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From "Masanz, James J." <Masanz.Ja...@mayo.edu>
Subject RE: Using PEAR Installer with cTAKES 3.1.1
Date Mon, 10 Mar 2014 20:48:43 GMT
Hi Sean,

If it were me, it would depend on the use case.

If you plan to release the new component as part of the opensource cTAKES, I would try creating
a new maven module
https://cwiki.apache.org/confluence/display/CTAKES/Adding+a+New+Component
probably starting with it under the sandbox branch.
That also assumes it can be licensed under Apache License, Version 2.0

Hopefully someone with more background knowledge of maven will expand on that.

If this is something that is not likely to become part of cTAKES in the future, I would not
use the pear installer but I would create a zip that includes the files from the cTAKES convenience
binary and your new code and resources.

For the second part, it looks like you are setting the classpath yourself. Have you double-checked
that your version of UIMA is the same as what cTAKES was built with. Or even better, just
use the uima jars that are within the lib directory of the cTAKES binary distribution. To
use the same classpath order, I would suggest you copy bin/runctakesCPE.bat and add in whatever
you want added that is specific to your new code and resources, and use that to launch your
program

-- James


-----Original Message-----
From: Murphy, Sean P. [RO BIT] 
Sent: Monday, March 10, 2014 2:01 PM
To: dev@ctakes.apache.org
Subject: Using PEAR Installer with cTAKES 3.1.1

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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