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. <[email protected]>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: [email protected] [mailto: > dev- > > [email protected]] On Behalf Of Kannan > > Thiagarajan > > Sent: Friday, April 12, 2013 12:03 PM > > To: [email protected] > > 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. > > <[email protected]>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: [email protected][mailto: > > > dev- > > > > [email protected]] On Behalf Of > > > > Kannan Thiagarajan > > > > Sent: Friday, April 12, 2013 9:57 AM > > > > To: [email protected] > > > > 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
