date:20140611

Re: Preparing for an Apache cTAKES 3.2 Release?

2014-06-11 Thread andy mcmurry

"2" doesn't mean much. The newer NER should have in its name the Behavior...

Perhaps something like MetaMap Usage
 "--allow_overmatches" or
 "--allow_concept_gaps" or .other?

Since yTex already provides a pluggable *DictionaryLookup, *that seems like
the best place to define the differing Behavior /  Usage.

https://cwiki.apache.org/confluence/display/CTAKES/User's+Guide
https://code.google.com/p/ytex/wiki/DictionaryLookup_V05


AndyMC

On Tue, Jun 10, 2014 at 9:55 AM, britt fitch  wrote:

> I don’t have an issue with the *-2 name. I also don’t have any objections
> to renaming it.
>
> It might be nice to keep the old dictionary code around for a
> release-worth of time but after that I would vote purging it.
> If someone needs it after that it’ll be accessible in the archived
> releases.
>
>
>
> On Jun 10, 2014, at 12:48 PM, Chen, Pei 
> wrote:
>
> > I think James has a fair point here.
> > It may be worthwhile biting the bullet here and push forward.
> >
> > Since this essentially will be a full replacement of the
> ctakes-dictionary-lookup module, a good option maybe to just replace the
> entire module now and rename the existing module to * _deprecated.
> > How do folks feel about that?  In a nutshell, ctakes-dictionary-lookup-2
> is a faster algorithm with a simpler code base- and comparable results
> (Sean has a full comparison in the documentation for those who are curious).
> >
> > --Pei
> >
> >> -Original Message-
> >> From: britt fitch [mailto:britt.fi...@gmail.com]
> >> Sent: Monday, June 09, 2014 5:42 PM
> >> To: dev@ctakes.apache.org
> >> Subject: Re: Preparing for an Apache cTAKES 3.2 Release?
> >>
> >> There is some documentation in the dictionary2 module under
> >> /doc/DictionaryLookupHelp.{txt | docx} that gives some some details of
> the
> >> different lookup implementation options within that module that I found
> >> helpful.
> >>
> >>
> >> On Jun 9, 2014, at 5:17 PM, Masanz, James J. 
> >> wrote:
> >>
> >>>
> >>> Will ctakes-dictionary-lookup2 remain the name for the new dictionary
> >> lookup or will it have a name that reflects the algorithm?
> >>>
> >>> Is there a description of it that will help users to decide when to
> use one
> >> dictionary lookup component vs. the other.
> >>>
> >>> -- James
> >>>
> >>> -Original Message-
> >>> From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu]
> >>> Sent: Friday, June 06, 2014 12:34 PM
> >>> To: dev@ctakes.apache.org
> >>> Subject: Preparing for an Apache cTAKES 3.2 Release?
> >>>
> >>> Hi,
> >>> The 3.2 release was slated to be release end of this month (Jun 21).
> >>> Since I volunteered to be the RM for this release, just like the past
> >> releases, I was planning to create a branch/tag next week from trunk and
> >> dev can continue.
> >>> Feel free to take a look at any outstanding Jira issues [1] that you
> may want
> >> to be included in this release.
> >>>
> >>> Major changes include:
> >>> CTAKES-197Upgrade cTAKES to Java 7
> >>> CTAKES-292Integrate YTEX with cTAKES
> >>> CTAKES-82  Add ctakes-temporal module (Time and Event
> Annotator +
> >> DocTimeRel Property only?)
> >>>
> >>> [1]
> >>> https://issues.apache.org/jira/browse/CTAKES-
> >> 298?jql=fixVersion%20%3D%
> >>> 203.2.0%20AND%20project%20%3D%20CTAKES
> >>>
>  -Original Message-
>  From: Masanz, James J. [mailto:masanz.ja...@mayo.edu]
>  Sent: Wednesday, March 26, 2014 9:34 PM
>  To: 'dev@ctakes.apache.org'
>  Subject: RE: Apache cTAKES 3.2 Release?
> 
>  +1 to naming it 3.2
> 
>  I'll review my JIRA items this week.
> 
>  -- James
> 
>  -Original Message-
>  From: Pei Chen [mailto:chen...@apache.org]
>  Sent: Wednesday, March 26, 2014 10:14 AM
>  To: dev@ctakes.apache.org
>  Subject: Apache cTAKES 3.2 Release?
> 
>  Hi,
> 
>  I think there are a lot of items slated for the next release, I
>  suggest we make it 3.2 instead of another patch release.
> 
>  I can volunteer to be the RM unless someone would like to take that
> up...
> 
> 
> 
>  Main Changes pending for 3.2:
> 
>  CTAKES-197Upgrade cTAKES to Java 7
> 
>  CTAKES-292Integrate YTEX with cTAKES
> 
>  CTAKES-82  Add ctakes-temporal module (Time and Event
> Annotator
> >> +
>  DocTimeRel Property only?)
> 
>  CTAKES-275some of the older junit tests don't have the right
>  Project name in the run configurations
> 
>  CTAKES-268Fix SentenceDetector training with updated OpenNLP
> API
> 
>  CTAKES-162Command line scripts leave the user back one
> directory
> 
>  CTAKES-241NullPointerException in ctakes-assertion
> 
>  CTAKES-288Severity not set for DiseaseDisorderMention
> 
>  CTAKES-239Medication Modifiers do not have the offsets
> populated
> >>

RE: Preparing for an Apache cTAKES 3.2 Release?

2014-06-11 Thread Finan, Sean

>. The newer NER should have in its name the Behavior...

I agree, but the *2 module is a complete replacement for the current lookup.  
It does not (really) have any different behavior, just a different 
implementation and performance.  We plan to swap out the old with the new in 
the next release and get rid of the *2 suffix.  So, any name provided now is 
just temporary - unless people don't like the name "dictionary-lookup" at all.

In my original sandbox it was named "RareWordLookup", a nod to its 
implementation.  However, this doesn't help any users.

Sean

-Original Message-
From: andy mcmurry [mailto:mcmurry.a...@gmail.com] 
Sent: Wednesday, June 11, 2014 3:09 AM
To: dev@ctakes.apache.org
Subject: Re: Preparing for an Apache cTAKES 3.2 Release?

"2" doesn't mean much. The newer NER should have in its name the Behavior...

Perhaps something like MetaMap Usage
 "--allow_overmatches" or  
"--allow_concept_gaps" or .other?

