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Posted to dev@ctakes.apache.org by "Dligach, Dmitriy" <dd...@luc.edu> on 2017/04/14 16:16:50 UTC
URI is not hierarchical
Dear cTAKES developers,
I am trying to run a simple pipeline that involves dictionary lookup:
https://github.com/dmitriydligach/ctakes-misc/blob/master/src/main/java/org/apache/ctakes/pipelines/UmlsLookupPipeline.java
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://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user dmitriydligach:
.14 Apr 2017 11:04:26 INFO UmlsUserApprover - UMLS Account at https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser 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] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
Re: URI is not hierarchical
Posted by "Dligach, Dmitriy" <dd...@luc.edu>.
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 <Se...@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:ddligach@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 <Se...@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:ddligach@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=
>
>
>
RE: URI is not hierarchical
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
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:ddligach@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 <Se...@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:ddligach@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=
Re: URI is not hierarchical
Posted by "Dligach, Dmitriy" <dd...@luc.edu>.
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 <Se...@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:ddligach@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=
RE: URI is not hierarchical [SUSPICIOUS]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
It is probably worth mentioning ....
I am revealing ctakes 4.0 (or trunk) functionality. Piper files do not exist in previous versions.
-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: Friday, April 14, 2017 12:35 PM
To: dev@ctakes.apache.org
Subject: RE: URI is not hierarchical [SUSPICIOUS]
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=a-8ZmA-W32ENsp3hDthi4tfII3KqNWZVSq67Gv3jMIo&s=rIpc1mhiMVLsL7pKOK2x2Fi2gBFJOhrb019O4xbuA7Y&e=
-----Original Message-----
From: Dligach, Dmitriy [mailto:ddligach@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=
RE: URI is not hierarchical
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Dima,
Ok, thanks.
I use ctakes some jars pulled from maven central for a couple of projects. I admit that they don't use lvg. However, I simply declare dependencies in a pom and they are pulled down. I then run piper files from ide or cli. For one project I do run simply from command line, but it is using a maven profile. For multiple entry points (development) this is not ideal. I only used mvn exec:java two or three times, but I agree with you that it is one good way to go for development if you are trying to build and run outside an IDE. It is almost as good as writing a script that accepts a main class name. 64 ways to skin a crayola pack of cats.
I think trust James will be able to bring ctakes-lvg into this decade and then you can try using ctakes jars from maven central. Between the FileLocator and possible usable lvg 2016 improvements it shouldn't take too much kludge. Flw.
Sean
-----Original Message-----
From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
Sent: Friday, April 28, 2017 1:52 PM
To: dev@ctakes.apache.org
Subject: Re: URI is not hierarchical
Hi Sean,
My goal is just to run the pipelines in ctakes-misc on a remote server. I only have SSH access to this server, so I’d like to run these pipelines from command line. I will not need to modify ctakes code.
I have not been able yet to get ctakes-misc to compile without a ctakes installation, but I am working on it (I started a separate email thread related to this and you had some suggestions which I’m trying now).
Dima
> On Apr 28, 2017, at 11:54, Finan, Sean <Se...@childrens.harvard.edu> wrote:
>
> Hi Dima,
> I have a question:
>
> Are you running ctakes-misc directly or do you have a master pom (like misc_pom.xml) that includes ctakes-misc(-master) as a dependency along with other ctakes modules?
> In other words, are you trying to run using ctakes source code/resources or ctakes jars? To put it another way, do you have a need to modify ctakes code as you develop -misc?
>
> If you are running with ctakes "as an api" then I think that I may have misunderstood your entire goal here ...
>
> -----Original Message-----
> From: James Masanz [mailto:masanz.james@gmail.com]
> Sent: Friday, April 28, 2017 12:28 PM
> To: dev@ctakes.apache.org
> Subject: Re: URI is not hierarchical
>
> Going back to your original email, I notice cTAKES is referencing
> lvg.properties as being within a jar
>
> 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
>
> But I also see in LvgCmdApiResourceImpl.java the following code, which
> is trying to handle it as a File, not a stream. :(
>
> File configFile = new File(dr.getUri());
> configFileName = configFile.getPath();
>
> At first glance, looks like LvgCmdApiResourceImpl needs updating.
>
> As a workaround, you could try extracting the lvg subdirectory from
> ctakes-resources-4.0-bin.zip that's on sourceforge [1] into something
> on the classpath so the lvg.propertiesfile appears under
>
> org/apache/ctakes/lvg/data/config/lvg.properties
>
> You might also need to have the rest of the files and directories under org/apache/ctakes/lvg/data to also be outside the jar, not sure offhand.
>
> I can try that out this afternoon.
>
> [1]
> https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_p
> rojects_ctakesresources_files_ctakes-2Dresources-2D4.0-2Dbin.zip_downl
> oad&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZ
> stTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ra9HfnuMGpOujoaSUtQA9mL4u6gpme6fd
> --2pbUGohc&s=fqcKKFIrMw69bxvC7tXm0ZWex5PvIsP32HivEqbJZrc&e=
>
>
> On Wed, Apr 26, 2017 at 3:29 PM, Dligach, Dmitriy <dd...@luc.edu> wrote:
>
>> Hi Sean,
>>
>> First of all, a huge thank you for taking time to debug this issue. I
>> really appreciate your help.
>>
>> Second, I think my main message somehow got lost in translation
>> (sorry, I should’ve included it for clarity with my recent emails). I
>> never had any trouble running this pipeline in Eclipse. The “URI is not hierarchical”
>> error only happens when I run it from command line.
>>
>> I run it using the following maven command:
>>
>> mvn exec:java -Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline"
>> -Dexec.args="" -Dctakes.umlsuser=<my umls login name>
>> -Dctakes.umlspw=<my umls password>
>>
>> As I said in my previous email, the other pipeline (that does not
>> have dictionary lookup) runs fine at command line. The error only
>> happens when I run pipelines containing dictionary lookup.
>>
>> Dima
>>
>>
>>
>>> On Apr 26, 2017, at 13:36, Finan, Sean
>>> <Se...@childrens.harvard.edu>
>> wrote:
>>>
>>> Hi Dima,
>>>
>>> Good news: no uri hierarchical error.
>>>
>>> All that I did was import your ctakes-misc pom as a maven project in
>> intellij. Then I created a run configuration with my sandbox as the
>> working directory, ctakes-misc as the classpath module, and my umls
>> credentials in the environment.
>>> All database files were found, the pipeline ran, and I got output:
>>> total 2448
>>> drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:19 .
>>> drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:18 ..
>>> -rwxrwx---+ 1 Administrators Domain Users 187675 Apr 26 14:19
>> GenSurg_UmbilicalHernia_1.rtf.xmi
>>> -rwxrwx---+ 1 Administrators Domain Users 238984 Apr 26 14:19
>> OBGYN_Gen_Abscess_1.rtf.xmi
>>> -rwxrwx---+ 1 Administrators Domain Users 82308 Apr 26 14:19
>> OBGYN_HysterectomyAndBSO_1.rtf.xmi
>>> -rwxrwx---+ 1 Administrators Domain Users 115983 Apr 26 14:19
>> OBGYN_IUD_1.rtf.xmi
>>> -rwxrwx---+ 1 Administrators Domain Users 35919 Apr 26 14:19
>> OBGYN_LaborProgressNote_1.rtf.xmi
>>> -rwxrwx---+ 1 Administrators Domain Users 112460 Apr 26 14:19
>> OBGYN_MVAPrego_1.rtf.xmi
>>> -rwxrwx---+ 1 Administrators Domain Users 173695 Apr 26 14:19
>> OBGYN_PROMCheck_1.rtf.xmi
>>> -rwxrwx---+ 1 Administrators Domain Users 340626 Apr 26 14:19
>> Peds_Dysphagia_1.rtf.xmi
>>> -rwxrwx---+ 1 Administrators Domain Users 390928 Apr 26 14:19
>> Peds_FebrileSez_1.rtf.xmi
>>> -rwxrwx---+ 1 Administrators Domain Users 115064 Apr 26 14:19
>> Peds_RoutBirthNote_1.rtf.xmi
>>> -rwxrwx---+ 1 Administrators Domain Users 101234 Apr 26 14:19
>> VascSurg_AAA_Leak_1.rtf.xmi
>>> -rwxrwx---+ 1 Administrators Domain Users 98015 Apr 26 14:19
>> VascSurg_FollowUp_1.rtf.xmi
>>> -rwxrwx---+ 1 Administrators Domain Users 218863 Apr 26 14:19
>> VascSurg_PVD_1.rtf.xmi
>>> -rwxrwx---+ 1 Administrators Domain Users 72902 Apr 26 14:19
>> VascSurg_RO-AAA_1.rtf.xmi
>>> -rwxrwx---+ 1 Administrators Domain Users 90825 Apr 26 14:19
>> VascSurg_RO-DVT.rtf.xmi
>>> -rwxrwx---+ 1 Administrators Domain Users 90827 Apr 26 14:19
>> VascSurg_RO-DVT_1.rtf.xmi
>>>
>>>
>>>
>>>
>>> Bad news: it looks like the hsqldb port of lvg2008 is not working.
>>>
>>> Caused by: org.hsqldb.HsqlException: error in script file line: 61
>> C:\Spiffy\prj_ctakes_401\dev\ctakes-lvg-res\target\classes\
>> org\apache\ctakes\lvg\data\HSqlDb\lvg2008 java.io.IOException: read
>> beyond end of file in statement [SET TABLE PUBLIC.INFLECTION INDEX
>> '3198299
>> 60557 3198299 53129 0 0 0 0 1210464']
>>>
>>> Caused by: org.hsqldb.HsqlException: Caused by: java.io.IOException:
>> read beyond end of file
>>>
>>>
>>> At any rate, the code works but I think that something is missing
>>> from
>> your configuration.
>>> Since it is a personal development environment you are kind of on
>>> your
>> own.
>>> Good luck,
>>> Sean
>>>
>>> P.S. Get rid of the ctakes-resources-umls2011ab artifact in your pom.
>> It isn't doing anything.
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
>>> Sent: Wednesday, April 26, 2017 12:46 PM
>>> To: dev@ctakes.apache.org
>>> Subject: Re: URI is not hierarchical
>>>
>>> I am definitely still seeing the “URI is not hierarchical” issue.
>>> Here’s
>> a piece of information that might help you figure out what the problem is:
>>>
>>>
>>>
>>> It only happens if the pipeline includes dictionary lookup. For
>> instance, this one fails:
>>>
>>>
>>>
>>> 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=Cv-_Ac9CLY7wNnflevRAn-
>> a92vTj9x79u08OjKfQ9U4&s=MKa09-UzlhjAB_1jVyGOpVo1UHWrMDqjWiVAnk0jfPE&e
>> =
>>>
>>>
>>>
>>> But this one succeeds:
>>>
>>>
>>>
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
>> com_dmitriydligach_ctakes-2Dmisc_blob_master_src_main_
>> java_org_apache_ctakes_pipelines_BasicPipeline.java&
>> d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=
>> fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevRAn-
>> a92vTj9x79u08OjKfQ9U4&s=U0zGx-soIiYY64nHK_tIAIpeind9vdIrAuDQIxh-4ek&e
>> =
>>>
>>>
>>>
>>> (it’s the same as the first one, but the dictionary lookup part is
>> removed).
>>>
>>>
>>>
>>> Dima
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>> On Apr 26, 2017, at 11:37, Finan, Sean <Sean.Finan@childrens.harvard.
>> edu> wrote:
>>>
>>>>
>>>
>>>> Hi again Dima,
>>>
>>>>
>>>
>>>> The piper files are not meant to replace uimafit. Uimafit is great
>>>> for
>> many purposes.
>>>
>>>>
>>>
>>>> As for that annoying old "URI is not hierarchical" bug, a while
>>>> back I
>> checked in a fix that worked for me. Since then I cannot duplicate it.
>>>
>>>>
>>>
>>>> Sean
>>>
>>>>
>>>
>>>> -----Original Message-----
>>>
>>>> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
>>>
>>>> Sent: Wednesday, April 26, 2017 12:18 PM
>>>
>>>> To: dev@ctakes.apache.org
>>>
>>>> Subject: Re: URI is not hierarchical
>>>
>>>>
>>>
>>>> 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.Finan@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:ddligach@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.Finan@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:ddligach@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/ctake
>> s
>> - 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=qS4goWBT7poplM69z
>> y _ 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bc
>> pKGd4f7d4gTao&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=qS4goWBT7poplM69z
>> y _ 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bc
>> pKGd4f7d4gTao&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.initializeAggregateAnalysisEng
>> ine(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=https-3A__urldefense.proofpoint&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ra9HfnuMGpOujoaSUtQA9mL4u6gpme6fd--2pbUGohc&s=YQ9ZF9smiNYo-O3hS6Q5Ig98tZLemJD5aRphQazqOkI&e= .
>> com/v2/url?u=http-3A__cwiki.apache.org_confluence_display_
>> MAVEN_MojoExecutionException&d=DwIGaQ&c=qS4goWBT7poplM69zy_
>> 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bc
>> pKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q303b0Q&s=JfA-
>> JsX45OHwuDl_DNkICQUwoIOMrYhdSxNKV1k_Ig4&e=
>>>
>>>>>
>>>
>>>>>
>>>
>>>>>
>>>
>>>>
>>>
>>>
>>>
>>
>>
Re: URI is not hierarchical
Posted by "Dligach, Dmitriy" <dd...@luc.edu>.
Hi Sean,
My goal is just to run the pipelines in ctakes-misc on a remote server. I only have SSH access to this server, so I’d like to run these pipelines from command line. I will not need to modify ctakes code.
I have not been able yet to get ctakes-misc to compile without a ctakes installation, but I am working on it (I started a separate email thread related to this and you had some suggestions which I’m trying now).
Dima
> On Apr 28, 2017, at 11:54, Finan, Sean <Se...@childrens.harvard.edu> wrote:
>
> Hi Dima,
> I have a question:
>
> Are you running ctakes-misc directly or do you have a master pom (like misc_pom.xml) that includes ctakes-misc(-master) as a dependency along with other ctakes modules?
> In other words, are you trying to run using ctakes source code/resources or ctakes jars? To put it another way, do you have a need to modify ctakes code as you develop -misc?
>
> If you are running with ctakes "as an api" then I think that I may have misunderstood your entire goal here ...
>
> -----Original Message-----
> From: James Masanz [mailto:masanz.james@gmail.com]
> Sent: Friday, April 28, 2017 12:28 PM
> To: dev@ctakes.apache.org
> Subject: Re: URI is not hierarchical
>
> Going back to your original email, I notice cTAKES is referencing lvg.properties as being within a jar
>
> 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
>
> But I also see in LvgCmdApiResourceImpl.java the following code, which is trying to handle it as a File, not a stream. :(
>
> File configFile = new File(dr.getUri());
> configFileName = configFile.getPath();
>
> At first glance, looks like LvgCmdApiResourceImpl needs updating.
>
> As a workaround, you could try extracting the lvg subdirectory from ctakes-resources-4.0-bin.zip that's on sourceforge [1] into something on the classpath so the lvg.propertiesfile appears under
>
> org/apache/ctakes/lvg/data/config/lvg.properties
>
> You might also need to have the rest of the files and directories under org/apache/ctakes/lvg/data to also be outside the jar, not sure offhand.
>
> I can try that out this afternoon.
>
> [1]
> https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_ctakesresources_files_ctakes-2Dresources-2D4.0-2Dbin.zip_download&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ra9HfnuMGpOujoaSUtQA9mL4u6gpme6fd--2pbUGohc&s=fqcKKFIrMw69bxvC7tXm0ZWex5PvIsP32HivEqbJZrc&e=
>
>
> On Wed, Apr 26, 2017 at 3:29 PM, Dligach, Dmitriy <dd...@luc.edu> wrote:
>
>> Hi Sean,
>>
>> First of all, a huge thank you for taking time to debug this issue. I
>> really appreciate your help.
>>
>> Second, I think my main message somehow got lost in translation
>> (sorry, I should’ve included it for clarity with my recent emails). I
>> never had any trouble running this pipeline in Eclipse. The “URI is not hierarchical”
>> error only happens when I run it from command line.
>>
>> I run it using the following maven command:
>>
>> mvn exec:java -Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline"
>> -Dexec.args="" -Dctakes.umlsuser=<my umls login name>
>> -Dctakes.umlspw=<my umls password>
>>
>> As I said in my previous email, the other pipeline (that does not have
>> dictionary lookup) runs fine at command line. The error only happens
>> when I run pipelines containing dictionary lookup.
>>
>> Dima
>>
>>
>>
>>> On Apr 26, 2017, at 13:36, Finan, Sean
>>> <Se...@childrens.harvard.edu>
>> wrote:
>>>
>>> Hi Dima,
>>>
>>> Good news: no uri hierarchical error.
>>>
>>> All that I did was import your ctakes-misc pom as a maven project in
>> intellij. Then I created a run configuration with my sandbox as the
>> working directory, ctakes-misc as the classpath module, and my umls
>> credentials in the environment.
>>> All database files were found, the pipeline ran, and I got output:
>>> total 2448
>>> drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:19 .
>>> drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:18 ..
>>> -rwxrwx---+ 1 Administrators Domain Users 187675 Apr 26 14:19
>> GenSurg_UmbilicalHernia_1.rtf.xmi
>>> -rwxrwx---+ 1 Administrators Domain Users 238984 Apr 26 14:19
>> OBGYN_Gen_Abscess_1.rtf.xmi
>>> -rwxrwx---+ 1 Administrators Domain Users 82308 Apr 26 14:19
>> OBGYN_HysterectomyAndBSO_1.rtf.xmi
>>> -rwxrwx---+ 1 Administrators Domain Users 115983 Apr 26 14:19
>> OBGYN_IUD_1.rtf.xmi
>>> -rwxrwx---+ 1 Administrators Domain Users 35919 Apr 26 14:19
>> OBGYN_LaborProgressNote_1.rtf.xmi
>>> -rwxrwx---+ 1 Administrators Domain Users 112460 Apr 26 14:19
>> OBGYN_MVAPrego_1.rtf.xmi
>>> -rwxrwx---+ 1 Administrators Domain Users 173695 Apr 26 14:19
>> OBGYN_PROMCheck_1.rtf.xmi
>>> -rwxrwx---+ 1 Administrators Domain Users 340626 Apr 26 14:19
>> Peds_Dysphagia_1.rtf.xmi
>>> -rwxrwx---+ 1 Administrators Domain Users 390928 Apr 26 14:19
>> Peds_FebrileSez_1.rtf.xmi
>>> -rwxrwx---+ 1 Administrators Domain Users 115064 Apr 26 14:19
>> Peds_RoutBirthNote_1.rtf.xmi
>>> -rwxrwx---+ 1 Administrators Domain Users 101234 Apr 26 14:19
>> VascSurg_AAA_Leak_1.rtf.xmi
>>> -rwxrwx---+ 1 Administrators Domain Users 98015 Apr 26 14:19
>> VascSurg_FollowUp_1.rtf.xmi
>>> -rwxrwx---+ 1 Administrators Domain Users 218863 Apr 26 14:19
>> VascSurg_PVD_1.rtf.xmi
>>> -rwxrwx---+ 1 Administrators Domain Users 72902 Apr 26 14:19
>> VascSurg_RO-AAA_1.rtf.xmi
>>> -rwxrwx---+ 1 Administrators Domain Users 90825 Apr 26 14:19
>> VascSurg_RO-DVT.rtf.xmi
>>> -rwxrwx---+ 1 Administrators Domain Users 90827 Apr 26 14:19
>> VascSurg_RO-DVT_1.rtf.xmi
>>>
>>>
>>>
>>>
>>> Bad news: it looks like the hsqldb port of lvg2008 is not working.
>>>
>>> Caused by: org.hsqldb.HsqlException: error in script file line: 61
>> C:\Spiffy\prj_ctakes_401\dev\ctakes-lvg-res\target\classes\
>> org\apache\ctakes\lvg\data\HSqlDb\lvg2008 java.io.IOException: read
>> beyond end of file in statement [SET TABLE PUBLIC.INFLECTION INDEX
>> '3198299
>> 60557 3198299 53129 0 0 0 0 1210464']
>>>
>>> Caused by: org.hsqldb.HsqlException: Caused by: java.io.IOException:
>> read beyond end of file
>>>
>>>
>>> At any rate, the code works but I think that something is missing
>>> from
>> your configuration.
>>> Since it is a personal development environment you are kind of on
>>> your
>> own.
>>> Good luck,
>>> Sean
>>>
>>> P.S. Get rid of the ctakes-resources-umls2011ab artifact in your pom.
>> It isn't doing anything.
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
>>> Sent: Wednesday, April 26, 2017 12:46 PM
>>> To: dev@ctakes.apache.org
>>> Subject: Re: URI is not hierarchical
>>>
>>> I am definitely still seeing the “URI is not hierarchical” issue.
>>> Here’s
>> a piece of information that might help you figure out what the problem is:
>>>
>>>
>>>
>>> It only happens if the pipeline includes dictionary lookup. For
>> instance, this one fails:
>>>
>>>
>>>
>>> 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=Cv-_Ac9CLY7wNnflevRAn-
>> a92vTj9x79u08OjKfQ9U4&s=MKa09-UzlhjAB_1jVyGOpVo1UHWrMDqjWiVAnk0jfPE&e=
>>>
>>>
>>>
>>> But this one succeeds:
>>>
>>>
>>>
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
>> com_dmitriydligach_ctakes-2Dmisc_blob_master_src_main_
>> java_org_apache_ctakes_pipelines_BasicPipeline.java&
>> d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=
>> fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevRAn-
>> a92vTj9x79u08OjKfQ9U4&s=U0zGx-soIiYY64nHK_tIAIpeind9vdIrAuDQIxh-4ek&e=
>>>
>>>
>>>
>>> (it’s the same as the first one, but the dictionary lookup part is
>> removed).
>>>
>>>
>>>
>>> Dima
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>> On Apr 26, 2017, at 11:37, Finan, Sean <Sean.Finan@childrens.harvard.
>> edu> wrote:
>>>
>>>>
>>>
>>>> Hi again Dima,
>>>
>>>>
>>>
>>>> The piper files are not meant to replace uimafit. Uimafit is great
>>>> for
>> many purposes.
>>>
>>>>
>>>
>>>> As for that annoying old "URI is not hierarchical" bug, a while
>>>> back I
>> checked in a fix that worked for me. Since then I cannot duplicate it.
>>>
>>>>
>>>
>>>> Sean
>>>
>>>>
>>>
>>>> -----Original Message-----
>>>
>>>> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
>>>
>>>> Sent: Wednesday, April 26, 2017 12:18 PM
>>>
>>>> To: dev@ctakes.apache.org
>>>
>>>> Subject: Re: URI is not hierarchical
>>>
>>>>
>>>
>>>> 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.Finan@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:ddligach@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.Finan@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:ddligach@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=fs67GvlGZstTpyIisCYNYmQCP6r0bc
>> pKGd4f7d4gTao&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=fs67GvlGZstTpyIisCYNYmQCP6r0bc
>> pKGd4f7d4gTao&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.initializeAggregateAnalysisEng
>> ine(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=https-3A__urldefense.proofpoint&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ra9HfnuMGpOujoaSUtQA9mL4u6gpme6fd--2pbUGohc&s=YQ9ZF9smiNYo-O3hS6Q5Ig98tZLemJD5aRphQazqOkI&e= .
>> com/v2/url?u=http-3A__cwiki.apache.org_confluence_display_
>> MAVEN_MojoExecutionException&d=DwIGaQ&c=qS4goWBT7poplM69zy_
>> 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bc
>> pKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q303b0Q&s=JfA-
>> JsX45OHwuDl_DNkICQUwoIOMrYhdSxNKV1k_Ig4&e=
>>>
>>>>>
>>>
>>>>>
>>>
>>>>>
>>>
>>>>
>>>
>>>
>>>
>>
>>
RE: URI is not hierarchical
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Dima,
I have a question:
Are you running ctakes-misc directly or do you have a master pom (like misc_pom.xml) that includes ctakes-misc(-master) as a dependency along with other ctakes modules?
In other words, are you trying to run using ctakes source code/resources or ctakes jars? To put it another way, do you have a need to modify ctakes code as you develop -misc?
If you are running with ctakes "as an api" then I think that I may have misunderstood your entire goal here ...
-----Original Message-----
From: James Masanz [mailto:masanz.james@gmail.com]
Sent: Friday, April 28, 2017 12:28 PM
To: dev@ctakes.apache.org
Subject: Re: URI is not hierarchical
Going back to your original email, I notice cTAKES is referencing lvg.properties as being within a jar
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
But I also see in LvgCmdApiResourceImpl.java the following code, which is trying to handle it as a File, not a stream. :(
File configFile = new File(dr.getUri());
configFileName = configFile.getPath();
At first glance, looks like LvgCmdApiResourceImpl needs updating.
As a workaround, you could try extracting the lvg subdirectory from ctakes-resources-4.0-bin.zip that's on sourceforge [1] into something on the classpath so the lvg.propertiesfile appears under
org/apache/ctakes/lvg/data/config/lvg.properties
You might also need to have the rest of the files and directories under org/apache/ctakes/lvg/data to also be outside the jar, not sure offhand.
I can try that out this afternoon.
[1]
https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_ctakesresources_files_ctakes-2Dresources-2D4.0-2Dbin.zip_download&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ra9HfnuMGpOujoaSUtQA9mL4u6gpme6fd--2pbUGohc&s=fqcKKFIrMw69bxvC7tXm0ZWex5PvIsP32HivEqbJZrc&e=
On Wed, Apr 26, 2017 at 3:29 PM, Dligach, Dmitriy <dd...@luc.edu> wrote:
> Hi Sean,
>
> First of all, a huge thank you for taking time to debug this issue. I
> really appreciate your help.
>
> Second, I think my main message somehow got lost in translation
> (sorry, I should’ve included it for clarity with my recent emails). I
> never had any trouble running this pipeline in Eclipse. The “URI is not hierarchical”
> error only happens when I run it from command line.
>
> I run it using the following maven command:
>
> mvn exec:java -Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline"
> -Dexec.args="" -Dctakes.umlsuser=<my umls login name>
> -Dctakes.umlspw=<my umls password>
>
> As I said in my previous email, the other pipeline (that does not have
> dictionary lookup) runs fine at command line. The error only happens
> when I run pipelines containing dictionary lookup.
>
> Dima
>
>
>
> > On Apr 26, 2017, at 13:36, Finan, Sean
> > <Se...@childrens.harvard.edu>
> wrote:
> >
> > Hi Dima,
> >
> > Good news: no uri hierarchical error.
> >
> > All that I did was import your ctakes-misc pom as a maven project in
> intellij. Then I created a run configuration with my sandbox as the
> working directory, ctakes-misc as the classpath module, and my umls
> credentials in the environment.
> > All database files were found, the pipeline ran, and I got output:
> > total 2448
> > drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:19 .
> > drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:18 ..
> > -rwxrwx---+ 1 Administrators Domain Users 187675 Apr 26 14:19
> GenSurg_UmbilicalHernia_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 238984 Apr 26 14:19
> OBGYN_Gen_Abscess_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 82308 Apr 26 14:19
> OBGYN_HysterectomyAndBSO_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 115983 Apr 26 14:19
> OBGYN_IUD_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 35919 Apr 26 14:19
> OBGYN_LaborProgressNote_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 112460 Apr 26 14:19
> OBGYN_MVAPrego_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 173695 Apr 26 14:19
> OBGYN_PROMCheck_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 340626 Apr 26 14:19
> Peds_Dysphagia_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 390928 Apr 26 14:19
> Peds_FebrileSez_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 115064 Apr 26 14:19
> Peds_RoutBirthNote_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 101234 Apr 26 14:19
> VascSurg_AAA_Leak_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 98015 Apr 26 14:19
> VascSurg_FollowUp_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 218863 Apr 26 14:19
> VascSurg_PVD_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 72902 Apr 26 14:19
> VascSurg_RO-AAA_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 90825 Apr 26 14:19
> VascSurg_RO-DVT.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 90827 Apr 26 14:19
> VascSurg_RO-DVT_1.rtf.xmi
> >
> >
> >
> >
> > Bad news: it looks like the hsqldb port of lvg2008 is not working.
> >
> > Caused by: org.hsqldb.HsqlException: error in script file line: 61
> C:\Spiffy\prj_ctakes_401\dev\ctakes-lvg-res\target\classes\
> org\apache\ctakes\lvg\data\HSqlDb\lvg2008 java.io.IOException: read
> beyond end of file in statement [SET TABLE PUBLIC.INFLECTION INDEX
> '3198299
> 60557 3198299 53129 0 0 0 0 1210464']
> >
> > Caused by: org.hsqldb.HsqlException: Caused by: java.io.IOException:
> read beyond end of file
> >
> >
> > At any rate, the code works but I think that something is missing
> > from
> your configuration.
> > Since it is a personal development environment you are kind of on
> > your
> own.
> > Good luck,
> > Sean
> >
> > P.S. Get rid of the ctakes-resources-umls2011ab artifact in your pom.
> It isn't doing anything.
> >
> >
> >
> > -----Original Message-----
> > From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
> > Sent: Wednesday, April 26, 2017 12:46 PM
> > To: dev@ctakes.apache.org
> > Subject: Re: URI is not hierarchical
> >
> > I am definitely still seeing the “URI is not hierarchical” issue.
> > Here’s
> a piece of information that might help you figure out what the problem is:
> >
> >
> >
> > It only happens if the pipeline includes dictionary lookup. For
> instance, this one fails:
> >
> >
> >
> > 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=Cv-_Ac9CLY7wNnflevRAn-
> a92vTj9x79u08OjKfQ9U4&s=MKa09-UzlhjAB_1jVyGOpVo1UHWrMDqjWiVAnk0jfPE&e=
> >
> >
> >
> > But this one succeeds:
> >
> >
> >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
> com_dmitriydligach_ctakes-2Dmisc_blob_master_src_main_
> java_org_apache_ctakes_pipelines_BasicPipeline.java&
> d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=
> fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevRAn-
> a92vTj9x79u08OjKfQ9U4&s=U0zGx-soIiYY64nHK_tIAIpeind9vdIrAuDQIxh-4ek&e=
> >
> >
> >
> > (it’s the same as the first one, but the dictionary lookup part is
> removed).
> >
> >
> >
> > Dima
> >
> >
> >
> >
> >
> >
> >
> >> On Apr 26, 2017, at 11:37, Finan, Sean <Sean.Finan@childrens.harvard.
> edu> wrote:
> >
> >>
> >
> >> Hi again Dima,
> >
> >>
> >
> >> The piper files are not meant to replace uimafit. Uimafit is great
> >> for
> many purposes.
> >
> >>
> >
> >> As for that annoying old "URI is not hierarchical" bug, a while
> >> back I
> checked in a fix that worked for me. Since then I cannot duplicate it.
> >
> >>
> >
> >> Sean
> >
> >>
> >
> >> -----Original Message-----
> >
> >> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
> >
> >> Sent: Wednesday, April 26, 2017 12:18 PM
> >
> >> To: dev@ctakes.apache.org
> >
> >> Subject: Re: URI is not hierarchical
> >
> >>
> >
> >> 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.Finan@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:ddligach@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.Finan@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:ddligach@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=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> pKGd4f7d4gTao&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=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> pKGd4f7d4gTao&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.initializeAggregateAnalysisEng
> ine(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=https-3A__urldefense.proofpoint&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ra9HfnuMGpOujoaSUtQA9mL4u6gpme6fd--2pbUGohc&s=YQ9ZF9smiNYo-O3hS6Q5Ig98tZLemJD5aRphQazqOkI&e= .
