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Date: Thu, 12 Oct 2017 20:00:00 +0000 (UTC)
From: "Sirisha (JIRA)" <jira@apache.org>
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Message-ID: <JIRA.13108613.1507729724000.44179.1507838400439@Atlassian.JIRA>
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Subject: [jira] [Updated] (CTAKES-466) cTAKES does not write xmi file in the
 output directory
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archived-at: Thu, 12 Oct 2017 20:00:06 -0000


     [ https://issues.apache.org/jira/browse/CTAKES-466?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]

Sirisha updated CTAKES-466:
---------------------------
    Attachment: RE_ [External] RE_ ctakes clinical default pipeline issue - CTAKES-466 [EXTERNAL]

Hi Alex,
Problem was with having "/" infront of "output" directory. After removing /, we were able to write .xmi files to the "output" folder.

Thanks for your input.

I have another question on how to get "Entity Recognition Codes" from CDA xml file, please let me know of any pointers to get additional details.

Attaching the email I sent to Sean regarding the same.

Thank you
Sirisha


> 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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