Since yTex already provides a pluggable *DictionaryLookup, *that seems like the 
best place to define the differing Behavior /  Usage.

https://cwiki.apache.org/confluence/display/CTAKES/User's+Guide
https://code.google.com/p/ytex/wiki/DictionaryLookup_V05


AndyMC

On Tue, Jun 10, 2014 at 9:55 AM, britt fitch  wrote:

> I don’t have an issue with the *-2 name. I also don’t have any 
> objections to renaming it.
>
> It might be nice to keep the old dictionary code around for a 
> release-worth of time but after that I would vote purging it.
> If someone needs it after that it’ll be accessible in the archived 
> releases.
>
>
>
> On Jun 10, 2014, at 12:48 PM, Chen, Pei 
> 
> wrote:
>
> > I think James has a fair point here.
> > It may be worthwhile biting the bullet here and push forward.
> >
> > Since this essentially will be a full replacement of the
> ctakes-dictionary-lookup module, a good option maybe to just replace 
> the entire module now and rename the existing module to * _deprecated.
> > How do folks feel about that?  In a nutshell, 
> > ctakes-dictionary-lookup-2
> is a faster algorithm with a simpler code base- and comparable results 
> (Sean has a full comparison in the documentation for those who are curious).
> >
> > --Pei
> >
> >> -Original Message-
> >> From: britt fitch [mailto:britt.fi...@gmail.com]
> >> Sent: Monday, June 09, 2014 5:42 PM
> >> To: dev@ctakes.apache.org
> >> Subject: Re: Preparing for an Apache cTAKES 3.2 Release?
> >>
> >> There is some documentation in the dictionary2 module under 
> >> /doc/DictionaryLookupHelp.{txt | docx} that gives some some details 
> >> of
> the
> >> different lookup implementation options within that module that I 
> >> found helpful.
> >>
> >>
> >> On Jun 9, 2014, at 5:17 PM, Masanz, James J. 
> >> 
> >> wrote:
> >>
> >>>
> >>> Will ctakes-dictionary-lookup2 remain the name for the new 
> >>> dictionary
> >> lookup or will it have a name that reflects the algorithm?
> >>>
> >>> Is there a description of it that will help users to decide when 
> >>> to
> use one
> >> dictionary lookup component vs. the other.
> >>>
> >>> -- James
> >>>
> >>> -Original Message-
> >>> From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu]
> >>> Sent: Friday, June 06, 2014 12:34 PM
> >>> To: dev@ctakes.apache.org
> >>> Subject: Preparing for an Apache cTAKES 3.2 Release?
> >>>
> >>> Hi,
> >>> The 3.2 release was slated to be release end of this month (Jun 21).
> >>> Since I volunteered to be the RM for this release, just like the 
> >>> past
> >> releases, I was planning to create a branch/tag next week from 
> >> trunk and dev can continue.
> >>> Feel free to take a look at any outstanding Jira issues [1] that 
> >>> you
> may want
> >> to be included in this release.
> >>>
> >>> Major changes include:
> >>> CTAKES-197Upgrade cTAKES to Java 7
> >>> CTAKES-292Integrate YTEX with cTAKES
> >>> CTAKES-82  Add ctakes-temporal module (Time and Event
> Annotator +
> >> DocTimeRel Property only?)
> >>>
> >>> [1]
> >>> https://issues.apache.org/jira/browse/CTAKES-
> >> 298?jql=fixVersion%20%3D%
> >>> 203.2.0%20AND%20project%20%3D%20CTAKES
> >>>
>  -Original Message-
>  From: Masanz, James J. [mailto:masanz.ja...@mayo.edu]
>  Sent: Wednesday, March 26, 2014 9:34 PM
>  To: 'dev@ctakes.apache.org'
>  Subject: RE: Apache cTAKES 3.2 Release?
> 
>  +1 to naming it 3.2
> 
>  I'll review my JIRA items this week.
> 
>  -- James
> 
>  -Original Message-
>  From: Pei Chen [mailto:chen...@apache.org]
>  Sent: Wednesday, March 26, 2014 10:14 AM
>  To: dev@ctakes.apache.org
>  Subject: Apache cTAKES 3.2 Release?
> 
>  Hi,
> 
>  I think there are a lot of items slated for the next release, I 
>  suggest we make it 3.2 instead of another patch release.
> 
>  I can volunteer to be the RM unless someone would like to take 
>  that
> up...
> 
> >>>

Re: Preparing for an Apache cTAKES 3.2 Release?

2014-06-11 Thread vijay garla

regardless of the name, I think it would be incredibly helpful to have
thorough documentation on the dictionary lookup, how to configure it, and
how to create new dictionaries.  I would venture to say that this is the
most important component in cTAKES, and probably the one that has generated
the most questions on the newsgroup.



On Wed, Jun 11, 2014 at 9:21 AM, Finan, Sean <
sean.fi...@childrens.harvard.edu> wrote:

> >. The newer NER should have in its name the Behavior...
>
> I agree, but the *2 module is a complete replacement for the current
> lookup.  It does not (really) have any different behavior, just a different
> implementation and performance.  We plan to swap out the old with the new
> in the next release and get rid of the *2 suffix.  So, any name provided
> now is just temporary - unless people don't like the name
> "dictionary-lookup" at all.
>
> In my original sandbox it was named "RareWordLookup", a nod to its
> implementation.  However, this doesn't help any users.
>
> Sean
>
> -Original Message-
> From: andy mcmurry [mailto:mcmurry.a...@gmail.com]
> Sent: Wednesday, June 11, 2014 3:09 AM
> To: dev@ctakes.apache.org
> Subject: Re: Preparing for an Apache cTAKES 3.2 Release?
>
> "2" doesn't mean much. The newer NER should have in its name the
> Behavior...
>
> Perhaps something like MetaMap Usage
>  "--allow_overmatches"
> or  "--allow_concept_gaps" or .other?
>
> Since yTex already provides a pluggable *DictionaryLookup, *that seems
> like the best place to define the differing Behavior /  Usage.
>
> https://cwiki.apache.org/confluence/display/CTAKES/User's+Guide
> https://code.google.com/p/ytex/wiki/DictionaryLookup_V05
>
>
> AndyMC
>
> On Tue, Jun 10, 2014 at 9:55 AM, britt fitch 
> wrote:
>
> > I don’t have an issue with the *-2 name. I also don’t have any
> > objections to renaming it.
> >
> > It might be nice to keep the old dictionary code around for a
> > release-worth of time but after that I would vote purging it.
> > If someone needs it after that it’ll be accessible in the archived
> > releases.
> >
> >
> >
> > On Jun 10, 2014, at 12:48 PM, Chen, Pei
> > 
> > wrote:
> >
> > > I think James has a fair point here.
> > > It may be worthwhile biting the bullet here and push forward.
> > >
> > > Since this essentially will be a full replacement of the
> > ctakes-dictionary-lookup module, a good option maybe to just replace
> > the entire module now and rename the existing module to * _deprecated.
> > > How do folks feel about that?  In a nutshell,
> > > ctakes-dictionary-lookup-2
> > is a faster algorithm with a simpler code base- and comparable results
> > (Sean has a full comparison in the documentation for those who are
> curious).
> > >
> > > --Pei
> > >
> > >> -Original Message-
> > >> From: britt fitch [mailto:britt.fi...@gmail.com]
> > >> Sent: Monday, June 09, 2014 5:42 PM
> > >> To: dev@ctakes.apache.org
> > >> Subject: Re: Preparing for an Apache cTAKES 3.2 Release?
> > >>
> > >> There is some documentation in the dictionary2 module under
> > >> /doc/DictionaryLookupHelp.{txt | docx} that gives some some details
> > >> of
> > the
> > >> different lookup implementation options within that module that I
> > >> found helpful.
> > >>
> > >>
> > >> On Jun 9, 2014, at 5:17 PM, Masanz, James J.
> > >> 
> > >> wrote:
> > >>
> > >>>
> > >>> Will ctakes-dictionary-lookup2 remain the name for the new
> > >>> dictionary
> > >> lookup or will it have a name that reflects the algorithm?
> > >>>
> > >>> Is there a description of it that will help users to decide when
> > >>> to
> > use one
> > >> dictionary lookup component vs. the other.
> > >>>
> > >>> -- James
> > >>>
> > >>> -Original Message-
> > >>> From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu]
> > >>> Sent: Friday, June 06, 2014 12:34 PM
> > >>> To: dev@ctakes.apache.org
> > >>> Subject: Preparing for an Apache cTAKES 3.2 Release?
> > >>>
> > >>> Hi,
> > >>> The 3.2 release was slated to be release end of this month (Jun 21).
> > >>> Since I volunteered to be the RM for this release, just like the
> > >>> past
> > >> releases, I was planning to create a branch/tag next week from
> > >> trunk and dev can continue.
> > >>> Feel free to take a look at any outstanding Jira issues [1] that
> > >>> you
> > may want
> > >> to be included in this release.
> > >>>
> > >>> Major changes include:
> > >>> CTAKES-197Upgrade cTAKES to Java 7
> > >>> CTAKES-292Integrate YTEX with cTAKES
> > >>> CTAKES-82  Add ctakes-temporal module (Time and Event
> > Annotator +
> > >> DocTimeRel Property only?)
> > >>>
> > >>> [1]
> > >>> https://issues.apache.org/jira/browse/CTAKES-
> > >> 298?jql=fixVersion%20%3D%
> > >>> 203.2.0%20AND%20project%20%3D%20CTAKES
> > >>>
> >  -Original Message-
> >  From: Masanz, James J. [mailto:masanz.ja...@mayo.edu]
> >  Sent: Wednesday, March 26, 2014 9:34 PM
> >  To: 'dev@ctakes.apache

