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From "Murphy, Sean P." <Murphy.S...@mayo.edu>
Subject Using PEAR Installer with cTAKES 3.1.1
Date Mon, 10 Mar 2014 19:01:03 GMT
Hello,
                Is there a Maven build process that is recommended in place of the legacy
PEAR installer processes?

I've been going through the painstaking process of getting a stand-alone project to correctly
install and deploy when using the PEAR installer to build the environment to be run alongside
a binary cTAKES installation.

I realize Maven has been utilized to replace many of the build functions within cTAKES, but
I'm wondering if the PEAR install approach should still be valid?

The problem I see when installing via 'runPearInstaller.bat' is the following: org.apache.uima.resource.ResourceInitializationException:
The class org.apache.ctakes.core.resource.FileResourceImpl does not implement org.apache.uima.resource.SharedResourceObject.

I should not need to change the FileResourceImpl or is there something else that may be causing
this (?).


Secondly, if I just use the installation 'as is' and run a command to kick off the CPE (see
below) I see:
Caused by: org.apache.uima.resource.ResourceInitializationException: The class edu.mayo.bmi.metakes.ssri.ae.SSRIHitAnnotator
is not a valid Analysis Component.  You must specify an Annotator, CAS Consumer, Collection
Reader, or CAS Multiplier. If you are calling ResourceManager.setExtensionClassPath
, this error can also be caused if you have put UIMA framework jar files on the extension
classpath, which is not allowed. (Descriptor: file:/C:/Temp/apache-ctakes-3.1.1-bin/apache-ctakes-3.1.1/PHONT_SSRI_term_spotter/desc/analysis_engine/PHONT_Hit.xml)

I'm am not utilizing the "ResourceManager.setExtensionClassPath" and the UIMA framework classes
haven't changed as far as I can tell.

java -cp ^
"%UIMA_HOME%/lib/uima-core.jar;^
%UIMA_HOME%/lib/uima-cpe.jar;^
%UIMA_HOME%/lib/uima-tools.jar;^
%UIMA_HOME%/lib/uima-document-annotations.jar;^
%UIMA_HOME%/lib/uima-examples.jar;^
lib/ctakes-chunker-3.1.1.jar;^
lib/ctakes-clinical-pipeline-3.1.1.jar;^
lib/ctakes-context-tokenizer-3.1.1.jar;^
lib/ctakes-core-3.1.1.jar;^
lib/ctakes-dictionary-lookup-3.1.1.jar;^
lib/ctakes-preprocessor-3.1.1.jar;^
lib/ctakes-lvg-3.1.1.jar;^
lib/ctakes-ne-contexts-3.1.1.jar;^
lib/ctakes-pos-tagger-3.1.1.jar;^
lib/ctakes-type-system-3.1.1.jar;^
PHONT_SSRI_term_spotter/bin;^
PHONT_SSRI_term_spotter/target/classes;^
PHONT_SSRI_term_spotter/target/generated-sources/jcasgen;^
PHONT_SSRI_term_spotter/resources;^
lib/log4j-1.2.16.jar;^
lib/jdom-1.0.jar;^
lib/lucene-core-4.0.0.jar;^
lib/opennlp-tools-1.5.2-incubating.jar;^
lib/opennlp-maxent-3.2.0-incubating.jar;^
lib/openaifsm-0.0.1.jar;^
lib/lvg2010dist-0.0.1.jar;^
lib/xercesImpl-2.10.0.jar;^
lib/xml-apis-1.4.01.jar;^
lib/ctakes-chunker-3.1.1-res.jar;^
lib/ctakes-clinical-pipeline-3.1.1-res.jar;^
lib/ctakes-context-tokenizer-3.1.1-res.jar;^
lib/ctakes-core-3.1.1-res.jar;^
lib/ctakes-dictionary-lookup-3.1.1-res.jar;^
lib/ctakes-preprocessor-3.1.1-res.jar;^
lib/ctakes-lvg-3.1.1-res.jar;^
lib/ctakes-ne-contexts-3.1.1-res.jar;^
lib/ctakes-pos-tagger-3.1.1-res.jar" org.apache.uima.tools.cpm.CpmFrame

                Thanks,
                                ~Sean

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