> com/v2/url?u=http-3A__cwiki.apache.org_confluence_display_
> MAVEN_MojoExecutionException&d=DwIGaQ&c=qS4goWBT7poplM69zy_
> 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> pKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q303b0Q&s=JfA-
> JsX45OHwuDl_DNkICQUwoIOMrYhdSxNKV1k_Ig4&e=
> >
> >>>
> >
> >>>
> >
> >>>
> >
> >>
> >
> >
> >
>
>
RE: URI is not hierarchical
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi James,
There is a trick to get around changing your ctakes (or other) main pom.xml for troubleshooting / using modules that aren't normally in the main project:
Make a copy of the ctakes pom.xml in the ctakes root directory. Name it "dima_pom.xml" or whatever. Add the module and dependency "ctakes-misc".
Use
mvn -f dima_pom.xml ...
and maven should pretend that dima_pom is your main pom.
That way you don't need to set svn ignore on your ctakes pom.xml or otherwise exclude it from checkins, etc.
Sean
-----Original Message-----
From: James Masanz [mailto:masanz.james@gmail.com]
Sent: Friday, April 28, 2017 5:31 PM
To: dev@ctakes.apache.org
Subject: Re: URI is not hierarchical
Hi Dima,
Just to let you know I am taking a look at this. More later, if not today, then tomorrow. FYI here is where I'm at so far.
I checked out a fresh copy of ctakes trunk and put files from your ctakes-misc into a subdirectory called ctakes-misc, and I updated my local copy of the main pom.xml for ctakes to include ctakes-misc.
I am able to reproduce getting URI is not hierarchical just by letting tests run during "mvn clean install":
Tests in error:
testPipeline(org.apache.ctakes.temporal.ae.BackwardsTimeAnnotatorTest):
URI is not hierarchical
testPipeline(org.apache.ctakes.temporal.ae.ContextualModalityAnnotatorTest):
URI is not hierarchical
testPipeline(org.apache.ctakes.temporal.ae.EventAnnotatorTest): URI is not hierarchical
testPipeline(org.apache.ctakes.temporal.ae.EventEventRelationAnnotatorTest):
URI is not hierarchical
testPipeline(org.apache.ctakes.temporal.ae.EventTimeRelationAnnotatorTest):
URI is not hierarchical
On Fri, Apr 28, 2017 at 12:27 PM, James Masanz <ma...@gmail.com>
wrote:
>
> Going back to your original email, I notice cTAKES is referencing
> lvg.properties as being within a jar
>
> 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
>
> But I also see in LvgCmdApiResourceImpl.java the following code, which
> is trying to handle it as a File, not a stream. :(
>
> File configFile = new File(dr.getUri());
> configFileName = configFile.getPath();
>
> At first glance, looks like LvgCmdApiResourceImpl needs updating.
>
> As a workaround, you could try extracting the lvg subdirectory from
> ctakes-resources-4.0-bin.zip that's on sourceforge [1] into something
> on the classpath so the lvg.propertiesfile appears under
>
> org/apache/ctakes/lvg/data/config/lvg.properties
>
> You might also need to have the rest of the files and directories
> under org/apache/ctakes/lvg/data to also be outside the jar, not sure offhand.
>
> I can try that out this afternoon.
>
> [1]
> https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_p
> rojects_ctakesresources_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdi
> oCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=g4ggohGOalAr
> RAS4TXlxJ30BA3Yn_OLtsw6K9n-z-hs&s=36cGmBLIcvvcyxkXHT4yV0EmP1nhZj1Hxt0P
> pAhOimk&e= files/ctakes-resources-4.0-bin.zip/download
>
>
> On Wed, Apr 26, 2017 at 3:29 PM, Dligach, Dmitriy <dd...@luc.edu>
> wrote:
>
>> Hi Sean,
>>
>> First of all, a huge thank you for taking time to debug this issue. I
>> really appreciate your help.
>>
>> Second, I think my main message somehow got lost in translation
>> (sorry, I should’ve included it for clarity with my recent emails). I
>> never had any trouble running this pipeline in Eclipse. The “URI is not hierarchical”
>> error only happens when I run it from command line.
>>
>> I run it using the following maven command:
>>
>> mvn exec:java -Dexec.mainClass="org.apache.c
>> takes.pipelines.UmlsLookupPipeline" -Dexec.args=""
>> -Dctakes.umlsuser=<my umls login name> -Dctakes.umlspw=<my umls
>> password>
>>
>> As I said in my previous email, the other pipeline (that does not
>> have dictionary lookup) runs fine at command line. The error only
>> happens when I run pipelines containing dictionary lookup.
>>
>> Dima
>>
>>
>>
>> > On Apr 26, 2017, at 13:36, Finan, Sean <Sean.Finan@childrens.harvard.
>> edu> wrote:
>> >
>> > Hi Dima,
>> >
>> > Good news: no uri hierarchical error.
>> >
>> > All that I did was import your ctakes-misc pom as a maven project
>> > in
>> intellij. Then I created a run configuration with my sandbox as the
>> working directory, ctakes-misc as the classpath module, and my umls
>> credentials in the environment.
>> > All database files were found, the pipeline ran, and I got output:
>> > total 2448
>> > drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:19 .
>> > drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:18 ..
>> > -rwxrwx---+ 1 Administrators Domain Users 187675 Apr 26 14:19
>> GenSurg_UmbilicalHernia_1.rtf.xmi
>> > -rwxrwx---+ 1 Administrators Domain Users 238984 Apr 26 14:19
>> OBGYN_Gen_Abscess_1.rtf.xmi
>> > -rwxrwx---+ 1 Administrators Domain Users 82308 Apr 26 14:19
>> OBGYN_HysterectomyAndBSO_1.rtf.xmi
>> > -rwxrwx---+ 1 Administrators Domain Users 115983 Apr 26 14:19
>> OBGYN_IUD_1.rtf.xmi
>> > -rwxrwx---+ 1 Administrators Domain Users 35919 Apr 26 14:19
>> OBGYN_LaborProgressNote_1.rtf.xmi
>> > -rwxrwx---+ 1 Administrators Domain Users 112460 Apr 26 14:19
>> OBGYN_MVAPrego_1.rtf.xmi
>> > -rwxrwx---+ 1 Administrators Domain Users 173695 Apr 26 14:19
>> OBGYN_PROMCheck_1.rtf.xmi
>> > -rwxrwx---+ 1 Administrators Domain Users 340626 Apr 26 14:19
>> Peds_Dysphagia_1.rtf.xmi
>> > -rwxrwx---+ 1 Administrators Domain Users 390928 Apr 26 14:19
>> Peds_FebrileSez_1.rtf.xmi
>> > -rwxrwx---+ 1 Administrators Domain Users 115064 Apr 26 14:19
>> Peds_RoutBirthNote_1.rtf.xmi
>> > -rwxrwx---+ 1 Administrators Domain Users 101234 Apr 26 14:19
>> VascSurg_AAA_Leak_1.rtf.xmi
>> > -rwxrwx---+ 1 Administrators Domain Users 98015 Apr 26 14:19
>> VascSurg_FollowUp_1.rtf.xmi
>> > -rwxrwx---+ 1 Administrators Domain Users 218863 Apr 26 14:19
>> VascSurg_PVD_1.rtf.xmi
>> > -rwxrwx---+ 1 Administrators Domain Users 72902 Apr 26 14:19
>> VascSurg_RO-AAA_1.rtf.xmi
>> > -rwxrwx---+ 1 Administrators Domain Users 90825 Apr 26 14:19
>> VascSurg_RO-DVT.rtf.xmi
>> > -rwxrwx---+ 1 Administrators Domain Users 90827 Apr 26 14:19
>> VascSurg_RO-DVT_1.rtf.xmi
>> >
>> >
>> >
>> >
>> > Bad news: it looks like the hsqldb port of lvg2008 is not working.
>> >
>> > Caused by: org.hsqldb.HsqlException: error in script file line: 61
>> C:\Spiffy\prj_ctakes_401\dev\ctakes-lvg-res\target\classes\o
>> rg\apache\ctakes\lvg\data\HSqlDb\lvg2008 java.io.IOException: read
>> beyond end of file in statement [SET TABLE PUBLIC.INFLECTION INDEX
>> '3198299
>> 60557 3198299 53129 0 0 0 0 1210464']
>> >
>> > Caused by: org.hsqldb.HsqlException: Caused by: java.io.IOException:
>> read beyond end of file
>> >
>> >
>> > At any rate, the code works but I think that something is missing
>> > from
>> your configuration.
>> > Since it is a personal development environment you are kind of on
>> > your
>> own.
>> > Good luck,
>> > Sean
>> >
>> > P.S. Get rid of the ctakes-resources-umls2011ab artifact in your pom.
>> It isn't doing anything.
>> >
>> >
>> >
>> > -----Original Message-----
>> > From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
>> > Sent: Wednesday, April 26, 2017 12:46 PM
>> > To: dev@ctakes.apache.org
>> > Subject: Re: URI is not hierarchical
>> >
>> > I am definitely still seeing the “URI is not hierarchical” issue.
>> Here’s a piece of information that might help you figure out what the
>> problem is:
>> >
>> >
>> >
>> > It only happens if the pipeline includes dictionary lookup. For
>> instance, this one fails:
>> >
>> >
>> >
>> > 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=fs67G
>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevR
>> An-a92vTj9x79u08OjKfQ9U4&s=MKa09-UzlhjAB_1jVyGOpVo1UHWrMDqjWiVAnk0jfP
>> E&e=
>> >
>> >
>> >
>> > But this one succeeds:
>> >
>> >
>> >
>> > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
>> com_dmitriydligach_ctakes-2Dmisc_blob_master_src_main_java_
>> org_apache_ctakes_pipelines_BasicPipeline.java&d=DwIGaQ&c=
>> qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpy
>> IisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevRAn-a92vTj
>> 9x79u08OjKfQ9U4&s=U0zGx-soIiYY64nHK_tIAIpeind9vdIrAuDQIxh-4ek&e=
>> >
>> >
>> >
>> > (it’s the same as the first one, but the dictionary lookup part is
>> removed).
>> >
>> >
>> >
>> > Dima
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >> On Apr 26, 2017, at 11:37, Finan, Sean <Sean.Finan@childrens.harvard.
>> edu> wrote:
>> >
>> >>
>> >
>> >> Hi again Dima,
>> >
>> >>
>> >
>> >> The piper files are not meant to replace uimafit. Uimafit is
>> >> great
>> for many purposes.
>> >
>> >>
>> >
>> >> As for that annoying old "URI is not hierarchical" bug, a while
>> >> back I
>> checked in a fix that worked for me. Since then I cannot duplicate it.
>> >
>> >>
>> >
>> >> Sean
>> >
>> >>
>> >
>> >> -----Original Message-----
>> >
>> >> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
>> >
>> >> Sent: Wednesday, April 26, 2017 12:18 PM
>> >
>> >> To: dev@ctakes.apache.org
>> >
>> >> Subject: Re: URI is not hierarchical
>> >
>> >>
>> >
>> >> 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.Finan@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:ddligach@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=fs67G
>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=xe6RaWm66aSyUeXjU20
>> x8dEc3xfYTHbadlwhgSdrIsw&s=ixO9vX_WJ7p-dpJc0RdnzRfjwQqbNw4gkLwf0SSpp0
>> I&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.Finan@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.a
>> pache.org_confluence_display_CTAKES_Piper-2BFiles&d=DwIGaQ&c
>> =qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTp
>> yIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=xe6RaWm66aSyUeXjU20x8dEc3xf
>> YTHbadlwhgSdrIsw&s=pNVLJSOBMk5orJZ4Oy4ZwtpkPp0tU48-g1qxtpIBucw&e=
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>> -----Original Message-----
>> >
>> >>>
>> >
>> >>>> From: Dligach, Dmitriy [mailto:ddligach@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=fs67G
>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf
>> _qgdQj3HYIeLCeKr9Q303b0Q&s=NWoDwPNChJkDhFseM3j8Gi7KNDdVqzi1BFt0onalf9
>> I&e=
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>> from command line as follows:
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>> mvn exec:java -Dexec.mainClass=“org.apache.c
>> takes.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/ctakesresour
>> ces/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/resource
>> s/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.t
>> ype.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/l
>> ookup/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-2Dw
>> s.nlm.nih.gov_restful_isValidUMLSUser&d=DwIGaQ&c=qS4goWBT7po
>> plM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP
>> 6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q30
>> 3b0Q&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-2Dw
>> s.nlm.nih.gov_restful_isValidUMLSUser&d=DwIGaQ&c=qS4goWBT7po
>> plM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP
>> 6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q30
>> 3b0Q&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/look
>> up/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(Lv
>> gCmdApiResourceImpl.java:65)
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>> at
>> >>>> org.apache.uima.resource.impl.ResourceManager_impl.registerR
>> esource(ResourceManager_impl.java:628)
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>> at
>> >>>> org.apache.uima.resource.impl.ResourceManager_impl.initializ
>> eExternalResources(ResourceManager_impl.java:464)
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>> at
>> >>>> org.apache.uima.resource.Resource_ImplBase.initialize(Resour
>> ce_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.produceResou
>> rce(AnalysisEngineFactory_impl.java:94)
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>> at
>> >>>> org.apache.uima.impl.CompositeResourceFactory_impl.produceRe
>> source(CompositeResourceFactory_impl.java:62)
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.
>> java:279)
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>> at
>> >>>> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFram
>> ework.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.createEngi
>> ne(AnalysisEngineFactory.java:711)
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>> at
>> >>>> org.apache.uima.fit.factory.AggregateBuilder.createAggregate
>> (AggregateBuilder.java:207)
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>> at
>> >>>> org.apache.ctakes.pipelines.UmlsLookupPipeline.main(UmlsLook
>> upPipeline.java:66)
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native
>> >>>> Method)
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>> at
>> >>>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAcce
>> ssorImpl.java:62)
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>> at
>> >>>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMe
>> thodAccessorImpl.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=https-3A__urldefense.proofpoint&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=g4ggohGOalArRAS4TXlxJ30BA3Yn_OLtsw6K9n-z-hs&s=aETx6GOCDxykGTRd5MPInU0fiGsfSwrxVzVk-cRTMdU&e= .
>> com/v2/url?u=http-3A__cwiki.apache.org_confluence_display_MA
>> VEN_MojoExecutionException&d=DwIGaQ&c=qS4goWBT7poplM69zy_3x
>> hKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4
>> f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q303b0Q&s=
>> JfA-JsX45OHwuDl_DNkICQUwoIOMrYhdSxNKV1k_Ig4&e=
>> >
>> >>>
>> >
>> >>>
>> >
>> >>>
>> >
>> >>
>> >
>> >
>> >
>>
>>
>
Re: URI is not hierarchical
Posted by "Dligach, Dmitriy" <dd...@luc.edu>.
James,
I was able to get around the “URI not hierarchical” issue by doing what you suggested!
I checked out lvg from svn.code.sf.net/p/ctakesresources/code/trunk/ctakes-resources-lvg2008/src/main/resources/org/apache/ctakes/lvg/ and put it in target/classes/org/apache/ctakes/.
Thank you so much, you made my day today :)
Dima
> On Apr 29, 2017, at 01:57, James Masanz <ma...@gmail.com> wrote:
>
> Hi Dima,
>
> I modified my local copy of FileLocator to avoid the
> StringIndexOutOfBoundsException I was seeing using HEAD, and here's the
> workaround for the problem you were seeing until the code change is made to
> LvgCmdApiResourceImpl:
>
> Copy the lvg directory that's in
>
> %CTAKES_HOME%/resources/org/apache/ctakes/
>
> to be under the target/classes/org/apache/ctakes directory that's within
> your local copy of ctakes-misc
>
> so for example, on my system, after the copy, I see
> C:\from.svn\ctakes-misc.git\trunk\target\classes\org\
> apache\ctakes\lvg\data\config\lvg.properties
>
> (For anyone else reading this, that resources directory will show up when
> you do mvn clean install of cTAKES)
>
> If you want lvg to use the actual lvg resources, you can't just copy the
> lvg.properties file for this workaround, you have to copy the entire
> subtree, or it will create an empty lvg database.
>
>
> I'll check out the StringIndexOutOfBoundsException on Monday unless someone
> else beats me to it before then.
>
>
> FYI, to test this workaround, before I did the copy, I was seeing
>
> 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)
>
> After I copied that lvg directory, I was then able see output in the
> outputDirectory
> defined by UmlsLookupPipeline.java
>
> FYI #2, I'm using Win 7 Pro. This workaround should work for linux/mac but
> was not tested there.
>
> FYI #3, this was using your idea of not having ctakes-misc be under ctakes.
> thanks for that tip! keeps things nicely separated - no need to update
> the parent pom at all.
>
>
>
> On Sat, Apr 29, 2017 at 2:00 AM, James Masanz <ma...@gmail.com>
> wrote:
>
>> Hi Dima,
>>
>> what revision of trunk are you using? I'm getting an error you weren't
>> seeing so I'm guessing it's because I checked out ctakes just today.
>>
>> Caused by: java.lang.StringIndexOutOfBoundsException: String index out of
>> range: -7
>> at java.lang.String.substring(String.java:1967)
>> at org.apache.ctakes.dictionary.lookup2.util.
>> JdbcConnectionFactory.getConnectionUrl(JdbcConnectionFactory.java:110)
>> at org.apache.ctakes.dictionary.lookup2.util.
>> JdbcConnectionFactory.getConnection(JdbcConnectionFactory.java:63)
>> at org.apache.ctakes.dictionary.lookup2.dictionary.
>> JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:91)
>> at org.apache.ctakes.dictionary.lookup2.dictionary.
>> JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:72)
>> at org.apache.ctakes.dictionary.lookup2.dictionary.
>> UmlsJdbcRareWordDictionary.<init>(UmlsJdbcRareWordDictionary.java:31)
>> ... 27 more
>>
>> FYI, I created the directories needed by UmlsLookupPipeline.java for
>> chunker-model.zip and inputDirectory and outputDirectory, and I get
>> the above regardless of whether I use text input file containing just "pain
>> in left knee started on Wednesday." or if I use
>> GenSurg_UmbilicalHernia_1.rtf as the input file instead.
>>
>>
>> On Fri, Apr 28, 2017 at 5:48 PM, Dligach, Dmitriy <dd...@luc.edu>
>> wrote:
>>
>>> Hi James,
>>>
>>> Thank you so much for looking into this!
>>>
>>> Your general setup matches mine. I also do:
>>>
>>> 1. svn co https://svn.apache.org/repos/asf/ctakes/trunk/
>>> 2. git clone https://github.com/dmitriydligach/ctakes-misc.git (in
>>> trunk/)
>>> 3. mvn clean compile (in trunk/)
>>> 4. mvn clean compile (in ctakes-misc/)
>>>
>>> BTW, I just discovered that it’s not necessary to check out a fresh copy
>>> of ctakes-misc into a subdirectory in trunk. It will build no matter where
>>> it is on your system as long as you first do an ‘mvn clean compile’ in
>>> trunk/ (without it, ctakes-misc/ will not build).
>>>
>>> Thanks again, James.
>>>
>>> Dima
>>>
>>>
>>>
>>>> On Apr 28, 2017, at 16:30, James Masanz <ma...@gmail.com> wrote:
>>>>
>>>> Hi Dima,
>>>>
>>>> Just to let you know I am taking a look at this. More later, if not
>>> today,
>>>> then tomorrow. FYI here is where I'm at so far.
>>>>
>>>> I checked out a fresh copy of ctakes trunk and put files from your
>>>> ctakes-misc into a subdirectory called ctakes-misc, and I updated my
>>> local
>>>> copy of the main pom.xml for ctakes to include ctakes-misc.
>>>>
>>>> I am able to reproduce getting URI is not hierarchical just by letting
>>>> tests run during "mvn clean install":
>>>>
>>>> Tests in error:
>>>> testPipeline(org.apache.ctakes.temporal.ae.BackwardsTimeAnno
>>> tatorTest):
>>>> URI is not hierarchical
>>>>
>>>> testPipeline(org.apache.ctakes.temporal.ae.ContextualModalit
>>> yAnnotatorTest):
>>>> URI is not hierarchical
>>>> testPipeline(org.apache.ctakes.temporal.ae.EventAnnotatorTest): URI is
>>>> not hierarchical
>>>>
>>>> testPipeline(org.apache.ctakes.temporal.ae.EventEventRelatio
>>> nAnnotatorTest):
>>>> URI is not hierarchical
>>>>
>>>> testPipeline(org.apache.ctakes.temporal.ae.EventTimeRelation
>>> AnnotatorTest):
>>>> URI is not hierarchical
>>>>
>>>>
>>>> On Fri, Apr 28, 2017 at 12:27 PM, James Masanz <ma...@gmail.com>
>>>> wrote:
>>>>
>>>>>
>>>>> Going back to your original email, I notice cTAKES is referencing
>>> lvg.properties
>>>>> as being within a jar
>>>>>
>>>>> 14 Apr 2017 11:04:24 INFO LvgAnnotator - URL for lvg.properties
>>>>> =file:/home/dima/.m2/repository/net/sourceforge/ctakesresour
>>> ces/ctakes-
>>>>> resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.
>>>>> 0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
>>>>>
>>>>> But I also see in LvgCmdApiResourceImpl.java the following code, which
>>> is
>>>>> trying to handle it as a File, not a stream. :(
>>>>>
>>>>> File configFile = new File(dr.getUri());
>>>>> configFileName = configFile.getPath();
>>>>>
>>>>> At first glance, looks like LvgCmdApiResourceImpl needs updating.
>>>>>
>>>>> As a workaround, you could try extracting the lvg subdirectory from
>>>>> ctakes-resources-4.0-bin.zip that's on sourceforge [1] into something
>>> on
>>>>> the classpath so the lvg.propertiesfile appears under
>>>>>
>>>>> org/apache/ctakes/lvg/data/config/lvg.properties
>>>>>
>>>>> You might also need to have the rest of the files and directories under
>>>>> org/apache/ctakes/lvg/data to also be outside the jar, not sure
>>> offhand.
>>>>>
>>>>> I can try that out this afternoon.
>>>>>
>>>>> [1] https://sourceforge.net/projects/ctakesresources/
>>>>> files/ctakes-resources-4.0-bin.zip/download
>>>>>
>>>>>
>>>>> On Wed, Apr 26, 2017 at 3:29 PM, Dligach, Dmitriy <dd...@luc.edu>
>>>>> wrote:
>>>>>
>>>>>> Hi Sean,
>>>>>>
>>>>>> First of all, a huge thank you for taking time to debug this issue. I
>>>>>> really appreciate your help.
>>>>>>
>>>>>> Second, I think my main message somehow got lost in translation
>>> (sorry, I
>>>>>> should’ve included it for clarity with my recent emails). I never had
>>> any
>>>>>> trouble running this pipeline in Eclipse. The “URI is not
>>> hierarchical”
>>>>>> error only happens when I run it from command line.
>>>>>>
>>>>>> I run it using the following maven command:
>>>>>>
>>>>>> mvn exec:java -Dexec.mainClass="org.apache.c
>>>>>> takes.pipelines.UmlsLookupPipeline" -Dexec.args=""
>>> -Dctakes.umlsuser=<my
>>>>>> umls login name> -Dctakes.umlspw=<my umls password>
>>>>>>
>>>>>> As I said in my previous email, the other pipeline (that does not have
>>>>>> dictionary lookup) runs fine at command line. The error only happens
>>> when I
>>>>>> run pipelines containing dictionary lookup.
>>>>>>
>>>>>> Dima
>>>>>>
>>>>>>
>>>>>>
>>>>>>> On Apr 26, 2017, at 13:36, Finan, Sean <Sean.Finan@childrens.harvard.
>>>>>> edu> wrote:
>>>>>>>
>>>>>>> Hi Dima,
>>>>>>>
>>>>>>> Good news: no uri hierarchical error.
>>>>>>>
>>>>>>> All that I did was import your ctakes-misc pom as a maven project in
>>>>>> intellij. Then I created a run configuration with my sandbox as the
>>>>>> working directory, ctakes-misc as the classpath module, and my umls
>>>>>> credentials in the environment.
>>>>>>> All database files were found, the pipeline ran, and I got output:
>>>>>>> total 2448
>>>>>>> drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:19 .
>>>>>>> drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:18 ..
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 187675 Apr 26 14:19
>>>>>> GenSurg_UmbilicalHernia_1.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 238984 Apr 26 14:19
>>>>>> OBGYN_Gen_Abscess_1.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 82308 Apr 26 14:19
>>>>>> OBGYN_HysterectomyAndBSO_1.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 115983 Apr 26 14:19
>>>>>> OBGYN_IUD_1.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 35919 Apr 26 14:19
>>>>>> OBGYN_LaborProgressNote_1.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 112460 Apr 26 14:19
>>>>>> OBGYN_MVAPrego_1.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 173695 Apr 26 14:19
>>>>>> OBGYN_PROMCheck_1.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 340626 Apr 26 14:19
>>>>>> Peds_Dysphagia_1.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 390928 Apr 26 14:19
>>>>>> Peds_FebrileSez_1.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 115064 Apr 26 14:19
>>>>>> Peds_RoutBirthNote_1.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 101234 Apr 26 14:19
>>>>>> VascSurg_AAA_Leak_1.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 98015 Apr 26 14:19
>>>>>> VascSurg_FollowUp_1.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 218863 Apr 26 14:19
>>>>>> VascSurg_PVD_1.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 72902 Apr 26 14:19
>>>>>> VascSurg_RO-AAA_1.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 90825 Apr 26 14:19
>>>>>> VascSurg_RO-DVT.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 90827 Apr 26 14:19
>>>>>> VascSurg_RO-DVT_1.rtf.xmi
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Bad news: it looks like the hsqldb port of lvg2008 is not working.
>>>>>>>
>>>>>>> Caused by: org.hsqldb.HsqlException: error in script file line: 61
>>>>>> C:\Spiffy\prj_ctakes_401\dev\ctakes-lvg-res\target\classes\o
>>>>>> rg\apache\ctakes\lvg\data\HSqlDb\lvg2008 java.io.IOException: read
>>>>>> beyond end of file in statement [SET TABLE PUBLIC.INFLECTION INDEX
>>> '3198299
>>>>>> 60557 3198299 53129 0 0 0 0 1210464']
>>>>>>>
>>>>>>> Caused by: org.hsqldb.HsqlException: Caused by: java.io.IOException:
>>>>>> read beyond end of file
>>>>>>>
>>>>>>>
>>>>>>> At any rate, the code works but I think that something is missing
>>> from
>>>>>> your configuration.
>>>>>>> Since it is a personal development environment you are kind of on
>>> your
>>>>>> own.
>>>>>>> Good luck,
>>>>>>> Sean
>>>>>>>
>>>>>>> P.S. Get rid of the ctakes-resources-umls2011ab artifact in your
>>> pom.
>>>>>> It isn't doing anything.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> -----Original Message-----
>>>>>>> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
>>>>>>> Sent: Wednesday, April 26, 2017 12:46 PM
>>>>>>> To: dev@ctakes.apache.org
>>>>>>> Subject: Re: URI is not hierarchical
>>>>>>>
>>>>>>> I am definitely still seeing the “URI is not hierarchical” issue.
>>>>>> Here’s a piece of information that might help you figure out what the
>>>>>> problem is:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> It only happens if the pipeline includes dictionary lookup. For
>>>>>> instance, this one fails:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> 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=fs67G
>>>>>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevR
>>>>>> An-a92vTj9x79u08OjKfQ9U4&s=MKa09-UzlhjAB_1jVyGOpVo1UHWrMDqjW
>>> iVAnk0jfPE&e=
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> But this one succeeds:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
>>>>>> com_dmitriydligach_ctakes-2Dmisc_blob_master_src_main_java_
>>>>>> org_apache_ctakes_pipelines_BasicPipeline.java&d=DwIGaQ&c=
>>>>>> qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpy
>>>>>> IisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevRAn-a92vTj
>>>>>> 9x79u08OjKfQ9U4&s=U0zGx-soIiYY64nHK_tIAIpeind9vdIrAuDQIxh-4ek&e=
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> (it’s the same as the first one, but the dictionary lookup part is
>>>>>> removed).
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Dima
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>> On Apr 26, 2017, at 11:37, Finan, Sean
>>> <Sean.Finan@childrens.harvard.
>>>>>> edu> wrote:
>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>> Hi again Dima,
>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>> The piper files are not meant to replace uimafit. Uimafit is great
>>>>>> for many purposes.
>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>> As for that annoying old "URI is not hierarchical" bug, a while
>>> back I
>>>>>> checked in a fix that worked for me. Since then I cannot duplicate
>>> it.
>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>> Sean
>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>> -----Original Message-----
>>>>>>>
>>>>>>>> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
>>>>>>>
>>>>>>>> Sent: Wednesday, April 26, 2017 12:18 PM
>>>>>>>
>>>>>>>> To: dev@ctakes.apache.org
>>>>>>>
>>>>>>>> Subject: Re: URI is not hierarchical
>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>> 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.Finan@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:ddligach@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=fs67G
>>>>>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=xe6RaWm66aSyUeXjU20
>>>>>> x8dEc3xfYTHbadlwhgSdrIsw&s=ixO9vX_WJ7p-dpJc0RdnzRfjwQqbNw4gk
>>> Lwf0SSpp0I&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.Finan@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.a
>>>>>> pache.org_confluence_display_CTAKES_Piper-2BFiles&d=DwIGaQ&c
>>>>>> =qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTp
>>>>>> yIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=xe6RaWm66aSyUeXjU20x8dEc3xf
>>>>>> YTHbadlwhgSdrIsw&s=pNVLJSOBMk5orJZ4Oy4ZwtpkPp0tU48-g1qxtpIBucw&e=
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>> -----Original Message-----
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>> From: Dligach, Dmitriy [mailto:ddligach@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=fs67G
>>>>>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf
>>>>>> _qgdQj3HYIeLCeKr9Q303b0Q&s=NWoDwPNChJkDhFseM3j8Gi7KNDdVqzi1B
>>> Ft0onalf9I&e=
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>> from command line as follows:
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>> mvn exec:java -Dexec.mainClass=“org.apache.c
>>>>>> takes.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/ctakesresour
>>>>>> ces/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/resource
>>>>>> s/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.t
>>>>>> ype.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/l
>>>>>> ookup/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-2Dw
>>>>>> s.nlm.nih.gov_restful_isValidUMLSUser&d=DwIGaQ&c=qS4goWBT7po
>>>>>> plM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP
>>>>>> 6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q30
>>>>>> 3b0Q&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-2Dw
>>>>>> s.nlm.nih.gov_restful_isValidUMLSUser&d=DwIGaQ&c=qS4goWBT7po
>>>>>> plM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP
>>>>>> 6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q30
>>>>>> 3b0Q&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/look
>>>>>> up/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(Lv
>>>>>> gCmdApiResourceImpl.java:65)
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>> at org.apache.uima.resource.impl.ResourceManager_impl.registerR
>>>>>> esource(ResourceManager_impl.java:628)
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>> at org.apache.uima.resource.impl.ResourceManager_impl.initializ
>>>>>> eExternalResources(ResourceManager_impl.java:464)
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>> at org.apache.uima.resource.Resource_ImplBase.initialize(Resour
>>>>>> ce_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.produceResou
>>>>>> rce(AnalysisEngineFactory_impl.java:94)
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>> at org.apache.uima.impl.CompositeResourceFactory_impl.produceRe
>>>>>> source(CompositeResourceFactory_impl.java:62)
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.