Re: Preparing for an Apache cTAKES 3.2 Release?

2014-06-11 Thread Karthik Sarma

Agreed

On Wednesday, June 11, 2014, vijay garla  wrote:

> regardless of the name, I think it would be incredibly helpful to have
> thorough documentation on the dictionary lookup, how to configure it, and
> how to create new dictionaries.  I would venture to say that this is the
> most important component in cTAKES, and probably the one that has generated
> the most questions on the newsgroup.
>
>
>
> On Wed, Jun 11, 2014 at 9:21 AM, Finan, Sean <
> sean.fi...@childrens.harvard.edu> wrote:
>
> > >. The newer NER should have in its name the Behavior...
> >
> > I agree, but the *2 module is a complete replacement for the current
> > lookup.  It does not (really) have any different behavior, just a
> different
> > implementation and performance.  We plan to swap out the old with the new
> > in the next release and get rid of the *2 suffix.  So, any name provided
> > now is just temporary - unless people don't like the name
> > "dictionary-lookup" at all.
> >
> > In my original sandbox it was named "RareWordLookup", a nod to its
> > implementation.  However, this doesn't help any users.
> >
> > Sean
> >
> > -Original Message-
> > From: andy mcmurry [mailto:mcmurry.a...@gmail.com]
> > Sent: Wednesday, June 11, 2014 3:09 AM
> > To: dev@ctakes.apache.org
> > Subject: Re: Preparing for an Apache cTAKES 3.2 Release?
> >
> > "2" doesn't mean much. The newer NER should have in its name the
> > Behavior...
> >
> > Perhaps something like MetaMap Usage
> >  "--allow_overmatches"
> > or  "--allow_concept_gaps" or .other?
> >
> > Since yTex already provides a pluggable *DictionaryLookup, *that seems
> > like the best place to define the differing Behavior /  Usage.
> >
> > https://cwiki.apache.org/confluence/display/CTAKES/User's+Guide
> > https://code.google.com/p/ytex/wiki/DictionaryLookup_V05
> >
> >
> > AndyMC
> >
> > On Tue, Jun 10, 2014 at 9:55 AM, britt fitch 
> > wrote:
> >
> > > I don’t have an issue with the *-2 name. I also don’t have any
> > > objections to renaming it.
> > >
> > > It might be nice to keep the old dictionary code around for a
> > > release-worth of time but after that I would vote purging it.
> > > If someone needs it after that it’ll be accessible in the archived
> > > releases.
> > >
> > >
> > >
> > > On Jun 10, 2014, at 12:48 PM, Chen, Pei
> > > 
> > > wrote:
> > >
> > > > I think James has a fair point here.
> > > > It may be worthwhile biting the bullet here and push forward.
> > > >
> > > > Since this essentially will be a full replacement of the
> > > ctakes-dictionary-lookup module, a good option maybe to just replace
> > > the entire module now and rename the existing module to * _deprecated.
> > > > How do folks feel about that?  In a nutshell,
> > > > ctakes-dictionary-lookup-2
> > > is a faster algorithm with a simpler code base- and comparable results
> > > (Sean has a full comparison in the documentation for those who are
> > curious).
> > > >
> > > > --Pei
> > > >
> > > >> -Original Message-
> > > >> From: britt fitch [mailto:britt.fi...@gmail.com]
> > > >> Sent: Monday, June 09, 2014 5:42 PM
> > > >> To: dev@ctakes.apache.org
> > > >> Subject: Re: Preparing for an Apache cTAKES 3.2 Release?
> > > >>
> > > >> There is some documentation in the dictionary2 module under
> > > >> /doc/DictionaryLookupHelp.{txt | docx} that gives some some details
> > > >> of
> > > the
> > > >> different lookup implementation options within that module that I
> > > >> found helpful.
> > > >>
> > > >>
> > > >> On Jun 9, 2014, at 5:17 PM, Masanz, James J.
> > > >> <



-- 




--
Karthik Sarma
UCLA Medical Scientist Training Program Class of 20??
Member, UCLA Medical Imaging & Informatics Lab
Member, CA Delegation to the House of Delegates of the American Medical
Association
ksa...@ksarma.com
gchat: ksa...@gmail.com
linkedin: www.linkedin.com/in/ksarma

RE: Preparing for an Apache cTAKES 3.2 Release?

2014-06-11 Thread Finan, Sean

> it would be incredibly helpful to have thorough documentation

I agree.  There is some documentation in the module's doc/ directory, but it is 
very brief.  There are also some example descriptors in the example/ directory. 
 The -resource also has some example xmls and dictionaries.

