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Posted to dev@ctakes.apache.org by Steven Bethard <st...@Colorado.EDU> on 2012/10/02 22:46:41 UTC
cTAKES resources and the classpath
On Sep 25, 2012, at 3:22 PM, "Chen, Pei" <Pe...@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 = 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
Re: cTAKES resources and the classpath
Posted by "Wu, Stephen T., Ph.D." <Wu...@mayo.edu>.
I tried it in two workspaces, the one I checked out from SVN, and another
where I did the "existing maven projects".
Unfortunately, I checked out through the SVN Repository View rather than
importing "existing maven project from SVN" -- I wasn't even aware that we
were using maven when I first checked out.
Would that do it? Do I need to re-import for a few more hours? =P
stephen
On 10/5/12 9:52 AM, "Chen, Pei" <Pe...@childrens.harvard.edu> wrote:
> Within Eclipse, did you import "existing maven projects"? or import existing
> 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
>>
>> I tried all the different launches. I should've posted my error:
>>
>> Launch configuration UIMA_CVD--clinical_documents_pipeline references
>> non-existing project ctakes-clinical-pipeline.
>>
>> I get the same thing for any of the things in resources/launch.
>>
>> 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 kind of
>> directory structure?
>>
>> stephen
>>
>>
>>
>> On 10/5/12 9:40 AM, "Chen, Pei" <Pe...@childrens.harvard.edu> wrote:
>>
>>> 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" <Pe...@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"
>>>>>> <Pe...@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"
>>>>>>>> <Pe...@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 =
>>>>>>>> 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
>>>>>>>
>>>>>
>>>
>
RE: cTAKES resources and the classpath
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
Within Eclipse, did you import "existing maven projects"? or import existing 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
>
> I tried all the different launches. I should've posted my error:
>
> Launch configuration UIMA_CVD--clinical_documents_pipeline references
> non-existing project ctakes-clinical-pipeline.
>
> I get the same thing for any of the things in resources/launch.
>
> 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 kind of
> directory structure?
>
> stephen
>
>
>
> On 10/5/12 9:40 AM, "Chen, Pei" <Pe...@childrens.harvard.edu> wrote:
>
> > 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" <Pe...@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"
> >>>> <Pe...@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"
> >>>>>> <Pe...@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 =
> >>>>>> 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
> >>>>>
> >>>
> >
Re: cTAKES resources and the classpath
Posted by "Wu, Stephen T., Ph.D." <Wu...@mayo.edu>.
I tried all the different launches. I should've posted my error:
Launch configuration UIMA_CVD--clinical_documents_pipeline references
non-existing project ctakes-clinical-pipeline.
I get the same thing for any of the things in resources/launch.
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 kind
of directory structure?
stephen
On 10/5/12 9:40 AM, "Chen, Pei" <Pe...@childrens.harvard.edu> wrote:
> I used
> /ctakes/trunk/ctakes-clinical-pipeline/resources/launch/UIMA_CVD--clinical_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" <Pe...@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"
>>>> <Pe...@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"
>>>>>> <Pe...@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 =
>>>>>> 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
>>>>>
>>>
>
RE: cTAKES resources and the classpath
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
I used
/ctakes/trunk/ctakes-clinical-pipeline/resources/launch/UIMA_CVD--clinical_documents_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" <Pe...@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"
> >> <Pe...@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"
> >>>> <Pe...@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 =
> >>>> 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
> >>>
> >
RE: cTAKES resources and the classpath
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
Ohh, you meant Type System Descriptors files (my apologies- I misread that).
Yes absolutely agree on that point!
> -----Original Message-----
> From: Steven Bethard [mailto:steven.bethard@Colorado.EDU]
> Sent: Thursday, October 04, 2012 6:50 PM
> To: ctakes-dev@incubator.apache.org
> Subject: Re: cTAKES resources and the classpath
>
> On Oct 4, 2012, at 4:44 PM, "Chen, Pei" <Pe...@childrens.harvard.edu>
> wrote:
> >> The other thing that should probably be moved into src/main/resources
> >> are the type system descriptor files. You can reference those on the
> >> class path, so they definitely belong in the jar as well.
> >
> > Yes, just need to mull over that just for a bit more (putting configuration
> files inside jars). With my end-user hat on: some of those xml contain simple
> configuration parameters such as max permutation where end-users may
> just want to tweak without rebuilding code.
>
> But I wasn't talking about the analysis engine descriptor files. Just the type
> system descriptor files. People definitely shouldn't be tweaking the type
> system - changes to the type system will almost certainly break cTAKES code.
>
> Steve
>
>
> > When those xml's are outside of the jars, it's very easy to do and
> > re-run a pipeline. If we distribute and package these up, we may need
> > to provide some mechanism for end-users to easily modify configuration
> > parameters (either thru uiafit style or gui of some sort.)
> >
> > Yes, even if it's in src/main/resources, we can always configure maven to
> move it anywhere during assembly time, but just wanted clearly on this
> before opening up Eclipse again.
> >
> >> -----Original Message-----
> >> From: Steven Bethard [mailto:steven.bethard@Colorado.EDU]
> >> Sent: Thursday, October 04, 2012 6:30 PM
> >> To: ctakes-dev@incubator.apache.org
> >> Subject: Re: cTAKES resources and the classpath
> >>
> >> On Oct 4, 2012, at 4:26 PM, "Chen, Pei"
> >> <Pe...@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).