>>>>>> java:279)
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFram
>>>>>> ework.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.createEngi
>>>>>> ne(AnalysisEngineFactory.java:711)
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>> at org.apache.uima.fit.factory.AggregateBuilder.createAggregate
>>>>>> (AggregateBuilder.java:207)
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>> at org.apache.ctakes.pipelines.UmlsLookupPipeline.main(UmlsLook
>>>>>> upPipeline.java:66)
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAcce
>>>>>> ssorImpl.java:62)
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMe
>>>>>> thodAccessorImpl.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-p
>>> lugin: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_MA
>>>>>> VEN_MojoExecutionException&d=DwIGaQ&c=qS4goWBT7poplM69zy_3x
>>>>>> hKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4
>>>>>> f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q303b0Q&s=
>>>>>> JfA-JsX45OHwuDl_DNkICQUwoIOMrYhdSxNKV1k_Ig4&e=
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>
>>>
>>
Re: URI is not hierarchical
Posted by James Masanz <ma...@gmail.com>.
Hmmm, sorry.
Instead of copying from %CTAKES_HOME%/resources, try checking out a copy of
the lvg resources from sourceforge
svn checkout svn://
svn.code.sf.net/p/ctakesresources/code/trunk/ctakes-resources-lvg2008/src/main/resources/org/apache/ctakes/lvg/
-- James
On Sat, Apr 29, 2017 at 2:23 PM, Dligach, Dmitriy <dd...@luc.edu> wrote:
> Hi James,
>
> > Copy the lvg directory that's in
> >
> > %CTAKES_HOME%/resources/org/apache/ctakes/
>
> Sorry, in my case, I am only seeing one directory here called
> ‘dictionary’. Is that the one or should there be something called ‘lvg’?
>
> Dima
>
>
> > to be under the target/classes/org/apache/ctakes directory that's
> within
> > your local copy of ctakes-misc
> >
> > so for example, on my system, after the copy, I see
> > C:\from.svn\ctakes-misc.git\trunk\target\classes\org\
> > apache\ctakes\lvg\data\config\lvg.properties
> >
> > (For anyone else reading this, that resources directory will show up when
> > you do mvn clean install of cTAKES)
> >
> > If you want lvg to use the actual lvg resources, you can't just copy the
> > lvg.properties file for this workaround, you have to copy the entire
> > subtree, or it will create an empty lvg database.
> >
> >
> > I'll check out the StringIndexOutOfBoundsException on Monday unless
> someone
> > else beats me to it before then.
> >
> >
> > FYI, to test this workaround, before I did the copy, I was seeing
> >
> > 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)
> >
> > After I copied that lvg directory, I was then able see output in the
> > outputDirectory
> > defined by UmlsLookupPipeline.java
> >
> > FYI #2, I'm using Win 7 Pro. This workaround should work for linux/mac
> but
> > was not tested there.
> >
> > FYI #3, this was using your idea of not having ctakes-misc be under
> ctakes.
> > thanks for that tip! keeps things nicely separated - no need to update
> > the parent pom at all.
> >
> >
> >
> > On Sat, Apr 29, 2017 at 2:00 AM, James Masanz <ma...@gmail.com>
> > wrote:
> >
> >> Hi Dima,
> >>
> >> what revision of trunk are you using? I'm getting an error you weren't
> >> seeing so I'm guessing it's because I checked out ctakes just today.
> >>
> >> Caused by: java.lang.StringIndexOutOfBoundsException: String index out
> of
> >> range: -7
> >> at java.lang.String.substring(String.java:1967)
> >> at org.apache.ctakes.dictionary.lookup2.util.
> >> JdbcConnectionFactory.getConnectionUrl(JdbcConnectionFactory.java:110)
> >> at org.apache.ctakes.dictionary.lookup2.util.
> >> JdbcConnectionFactory.getConnection(JdbcConnectionFactory.java:63)
> >> at org.apache.ctakes.dictionary.lookup2.dictionary.
> >> JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:91)
> >> at org.apache.ctakes.dictionary.lookup2.dictionary.
> >> JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:72)
> >> at org.apache.ctakes.dictionary.lookup2.dictionary.
> >> UmlsJdbcRareWordDictionary.<init>(UmlsJdbcRareWordDictionary.java:31)
> >> ... 27 more
> >>
> >> FYI, I created the directories needed by UmlsLookupPipeline.java for
> >> chunker-model.zip and inputDirectory and outputDirectory, and I
> get
> >> the above regardless of whether I use text input file containing just
> "pain
> >> in left knee started on Wednesday." or if I use
> >> GenSurg_UmbilicalHernia_1.rtf as the input file instead.
> >>
> >>
> >> On Fri, Apr 28, 2017 at 5:48 PM, Dligach, Dmitriy <dd...@luc.edu>
> >> wrote:
> >>
> >>> Hi James,
> >>>
> >>> Thank you so much for looking into this!
> >>>
> >>> Your general setup matches mine. I also do:
> >>>
> >>> 1. svn co https://svn.apache.org/repos/asf/ctakes/trunk/
> >>> 2. git clone https://github.com/dmitriydligach/ctakes-misc.git (in
> >>> trunk/)
> >>> 3. mvn clean compile (in trunk/)
> >>> 4. mvn clean compile (in ctakes-misc/)
> >>>
> >>> BTW, I just discovered that it’s not necessary to check out a fresh
> copy
> >>> of ctakes-misc into a subdirectory in trunk. It will build no matter
> where
> >>> it is on your system as long as you first do an ‘mvn clean compile’ in
> >>> trunk/ (without it, ctakes-misc/ will not build).
> >>>
> >>> Thanks again, James.
> >>>
> >>> Dima
> >>>
> >>>
> >>>
> >>>> On Apr 28, 2017, at 16:30, James Masanz <ma...@gmail.com>
> wrote:
> >>>>
> >>>> Hi Dima,
> >>>>
> >>>> Just to let you know I am taking a look at this. More later, if not
> >>> today,
> >>>> then tomorrow. FYI here is where I'm at so far.
> >>>>
> >>>> I checked out a fresh copy of ctakes trunk and put files from your
> >>>> ctakes-misc into a subdirectory called ctakes-misc, and I updated my
> >>> local
> >>>> copy of the main pom.xml for ctakes to include ctakes-misc.
> >>>>
> >>>> I am able to reproduce getting URI is not hierarchical just by letting
> >>>> tests run during "mvn clean install":
> >>>>
> >>>> Tests in error:
> >>>> testPipeline(org.apache.ctakes.temporal.ae.BackwardsTimeAnno
> >>> tatorTest):
> >>>> URI is not hierarchical
> >>>>
> >>>> testPipeline(org.apache.ctakes.temporal.ae.ContextualModalit
> >>> yAnnotatorTest):
> >>>> URI is not hierarchical
> >>>> testPipeline(org.apache.ctakes.temporal.ae.EventAnnotatorTest): URI
> is
> >>>> not hierarchical
> >>>>
> >>>> testPipeline(org.apache.ctakes.temporal.ae.EventEventRelatio
> >>> nAnnotatorTest):
> >>>> URI is not hierarchical
> >>>>
> >>>> testPipeline(org.apache.ctakes.temporal.ae.EventTimeRelation
> >>> AnnotatorTest):
> >>>> URI is not hierarchical
> >>>>
> >>>>
> >>>> On Fri, Apr 28, 2017 at 12:27 PM, James Masanz <
> masanz.james@gmail.com>
> >>>> wrote:
> >>>>
> >>>>>
> >>>>> Going back to your original email, I notice cTAKES is referencing
> >>> lvg.properties
> >>>>> as being within a jar
> >>>>>
> >>>>> 14 Apr 2017 11:04:24 INFO LvgAnnotator - URL for lvg.properties
> >>>>> =file:/home/dima/.m2/repository/net/sourceforge/ctakesresour
> >>> ces/ctakes-
> >>>>> resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.
> >>>>> 0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
> >>>>>
> >>>>> But I also see in LvgCmdApiResourceImpl.java the following code,
> which
> >>> is
> >>>>> trying to handle it as a File, not a stream. :(
> >>>>>
> >>>>> File configFile = new File(dr.getUri());
> >>>>> configFileName = configFile.getPath();
> >>>>>
> >>>>> At first glance, looks like LvgCmdApiResourceImpl needs updating.
> >>>>>
> >>>>> As a workaround, you could try extracting the lvg subdirectory from
> >>>>> ctakes-resources-4.0-bin.zip that's on sourceforge [1] into something
> >>> on
> >>>>> the classpath so the lvg.propertiesfile appears under
> >>>>>
> >>>>> org/apache/ctakes/lvg/data/config/lvg.properties
> >>>>>
> >>>>> You might also need to have the rest of the files and directories
> under
> >>>>> org/apache/ctakes/lvg/data to also be outside the jar, not sure
> >>> offhand.
> >>>>>
> >>>>> I can try that out this afternoon.
> >>>>>
> >>>>> [1] https://sourceforge.net/projects/ctakesresources/
> >>>>> files/ctakes-resources-4.0-bin.zip/download
> >>>>>
> >>>>>
> >>>>> On Wed, Apr 26, 2017 at 3:29 PM, Dligach, Dmitriy <dd...@luc.edu>
> >>>>> wrote:
> >>>>>
> >>>>>> Hi Sean,
> >>>>>>
> >>>>>> First of all, a huge thank you for taking time to debug this issue.
> I
> >>>>>> really appreciate your help.
> >>>>>>
> >>>>>> Second, I think my main message somehow got lost in translation
> >>> (sorry, I
> >>>>>> should’ve included it for clarity with my recent emails). I never
> had
> >>> any
> >>>>>> trouble running this pipeline in Eclipse. The “URI is not
> >>> hierarchical”
> >>>>>> error only happens when I run it from command line.
> >>>>>>
> >>>>>> I run it using the following maven command:
> >>>>>>
> >>>>>> mvn exec:java -Dexec.mainClass="org.apache.c
> >>>>>> takes.pipelines.UmlsLookupPipeline" -Dexec.args=""
> >>> -Dctakes.umlsuser=<my
> >>>>>> umls login name> -Dctakes.umlspw=<my umls password>
> >>>>>>
> >>>>>> As I said in my previous email, the other pipeline (that does not
> have
> >>>>>> dictionary lookup) runs fine at command line. The error only happens
> >>> when I
> >>>>>> run pipelines containing dictionary lookup.
> >>>>>>
> >>>>>> Dima
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>> On Apr 26, 2017, at 13:36, Finan, Sean
> <Sean.Finan@childrens.harvard.
> >>>>>> edu> wrote:
> >>>>>>>
> >>>>>>> Hi Dima,
> >>>>>>>
> >>>>>>> Good news: no uri hierarchical error.
> >>>>>>>
> >>>>>>> All that I did was import your ctakes-misc pom as a maven project
> in
> >>>>>> intellij. Then I created a run configuration with my sandbox as the
> >>>>>> working directory, ctakes-misc as the classpath module, and my umls
> >>>>>> credentials in the environment.
> >>>>>>> All database files were found, the pipeline ran, and I got output:
> >>>>>>> total 2448
> >>>>>>> drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:19 .
> >>>>>>> drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:18 ..
> >>>>>>> -rwxrwx---+ 1 Administrators Domain Users 187675 Apr 26 14:19
> >>>>>> GenSurg_UmbilicalHernia_1.rtf.xmi
> >>>>>>> -rwxrwx---+ 1 Administrators Domain Users 238984 Apr 26 14:19
> >>>>>> OBGYN_Gen_Abscess_1.rtf.xmi
> >>>>>>> -rwxrwx---+ 1 Administrators Domain Users 82308 Apr 26 14:19
> >>>>>> OBGYN_HysterectomyAndBSO_1.rtf.xmi
> >>>>>>> -rwxrwx---+ 1 Administrators Domain Users 115983 Apr 26 14:19
> >>>>>> OBGYN_IUD_1.rtf.xmi
> >>>>>>> -rwxrwx---+ 1 Administrators Domain Users 35919 Apr 26 14:19
> >>>>>> OBGYN_LaborProgressNote_1.rtf.xmi
> >>>>>>> -rwxrwx---+ 1 Administrators Domain Users 112460 Apr 26 14:19
> >>>>>> OBGYN_MVAPrego_1.rtf.xmi
> >>>>>>> -rwxrwx---+ 1 Administrators Domain Users 173695 Apr 26 14:19
> >>>>>> OBGYN_PROMCheck_1.rtf.xmi
> >>>>>>> -rwxrwx---+ 1 Administrators Domain Users 340626 Apr 26 14:19
> >>>>>> Peds_Dysphagia_1.rtf.xmi
> >>>>>>> -rwxrwx---+ 1 Administrators Domain Users 390928 Apr 26 14:19
> >>>>>> Peds_FebrileSez_1.rtf.xmi
> >>>>>>> -rwxrwx---+ 1 Administrators Domain Users 115064 Apr 26 14:19
> >>>>>> Peds_RoutBirthNote_1.rtf.xmi
> >>>>>>> -rwxrwx---+ 1 Administrators Domain Users 101234 Apr 26 14:19
> >>>>>> VascSurg_AAA_Leak_1.rtf.xmi
> >>>>>>> -rwxrwx---+ 1 Administrators Domain Users 98015 Apr 26 14:19
> >>>>>> VascSurg_FollowUp_1.rtf.xmi
> >>>>>>> -rwxrwx---+ 1 Administrators Domain Users 218863 Apr 26 14:19
> >>>>>> VascSurg_PVD_1.rtf.xmi
> >>>>>>> -rwxrwx---+ 1 Administrators Domain Users 72902 Apr 26 14:19
> >>>>>> VascSurg_RO-AAA_1.rtf.xmi
> >>>>>>> -rwxrwx---+ 1 Administrators Domain Users 90825 Apr 26 14:19
> >>>>>> VascSurg_RO-DVT.rtf.xmi
> >>>>>>> -rwxrwx---+ 1 Administrators Domain Users 90827 Apr 26 14:19
> >>>>>> VascSurg_RO-DVT_1.rtf.xmi
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> Bad news: it looks like the hsqldb port of lvg2008 is not working.
> >>>>>>>
> >>>>>>> Caused by: org.hsqldb.HsqlException: error in script file line: 61
> >>>>>> C:\Spiffy\prj_ctakes_401\dev\ctakes-lvg-res\target\classes\o
> >>>>>> rg\apache\ctakes\lvg\data\HSqlDb\lvg2008 java.io.IOException: read
> >>>>>> beyond end of file in statement [SET TABLE PUBLIC.INFLECTION INDEX
> >>> '3198299
> >>>>>> 60557 3198299 53129 0 0 0 0 1210464']
> >>>>>>>
> >>>>>>> Caused by: org.hsqldb.HsqlException: Caused by:
> java.io.IOException:
> >>>>>> read beyond end of file
> >>>>>>>
> >>>>>>>
> >>>>>>> At any rate, the code works but I think that something is missing
> >>> from
> >>>>>> your configuration.
> >>>>>>> Since it is a personal development environment you are kind of on
> >>> your
> >>>>>> own.
> >>>>>>> Good luck,
> >>>>>>> Sean
> >>>>>>>
> >>>>>>> P.S. Get rid of the ctakes-resources-umls2011ab artifact in your
> >>> pom.
> >>>>>> It isn't doing anything.
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> -----Original Message-----
> >>>>>>> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
> >>>>>>> Sent: Wednesday, April 26, 2017 12:46 PM
> >>>>>>> To: dev@ctakes.apache.org
> >>>>>>> Subject: Re: URI is not hierarchical
> >>>>>>>
> >>>>>>> I am definitely still seeing the “URI is not hierarchical” issue.
> >>>>>> Here’s a piece of information that might help you figure out what
> the
> >>>>>> problem is:
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> It only happens if the pipeline includes dictionary lookup. For
> >>>>>> instance, this one fails:
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> 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=fs67G
> >>>>>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevR
> >>>>>> An-a92vTj9x79u08OjKfQ9U4&s=MKa09-UzlhjAB_1jVyGOpVo1UHWrMDqjW
> >>> iVAnk0jfPE&e=
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> But this one succeeds:
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
> >>>>>> com_dmitriydligach_ctakes-2Dmisc_blob_master_src_main_java_
> >>>>>> org_apache_ctakes_pipelines_BasicPipeline.java&d=DwIGaQ&c=
> >>>>>> qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpy
> >>>>>> IisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevRAn-a92vTj
> >>>>>> 9x79u08OjKfQ9U4&s=U0zGx-soIiYY64nHK_tIAIpeind9vdIrAuDQIxh-4ek&e=
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> (it’s the same as the first one, but the dictionary lookup part is
> >>>>>> removed).
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> Dima
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>> On Apr 26, 2017, at 11:37, Finan, Sean
> >>> <Sean.Finan@childrens.harvard.
> >>>>>> edu> wrote:
> >>>>>>>
> >>>>>>>>
> >>>>>>>
> >>>>>>>> Hi again Dima,
> >>>>>>>
> >>>>>>>>
> >>>>>>>
> >>>>>>>> The piper files are not meant to replace uimafit. Uimafit is
> great
> >>>>>> for many purposes.
> >>>>>>>
> >>>>>>>>
> >>>>>>>
> >>>>>>>> As for that annoying old "URI is not hierarchical" bug, a while
> >>> back I
> >>>>>> checked in a fix that worked for me. Since then I cannot duplicate
> >>> it.
> >>>>>>>
> >>>>>>>>
> >>>>>>>
> >>>>>>>> Sean
> >>>>>>>
> >>>>>>>>
> >>>>>>>
> >>>>>>>> -----Original Message-----
> >>>>>>>
> >>>>>>>> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
> >>>>>>>
> >>>>>>>> Sent: Wednesday, April 26, 2017 12:18 PM
> >>>>>>>
> >>>>>>>> To: dev@ctakes.apache.org
> >>>>>>>
> >>>>>>>> Subject: Re: URI is not hierarchical
> >>>>>>>
> >>>>>>>>
> >>>>>>>
> >>>>>>>> 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.Finan@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:ddligach@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=fs67G
> >>>>>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=xe6RaWm66aSyUeXjU20
> >>>>>> x8dEc3xfYTHbadlwhgSdrIsw&s=ixO9vX_WJ7p-dpJc0RdnzRfjwQqbNw4gk
> >>> Lwf0SSpp0I&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.Finan@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.a
> >>>>>> pache.org_confluence_display_CTAKES_Piper-2BFiles&d=DwIGaQ&c
> >>>>>> =qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTp
> >>>>>> yIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=xe6RaWm66aSyUeXjU20x8dEc3xf
> >>>>>> YTHbadlwhgSdrIsw&s=pNVLJSOBMk5orJZ4Oy4ZwtpkPp0tU48-g1qxtpIBucw&e=
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> -----Original Message-----
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> From: Dligach, Dmitriy [mailto:ddligach@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=fs67G
> >>>>>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf
> >>>>>> _qgdQj3HYIeLCeKr9Q303b0Q&s=NWoDwPNChJkDhFseM3j8Gi7KNDdVqzi1B
> >>> Ft0onalf9I&e=
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> from command line as follows:
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> mvn exec:java -Dexec.mainClass=“org.apache.c
> >>>>>> takes.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/ctakesresour
> >>>>>> ces/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/resource
> >>>>>> s/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.t
> >>>>>> ype.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/l
> >>>>>> ookup/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-2Dw
> >>>>>> s.nlm.nih.gov_restful_isValidUMLSUser&d=DwIGaQ&c=qS4goWBT7po
> >>>>>> plM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP
> >>>>>> 6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q30
> >>>>>> 3b0Q&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-2Dw
> >>>>>> s.nlm.nih.gov_restful_isValidUMLSUser&d=DwIGaQ&c=qS4goWBT7po
> >>>>>> plM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP
> >>>>>> 6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q30
> >>>>>> 3b0Q&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/look
> >>>>>> up/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(Lv
> >>>>>> gCmdApiResourceImpl.java:65)
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> at org.apache.uima.resource.impl.
> ResourceManager_impl.registerR
> >>>>>> esource(ResourceManager_impl.java:628)
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> at org.apache.uima.resource.impl.
> ResourceManager_impl.initializ
> >>>>>> eExternalResources(ResourceManager_impl.java:464)
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> at org.apache.uima.resource.Resource_ImplBase.initialize(
> Resour
> >>>>>> ce_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.
> produceResou
> >>>>>> rce(AnalysisEngineFactory_impl.java:94)
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> at org.apache.uima.impl.CompositeResourceFactory_impl.
> produceRe
> >>>>>> source(CompositeResourceFactory_impl.java:62)
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> at org.apache.uima.UIMAFramework.
> produceResource(UIMAFramework.
> >>>>>> java:279)
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> at org.apache.uima.UIMAFramework.
> produceAnalysisEngine(UIMAFram
> >>>>>> ework.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.
> createEngi
> >>>>>> ne(AnalysisEngineFactory.java:711)
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> at org.apache.uima.fit.factory.AggregateBuilder.
> createAggregate
> >>>>>> (AggregateBuilder.java:207)
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> at org.apache.ctakes.pipelines.UmlsLookupPipeline.main(
> UmlsLook
> >>>>>> upPipeline.java:66)
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> at sun.reflect.NativeMethodAccessorImpl.
> invoke(NativeMethodAcce
> >>>>>> ssorImpl.java:62)
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>> at sun.reflect.DelegatingMethodAccessorImpl.
> invoke(DelegatingMe
> >>>>>> thodAccessorImpl.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-p
> >>> lugin: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_MA
> >>>>>> VEN_MojoExecutionException&d=DwIGaQ&c=qS4goWBT7poplM69zy_3x
> >>>>>> hKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4
> >>>>>> f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q303b0Q&s=
> >>>>>> JfA-JsX45OHwuDl_DNkICQUwoIOMrYhdSxNKV1k_Ig4&e=
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>>
> >>>>>>>
> >>>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>
> >>>>>>
> >>>>>
> >>>
> >>>
> >>
>
>
Re: URI is not hierarchical
Posted by "Dligach, Dmitriy" <dd...@luc.edu>.
Hi James,
> Copy the lvg directory that's in
>
> %CTAKES_HOME%/resources/org/apache/ctakes/
Sorry, in my case, I am only seeing one directory here called ‘dictionary’. Is that the one or should there be something called ‘lvg’?
Dima
> to be under the target/classes/org/apache/ctakes directory that's within
> your local copy of ctakes-misc
>
> so for example, on my system, after the copy, I see
> C:\from.svn\ctakes-misc.git\trunk\target\classes\org\
> apache\ctakes\lvg\data\config\lvg.properties
>
> (For anyone else reading this, that resources directory will show up when
> you do mvn clean install of cTAKES)
>
> If you want lvg to use the actual lvg resources, you can't just copy the
> lvg.properties file for this workaround, you have to copy the entire
> subtree, or it will create an empty lvg database.
>
>
> I'll check out the StringIndexOutOfBoundsException on Monday unless someone
> else beats me to it before then.
>
>
> FYI, to test this workaround, before I did the copy, I was seeing
>
> 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)
>
> After I copied that lvg directory, I was then able see output in the
> outputDirectory
> defined by UmlsLookupPipeline.java
>
> FYI #2, I'm using Win 7 Pro. This workaround should work for linux/mac but
> was not tested there.
>
> FYI #3, this was using your idea of not having ctakes-misc be under ctakes.
> thanks for that tip! keeps things nicely separated - no need to update
> the parent pom at all.
>
>
>
> On Sat, Apr 29, 2017 at 2:00 AM, James Masanz <ma...@gmail.com>
> wrote:
>
>> Hi Dima,
>>
>> what revision of trunk are you using? I'm getting an error you weren't
>> seeing so I'm guessing it's because I checked out ctakes just today.
>>
>> Caused by: java.lang.StringIndexOutOfBoundsException: String index out of
>> range: -7
>> at java.lang.String.substring(String.java:1967)
>> at org.apache.ctakes.dictionary.lookup2.util.
>> JdbcConnectionFactory.getConnectionUrl(JdbcConnectionFactory.java:110)
>> at org.apache.ctakes.dictionary.lookup2.util.
>> JdbcConnectionFactory.getConnection(JdbcConnectionFactory.java:63)
>> at org.apache.ctakes.dictionary.lookup2.dictionary.
>> JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:91)
>> at org.apache.ctakes.dictionary.lookup2.dictionary.
>> JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:72)
>> at org.apache.ctakes.dictionary.lookup2.dictionary.
>> UmlsJdbcRareWordDictionary.<init>(UmlsJdbcRareWordDictionary.java:31)
>> ... 27 more
>>
>> FYI, I created the directories needed by UmlsLookupPipeline.java for
>> chunker-model.zip and inputDirectory and outputDirectory, and I get
>> the above regardless of whether I use text input file containing just "pain
>> in left knee started on Wednesday." or if I use
>> GenSurg_UmbilicalHernia_1.rtf as the input file instead.
>>
>>
>> On Fri, Apr 28, 2017 at 5:48 PM, Dligach, Dmitriy <dd...@luc.edu>
>> wrote:
>>
>>> Hi James,
>>>
>>> Thank you so much for looking into this!
>>>
>>> Your general setup matches mine. I also do:
>>>
>>> 1. svn co https://svn.apache.org/repos/asf/ctakes/trunk/
>>> 2. git clone https://github.com/dmitriydligach/ctakes-misc.git (in
>>> trunk/)
>>> 3. mvn clean compile (in trunk/)
>>> 4. mvn clean compile (in ctakes-misc/)
>>>
>>> BTW, I just discovered that it’s not necessary to check out a fresh copy
>>> of ctakes-misc into a subdirectory in trunk. It will build no matter where
>>> it is on your system as long as you first do an ‘mvn clean compile’ in
>>> trunk/ (without it, ctakes-misc/ will not build).
>>>
>>> Thanks again, James.
>>>
>>> Dima
>>>
>>>
>>>
>>>> On Apr 28, 2017, at 16:30, James Masanz <ma...@gmail.com> wrote:
>>>>
>>>> Hi Dima,
>>>>
>>>> Just to let you know I am taking a look at this. More later, if not
>>> today,
>>>> then tomorrow. FYI here is where I'm at so far.
>>>>
>>>> I checked out a fresh copy of ctakes trunk and put files from your
>>>> ctakes-misc into a subdirectory called ctakes-misc, and I updated my
>>> local
>>>> copy of the main pom.xml for ctakes to include ctakes-misc.
>>>>
>>>> I am able to reproduce getting URI is not hierarchical just by letting
>>>> tests run during "mvn clean install":
>>>>
>>>> Tests in error:
>>>> testPipeline(org.apache.ctakes.temporal.ae.BackwardsTimeAnno
>>> tatorTest):
>>>> URI is not hierarchical
>>>>
>>>> testPipeline(org.apache.ctakes.temporal.ae.ContextualModalit
>>> yAnnotatorTest):
>>>> URI is not hierarchical
>>>> testPipeline(org.apache.ctakes.temporal.ae.EventAnnotatorTest): URI is
>>>> not hierarchical
>>>>
>>>> testPipeline(org.apache.ctakes.temporal.ae.EventEventRelatio
>>> nAnnotatorTest):
>>>> URI is not hierarchical
>>>>
>>>> testPipeline(org.apache.ctakes.temporal.ae.EventTimeRelation
>>> AnnotatorTest):
>>>> URI is not hierarchical
>>>>
>>>>
>>>> On Fri, Apr 28, 2017 at 12:27 PM, James Masanz <ma...@gmail.com>
>>>> wrote:
>>>>
>>>>>
>>>>> Going back to your original email, I notice cTAKES is referencing
>>> lvg.properties
>>>>> as being within a jar
>>>>>
>>>>> 14 Apr 2017 11:04:24 INFO LvgAnnotator - URL for lvg.properties
>>>>> =file:/home/dima/.m2/repository/net/sourceforge/ctakesresour
>>> ces/ctakes-
>>>>> resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.
>>>>> 0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
>>>>>
>>>>> But I also see in LvgCmdApiResourceImpl.java the following code, which
>>> is
>>>>> trying to handle it as a File, not a stream. :(
>>>>>
>>>>> File configFile = new File(dr.getUri());
>>>>> configFileName = configFile.getPath();
>>>>>
>>>>> At first glance, looks like LvgCmdApiResourceImpl needs updating.
>>>>>
>>>>> As a workaround, you could try extracting the lvg subdirectory from
>>>>> ctakes-resources-4.0-bin.zip that's on sourceforge [1] into something
>>> on
>>>>> the classpath so the lvg.propertiesfile appears under
>>>>>
>>>>> org/apache/ctakes/lvg/data/config/lvg.properties
>>>>>
>>>>> You might also need to have the rest of the files and directories under
>>>>> org/apache/ctakes/lvg/data to also be outside the jar, not sure
>>> offhand.
>>>>>
>>>>> I can try that out this afternoon.
>>>>>
>>>>> [1] https://sourceforge.net/projects/ctakesresources/
>>>>> files/ctakes-resources-4.0-bin.zip/download
>>>>>
>>>>>
>>>>> On Wed, Apr 26, 2017 at 3:29 PM, Dligach, Dmitriy <dd...@luc.edu>
>>>>> wrote:
>>>>>
>>>>>> Hi Sean,
>>>>>>
>>>>>> First of all, a huge thank you for taking time to debug this issue. I
>>>>>> really appreciate your help.
>>>>>>
>>>>>> Second, I think my main message somehow got lost in translation
>>> (sorry, I
>>>>>> should’ve included it for clarity with my recent emails). I never had
>>> any
>>>>>> trouble running this pipeline in Eclipse. The “URI is not
>>> hierarchical”
>>>>>> error only happens when I run it from command line.
>>>>>>
>>>>>> I run it using the following maven command:
>>>>>>
>>>>>> mvn exec:java -Dexec.mainClass="org.apache.c
>>>>>> takes.pipelines.UmlsLookupPipeline" -Dexec.args=""
>>> -Dctakes.umlsuser=<my
>>>>>> umls login name> -Dctakes.umlspw=<my umls password>
>>>>>>
>>>>>> As I said in my previous email, the other pipeline (that does not have
>>>>>> dictionary lookup) runs fine at command line. The error only happens
>>> when I
>>>>>> run pipelines containing dictionary lookup.
>>>>>>
>>>>>> Dima
>>>>>>
>>>>>>
>>>>>>
>>>>>>> On Apr 26, 2017, at 13:36, Finan, Sean <Sean.Finan@childrens.harvard.
>>>>>> edu> wrote:
>>>>>>>
>>>>>>> Hi Dima,
>>>>>>>
>>>>>>> Good news: no uri hierarchical error.
>>>>>>>
>>>>>>> All that I did was import your ctakes-misc pom as a maven project in
>>>>>> intellij. Then I created a run configuration with my sandbox as the
>>>>>> working directory, ctakes-misc as the classpath module, and my umls
>>>>>> credentials in the environment.
>>>>>>> All database files were found, the pipeline ran, and I got output:
>>>>>>> total 2448
>>>>>>> drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:19 .
>>>>>>> drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:18 ..
