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Posted to dev@ctakes.apache.org by "Dligach, Dmitriy" <dd...@luc.edu> on 2017/04/14 14:48:03 UTC
cTAKES as a dependency
Hello,
Has anybody tried to run a cTAKES pipeline without having a local cTAKES installation? In other words, is it possible to set up a maven project that will use cTAKES as an external dependency?
Dima
Re: cTAKES as a dependency
Posted by "Dligach, Dmitriy" <dd...@luc.edu>.
Sean, this is very helpful, thanks!
Will give it a try.
Dima
> On Apr 14, 2017, at 10:04, Finan, Sean <Se...@childrens.harvard.edu> wrote:
>
> Yes indeed. The chip-nlp and upmc Deep Phenome team uses ctakes as a maven dependency.
>
> If the project uses maven just add ctakes poms as dependencies. For instance, if you want to add everything necessary for the clinical pipeline:
> <dependency>
> <groupId>org.apache.ctakes</groupId>
> <artifactId>ctakes-clinical-pipeline</artifactId>
> <version>${ctakes.version}</version>
> </dependency>
>
> To add individual modules:
> <dependency>
> <groupId>org.apache.ctakes</groupId>
> <artifactId>ctakes-temporal</artifactId>
> <version>${ctakes.version}</version>
> </dependency>
>
> Either hardcode the version or use (with your desired version):
> <properties>
> <ctakes.version>3.2.3-SNAPSHOT</ctakes.version>
> ...
> </properties>
>
> You can find the available modules here:
> https://mvnrepository.com/artifact/org.apache.ctakes
>
> There is a tiny module in ctakes sandbox named ctakes-the-api. It consists of a simple pom.xml that can be used to do exactly what interests you. Download that pom and look at the comments inside. It should be pretty self-explanatory.
>
> If you aren't using maven you can download the jar files that you want from the same site (https://mvnrepository.com/artifact/org.apache.ctakes ). Click on a module then a version. There will be -code- for various build systems.
> If your build is manual, click "Download (JAR)". If you go the jar route you will also need to download all of the "compile dependencies" below.
>
> Sean
>
>
> -----Original Message-----
> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
> Sent: Friday, April 14, 2017 10:48 AM
> To: cTAKES Developer list
> Subject: cTAKES as a dependency
>
> Hello,
>
> Has anybody tried to run a cTAKES pipeline without having a local cTAKES installation? In other words, is it possible to set up a maven project that will use cTAKES as an external dependency?
>
> Dima
>
>
>
RE: cTAKES as a dependency
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Huh, that is a bit odd. That sandbox module worked when I made it. Obviously something else needs to be changed/fixed.
Ok, sorry for the misdirect, you can stop running down that road. I chatted with James a little earlier and he was making great progress with the whole lvg update. We may trade back and forth with a fix on that this weekend. All in all, that is the root of the problem, so that is our immediate focus.
So glad that James is back in the ctakes family ...
Three cheers for Guergana wrt his recruitment ...
Hopefully once we get the root of this problem (the old lvg module) under control we can move forward and make that crayola pack of ctakes pretty.
Sean
-----Original Message-----
From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
Sent: Friday, April 28, 2017 7:48 PM
To: dev@ctakes.apache.org
Subject: Re: cTAKES as a dependency
>
> Most likely things are now out-of-sync since we have 4.0.1-SNAPSHOT.
>
Yes, that’s what I thought too at first. I forgot to mention that even if you update everything to the latest version, I still get the same error ("Non-resolvable parent POM…”).
Dima
> Since it is just a sandbox project I didn't pay it any attention wrt the 4.0 release. It probably needs to be updated.
>
> Anyway, you probably get the idea - instead of just adding "ctakes-clinical-pipeline" as a dependency, one can grab this pom, rename and uncomment as necessary.
>
> Thanks for the update. When Trump lands us on Mars I'll update the sandbox project.
>
> Sean
>
> -----Original Message-----
> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
> Sent: Friday, April 28, 2017 6:00 PM
> To: dev@ctakes.apache.org
> Subject: Re: cTAKES as a dependency
>
> Hi Sean,
>
>
>
> Thanks for the pointers.
>
>
>
>> There is a tiny module in ctakes sandbox named ctakes-the-api. It consists of a simple pom.xml that can be used to do exactly what interests you. Download that pom and look at the comments inside. It should be pretty self-explanatory.
>
>
>
> I tried this. It works, but only if I run ‘mvn clean compile’ in ctakes trunk first (which deposits a bunch of jars into my .m2 directory). If I remove .m2 and try to build an empty directory with you pom.xml file, I get an error (pasted below). Is it possible it build fine on your end because there’s already ctakes-related stuff in your .m2?
