Hi Sean, The pipeline I am trying to run is this:
https://github.com/dmitriydligach/ctakes-misc/blob/master/src/main/java/org/apache/ctakes/pipelines/UmlsLookupPipeline.java (This is the UmlsLookupPipeline class). It runs fine in Eclipse but fails when I run from command line. I will look into the solution you are suggesting (thanks!). 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://cwiki.apache.org/confluence/display/CTAKES/Piper+Files > > > -----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= >
