Sirisha created CTAKES-466:
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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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