:32-05:00 > >> > >> [INFO] Final Memory: 510M/1455M > >> > >> [INFO] >> ------------------------------------------------------------------------ > >> > >> [ERROR] Failed to execute goal >> org.codehaus.mojo:exec-maven-plugin:1.6.0:java (default-cli) on project >> ctakes-misc: An exception occured while executing the Java class. URI is not >> hierarchical -> [Help 1] > >> > >> [ERROR] > >> > >> [ERROR] To see the full stack trace of the errors, re-run Maven with the -e >> switch. > >> > >> [ERROR] Re-run Maven using the -X switch to enable full debug logging. > >> > >> [ERROR] > >> > >> [ERROR] For more information about the errors and possible solutions, please >> read the following articles: > >> > >> [ERROR] [Help 1] >> https://urldefense.proofpoint.com/v2/url?u=http-3A__cwiki.apache.org_confluence_display_MAVEN_MojoExecutionException&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q303b0Q&s=JfA-JsX45OHwuDl_DNkICQUwoIOMrYhdSxNKV1k_Ig4&e= >> > > >
