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From "James Joseph Masanz (JIRA)" <j...@apache.org>
Subject [jira] [Commented] (CTAKES-445) java.lang.IllegalArgumentException: URI is not hierarchical - org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl.load
Date Sun, 30 Jul 2017 23:07:02 GMT

    [ https://issues.apache.org/jira/browse/CTAKES-445?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16106689#comment-16106689
] 

James Joseph Masanz commented on CTAKES-445:
--------------------------------------------

I've been out on an unexpected, extended medical leave, and don't remember exactly where I
left off. 

Some code within cTAKES will copy files out of jars when there is something that uses File
instead of Stream.  However, with the LVG database being fairly large, I don't think that
would make a good long term solution.

The workaround (if remember correctly) is to check out everything under
svn.code.sf.net/p/ctakesresources/code/trunk/ctakes-resources-lvg2008/src/main/resources/org/apache/ctakes/lvg/
(or extract all the contents from the ctakes-resources-lvg2008 4.0 jar)
and put that org directory in something on your classpath so you have 

SOME.CLASSPATH.DIR/org/apache/ctakes/lvg/data

Once that is done you should have a number of files and subdirectories including the following

SOME.CLASSPATH.DIR\org\apache\ctakes\lvg\data\config\lvg.properties
SOME.CLASSPATH.DIR\org\apache\ctakes\lvg\data\HSqlDb\

I'll try to test that and add more details sometime this week if no one else beats me to it.

Note, if you want lvg to use the actual lvg resources, you can't just copy/extract the lvg.properties
file for this workaround, you have to copy/extract the entire subtree, or it will create an
empty lvg database.

> java.lang.IllegalArgumentException: URI is not hierarchical - org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl.load
> -----------------------------------------------------------------------------------------------------------------------
>
>                 Key: CTAKES-445
>                 URL: https://issues.apache.org/jira/browse/CTAKES-445
>             Project: cTAKES
>          Issue Type: Bug
>          Components: ctakes-lvg
>    Affects Versions: 4.0.0
>            Reporter: James Joseph Masanz
>            Assignee: James Joseph Masanz
>             Fix For: 4.0.1
>
>
> Dima reported this on the dev@ list:
> http://markmail.org/message/l6mct3btk3nb43ld
> http://mail-archives.apache.org/mod_mbox/ctakes-dev/201704.mbox/%3CF00347B9-4228-4407-B566-4EB2774B21B5%40luc.edu%3E
> When using cTAKES as maven dependency and invoking his (Dima's) program using:
> mvn exec:java -Dexec.mainClass=“org.apache.ctakes.pipelines.UmlsLookupPipeline” 
> Not sure which release this originated in. reproduced it in 4.0



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