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Posted to dev@ctakes.apache.org by "Chen, Pei" <Pe...@childrens.harvard.edu> on 2013/02/06 23:39:31 UTC
RE: cTAKES 3.0 developer guide review
Hi Troy,
Thanks for putting the developers guide together.
Just an FYI, the UMLS resources, Full LVG, Models are available as a single download now. (i.e. users won't need to do anything special to download the full LVG, etc.)
The downloads page have been updated with a link to SF, but I presume the doc should as well:
http://incubator.apache.org/ctakes/downloads.html
Resources & Models
The trained models and resources are required to run cTAKES. They are available for download from SourceForge: ctakes-resources-3.0.1.zip.
Please download, unzip and add/merge the contents to the existing resources directory.
--Pei
> -----Original Message-----
> From: Bleeker, Troy C. [mailto:Bleeker.Troy@mayo.edu]
> Sent: Friday, January 18, 2013 5:49 PM
> To: 'ctakes-dev@incubator.apache.org'
> Subject: cTAKES 3.0 developer guide review
>
> The developer guide is pretty close to complete then. If anyone could take
> the time to review it, make changes. There are both expert install
> instructions and step by step.
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+Develope
> r+Guide
>
> I used what we think will be the URL for check out based on what James said.
>
> Fill me in on how to select which run configuration and I can add it - or the
> beauty of the wiki - you can too.
>
> I assume someone will take care of deleting the empty directories at some
> point.
>
> For the launch files I think there should only be 2 as well. Are these names
> better than what's there now, more descriptive in the short space?
> UIMA_GUI_collection_processing_engine.launch
> UIMA_GUI_CAS_visual_debugger.launch
>
>
> Thanks
> Troy
>
> -----Original Message-----
> From: ctakes-dev-return-1053-
> Bleeker.Troy=mayo.edu@incubator.apache.org [mailto:ctakes-dev-return-
> 1053-Bleeker.Troy=mayo.edu@incubator.apache.org] On Behalf Of Masanz,
> James J.
> Sent: Friday, January 18, 2013 12:08 PM
> To: 'ctakes-dev@incubator.apache.org'
> Subject: RE: cTAKES 3.0 questions
>
>
> There is a branch for 3.0
> https://svn.apache.org/repos/asf/incubator/ctakes/branches/ctakes-3.0.0-
> incubating
>
> For each release candidate there is a tag such as
> https://svn.apache.org/repos/asf/incubator/ctakes/tags/ctakes-3.0.0-
> incubating-rc5
>
> I'm assuming we will create a tag for the release without 'rcX' on the end
> once the release is approved.
>
> I don't think we need to document all the run configurations. I think we
> should just document how to select which one of the twin to select Within
> the Run Configurations popup, look at the Shared file field on the Common
> tab.
>
> Yes, all the institutional directories are supposed to be gone. Looks like we
> missed an empty one.
>
> Regards,
> James Masanz
>
>
> > -----Original Message-----
> > From:
> > ctakes-dev-return-1048-Masanz.James=mayo.edu@incubator.apache.org
> > [mailto:ctakes-dev-return-1048-
> Masanz.James=mayo.edu@incubator.apache.
> > org]
> > On Behalf Of Bleeker, Troy C.
> > Sent: Friday, January 18, 2013 11:29 AM
> > To: ctakes-dev@incubator.apache.org
> > Subject: cTAKES 3.0 questions
> >
> > Working through the dev install instructions I've come up with a
> > number of questions. Could the group help me out ...
> >
> > Where will the non-volatile cTAKES 3.0 trunk be? Seems like the code
> > here keeps changing:
> > https://svn.apache.org/repos/asf/incubator/ctakes/trunk
> > Once released will the code freeze at a particular place and will it
> > have
> > 3.0 in the URL in order to distinguish this release from an inevitable
> > future release?
> >
> > Why are there 4 .launch files under ctakes-clicnical-
> > pipeline/resources/launch? What's the difference?
> > CPE cTAKES.launch
> > CVD cTAKES.launch
> > UIMA_CPE_GUI--clinical_documents_pipeline.launch
> > UIMA_CVD--clinical_documents_pipeline.launch
> >
> > There are lots of Run Configurations now. Do we need a place to
> > document all of those? All of them in my checkout on 1/14 appear to have a
> twin.
> >
> > Ctakes/ctakes-ne-contexts/target/classes/edu/mayo/bmi is created in my
> > Eclipse projects upon checkout. Are not all the institutional
> > directories supposed to be gone?
> >
> > Troy Bleeker * Senior Business Analyst CBAP(r) * Biomedical Statistics
> > and Informatics
> > Phone: 507-293-1574 * Fax: 507-284-0360 * bleeker.troy@mayo.edu Mayo
> > Clinic * 200 First Street SW * Rochester, MN 55905 * www.mayoclinic.org
Re: cTAKES 3.0 developer guide review
Posted by Andy McMurry <mc...@gmail.com>.
