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From "Alex Zbarcea (JIRA)" <j...@apache.org>
Subject [jira] [Commented] (CTAKES-466) cTAKES does not write xmi file in the output directory
Date Thu, 12 Oct 2017 20:34:00 GMT

    [ https://issues.apache.org/jira/browse/CTAKES-466?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16202582#comment-16202582
] 

Alex Zbarcea commented on CTAKES-466:
-------------------------------------

What do you have in your {{/testdata}} directory? Trying to reproduce what you have:

either use the stable {{4.0.0}} or the trunk. If I use the trunk:

{code}
$ mvn clean install
$ cd ctakes-distribution/target
$ tar -xvf apache-ctakes-4.0.1-SNAPSHOT-bin.tar.gz
$ cd apache-ctakes-4.0.1-SNAPSHOT
$ mkdir -p testdata output
$ bin/runClinicalPipeline.sh -i testdata/ --xmiOut output/ --user xxx --pass xxxx
log4j: reset attribute= "false".
log4j: Threshold ="null".
log4j: Retreiving an instance of org.apache.log4j.Logger.
log4j: Setting [ProgressAppender] additivity to [false].
log4j: Level value for ProgressAppender is  [INFO].
log4j: ProgressAppender level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%m].
log4j: Adding appender named [noEolAppender] to category [ProgressAppender].
log4j: Retreiving an instance of org.apache.log4j.Logger.
log4j: Setting [ProgressDone] additivity to [false].
log4j: Level value for ProgressDone is  [INFO].
log4j: ProgressDone level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%m%n].
log4j: Adding appender named [eolAppender] to category [ProgressDone].
log4j: Level value for root is  [INFO].
log4j: root level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%d{dd MMM yyyy HH:mm:ss} %5p %c{1} - %m%n].
log4j: Adding appender named [consoleAppender] to category [root].
12 Oct 2017 16:13:07  INFO SentenceDetector - Sentence detector model file: org/apache/ctakes/core/sentdetect/sd-med-model.zip
12 Oct 2017 16:13:07  INFO TokenizerAnnotatorPTB - Initializing org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
12 Oct 2017 16:13:07  INFO ContextDependentTokenizerAnnotator - Finite state machines loaded.
12 Oct 2017 16:13:07  INFO POSTagger - POS tagger model file: org/apache/ctakes/postagger/models/mayo-pos.zip
12 Oct 2017 16:13:08  INFO Chunker - Chunker model file: org/apache/ctakes/chunker/models/chunker-model.zip
12 Oct 2017 16:13:08  INFO AbstractJCasTermAnnotator - Using dictionary lookup window type:
org.apache.ctakes.typesystem.type.textspan.Sentence
12 Oct 2017 16:13:08  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 
12 Oct 2017 16:13:08  INFO AbstractJCasTermAnnotator - Using minimum term text span: 3
12 Oct 2017 16:13:08  INFO AbstractJCasTermAnnotator - Using Dictionary Descriptor: org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml
12 Oct 2017 16:13:08  INFO DictionaryDescriptorParser - Parsing dictionary specifications:

12 Oct 2017 16:13:08  INFO UmlsUserApprover - Checking UMLS Account at https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser:
.12 Oct 2017 16:13:09  INFO UmlsUserApprover -   UMLS Account has been validated

