Can you, as the user running ctakes, do a "touch /output/TestSample1.xml.xmi" ?
-----Original Message----- From: Sirisha Pulivarthi [mailto:[email protected]] Sent: Wednesday, October 11, 2017 11:22 AM To: [email protected] 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 *********************************************************** This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use, or distribution of the information included in this message is prohibited -- please immediately and permanently delete this message. ***********************************************************