Suggestion:
"Apache cTAKES requires Java level 1.6; it has been tested with Sun Java SDK v6.0, IBM Java 6.0, and OpenJDK 6.0.
Running the Eclipse plugin tooling for UIMA requires you start Eclipse.
The supported platforms are: Windows, Linux, Solaris, AIX and Mac OS X.
Other platforms and Java (1.7 or 1.8) implementations should work, but have not been significantly tested."
My idea is simply to adopt/adopt the UIMA "supported platforms" statement specifically for cTAKES .
http://svn.apache.org/repos/asf/uima/uimaj/trunk/README
"Apache UIMA requires Java level 1.5; it has been tested with Sun Java SDK v5.0 and v6.0, and IBM Java 6.0.
Running the Eclipse plugin tooling for UIMA requires you start Eclipse using a Java 1.5 or later, as well.
The supported platforms are: Windows, Linux, Solaris, AIX and Mac OS X.
Other platforms and Java (1.5+) implementations should work, but have not been significantly tested.
Many of the scripts in the /bin directory invoke Java. They use the value of the environment variable, JAVA_HOME,
to locate the Java to use; if it is not set, they invoke "java" expecting to find an appropriate Java in your PATH."
On Feb 13, 2013, at 12:16 AM, Jörn Kottmann <ko...@gmail.com> wrote:
> On 02/13/2013 12:38 AM, Andy McMurry wrote:
>> I suggest changing the Java supported versions from "JDK 1.6+" to the UIMA supported versions (minus JDK 1.5).
>> http://svn.apache.org/repos/asf/uima/uimaj/trunk/README
>>
>> Worth noting that Java 1.6 is facing end of life and Java 1.8 would likely be very experimental.
>> (Unless of course cTakes is been thoroughly tested on Java 1.7 and 1.8 )
>
> Why do you think it should be switched back to 1.5? Java is backward compatible, cTAKES should
> run fine on 1.7 or 1.8 when its out.
>
> Do you have to run on 1.5 in your production system?
>
> Jörn
Re: cTAKES 3.0 developer guide review
Posted by Jörn Kottmann <ko...@gmail.com>.
On 02/13/2013 12:38 AM, Andy McMurry wrote:
> I suggest changing the Java supported versions from "JDK 1.6+" to the UIMA supported versions (minus JDK 1.5).
> http://svn.apache.org/repos/asf/uima/uimaj/trunk/README
>
> Worth noting that Java 1.6 is facing end of life and Java 1.8 would likely be very experimental.
> (Unless of course cTakes is been thoroughly tested on Java 1.7 and 1.8 )
Why do you think it should be switched back to 1.5? Java is backward
compatible, cTAKES should
run fine on 1.7 or 1.8 when its out.
Do you have to run on 1.5 in your production system?
Jörn
Re: cTAKES 3.0 developer guide review
Posted by Andy McMurry <mc...@gmail.com>.
Thanks Troy, this looks nice!
I suggest changing the Java supported versions from "JDK 1.6+" to the UIMA supported versions (minus JDK 1.5).
http://svn.apache.org/repos/asf/uima/uimaj/trunk/README
Worth noting that Java 1.6 is facing end of life and Java 1.8 would likely be very experimental.
(Unless of course cTakes is been thoroughly tested on Java 1.7 and 1.8 )
cheers,
--andy
On Feb 6, 2013, at 2:39 PM, "Chen, Pei" <Pe...@childrens.harvard.edu> wrote:
> Hi Troy,
> Thanks for putting the developers guide together.
> Just an FYI, the UMLS resources, Full LVG, Models are available as a single download now. (i.e. users won't need to do anything special to download the full LVG, etc.)
>
> The downloads page have been updated with a link to SF, but I presume the doc should as well:
> http://incubator.apache.org/ctakes/downloads.html
>
> Resources & Models
> The trained models and resources are required to run cTAKES. They are available for download from SourceForge: ctakes-resources-3.0.1.zip.
> Please download, unzip and add/merge the contents to the existing resources directory.
>
> --Pei
>
>> -----Original Message-----
>> From: Bleeker, Troy C. [mailto:Bleeker.Troy@mayo.edu]
>> Sent: Friday, January 18, 2013 5:49 PM
>> To: 'ctakes-dev@incubator.apache.org'
>> Subject: cTAKES 3.0 developer guide review
>>
>> The developer guide is pretty close to complete then. If anyone could take
>> the time to review it, make changes. There are both expert install
>> instructions and step by step.
>> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+Develope
>> r+Guide
>>
>> I used what we think will be the URL for check out based on what James said.