It isn't much, but I have a small plate heaped with large portions of many 
courses and very little time to document.  If there are questions please write 
me and I'll update the documentation as necessary.  Anybody else that feels 
inclined can also add to the docs.  Eventually the documentation should be 
moved to reside with the rest of the cTakes docs.

Sean

-Original Message-
From: vijay garla [mailto:vnga...@gmail.com] 
Sent: Wednesday, June 11, 2014 9:33 AM
To: dev@ctakes.apache.org
Subject: Re: Preparing for an Apache cTAKES 3.2 Release?

regardless of the name, I think it would be incredibly helpful to have thorough 
documentation on the dictionary lookup, how to configure it, and how to create 
new dictionaries.  I would venture to say that this is the most important 
component in cTAKES, and probably the one that has generated the most questions 
on the newsgroup.



On Wed, Jun 11, 2014 at 9:21 AM, Finan, Sean < 
sean.fi...@childrens.harvard.edu> wrote:

> >. The newer NER should have in its name the Behavior...
>
> I agree, but the *2 module is a complete replacement for the current 
> lookup.  It does not (really) have any different behavior, just a 
> different implementation and performance.  We plan to swap out the old 
> with the new in the next release and get rid of the *2 suffix.  So, 
> any name provided now is just temporary - unless people don't like the 
> name "dictionary-lookup" at all.
>
> In my original sandbox it was named "RareWordLookup", a nod to its 
> implementation.  However, this doesn't help any users.
>
> Sean
>
> -Original Message-
> From: andy mcmurry [mailto:mcmurry.a...@gmail.com]
> Sent: Wednesday, June 11, 2014 3:09 AM
> To: dev@ctakes.apache.org
> Subject: Re: Preparing for an Apache cTAKES 3.2 Release?
>
> "2" doesn't mean much. The newer NER should have in its name the 
> Behavior...
>
> Perhaps something like MetaMap Usage
>  "--allow_overmatches"
> or  "--allow_concept_gaps" or .other?
>
> Since yTex already provides a pluggable *DictionaryLookup, *that seems 
> like the best place to define the differing Behavior /  Usage.
>
> https://cwiki.apache.org/confluence/display/CTAKES/User's+Guide
> https://code.google.com/p/ytex/wiki/DictionaryLookup_V05
>
>
> AndyMC
>
> On Tue, Jun 10, 2014 at 9:55 AM, britt fitch 
> wrote:
>
> > I don’t have an issue with the *-2 name. I also don’t have any 
> > objections to renaming it.
> >
> > It might be nice to keep the old dictionary code around for a 
> > release-worth of time but after that I would vote purging it.
> > If someone needs it after that it’ll be accessible in the archived 
> > releases.
> >
> >
> >
> > On Jun 10, 2014, at 12:48 PM, Chen, Pei 
> > 
> > wrote:
> >
> > > I think James has a fair point here.
> > > It may be worthwhile biting the bullet here and push forward.
> > >
> > > Since this essentially will be a full replacement of the
> > ctakes-dictionary-lookup module, a good option maybe to just replace 
> > the entire module now and rename the existing module to * _deprecated.
> > > How do folks feel about that?  In a nutshell,
> > > ctakes-dictionary-lookup-2
> > is a faster algorithm with a simpler code base- and comparable 
> > results (Sean has a full comparison in the documentation for those 
> > who are
> curious).
> > >
> > > --Pei
> > >
> > >> -Original Message-
> > >> From: britt fitch [mailto:britt.fi...@gmail.com]
> > >> Sent: Monday, June 09, 2014 5:42 PM
> > >> To: dev@ctakes.apache.org
> > >> Subject: Re: Preparing for an Apache cTAKES 3.2 Release?
> > >>
> > >> There is some documentation in the dictionary2 module under 
> > >> /doc/DictionaryLookupHelp.{txt | docx} that gives some some 
> > >> details of
> > the
> > >> different lookup implementation options within that module that I 
> > >> found helpful.
> > >>
> > >>
> > >> On Jun 9, 2014, at 5:17 PM, Masanz, James J.
> > >> 
> > >> wrote:
> > >>
> > >>>
> > >>> Will ctakes-dictionary-lookup2 remain the name for the new 
> > >>> dictionary
> > >> lookup or will it have a name that reflects the algorithm?
> > >>>
> > >>> Is there a description of it that will help users to decide when 
> > >>> to
> > use one
> > >> dictionary lookup component vs. the other.
> > >>>
> > >>> -- James
> > >>>
> > >>> -Original Message-
> > >>> From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu]
> > >>> Sent: Friday, June 06, 2014 12:34 PM
> > >>> To: dev@ctakes.apache.org
> > >>> Subject: Preparing for an Apache cTAKES 3.2 Release?
> > >>>
> > >>> Hi,
> > >>> The 3.2 release was slated to be release end of this month (Jun 21).
> > >>> Since I volunteered to be the RM for this rel

ApacheCon CFP closes June 25

2014-06-11 Thread Chen, Pei

Dear cTAKES enthusiast,



As you may be aware, ApacheCon will be held this year in Budapest, on November 
17-23. (See http://apachecon.eu for more info.)



The Call For Papers for that conference is still open, but will be closing 
soon. We need you talk proposals, to represent cTAKES at ApacheCon. We need all 
kinds of talks - deep technical talks, hands-on tutorials, introductions for 
beginners, or case studies about the awesome stuff you're doing with cTAKES.



Please consider submitting a proposal, at 
http://events.linuxfoundation.org//events/apachecon-europe/program/cfp



Thanks!

query

2014-06-11 Thread Harpreet Khanduja

Hello,
  I am trying to use ctakes as a developer. I am not able to use UMLS
resources when I run
  the AEs which use UMLS Dictionary.
  I have signed up on the UMLS website and I am using the correct email and
password.
  I have specified username and password in

   Dictionary Lookup: /desc/ctakes-dictionary-
 lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml*


  But I keep getting the exception. I would really appreciate any help on
this.