>
>
>
> [INFO] Scanning for projects...
>
> [ERROR] [ERROR] Some problems were encountered while processing the POMs:
>
> [FATAL] Non-resolvable parent POM for org.apache.ctakes:ctakes-the-api:[unknown-version]: Could not find artifact org.apache.ctakes:ctakes:pom:3.2.3-SNAPSHOT and 'parent.relativePath' points at wrong local POM @ line 6, column 12
>
> @
>
> [ERROR] The build could not read 1 project -> [Help 1]
>
> [ERROR]
>
> [ERROR] The project org.apache.ctakes:ctakes-the-api:[unknown-version] (/home/dima/Temp/pom.xml) has 1 error
>
> [ERROR] Non-resolvable parent POM for org.apache.ctakes:ctakes-the-api:[unknown-version]: Could not find artifact org.apache.ctakes:ctakes:pom:3.2.3-SNAPSHOT and 'parent.relativePath' points at wrong local POM @ line 6, column 12 -> [Help 2]
>
> [ERROR]
>
> [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
>
> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
>
> [ERROR]
>
> [ERROR] For more information about the errors and possible solutions, please read the following articles:
>
> [ERROR] [Help 1] https://urldefense.proofpoint.com/v2/url?u=http-3A__cwiki.apache.org_confluence_display_MAVEN_ProjectBuildingException&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=_cciP59cAVa5JVLoMznmZU7g0s6FlhjClbuWDboQjkw&s=Vaf6Gt1ysN0Lsva2fO-HqYsucLD39WUyqox3r1K9uxU&e=
>
> [ERROR] [Help 2] https://urldefense.proofpoint.com/v2/url?u=http-3A__cwiki.apache.org_confluence_display_MAVEN_UnresolvableModelException&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=_cciP59cAVa5JVLoMznmZU7g0s6FlhjClbuWDboQjkw&s=tY0paD2j0h-Ot0HDbVi8UM20cBgK_zmgAJCMIF5stvw&e=
Re: cTAKES as a dependency
Posted by "Dligach, Dmitriy" <dd...@luc.edu>.
>
> Most likely things are now out-of-sync since we have 4.0.1-SNAPSHOT.
>
Yes, that’s what I thought too at first. I forgot to mention that even if you update everything to the latest version, I still get the same error ("Non-resolvable parent POM…”).
Dima
> Since it is just a sandbox project I didn't pay it any attention wrt the 4.0 release. It probably needs to be updated.
>
> Anyway, you probably get the idea - instead of just adding "ctakes-clinical-pipeline" as a dependency, one can grab this pom, rename and uncomment as necessary.
>
> Thanks for the update. When Trump lands us on Mars I'll update the sandbox project.
>
> Sean
>
> -----Original Message-----
> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
> Sent: Friday, April 28, 2017 6:00 PM
> To: dev@ctakes.apache.org
> Subject: Re: cTAKES as a dependency
>
> Hi Sean,
>
>
>
> Thanks for the pointers.
>
>
>
>> There is a tiny module in ctakes sandbox named ctakes-the-api. It consists of a simple pom.xml that can be used to do exactly what interests you. Download that pom and look at the comments inside. It should be pretty self-explanatory.
>
>
>
> I tried this. It works, but only if I run ‘mvn clean compile’ in ctakes trunk first (which deposits a bunch of jars into my .m2 directory). If I remove .m2 and try to build an empty directory with you pom.xml file, I get an error (pasted below). Is it possible it build fine on your end because there’s already ctakes-related stuff in your .m2?
>
>
>
> [INFO] Scanning for projects...