>>
>> Fill me in on how to select which run configuration and I can add it - or the
>> beauty of the wiki - you can too.
>>
>> I assume someone will take care of deleting the empty directories at some
>> point.
>>
>> For the launch files I think there should only be 2 as well. Are these names
>> better than what's there now, more descriptive in the short space?
>> UIMA_GUI_collection_processing_engine.launch
>> UIMA_GUI_CAS_visual_debugger.launch
>>
>>
>> Thanks
>> Troy
>>
>> -----Original Message-----
>> From: ctakes-dev-return-1053-
>> Bleeker.Troy=mayo.edu@incubator.apache.org [mailto:ctakes-dev-return-
>> 1053-Bleeker.Troy=mayo.edu@incubator.apache.org] On Behalf Of Masanz,
>> James J.
>> Sent: Friday, January 18, 2013 12:08 PM
>> To: 'ctakes-dev@incubator.apache.org'
>> Subject: RE: cTAKES 3.0 questions
>>
>>
>> There is a branch for 3.0
>> https://svn.apache.org/repos/asf/incubator/ctakes/branches/ctakes-3.0.0-
>> incubating
>>
>> For each release candidate there is a tag such as
>> https://svn.apache.org/repos/asf/incubator/ctakes/tags/ctakes-3.0.0-
>> incubating-rc5
>>
>> I'm assuming we will create a tag for the release without 'rcX' on the end
>> once the release is approved.
>>
>> I don't think we need to document all the run configurations. I think we
>> should just document how to select which one of the twin to select Within
>> the Run Configurations popup, look at the Shared file field on the Common
>> tab.
>>
>> Yes, all the institutional directories are supposed to be gone. Looks like we
>> missed an empty one.
>>
>> Regards,
>> James Masanz
>>
>>
>>> -----Original Message-----
>>> From:
>>> ctakes-dev-return-1048-Masanz.James=mayo.edu@incubator.apache.org
>>> [mailto:ctakes-dev-return-1048-
>> Masanz.James=mayo.edu@incubator.apache.
>>> org]
>>> On Behalf Of Bleeker, Troy C.
>>> Sent: Friday, January 18, 2013 11:29 AM
>>> To: ctakes-dev@incubator.apache.org
>>> Subject: cTAKES 3.0 questions
>>>
>>> Working through the dev install instructions I've come up with a
>>> number of questions. Could the group help me out ...
>>>
>>> Where will the non-volatile cTAKES 3.0 trunk be? Seems like the code
>>> here keeps changing:
>>> https://svn.apache.org/repos/asf/incubator/ctakes/trunk
>>> Once released will the code freeze at a particular place and will it
>>> have
>>> 3.0 in the URL in order to distinguish this release from an inevitable
>>> future release?
>>>
>>> Why are there 4 .launch files under ctakes-clicnical-
>>> pipeline/resources/launch? What's the difference?
>>> CPE cTAKES.launch
>>> CVD cTAKES.launch
>>> UIMA_CPE_GUI--clinical_documents_pipeline.launch
>>> UIMA_CVD--clinical_documents_pipeline.launch
>>>
>>> There are lots of Run Configurations now. Do we need a place to
>>> document all of those? All of them in my checkout on 1/14 appear to have a
>> twin.
>>>
>>> Ctakes/ctakes-ne-contexts/target/classes/edu/mayo/bmi is created in my
>>> Eclipse projects upon checkout. Are not all the institutional
>>> directories supposed to be gone?
>>>
>>> Troy Bleeker * Senior Business Analyst CBAP(r) * Biomedical Statistics
>>> and Informatics
>>> Phone: 507-293-1574 * Fax: 507-284-0360 * bleeker.troy@mayo.edu Mayo
>>> Clinic * 200 First Street SW * Rochester, MN 55905 * www.mayoclinic.org
>
RE: cTAKES 3.0 developer guide review
Posted by "Bleeker, Troy C." <Bl...@mayo.edu>.
Pei,
The downloads page already had a section for the cTAKES resources ZIP file location near to the bottom. Could you reconcile those two sections? The bottom one was added when the resources were optional. Now they are not so perhaps it just gets removed.
> Please download, unzip and add/merge the contents to the existing resources directory.
I have tried this and do not see a high-level, existing "resources" directory in a clean RC7 download. The README in the ZIP says the same thing. Could you help me locate this?
Thanks
Troy
-----Original Message-----
From: ctakes-dev-return-1166-Bleeker.Troy=mayo.edu@incubator.apache.org [mailto:ctakes-dev-return-1166-Bleeker.Troy=mayo.edu@incubator.apache.org] On Behalf Of Chen, Pei
Sent: Wednesday, February 06, 2013 4:40 PM
To: ctakes-dev@incubator.apache.org
Subject: RE: cTAKES 3.0 developer guide review
Hi Troy,
Thanks for putting the developers guide together.
