Did you by chance miss the step where you "Download the cTAKES resources ZIP file with a matching version from the ctakesresources project"
Do you have a directory such as resources/org/apache/ctakes/dictionary/lookup/umls* such as resources/org/apache/ctakes/dictionary/lookup/umls2011ab -----Original Message----- From: Abraham Tom [mailto:a...@practicefusion.com] Sent: Sunday, April 13, 2014 11:49 AM To: dev@ctakes.apache.org Subject: RE: Command line invocation Thanks for the information I was on the developer version, but now I have reverted to the user version I reinstalled cTakes, specifically apache-ctakes-3.1.0-bin.tar.gz and followed the instructions from https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1+User+Install+Guide Then I tried to execute the following java -cp $CTAKES_HOME/lib/*:$CTAKES_HOME/desc/:$CTAKES_HOME/resources/ -Xms512M -Xmx1024M org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls and I got the following message Exception in thread "main" org.apache.uima.resource.ResourceInitializationException Then I tried to invoke the jar intself java -jar -Xms512M -Xmx1024M ./lib/ctakes-clinical-pipeline-3.1.0.jar but I got the following error Failed to load Main-Class manifest attribute from ./lib/ctakes-clinical-pipeline-3.1.0.jar Groovy is an option if I there are instructions on how to use it I would not mind helping to build those instructions to invoke specific classes Best regards, Abraham Tom ____________________________ Abraham Tom Data Warehouse Engineer -----Original Message----- From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] Sent: Sunday, April 13, 2014 5:32 AM To: 'dev@ctakes.apache.org' Subject: RE: Command line invocation Yes, that's possible. You need more things on your classpath - you can take a look at the classpath within runctakesCVD.bat Or if you are open to using groovy, take a look at the scripts directory within ctakes-core -----Original Message----- From: Abraham Tom [mailto:a...@practicefusion.com] Sent: Saturday, April 12, 2014 10:55 AM To: dev@ctakes.apache.org Subject: Command line invocation I am not a core java developer, I am a Hadoop data guy We are experimenting with using cTakes and we have no Java developers in house I am trying to invoke ClinicalPipelineWithUmls on a server where I installed the developer cTakes. This invocation is done via the following command line java -verbose -cp "/opt/cTAKES-3.1.1/ctakes-clinical-pipeline/target/classes;/home/mapr/.m2/repository/org/cleartk/cleartk-util/0.9.2/cleartk-util-0.9.2.jar" org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls but I am getting a Class not found error I would like to invoke via command line so that I can wrap a shell script around it and automate the processing of various docs. This should be possible shouldn't it? Best regards, Abraham Tom