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 187675 Apr 26 14:19
>>>>>> GenSurg_UmbilicalHernia_1.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 238984 Apr 26 14:19
>>>>>> OBGYN_Gen_Abscess_1.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 82308 Apr 26 14:19
>>>>>> OBGYN_HysterectomyAndBSO_1.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 115983 Apr 26 14:19
>>>>>> OBGYN_IUD_1.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 35919 Apr 26 14:19
>>>>>> OBGYN_LaborProgressNote_1.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 112460 Apr 26 14:19
>>>>>> OBGYN_MVAPrego_1.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 173695 Apr 26 14:19
>>>>>> OBGYN_PROMCheck_1.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 340626 Apr 26 14:19
>>>>>> Peds_Dysphagia_1.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 390928 Apr 26 14:19
>>>>>> Peds_FebrileSez_1.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 115064 Apr 26 14:19
>>>>>> Peds_RoutBirthNote_1.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 101234 Apr 26 14:19
>>>>>> VascSurg_AAA_Leak_1.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 98015 Apr 26 14:19
>>>>>> VascSurg_FollowUp_1.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 218863 Apr 26 14:19
>>>>>> VascSurg_PVD_1.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 72902 Apr 26 14:19
>>>>>> VascSurg_RO-AAA_1.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 90825 Apr 26 14:19
>>>>>> VascSurg_RO-DVT.rtf.xmi
>>>>>>> -rwxrwx---+ 1 Administrators Domain Users 90827 Apr 26 14:19
>>>>>> VascSurg_RO-DVT_1.rtf.xmi
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Bad news: it looks like the hsqldb port of lvg2008 is not working.
>>>>>>>
>>>>>>> Caused by: org.hsqldb.HsqlException: error in script file line: 61
>>>>>> C:\Spiffy\prj_ctakes_401\dev\ctakes-lvg-res\target\classes\o
>>>>>> rg\apache\ctakes\lvg\data\HSqlDb\lvg2008 java.io.IOException: read
>>>>>> beyond end of file in statement [SET TABLE PUBLIC.INFLECTION INDEX
>>> '3198299
>>>>>> 60557 3198299 53129 0 0 0 0 1210464']
>>>>>>>
>>>>>>> Caused by: org.hsqldb.HsqlException: Caused by: java.io.IOException:
>>>>>> read beyond end of file
>>>>>>>
>>>>>>>
>>>>>>> At any rate, the code works but I think that something is missing
>>> from
>>>>>> your configuration.
>>>>>>> Since it is a personal development environment you are kind of on
>>> your
>>>>>> own.
>>>>>>> Good luck,
>>>>>>> Sean
>>>>>>>
>>>>>>> P.S. Get rid of the ctakes-resources-umls2011ab artifact in your
>>> pom.
>>>>>> It isn't doing anything.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> -----Original Message-----
>>>>>>> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
>>>>>>> Sent: Wednesday, April 26, 2017 12:46 PM
>>>>>>> To: dev@ctakes.apache.org
>>>>>>> Subject: Re: URI is not hierarchical
>>>>>>>
>>>>>>> I am definitely still seeing the “URI is not hierarchical” issue.
>>>>>> Here’s a piece of information that might help you figure out what the
>>>>>> problem is:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> It only happens if the pipeline includes dictionary lookup. For
>>>>>> instance, this one fails:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> 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=fs67G
>>>>>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevR
>>>>>> An-a92vTj9x79u08OjKfQ9U4&s=MKa09-UzlhjAB_1jVyGOpVo1UHWrMDqjW
>>> iVAnk0jfPE&e=
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> But this one succeeds:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
>>>>>> com_dmitriydligach_ctakes-2Dmisc_blob_master_src_main_java_
>>>>>> org_apache_ctakes_pipelines_BasicPipeline.java&d=DwIGaQ&c=
>>>>>> qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpy
>>>>>> IisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevRAn-a92vTj
>>>>>> 9x79u08OjKfQ9U4&s=U0zGx-soIiYY64nHK_tIAIpeind9vdIrAuDQIxh-4ek&e=
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> (it’s the same as the first one, but the dictionary lookup part is
>>>>>> removed).
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Dima
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>> On Apr 26, 2017, at 11:37, Finan, Sean
>>> <Sean.Finan@childrens.harvard.
>>>>>> edu> wrote:
>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>> Hi again Dima,
>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>> The piper files are not meant to replace uimafit. Uimafit is great
>>>>>> for many purposes.
>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>> As for that annoying old "URI is not hierarchical" bug, a while
>>> back I
>>>>>> checked in a fix that worked for me. Since then I cannot duplicate
>>> it.
>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>> Sean
>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>> -----Original Message-----
>>>>>>>
>>>>>>>> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
>>>>>>>
>>>>>>>> Sent: Wednesday, April 26, 2017 12:18 PM
>>>>>>>
>>>>>>>> To: dev@ctakes.apache.org
>>>>>>>
>>>>>>>> Subject: Re: URI is not hierarchical
>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>> 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.Finan@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:ddligach@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=fs67G
>>>>>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=xe6RaWm66aSyUeXjU20
>>>>>> x8dEc3xfYTHbadlwhgSdrIsw&s=ixO9vX_WJ7p-dpJc0RdnzRfjwQqbNw4gk
>>> Lwf0SSpp0I&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.Finan@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.a
>>>>>> pache.org_confluence_display_CTAKES_Piper-2BFiles&d=DwIGaQ&c
>>>>>> =qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTp
>>>>>> yIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=xe6RaWm66aSyUeXjU20x8dEc3xf
>>>>>> YTHbadlwhgSdrIsw&s=pNVLJSOBMk5orJZ4Oy4ZwtpkPp0tU48-g1qxtpIBucw&e=
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>> -----Original Message-----
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>> From: Dligach, Dmitriy [mailto:ddligach@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=fs67G
>>>>>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf
>>>>>> _qgdQj3HYIeLCeKr9Q303b0Q&s=NWoDwPNChJkDhFseM3j8Gi7KNDdVqzi1B
>>> Ft0onalf9I&e=
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>> from command line as follows:
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>> mvn exec:java -Dexec.mainClass=“org.apache.c
>>>>>> takes.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/ctakesresour
>>>>>> ces/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/resource
>>>>>> s/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.t
>>>>>> ype.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/l
>>>>>> ookup/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-2Dw
>>>>>> s.nlm.nih.gov_restful_isValidUMLSUser&d=DwIGaQ&c=qS4goWBT7po
>>>>>> plM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP
>>>>>> 6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q30
>>>>>> 3b0Q&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-2Dw
>>>>>> s.nlm.nih.gov_restful_isValidUMLSUser&d=DwIGaQ&c=qS4goWBT7po
>>>>>> plM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP
>>>>>> 6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q30
>>>>>> 3b0Q&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/look
>>>>>> up/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(Lv
>>>>>> gCmdApiResourceImpl.java:65)
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>> at org.apache.uima.resource.impl.ResourceManager_impl.registerR
>>>>>> esource(ResourceManager_impl.java:628)
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>> at org.apache.uima.resource.impl.ResourceManager_impl.initializ
>>>>>> eExternalResources(ResourceManager_impl.java:464)
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>> at org.apache.uima.resource.Resource_ImplBase.initialize(Resour
>>>>>> ce_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.produceResou
>>>>>> rce(AnalysisEngineFactory_impl.java:94)
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>> at org.apache.uima.impl.CompositeResourceFactory_impl.produceRe
>>>>>> source(CompositeResourceFactory_impl.java:62)
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.
>>>>>> java:279)
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFram
>>>>>> ework.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.createEngi
>>>>>> ne(AnalysisEngineFactory.java:711)
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>> at org.apache.uima.fit.factory.AggregateBuilder.createAggregate
>>>>>> (AggregateBuilder.java:207)
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>> at org.apache.ctakes.pipelines.UmlsLookupPipeline.main(UmlsLook
>>>>>> upPipeline.java:66)
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAcce
>>>>>> ssorImpl.java:62)
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMe
>>>>>> thodAccessorImpl.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-p
>>> lugin: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_MA
>>>>>> VEN_MojoExecutionException&d=DwIGaQ&c=qS4goWBT7poplM69zy_3x
>>>>>> hKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4
>>>>>> f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q303b0Q&s=
>>>>>> JfA-JsX45OHwuDl_DNkICQUwoIOMrYhdSxNKV1k_Ig4&e=
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>
>>>
>>
Re: URI is not hierarchical
Posted by James Masanz <ma...@gmail.com>.
Hi Dima,
I modified my local copy of FileLocator to avoid the
StringIndexOutOfBoundsException I was seeing using HEAD, and here's the
workaround for the problem you were seeing until the code change is made to
LvgCmdApiResourceImpl:
Copy the lvg directory that's in
%CTAKES_HOME%/resources/org/apache/ctakes/
to be under the target/classes/org/apache/ctakes directory that's within
your local copy of ctakes-misc
so for example, on my system, after the copy, I see
C:\from.svn\ctakes-misc.git\trunk\target\classes\org\
apache\ctakes\lvg\data\config\lvg.properties
(For anyone else reading this, that resources directory will show up when
you do mvn clean install of cTAKES)
If you want lvg to use the actual lvg resources, you can't just copy the
lvg.properties file for this workaround, you have to copy the entire
subtree, or it will create an empty lvg database.
I'll check out the StringIndexOutOfBoundsException on Monday unless someone
else beats me to it before then.
FYI, to test this workaround, before I did the copy, I was seeing
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)
After I copied that lvg directory, I was then able see output in the
outputDirectory
defined by UmlsLookupPipeline.java
FYI #2, I'm using Win 7 Pro. This workaround should work for linux/mac but
was not tested there.
FYI #3, this was using your idea of not having ctakes-misc be under ctakes.
thanks for that tip! keeps things nicely separated - no need to update
the parent pom at all.
On Sat, Apr 29, 2017 at 2:00 AM, James Masanz <ma...@gmail.com>
wrote:
> Hi Dima,
>
> what revision of trunk are you using? I'm getting an error you weren't
> seeing so I'm guessing it's because I checked out ctakes just today.
>
> Caused by: java.lang.StringIndexOutOfBoundsException: String index out of
> range: -7
> at java.lang.String.substring(String.java:1967)
> at org.apache.ctakes.dictionary.lookup2.util.
> JdbcConnectionFactory.getConnectionUrl(JdbcConnectionFactory.java:110)
> at org.apache.ctakes.dictionary.lookup2.util.
> JdbcConnectionFactory.getConnection(JdbcConnectionFactory.java:63)
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:91)
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:72)
> at org.apache.ctakes.dictionary.lookup2.dictionary.
> UmlsJdbcRareWordDictionary.<init>(UmlsJdbcRareWordDictionary.java:31)
> ... 27 more
>
> FYI, I created the directories needed by UmlsLookupPipeline.java for
> chunker-model.zip and inputDirectory and outputDirectory, and I get
> the above regardless of whether I use text input file containing just "pain
> in left knee started on Wednesday." or if I use
> GenSurg_UmbilicalHernia_1.rtf as the input file instead.
>
>
> On Fri, Apr 28, 2017 at 5:48 PM, Dligach, Dmitriy <dd...@luc.edu>
> wrote:
>
>> Hi James,
>>
>> Thank you so much for looking into this!
>>
>> Your general setup matches mine. I also do:
>>
>> 1. svn co https://svn.apache.org/repos/asf/ctakes/trunk/
>> 2. git clone https://github.com/dmitriydligach/ctakes-misc.git (in
>> trunk/)
>> 3. mvn clean compile (in trunk/)
>> 4. mvn clean compile (in ctakes-misc/)
>>
>> BTW, I just discovered that it’s not necessary to check out a fresh copy
>> of ctakes-misc into a subdirectory in trunk. It will build no matter where
>> it is on your system as long as you first do an ‘mvn clean compile’ in
>> trunk/ (without it, ctakes-misc/ will not build).
>>
>> Thanks again, James.
>>
>> Dima
>>
>>
>>
>> > On Apr 28, 2017, at 16:30, James Masanz <ma...@gmail.com> wrote:
>> >
>> > Hi Dima,
>> >
>> > Just to let you know I am taking a look at this. More later, if not
>> today,
>> > then tomorrow. FYI here is where I'm at so far.
>> >
>> > I checked out a fresh copy of ctakes trunk and put files from your
>> > ctakes-misc into a subdirectory called ctakes-misc, and I updated my
>> local
>> > copy of the main pom.xml for ctakes to include ctakes-misc.
>> >
>> > I am able to reproduce getting URI is not hierarchical just by letting
>> > tests run during "mvn clean install":
>> >
>> > Tests in error:
>> > testPipeline(org.apache.ctakes.temporal.ae.BackwardsTimeAnno
>> tatorTest):
>> > URI is not hierarchical
>> >
>> > testPipeline(org.apache.ctakes.temporal.ae.ContextualModalit
>> yAnnotatorTest):
>> > URI is not hierarchical
>> > testPipeline(org.apache.ctakes.temporal.ae.EventAnnotatorTest): URI is
>> > not hierarchical
>> >
>> > testPipeline(org.apache.ctakes.temporal.ae.EventEventRelatio
>> nAnnotatorTest):
>> > URI is not hierarchical
>> >
>> > testPipeline(org.apache.ctakes.temporal.ae.EventTimeRelation
>> AnnotatorTest):
>> > URI is not hierarchical
>> >
>> >
>> > On Fri, Apr 28, 2017 at 12:27 PM, James Masanz <ma...@gmail.com>
>> > wrote:
>> >
>> >>
>> >> Going back to your original email, I notice cTAKES is referencing
>> lvg.properties
>> >> as being within a jar
>> >>
>> >> 14 Apr 2017 11:04:24 INFO LvgAnnotator - URL for lvg.properties
>> >> =file:/home/dima/.m2/repository/net/sourceforge/ctakesresour
>> ces/ctakes-
>> >> resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.
>> >> 0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
>> >>
>> >> But I also see in LvgCmdApiResourceImpl.java the following code, which
>> is
>> >> trying to handle it as a File, not a stream. :(
>> >>
>> >> File configFile = new File(dr.getUri());
>> >> configFileName = configFile.getPath();
>> >>
>> >> At first glance, looks like LvgCmdApiResourceImpl needs updating.
>> >>
>> >> As a workaround, you could try extracting the lvg subdirectory from
>> >> ctakes-resources-4.0-bin.zip that's on sourceforge [1] into something
>> on
>> >> the classpath so the lvg.propertiesfile appears under
>> >>
>> >> org/apache/ctakes/lvg/data/config/lvg.properties
>> >>
>> >> You might also need to have the rest of the files and directories under
>> >> org/apache/ctakes/lvg/data to also be outside the jar, not sure
>> offhand.
>> >>
>> >> I can try that out this afternoon.
>> >>
>> >> [1] https://sourceforge.net/projects/ctakesresources/
>> >> files/ctakes-resources-4.0-bin.zip/download
>> >>
>> >>
>> >> On Wed, Apr 26, 2017 at 3:29 PM, Dligach, Dmitriy <dd...@luc.edu>
>> >> wrote:
>> >>
>> >>> Hi Sean,
>> >>>
>> >>> First of all, a huge thank you for taking time to debug this issue. I
>> >>> really appreciate your help.
>> >>>
>> >>> Second, I think my main message somehow got lost in translation
>> (sorry, I
>> >>> should’ve included it for clarity with my recent emails). I never had
>> any
>> >>> trouble running this pipeline in Eclipse. The “URI is not
>> hierarchical”
>> >>> error only happens when I run it from command line.
>> >>>
>> >>> I run it using the following maven command:
>> >>>
>> >>> mvn exec:java -Dexec.mainClass="org.apache.c
>> >>> takes.pipelines.UmlsLookupPipeline" -Dexec.args=""
>> -Dctakes.umlsuser=<my
>> >>> umls login name> -Dctakes.umlspw=<my umls password>
>> >>>
>> >>> As I said in my previous email, the other pipeline (that does not have
>> >>> dictionary lookup) runs fine at command line. The error only happens
>> when I
>> >>> run pipelines containing dictionary lookup.
>> >>>
>> >>> Dima
>> >>>
>> >>>
>> >>>
>> >>>> On Apr 26, 2017, at 13:36, Finan, Sean <Sean.Finan@childrens.harvard.
>> >>> edu> wrote:
>> >>>>
>> >>>> Hi Dima,
>> >>>>
>> >>>> Good news: no uri hierarchical error.
>> >>>>
>> >>>> All that I did was import your ctakes-misc pom as a maven project in
>> >>> intellij. Then I created a run configuration with my sandbox as the
>> >>> working directory, ctakes-misc as the classpath module, and my umls
>> >>> credentials in the environment.
>> >>>> All database files were found, the pipeline ran, and I got output:
>> >>>> total 2448
>> >>>> drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:19 .
>> >>>> drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:18 ..
>> >>>> -rwxrwx---+ 1 Administrators Domain Users 187675 Apr 26 14:19
>> >>> GenSurg_UmbilicalHernia_1.rtf.xmi
>> >>>> -rwxrwx---+ 1 Administrators Domain Users 238984 Apr 26 14:19
>> >>> OBGYN_Gen_Abscess_1.rtf.xmi
>> >>>> -rwxrwx---+ 1 Administrators Domain Users 82308 Apr 26 14:19
>> >>> OBGYN_HysterectomyAndBSO_1.rtf.xmi
>> >>>> -rwxrwx---+ 1 Administrators Domain Users 115983 Apr 26 14:19
>> >>> OBGYN_IUD_1.rtf.xmi
>> >>>> -rwxrwx---+ 1 Administrators Domain Users 35919 Apr 26 14:19
>> >>> OBGYN_LaborProgressNote_1.rtf.xmi
>> >>>> -rwxrwx---+ 1 Administrators Domain Users 112460 Apr 26 14:19
>> >>> OBGYN_MVAPrego_1.rtf.xmi
>> >>>> -rwxrwx---+ 1 Administrators Domain Users 173695 Apr 26 14:19
>> >>> OBGYN_PROMCheck_1.rtf.xmi
>> >>>> -rwxrwx---+ 1 Administrators Domain Users 340626 Apr 26 14:19
>> >>> Peds_Dysphagia_1.rtf.xmi
>> >>>> -rwxrwx---+ 1 Administrators Domain Users 390928 Apr 26 14:19
>> >>> Peds_FebrileSez_1.rtf.xmi
>> >>>> -rwxrwx---+ 1 Administrators Domain Users 115064 Apr 26 14:19
>> >>> Peds_RoutBirthNote_1.rtf.xmi
>> >>>> -rwxrwx---+ 1 Administrators Domain Users 101234 Apr 26 14:19
>> >>> VascSurg_AAA_Leak_1.rtf.xmi
>> >>>> -rwxrwx---+ 1 Administrators Domain Users 98015 Apr 26 14:19
>> >>> VascSurg_FollowUp_1.rtf.xmi
>> >>>> -rwxrwx---+ 1 Administrators Domain Users 218863 Apr 26 14:19
>> >>> VascSurg_PVD_1.rtf.xmi
>> >>>> -rwxrwx---+ 1 Administrators Domain Users 72902 Apr 26 14:19
>> >>> VascSurg_RO-AAA_1.rtf.xmi
>> >>>> -rwxrwx---+ 1 Administrators Domain Users 90825 Apr 26 14:19
>> >>> VascSurg_RO-DVT.rtf.xmi
>> >>>> -rwxrwx---+ 1 Administrators Domain Users 90827 Apr 26 14:19
>> >>> VascSurg_RO-DVT_1.rtf.xmi
>> >>>>
>> >>>>
>> >>>>
>> >>>>
>> >>>> Bad news: it looks like the hsqldb port of lvg2008 is not working.
>> >>>>
>> >>>> Caused by: org.hsqldb.HsqlException: error in script file line: 61
>> >>> C:\Spiffy\prj_ctakes_401\dev\ctakes-lvg-res\target\classes\o
>> >>> rg\apache\ctakes\lvg\data\HSqlDb\lvg2008 java.io.IOException: read
>> >>> beyond end of file in statement [SET TABLE PUBLIC.INFLECTION INDEX
>> '3198299
>> >>> 60557 3198299 53129 0 0 0 0 1210464']
>> >>>>
>> >>>> Caused by: org.hsqldb.HsqlException: Caused by: java.io.IOException:
>> >>> read beyond end of file
>> >>>>
>> >>>>
>> >>>> At any rate, the code works but I think that something is missing
>> from
>> >>> your configuration.
>> >>>> Since it is a personal development environment you are kind of on
>> your
>> >>> own.
>> >>>> Good luck,
>> >>>> Sean
>> >>>>
>> >>>> P.S. Get rid of the ctakes-resources-umls2011ab artifact in your
>> pom.
>> >>> It isn't doing anything.
>> >>>>
>> >>>>
>> >>>>
>> >>>> -----Original Message-----
>> >>>> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
>> >>>> Sent: Wednesday, April 26, 2017 12:46 PM
>> >>>> To: dev@ctakes.apache.org
>> >>>> Subject: Re: URI is not hierarchical
>> >>>>
>> >>>> I am definitely still seeing the “URI is not hierarchical” issue.
>> >>> Here’s a piece of information that might help you figure out what the
>> >>> problem is:
>> >>>>
>> >>>>
>> >>>>
>> >>>> It only happens if the pipeline includes dictionary lookup. For
>> >>> instance, this one fails:
>> >>>>
>> >>>>
>> >>>>
>> >>>> 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=fs67G
>> >>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevR
>> >>> An-a92vTj9x79u08OjKfQ9U4&s=MKa09-UzlhjAB_1jVyGOpVo1UHWrMDqjW
>> iVAnk0jfPE&e=
>> >>>>
>> >>>>
>> >>>>
>> >>>> But this one succeeds:
>> >>>>
>> >>>>
>> >>>>
>> >>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
>> >>> com_dmitriydligach_ctakes-2Dmisc_blob_master_src_main_java_
>> >>> org_apache_ctakes_pipelines_BasicPipeline.java&d=DwIGaQ&c=
>> >>> qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpy
>> >>> IisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevRAn-a92vTj
>> >>> 9x79u08OjKfQ9U4&s=U0zGx-soIiYY64nHK_tIAIpeind9vdIrAuDQIxh-4ek&e=
>> >>>>
>> >>>>
>> >>>>
>> >>>> (it’s the same as the first one, but the dictionary lookup part is
>> >>> removed).
>> >>>>
>> >>>>
>> >>>>
>> >>>> Dima
>> >>>>
>> >>>>
>> >>>>
>> >>>>
>> >>>>
>> >>>>
>> >>>>
>> >>>>> On Apr 26, 2017, at 11:37, Finan, Sean
>> <Sean.Finan@childrens.harvard.
>> >>> edu> wrote:
>> >>>>
>> >>>>>
>> >>>>
>> >>>>> Hi again Dima,
>> >>>>
>> >>>>>
>> >>>>
>> >>>>> The piper files are not meant to replace uimafit. Uimafit is great
>> >>> for many purposes.
>> >>>>
>> >>>>>
>> >>>>
>> >>>>> As for that annoying old "URI is not hierarchical" bug, a while
>> back I
>> >>> checked in a fix that worked for me. Since then I cannot duplicate
>> it.
>> >>>>
>> >>>>>
>> >>>>
>> >>>>> Sean
>> >>>>
>> >>>>>
>> >>>>
>> >>>>> -----Original Message-----
>> >>>>
>> >>>>> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
>> >>>>
>> >>>>> Sent: Wednesday, April 26, 2017 12:18 PM
>> >>>>
>> >>>>> To: dev@ctakes.apache.org
>> >>>>
>> >>>>> Subject: Re: URI is not hierarchical
>> >>>>
>> >>>>>
>> >>>>
>> >>>>> 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.Finan@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:ddligach@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=fs67G
>> >>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=xe6RaWm66aSyUeXjU20
>> >>> x8dEc3xfYTHbadlwhgSdrIsw&s=ixO9vX_WJ7p-dpJc0RdnzRfjwQqbNw4gk
>> Lwf0SSpp0I&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.Finan@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.a
>> >>> pache.org_confluence_display_CTAKES_Piper-2BFiles&d=DwIGaQ&c
>> >>> =qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTp
>> >>> yIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=xe6RaWm66aSyUeXjU20x8dEc3xf
>> >>> YTHbadlwhgSdrIsw&s=pNVLJSOBMk5orJZ4Oy4ZwtpkPp0tU48-g1qxtpIBucw&e=
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>>
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>>
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>> -----Original Message-----
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>> From: Dligach, Dmitriy [mailto:ddligach@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=fs67G
>> >>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf
>> >>> _qgdQj3HYIeLCeKr9Q303b0Q&s=NWoDwPNChJkDhFseM3j8Gi7KNDdVqzi1B
>> Ft0onalf9I&e=
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>>
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>>
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>>
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>> from command line as follows:
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>>
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>>
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>>
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>> mvn exec:java -Dexec.mainClass=“org.apache.c
>> >>> takes.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/ctakesresour
>> >>> ces/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/resource
>> >>> s/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.t
>> >>> ype.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/l
>> >>> ookup/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-2Dw
>> >>> s.nlm.nih.gov_restful_isValidUMLSUser&d=DwIGaQ&c=qS4goWBT7po
>> >>> plM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP
>> >>> 6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q30
>> >>> 3b0Q&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-2Dw
>> >>> s.nlm.nih.gov_restful_isValidUMLSUser&d=DwIGaQ&c=qS4goWBT7po
>> >>> plM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP
>> >>> 6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q30
>> >>> 3b0Q&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/look
>> >>> up/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(Lv
>> >>> gCmdApiResourceImpl.java:65)
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>>
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>> at org.apache.uima.resource.impl.ResourceManager_impl.registerR
>> >>> esource(ResourceManager_impl.java:628)
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>>
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>> at org.apache.uima.resource.impl.ResourceManager_impl.initializ
>> >>> eExternalResources(ResourceManager_impl.java:464)
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>>
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>> at org.apache.uima.resource.Resource_ImplBase.initialize(Resour
>> >>> ce_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.produceResou
>> >>> rce(AnalysisEngineFactory_impl.java:94)
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>>
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>> at org.apache.uima.impl.CompositeResourceFactory_impl.produceRe
>> >>> source(CompositeResourceFactory_impl.java:62)
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>>
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.
>> >>> java:279)
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>>
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFram
>> >>> ework.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.createEngi
>> >>> ne(AnalysisEngineFactory.java:711)
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>>
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>> at org.apache.uima.fit.factory.AggregateBuilder.createAggregate
>> >>> (AggregateBuilder.java:207)
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>>
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>> at org.apache.ctakes.pipelines.UmlsLookupPipeline.main(UmlsLook
>> >>> upPipeline.java:66)
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>>
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>>
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAcce
>> >>> ssorImpl.java:62)
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>>
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMe
>> >>> thodAccessorImpl.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-p
>> lugin: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_MA
>> >>> VEN_MojoExecutionException&d=DwIGaQ&c=qS4goWBT7poplM69zy_3x
>> >>> hKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4
>> >>> f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q303b0Q&s=
>> >>> JfA-JsX45OHwuDl_DNkICQUwoIOMrYhdSxNKV1k_Ig4&e=
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>>
>> >>>>
>> >>>>>
>> >>>>
>> >>>>
>> >>>>
>> >>>
>> >>>
>> >>
>>
>>
>
RE: URI is not hierarchical
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Ok thanks, I found the problem and checked in a fix.
From: James Masanz [mailto:masanz.james@gmail.com]
Sent: Saturday, April 29, 2017 10:59 AM
To: dev@ctakes.apache.org
Subject: Re: URI is not hierarchical
Attached is a snippet of the console messages
On Sat, Apr 29, 2017 at 9:18 AM, Finan, Sean <Se...@childrens.harvard.edu>> wrote:
Woah, I've never seen that. How did that happen? Is there another bug? The FileLocator should have logged a very long message saying "I couldn't find it here or there or the other place ..." and then thrown a FileNotFoundException.
-----Original Message-----
From: James Masanz [mailto:masanz.james@gmail.com<ma...@gmail.com>]
Sent: Saturday, April 29, 2017 2:00 AM
To: dev@ctakes.apache.org<ma...@ctakes.apache.org>
Subject: Re: URI is not hierarchical
Hi Dima,
what revision of trunk are you using? I'm getting an error you weren't seeing so I'm guessing it's because I checked out ctakes just today.
Caused by: java.lang.StringIndexOutOfBoundsException: String index out of
range: -7
at java.lang.String.substring(String.java:1967)
at
org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnectionUrl(JdbcConnectionFactory.java:110)
at
org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnection(JdbcConnectionFactory.java:63)
at
org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:91)
at
org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:72)
at
org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary.<init>(UmlsJdbcRareWordDictionary.java:31)
... 27 more
FYI, I created the directories needed by UmlsLookupPipeline.java for
chunker-model.zip and inputDirectory and outputDirectory, and I get
the above regardless of whether I use text input file containing just "pain in left knee started on Wednesday." or if I use GenSurg_UmbilicalHernia_1.rtf as the input file instead.
On Fri, Apr 28, 2017 at 5:48 PM, Dligach, Dmitriy <dd...@luc.edu>> wrote:
> Hi James,
>
> Thank you so much for looking into this!
>
> Your general setup matches mine. I also do:
>
> 1. svn co
> https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_re
> pos_asf_ctakes_trunk_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCo
> ppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Lc9XlOnpIxXTTjv
> RKjUkyEK6iZXUXjRQhnbtKubbuQQ&s=ulRVEvEVpyQ8zZjXbCF2pY_ejjjoFaDYOnMk1l0
> Fez0&e= 2. git clone
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_dmitri
> ydligach_ctakes-2Dmisc.git&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMS
> dioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Lc9XlOnpIx
> XTTjvRKjUkyEK6iZXUXjRQhnbtKubbuQQ&s=vwWZxpuAYNjunq6khejHsCaw12XBURfSRj
> mZvfbA8TA&e= (in trunk/) 3. mvn clean compile (in trunk/) 4. mvn
> clean compile (in ctakes-misc/)
>
> BTW, I just discovered that it’s not necessary to check out a fresh
> copy of ctakes-misc into a subdirectory in trunk. It will build no
> matter where it is on your system as long as you first do an ‘mvn
> clean compile’ in trunk/ (without it, ctakes-misc/ will not build).
>
> Thanks again, James.
>
> Dima
>
>
>
> > On Apr 28, 2017, at 16:30, James Masanz <ma...@gmail.com>> wrote:
> >
> > Hi Dima,
> >
> > Just to let you know I am taking a look at this. More later, if not
> today,
> > then tomorrow. FYI here is where I'm at so far.
> >
> > I checked out a fresh copy of ctakes trunk and put files from your
> > ctakes-misc into a subdirectory called ctakes-misc, and I updated my
> local
> > copy of the main pom.xml for ctakes to include ctakes-misc.
> >
> > I am able to reproduce getting URI is not hierarchical just by
> > letting tests run during "mvn clean install":
> >
> > Tests in error:
> > testPipeline(org.apache.ctakes.temporal.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__ctakes.temporal.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=fnp4lyT_3SV-Jso9YCBz41xa9CJnHxke0J20sjdWqZM&s=Akb9JcogedoWi_H0Ci3qCN1JhvlJ_djwdkHcfBcDOlA&e=>.BackwardsTimeAnnotatorTest):
> > URI is not hierarchical
> >
> > testPipeline(org.apache.ctakes.temporal.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__org.apache.ctakes.temporal.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=fnp4lyT_3SV-Jso9YCBz41xa9CJnHxke0J20sjdWqZM&s=1yjOzRNpKYbwnF6GMk0tilvpRgjcyFahqgsCtlgXuCI&e=>.
