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=
>>  
> 
> 
> 

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