As I said in my previous email, the piper approach looks very promising. However many of us probably still have lots of existing uimaFIT pipelines and it would be nice to be able to run them from command line.
So, are there any plans to finally fix this old “URI is not hierarchical” problem? Do we at least know what’s causing it? Dima > On Apr 14, 2017, at 12:14, Finan, Sean <sean.fi...@childrens.harvard.edu> > wrote: > > Ok, thanks. For your original question: > >> 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? > > I thought that I had already fixed it. So much for my thorough testing. > > Let me know what happens with the piper approach. > Sean > > > -----Original Message----- > From: Dligach, Dmitriy [mailto:ddlig...@luc.edu] > Sent: Friday, April 14, 2017 12:47 PM > To: dev@ctakes.apache.org > Subject: Re: URI is not hierarchical > > Hi Sean, > > > > The pipeline I am trying to run is this: > > > > 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=xe6RaWm66aSyUeXjU20x8dEc3xfYTHbadlwhgSdrIsw&s=ixO9vX_WJ7p-dpJc0RdnzRfjwQqbNw4gkLwf0SSpp0I&e= > > > > > (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://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_Piper-2BFiles&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=xe6RaWm66aSyUeXjU20x8dEc3xfYTHbadlwhgSdrIsw&s=pNVLJSOBMk5orJZ4Oy4ZwtpkPp0tU48-g1qxtpIBucw&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= >> > > >
