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From "Masanz, James J." <Masanz.Ja...@mayo.edu>
Subject RE: FileNotFoundException: org/apache/ctakes/dictionary/lookup/rxnorm_index
Date Fri, 12 Apr 2013 17:54:31 GMT
Thanks for your answers. 

We have several different types of resources.
The models built by machine learning algorithms will be the *res projects.
As well as the LVG database.

Unfortunately the license for the UMLS resources come with additional restrictions, so as
I understand it, we cannot simply include the UMLS resources in our SVN.

I seem to have my workspace messed up at the moment.  I will try the steps below once a fresh
check-out finishes, and post results. I post them now in case you'd like to try them yourself
without waiting.

Please extract things from the downloaded resources zip to somewhere temporary.
Then move (merge) the resources/org from that temporary place into ctakes-dictionary-lookup-res/src/main/resources/

After the merge you should end up with a directory
ctakes-dictionary-lookup-res/src/main/resources/org/apache/ctakes/dictionary/lookup/rxnorm_index

Also if you are using the supplied run configuration, be sure to use the one that has Project
set to ctakes-drug-ner

If the above doesn't work for some reason, let me know. 

That's a temporary workaround. 

-- James



> -----Original Message-----
> From: dev-return-1511-Masanz.James=mayo.edu@ctakes.apache.org [mailto:dev-
> return-1511-Masanz.James=mayo.edu@ctakes.apache.org] On Behalf Of Kannan
> Thiagarajan
> Sent: Friday, April 12, 2013 12:03 PM
> To: dev@ctakes.apache.org
> Subject: Re: FileNotFoundException:
> org/apache/ctakes/dictionary/lookup/rxnorm_index
> 
> James,
> 
> Thanks for getting back.
> 
> I checked out from SVN.
> I have not tried other UMLS pipelines
> I downloaded the ZIP, but did not extract/merge into workspace  since I
> saw a bunch of "-res" folders in the workspace, I was not sure if this
> step was needed anymore.
> 
> Thanks for looking into this.
> 
> Best Regards
> Kannan Thiagarajan
> 
> 
> 
> 
> On Fri, Apr 12, 2013 at 11:42 AM, Masanz, James J.
> <Masanz.James@mayo.edu>wrote:
> 
> > I too see that error in my workspace that I checked out from SVN when
> > I try to use that pipeline.
> >
> > Some questions so I can describe corrective steps appropriately
> > - did you check out from SVN or did you download and install from an
> > install artifact?
> > - have you been able to run any other *UMLSProcessor pipelines?
> > - if you downloaded the external resources described in the  "Download
> > cTAKES 3.0 Dictionaries and models" step [1], where did you extract them
> to?
> >
> >
> > [1] http://s.apache.org/ctakes3.0resourcesStep
> >
> >
> > -- James
> >
> >
> > > -----Original Message-----
> > > From: dev-return-1509-Masanz.James=mayo.edu@ctakes.apache.org [mailto:
> > dev-
> > > return-1509-Masanz.James=mayo.edu@ctakes.apache.org] On Behalf Of
> > > Kannan Thiagarajan
> > > Sent: Friday, April 12, 2013 9:57 AM
> > > To: dev@ctakes.apache.org
> > > Subject: FileNotFoundException:
> > > org/apache/ctakes/dictionary/lookup/rxnorm_index
> > >
> > > Hello Team,
> > >
> > > I was trying out the CVD on the DrugNER
> > > (DrugAggregatePlaintextUMLSProcessor.xml) pipeline and I got a
> > > FileNotFoundException on the rxnorm_index.
> > >
> > > First I was suspecting a Workspace setup issue on my part but then I
> > > noticed the following JIRA
> > >
> > > https://issues.apache.org/jira/browse/CTAKES-156
> > >
> > > I'm guessing a fix maybe available in a future release. My question
> > > is,
> > is
> > > there a workaround or a quick fix I can perform in my workspace.
> > >
> > > Appreciate any pointers to get around this issue.
> > >
> > > Thanks & Best Regards
> > > Kannan Thiagarajan
> >
> 
> 
> 
> --
> Best Regards
> Kannan Thiagarajan

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