> >>
> >> Thanks for doing this!
> >>
> >>
> >> Steve
> >>
> >>> 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"
> >>>> <Pe...@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"
> >>>>>> <Pe...@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 =
> >>>>>> 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
> >>>>>
> >>>
> >
Re: cTAKES resources and the classpath
Posted by Steven Bethard <st...@Colorado.EDU>.
On Oct 4, 2012, at 4:44 PM, "Chen, Pei" <Pe...@childrens.harvard.edu> wrote:
>> The other thing that should probably be moved into src/main/resources are
>> the type system descriptor files. You can reference those on the class path,
>> so they definitely belong in the jar as well.
>
> Yes, just need to mull over that just for a bit more (putting configuration files inside jars). With my end-user hat on: some of those xml contain simple configuration parameters such as max permutation where end-users may just want to tweak without rebuilding code.
But I wasn't talking about the analysis engine descriptor files. Just the type system descriptor files. People definitely shouldn't be tweaking the type system - changes to the type system will almost certainly break cTAKES code.
Steve
> When those xml's are outside of the jars, it's very easy to do and re-run a pipeline. If we distribute and package these up, we may need to provide some mechanism for end-users to easily modify configuration parameters (either thru uiafit style or gui of some sort.)
>
> Yes, even if it's in src/main/resources, we can always configure maven to move it anywhere during assembly time, but just wanted clearly on this before opening up Eclipse again.
>
>> -----Original Message-----
>> From: Steven Bethard [mailto:steven.bethard@Colorado.EDU]
>> Sent: Thursday, October 04, 2012 6:30 PM
>> To: ctakes-dev@incubator.apache.org
>> Subject: Re: cTAKES resources and the classpath
>>
>> On Oct 4, 2012, at 4:26 PM, "Chen, Pei" <Pe...@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).
>>
>> Thanks for doing this!
>>
>>
>> Steve
>>
>>> 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"
>>>> <Pe...@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"
>>>>>> <Pe...@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 =
>>>>>> 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
>>>>>
>>>
>
RE: cTAKES resources and the classpath
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
> The other thing that should probably be moved into src/main/resources are
> the type system descriptor files. You can reference those on the class path,
> so they definitely belong in the jar as well.
Yes, just need to mull over that just for a bit more (putting configuration files inside jars). With my end-user hat on: some of those xml contain simple configuration parameters such as max permutation where end-users may just want to tweak without rebuilding code. When those xml's are outside of the jars, it's very easy to do and re-run a pipeline. If we distribute and package these up, we may need to provide some mechanism for end-users to easily modify configuration parameters (either thru uiafit style or gui of some sort.)
Yes, even if it's in src/main/resources, we can always configure maven to move it anywhere during assembly time, but just wanted clearly on this before opening up Eclipse again.
> -----Original Message-----
> From: Steven Bethard [mailto:steven.bethard@Colorado.EDU]
> Sent: Thursday, October 04, 2012 6:30 PM
> To: ctakes-dev@incubator.apache.org
> Subject: Re: cTAKES resources and the classpath
>
> On Oct 4, 2012, at 4:26 PM, "Chen, Pei" <Pe...@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).
>
> Thanks for doing this!
>
>
> Steve
>
> > 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"
> >> <Pe...@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"
> >>>> <Pe...@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 =
> >>>> 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
> >>>
> >
Re: cTAKES resources and the classpath
Posted by Steven Bethard <st...@Colorado.EDU>.
On Oct 4, 2012, at 4:26 PM, "Chen, Pei" <Pe...@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).
Thanks for doing this!
The other thing that should probably be moved into src/main/resources are the type system descriptor files. You can reference those on the class path, so they definitely belong in the jar as well.
Steve
> 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" <Pe...@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"
>>>> <Pe...@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 =
>>>> 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
>>>
>
Re: cTAKES resources and the classpath
Posted by Jörn Kottmann <ko...@gmail.com>.
The lastest UIMA release contains an eclipse launcher for
AEs and AAEs. Depending on your use case that is easier to
use than CVD or CPE.
As input you can specify text or xmi files in the launch configuration
and the output can optionally written to a folder.
The xmi files can be viewed and edited with the Cas Editor (another
eclipse plugin).
HTH,
Jörn
On 10/05/2012 04:23 PM, Wu, Stephen T., Ph.D. wrote:
> 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" <Pe...@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" <Pe...@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"
>>>>> <Pe...@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 =
>>>>> 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
Re: cTAKES resources and the classpath
Posted by "Wu, Stephen T., Ph.D." <Wu...@mayo.edu>.
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" <Pe...@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" <Pe...@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"
>>>> <Pe...@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 =
>>>> 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
>>>
>
RE: cTAKES resources and the classpath
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
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" <Pe...@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"
> >> <Pe...@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 =
> >> 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
> >
Re: cTAKES resources and the classpath
Posted by Steven Bethard <st...@Colorado.EDU>.
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" <Pe...@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" <Pe...@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 =
>> 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
>
RE: cTAKES resources and the classpath
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
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" <Pe...@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 =
> 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