[CTAKES-466] cTAKES does not write xmi file in the output directory

• Type: Bug
• Status: Closed
• Priority: Major
• Resolution: Invalid
• Component/s: ctakes-clinical-pipeline
• Assignee: Unassigned
• Reporter: Sirisha
• Created: 11/Oct/17 13:48
• Updated: 12/Oct/17 20:33
• Resolved: 11/Oct/17 18:12

Description

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)