>
> [ERROR] [ERROR] Some problems were encountered while processing the POMs:
>
> [FATAL] Non-resolvable parent POM for org.apache.ctakes:ctakes-the-api:[unknown-version]: Could not find artifact org.apache.ctakes:ctakes:pom:3.2.3-SNAPSHOT and 'parent.relativePath' points at wrong local POM @ line 6, column 12
>
> @
>
> [ERROR] The build could not read 1 project -> [Help 1]
>
> [ERROR]
>
> [ERROR] The project org.apache.ctakes:ctakes-the-api:[unknown-version] (/home/dima/Temp/pom.xml) has 1 error
>
> [ERROR] Non-resolvable parent POM for org.apache.ctakes:ctakes-the-api:[unknown-version]: Could not find artifact org.apache.ctakes:ctakes:pom:3.2.3-SNAPSHOT and 'parent.relativePath' points at wrong local POM @ line 6, column 12 -> [Help 2]
>
> [ERROR]
>
> [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
>
> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
>
> [ERROR]
>
> [ERROR] For more information about the errors and possible solutions, please read the following articles:
>
> [ERROR] [Help 1] https://urldefense.proofpoint.com/v2/url?u=http-3A__cwiki.apache.org_confluence_display_MAVEN_ProjectBuildingException&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=_cciP59cAVa5JVLoMznmZU7g0s6FlhjClbuWDboQjkw&s=Vaf6Gt1ysN0Lsva2fO-HqYsucLD39WUyqox3r1K9uxU&e=
>
> [ERROR] [Help 2] https://urldefense.proofpoint.com/v2/url?u=http-3A__cwiki.apache.org_confluence_display_MAVEN_UnresolvableModelException&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=_cciP59cAVa5JVLoMznmZU7g0s6FlhjClbuWDboQjkw&s=tY0paD2j0h-Ot0HDbVi8UM20cBgK_zmgAJCMIF5stvw&e=
RE: cTAKES as a dependency
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Dima,
Most likely things are now out-of-sync since we have 4.0.1-SNAPSHOT.
Since it is just a sandbox project I didn't pay it any attention wrt the 4.0 release. It probably needs to be updated.
Anyway, you probably get the idea - instead of just adding "ctakes-clinical-pipeline" as a dependency, one can grab this pom, rename and uncomment as necessary.
Thanks for the update. When Trump lands us on Mars I'll update the sandbox project.
Sean
-----Original Message-----
From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
Sent: Friday, April 28, 2017 6:00 PM
To: dev@ctakes.apache.org
Subject: Re: cTAKES as a dependency
Hi Sean,
Thanks for the pointers.
> There is a tiny module in ctakes sandbox named ctakes-the-api. It consists of a simple pom.xml that can be used to do exactly what interests you. Download that pom and look at the comments inside. It should be pretty self-explanatory.
I tried this. It works, but only if I run ‘mvn clean compile’ in ctakes trunk first (which deposits a bunch of jars into my .m2 directory). If I remove .m2 and try to build an empty directory with you pom.xml file, I get an error (pasted below). Is it possible it build fine on your end because there’s already ctakes-related stuff in your .m2?
[INFO] Scanning for projects...
[ERROR] [ERROR] Some problems were encountered while processing the POMs:
[FATAL] Non-resolvable parent POM for org.apache.ctakes:ctakes-the-api:[unknown-version]: Could not find artifact org.apache.ctakes:ctakes:pom:3.2.3-SNAPSHOT and 'parent.relativePath' points at wrong local POM @ line 6, column 12
@
[ERROR] The build could not read 1 project -> [Help 1]
[ERROR]
[ERROR] The project org.apache.ctakes:ctakes-the-api:[unknown-version] (/home/dima/Temp/pom.xml) has 1 error
[ERROR] Non-resolvable parent POM for org.apache.ctakes:ctakes-the-api:[unknown-version]: Could not find artifact org.apache.ctakes:ctakes:pom:3.2.3-SNAPSHOT and 'parent.relativePath' points at wrong local POM @ line 6, column 12 -> [Help 2]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] https://urldefense.proofpoint.com/v2/url?u=http-3A__cwiki.apache.org_confluence_display_MAVEN_ProjectBuildingException&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=_cciP59cAVa5JVLoMznmZU7g0s6FlhjClbuWDboQjkw&s=Vaf6Gt1ysN0Lsva2fO-HqYsucLD39WUyqox3r1K9uxU&e=
[ERROR] [Help 2] https://urldefense.proofpoint.com/v2/url?u=http-3A__cwiki.apache.org_confluence_display_MAVEN_UnresolvableModelException&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=_cciP59cAVa5JVLoMznmZU7g0s6FlhjClbuWDboQjkw&s=tY0paD2j0h-Ot0HDbVi8UM20cBgK_zmgAJCMIF5stvw&e=
Re: cTAKES as a dependency
Posted by "Dligach, Dmitriy" <dd...@luc.edu>.
Hi Sean,
Thanks for the pointers.
> There is a tiny module in ctakes sandbox named ctakes-the-api. It consists of a simple pom.xml that can be used to do exactly what interests you. Download that pom and look at the comments inside. It should be pretty self-explanatory.
I tried this. It works, but only if I run ‘mvn clean compile’ in ctakes trunk first (which deposits a bunch of jars into my .m2 directory). If I remove .m2 and try to build an empty directory with you pom.xml file, I get an error (pasted below). Is it possible it build fine on your end because there’s already ctakes-related stuff in your .m2?