 OUTPUT THAT I GET  on running AggregatePlaintextUMLSProcessor.xml :


  log4j: reset attribute= "false".
log4j: Threshold ="null".
log4j: Level value for root is  [INFO].
log4j: root level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%d{dd MMM  HH:mm:ss}
%5p %c{1} - %m%n].
log4j: Adding appender named [consoleAppender] to category [root].
11 Jun 2014 13:07:01  INFO TokenizerAnnotatorPTB - Initializing
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
11 Jun 2014 13:07:01  INFO POSTagger - POS tagger model file:
org/apache/ctakes/postagger/models/mayo-pos.zip
11 Jun 2014 13:07:01  INFO ContextDependentTokenizerAnnotator - Finite
state machines loaded.
11 Jun 2014 13:07:01  INFO Chunker - Chunker model file:
org/apache/ctakes/chunker/models/chunker-model.zip
11 Jun 2014 13:07:03  INFO SentenceDetector - Sentence detector model file:
org/apache/ctakes/core/sentdetect/sd-med-model.zip
11 Jun 2014 13:07:03  INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg
with config file =
D:\workspaces\workspace_cTakes\ctakes\ctakes-dictionary-lookup\resources\org\apache\ctakes\lvg\data\config\lvg.properties
11 Jun 2014 13:07:03  INFO LvgCmdApiResourceImpl -   config file absolute
path =
D:\workspaces\workspace_cTakes\ctakes\ctakes-dictionary-lookup\resources\org\apache\ctakes\lvg\data\config\lvg.properties
11 Jun 2014 13:07:03  INFO LvgCmdApiResourceImpl - cwd =
D:\workspaces\workspace_cTakes\ctakes\ctakes-clinical-pipeline
11 Jun 2014 13:07:03  INFO LvgCmdApiResourceImpl - cd
D:\workspaces\workspace_cTakes\ctakes\ctakes-dictionary-lookup\resources\org\apache\ctakes\lvg\
11 Jun 2014 13:07:03  INFO LvgCmdApiResourceImpl - cd
D:\workspaces\workspace_cTakes\ctakes\ctakes-clinical-pipeline
11 Jun 2014 13:07:04  INFO JdbcConnectionResourceImpl - Connection
established to:
jdbc:hsqldb:res:/org/apache/ctakes/dictionary/lookup/umls2011ab/umls
Exception in thread "main"
org.apache.uima.resource.ResourceInitializationException
at
org.apache.ctakes.core.resource.JdbcConnectionResourceImpl.load(JdbcConnectionResourceImpl.java:130)
at
org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:603)
at
org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442)
at
org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153)
at
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.java:157)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:123)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory

Re: query

2014-06-11 Thread Pei Chen

Harpreet,
Ensure that you have downloaded the dictionaries (umls) per download page:
http://ctakes.apache.org/downloads.cgi
Resources

Resources are required to run most of cTAKES. They are available for
download from SourceForge: ctakes-resources-3.1.0.zip

.

Please download, unzip and add/merge the contents to the existing resources
directory. Follow the User 
 or Developer  Install Guide
to direct you through the installation process.


On Wed, Jun 11, 2014 at 1:45 PM, Harpreet Khanduja  wrote:

> Hello,
>   I am trying to use ctakes as a developer. I am not able to use UMLS
> resources when I run
>   the AEs which use UMLS Dictionary.
>   I have signed up on the UMLS website and I am using the correct email and
> password.
>   I have specified username and password in
>
>Dictionary Lookup: /desc/ctakes-dictionary-
>  lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml*
>
>
>   But I keep getting the exception. I would really appreciate any help on
> this.
>
>  OUTPUT THAT I GET  on running AggregatePlaintextUMLSProcessor.xml :
>
>
>   log4j: reset attribute= "false".
> log4j: Threshold ="null".
> log4j: Level value for root is  [INFO].
> log4j: root level set to INFO
> log4j: Class name: [org.apache.log4j.ConsoleAppender]
> log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
> log4j: Setting property [conversionPattern] to [%d{dd MMM  HH:mm:ss}
> %5p %c{1} - %m%n].
> log4j: Adding appender named [consoleAppender] to category [root].
> 11 Jun 2014 13:07:01  INFO TokenizerAnnotatorPTB - Initializing
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 11 Jun 2014 13:07:01  INFO POSTagger - POS tagger model file:
> org/apache/ctakes/postagger/models/mayo-pos.zip
> 11 Jun 2014 13:07:01  INFO ContextDependentTokenizerAnnotator - Finite
> state machines loaded.
> 11 Jun 2014 13:07:01  INFO Chunker - Chunker model file:
> org/apache/ctakes/chunker/models/chunker-model.zip
> 11 Jun 2014 13:07:03  INFO SentenceDetector - Sentence detector model file:
> org/apache/ctakes/core/sentdetect/sd-med-model.zip
> 11 Jun 2014 13:07:03  INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg
> with config file =
>
> D:\workspaces\workspace_cTakes\ctakes\ctakes-dictionary-lookup\resources\org\apache\ctakes\lvg\data\config\lvg.properties
> 11 Jun 2014 13:07:03  INFO LvgCmdApiResourceImpl -   config file absolute
> path =
>
> D:\workspaces\workspace_cTakes\ctakes\ctakes-dictionary-lookup\resources\org\apache\ctakes\lvg\data\config\lvg.properties
> 11 Jun 2014 13:07:03  INFO LvgCmdApiResourceImpl - cwd =
> D:\workspaces\workspace_cTakes\ctakes\ctakes-clinical-pipeline
> 11 Jun 2014 13:07:03  INFO LvgCmdApiResourceImpl - cd
>
> D:\workspaces\workspace_cTakes\ctakes\ctakes-dictionary-lookup\resources\org\apache\ctakes\lvg\
> 11 Jun 2014 13:07:03  INFO LvgCmdApiResourceImpl - cd
> D:\workspaces\workspace_cTakes\ctakes\ctakes-clinical-pipeline
> 11 Jun 2014 13:07:04  INFO JdbcConnectionResourceImpl - Connection
> established to:
> jdbc:hsqldb:res:/org/apache/ctakes/dictionary/lookup/umls2011ab/umls
> Exception in thread "main"
> org.apache.uima.resource.ResourceInitializationException
> at
>
> org.apache.ctakes.core.resource.JdbcConnectionResourceImpl.load(JdbcConnectionResourceImpl.java:130)
> at
>
> org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:603)
> at
>
> org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442)
> at
>
> org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153)
> at
>
> org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.java:157)
> at
>
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:123)
> at
>
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> at
>
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
> at
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
> at
> org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
> at
>
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
> at
>
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
> at
>
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
> at
>
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> at
>
> org.apache.uima.impl.Compo

Re: query

2014-06-11 Thread Harpreet Khanduja

Hello,
   Thanks for the reply, but I have already done that and I made sure that
   these resources are there all over again.

