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From: "Chen, Pei" <Pei.Chen@childrens.harvard.edu>
To: "ctakes-dev@incubator.apache.org" <ctakes-dev@incubator.apache.org>
Subject: RE: cTAKES resources and the classpath
Thread-Topic: cTAKES resources and the classpath
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Date: Fri, 5 Oct 2012 14:52:45 +0000
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Within Eclipse, did you import "existing maven projects"?  or import existi=
ng maven projects from SVN?


> -----Original Message-----
> From: Wu, Stephen T., Ph.D. [mailto:Wu.Stephen@mayo.edu]
> Sent: Friday, October 05, 2012 10:50 AM
> To: ctakes-dev@incubator.apache.org
> Subject: Re: cTAKES resources and the classpath
>=20
> I tried all the different launches.  I should've posted my error:
>=20
> Launch configuration UIMA_CVD--clinical_documents_pipeline references
> non-existing project ctakes-clinical-pipeline.
>=20
> I get the same thing for any of the things in resources/launch.
>=20
> I figure since I checked out at trunk, eclipse is not recognizing each
> ctakes-* as a project and doesn't know where the src, bin, and other
> directories are.  This seems to be normal for maven projects and this kin=
d of
> directory structure?
>=20
> stephen
>=20
>=20
>=20
> On 10/5/12 9:40 AM, "Chen, Pei" <Pei.Chen@childrens.harvard.edu> wrote:
>=20
> > I used
> > /ctakes/trunk/ctakes-clinical-pipeline/resources/launch/UIMA_CVD--clin
> > ical_doc
> > uments_pipeline.launch
> > Not sure what the differences are, but some housekeeping is probably
> > in order...
> >
> >> -----Original Message-----
> >> From: Wu, Stephen T., Ph.D. [mailto:Wu.Stephen@mayo.edu]
> >> Sent: Friday, October 05, 2012 10:24 AM
> >> To: ctakes-dev@incubator.apache.org
> >> Subject: Re: cTAKES resources and the classpath
> >>
> >> Being new to maven (and maven in eclipse)... How do you run the
> >> default pipeline with CVD?  I've checked out, and tried going to
> >>   /ctakes/ctakes-clinical-pipeline/resources/launch/CVD cTAKES.launch
> >> but that doesn't work.
> >>
> >> stephen
> >>
> >>
> >> On 10/4/12 5:26 PM, "Chen, Pei" <Pei.Chen@childrens.harvard.edu>
> wrote:
> >>
> >>> The individual resources have been moved to src/main/resources so
> >>> that maven will automatically add it to the classpath and individual =
jar(s).
> >>> It was also an opportunity to add a fully qualified namespace such
> >>> as /org/apach/ctakes/{project}/somemodelsresourcedirectory.  This
> >>> will be important to avoid clashes if we decide to distribute some
> >>> uber-jar/war or move resources around again. [Even though the
> >>> resources were updated in the descriptor xml files, still haven't
> >>> decided to move those yet since it's working now and we may move to
> >>> uimaFIT style in the future.]
> >>>
> >>> I just tested the default clinical documents pipeline in trunk with
> >>> the CVD and it should be working now.
> >>> Feel free to check out and work off trunk in ASF SVN now: svn co
> >>> https://svn.apache.org/repos/asf/incubator/ctakes/trunk
> >>> (The OrangeBook will still require Lucene 3.0.2 so you might have to
> >>> update that from 3.5.0 if you plan to use the dictionary lookup)
> >>>
> >>> [Disclaimer: over ~5000-6000 files were touched since we updated
> >>> java namespaces, license headers, resource paths, etc. and wouldn't
> >>> be surprised if we missed something.  Feel free to let us know if
> >>> you encounter any issues or even better- open up a Jira and fix it
> >>> :)]
> >>>
> >>> <-- Will get some coffee and start looking into some of the open
> >>> Jira issues now.  I think we should have a Release Candidate for
> >>> 3.0.0-incubating or a baseline within ASF very soon.
> >>>
> >>> --Pei
> >>>
> >>>> -----Original Message-----
> >>>> From: Steven Bethard [mailto:steven.bethard@Colorado.EDU]
> >>>> Sent: Tuesday, October 02, 2012 5:25 PM
> >>>> To: ctakes-dev@incubator.apache.org
> >>>> Subject: Re: cTAKES resources and the classpath
> >>>>
> >>>> Yeah, I'm going to commit a change to the dependency parser that
> >>>> allows me to do this. (Currently the location of the lemmatized
> >>>> data file is hard
> >>>> coded.)
> >>>>
> >>>> Steve
> >>>>
> >>>> On Oct 2, 2012, at 3:12 PM, "Chen, Pei"
> >>>> <Pei.Chen@childrens.harvard.edu>
> >>>> wrote:
> >>>>
> >>>>> Hi Steve,
> >>>>> I didn't get a chance to do this last week, but will work on it
> >>>>> tonight and
> >>>> tomorrow.
> >>>>> Don't want this to stop you though, so feel free to read in the
> >>>>> resource
> >>>> from an another location temporarily...
> >>>>> --Pei
> >>>>>
> >>>>>> -----Original Message-----
> >>>>>> From: Steven Bethard [mailto:steven.bethard@Colorado.EDU]
> >>>>>> Sent: Tuesday, October 02, 2012 4:47 PM
> >>>>>> To: ctakes-dev@incubator.apache.org
> >>>>>> Subject: cTAKES resources and the classpath
> >>>>>>
> >>>>>> On Sep 25, 2012, at 3:22 PM, "Chen, Pei"
> >>>>>> <Pei.Chen@childrens.harvard.edu>
> >>>>>> wrote:
> >>>>>>> I think Brandyn and others had a reasonable suggestion to use
> >>>>>>> the name
> >>>>>> instead of location paths in those pesky descriptor xml files-
> >>>>>> Assuming they're in the classpath (placed in src/main/resources).
> >>>>>>> I'll take a stab at this later this week if I get a chance.
> >>>>>>
> >>>>>> Pei, are you still working on this? I'm currently unable to use
> >>>>>> the dependency parser from another project because it can't find
> >>>>>> it's resources. Specifically, it fails on this line:
> >>>>>>
> >>>>>> URL lemmatizerDataFileURL =3D
> >>>>>> this.getClass().getResource(ENG_LEMMATIZER_DATA_FILE);
> >>>>>>
> >>>>>> I would take a stab at fixing these myself, but the JCasGen issue
> >>>>>> makes these kind of broad changes really difficult for me.
> >>>>>>
> >>>>>> Steve
> >>>>>
> >>>
> >