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From "Sirisha (JIRA)" <j...@apache.org>
Subject [jira] [Created] (CTAKES-466) cTAKES does not xmi file in the output directory
Date Wed, 11 Oct 2017 13:49:00 GMT
Sirisha created CTAKES-466:
------------------------------

             Summary: cTAKES does not 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


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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