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From Kannan Thiagarajan <kanna...@gmail.com>
Subject Re: FileNotFoundException: org/apache/ctakes/dictionary/lookup/rxnorm_index
Date Fri, 12 Apr 2013 18:25:58 GMT
James,

Thank you for the detailed response.

That worked perfectly.

I think the Doc may need to be updated to mention
"ctakes-dictionary-lookup-res"
as opposed to "ctakes-dictionary-lookup" as the destination folder for
dictionary resources. I understand this is work-in-progress, but thought
its worth mentioning here.

You guys are doing a great job!

Best Regards
Kannan


On Fri, Apr 12, 2013 at 12:54 PM, Masanz, James J. <Masanz.James@mayo.edu>wrote:

> 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
>



-- 
Best Regards
Kannan Thiagarajan

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