> ContextualModalityAnnotatorTest):
> > URI is not hierarchical
> > testPipeline(org.apache.ctakes.temporal.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__ctakes.temporal.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=fnp4lyT_3SV-Jso9YCBz41xa9CJnHxke0J20sjdWqZM&s=Akb9JcogedoWi_H0Ci3qCN1JhvlJ_djwdkHcfBcDOlA&e=>.EventAnnotatorTest): URI
> > is not hierarchical
> >
> > testPipeline(org.apache.ctakes.temporal.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__org.apache.ctakes.temporal.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=fnp4lyT_3SV-Jso9YCBz41xa9CJnHxke0J20sjdWqZM&s=1yjOzRNpKYbwnF6GMk0tilvpRgjcyFahqgsCtlgXuCI&e=>.
> EventEventRelationAnnotatorTest):
> > URI is not hierarchical
> >
> > testPipeline(org.apache.ctakes.temporal.ae<https://urldefense.proofpoint.com/v2/url?u=http-3A__org.apache.ctakes.temporal.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=fnp4lyT_3SV-Jso9YCBz41xa9CJnHxke0J20sjdWqZM&s=1yjOzRNpKYbwnF6GMk0tilvpRgjcyFahqgsCtlgXuCI&e=>.
> EventTimeRelationAnnotatorTest):
> > URI is not hierarchical
> >
> >
> > On Fri, Apr 28, 2017 at 12:27 PM, James Masanz
> > <ma...@gmail.com>>
> > wrote:
> >
> >>
> >> Going back to your original email, I notice cTAKES is referencing
> lvg.properties
> >> as being within a jar
> >>
> >> 14 Apr 2017 11:04:24 INFO LvgAnnotator - URL for lvg.properties
> >> =file:/home/dima/.m2/repository/net/sourceforge/ctakesresources/cta
> >> kes- resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.
> >> 0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
> >>
> >> But I also see in LvgCmdApiResourceImpl.java the following code,
> >> which
> is
> >> trying to handle it as a File, not a stream. :(
> >>
> >> File configFile = new File(dr.getUri());
> >> configFileName = configFile.getPath();
> >>
> >> At first glance, looks like LvgCmdApiResourceImpl needs updating.
> >>
> >> As a workaround, you could try extracting the lvg subdirectory from
> >> ctakes-resources-4.0-bin.zip that's on sourceforge [1] into
> >> something on the classpath so the lvg.propertiesfile appears under
> >>
> >> org/apache/ctakes/lvg/data/config/lvg.properties
> >>
> >> You might also need to have the rest of the files and directories
> >> under org/apache/ctakes/lvg/data to also be outside the jar, not
> >> sure
> offhand.
> >>
> >> I can try that out this afternoon.
> >>
> >> [1]
> >> https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.ne
> >> t_projects_ctakesresources_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14
> >> JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Lc9
> >> XlOnpIxXTTjvRKjUkyEK6iZXUXjRQhnbtKubbuQQ&s=dKDOAG-k6QNwD3cIsI31U4zH
> >> k2lGmqXzRjKXI4ySz_s&e= files/ctakes-resources-4.0-bin.zip/download
> >>
> >>
> >> On Wed, Apr 26, 2017 at 3:29 PM, Dligach, Dmitriy
> >> <dd...@luc.edu>>
> >> wrote:
> >>
> >>> Hi Sean,
> >>>
> >>> First of all, a huge thank you for taking time to debug this
> >>> issue. I really appreciate your help.
> >>>
> >>> Second, I think my main message somehow got lost in translation
> (sorry, I
> >>> should’ve included it for clarity with my recent emails). I never
> >>> had
> any
> >>> trouble running this pipeline in Eclipse. The “URI is not hierarchical”
> >>> error only happens when I run it from command line.
> >>>
> >>> I run it using the following maven command:
> >>>
> >>> mvn exec:java -Dexec.mainClass="org.apache.c
> >>> takes.pipelines.UmlsLookupPipeline" -Dexec.args=""
> -Dctakes.umlsuser=<my
> >>> umls login name> -Dctakes.umlspw=<my umls password>
> >>>
> >>> As I said in my previous email, the other pipeline (that does not
> >>> have dictionary lookup) runs fine at command line. The error only
> >>> happens
> when I
> >>> run pipelines containing dictionary lookup.
> >>>
> >>> Dima
> >>>
> >>>
> >>>
> >>>> On Apr 26, 2017, at 13:36, Finan, Sean <Sean.Finan@childrens.harvard.
<mailto:Sean.Finan@childrens.harvard.%0b>> >>> edu> wrote:
> >>>>
> >>>> Hi Dima,
> >>>>
> >>>> Good news: no uri hierarchical error.
> >>>>
> >>>> All that I did was import your ctakes-misc pom as a maven project
> >>>> in
> >>> intellij. Then I created a run configuration with my sandbox as
> >>> the working directory, ctakes-misc as the classpath module, and my
> >>> umls credentials in the environment.
> >>>> All database files were found, the pipeline ran, and I got output:
> >>>> total 2448
> >>>> drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:19 .
> >>>> drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:18 ..
> >>>> -rwxrwx---+ 1 Administrators Domain Users 187675 Apr 26 14:19
> >>> GenSurg_UmbilicalHernia_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 238984 Apr 26 14:19
> >>> OBGYN_Gen_Abscess_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 82308 Apr 26 14:19
> >>> OBGYN_HysterectomyAndBSO_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 115983 Apr 26 14:19
> >>> OBGYN_IUD_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 35919 Apr 26 14:19
> >>> OBGYN_LaborProgressNote_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 112460 Apr 26 14:19
> >>> OBGYN_MVAPrego_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 173695 Apr 26 14:19
> >>> OBGYN_PROMCheck_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 340626 Apr 26 14:19
> >>> Peds_Dysphagia_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 390928 Apr 26 14:19
> >>> Peds_FebrileSez_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 115064 Apr 26 14:19
> >>> Peds_RoutBirthNote_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 101234 Apr 26 14:19
> >>> VascSurg_AAA_Leak_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 98015 Apr 26 14:19
> >>> VascSurg_FollowUp_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 218863 Apr 26 14:19
> >>> VascSurg_PVD_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 72902 Apr 26 14:19
> >>> VascSurg_RO-AAA_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 90825 Apr 26 14:19
> >>> VascSurg_RO-DVT.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 90827 Apr 26 14:19
> >>> VascSurg_RO-DVT_1.rtf.xmi
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> Bad news: it looks like the hsqldb port of lvg2008 is not working.
> >>>>
> >>>> Caused by: org.hsqldb.HsqlException: error in script file line:
> >>>> 61
> >>> C:\Spiffy\prj_ctakes_401\dev\ctakes-lvg-res\target\classes\o
> >>> rg\apache\ctakes\lvg\data\HSqlDb\lvg2008 java.io.IOException: read
> >>> beyond end of file in statement [SET TABLE PUBLIC.INFLECTION INDEX
> '3198299
> >>> 60557 3198299 53129 0 0 0 0 1210464']
> >>>>
> >>>> Caused by: org.hsqldb.HsqlException: Caused by: java.io.IOException:
> >>> read beyond end of file
> >>>>
> >>>>
> >>>> At any rate, the code works but I think that something is missing
> >>>> from
> >>> your configuration.
> >>>> Since it is a personal development environment you are kind of on
> >>>> your
> >>> own.
> >>>> Good luck,
> >>>> Sean
> >>>>
> >>>> P.S. Get rid of the ctakes-resources-umls2011ab artifact in your pom.
> >>> It isn't doing anything.
> >>>>
> >>>>
> >>>>
> >>>> -----Original Message-----
> >>>> From: Dligach, Dmitriy [mailto:ddligach@luc.edu<ma...@luc.edu>]
> >>>> Sent: Wednesday, April 26, 2017 12:46 PM
> >>>> To: dev@ctakes.apache.org<ma...@ctakes.apache.org>
> >>>> Subject: Re: URI is not hierarchical
> >>>>
> >>>> I am definitely still seeing the “URI is not hierarchical” issue.
> >>> Here’s a piece of information that might help you figure out what
> >>> the problem is:
> >>>>
> >>>>
> >>>>
> >>>> It only happens if the pipeline includes dictionary lookup. For
> >>> instance, this one fails:
> >>>>
> >>>>
> >>>>
> >>>> 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=fs67G
> >>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevR
> >>> An-a92vTj9x79u08OjKfQ9U4&s=MKa09-UzlhjAB_
> 1jVyGOpVo1UHWrMDqjWiVAnk0jfPE&e=
> >>>>
> >>>>
> >>>>
> >>>> But this one succeeds:
> >>>>
> >>>>
> >>>>
> >>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
> >>> com_dmitriydligach_ctakes-2Dmisc_blob_master_src_main_java_
> >>> org_apache_ctakes_pipelines_BasicPipeline.java&d=DwIGaQ&c=
> >>> qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpy
> >>> IisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevRAn-a92vTj
> >>> 9x79u08OjKfQ9U4&s=U0zGx-soIiYY64nHK_tIAIpeind9vdIrAuDQIxh-4ek&e=
> >>>>
> >>>>
> >>>>
> >>>> (it’s the same as the first one, but the dictionary lookup part
> >>>> is
> >>> removed).
> >>>>
> >>>>
> >>>>
> >>>> Dima
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>> On Apr 26, 2017, at 11:37, Finan, Sean <Sean.Finan@childrens.harvard.
<mailto:Sean.Finan@childrens.harvard.%0b>> >>> edu> wrote:
> >>>>
> >>>>>
> >>>>
> >>>>> Hi again Dima,
> >>>>
> >>>>>
> >>>>
> >>>>> The piper files are not meant to replace uimafit. Uimafit is
> >>>>> great
> >>> for many purposes.
> >>>>
> >>>>>
> >>>>
> >>>>> As for that annoying old "URI is not hierarchical" bug, a while
> >>>>> back
> I
> >>> checked in a fix that worked for me. Since then I cannot duplicate it.
> >>>>
> >>>>>
> >>>>
> >>>>> Sean
> >>>>
> >>>>>
> >>>>
> >>>>> -----Original Message-----
> >>>>
> >>>>> From: Dligach, Dmitriy [mailto:ddligach@luc.edu<ma...@luc.edu>]
> >>>>
> >>>>> Sent: Wednesday, April 26, 2017 12:18 PM
> >>>>
> >>>>> To: dev@ctakes.apache.org<ma...@ctakes.apache.org>
> >>>>
> >>>>> Subject: Re: URI is not hierarchical
> >>>>
> >>>>>
> >>>>
> >>>>> 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.Finan@childrens.harvard.
<mailto:Sean.Finan@childrens.harvard.%0b>> >>> 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:ddligach@luc.edu<ma...@luc.edu>]
> >>>>
> >>>>>> Sent: Friday, April 14, 2017 12:47 PM
> >>>>
> >>>>>> To: dev@ctakes.apache.org<ma...@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=fs67G
> >>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=xe6RaWm66aSyUeXjU20
> >>> x8dEc3xfYTHbadlwhgSdrIsw&s=ixO9vX_WJ7p-dpJc0RdnzRfjwQqbNw4gkLwf0SS
> >>> pp0
> I&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.Finan@childrens.harvard.edu<ma...@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.a
> >>> pache.org_confluence_display_CTAKES_Piper-2BFiles&d=DwIGaQ&c
> >>> =qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTp
> >>> yIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=xe6RaWm66aSyUeXjU20x8dEc3xf
> >>> YTHbadlwhgSdrIsw&s=pNVLJSOBMk5orJZ4Oy4ZwtpkPp0tU48-g1qxtpIBucw&e=
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> -----Original Message-----
> >>>>
> >>>>>>
> >>>>
> >>>>>>> From: Dligach, Dmitriy [mailto:ddligach@luc.edu<ma...@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=fs67G
> >>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf
> >>> _qgdQj3HYIeLCeKr9Q303b0Q&s=NWoDwPNChJkDhFseM3j8Gi7KNDdVqz
> i1BFt0onalf9I&e=
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> from command line as follows:
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> mvn exec:java -Dexec.mainClass=“org.apache.c
> >>> takes.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/ctakesresour
> >>> ces/ctakes-resources-lvg2008/4.0.0/ctakes-resources-
> >>> lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.propertie
> >>> s
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> 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<https://urldefense.proofpoint.com/v2/url?u=http-3A__org.apache.ctakes.core.ae&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=fnp4lyT_3SV-Jso9YCBz41xa9CJnHxke0J20sjdWqZM&s=lHErPP1yP11Hsd2BuxxnZRzp6-97NpdVqhptXbt0NjM&e=>.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/resource
> >>> s/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.t
> >>> ype.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/l
> >>> ookup/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-2Dw
> >>> s.nlm.nih.gov_restful_isValidUMLSUser&d=DwIGaQ&c=qS4goWBT7po
> >>> plM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP
> >>> 6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q30
> >>> 3b0Q&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-2Dw
> >>> s.nlm.nih.gov_restful_isValidUMLSUser&d=DwIGaQ&c=qS4goWBT7po
> >>> plM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP
> >>> 6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q30
> >>> 3b0Q&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/look
> >>> up/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(Lv
> >>> gCmdApiResourceImpl.java:65)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at
> >>>>>>> org.apache.uima.resource.impl.ResourceManager_impl.registerR
> >>> esource(ResourceManager_impl.java:628)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at
> >>>>>>> org.apache.uima.resource.impl.ResourceManager_impl.initializ
> >>> eExternalResources(ResourceManager_impl.java:464)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at
> >>>>>>> org.apache.uima.resource.Resource_ImplBase.initialize(Resour
> >>> ce_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.produceResou
> >>> rce(AnalysisEngineFactory_impl.java:94)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at
> >>>>>>> org.apache.uima.impl.CompositeResourceFactory_impl.produceRe
> >>> source(CompositeResourceFactory_impl.java:62)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.
> >>> java:279)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at
> >>>>>>> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFram
> >>> ework.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.createEngi
> >>> ne(AnalysisEngineFactory.java:711)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at
> >>>>>>> org.apache.uima.fit.factory.AggregateBuilder.createAggregate
> >>> (AggregateBuilder.java:207)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at
> >>>>>>> org.apache.ctakes.pipelines.UmlsLookupPipeline.main(UmlsLook
> >>> upPipeline.java:66)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native
> >>>>>>> Method)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at
> >>>>>>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAcce
> >>> ssorImpl.java:62)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at
> >>>>>>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMe
> >>> thodAccessorImpl.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=https-3A__urldefense.proofpoint&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Lc9XlOnpIxXTTjvRKjUkyEK6iZXUXjRQhnbtKubbuQQ&s=qORzTUT4mGAcaxRvrlTVH7hUZDSxp3VJQ6v6oiaYND8&e= .
> >>> com/v2/url?u=http-3A__cwiki.apache.org_confluence_display_MA
> >>> VEN_MojoExecutionException&d=DwIGaQ&c=qS4goWBT7poplM69zy_3x
> >>> hKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4
> >>> f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q303b0Q&s=
> >>> JfA-JsX45OHwuDl_DNkICQUwoIOMrYhdSxNKV1k_Ig4&e=
> >>>>
> >>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>
> >>>>
> >>>>
> >>>>
> >>>
> >>>
> >>
>
>
Re: URI is not hierarchical
Posted by James Masanz <ma...@gmail.com>.
Attached is a snippet of the console messages
On Sat, Apr 29, 2017 at 9:18 AM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:
> Woah, I've never seen that. How did that happen? Is there another bug?
> The FileLocator should have logged a very long message saying "I couldn't
> find it here or there or the other place ..." and then thrown a
> FileNotFoundException.
>
>
>
> -----Original Message-----
> From: James Masanz [mailto:masanz.james@gmail.com]
> Sent: Saturday, April 29, 2017 2:00 AM
> To: dev@ctakes.apache.org
> Subject: Re: URI is not hierarchical
>
> Hi Dima,
>
> what revision of trunk are you using? I'm getting an error you weren't
> seeing so I'm guessing it's because I checked out ctakes just today.
>
> Caused by: java.lang.StringIndexOutOfBoundsException: String index out of
> range: -7
> at java.lang.String.substring(String.java:1967)
> at
> org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.
> getConnectionUrl(JdbcConnectionFactory.java:110)
> at
> org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.
> getConnection(JdbcConnectionFactory.java:63)
> at
> org.apache.ctakes.dictionary.lookup2.dictionary.
> JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:91)
> at
> org.apache.ctakes.dictionary.lookup2.dictionary.
> JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:72)
> at
> org.apache.ctakes.dictionary.lookup2.dictionary.
> UmlsJdbcRareWordDictionary.<init>(UmlsJdbcRareWordDictionary.java:31)
> ... 27 more
>
> FYI, I created the directories needed by UmlsLookupPipeline.java for
> chunker-model.zip and inputDirectory and outputDirectory, and I get
> the above regardless of whether I use text input file containing just
> "pain in left knee started on Wednesday." or if I use
> GenSurg_UmbilicalHernia_1.rtf as the input file instead.
>
>
> On Fri, Apr 28, 2017 at 5:48 PM, Dligach, Dmitriy <dd...@luc.edu>
> wrote:
>
> > Hi James,
> >
> > Thank you so much for looking into this!
> >
> > Your general setup matches mine. I also do:
> >
> > 1. svn co
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_re
> > pos_asf_ctakes_trunk_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCo
> > ppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Lc9XlOnpIxXTTjv
> > RKjUkyEK6iZXUXjRQhnbtKubbuQQ&s=ulRVEvEVpyQ8zZjXbCF2pY_ejjjoFaDYOnMk1l0
> > Fez0&e= 2. git clone
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_dmitri
> > ydligach_ctakes-2Dmisc.git&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMS
> > dioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Lc9XlOnpIx
> > XTTjvRKjUkyEK6iZXUXjRQhnbtKubbuQQ&s=vwWZxpuAYNjunq6khejHsCaw12XBURfSRj
> > mZvfbA8TA&e= (in trunk/) 3. mvn clean compile (in trunk/) 4. mvn
> > clean compile (in ctakes-misc/)
> >
> > BTW, I just discovered that it’s not necessary to check out a fresh
> > copy of ctakes-misc into a subdirectory in trunk. It will build no
> > matter where it is on your system as long as you first do an ‘mvn
> > clean compile’ in trunk/ (without it, ctakes-misc/ will not build).
> >
> > Thanks again, James.
> >
> > Dima
> >
> >
> >
> > > On Apr 28, 2017, at 16:30, James Masanz <ma...@gmail.com>
> wrote:
> > >
> > > Hi Dima,
> > >
> > > Just to let you know I am taking a look at this. More later, if not
> > today,
> > > then tomorrow. FYI here is where I'm at so far.
> > >
> > > I checked out a fresh copy of ctakes trunk and put files from your
> > > ctakes-misc into a subdirectory called ctakes-misc, and I updated my
> > local
> > > copy of the main pom.xml for ctakes to include ctakes-misc.
> > >
> > > I am able to reproduce getting URI is not hierarchical just by
> > > letting tests run during "mvn clean install":
> > >
> > > Tests in error:
> > > testPipeline(org.apache.ctakes.temporal.ae.
> BackwardsTimeAnnotatorTest):
> > > URI is not hierarchical
> > >
> > > testPipeline(org.apache.ctakes.temporal.ae.
> > ContextualModalityAnnotatorTest):
> > > URI is not hierarchical
> > > testPipeline(org.apache.ctakes.temporal.ae.EventAnnotatorTest): URI
> > > is not hierarchical
> > >
> > > testPipeline(org.apache.ctakes.temporal.ae.
> > EventEventRelationAnnotatorTest):
> > > URI is not hierarchical
> > >
> > > testPipeline(org.apache.ctakes.temporal.ae.
> > EventTimeRelationAnnotatorTest):
> > > URI is not hierarchical
> > >
> > >
> > > On Fri, Apr 28, 2017 at 12:27 PM, James Masanz
> > > <ma...@gmail.com>
> > > wrote:
> > >
> > >>
> > >> Going back to your original email, I notice cTAKES is referencing
> > lvg.properties
> > >> as being within a jar
> > >>
> > >> 14 Apr 2017 11:04:24 INFO LvgAnnotator - URL for lvg.properties
> > >> =file:/home/dima/.m2/repository/net/sourceforge/ctakesresources/cta
> > >> kes- resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.
> > >> 0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
> > >>
> > >> But I also see in LvgCmdApiResourceImpl.java the following code,
> > >> which
> > is
> > >> trying to handle it as a File, not a stream. :(
> > >>
> > >> File configFile = new File(dr.getUri());
> > >> configFileName = configFile.getPath();
> > >>
> > >> At first glance, looks like LvgCmdApiResourceImpl needs updating.
> > >>
> > >> As a workaround, you could try extracting the lvg subdirectory from
> > >> ctakes-resources-4.0-bin.zip that's on sourceforge [1] into
> > >> something on the classpath so the lvg.propertiesfile appears under
> > >>
> > >> org/apache/ctakes/lvg/data/config/lvg.properties
> > >>
> > >> You might also need to have the rest of the files and directories
> > >> under org/apache/ctakes/lvg/data to also be outside the jar, not
> > >> sure
> > offhand.
> > >>
> > >> I can try that out this afternoon.
> > >>
> > >> [1]
> > >> https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.ne
> > >> t_projects_ctakesresources_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14
> > >> JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Lc9
> > >> XlOnpIxXTTjvRKjUkyEK6iZXUXjRQhnbtKubbuQQ&s=dKDOAG-k6QNwD3cIsI31U4zH
> > >> k2lGmqXzRjKXI4ySz_s&e= files/ctakes-resources-4.0-bin.zip/download
> > >>
> > >>
> > >> On Wed, Apr 26, 2017 at 3:29 PM, Dligach, Dmitriy
> > >> <dd...@luc.edu>
> > >> wrote:
> > >>
> > >>> Hi Sean,
> > >>>
> > >>> First of all, a huge thank you for taking time to debug this
> > >>> issue. I really appreciate your help.
> > >>>
> > >>> Second, I think my main message somehow got lost in translation
> > (sorry, I
> > >>> should’ve included it for clarity with my recent emails). I never
> > >>> had
> > any
> > >>> trouble running this pipeline in Eclipse. The “URI is not
> hierarchical”
> > >>> error only happens when I run it from command line.
> > >>>
> > >>> I run it using the following maven command:
> > >>>
> > >>> mvn exec:java -Dexec.mainClass="org.apache.c
> > >>> takes.pipelines.UmlsLookupPipeline" -Dexec.args=""
> > -Dctakes.umlsuser=<my
> > >>> umls login name> -Dctakes.umlspw=<my umls password>
> > >>>
> > >>> As I said in my previous email, the other pipeline (that does not
> > >>> have dictionary lookup) runs fine at command line. The error only
> > >>> happens
> > when I
> > >>> run pipelines containing dictionary lookup.
> > >>>
> > >>> Dima
> > >>>
> > >>>
> > >>>
> > >>>> On Apr 26, 2017, at 13:36, Finan, Sean
> <Sean.Finan@childrens.harvard.
> > >>> edu> wrote:
> > >>>>
> > >>>> Hi Dima,
> > >>>>
> > >>>> Good news: no uri hierarchical error.
> > >>>>
> > >>>> All that I did was import your ctakes-misc pom as a maven project
> > >>>> in
> > >>> intellij. Then I created a run configuration with my sandbox as
> > >>> the working directory, ctakes-misc as the classpath module, and my
> > >>> umls credentials in the environment.
> > >>>> All database files were found, the pipeline ran, and I got output:
> > >>>> total 2448
> > >>>> drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:19 .
> > >>>> drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:18 ..
> > >>>> -rwxrwx---+ 1 Administrators Domain Users 187675 Apr 26 14:19
> > >>> GenSurg_UmbilicalHernia_1.rtf.xmi
> > >>>> -rwxrwx---+ 1 Administrators Domain Users 238984 Apr 26 14:19
> > >>> OBGYN_Gen_Abscess_1.rtf.xmi
> > >>>> -rwxrwx---+ 1 Administrators Domain Users 82308 Apr 26 14:19
> > >>> OBGYN_HysterectomyAndBSO_1.rtf.xmi
> > >>>> -rwxrwx---+ 1 Administrators Domain Users 115983 Apr 26 14:19
> > >>> OBGYN_IUD_1.rtf.xmi
> > >>>> -rwxrwx---+ 1 Administrators Domain Users 35919 Apr 26 14:19
> > >>> OBGYN_LaborProgressNote_1.rtf.xmi
> > >>>> -rwxrwx---+ 1 Administrators Domain Users 112460 Apr 26 14:19
> > >>> OBGYN_MVAPrego_1.rtf.xmi
> > >>>> -rwxrwx---+ 1 Administrators Domain Users 173695 Apr 26 14:19
> > >>> OBGYN_PROMCheck_1.rtf.xmi
> > >>>> -rwxrwx---+ 1 Administrators Domain Users 340626 Apr 26 14:19
> > >>> Peds_Dysphagia_1.rtf.xmi
> > >>>> -rwxrwx---+ 1 Administrators Domain Users 390928 Apr 26 14:19
> > >>> Peds_FebrileSez_1.rtf.xmi
> > >>>> -rwxrwx---+ 1 Administrators Domain Users 115064 Apr 26 14:19
> > >>> Peds_RoutBirthNote_1.rtf.xmi
> > >>>> -rwxrwx---+ 1 Administrators Domain Users 101234 Apr 26 14:19
> > >>> VascSurg_AAA_Leak_1.rtf.xmi
> > >>>> -rwxrwx---+ 1 Administrators Domain Users 98015 Apr 26 14:19
> > >>> VascSurg_FollowUp_1.rtf.xmi
> > >>>> -rwxrwx---+ 1 Administrators Domain Users 218863 Apr 26 14:19
> > >>> VascSurg_PVD_1.rtf.xmi
> > >>>> -rwxrwx---+ 1 Administrators Domain Users 72902 Apr 26 14:19
> > >>> VascSurg_RO-AAA_1.rtf.xmi
> > >>>> -rwxrwx---+ 1 Administrators Domain Users 90825 Apr 26 14:19
> > >>> VascSurg_RO-DVT.rtf.xmi
> > >>>> -rwxrwx---+ 1 Administrators Domain Users 90827 Apr 26 14:19
> > >>> VascSurg_RO-DVT_1.rtf.xmi
> > >>>>
> > >>>>
> > >>>>
> > >>>>
> > >>>> Bad news: it looks like the hsqldb port of lvg2008 is not working.
> > >>>>
> > >>>> Caused by: org.hsqldb.HsqlException: error in script file line:
> > >>>> 61
> > >>> C:\Spiffy\prj_ctakes_401\dev\ctakes-lvg-res\target\classes\o
> > >>> rg\apache\ctakes\lvg\data\HSqlDb\lvg2008 java.io.IOException: read
> > >>> beyond end of file in statement [SET TABLE PUBLIC.INFLECTION INDEX
> > '3198299
> > >>> 60557 3198299 53129 0 0 0 0 1210464']
> > >>>>
> > >>>> Caused by: org.hsqldb.HsqlException: Caused by: java.io.IOException:
> > >>> read beyond end of file
> > >>>>
> > >>>>
> > >>>> At any rate, the code works but I think that something is missing
> > >>>> from
> > >>> your configuration.
> > >>>> Since it is a personal development environment you are kind of on
> > >>>> your
> > >>> own.
> > >>>> Good luck,
> > >>>> Sean
> > >>>>
> > >>>> P.S. Get rid of the ctakes-resources-umls2011ab artifact in your
> pom.
> > >>> It isn't doing anything.
> > >>>>
> > >>>>
> > >>>>
> > >>>> -----Original Message-----
> > >>>> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
> > >>>> Sent: Wednesday, April 26, 2017 12:46 PM
> > >>>> To: dev@ctakes.apache.org
> > >>>> Subject: Re: URI is not hierarchical
> > >>>>
> > >>>> I am definitely still seeing the “URI is not hierarchical” issue.
> > >>> Here’s a piece of information that might help you figure out what
> > >>> the problem is:
> > >>>>
> > >>>>
> > >>>>
> > >>>> It only happens if the pipeline includes dictionary lookup. For
> > >>> instance, this one fails:
> > >>>>
> > >>>>
> > >>>>
> > >>>> 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=fs67G
> > >>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevR
> > >>> An-a92vTj9x79u08OjKfQ9U4&s=MKa09-UzlhjAB_
> > 1jVyGOpVo1UHWrMDqjWiVAnk0jfPE&e=
> > >>>>
> > >>>>
> > >>>>
> > >>>> But this one succeeds:
> > >>>>
> > >>>>
> > >>>>
> > >>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
> > >>> com_dmitriydligach_ctakes-2Dmisc_blob_master_src_main_java_
> > >>> org_apache_ctakes_pipelines_BasicPipeline.java&d=DwIGaQ&c=
> > >>> qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpy
> > >>> IisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevRAn-a92vTj
> > >>> 9x79u08OjKfQ9U4&s=U0zGx-soIiYY64nHK_tIAIpeind9vdIrAuDQIxh-4ek&e=
> > >>>>
> > >>>>
> > >>>>
> > >>>> (it’s the same as the first one, but the dictionary lookup part
> > >>>> is
> > >>> removed).
> > >>>>
> > >>>>
> > >>>>
> > >>>> Dima
> > >>>>
> > >>>>
> > >>>>
> > >>>>
> > >>>>
> > >>>>
> > >>>>
> > >>>>> On Apr 26, 2017, at 11:37, Finan, Sean
> <Sean.Finan@childrens.harvard.
> > >>> edu> wrote:
> > >>>>
> > >>>>>
> > >>>>
> > >>>>> Hi again Dima,
> > >>>>
> > >>>>>
> > >>>>
> > >>>>> The piper files are not meant to replace uimafit. Uimafit is
> > >>>>> great
> > >>> for many purposes.
> > >>>>
> > >>>>>
> > >>>>
> > >>>>> As for that annoying old "URI is not hierarchical" bug, a while
> > >>>>> back
> > I
> > >>> checked in a fix that worked for me. Since then I cannot duplicate
> it.
