RE: [External] RE: ctakes clinical default pipeline issue - CTAKES-466 [EXTERNAL]

[Sirisha Pulivarthi <Si...@horizonblue.com.INVALID>]

Hi 
I have closed this issue. It has to do with writing to a different folder.

Thank you Sean and Gandhi for the prompt response.

-----Original Message-----
From: Gandhi Rajan Natarajan [mailto:Gandhi.Natarajan@arisglobal.com] 
Sent: Wednesday, October 11, 2017 2:09 PM
To: dev@ctakes.apache.org
Subject: [External] RE: ctakes clinical default pipeline issue - CTAKES-466 [EXTERNAL]

Hi Sirisha,

I tried executing this in my windows machine and it works fine. The execution also creates the output folder itself. So as Sean suggested this could be an issue with file permissions or folder creation permissions.

Regards,
Gandhi

-----Original Message-----
From: Finan, Sean [mailto:Sean.Finan@childrens.harvard.edu]
Sent: Wednesday, October 11, 2017 9:24 PM
To: dev@ctakes.apache.org
Subject: RE: ctakes clinical default pipeline issue - CTAKES-466 [EXTERNAL]

Can you, as the user running ctakes, do a "touch /output/TestSample1.xml.xmi" ?

-----Original Message-----
From: Sirisha Pulivarthi [mailto:Sirisha_Pulivarthi@horizonblue.com.INVALID]
Sent: Wednesday, October 11, 2017 11:22 AM
To: dev@ctakes.apache.org
Subject: ctakes clinical default pipeline issue - CTAKES-466 [EXTERNAL]

Hi,

I'm working on doing a POC using Ctakes 4.0.0 - below is what I'm trying to do "Ingest a CDA document containing free form text, run it through a Clinical Document processing pipeline and spit out a converted result".

I have downloaded and installed user guide, tried below command with one of the test document bin/runClinicalPipeline.sh  -i /testdata  --xmiOut  /output  --user xxx  --pass xxx

However, I'm running into below exception

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)
Activity

I have created CTAKES-466 this morning. Would appreciate your help on this.

Thank you
Sirisha

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