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.fi...@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_pulivar...@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 *********************************************************** 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. *********************************************************** This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