> > >>>>
> > >>>>>
> > >>>>
> > >>>>> Sean
> > >>>>
> > >>>>>
> > >>>>
> > >>>>> -----Original Message-----
> > >>>>
> > >>>>> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
> > >>>>
> > >>>>> Sent: Wednesday, April 26, 2017 12:18 PM
> > >>>>
> > >>>>> To: dev@ctakes.apache.org
> > >>>>
> > >>>>> Subject: Re: URI is not hierarchical
> > >>>>
> > >>>>>
> > >>>>
> > >>>>> 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.Finan@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:ddligach@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=fs67G
> > >>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=xe6RaWm66aSyUeXjU20
> > >>> x8dEc3xfYTHbadlwhgSdrIsw&s=ixO9vX_WJ7p-dpJc0RdnzRfjwQqbNw4gkLwf0SS
> > >>> pp0
> > I&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.Finan@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.a
> > >>> pache.org_confluence_display_CTAKES_Piper-2BFiles&d=DwIGaQ&c
> > >>> =qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTp
> > >>> yIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=xe6RaWm66aSyUeXjU20x8dEc3xf
> > >>> YTHbadlwhgSdrIsw&s=pNVLJSOBMk5orJZ4Oy4ZwtpkPp0tU48-g1qxtpIBucw&e=
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>>
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>>
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>> -----Original Message-----
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>> From: Dligach, Dmitriy [mailto:ddligach@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=fs67G
> > >>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf
> > >>> _qgdQj3HYIeLCeKr9Q303b0Q&s=NWoDwPNChJkDhFseM3j8Gi7KNDdVqz
> > i1BFt0onalf9I&e=
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>>
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>>
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>>
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>> from command line as follows:
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>>
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>>
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>>
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>> mvn exec:java -Dexec.mainClass=“org.apache.c
> > >>> takes.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/ctakesresour
> > >>> ces/ctakes-resources-lvg2008/4.0.0/ctakes-resources-
> > >>> lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.propertie
> > >>> s
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>>
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>> 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/resource
> > >>> s/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.t
> > >>> ype.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/l
> > >>> ookup/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-2Dw
> > >>> s.nlm.nih.gov_restful_isValidUMLSUser&d=DwIGaQ&c=qS4goWBT7po
> > >>> plM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP
> > >>> 6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q30
> > >>> 3b0Q&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-2Dw
> > >>> s.nlm.nih.gov_restful_isValidUMLSUser&d=DwIGaQ&c=qS4goWBT7po
> > >>> plM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP
> > >>> 6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q30
> > >>> 3b0Q&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/look
> > >>> up/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(Lv
> > >>> gCmdApiResourceImpl.java:65)
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>>
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>> at
> > >>>>>>> org.apache.uima.resource.impl.ResourceManager_impl.registerR
> > >>> esource(ResourceManager_impl.java:628)
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>>
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>> at
> > >>>>>>> org.apache.uima.resource.impl.ResourceManager_impl.initializ
> > >>> eExternalResources(ResourceManager_impl.java:464)
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>>
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>> at
> > >>>>>>> org.apache.uima.resource.Resource_ImplBase.initialize(Resour
> > >>> ce_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.produceResou
> > >>> rce(AnalysisEngineFactory_impl.java:94)
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>>
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>> at
> > >>>>>>> org.apache.uima.impl.CompositeResourceFactory_impl.produceRe
> > >>> source(CompositeResourceFactory_impl.java:62)
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>>
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>> at org.apache.uima.UIMAFramework.
> produceResource(UIMAFramework.
> > >>> java:279)
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>>
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>> at
> > >>>>>>> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFram
> > >>> ework.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.createEngi
> > >>> ne(AnalysisEngineFactory.java:711)
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>>
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>> at
> > >>>>>>> org.apache.uima.fit.factory.AggregateBuilder.createAggregate
> > >>> (AggregateBuilder.java:207)
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>>
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>> at
> > >>>>>>> org.apache.ctakes.pipelines.UmlsLookupPipeline.main(UmlsLook
> > >>> upPipeline.java:66)
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>>
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native
> > >>>>>>> Method)
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>>
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>> at
> > >>>>>>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAcce
> > >>> ssorImpl.java:62)
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>>
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>> at
> > >>>>>>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMe
> > >>> thodAccessorImpl.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=https-3A__urldefense.proofpoint&d=
> DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=
> fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> Lc9XlOnpIxXTTjvRKjUkyEK6iZXUXjRQhnbtKubbuQQ&s=
> qORzTUT4mGAcaxRvrlTVH7hUZDSxp3VJQ6v6oiaYND8&e= .
> > >>> com/v2/url?u=http-3A__cwiki.apache.org_confluence_display_MA
> > >>> VEN_MojoExecutionException&d=DwIGaQ&c=qS4goWBT7poplM69zy_3x
> > >>> hKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4
> > >>> f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q303b0Q&s=
> > >>> JfA-JsX45OHwuDl_DNkICQUwoIOMrYhdSxNKV1k_Ig4&e=
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>>
> > >>>>
> > >>>>>
> > >>>>
> > >>>>
> > >>>>
> > >>>
> > >>>
> > >>
> >
> >
>
RE: URI is not hierarchical
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Woah, I've never seen that. How did that happen? Is there another bug? The FileLocator should have logged a very long message saying "I couldn't find it here or there or the other place ..." and then thrown a FileNotFoundException.
-----Original Message-----
From: James Masanz [mailto:masanz.james@gmail.com]
Sent: Saturday, April 29, 2017 2:00 AM
To: dev@ctakes.apache.org
Subject: Re: URI is not hierarchical
Hi Dima,
what revision of trunk are you using? I'm getting an error you weren't seeing so I'm guessing it's because I checked out ctakes just today.
Caused by: java.lang.StringIndexOutOfBoundsException: String index out of
range: -7
at java.lang.String.substring(String.java:1967)
at
org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnectionUrl(JdbcConnectionFactory.java:110)
at
org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnection(JdbcConnectionFactory.java:63)
at
org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:91)
at
org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:72)
at
org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary.<init>(UmlsJdbcRareWordDictionary.java:31)
... 27 more
FYI, I created the directories needed by UmlsLookupPipeline.java for
chunker-model.zip and inputDirectory and outputDirectory, and I get
the above regardless of whether I use text input file containing just "pain in left knee started on Wednesday." or if I use GenSurg_UmbilicalHernia_1.rtf as the input file instead.
On Fri, Apr 28, 2017 at 5:48 PM, Dligach, Dmitriy <dd...@luc.edu> wrote:
> Hi James,
>
> Thank you so much for looking into this!
>
> Your general setup matches mine. I also do:
>
> 1. svn co
> https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_re
> pos_asf_ctakes_trunk_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCo
> ppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Lc9XlOnpIxXTTjv
> RKjUkyEK6iZXUXjRQhnbtKubbuQQ&s=ulRVEvEVpyQ8zZjXbCF2pY_ejjjoFaDYOnMk1l0
> Fez0&e= 2. git clone
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_dmitri
> ydligach_ctakes-2Dmisc.git&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMS
> dioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Lc9XlOnpIx
> XTTjvRKjUkyEK6iZXUXjRQhnbtKubbuQQ&s=vwWZxpuAYNjunq6khejHsCaw12XBURfSRj
> mZvfbA8TA&e= (in trunk/) 3. mvn clean compile (in trunk/) 4. mvn
> clean compile (in ctakes-misc/)
>
> BTW, I just discovered that it’s not necessary to check out a fresh
> copy of ctakes-misc into a subdirectory in trunk. It will build no
> matter where it is on your system as long as you first do an ‘mvn
> clean compile’ in trunk/ (without it, ctakes-misc/ will not build).
>
> Thanks again, James.
>
> Dima
>
>
>
> > On Apr 28, 2017, at 16:30, James Masanz <ma...@gmail.com> wrote:
> >
> > Hi Dima,
> >
> > Just to let you know I am taking a look at this. More later, if not
> today,
> > then tomorrow. FYI here is where I'm at so far.
> >
> > I checked out a fresh copy of ctakes trunk and put files from your
> > ctakes-misc into a subdirectory called ctakes-misc, and I updated my
> local
> > copy of the main pom.xml for ctakes to include ctakes-misc.
> >
> > I am able to reproduce getting URI is not hierarchical just by
> > letting tests run during "mvn clean install":
> >
> > Tests in error:
> > testPipeline(org.apache.ctakes.temporal.ae.BackwardsTimeAnnotatorTest):
> > URI is not hierarchical
> >
> > testPipeline(org.apache.ctakes.temporal.ae.
> ContextualModalityAnnotatorTest):
> > URI is not hierarchical
> > testPipeline(org.apache.ctakes.temporal.ae.EventAnnotatorTest): URI
> > is not hierarchical
> >
> > testPipeline(org.apache.ctakes.temporal.ae.
> EventEventRelationAnnotatorTest):
> > URI is not hierarchical
> >
> > testPipeline(org.apache.ctakes.temporal.ae.
> EventTimeRelationAnnotatorTest):
> > URI is not hierarchical
> >
> >
> > On Fri, Apr 28, 2017 at 12:27 PM, James Masanz
> > <ma...@gmail.com>
> > wrote:
> >
> >>
> >> Going back to your original email, I notice cTAKES is referencing
> lvg.properties
> >> as being within a jar
> >>
> >> 14 Apr 2017 11:04:24 INFO LvgAnnotator - URL for lvg.properties
> >> =file:/home/dima/.m2/repository/net/sourceforge/ctakesresources/cta
> >> kes- resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.
> >> 0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
> >>
> >> But I also see in LvgCmdApiResourceImpl.java the following code,
> >> which
> is
> >> trying to handle it as a File, not a stream. :(
> >>
> >> File configFile = new File(dr.getUri());
> >> configFileName = configFile.getPath();
> >>
> >> At first glance, looks like LvgCmdApiResourceImpl needs updating.
> >>
> >> As a workaround, you could try extracting the lvg subdirectory from
> >> ctakes-resources-4.0-bin.zip that's on sourceforge [1] into
> >> something on the classpath so the lvg.propertiesfile appears under
> >>
> >> org/apache/ctakes/lvg/data/config/lvg.properties
> >>
> >> You might also need to have the rest of the files and directories
> >> under org/apache/ctakes/lvg/data to also be outside the jar, not
> >> sure
> offhand.
> >>
> >> I can try that out this afternoon.
> >>
> >> [1]
> >> https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.ne
> >> t_projects_ctakesresources_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14
> >> JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Lc9
> >> XlOnpIxXTTjvRKjUkyEK6iZXUXjRQhnbtKubbuQQ&s=dKDOAG-k6QNwD3cIsI31U4zH
> >> k2lGmqXzRjKXI4ySz_s&e= files/ctakes-resources-4.0-bin.zip/download
> >>
> >>
> >> On Wed, Apr 26, 2017 at 3:29 PM, Dligach, Dmitriy
> >> <dd...@luc.edu>
> >> wrote:
> >>
> >>> Hi Sean,
> >>>
> >>> First of all, a huge thank you for taking time to debug this
> >>> issue. I really appreciate your help.
> >>>
> >>> Second, I think my main message somehow got lost in translation
> (sorry, I
> >>> should’ve included it for clarity with my recent emails). I never
> >>> had
> any
> >>> trouble running this pipeline in Eclipse. The “URI is not hierarchical”
> >>> error only happens when I run it from command line.
> >>>
> >>> I run it using the following maven command:
> >>>
> >>> mvn exec:java -Dexec.mainClass="org.apache.c
> >>> takes.pipelines.UmlsLookupPipeline" -Dexec.args=""
> -Dctakes.umlsuser=<my
> >>> umls login name> -Dctakes.umlspw=<my umls password>
> >>>
> >>> As I said in my previous email, the other pipeline (that does not
> >>> have dictionary lookup) runs fine at command line. The error only
> >>> happens
> when I
> >>> run pipelines containing dictionary lookup.
> >>>
> >>> Dima
> >>>
> >>>
> >>>
> >>>> On Apr 26, 2017, at 13:36, Finan, Sean <Sean.Finan@childrens.harvard.
> >>> edu> wrote:
> >>>>
> >>>> Hi Dima,
> >>>>
> >>>> Good news: no uri hierarchical error.
> >>>>
> >>>> All that I did was import your ctakes-misc pom as a maven project
> >>>> in
> >>> intellij. Then I created a run configuration with my sandbox as
> >>> the working directory, ctakes-misc as the classpath module, and my
> >>> umls credentials in the environment.
> >>>> All database files were found, the pipeline ran, and I got output:
> >>>> total 2448
> >>>> drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:19 .
> >>>> drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:18 ..
> >>>> -rwxrwx---+ 1 Administrators Domain Users 187675 Apr 26 14:19
> >>> GenSurg_UmbilicalHernia_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 238984 Apr 26 14:19
> >>> OBGYN_Gen_Abscess_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 82308 Apr 26 14:19
> >>> OBGYN_HysterectomyAndBSO_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 115983 Apr 26 14:19
> >>> OBGYN_IUD_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 35919 Apr 26 14:19
> >>> OBGYN_LaborProgressNote_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 112460 Apr 26 14:19
> >>> OBGYN_MVAPrego_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 173695 Apr 26 14:19
> >>> OBGYN_PROMCheck_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 340626 Apr 26 14:19
> >>> Peds_Dysphagia_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 390928 Apr 26 14:19
> >>> Peds_FebrileSez_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 115064 Apr 26 14:19
> >>> Peds_RoutBirthNote_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 101234 Apr 26 14:19
> >>> VascSurg_AAA_Leak_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 98015 Apr 26 14:19
> >>> VascSurg_FollowUp_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 218863 Apr 26 14:19
> >>> VascSurg_PVD_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 72902 Apr 26 14:19
> >>> VascSurg_RO-AAA_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 90825 Apr 26 14:19
> >>> VascSurg_RO-DVT.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 90827 Apr 26 14:19
> >>> VascSurg_RO-DVT_1.rtf.xmi
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> Bad news: it looks like the hsqldb port of lvg2008 is not working.
> >>>>
> >>>> Caused by: org.hsqldb.HsqlException: error in script file line:
> >>>> 61
> >>> C:\Spiffy\prj_ctakes_401\dev\ctakes-lvg-res\target\classes\o
> >>> rg\apache\ctakes\lvg\data\HSqlDb\lvg2008 java.io.IOException: read
> >>> beyond end of file in statement [SET TABLE PUBLIC.INFLECTION INDEX
> '3198299
> >>> 60557 3198299 53129 0 0 0 0 1210464']
> >>>>
> >>>> Caused by: org.hsqldb.HsqlException: Caused by: java.io.IOException:
> >>> read beyond end of file
> >>>>
> >>>>
> >>>> At any rate, the code works but I think that something is missing
> >>>> from
> >>> your configuration.
> >>>> Since it is a personal development environment you are kind of on
> >>>> your
> >>> own.
> >>>> Good luck,
> >>>> Sean
> >>>>
> >>>> P.S. Get rid of the ctakes-resources-umls2011ab artifact in your pom.
> >>> It isn't doing anything.
> >>>>
> >>>>
> >>>>
> >>>> -----Original Message-----
> >>>> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
> >>>> Sent: Wednesday, April 26, 2017 12:46 PM
> >>>> To: dev@ctakes.apache.org
> >>>> Subject: Re: URI is not hierarchical
> >>>>
> >>>> I am definitely still seeing the “URI is not hierarchical” issue.
> >>> Here’s a piece of information that might help you figure out what
> >>> the problem is:
> >>>>
> >>>>
> >>>>
> >>>> It only happens if the pipeline includes dictionary lookup. For
> >>> instance, this one fails:
> >>>>
> >>>>
> >>>>
> >>>> 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=fs67G
> >>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevR
> >>> An-a92vTj9x79u08OjKfQ9U4&s=MKa09-UzlhjAB_
> 1jVyGOpVo1UHWrMDqjWiVAnk0jfPE&e=
> >>>>
> >>>>
> >>>>
> >>>> But this one succeeds:
> >>>>
> >>>>
> >>>>
> >>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
> >>> com_dmitriydligach_ctakes-2Dmisc_blob_master_src_main_java_
> >>> org_apache_ctakes_pipelines_BasicPipeline.java&d=DwIGaQ&c=
> >>> qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpy
> >>> IisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevRAn-a92vTj
> >>> 9x79u08OjKfQ9U4&s=U0zGx-soIiYY64nHK_tIAIpeind9vdIrAuDQIxh-4ek&e=
> >>>>
> >>>>
> >>>>
> >>>> (it’s the same as the first one, but the dictionary lookup part
> >>>> is
> >>> removed).
> >>>>
> >>>>
> >>>>
> >>>> Dima
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>> On Apr 26, 2017, at 11:37, Finan, Sean <Sean.Finan@childrens.harvard.
> >>> edu> wrote:
> >>>>
> >>>>>
> >>>>
> >>>>> Hi again Dima,
> >>>>
> >>>>>
> >>>>
> >>>>> The piper files are not meant to replace uimafit. Uimafit is
> >>>>> great
> >>> for many purposes.
> >>>>
> >>>>>
> >>>>
> >>>>> As for that annoying old "URI is not hierarchical" bug, a while
> >>>>> back
> I
> >>> checked in a fix that worked for me. Since then I cannot duplicate it.
> >>>>
> >>>>>
> >>>>
> >>>>> Sean
> >>>>
> >>>>>
> >>>>
> >>>>> -----Original Message-----
> >>>>
> >>>>> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
> >>>>
> >>>>> Sent: Wednesday, April 26, 2017 12:18 PM
> >>>>
> >>>>> To: dev@ctakes.apache.org
> >>>>
> >>>>> Subject: Re: URI is not hierarchical
> >>>>
> >>>>>
> >>>>
> >>>>> 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.Finan@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:ddligach@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=fs67G
> >>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=xe6RaWm66aSyUeXjU20
> >>> x8dEc3xfYTHbadlwhgSdrIsw&s=ixO9vX_WJ7p-dpJc0RdnzRfjwQqbNw4gkLwf0SS
> >>> pp0
> I&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.Finan@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.a
> >>> pache.org_confluence_display_CTAKES_Piper-2BFiles&d=DwIGaQ&c
> >>> =qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTp
> >>> yIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=xe6RaWm66aSyUeXjU20x8dEc3xf
> >>> YTHbadlwhgSdrIsw&s=pNVLJSOBMk5orJZ4Oy4ZwtpkPp0tU48-g1qxtpIBucw&e=
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> -----Original Message-----
> >>>>
> >>>>>>
> >>>>
> >>>>>>> From: Dligach, Dmitriy [mailto:ddligach@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=fs67G
> >>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf
> >>> _qgdQj3HYIeLCeKr9Q303b0Q&s=NWoDwPNChJkDhFseM3j8Gi7KNDdVqz
> i1BFt0onalf9I&e=
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> from command line as follows:
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> mvn exec:java -Dexec.mainClass=“org.apache.c
> >>> takes.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/ctakesresour
> >>> ces/ctakes-resources-lvg2008/4.0.0/ctakes-resources-
> >>> lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.propertie
> >>> s
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> 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/resource
> >>> s/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.t
> >>> ype.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/l
> >>> ookup/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-2Dw
> >>> s.nlm.nih.gov_restful_isValidUMLSUser&d=DwIGaQ&c=qS4goWBT7po
> >>> plM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP
> >>> 6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q30
> >>> 3b0Q&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-2Dw
> >>> s.nlm.nih.gov_restful_isValidUMLSUser&d=DwIGaQ&c=qS4goWBT7po
> >>> plM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP
> >>> 6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q30
> >>> 3b0Q&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/look
> >>> up/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(Lv
> >>> gCmdApiResourceImpl.java:65)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at
> >>>>>>> org.apache.uima.resource.impl.ResourceManager_impl.registerR
> >>> esource(ResourceManager_impl.java:628)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at
> >>>>>>> org.apache.uima.resource.impl.ResourceManager_impl.initializ
> >>> eExternalResources(ResourceManager_impl.java:464)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at
> >>>>>>> org.apache.uima.resource.Resource_ImplBase.initialize(Resour
> >>> ce_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.produceResou
> >>> rce(AnalysisEngineFactory_impl.java:94)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at
> >>>>>>> org.apache.uima.impl.CompositeResourceFactory_impl.produceRe
> >>> source(CompositeResourceFactory_impl.java:62)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.
> >>> java:279)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at
> >>>>>>> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFram
> >>> ework.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.createEngi
> >>> ne(AnalysisEngineFactory.java:711)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at
> >>>>>>> org.apache.uima.fit.factory.AggregateBuilder.createAggregate
> >>> (AggregateBuilder.java:207)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at
> >>>>>>> org.apache.ctakes.pipelines.UmlsLookupPipeline.main(UmlsLook
> >>> upPipeline.java:66)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native
> >>>>>>> Method)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at
> >>>>>>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAcce
> >>> ssorImpl.java:62)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at
> >>>>>>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMe
> >>> thodAccessorImpl.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=https-3A__urldefense.proofpoint&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Lc9XlOnpIxXTTjvRKjUkyEK6iZXUXjRQhnbtKubbuQQ&s=qORzTUT4mGAcaxRvrlTVH7hUZDSxp3VJQ6v6oiaYND8&e= .
> >>> com/v2/url?u=http-3A__cwiki.apache.org_confluence_display_MA
> >>> VEN_MojoExecutionException&d=DwIGaQ&c=qS4goWBT7poplM69zy_3x
> >>> hKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4
> >>> f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q303b0Q&s=
> >>> JfA-JsX45OHwuDl_DNkICQUwoIOMrYhdSxNKV1k_Ig4&e=
> >>>>
> >>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>
> >>>>
> >>>>
> >>>>
> >>>
> >>>
> >>
>
>
Re: URI is not hierarchical
Posted by James Masanz <ma...@gmail.com>.
Hi Dima,
what revision of trunk are you using? I'm getting an error you weren't
seeing so I'm guessing it's because I checked out ctakes just today.
Caused by: java.lang.StringIndexOutOfBoundsException: String index out of
range: -7
at java.lang.String.substring(String.java:1967)
at
org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnectionUrl(JdbcConnectionFactory.java:110)
at
org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnection(JdbcConnectionFactory.java:63)
at
org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:91)
at
org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:72)
at
org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary.<init>(UmlsJdbcRareWordDictionary.java:31)
... 27 more
FYI, I created the directories needed by UmlsLookupPipeline.java for
chunker-model.zip and inputDirectory and outputDirectory, and I get
the above regardless of whether I use text input file containing just "pain
in left knee started on Wednesday." or if I use
GenSurg_UmbilicalHernia_1.rtf as the input file instead.
On Fri, Apr 28, 2017 at 5:48 PM, Dligach, Dmitriy <dd...@luc.edu> wrote:
> Hi James,
>
> Thank you so much for looking into this!
>
> Your general setup matches mine. I also do:
>
> 1. svn co https://svn.apache.org/repos/asf/ctakes/trunk/
> 2. git clone https://github.com/dmitriydligach/ctakes-misc.git (in trunk/)
> 3. mvn clean compile (in trunk/)
> 4. mvn clean compile (in ctakes-misc/)
>
> BTW, I just discovered that it’s not necessary to check out a fresh copy
> of ctakes-misc into a subdirectory in trunk. It will build no matter where
> it is on your system as long as you first do an ‘mvn clean compile’ in
> trunk/ (without it, ctakes-misc/ will not build).
>
> Thanks again, James.
>
> Dima
>
>
>
> > On Apr 28, 2017, at 16:30, James Masanz <ma...@gmail.com> wrote:
> >
> > Hi Dima,
> >
> > Just to let you know I am taking a look at this. More later, if not
> today,
> > then tomorrow. FYI here is where I'm at so far.
> >
> > I checked out a fresh copy of ctakes trunk and put files from your
> > ctakes-misc into a subdirectory called ctakes-misc, and I updated my
> local
> > copy of the main pom.xml for ctakes to include ctakes-misc.
> >
> > I am able to reproduce getting URI is not hierarchical just by letting
> > tests run during "mvn clean install":
> >
> > Tests in error:
> > testPipeline(org.apache.ctakes.temporal.ae.BackwardsTimeAnnotatorTest):
> > URI is not hierarchical
> >
> > testPipeline(org.apache.ctakes.temporal.ae.
> ContextualModalityAnnotatorTest):
> > URI is not hierarchical
> > testPipeline(org.apache.ctakes.temporal.ae.EventAnnotatorTest): URI is
> > not hierarchical
> >
> > testPipeline(org.apache.ctakes.temporal.ae.
> EventEventRelationAnnotatorTest):
> > URI is not hierarchical
> >
> > testPipeline(org.apache.ctakes.temporal.ae.
> EventTimeRelationAnnotatorTest):
> > URI is not hierarchical
> >
> >
> > On Fri, Apr 28, 2017 at 12:27 PM, James Masanz <ma...@gmail.com>
> > wrote:
> >
> >>
> >> Going back to your original email, I notice cTAKES is referencing
> lvg.properties
> >> as being within a jar
> >>
> >> 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
> >>
> >> But I also see in LvgCmdApiResourceImpl.java the following code, which
> is
> >> trying to handle it as a File, not a stream. :(
> >>
> >> File configFile = new File(dr.getUri());
> >> configFileName = configFile.getPath();
> >>
> >> At first glance, looks like LvgCmdApiResourceImpl needs updating.
> >>
> >> As a workaround, you could try extracting the lvg subdirectory from
> >> ctakes-resources-4.0-bin.zip that's on sourceforge [1] into something on
> >> the classpath so the lvg.propertiesfile appears under
> >>
> >> org/apache/ctakes/lvg/data/config/lvg.properties
> >>
> >> You might also need to have the rest of the files and directories under
> >> org/apache/ctakes/lvg/data to also be outside the jar, not sure
> offhand.
> >>
> >> I can try that out this afternoon.
> >>
> >> [1] https://sourceforge.net/projects/ctakesresources/
> >> files/ctakes-resources-4.0-bin.zip/download
> >>
> >>
> >> On Wed, Apr 26, 2017 at 3:29 PM, Dligach, Dmitriy <dd...@luc.edu>
> >> wrote:
> >>
> >>> Hi Sean,
> >>>
> >>> First of all, a huge thank you for taking time to debug this issue. I
> >>> really appreciate your help.
> >>>
> >>> Second, I think my main message somehow got lost in translation
> (sorry, I
> >>> should’ve included it for clarity with my recent emails). I never had
> any
> >>> trouble running this pipeline in Eclipse. The “URI is not hierarchical”
> >>> error only happens when I run it from command line.
> >>>
> >>> I run it using the following maven command:
> >>>
> >>> mvn exec:java -Dexec.mainClass="org.apache.c
> >>> takes.pipelines.UmlsLookupPipeline" -Dexec.args=""
> -Dctakes.umlsuser=<my
> >>> umls login name> -Dctakes.umlspw=<my umls password>
> >>>
> >>> As I said in my previous email, the other pipeline (that does not have
> >>> dictionary lookup) runs fine at command line. The error only happens
> when I
> >>> run pipelines containing dictionary lookup.
> >>>
> >>> Dima
> >>>
> >>>
> >>>
> >>>> On Apr 26, 2017, at 13:36, Finan, Sean <Sean.Finan@childrens.harvard.
> >>> edu> wrote:
> >>>>
> >>>> Hi Dima,
> >>>>
> >>>> Good news: no uri hierarchical error.
> >>>>
> >>>> All that I did was import your ctakes-misc pom as a maven project in
> >>> intellij. Then I created a run configuration with my sandbox as the
> >>> working directory, ctakes-misc as the classpath module, and my umls
> >>> credentials in the environment.
> >>>> All database files were found, the pipeline ran, and I got output:
> >>>> total 2448
> >>>> drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:19 .
> >>>> drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:18 ..
> >>>> -rwxrwx---+ 1 Administrators Domain Users 187675 Apr 26 14:19
> >>> GenSurg_UmbilicalHernia_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 238984 Apr 26 14:19
> >>> OBGYN_Gen_Abscess_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 82308 Apr 26 14:19
> >>> OBGYN_HysterectomyAndBSO_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 115983 Apr 26 14:19
> >>> OBGYN_IUD_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 35919 Apr 26 14:19
> >>> OBGYN_LaborProgressNote_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 112460 Apr 26 14:19
> >>> OBGYN_MVAPrego_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 173695 Apr 26 14:19
> >>> OBGYN_PROMCheck_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 340626 Apr 26 14:19
> >>> Peds_Dysphagia_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 390928 Apr 26 14:19
> >>> Peds_FebrileSez_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 115064 Apr 26 14:19
> >>> Peds_RoutBirthNote_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 101234 Apr 26 14:19
> >>> VascSurg_AAA_Leak_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 98015 Apr 26 14:19
> >>> VascSurg_FollowUp_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 218863 Apr 26 14:19
> >>> VascSurg_PVD_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 72902 Apr 26 14:19
> >>> VascSurg_RO-AAA_1.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 90825 Apr 26 14:19
> >>> VascSurg_RO-DVT.rtf.xmi
> >>>> -rwxrwx---+ 1 Administrators Domain Users 90827 Apr 26 14:19
> >>> VascSurg_RO-DVT_1.rtf.xmi
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> Bad news: it looks like the hsqldb port of lvg2008 is not working.
> >>>>
> >>>> Caused by: org.hsqldb.HsqlException: error in script file line: 61
> >>> C:\Spiffy\prj_ctakes_401\dev\ctakes-lvg-res\target\classes\o
> >>> rg\apache\ctakes\lvg\data\HSqlDb\lvg2008 java.io.IOException: read
> >>> beyond end of file in statement [SET TABLE PUBLIC.INFLECTION INDEX
> '3198299
> >>> 60557 3198299 53129 0 0 0 0 1210464']
> >>>>
> >>>> Caused by: org.hsqldb.HsqlException: Caused by: java.io.IOException:
> >>> read beyond end of file
> >>>>
> >>>>
> >>>> At any rate, the code works but I think that something is missing from
> >>> your configuration.
> >>>> Since it is a personal development environment you are kind of on your
> >>> own.
> >>>> Good luck,
> >>>> Sean
> >>>>
> >>>> P.S. Get rid of the ctakes-resources-umls2011ab artifact in your pom.
> >>> It isn't doing anything.
> >>>>
> >>>>
> >>>>
> >>>> -----Original Message-----
> >>>> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
> >>>> Sent: Wednesday, April 26, 2017 12:46 PM
> >>>> To: dev@ctakes.apache.org
> >>>> Subject: Re: URI is not hierarchical
> >>>>
> >>>> I am definitely still seeing the “URI is not hierarchical” issue.
> >>> Here’s a piece of information that might help you figure out what the
> >>> problem is:
> >>>>
> >>>>
> >>>>
> >>>> It only happens if the pipeline includes dictionary lookup. For
> >>> instance, this one fails:
> >>>>
> >>>>
> >>>>
> >>>> 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=fs67G
> >>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevR
> >>> An-a92vTj9x79u08OjKfQ9U4&s=MKa09-UzlhjAB_
> 1jVyGOpVo1UHWrMDqjWiVAnk0jfPE&e=
> >>>>
> >>>>
> >>>>
> >>>> But this one succeeds:
> >>>>
> >>>>
> >>>>
> >>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
> >>> com_dmitriydligach_ctakes-2Dmisc_blob_master_src_main_java_
> >>> org_apache_ctakes_pipelines_BasicPipeline.java&d=DwIGaQ&c=
> >>> qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpy
> >>> IisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevRAn-a92vTj
> >>> 9x79u08OjKfQ9U4&s=U0zGx-soIiYY64nHK_tIAIpeind9vdIrAuDQIxh-4ek&e=
> >>>>
> >>>>
> >>>>
> >>>> (it’s the same as the first one, but the dictionary lookup part is
> >>> removed).
> >>>>
> >>>>
> >>>>
> >>>> Dima
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>> On Apr 26, 2017, at 11:37, Finan, Sean <Sean.Finan@childrens.harvard.
> >>> edu> wrote:
> >>>>
> >>>>>
> >>>>
> >>>>> Hi again Dima,
> >>>>
> >>>>>
> >>>>
> >>>>> The piper files are not meant to replace uimafit. Uimafit is great
> >>> for many purposes.
> >>>>
> >>>>>
> >>>>
> >>>>> As for that annoying old "URI is not hierarchical" bug, a while back
> I
> >>> checked in a fix that worked for me. Since then I cannot duplicate it.