[INFO] Scanning for projects...
[ERROR] [ERROR] Some problems were encountered while processing the POMs:
[FATAL] Non-resolvable parent POM for org.apache.ctakes:ctakes-the-api:[unknown-version]: Could not find artifact org.apache.ctakes:ctakes:pom:3.2.3-SNAPSHOT and 'parent.relativePath' points at wrong local POM @ line 6, column 12
@
[ERROR] The build could not read 1 project -> [Help 1]
[ERROR]
[ERROR] The project org.apache.ctakes:ctakes-the-api:[unknown-version] (/home/dima/Temp/pom.xml) has 1 error
[ERROR] Non-resolvable parent POM for org.apache.ctakes:ctakes-the-api:[unknown-version]: Could not find artifact org.apache.ctakes:ctakes:pom:3.2.3-SNAPSHOT and 'parent.relativePath' points at wrong local POM @ line 6, column 12 -> [Help 2]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException
[ERROR] [Help 2] http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException
RE: cTAKES as a dependency
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Sally,
Many thanks. As far as I know our pmc has no formal process for adding 3rd party mentions no the website. So I just wrote a howbout email to the @private and we shall see what happens. If we already do have some process then I'm sure that one of them will let me know.
You have been a great help!
Sean
-----Original Message-----
From: Sally Khudairi [mailto:sk@apache.org]
Sent: Monday, May 01, 2017 9:25 AM
To: Savova, Guergana; dev@ctakes.apache.org
Subject: Re: cTAKES as a dependency
Thanks so much, Guergana, and hello, everyone.
Yes, by all means --we encourage users of Apache projects to be added to their "Used/Powered By" lists and use the "Powered By" logo as well.
There is no formal vetting process by ASF Marketing & Publicity; it's actually up to each Apache project to decide how to best maintain their user lists.
So back to you, Guergana: however the PMC updates their site content, feel free to go ahead. Some projects have a specific process for site updates (and assigned individuals with editing credentials), so I'd start with the PMC to see how this can be done.
Warmest regards,
Sally
- - -
Vice President Marketing & Publicity
The Apache Software Foundation
Tel +1 617 921 8656
Skype sallykhudairi
On Mon, May 1, 2017, at 08:52, Savova, Guergana wrote:
> We probably need to reach out to Sally Khudairi for guidance (copied).
>
> Sally,
> What would be your recommendation?
> Thanks,
> --Guergana
>
>
> Guergana Savova, PhD, FACMI
> Associate Professor
> PI Natural Language Processing Lab
> Boston Children's Hospital and Harvard Medical School
> 300 Longwood Avenue
> Mailstop: BCH3092
> Enders 144.1
> Boston, MA 02115
> Tel: (617) 919-2972
> Fax: (617) 730-0817
> Guergana.Savova@childrens.harvard.edu
> Harvard Scholar: https://urldefense.proofpoint.com/v2/url?u=http-3A__scholar.harvard.edu_guergana-5Fk-5Fsavova_biocv&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=w0fPa3mfkGjZfYSzUtAcqQDqeeqSsmqE71AwHMnoopw&s=yeGBq8FL6fG6sJNiYBaGrP4dZ7bjY8SM8rkJ2MmbDGo&e=
> https://urldefense.proofpoint.com/v2/url?u=http-3A__ctakes.apache.org&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=w0fPa3mfkGjZfYSzUtAcqQDqeeqSsmqE71AwHMnoopw&s=dGrqp2TJ0pVTKfotsQO6bMZ80Uk55E1JrosDiNlY8vQ&e=
> https://urldefense.proofpoint.com/v2/url?u=http-3A__thyme.healthnlp.or
> g&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZst
> TpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=w0fPa3mfkGjZfYSzUtAcqQDqeeqSsmqE71A
> wHMnoopw&s=rFXqUEjWEjwD8x5q8nCcjfgbiq2MMygEpwa8pE15KXU&e=
> https://urldefense.proofpoint.com/v2/url?u=http-3A__cancer.healthnlp.o
> rg&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZs
> tTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=w0fPa3mfkGjZfYSzUtAcqQDqeeqSsmqE71
> AwHMnoopw&s=6zXsieePXc_j4DP8yh3QNsBF9qxwnuDJFZFN5JpDmsQ&e=
> https://urldefense.proofpoint.com/v2/url?u=http-3A__share.healthnlp.org&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=w0fPa3mfkGjZfYSzUtAcqQDqeeqSsmqE71AwHMnoopw&s=OsFvXX2g0Ap0d_wEaiFA05svwk4zwxxIb-9YvTsuL7I&e=
> https://urldefense.proofpoint.com/v2/url?u=http-3A__center.healthnlp.org&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=w0fPa3mfkGjZfYSzUtAcqQDqeeqSsmqE71AwHMnoopw&s=FYlVTUtO7S8Vj6vFZxnQS2Vgf3rQMYNUQNoCuNjiYRA&e=
>
>
>
> -----Original Message-----
> From: Kean Kaufmann [mailto:kean@recordsone.com]
> Sent: Monday, May 1, 2017 8:46 AM
> To: dev@ctakes.apache.org
> Subject: Re: cTAKES as a dependency
>
> >
> > On Fri, Apr 28, 2017 at 9:53 PM, Finan, Sean <
> > Sean.Finan@childrens.harvard.edu> wrote:
> >
> Hey Kean,
> >
> > It is great to know that your project is out there!