Harpreet



On Wed, Jun 11, 2014 at 1:49 PM, Pei Chen  wrote:

> Harpreet,
> Ensure that you have downloaded the dictionaries (umls) per download page:
> http://ctakes.apache.org/downloads.cgi
> Resources
>
> Resources are required to run most of cTAKES. They are available for
> download from SourceForge: ctakes-resources-3.1.0.zip
> <
> http://sourceforge.net/projects/ctakesresources/files/ctakes-resources-3.1.0.zip/download
> >
> .
>
> Please download, unzip and add/merge the contents to the existing resources
> directory. Follow the User 
>  or Developer  Install Guide
> to direct you through the installation process.
>
>
> On Wed, Jun 11, 2014 at 1:45 PM, Harpreet Khanduja 
> wrote:
>
> > Hello,
> >   I am trying to use ctakes as a developer. I am not able to use UMLS
> > resources when I run
> >   the AEs which use UMLS Dictionary.
> >   I have signed up on the UMLS website and I am using the correct email
> and
> > password.
> >   I have specified username and password in
> >
> >Dictionary Lookup: /desc/ctakes-dictionary-
> >  lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml*
> >
> >
> >   But I keep getting the exception. I would really appreciate any help on
> > this.
> >
> >  OUTPUT THAT I GET  on running AggregatePlaintextUMLSProcessor.xml :
> >
> >
> >   log4j: reset attribute= "false".
> > log4j: Threshold ="null".
> > log4j: Level value for root is  [INFO].
> > log4j: root level set to INFO
> > log4j: Class name: [org.apache.log4j.ConsoleAppender]
> > log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
> > log4j: Setting property [conversionPattern] to [%d{dd MMM  HH:mm:ss}
> > %5p %c{1} - %m%n].
> > log4j: Adding appender named [consoleAppender] to category [root].
> > 11 Jun 2014 13:07:01  INFO TokenizerAnnotatorPTB - Initializing
> > org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> > 11 Jun 2014 13:07:01  INFO POSTagger - POS tagger model file:
> > org/apache/ctakes/postagger/models/mayo-pos.zip
> > 11 Jun 2014 13:07:01  INFO ContextDependentTokenizerAnnotator - Finite
> > state machines loaded.
> > 11 Jun 2014 13:07:01  INFO Chunker - Chunker model file:
> > org/apache/ctakes/chunker/models/chunker-model.zip
> > 11 Jun 2014 13:07:03  INFO SentenceDetector - Sentence detector model
> file:
> > org/apache/ctakes/core/sentdetect/sd-med-model.zip
> > 11 Jun 2014 13:07:03  INFO LvgCmdApiResourceImpl - Loading NLM Norm and
> Lvg
> > with config file =
> >
> >
> D:\workspaces\workspace_cTakes\ctakes\ctakes-dictionary-lookup\resources\org\apache\ctakes\lvg\data\config\lvg.properties
> > 11 Jun 2014 13:07:03  INFO LvgCmdApiResourceImpl -   config file absolute
> > path =
> >
> >
> D:\workspaces\workspace_cTakes\ctakes\ctakes-dictionary-lookup\resources\org\apache\ctakes\lvg\data\config\lvg.properties
> > 11 Jun 2014 13:07:03  INFO LvgCmdApiResourceImpl - cwd =
> > D:\workspaces\workspace_cTakes\ctakes\ctakes-clinical-pipeline
> > 11 Jun 2014 13:07:03  INFO LvgCmdApiResourceImpl - cd
> >
> >
> D:\workspaces\workspace_cTakes\ctakes\ctakes-dictionary-lookup\resources\org\apache\ctakes\lvg\
> > 11 Jun 2014 13:07:03  INFO LvgCmdApiResourceImpl - cd
> > D:\workspaces\workspace_cTakes\ctakes\ctakes-clinical-pipeline
> > 11 Jun 2014 13:07:04  INFO JdbcConnectionResourceImpl - Connection
> > established to:
> > jdbc:hsqldb:res:/org/apache/ctakes/dictionary/lookup/umls2011ab/umls
> > Exception in thread "main"
> > org.apache.uima.resource.ResourceInitializationException
> > at
> >
> >
> org.apache.ctakes.core.resource.JdbcConnectionResourceImpl.load(JdbcConnectionResourceImpl.java:130)
> > at
> >
> >
> org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:603)
> > at
> >
> >
> org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442)
> > at
> >
> >
> org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153)
> > at
> >
> >
> org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.java:157)
> > at
> >
> >
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:123)
> > at
> >
> >
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> > at
> >
> >
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
> > at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
> > at
> >
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
> > at
> >
> org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
> > at
> >
> >
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnaly

RE: query

2014-06-11 Thread Chen, Pei

Harpreet,
I had a closer look at your log file and it looks like you were actually trying 
to run it from Eclipse IDE?
If so, just ensure that the resources do exist in the classpath.
If it's within eclipse ide, the plugin should download and unpack the umls 
dictionaries automatically actually. (you can check the below to ensure it 
exists
target/classes/org/apache/ctakes/dictionary/lookup/umls2011ab/)
You can also try running 'mvn clean compile' from the command line as well.



> -Original Message-
> From: Harpreet Khanduja [mailto:hsk5...@rit.edu]
> Sent: Wednesday, June 11, 2014 2:09 PM
> To: dev@ctakes.apache.org
> Subject: Re: query
> 
> Hello,
>Thanks for the reply, but I have already done that and I made sure that
>these resources are there all over again.
> 
> Harpreet
> 
> 
> 
> On Wed, Jun 11, 2014 at 1:49 PM, Pei Chen  wrote:
> 
> > Harpreet,
> > Ensure that you have downloaded the dictionaries (umls) per download
> page:
> > http://ctakes.apache.org/downloads.cgi
> > Resources
> >
> > Resources are required to run most of cTAKES. They are available for
> > download from SourceForge: ctakes-resources-3.1.0.zip <
> > http://sourceforge.net/projects/ctakesresources/files/ctakes-resources
> > -3.1.0.zip/download
> > >
> > .
> >
> > Please download, unzip and add/merge the contents to the existing
> > resources directory. Follow the User
> > 
> >  or Developer  Install
> > Guide to direct you through the installation process.
> >
> >
> > On Wed, Jun 11, 2014 at 1:45 PM, Harpreet Khanduja 
> > wrote:
> >
> > > Hello,
> > >   I am trying to use ctakes as a developer. I am not able to use
> > > UMLS resources when I run
> > >   the AEs which use UMLS Dictionary.
> > >   I have signed up on the UMLS website and I am using the correct
> > > email
> > and
> > > password.
> > >   I have specified username and password in
> > >
> > >Dictionary Lookup: /desc/ctakes-dictionary-
> > >  lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml*
> > >
> > >
> > >   But I keep getting the exception. I would really appreciate any
> > > help on this.
> > >
> > >  OUTPUT THAT I GET  on running AggregatePlaintextUMLSProcessor.xml :
> > >
> > >
> > >   log4j: reset attribute= "false".
> > > log4j: Threshold ="null".
> > > log4j: Level value for root is  [INFO].
> > > log4j: root level set to INFO
> > > log4j: Class name: [org.apache.log4j.ConsoleAppender]
> > > log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
> > > log4j: Setting property [conversionPattern] to [%d{dd MMM 
> > > HH:mm:ss} %5p %c{1} - %m%n].
> > > log4j: Adding appender named [consoleAppender] to category [root].
> > > 11 Jun 2014 13:07:01  INFO TokenizerAnnotatorPTB - Initializing
> > > org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> > > 11 Jun 2014 13:07:01  INFO POSTagger - POS tagger model file:
> > > org/apache/ctakes/postagger/models/mayo-pos.zip
> > > 11 Jun 2014 13:07:01  INFO ContextDependentTokenizerAnnotator -
> > > Finite state machines loaded.
> > > 11 Jun 2014 13:07:01  INFO Chunker - Chunker model file:
> > > org/apache/ctakes/chunker/models/chunker-model.zip
> > > 11 Jun 2014 13:07:03  INFO SentenceDetector - Sentence detector
> > > model
> > file:
> > > org/apache/ctakes/core/sentdetect/sd-med-model.zip
> > > 11 Jun 2014 13:07:03  INFO LvgCmdApiResourceImpl - Loading NLM Norm
> > > and
> > Lvg
> > > with config file =
> > >
> > >
> > D:\workspaces\workspace_cTakes\ctakes\ctakes-dictionary-
> lookup\resourc
> > es\org\apache\ctakes\lvg\data\config\lvg.properties
> > > 11 Jun 2014 13:07:03  INFO LvgCmdApiResourceImpl -   config file absolute
> > > path =
> > >
> > >
> > D:\workspaces\workspace_cTakes\ctakes\ctakes-dictionary-
> lookup\resourc
> > es\org\apache\ctakes\lvg\data\config\lvg.properties
> > > 11 Jun 2014 13:07:03  INFO LvgCmdApiResourceImpl - cwd =
> > > D:\workspaces\workspace_cTakes\ctakes\ctakes-clinical-pipeline
> > > 11 Jun 2014 13:07:03  INFO LvgCmdApiResourceImpl - cd
> > >
> > >
> > D:\workspaces\workspace_cTakes\ctakes\ctakes-dictionary-
> lookup\resourc
> > es\org\apache\ctakes\lvg\
> > > 11 Jun 2014 13:07:03  INFO LvgCmdApiResourceImpl - cd
> > > D:\workspaces\workspace_cTakes\ctakes\ctakes-clinical-pipeline
> > > 11 Jun 2014 13:07:04  INFO JdbcConnectionResourceImpl - Connection
> > > established to:
> > > jdbc:hsqldb:res:/org/apache/ctakes/dictionary/lookup/umls2011ab/umls
> > > Exception in thread "main"
> > > org.apache.uima.resource.ResourceInitializationException
> > > at
> > >
> > >
> >
> org.apache.ctakes.core.resource.JdbcConnectionResourceImpl.load(JdbcCo
> > nnectionResourceImpl.java:130)
> > > at
> > >
> > >
> >
> org.apache.uima.resource.impl.ResourceManager_impl.registerResource(Re
> > sourceManager_impl.java:603)
> > > at
> > >
> > >
> > org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalR
> > esources(ResourceManager_impl.java:442)
> > > at
> >