> >>>>
> >>>>>
> >>>>
> >>>>> Sean
> >>>>
> >>>>>
> >>>>
> >>>>> -----Original Message-----
> >>>>
> >>>>> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
> >>>>
> >>>>> Sent: Wednesday, April 26, 2017 12:18 PM
> >>>>
> >>>>> To: dev@ctakes.apache.org
> >>>>
> >>>>> Subject: Re: URI is not hierarchical
> >>>>
> >>>>>
> >>>>
> >>>>> 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.Finan@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:ddligach@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=fs67G
> >>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=xe6RaWm66aSyUeXjU20
> >>> x8dEc3xfYTHbadlwhgSdrIsw&s=ixO9vX_WJ7p-dpJc0RdnzRfjwQqbNw4gkLwf0SSpp0
> I&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.Finan@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.a
> >>> pache.org_confluence_display_CTAKES_Piper-2BFiles&d=DwIGaQ&c
> >>> =qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTp
> >>> yIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=xe6RaWm66aSyUeXjU20x8dEc3xf
> >>> YTHbadlwhgSdrIsw&s=pNVLJSOBMk5orJZ4Oy4ZwtpkPp0tU48-g1qxtpIBucw&e=
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> -----Original Message-----
> >>>>
> >>>>>>
> >>>>
> >>>>>>> From: Dligach, Dmitriy [mailto:ddligach@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=fs67G
> >>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf
> >>> _qgdQj3HYIeLCeKr9Q303b0Q&s=NWoDwPNChJkDhFseM3j8Gi7KNDdVqz
> i1BFt0onalf9I&e=
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> from command line as follows:
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> mvn exec:java -Dexec.mainClass=“org.apache.c
> >>> takes.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/ctakesresour
> >>> ces/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/resource
> >>> s/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.t
> >>> ype.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/l
> >>> ookup/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-2Dw
> >>> s.nlm.nih.gov_restful_isValidUMLSUser&d=DwIGaQ&c=qS4goWBT7po
> >>> plM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP
> >>> 6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q30
> >>> 3b0Q&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-2Dw
> >>> s.nlm.nih.gov_restful_isValidUMLSUser&d=DwIGaQ&c=qS4goWBT7po
> >>> plM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP
> >>> 6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q30
> >>> 3b0Q&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/look
> >>> up/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(Lv
> >>> gCmdApiResourceImpl.java:65)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at org.apache.uima.resource.impl.ResourceManager_impl.registerR
> >>> esource(ResourceManager_impl.java:628)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at org.apache.uima.resource.impl.ResourceManager_impl.initializ
> >>> eExternalResources(ResourceManager_impl.java:464)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at org.apache.uima.resource.Resource_ImplBase.initialize(Resour
> >>> ce_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.produceResou
> >>> rce(AnalysisEngineFactory_impl.java:94)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at org.apache.uima.impl.CompositeResourceFactory_impl.produceRe
> >>> source(CompositeResourceFactory_impl.java:62)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.
> >>> java:279)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFram
> >>> ework.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.createEngi
> >>> ne(AnalysisEngineFactory.java:711)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at org.apache.uima.fit.factory.AggregateBuilder.createAggregate
> >>> (AggregateBuilder.java:207)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at org.apache.ctakes.pipelines.UmlsLookupPipeline.main(UmlsLook
> >>> upPipeline.java:66)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAcce
> >>> ssorImpl.java:62)
> >>>>
> >>>>>>
> >>>>
> >>>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMe
> >>> thodAccessorImpl.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_MA
> >>> VEN_MojoExecutionException&d=DwIGaQ&c=qS4goWBT7poplM69zy_3x
> >>> hKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4
> >>> f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q303b0Q&s=
> >>> JfA-JsX45OHwuDl_DNkICQUwoIOMrYhdSxNKV1k_Ig4&e=
> >>>>
> >>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>>
> >>>>
> >>>>>
> >>>>
> >>>>
> >>>>
> >>>
> >>>
> >>
>
>
Re: URI is not hierarchical
Posted by "Dligach, Dmitriy" <dd...@luc.edu>.
Hi James,
Thank you so much for looking into this!
Your general setup matches mine. I also do:
1. svn co https://svn.apache.org/repos/asf/ctakes/trunk/
2. git clone https://github.com/dmitriydligach/ctakes-misc.git (in trunk/)
3. mvn clean compile (in trunk/)
4. mvn clean compile (in ctakes-misc/)
BTW, I just discovered that it’s not necessary to check out a fresh copy of ctakes-misc into a subdirectory in trunk. It will build no matter where it is on your system as long as you first do an ‘mvn clean compile’ in trunk/ (without it, ctakes-misc/ will not build).
Thanks again, James.
Dima
> On Apr 28, 2017, at 16:30, James Masanz <ma...@gmail.com> wrote:
>
> Hi Dima,
>
> Just to let you know I am taking a look at this. More later, if not today,
> then tomorrow. FYI here is where I'm at so far.
>
> I checked out a fresh copy of ctakes trunk and put files from your
> ctakes-misc into a subdirectory called ctakes-misc, and I updated my local
> copy of the main pom.xml for ctakes to include ctakes-misc.
>
> I am able to reproduce getting URI is not hierarchical just by letting
> tests run during "mvn clean install":
>
> Tests in error:
> testPipeline(org.apache.ctakes.temporal.ae.BackwardsTimeAnnotatorTest):
> URI is not hierarchical
>
> testPipeline(org.apache.ctakes.temporal.ae.ContextualModalityAnnotatorTest):
> URI is not hierarchical
> testPipeline(org.apache.ctakes.temporal.ae.EventAnnotatorTest): URI is
> not hierarchical
>
> testPipeline(org.apache.ctakes.temporal.ae.EventEventRelationAnnotatorTest):
> URI is not hierarchical
>
> testPipeline(org.apache.ctakes.temporal.ae.EventTimeRelationAnnotatorTest):
> URI is not hierarchical
>
>
> On Fri, Apr 28, 2017 at 12:27 PM, James Masanz <ma...@gmail.com>
> wrote:
>
>>
>> Going back to your original email, I notice cTAKES is referencing lvg.properties
>> as being within a jar
>>
>> 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
>>
>> But I also see in LvgCmdApiResourceImpl.java the following code, which is
>> trying to handle it as a File, not a stream. :(
>>
>> File configFile = new File(dr.getUri());
>> configFileName = configFile.getPath();
>>
>> At first glance, looks like LvgCmdApiResourceImpl needs updating.
>>
>> As a workaround, you could try extracting the lvg subdirectory from
>> ctakes-resources-4.0-bin.zip that's on sourceforge [1] into something on
>> the classpath so the lvg.propertiesfile appears under
>>
>> org/apache/ctakes/lvg/data/config/lvg.properties
>>
>> You might also need to have the rest of the files and directories under
>> org/apache/ctakes/lvg/data to also be outside the jar, not sure offhand.
>>
>> I can try that out this afternoon.
>>
>> [1] https://sourceforge.net/projects/ctakesresources/
>> files/ctakes-resources-4.0-bin.zip/download
>>
>>
>> On Wed, Apr 26, 2017 at 3:29 PM, Dligach, Dmitriy <dd...@luc.edu>
>> wrote:
>>
>>> Hi Sean,
>>>
>>> First of all, a huge thank you for taking time to debug this issue. I
>>> really appreciate your help.
>>>
>>> Second, I think my main message somehow got lost in translation (sorry, I
>>> should’ve included it for clarity with my recent emails). I never had any
>>> trouble running this pipeline in Eclipse. The “URI is not hierarchical”
>>> error only happens when I run it from command line.
>>>
>>> I run it using the following maven command:
>>>
>>> mvn exec:java -Dexec.mainClass="org.apache.c
>>> takes.pipelines.UmlsLookupPipeline" -Dexec.args="" -Dctakes.umlsuser=<my
>>> umls login name> -Dctakes.umlspw=<my umls password>
>>>
>>> As I said in my previous email, the other pipeline (that does not have
>>> dictionary lookup) runs fine at command line. The error only happens when I
>>> run pipelines containing dictionary lookup.
>>>
>>> Dima
>>>
>>>
>>>
>>>> On Apr 26, 2017, at 13:36, Finan, Sean <Sean.Finan@childrens.harvard.
>>> edu> wrote:
>>>>
>>>> Hi Dima,
>>>>
>>>> Good news: no uri hierarchical error.
>>>>
>>>> All that I did was import your ctakes-misc pom as a maven project in
>>> intellij. Then I created a run configuration with my sandbox as the
>>> working directory, ctakes-misc as the classpath module, and my umls
>>> credentials in the environment.
>>>> All database files were found, the pipeline ran, and I got output:
>>>> total 2448
>>>> drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:19 .
>>>> drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:18 ..
>>>> -rwxrwx---+ 1 Administrators Domain Users 187675 Apr 26 14:19
>>> GenSurg_UmbilicalHernia_1.rtf.xmi
>>>> -rwxrwx---+ 1 Administrators Domain Users 238984 Apr 26 14:19
>>> OBGYN_Gen_Abscess_1.rtf.xmi
>>>> -rwxrwx---+ 1 Administrators Domain Users 82308 Apr 26 14:19
>>> OBGYN_HysterectomyAndBSO_1.rtf.xmi
>>>> -rwxrwx---+ 1 Administrators Domain Users 115983 Apr 26 14:19
>>> OBGYN_IUD_1.rtf.xmi
>>>> -rwxrwx---+ 1 Administrators Domain Users 35919 Apr 26 14:19
>>> OBGYN_LaborProgressNote_1.rtf.xmi
>>>> -rwxrwx---+ 1 Administrators Domain Users 112460 Apr 26 14:19
>>> OBGYN_MVAPrego_1.rtf.xmi
>>>> -rwxrwx---+ 1 Administrators Domain Users 173695 Apr 26 14:19
>>> OBGYN_PROMCheck_1.rtf.xmi
>>>> -rwxrwx---+ 1 Administrators Domain Users 340626 Apr 26 14:19
>>> Peds_Dysphagia_1.rtf.xmi
>>>> -rwxrwx---+ 1 Administrators Domain Users 390928 Apr 26 14:19
>>> Peds_FebrileSez_1.rtf.xmi
>>>> -rwxrwx---+ 1 Administrators Domain Users 115064 Apr 26 14:19
>>> Peds_RoutBirthNote_1.rtf.xmi
>>>> -rwxrwx---+ 1 Administrators Domain Users 101234 Apr 26 14:19
>>> VascSurg_AAA_Leak_1.rtf.xmi
>>>> -rwxrwx---+ 1 Administrators Domain Users 98015 Apr 26 14:19
>>> VascSurg_FollowUp_1.rtf.xmi
>>>> -rwxrwx---+ 1 Administrators Domain Users 218863 Apr 26 14:19
>>> VascSurg_PVD_1.rtf.xmi
>>>> -rwxrwx---+ 1 Administrators Domain Users 72902 Apr 26 14:19
>>> VascSurg_RO-AAA_1.rtf.xmi
>>>> -rwxrwx---+ 1 Administrators Domain Users 90825 Apr 26 14:19
>>> VascSurg_RO-DVT.rtf.xmi
>>>> -rwxrwx---+ 1 Administrators Domain Users 90827 Apr 26 14:19
>>> VascSurg_RO-DVT_1.rtf.xmi
>>>>
>>>>
>>>>
>>>>
>>>> Bad news: it looks like the hsqldb port of lvg2008 is not working.
>>>>
>>>> Caused by: org.hsqldb.HsqlException: error in script file line: 61
>>> C:\Spiffy\prj_ctakes_401\dev\ctakes-lvg-res\target\classes\o
>>> rg\apache\ctakes\lvg\data\HSqlDb\lvg2008 java.io.IOException: read
>>> beyond end of file in statement [SET TABLE PUBLIC.INFLECTION INDEX '3198299
>>> 60557 3198299 53129 0 0 0 0 1210464']
>>>>
>>>> Caused by: org.hsqldb.HsqlException: Caused by: java.io.IOException:
>>> read beyond end of file
>>>>
>>>>
>>>> At any rate, the code works but I think that something is missing from
>>> your configuration.
>>>> Since it is a personal development environment you are kind of on your
>>> own.
>>>> Good luck,
>>>> Sean
>>>>
>>>> P.S. Get rid of the ctakes-resources-umls2011ab artifact in your pom.
>>> It isn't doing anything.
>>>>
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
>>>> Sent: Wednesday, April 26, 2017 12:46 PM
>>>> To: dev@ctakes.apache.org
>>>> Subject: Re: URI is not hierarchical
>>>>
>>>> I am definitely still seeing the “URI is not hierarchical” issue.
>>> Here’s a piece of information that might help you figure out what the
>>> problem is:
>>>>
>>>>
>>>>
>>>> It only happens if the pipeline includes dictionary lookup. For
>>> instance, this one fails:
>>>>
>>>>
>>>>
>>>> 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=fs67G
>>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevR
>>> An-a92vTj9x79u08OjKfQ9U4&s=MKa09-UzlhjAB_1jVyGOpVo1UHWrMDqjWiVAnk0jfPE&e=
>>>>
>>>>
>>>>
>>>> But this one succeeds:
>>>>
>>>>
>>>>
>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
>>> com_dmitriydligach_ctakes-2Dmisc_blob_master_src_main_java_
>>> org_apache_ctakes_pipelines_BasicPipeline.java&d=DwIGaQ&c=
>>> qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpy
>>> IisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevRAn-a92vTj
>>> 9x79u08OjKfQ9U4&s=U0zGx-soIiYY64nHK_tIAIpeind9vdIrAuDQIxh-4ek&e=
>>>>
>>>>
>>>>
>>>> (it’s the same as the first one, but the dictionary lookup part is
>>> removed).
>>>>
>>>>
>>>>
>>>> Dima
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>> On Apr 26, 2017, at 11:37, Finan, Sean <Sean.Finan@childrens.harvard.
>>> edu> wrote:
>>>>
>>>>>
>>>>
>>>>> Hi again Dima,
>>>>
>>>>>
>>>>
>>>>> The piper files are not meant to replace uimafit. Uimafit is great
>>> for many purposes.
>>>>
>>>>>
>>>>
>>>>> As for that annoying old "URI is not hierarchical" bug, a while back I
>>> checked in a fix that worked for me. Since then I cannot duplicate it.
>>>>
>>>>>
>>>>
>>>>> Sean
>>>>
>>>>>
>>>>
>>>>> -----Original Message-----
>>>>
>>>>> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
>>>>
>>>>> Sent: Wednesday, April 26, 2017 12:18 PM
>>>>
>>>>> To: dev@ctakes.apache.org
>>>>
>>>>> Subject: Re: URI is not hierarchical
>>>>
>>>>>
>>>>
>>>>> 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.Finan@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:ddligach@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=fs67G
>>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=xe6RaWm66aSyUeXjU20
>>> x8dEc3xfYTHbadlwhgSdrIsw&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.Finan@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.a
>>> pache.org_confluence_display_CTAKES_Piper-2BFiles&d=DwIGaQ&c
>>> =qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTp
>>> yIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=xe6RaWm66aSyUeXjU20x8dEc3xf
>>> YTHbadlwhgSdrIsw&s=pNVLJSOBMk5orJZ4Oy4ZwtpkPp0tU48-g1qxtpIBucw&e=
>>>>
>>>>>>
>>>>
>>>>>>>
>>>>
>>>>>>
>>>>
>>>>>>>
>>>>
>>>>>>
>>>>
>>>>>>> -----Original Message-----
>>>>
>>>>>>
>>>>
>>>>>>> From: Dligach, Dmitriy [mailto:ddligach@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=fs67G
>>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf
>>> _qgdQj3HYIeLCeKr9Q303b0Q&s=NWoDwPNChJkDhFseM3j8Gi7KNDdVqzi1BFt0onalf9I&e=
>>>>
>>>>>>
>>>>
>>>>>>>
>>>>
>>>>>>
>>>>
>>>>>>>
>>>>
>>>>>>
>>>>
>>>>>>>
>>>>
>>>>>>
>>>>
>>>>>>> from command line as follows:
>>>>
>>>>>>
>>>>
>>>>>>>
>>>>
>>>>>>
>>>>
>>>>>>>
>>>>
>>>>>>
>>>>
>>>>>>>
>>>>
>>>>>>
>>>>
>>>>>>> mvn exec:java -Dexec.mainClass=“org.apache.c
>>> takes.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/ctakesresour
>>> ces/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/resource
>>> s/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.t
>>> ype.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/l
>>> ookup/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-2Dw
>>> s.nlm.nih.gov_restful_isValidUMLSUser&d=DwIGaQ&c=qS4goWBT7po
>>> plM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP
>>> 6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q30
>>> 3b0Q&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-2Dw
>>> s.nlm.nih.gov_restful_isValidUMLSUser&d=DwIGaQ&c=qS4goWBT7po
>>> plM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP
>>> 6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q30
>>> 3b0Q&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/look
>>> up/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(Lv
>>> gCmdApiResourceImpl.java:65)
>>>>
>>>>>>
>>>>
>>>>>>>
>>>>
>>>>>>
>>>>
>>>>>>> at org.apache.uima.resource.impl.ResourceManager_impl.registerR
>>> esource(ResourceManager_impl.java:628)
>>>>
>>>>>>
>>>>
>>>>>>>
>>>>
>>>>>>
>>>>
>>>>>>> at org.apache.uima.resource.impl.ResourceManager_impl.initializ
>>> eExternalResources(ResourceManager_impl.java:464)
>>>>
>>>>>>
>>>>
>>>>>>>
>>>>
>>>>>>
>>>>
>>>>>>> at org.apache.uima.resource.Resource_ImplBase.initialize(Resour
>>> ce_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.produceResou
>>> rce(AnalysisEngineFactory_impl.java:94)
>>>>
>>>>>>
>>>>
>>>>>>>
>>>>
>>>>>>
>>>>
>>>>>>> at org.apache.uima.impl.CompositeResourceFactory_impl.produceRe
>>> source(CompositeResourceFactory_impl.java:62)
>>>>
>>>>>>
>>>>
>>>>>>>
>>>>
>>>>>>
>>>>
>>>>>>> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.
>>> java:279)
>>>>
>>>>>>
>>>>
>>>>>>>
>>>>
>>>>>>
>>>>
>>>>>>> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFram
>>> ework.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.createEngi
>>> ne(AnalysisEngineFactory.java:711)
>>>>
>>>>>>
>>>>
>>>>>>>
>>>>
>>>>>>
>>>>
>>>>>>> at org.apache.uima.fit.factory.AggregateBuilder.createAggregate
>>> (AggregateBuilder.java:207)
>>>>
>>>>>>
>>>>
>>>>>>>
>>>>
>>>>>>
>>>>
>>>>>>> at org.apache.ctakes.pipelines.UmlsLookupPipeline.main(UmlsLook
>>> upPipeline.java:66)
>>>>
>>>>>>
>>>>
>>>>>>>
>>>>
>>>>>>
>>>>
>>>>>>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>>>
>>>>>>
>>>>
>>>>>>>
>>>>
>>>>>>
>>>>
>>>>>>> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAcce
>>> ssorImpl.java:62)
>>>>
>>>>>>
>>>>
>>>>>>>
>>>>
>>>>>>
>>>>
>>>>>>> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMe
>>> thodAccessorImpl.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_MA
>>> VEN_MojoExecutionException&d=DwIGaQ&c=qS4goWBT7poplM69zy_3x
>>> hKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4
>>> f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q303b0Q&s=
>>> JfA-JsX45OHwuDl_DNkICQUwoIOMrYhdSxNKV1k_Ig4&e=
>>>>
>>>>>>
>>>>
>>>>>>
>>>>
>>>>>>
>>>>
>>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>
Re: URI is not hierarchical
Posted by James Masanz <ma...@gmail.com>.
Hi Dima,
Just to let you know I am taking a look at this. More later, if not today,
then tomorrow. FYI here is where I'm at so far.
I checked out a fresh copy of ctakes trunk and put files from your
ctakes-misc into a subdirectory called ctakes-misc, and I updated my local
copy of the main pom.xml for ctakes to include ctakes-misc.
I am able to reproduce getting URI is not hierarchical just by letting
tests run during "mvn clean install":
Tests in error:
testPipeline(org.apache.ctakes.temporal.ae.BackwardsTimeAnnotatorTest):
URI is not hierarchical
testPipeline(org.apache.ctakes.temporal.ae.ContextualModalityAnnotatorTest):
URI is not hierarchical
testPipeline(org.apache.ctakes.temporal.ae.EventAnnotatorTest): URI is
not hierarchical
testPipeline(org.apache.ctakes.temporal.ae.EventEventRelationAnnotatorTest):
URI is not hierarchical
testPipeline(org.apache.ctakes.temporal.ae.EventTimeRelationAnnotatorTest):
URI is not hierarchical
On Fri, Apr 28, 2017 at 12:27 PM, James Masanz <ma...@gmail.com>
wrote:
>
> Going back to your original email, I notice cTAKES is referencing lvg.properties
> as being within a jar
>
> 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
>
> But I also see in LvgCmdApiResourceImpl.java the following code, which is
> trying to handle it as a File, not a stream. :(
>
> File configFile = new File(dr.getUri());
> configFileName = configFile.getPath();
>
> At first glance, looks like LvgCmdApiResourceImpl needs updating.
>
> As a workaround, you could try extracting the lvg subdirectory from
> ctakes-resources-4.0-bin.zip that's on sourceforge [1] into something on
> the classpath so the lvg.propertiesfile appears under
>
> org/apache/ctakes/lvg/data/config/lvg.properties
>
> You might also need to have the rest of the files and directories under
> org/apache/ctakes/lvg/data to also be outside the jar, not sure offhand.
>
> I can try that out this afternoon.
>
> [1] https://sourceforge.net/projects/ctakesresources/
> files/ctakes-resources-4.0-bin.zip/download
>
>
> On Wed, Apr 26, 2017 at 3:29 PM, Dligach, Dmitriy <dd...@luc.edu>
> wrote:
>
>> Hi Sean,
>>
>> First of all, a huge thank you for taking time to debug this issue. I
>> really appreciate your help.
>>
>> Second, I think my main message somehow got lost in translation (sorry, I
>> should’ve included it for clarity with my recent emails). I never had any
>> trouble running this pipeline in Eclipse. The “URI is not hierarchical”
>> error only happens when I run it from command line.
>>
>> I run it using the following maven command:
>>
>> mvn exec:java -Dexec.mainClass="org.apache.c
>> takes.pipelines.UmlsLookupPipeline" -Dexec.args="" -Dctakes.umlsuser=<my
>> umls login name> -Dctakes.umlspw=<my umls password>
>>
>> As I said in my previous email, the other pipeline (that does not have
>> dictionary lookup) runs fine at command line. The error only happens when I
>> run pipelines containing dictionary lookup.
>>
>> Dima
>>
>>
>>
>> > On Apr 26, 2017, at 13:36, Finan, Sean <Sean.Finan@childrens.harvard.
>> edu> wrote:
>> >
>> > Hi Dima,
>> >
>> > Good news: no uri hierarchical error.
>> >
>> > All that I did was import your ctakes-misc pom as a maven project in
>> intellij. Then I created a run configuration with my sandbox as the
>> working directory, ctakes-misc as the classpath module, and my umls
>> credentials in the environment.
>> > All database files were found, the pipeline ran, and I got output:
>> > total 2448
>> > drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:19 .
>> > drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:18 ..
>> > -rwxrwx---+ 1 Administrators Domain Users 187675 Apr 26 14:19
>> GenSurg_UmbilicalHernia_1.rtf.xmi
>> > -rwxrwx---+ 1 Administrators Domain Users 238984 Apr 26 14:19
>> OBGYN_Gen_Abscess_1.rtf.xmi
>> > -rwxrwx---+ 1 Administrators Domain Users 82308 Apr 26 14:19
>> OBGYN_HysterectomyAndBSO_1.rtf.xmi
>> > -rwxrwx---+ 1 Administrators Domain Users 115983 Apr 26 14:19
>> OBGYN_IUD_1.rtf.xmi
>> > -rwxrwx---+ 1 Administrators Domain Users 35919 Apr 26 14:19
>> OBGYN_LaborProgressNote_1.rtf.xmi
>> > -rwxrwx---+ 1 Administrators Domain Users 112460 Apr 26 14:19
>> OBGYN_MVAPrego_1.rtf.xmi
>> > -rwxrwx---+ 1 Administrators Domain Users 173695 Apr 26 14:19
>> OBGYN_PROMCheck_1.rtf.xmi
>> > -rwxrwx---+ 1 Administrators Domain Users 340626 Apr 26 14:19
>> Peds_Dysphagia_1.rtf.xmi
>> > -rwxrwx---+ 1 Administrators Domain Users 390928 Apr 26 14:19
>> Peds_FebrileSez_1.rtf.xmi
>> > -rwxrwx---+ 1 Administrators Domain Users 115064 Apr 26 14:19
>> Peds_RoutBirthNote_1.rtf.xmi
>> > -rwxrwx---+ 1 Administrators Domain Users 101234 Apr 26 14:19
>> VascSurg_AAA_Leak_1.rtf.xmi
>> > -rwxrwx---+ 1 Administrators Domain Users 98015 Apr 26 14:19
>> VascSurg_FollowUp_1.rtf.xmi
>> > -rwxrwx---+ 1 Administrators Domain Users 218863 Apr 26 14:19
>> VascSurg_PVD_1.rtf.xmi
>> > -rwxrwx---+ 1 Administrators Domain Users 72902 Apr 26 14:19
>> VascSurg_RO-AAA_1.rtf.xmi
>> > -rwxrwx---+ 1 Administrators Domain Users 90825 Apr 26 14:19
>> VascSurg_RO-DVT.rtf.xmi
>> > -rwxrwx---+ 1 Administrators Domain Users 90827 Apr 26 14:19
>> VascSurg_RO-DVT_1.rtf.xmi
>> >
>> >
>> >
>> >
>> > Bad news: it looks like the hsqldb port of lvg2008 is not working.
>> >
>> > Caused by: org.hsqldb.HsqlException: error in script file line: 61
>> C:\Spiffy\prj_ctakes_401\dev\ctakes-lvg-res\target\classes\o
>> rg\apache\ctakes\lvg\data\HSqlDb\lvg2008 java.io.IOException: read
>> beyond end of file in statement [SET TABLE PUBLIC.INFLECTION INDEX '3198299
>> 60557 3198299 53129 0 0 0 0 1210464']
>> >
>> > Caused by: org.hsqldb.HsqlException: Caused by: java.io.IOException:
>> read beyond end of file
>> >
>> >
>> > At any rate, the code works but I think that something is missing from
>> your configuration.
>> > Since it is a personal development environment you are kind of on your
>> own.
>> > Good luck,
>> > Sean
>> >
>> > P.S. Get rid of the ctakes-resources-umls2011ab artifact in your pom.
>> It isn't doing anything.
>> >
>> >
>> >
>> > -----Original Message-----
>> > From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
>> > Sent: Wednesday, April 26, 2017 12:46 PM
>> > To: dev@ctakes.apache.org
>> > Subject: Re: URI is not hierarchical
>> >
>> > I am definitely still seeing the “URI is not hierarchical” issue.
>> Here’s a piece of information that might help you figure out what the
>> problem is:
>> >
>> >
>> >
>> > It only happens if the pipeline includes dictionary lookup. For
>> instance, this one fails:
>> >
>> >
>> >
>> > 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=fs67G
>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevR
>> An-a92vTj9x79u08OjKfQ9U4&s=MKa09-UzlhjAB_1jVyGOpVo1UHWrMDqjWiVAnk0jfPE&e=
>> >
>> >
>> >
>> > But this one succeeds:
>> >
>> >
>> >
>> > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
>> com_dmitriydligach_ctakes-2Dmisc_blob_master_src_main_java_
>> org_apache_ctakes_pipelines_BasicPipeline.java&d=DwIGaQ&c=
>> qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpy
>> IisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevRAn-a92vTj
>> 9x79u08OjKfQ9U4&s=U0zGx-soIiYY64nHK_tIAIpeind9vdIrAuDQIxh-4ek&e=
>> >
>> >
>> >
>> > (it’s the same as the first one, but the dictionary lookup part is
>> removed).
>> >
>> >
>> >
>> > Dima
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >> On Apr 26, 2017, at 11:37, Finan, Sean <Sean.Finan@childrens.harvard.
>> edu> wrote:
>> >
>> >>
>> >
>> >> Hi again Dima,
>> >
>> >>
>> >
>> >> The piper files are not meant to replace uimafit. Uimafit is great
>> for many purposes.
>> >
>> >>
>> >
>> >> As for that annoying old "URI is not hierarchical" bug, a while back I
>> checked in a fix that worked for me. Since then I cannot duplicate it.
>> >
>> >>
>> >
>> >> Sean
>> >
>> >>
>> >
>> >> -----Original Message-----
>> >
>> >> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
>> >
>> >> Sent: Wednesday, April 26, 2017 12:18 PM
>> >
>> >> To: dev@ctakes.apache.org
>> >
>> >> Subject: Re: URI is not hierarchical
>> >
>> >>
>> >
>> >> 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.Finan@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:ddligach@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=fs67G
>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=xe6RaWm66aSyUeXjU20
>> x8dEc3xfYTHbadlwhgSdrIsw&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.Finan@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.a
>> pache.org_confluence_display_CTAKES_Piper-2BFiles&d=DwIGaQ&c
>> =qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTp
>> yIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=xe6RaWm66aSyUeXjU20x8dEc3xf
>> YTHbadlwhgSdrIsw&s=pNVLJSOBMk5orJZ4Oy4ZwtpkPp0tU48-g1qxtpIBucw&e=
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>> -----Original Message-----
>> >
>> >>>
>> >
>> >>>> From: Dligach, Dmitriy [mailto:ddligach@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=fs67G
>> vlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf
>> _qgdQj3HYIeLCeKr9Q303b0Q&s=NWoDwPNChJkDhFseM3j8Gi7KNDdVqzi1BFt0onalf9I&e=
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>> from command line as follows:
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>> mvn exec:java -Dexec.mainClass=“org.apache.c
>> takes.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/ctakesresour
>> ces/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/resource
>> s/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.t
>> ype.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/l
>> ookup/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-2Dw
>> s.nlm.nih.gov_restful_isValidUMLSUser&d=DwIGaQ&c=qS4goWBT7po
>> plM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP
>> 6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q30
>> 3b0Q&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-2Dw
>> s.nlm.nih.gov_restful_isValidUMLSUser&d=DwIGaQ&c=qS4goWBT7po
>> plM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP
>> 6r0bcpKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q30
>> 3b0Q&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/look
>> up/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(Lv
>> gCmdApiResourceImpl.java:65)
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>> at org.apache.uima.resource.impl.ResourceManager_impl.registerR
>> esource(ResourceManager_impl.java:628)
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>> at org.apache.uima.resource.impl.ResourceManager_impl.initializ
>> eExternalResources(ResourceManager_impl.java:464)
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>> at org.apache.uima.resource.Resource_ImplBase.initialize(Resour
>> ce_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.produceResou
>> rce(AnalysisEngineFactory_impl.java:94)
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>> at org.apache.uima.impl.CompositeResourceFactory_impl.produceRe
>> source(CompositeResourceFactory_impl.java:62)
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.
>> java:279)
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFram
>> ework.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.createEngi
>> ne(AnalysisEngineFactory.java:711)
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>> at org.apache.uima.fit.factory.AggregateBuilder.createAggregate
>> (AggregateBuilder.java:207)
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>> at org.apache.ctakes.pipelines.UmlsLookupPipeline.main(UmlsLook
>> upPipeline.java:66)
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAcce
>> ssorImpl.java:62)
>> >
>> >>>
>> >
>> >>>>
>> >
>> >>>
>> >
>> >>>> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMe
>> thodAccessorImpl.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_MA
>> VEN_MojoExecutionException&d=DwIGaQ&c=qS4goWBT7poplM69zy_3x
>> hKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4
>> f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q303b0Q&s=
>> JfA-JsX45OHwuDl_DNkICQUwoIOMrYhdSxNKV1k_Ig4&e=
>> >
>> >>>
>> >
>> >>>
>> >
>> >>>
>> >
>> >>
>> >
>> >
>> >
>>
>>
>
RE: URI is not hierarchical
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi James,
With a glance at LvgCmdApiResource ... good gods, do we still need this?