Just an FYI, the UMLS resources, Full LVG, Models are available as a single download now. (i.e. users won't need to do anything special to download the full LVG, etc.)
The downloads page have been updated with a link to SF, but I presume the doc should as well:
http://incubator.apache.org/ctakes/downloads.html
Resources & Models
The trained models and resources are required to run cTAKES. They are available for download from SourceForge: ctakes-resources-3.0.1.zip.
Please download, unzip and add/merge the contents to the existing resources directory.
--Pei
> -----Original Message-----
> From: Bleeker, Troy C. [mailto:Bleeker.Troy@mayo.edu]
> Sent: Friday, January 18, 2013 5:49 PM
> To: 'ctakes-dev@incubator.apache.org'
> Subject: cTAKES 3.0 developer guide review
>
> The developer guide is pretty close to complete then. If anyone could
> take the time to review it, make changes. There are both expert
> install instructions and step by step.
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+Develope
> r+Guide
>
> I used what we think will be the URL for check out based on what James said.
>
> Fill me in on how to select which run configuration and I can add it -
> or the beauty of the wiki - you can too.
>
> I assume someone will take care of deleting the empty directories at
> some point.
>
> For the launch files I think there should only be 2 as well. Are these
> names better than what's there now, more descriptive in the short space?
> UIMA_GUI_collection_processing_engine.launch
> UIMA_GUI_CAS_visual_debugger.launch
>
>
> Thanks
> Troy
>
> -----Original Message-----
> From: ctakes-dev-return-1053-
> Bleeker.Troy=mayo.edu@incubator.apache.org [mailto:ctakes-dev-return-
> 1053-Bleeker.Troy=mayo.edu@incubator.apache.org] On Behalf Of Masanz,
> James J.
> Sent: Friday, January 18, 2013 12:08 PM
> To: 'ctakes-dev@incubator.apache.org'
> Subject: RE: cTAKES 3.0 questions
>
>
> There is a branch for 3.0
> https://svn.apache.org/repos/asf/incubator/ctakes/branches/ctakes-3.0.
> 0-
> incubating
>
> For each release candidate there is a tag such as
> https://svn.apache.org/repos/asf/incubator/ctakes/tags/ctakes-3.0.0-
> incubating-rc5
>
> I'm assuming we will create a tag for the release without 'rcX' on the
> end once the release is approved.
>
> I don't think we need to document all the run configurations. I think
> we should just document how to select which one of the twin to select
> Within the Run Configurations popup, look at the Shared file field on
> the Common tab.
>
> Yes, all the institutional directories are supposed to be gone. Looks
> like we missed an empty one.
>
> Regards,
> James Masanz
>
>
> > -----Original Message-----
> > From:
> > ctakes-dev-return-1048-Masanz.James=mayo.edu@incubator.apache.org
> > [mailto:ctakes-dev-return-1048-
> Masanz.James=mayo.edu@incubator.apache.
> > org]
> > On Behalf Of Bleeker, Troy C.
> > Sent: Friday, January 18, 2013 11:29 AM
> > To: ctakes-dev@incubator.apache.org
> > Subject: cTAKES 3.0 questions
> >
> > Working through the dev install instructions I've come up with a
> > number of questions. Could the group help me out ...
> >
> > Where will the non-volatile cTAKES 3.0 trunk be? Seems like the code
> > here keeps changing:
> > https://svn.apache.org/repos/asf/incubator/ctakes/trunk
> > Once released will the code freeze at a particular place and will it
> > have
> > 3.0 in the URL in order to distinguish this release from an
> > inevitable future release?
> >
> > Why are there 4 .launch files under ctakes-clicnical-
> > pipeline/resources/launch? What's the difference?
> > CPE cTAKES.launch
> > CVD cTAKES.launch
> > UIMA_CPE_GUI--clinical_documents_pipeline.launch
> > UIMA_CVD--clinical_documents_pipeline.launch
> >
> > There are lots of Run Configurations now. Do we need a place to
> > document all of those? All of them in my checkout on 1/14 appear to
> > have a
> twin.
> >
> > Ctakes/ctakes-ne-contexts/target/classes/edu/mayo/bmi is created in
> > my Eclipse projects upon checkout. Are not all the institutional
> > directories supposed to be gone?
> >
> > Troy Bleeker * Senior Business Analyst CBAP(r) * Biomedical
> > Statistics and Informatics
> > Phone: 507-293-1574 * Fax: 507-284-0360 * bleeker.troy@mayo.edu Mayo
> > Clinic * 200 First Street SW * Rochester, MN 55905 * www.mayoclinic.org