Re: query

2014-06-11 Thread Harpreet Khanduja

Pei,
   I had provided the classpath = ctakes-dictionay-look-up/resources to all
the projects in ctakes.
   as it says in the documentation but there was nothing inside my target
folder in ctakes-clinical-pipeline directory.
   So, then I ran maven compile and I got following error.


 [ERROR] Failed to execute goal on project ctakes-clinical-pipeline: Could
not resolve dependencies for project
org.apache.ctakes:ctakes-clinical-pipeline:jar:3.1.2-SNAPSHOT: Failed to
collect dependencies for
[org.apache.ctakes:ctakes-type-system:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-core:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-utils:jar:3.1.2-SNAPSHOT (compile),
jdom:jdom:jar:1.0 (compile), junit:junit:jar:4.10 (test),
org.apache.ctakes:ctakes-context-tokenizer:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-dictionary-lookup:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-preprocessor:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-lvg:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-chunker:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-ne-contexts:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-pos-tagger:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-assertion:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-dependency-parser:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-dependency-parser-res:jar:3.1.2-SNAPSHOT
(compile), org.apache.ctakes:ctakes-ytex:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-ytex-res:jar:3.1.2-SNAPSHOT (compile),
org.apache.ctakes:ctakes-ytex-uima:jar:3.1.2-SNAPSHOT (compile)]: Failed to
read artifact descriptor for
org.apache.ctakes:ctakes-type-system:jar:3.1.2-SNAPSHOT: Failure to find
org.apache.ctakes:ctakes:pom:3.1.2-SNAPSHOT in
http://repository.apache.org/snapshots was cached in the local repository,
resolution will not be reattempted until the update interval of
apache.snapshots has elapsed or updates are forced -> [Help 1]
[ERROR]



On Wed, Jun 11, 2014 at 2:17 PM, Chen, Pei 
wrote:

> Harpreet,
> I had a closer look at your log file and it looks like you were actually
> trying to run it from Eclipse IDE?
> If so, just ensure that the resources do exist in the classpath.
> If it's within eclipse ide, the plugin should download and unpack the umls
> dictionaries automatically actually. (you can check the below to ensure it
> exists
> target/classes/org/apache/ctakes/dictionary/lookup/umls2011ab/)
> You can also try running 'mvn clean compile' from the command line as well.
>
>
>
> > -Original Message-
> > From: Harpreet Khanduja [mailto:hsk5...@rit.edu]
> > Sent: Wednesday, June 11, 2014 2:09 PM
> > To: dev@ctakes.apache.org
> > Subject: Re: query
> >
> > Hello,
> >Thanks for the reply, but I have already done that and I made sure
> that
> >these resources are there all over again.
> >
> > Harpreet
> >
> >
> >
> > On Wed, Jun 11, 2014 at 1:49 PM, Pei Chen  wrote:
> >
> > > Harpreet,
> > > Ensure that you have downloaded the dictionaries (umls) per download
> > page:
> > > http://ctakes.apache.org/downloads.cgi
> > > Resources
> > >
> > > Resources are required to run most of cTAKES. They are available for
> > > download from SourceForge: ctakes-resources-3.1.0.zip <
> > > http://sourceforge.net/projects/ctakesresources/files/ctakes-resources
> > > -3.1.0.zip/download
> > > >
> > > .
> > >
> > > Please download, unzip and add/merge the contents to the existing
> > > resources directory. Follow the User
> > > 
> > >  or Developer  Install
> > > Guide to direct you through the installation process.
> > >
> > >
> > > On Wed, Jun 11, 2014 at 1:45 PM, Harpreet Khanduja 
> > > wrote:
> > >
> > > > Hello,
> > > >   I am trying to use ctakes as a developer. I am not able to use
> > > > UMLS resources when I run
> > > >   the AEs which use UMLS Dictionary.
> > > >   I have signed up on the UMLS website and I am using the correct
> > > > email
> > > and
> > > > password.
> > > >   I have specified username and password in
> > > >
> > > >Dictionary Lookup: /desc/ctakes-dictionary-
> > > >  lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml*
> > > >
> > > >
> > > >   But I keep getting the exception. I would really appreciate any
> > > > help on this.
> > > >
> > > >  OUTPUT THAT I GET  on running AggregatePlaintextUMLSProcessor.xml :
> > > >
> > > >
> > > >   log4j: reset attribute= "false".
> > > > log4j: Threshold ="null".
> > > > log4j: Level value for root is  [INFO].
> > > > log4j: root level set to INFO
> > > > log4j: Class name: [org.apache.log4j.ConsoleAppender]
> > > > log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
> > > > log4j: Setting property [conversionPattern] to [%d{dd MMM 
> > > > HH:mm:ss} %5p %c{1} - %m%n].
> > > > log4j: Adding appender named [consoleAppender] to category [root].
> > > > 11 Jun 2014 13:07:01  INFO TokenizerAnnotatorPTB