Given that we updated to lvg 2016 it looks like half of lvg-res should be completely revamped and we can probably get rid of the hacky references. 4.1 ?
Sean
-----Original Message-----
From: James Masanz [mailto:masanz.james@gmail.com]
Sent: Friday, April 28, 2017 12:28 PM
To: dev@ctakes.apache.org
Subject: Re: URI is not hierarchical
Going back to your original email, I notice cTAKES is referencing
lvg.properties
as being within a jar
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
But I also see in LvgCmdApiResourceImpl.java the following code, which is
trying to handle it as a File, not a stream. :(
File configFile = new File(dr.getUri());
configFileName = configFile.getPath();
At first glance, looks like LvgCmdApiResourceImpl needs updating.
As a workaround, you could try extracting the lvg subdirectory from
ctakes-resources-4.0-bin.zip that's on sourceforge [1] into something on
the classpath so the lvg.propertiesfile appears under
org/apache/ctakes/lvg/data/config/lvg.properties
You might also need to have the rest of the files and directories under
org/apache/ctakes/lvg/data to also be outside the jar, not sure offhand.
I can try that out this afternoon.
[1]
https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_ctakesresources_files_ctakes-2Dresources-2D4.0-2Dbin.zip_download&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ra9HfnuMGpOujoaSUtQA9mL4u6gpme6fd--2pbUGohc&s=fqcKKFIrMw69bxvC7tXm0ZWex5PvIsP32HivEqbJZrc&e=
On Wed, Apr 26, 2017 at 3:29 PM, Dligach, Dmitriy <dd...@luc.edu> wrote:
> Hi Sean,
>
> First of all, a huge thank you for taking time to debug this issue. I
> really appreciate your help.
>
> Second, I think my main message somehow got lost in translation (sorry, I
> should’ve included it for clarity with my recent emails). I never had any
> trouble running this pipeline in Eclipse. The “URI is not hierarchical”
> error only happens when I run it from command line.
>
> I run it using the following maven command:
>
> mvn exec:java -Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline"
> -Dexec.args="" -Dctakes.umlsuser=<my umls login name> -Dctakes.umlspw=<my
> umls password>
>
> As I said in my previous email, the other pipeline (that does not have
> dictionary lookup) runs fine at command line. The error only happens when I
> run pipelines containing dictionary lookup.
>
> Dima
>
>
>
> > On Apr 26, 2017, at 13:36, Finan, Sean <Se...@childrens.harvard.edu>
> wrote:
> >
> > Hi Dima,
> >
> > Good news: no uri hierarchical error.
> >
> > All that I did was import your ctakes-misc pom as a maven project in
> intellij. Then I created a run configuration with my sandbox as the
> working directory, ctakes-misc as the classpath module, and my umls
> credentials in the environment.
> > All database files were found, the pipeline ran, and I got output:
> > total 2448
> > drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:19 .
> > drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:18 ..
> > -rwxrwx---+ 1 Administrators Domain Users 187675 Apr 26 14:19
> GenSurg_UmbilicalHernia_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 238984 Apr 26 14:19
> OBGYN_Gen_Abscess_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 82308 Apr 26 14:19
> OBGYN_HysterectomyAndBSO_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 115983 Apr 26 14:19
> OBGYN_IUD_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 35919 Apr 26 14:19
> OBGYN_LaborProgressNote_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 112460 Apr 26 14:19
> OBGYN_MVAPrego_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 173695 Apr 26 14:19
> OBGYN_PROMCheck_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 340626 Apr 26 14:19
> Peds_Dysphagia_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 390928 Apr 26 14:19
> Peds_FebrileSez_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 115064 Apr 26 14:19
> Peds_RoutBirthNote_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 101234 Apr 26 14:19
> VascSurg_AAA_Leak_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 98015 Apr 26 14:19
> VascSurg_FollowUp_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 218863 Apr 26 14:19
> VascSurg_PVD_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 72902 Apr 26 14:19
> VascSurg_RO-AAA_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 90825 Apr 26 14:19
> VascSurg_RO-DVT.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 90827 Apr 26 14:19
> VascSurg_RO-DVT_1.rtf.xmi
> >
> >
> >
> >
> > Bad news: it looks like the hsqldb port of lvg2008 is not working.
> >
> > Caused by: org.hsqldb.HsqlException: error in script file line: 61
> C:\Spiffy\prj_ctakes_401\dev\ctakes-lvg-res\target\classes\
> org\apache\ctakes\lvg\data\HSqlDb\lvg2008 java.io.IOException: read
> beyond end of file in statement [SET TABLE PUBLIC.INFLECTION INDEX '3198299
> 60557 3198299 53129 0 0 0 0 1210464']
> >
> > Caused by: org.hsqldb.HsqlException: Caused by: java.io.IOException:
> read beyond end of file
> >
> >
> > At any rate, the code works but I think that something is missing from
> your configuration.
> > Since it is a personal development environment you are kind of on your
> own.
> > Good luck,
> > Sean
> >
> > P.S. Get rid of the ctakes-resources-umls2011ab artifact in your pom.
> It isn't doing anything.
> >
> >
> >
> > -----Original Message-----
> > From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
> > Sent: Wednesday, April 26, 2017 12:46 PM
> > To: dev@ctakes.apache.org
> > Subject: Re: URI is not hierarchical
> >
> > I am definitely still seeing the “URI is not hierarchical” issue. Here’s
> a piece of information that might help you figure out what the problem is:
> >
> >
> >
> > It only happens if the pipeline includes dictionary lookup. For
> instance, this one fails:
> >
> >
> >
> > 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=Cv-_Ac9CLY7wNnflevRAn-
> a92vTj9x79u08OjKfQ9U4&s=MKa09-UzlhjAB_1jVyGOpVo1UHWrMDqjWiVAnk0jfPE&e=
> >
> >
> >
> > But this one succeeds:
> >
> >
> >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
> com_dmitriydligach_ctakes-2Dmisc_blob_master_src_main_
> java_org_apache_ctakes_pipelines_BasicPipeline.java&
> d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=
> fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevRAn-
> a92vTj9x79u08OjKfQ9U4&s=U0zGx-soIiYY64nHK_tIAIpeind9vdIrAuDQIxh-4ek&e=
> >
> >
> >
> > (it’s the same as the first one, but the dictionary lookup part is
> removed).
> >
> >
> >
> > Dima
> >
> >
> >
> >
> >
> >
> >
> >> On Apr 26, 2017, at 11:37, Finan, Sean <Sean.Finan@childrens.harvard.
> edu> wrote:
> >
> >>
> >
> >> Hi again Dima,
> >
> >>
> >
> >> The piper files are not meant to replace uimafit. Uimafit is great for
> many purposes.
> >
> >>
> >
> >> As for that annoying old "URI is not hierarchical" bug, a while back I
> checked in a fix that worked for me. Since then I cannot duplicate it.
> >
> >>
> >
> >> Sean
> >
> >>
> >
> >> -----Original Message-----
> >
> >> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
> >
> >> Sent: Wednesday, April 26, 2017 12:18 PM
> >
> >> To: dev@ctakes.apache.org
> >
> >> Subject: Re: URI is not hierarchical
> >
> >>
> >
> >> 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.Finan@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:ddligach@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.Finan@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:ddligach@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=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> pKGd4f7d4gTao&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=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> pKGd4f7d4gTao&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.initializeAggregateAnalysisEng
> ine(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=https-3A__urldefense.proofpoint&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=ra9HfnuMGpOujoaSUtQA9mL4u6gpme6fd--2pbUGohc&s=YQ9ZF9smiNYo-O3hS6Q5Ig98tZLemJD5aRphQazqOkI&e= .
> com/v2/url?u=http-3A__cwiki.apache.org_confluence_display_
> MAVEN_MojoExecutionException&d=DwIGaQ&c=qS4goWBT7poplM69zy_
> 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> pKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q303b0Q&s=JfA-
> JsX45OHwuDl_DNkICQUwoIOMrYhdSxNKV1k_Ig4&e=
> >
> >>>
> >
> >>>
> >
> >>>
> >
> >>
> >
> >
> >
>
>
Re: URI is not hierarchical
Posted by James Masanz <ma...@gmail.com>.
Going back to your original email, I notice cTAKES is referencing
lvg.properties
as being within a jar
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
But I also see in LvgCmdApiResourceImpl.java the following code, which is
trying to handle it as a File, not a stream. :(
File configFile = new File(dr.getUri());
configFileName = configFile.getPath();
At first glance, looks like LvgCmdApiResourceImpl needs updating.
As a workaround, you could try extracting the lvg subdirectory from
ctakes-resources-4.0-bin.zip that's on sourceforge [1] into something on
the classpath so the lvg.propertiesfile appears under
org/apache/ctakes/lvg/data/config/lvg.properties
You might also need to have the rest of the files and directories under
org/apache/ctakes/lvg/data to also be outside the jar, not sure offhand.
I can try that out this afternoon.
[1]
https://sourceforge.net/projects/ctakesresources/files/ctakes-resources-4.0-bin.zip/download
On Wed, Apr 26, 2017 at 3:29 PM, Dligach, Dmitriy <dd...@luc.edu> wrote:
> Hi Sean,
>
> First of all, a huge thank you for taking time to debug this issue. I
> really appreciate your help.
>
> Second, I think my main message somehow got lost in translation (sorry, I
> should’ve included it for clarity with my recent emails). I never had any
> trouble running this pipeline in Eclipse. The “URI is not hierarchical”
> error only happens when I run it from command line.
>
> I run it using the following maven command:
>
> mvn exec:java -Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline"
> -Dexec.args="" -Dctakes.umlsuser=<my umls login name> -Dctakes.umlspw=<my
> umls password>
>
> As I said in my previous email, the other pipeline (that does not have
> dictionary lookup) runs fine at command line. The error only happens when I
> run pipelines containing dictionary lookup.
>
> Dima
>
>
>
> > On Apr 26, 2017, at 13:36, Finan, Sean <Se...@childrens.harvard.edu>
> wrote:
> >
> > Hi Dima,
> >
> > Good news: no uri hierarchical error.
> >
> > All that I did was import your ctakes-misc pom as a maven project in
> intellij. Then I created a run configuration with my sandbox as the
> working directory, ctakes-misc as the classpath module, and my umls
> credentials in the environment.
> > All database files were found, the pipeline ran, and I got output:
> > total 2448
> > drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:19 .
> > drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:18 ..
> > -rwxrwx---+ 1 Administrators Domain Users 187675 Apr 26 14:19
> GenSurg_UmbilicalHernia_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 238984 Apr 26 14:19
> OBGYN_Gen_Abscess_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 82308 Apr 26 14:19
> OBGYN_HysterectomyAndBSO_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 115983 Apr 26 14:19
> OBGYN_IUD_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 35919 Apr 26 14:19
> OBGYN_LaborProgressNote_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 112460 Apr 26 14:19
> OBGYN_MVAPrego_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 173695 Apr 26 14:19
> OBGYN_PROMCheck_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 340626 Apr 26 14:19
> Peds_Dysphagia_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 390928 Apr 26 14:19
> Peds_FebrileSez_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 115064 Apr 26 14:19
> Peds_RoutBirthNote_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 101234 Apr 26 14:19
> VascSurg_AAA_Leak_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 98015 Apr 26 14:19
> VascSurg_FollowUp_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 218863 Apr 26 14:19
> VascSurg_PVD_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 72902 Apr 26 14:19
> VascSurg_RO-AAA_1.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 90825 Apr 26 14:19
> VascSurg_RO-DVT.rtf.xmi
> > -rwxrwx---+ 1 Administrators Domain Users 90827 Apr 26 14:19
> VascSurg_RO-DVT_1.rtf.xmi
> >
> >
> >
> >
> > Bad news: it looks like the hsqldb port of lvg2008 is not working.
> >
> > Caused by: org.hsqldb.HsqlException: error in script file line: 61
> C:\Spiffy\prj_ctakes_401\dev\ctakes-lvg-res\target\classes\
> org\apache\ctakes\lvg\data\HSqlDb\lvg2008 java.io.IOException: read
> beyond end of file in statement [SET TABLE PUBLIC.INFLECTION INDEX '3198299
> 60557 3198299 53129 0 0 0 0 1210464']
> >
> > Caused by: org.hsqldb.HsqlException: Caused by: java.io.IOException:
> read beyond end of file
> >
> >
> > At any rate, the code works but I think that something is missing from
> your configuration.
> > Since it is a personal development environment you are kind of on your
> own.
> > Good luck,
> > Sean
> >
> > P.S. Get rid of the ctakes-resources-umls2011ab artifact in your pom.
> It isn't doing anything.
> >
> >
> >
> > -----Original Message-----
> > From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
> > Sent: Wednesday, April 26, 2017 12:46 PM
> > To: dev@ctakes.apache.org
> > Subject: Re: URI is not hierarchical
> >
> > I am definitely still seeing the “URI is not hierarchical” issue. Here’s
> a piece of information that might help you figure out what the problem is:
> >
> >
> >
> > It only happens if the pipeline includes dictionary lookup. For
> instance, this one fails:
> >
> >
> >
> > 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=Cv-_Ac9CLY7wNnflevRAn-
> a92vTj9x79u08OjKfQ9U4&s=MKa09-UzlhjAB_1jVyGOpVo1UHWrMDqjWiVAnk0jfPE&e=
> >
> >
> >
> > But this one succeeds:
> >
> >
> >
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.
> com_dmitriydligach_ctakes-2Dmisc_blob_master_src_main_
> java_org_apache_ctakes_pipelines_BasicPipeline.java&
> d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=
> fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevRAn-
> a92vTj9x79u08OjKfQ9U4&s=U0zGx-soIiYY64nHK_tIAIpeind9vdIrAuDQIxh-4ek&e=
> >
> >
> >
> > (it’s the same as the first one, but the dictionary lookup part is
> removed).
> >
> >
> >
> > Dima
> >
> >
> >
> >
> >
> >
> >
> >> On Apr 26, 2017, at 11:37, Finan, Sean <Sean.Finan@childrens.harvard.
> edu> wrote:
> >
> >>
> >
> >> Hi again Dima,
> >
> >>
> >
> >> The piper files are not meant to replace uimafit. Uimafit is great for
> many purposes.
> >
> >>
> >
> >> As for that annoying old "URI is not hierarchical" bug, a while back I
> checked in a fix that worked for me. Since then I cannot duplicate it.
> >
> >>
> >
> >> Sean
> >
> >>
> >
> >> -----Original Message-----
> >
> >> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
> >
> >> Sent: Wednesday, April 26, 2017 12:18 PM
> >
> >> To: dev@ctakes.apache.org
> >
> >> Subject: Re: URI is not hierarchical
> >
> >>
> >
> >> 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.Finan@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:ddligach@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.Finan@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:ddligach@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=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> pKGd4f7d4gTao&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=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> pKGd4f7d4gTao&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.initializeAggregateAnalysisEng
> ine(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=fs67GvlGZstTpyIisCYNYmQCP6r0bc
> pKGd4f7d4gTao&m=-N-wYwlTFXbedV0kkcf_qgdQj3HYIeLCeKr9Q303b0Q&s=JfA-
> JsX45OHwuDl_DNkICQUwoIOMrYhdSxNKV1k_Ig4&e=
> >
> >>>
> >
> >>>
> >
> >>>
> >
> >>
> >
> >
> >
>
>
Re: URI is not hierarchical
Posted by "Dligach, Dmitriy" <dd...@luc.edu>.
Hi Sean,
First of all, a huge thank you for taking time to debug this issue. I really appreciate your help.
Second, I think my main message somehow got lost in translation (sorry, I should’ve included it for clarity with my recent emails). I never had any trouble running this pipeline in Eclipse. The “URI is not hierarchical” error only happens when I run it from command line.
I run it using the following maven command:
mvn exec:java -Dexec.mainClass="org.apache.ctakes.pipelines.UmlsLookupPipeline" -Dexec.args="" -Dctakes.umlsuser=<my umls login name> -Dctakes.umlspw=<my umls password>
As I said in my previous email, the other pipeline (that does not have dictionary lookup) runs fine at command line. The error only happens when I run pipelines containing dictionary lookup.
Dima
> On Apr 26, 2017, at 13:36, Finan, Sean <Se...@childrens.harvard.edu> wrote:
>
> Hi Dima,
>
> Good news: no uri hierarchical error.
>
> All that I did was import your ctakes-misc pom as a maven project in intellij. Then I created a run configuration with my sandbox as the working directory, ctakes-misc as the classpath module, and my umls credentials in the environment.
> All database files were found, the pipeline ran, and I got output:
> total 2448
> drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:19 .
> drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:18 ..
> -rwxrwx---+ 1 Administrators Domain Users 187675 Apr 26 14:19 GenSurg_UmbilicalHernia_1.rtf.xmi
> -rwxrwx---+ 1 Administrators Domain Users 238984 Apr 26 14:19 OBGYN_Gen_Abscess_1.rtf.xmi
> -rwxrwx---+ 1 Administrators Domain Users 82308 Apr 26 14:19 OBGYN_HysterectomyAndBSO_1.rtf.xmi
> -rwxrwx---+ 1 Administrators Domain Users 115983 Apr 26 14:19 OBGYN_IUD_1.rtf.xmi
> -rwxrwx---+ 1 Administrators Domain Users 35919 Apr 26 14:19 OBGYN_LaborProgressNote_1.rtf.xmi
> -rwxrwx---+ 1 Administrators Domain Users 112460 Apr 26 14:19 OBGYN_MVAPrego_1.rtf.xmi
> -rwxrwx---+ 1 Administrators Domain Users 173695 Apr 26 14:19 OBGYN_PROMCheck_1.rtf.xmi
> -rwxrwx---+ 1 Administrators Domain Users 340626 Apr 26 14:19 Peds_Dysphagia_1.rtf.xmi
> -rwxrwx---+ 1 Administrators Domain Users 390928 Apr 26 14:19 Peds_FebrileSez_1.rtf.xmi
> -rwxrwx---+ 1 Administrators Domain Users 115064 Apr 26 14:19 Peds_RoutBirthNote_1.rtf.xmi
> -rwxrwx---+ 1 Administrators Domain Users 101234 Apr 26 14:19 VascSurg_AAA_Leak_1.rtf.xmi
> -rwxrwx---+ 1 Administrators Domain Users 98015 Apr 26 14:19 VascSurg_FollowUp_1.rtf.xmi
> -rwxrwx---+ 1 Administrators Domain Users 218863 Apr 26 14:19 VascSurg_PVD_1.rtf.xmi
> -rwxrwx---+ 1 Administrators Domain Users 72902 Apr 26 14:19 VascSurg_RO-AAA_1.rtf.xmi
> -rwxrwx---+ 1 Administrators Domain Users 90825 Apr 26 14:19 VascSurg_RO-DVT.rtf.xmi
> -rwxrwx---+ 1 Administrators Domain Users 90827 Apr 26 14:19 VascSurg_RO-DVT_1.rtf.xmi
>
>
>
>
> Bad news: it looks like the hsqldb port of lvg2008 is not working.
>
> Caused by: org.hsqldb.HsqlException: error in script file line: 61 C:\Spiffy\prj_ctakes_401\dev\ctakes-lvg-res\target\classes\org\apache\ctakes\lvg\data\HSqlDb\lvg2008 java.io.IOException: read beyond end of file in statement [SET TABLE PUBLIC.INFLECTION INDEX '3198299 60557 3198299 53129 0 0 0 0 1210464']
>
> Caused by: org.hsqldb.HsqlException: Caused by: java.io.IOException: read beyond end of file
>
>
> At any rate, the code works but I think that something is missing from your configuration.
> Since it is a personal development environment you are kind of on your own.
> Good luck,
> Sean
>
> P.S. Get rid of the ctakes-resources-umls2011ab artifact in your pom. It isn't doing anything.
>
>
>
> -----Original Message-----
> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
> Sent: Wednesday, April 26, 2017 12:46 PM
> To: dev@ctakes.apache.org
> Subject: Re: URI is not hierarchical
>
> I am definitely still seeing the “URI is not hierarchical” issue. Here’s a piece of information that might help you figure out what the problem is:
>
>
>
> It only happens if the pipeline includes dictionary lookup. For instance, this one fails:
>
>
>
> 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=Cv-_Ac9CLY7wNnflevRAn-a92vTj9x79u08OjKfQ9U4&s=MKa09-UzlhjAB_1jVyGOpVo1UHWrMDqjWiVAnk0jfPE&e=
>
>
>
> But this one succeeds:
>
>
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_dmitriydligach_ctakes-2Dmisc_blob_master_src_main_java_org_apache_ctakes_pipelines_BasicPipeline.java&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevRAn-a92vTj9x79u08OjKfQ9U4&s=U0zGx-soIiYY64nHK_tIAIpeind9vdIrAuDQIxh-4ek&e=
>
>
>
> (it’s the same as the first one, but the dictionary lookup part is removed).
>
>
>
> Dima
>
>
>
>
>
>
>
>> On Apr 26, 2017, at 11:37, Finan, Sean <Se...@childrens.harvard.edu> wrote:
>
>>
>
>> Hi again Dima,
>
>>
>
>> The piper files are not meant to replace uimafit. Uimafit is great for many purposes.
>
>>
>
>> As for that annoying old "URI is not hierarchical" bug, a while back I checked in a fix that worked for me. Since then I cannot duplicate it.
>
>>
>
>> Sean
>
>>
>
>> -----Original Message-----
>
>> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
>
>> Sent: Wednesday, April 26, 2017 12:18 PM
>
>> To: dev@ctakes.apache.org
>
>> Subject: Re: URI is not hierarchical
>
>>
>
>> 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 <Se...@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:ddligach@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 <Se...@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:ddligach@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=
>
>>>
>
>>>
>
>>>
>
>>
>
>
>
RE: URI is not hierarchical
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Dima,
Good news: no uri hierarchical error.
All that I did was import your ctakes-misc pom as a maven project in intellij. Then I created a run configuration with my sandbox as the working directory, ctakes-misc as the classpath module, and my umls credentials in the environment.
All database files were found, the pipeline ran, and I got output:
total 2448
drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:19 .
drwxrwx---+ 1 Administrators Domain Users 0 Apr 26 14:18 ..
-rwxrwx---+ 1 Administrators Domain Users 187675 Apr 26 14:19 GenSurg_UmbilicalHernia_1.rtf.xmi
-rwxrwx---+ 1 Administrators Domain Users 238984 Apr 26 14:19 OBGYN_Gen_Abscess_1.rtf.xmi
-rwxrwx---+ 1 Administrators Domain Users 82308 Apr 26 14:19 OBGYN_HysterectomyAndBSO_1.rtf.xmi
-rwxrwx---+ 1 Administrators Domain Users 115983 Apr 26 14:19 OBGYN_IUD_1.rtf.xmi
-rwxrwx---+ 1 Administrators Domain Users 35919 Apr 26 14:19 OBGYN_LaborProgressNote_1.rtf.xmi
-rwxrwx---+ 1 Administrators Domain Users 112460 Apr 26 14:19 OBGYN_MVAPrego_1.rtf.xmi
-rwxrwx---+ 1 Administrators Domain Users 173695 Apr 26 14:19 OBGYN_PROMCheck_1.rtf.xmi
-rwxrwx---+ 1 Administrators Domain Users 340626 Apr 26 14:19 Peds_Dysphagia_1.rtf.xmi
-rwxrwx---+ 1 Administrators Domain Users 390928 Apr 26 14:19 Peds_FebrileSez_1.rtf.xmi
-rwxrwx---+ 1 Administrators Domain Users 115064 Apr 26 14:19 Peds_RoutBirthNote_1.rtf.xmi
-rwxrwx---+ 1 Administrators Domain Users 101234 Apr 26 14:19 VascSurg_AAA_Leak_1.rtf.xmi
-rwxrwx---+ 1 Administrators Domain Users 98015 Apr 26 14:19 VascSurg_FollowUp_1.rtf.xmi
-rwxrwx---+ 1 Administrators Domain Users 218863 Apr 26 14:19 VascSurg_PVD_1.rtf.xmi
-rwxrwx---+ 1 Administrators Domain Users 72902 Apr 26 14:19 VascSurg_RO-AAA_1.rtf.xmi
-rwxrwx---+ 1 Administrators Domain Users 90825 Apr 26 14:19 VascSurg_RO-DVT.rtf.xmi
-rwxrwx---+ 1 Administrators Domain Users 90827 Apr 26 14:19 VascSurg_RO-DVT_1.rtf.xmi
Bad news: it looks like the hsqldb port of lvg2008 is not working.
Caused by: org.hsqldb.HsqlException: error in script file line: 61 C:\Spiffy\prj_ctakes_401\dev\ctakes-lvg-res\target\classes\org\apache\ctakes\lvg\data\HSqlDb\lvg2008 java.io.IOException: read beyond end of file in statement [SET TABLE PUBLIC.INFLECTION INDEX '3198299 60557 3198299 53129 0 0 0 0 1210464']
Caused by: org.hsqldb.HsqlException: Caused by: java.io.IOException: read beyond end of file
At any rate, the code works but I think that something is missing from your configuration.
Since it is a personal development environment you are kind of on your own.
Good luck,
Sean
P.S. Get rid of the ctakes-resources-umls2011ab artifact in your pom. It isn't doing anything.
-----Original Message-----
From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
Sent: Wednesday, April 26, 2017 12:46 PM
To: dev@ctakes.apache.org
Subject: Re: URI is not hierarchical
I am definitely still seeing the “URI is not hierarchical” issue. Here’s a piece of information that might help you figure out what the problem is:
It only happens if the pipeline includes dictionary lookup. For instance, this one fails:
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=Cv-_Ac9CLY7wNnflevRAn-a92vTj9x79u08OjKfQ9U4&s=MKa09-UzlhjAB_1jVyGOpVo1UHWrMDqjWiVAnk0jfPE&e=
But this one succeeds:
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_dmitriydligach_ctakes-2Dmisc_blob_master_src_main_java_org_apache_ctakes_pipelines_BasicPipeline.java&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=Cv-_Ac9CLY7wNnflevRAn-a92vTj9x79u08OjKfQ9U4&s=U0zGx-soIiYY64nHK_tIAIpeind9vdIrAuDQIxh-4ek&e=
(it’s the same as the first one, but the dictionary lookup part is removed).
Dima
> On Apr 26, 2017, at 11:37, Finan, Sean <Se...@childrens.harvard.edu> wrote:
>
> Hi again Dima,
>
> The piper files are not meant to replace uimafit. Uimafit is great for many purposes.
>
> As for that annoying old "URI is not hierarchical" bug, a while back I checked in a fix that worked for me. Since then I cannot duplicate it.
>
> Sean
>
> -----Original Message-----
> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
> Sent: Wednesday, April 26, 2017 12:18 PM
> To: dev@ctakes.apache.org
> Subject: Re: URI is not hierarchical
>
> 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 <Se...@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:ddligach@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 <Se...@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:ddligach@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=
>>
>>
>>
>
Re: URI is not hierarchical
Posted by "Dligach, Dmitriy" <dd...@luc.edu>.
I am definitely still seeing the “URI is not hierarchical” issue. Here’s a piece of information that might help you figure out what the problem is:
It only happens if the pipeline includes dictionary lookup. For instance, this one fails:
https://github.com/dmitriydligach/ctakes-misc/blob/master/src/main/java/org/apache/ctakes/pipelines/UmlsLookupPipeline.java
But this one succeeds:
https://github.com/dmitriydligach/ctakes-misc/blob/master/src/main/java/org/apache/ctakes/pipelines/BasicPipeline.java
(it’s the same as the first one, but the dictionary lookup part is removed).
Dima
> On Apr 26, 2017, at 11:37, Finan, Sean <Se...@childrens.harvard.edu> wrote:
>
> Hi again Dima,
>
> The piper files are not meant to replace uimafit. Uimafit is great for many purposes.
>
> As for that annoying old "URI is not hierarchical" bug, a while back I checked in a fix that worked for me. Since then I cannot duplicate it.
>
> Sean
>
> -----Original Message-----
> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
> Sent: Wednesday, April 26, 2017 12:18 PM
> To: dev@ctakes.apache.org
> Subject: Re: URI is not hierarchical
>
> 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 <Se...@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:ddligach@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 <Se...@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:ddligach@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=
>>
>>
>>
>
RE: URI is not hierarchical
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi again Dima,
The piper files are not meant to replace uimafit. Uimafit is great for many purposes.
As for that annoying old "URI is not hierarchical" bug, a while back I checked in a fix that worked for me. Since then I cannot duplicate it.
Sean
-----Original Message-----
From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
Sent: Wednesday, April 26, 2017 12:18 PM
To: dev@ctakes.apache.org
Subject: Re: URI is not hierarchical
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 <Se...@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:ddligach@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 <Se...@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:ddligach@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=
>
>
>
RE: URI is not hierarchical
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Dima,
I don't know what to say. "Stop using Eclipse"? Just kidding.
When I run from command line I use scripts that set my classpath.
When I run from Intellij I specify the "working directory: ..." and "use classpath of module: ..." that encompass everything that I need.
I understand what you are saying: "dictionary doesn't work". What I am saying is "dictionary doesn't work as you are running it, and I don't know how you are running it. Code isn't everything." Does that make sense? I am going to pull your github code and see if it runs for me.
Sean
Just in case there is confusion on pipers and uimafit ... you can mix piper files (e.g. default clinical) with uimafit:
PiperFileReader r = new PiperFileReader( piperFilePath );
AnalysisEngineDescription aed = r.getBuilder().getAnalysisEngineDesc();
Your github class with the ~70 line method building a duplicate of the clinical pipeline could be reduced to:
protected static AggregateBuilder getXMIWritingPreprocessorAggregateBuilder()
throws Exception {
AggregateBuilder aggregateBuilder = new AggregateBuilder();
aggregateBuilder.add( AnalysisEngineFactory.createEngineDescription( UriToDocumentTextAnnotatorCtakes.class ) );
PiperFileReader reader = new PiperFileReader( clinicalPiperPath );
AnalysisEngineDescription clinical = r.getBuilder().getAnalysisEngineDesc();
aggregateBuilder.add( clinical );
aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(
XMIWriter.class,
XMIWriter.PARAM_XMI_DIRECTORY,
outputDirectory));
return aggregateBuilder;
}
Just to really confuse you, your entire custom pipeline can be run with something like:
PiperFileReader reader = new PiperFileReader();
PipelineBuilder builder
= reader.getBuilder()
.reader( UriCollectionReader.class, "files", files )
.add( UriToDocumentTextAnnotatorCtakes.class );
reader.loadPipelineFile( piperFilePath );
builder.writeXmis( outputDirectory )
.run();
-----Original Message-----
From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
Sent: Wednesday, April 26, 2017 12:18 PM
To: dev@ctakes.apache.org
Subject: Re: URI is not hierarchical
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 <Se...@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:ddligach@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 <Se...@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:ddligach@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=
>
>
>
Re: URI is not hierarchical
Posted by "Dligach, Dmitriy" <dd...@luc.edu>.
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 <Se...@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:ddligach@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 <Se...@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:ddligach@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=
>
>
>
RE: URI is not hierarchical
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
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:ddligach@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 <Se...@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:ddligach@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=
Re: URI is not hierarchical
Posted by "Dligach, Dmitriy" <dd...@luc.edu>.
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 <Se...@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:ddligach@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=
RE: URI is not hierarchical
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
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:ddligach@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=