12 Oct 2017 16:13:09  INFO JdbcConnectionFactory - Connecting to jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab:
..12 Oct 2017 16:13:10  INFO ENGINE - open start - state not modified
...................
12 Oct 2017 16:13:16  INFO JdbcConnectionFactory -  Database connected
12 Oct 2017 16:13:16  INFO JdbcRareWordDictionary - Connected to cui and term table CUI_TERMS
12 Oct 2017 16:13:16  INFO JdbcConceptFactory - Connected to concept table TUI with class
TUI
12 Oct 2017 16:13:16  INFO JdbcConceptFactory - Connected to concept table RXNORM with class
LONG
12 Oct 2017 16:13:16  INFO JdbcConceptFactory - Connected to concept table PREFTERM with class
PREFTERM
12 Oct 2017 16:13:16  INFO JdbcConceptFactory - Connected to concept table SNOMEDCT_US with
class LONG
Loading configuration.
Loading feature templates.
Loading lexica.
Loading model:
........................................................................................
12 Oct 2017 16:13:26  INFO ClearNLPDependencyParserAE - Initializing ClearNLP dependency parser,
using lemmatizer: true
12 Oct 2017 16:13:26  INFO ClearNLPSemanticRoleLabelerAE - Starting initializing
12 Oct 2017 16:13:26  INFO ClearNLPSemanticRoleLabelerAE - Initializing ClearNLP semantic
role labeler
Loading configuration.
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Loading model:
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Loading configuration.
Loading feature templates.
Loading lexica.
Loading model:
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.............................
12 Oct 2017 16:13:28  INFO ClearNLPSemanticRoleLabelerAE - Finished initializing
12 Oct 2017 16:13:28  INFO CleartkAnalysisEngine - Starting initializing for Assigning Attributes
12 Oct 2017 16:13:29  INFO CleartkAnalysisEngine - Finished initializing
{code}

As you can see, I use local {{testdata}} and not {{/testdata}}. The same as for {{output}}
instead of {{/output}}. 


> cTAKES does not write xmi file in the output directory
> ------------------------------------------------------
>
>                 Key: CTAKES-466
>                 URL: https://issues.apache.org/jira/browse/CTAKES-466
>             Project: cTAKES
>          Issue Type: Bug
>          Components: ctakes-clinical-pipeline
>            Reporter: Sirisha
>         Attachments: RE_ [External] RE_ ctakes clinical default pipeline issue - CTAKES-466
[EXTERNAL]
>
>
> When i run default clinical pipeline with sample data, not able to write xmi file to
the output directory. Below is the command line
> bin/runClinicalPipeline.sh  -i /testdata  --xmiOut  /output  --user XXXX  --pass XXXX
> i get below error 
> Oct 11, 2017 9:40:24 AM org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl
processAndOutputNewCASes(273)
> SEVERE: Exception occurred
> org.apache.uima.analysis_engine.AnalysisEngineProcessException
> 	at org.apache.ctakes.core.cc.AbstractOutputFileWriter.process(AbstractOutputFileWriter.java:84)
> 	at org.apache.uima.analysis_component.CasAnnotator_ImplBase.process(CasAnnotator_ImplBase.java:56)
> 	at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:396)
> 	at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:314)
> 	at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:570)
> 	at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:412)
> 	at org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:344)
> 	at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:265)
> 	at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:570)
> 	at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:412)
> 	at org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:344)
> 	at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:265)
> 	at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:269)
> 	at org.apache.uima.fit.pipeline.SimplePipeline.runPipeline(SimplePipeline.java:150)
> 	at org.apache.ctakes.core.pipeline.PipelineBuilder.run(PipelineBuilder.java:293)
> 	at org.apache.ctakes.core.pipeline.PiperFileRunner.main(PiperFileRunner.java:81)
> Caused by: java.io.IOException: java.io.FileNotFoundException: /output/TestSample1.xml.xmi
(No such file or directory)
> 	at org.apache.ctakes.core.cc.FileTreeXmiWriter.writeFile(FileTreeXmiWriter.java:45)
> 	at org.apache.ctakes.core.cc.AbstractOutputFileWriter.process(AbstractOutputFileWriter.java:82)
> 	... 15 more
> Caused by: java.io.FileNotFoundException: /output/TestSample1.xml.xmi (No such file or
directory)
> 	at java.io.FileOutputStream.open0(Native Method)
> 	at java.io.FileOutputStream.open(FileOutputStream.java:270)
> 	at java.io.FileOutputStream.<init>(FileOutputStream.java:213)



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