RE: query

2014-06-11 Thread Chen, Pei

Harpreet,
Just curious- is maven able to connect to the internet (maven central 
repositories)? i.e. did you have to set your ~/.m2/settings.xml with proxy info 
if behind a firewall?
If it was an intermittent issue, you can try clearing out the local 
~/.m2/repository?
--Pei

> -Original Message-
> From: Harpreet Khanduja [mailto:hsk5...@rit.edu]
> Sent: Wednesday, June 11, 2014 3:54 PM
> To: dev@ctakes.apache.org
> Subject: Re: query
> 
> Pei,
>I had provided the classpath = ctakes-dictionay-look-up/resources to all 
> the
> projects in ctakes.
>as it says in the documentation but there was nothing inside my target
> folder in ctakes-clinical-pipeline directory.
>So, then I ran maven compile and I got following error.
> 
> 
>  [ERROR] Failed to execute goal on project ctakes-clinical-pipeline: Could not
> resolve dependencies for project
> org.apache.ctakes:ctakes-clinical-pipeline:jar:3.1.2-SNAPSHOT: Failed to
> collect dependencies for [org.apache.ctakes:ctakes-type-system:jar:3.1.2-
> SNAPSHOT (compile), org.apache.ctakes:ctakes-core:jar:3.1.2-SNAPSHOT
> (compile), org.apache.ctakes:ctakes-utils:jar:3.1.2-SNAPSHOT (compile),
> jdom:jdom:jar:1.0 (compile), junit:junit:jar:4.10 (test),
> org.apache.ctakes:ctakes-context-tokenizer:jar:3.1.2-SNAPSHOT (compile),
> org.apache.ctakes:ctakes-dictionary-lookup:jar:3.1.2-SNAPSHOT (compile),
> org.apache.ctakes:ctakes-preprocessor:jar:3.1.2-SNAPSHOT (compile),
> org.apache.ctakes:ctakes-lvg:jar:3.1.2-SNAPSHOT (compile),
> org.apache.ctakes:ctakes-chunker:jar:3.1.2-SNAPSHOT (compile),
> org.apache.ctakes:ctakes-ne-contexts:jar:3.1.2-SNAPSHOT (compile),
> org.apache.ctakes:ctakes-pos-tagger:jar:3.1.2-SNAPSHOT (compile),
> org.apache.ctakes:ctakes-assertion:jar:3.1.2-SNAPSHOT (compile),
> org.apache.ctakes:ctakes-dependency-parser:jar:3.1.2-SNAPSHOT (compile),
> org.apache.ctakes:ctakes-dependency-parser-res:jar:3.1.2-SNAPSHOT
> (compile), org.apache.ctakes:ctakes-ytex:jar:3.1.2-SNAPSHOT (compile),
> org.apache.ctakes:ctakes-ytex-res:jar:3.1.2-SNAPSHOT (compile),
> org.apache.ctakes:ctakes-ytex-uima:jar:3.1.2-SNAPSHOT (compile)]: Failed
> to read artifact descriptor for
> org.apache.ctakes:ctakes-type-system:jar:3.1.2-SNAPSHOT: Failure to find
> org.apache.ctakes:ctakes:pom:3.1.2-SNAPSHOT in
> http://repository.apache.org/snapshots was cached in the local repository,
> resolution will not be reattempted until the update interval of
> apache.snapshots has elapsed or updates are forced -> [Help 1] [ERROR]
> 
> 
> 
> On Wed, Jun 11, 2014 at 2:17 PM, Chen, Pei
> 
> wrote:
> 
> > Harpreet,
> > I had a closer look at your log file and it looks like you were
> > actually trying to run it from Eclipse IDE?
> > If so, just ensure that the resources do exist in the classpath.
> > If it's within eclipse ide, the plugin should download and unpack the
> > umls dictionaries automatically actually. (you can check the below to
> > ensure it exists
> > target/classes/org/apache/ctakes/dictionary/lookup/umls2011ab/)
> > You can also try running 'mvn clean compile' from the command line as
> well.
> >
> >
> >
> > > -Original Message-
> > > From: Harpreet Khanduja [mailto:hsk5...@rit.edu]
> > > Sent: Wednesday, June 11, 2014 2:09 PM
> > > To: dev@ctakes.apache.org
> > > Subject: Re: query
> > >
> > > Hello,
> > >Thanks for the reply, but I have already done that and I made
> > > sure
> > that
> > >these resources are there all over again.
> > >
> > > Harpreet
> > >
> > >
> > >
> > > On Wed, Jun 11, 2014 at 1:49 PM, Pei Chen 
> wrote:
> > >
> > > > Harpreet,
> > > > Ensure that you have downloaded the dictionaries (umls) per
> > > > download
> > > page:
> > > > http://ctakes.apache.org/downloads.cgi
> > > > Resources
> > > >
> > > > Resources are required to run most of cTAKES. They are available
> > > > for download from SourceForge: ctakes-resources-3.1.0.zip <
> > > > http://sourceforge.net/projects/ctakesresources/files/ctakes-resou
> > > > rces
> > > > -3.1.0.zip/download
> > > > >
> > > > .
> > > >
> > > > Please download, unzip and add/merge the contents to the existing
> > > > resources directory. Follow the User
> > > > 
> > > >  or Developer 
> > > > Install Guide to direct you through the installation process.
> > > >
> > > >
> > > > On Wed, Jun 11, 2014 at 1:45 PM, Harpreet Khanduja
> > > > 
> > > > wrote:
> > > >
> > > > > Hello,
> > > > >   I am trying to use ctakes as a developer. I am not able to use
> > > > > UMLS resources when I run
> > > > >   the AEs which use UMLS Dictionary.
> > > > >   I have signed up on the UMLS website and I am using the
> > > > > correct email
> > > > and
> > > > > password.
> > > > >   I have specified username and password in
> > > > >
> > > > >Dictionary Lookup: /desc/ctakes-dictionary-
> > > > >
> lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml*
> > > > >
> > > > >
> > > > >   But I keep gettin

Re: Preparing for an Apache cTAKES 3.2 Release?

RE: Preparing for an Apache cTAKES 3.2 Release?

Re: Preparing for an Apache cTAKES 3.2 Release?

Re: Preparing for an Apache cTAKES 3.2 Release?

RE: Preparing for an Apache cTAKES 3.2 Release?

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