> >
>
> Hey Sean! Very kind of you. Speaking of which, our BizDevVeep would
> like to see RecordsOne listed under "Companies" on the "Users of cTAKES"
> page:
> https://urldefense.proofpoint.com/v2/url?u=http-3A__ctakes.apache.org_
> usedby.html&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=S
> eLHlpmrGNnJ9mI2WCgf_wwQk9zL4aIrVmfBoSi-j0kfEcrO4yRGmRCJNAr-rCmP&m=L8s4
> 22nQDPgdtmXx1GSp0EjFwLprtxHkVqV02XoSOl8&s=bxgVB9OYUOWATh5aPUDwAscheOLC
> 1vy_fj73rED16ZU&e=
> . Who should I ask about that?
>
> Many thanks...
Re: cTAKES as a dependency
Posted by Sally Khudairi <sk...@apache.org>.
Thanks so much, Guergana, and hello, everyone.
Yes, by all means --we encourage users of Apache projects to be added to
their "Used/Powered By" lists and use the "Powered By" logo as well.
There is no formal vetting process by ASF Marketing & Publicity; it's
actually up to each Apache project to decide how to best maintain their
user lists.
So back to you, Guergana: however the PMC updates their site content,
feel free to go ahead. Some projects have a specific process for site
updates (and assigned individuals with editing credentials), so I'd
start with the PMC to see how this can be done.
Warmest regards,
Sally
- - -
Vice President Marketing & Publicity
The Apache Software Foundation
Tel +1 617 921 8656
Skype sallykhudairi
On Mon, May 1, 2017, at 08:52, Savova, Guergana wrote:
> We probably need to reach out to Sally Khudairi for guidance (copied).
>
> Sally,
> What would be your recommendation?
> Thanks,
> --Guergana
>
>
> Guergana Savova, PhD, FACMI
> Associate Professor
> PI Natural Language Processing Lab
> Boston Children's Hospital and Harvard Medical School
> 300 Longwood Avenue
> Mailstop: BCH3092
> Enders 144.1
> Boston, MA 02115
> Tel: (617) 919-2972
> Fax: (617) 730-0817
> Guergana.Savova@childrens.harvard.edu
> Harvard Scholar: http://scholar.harvard.edu/guergana_k_savova/biocv
> http://ctakes.apache.org
> http://thyme.healthnlp.org
> http://cancer.healthnlp.org
> http://share.healthnlp.org
> http://center.healthnlp.org
>
>
>
> -----Original Message-----
> From: Kean Kaufmann [mailto:kean@recordsone.com]
> Sent: Monday, May 1, 2017 8:46 AM
> To: dev@ctakes.apache.org
> Subject: Re: cTAKES as a dependency
>
> >
> > On Fri, Apr 28, 2017 at 9:53 PM, Finan, Sean <
> > Sean.Finan@childrens.harvard.edu> wrote:
> >
> Hey Kean,
> >
> > It is great to know that your project is out there!
> >
>
> Hey Sean! Very kind of you. Speaking of which, our BizDevVeep would
> like to see RecordsOne listed under "Companies" on the "Users of cTAKES"
> page:
> https://urldefense.proofpoint.com/v2/url?u=http-3A__ctakes.apache.org_usedby.html&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=SeLHlpmrGNnJ9mI2WCgf_wwQk9zL4aIrVmfBoSi-j0kfEcrO4yRGmRCJNAr-rCmP&m=L8s422nQDPgdtmXx1GSp0EjFwLprtxHkVqV02XoSOl8&s=bxgVB9OYUOWATh5aPUDwAscheOLC1vy_fj73rED16ZU&e=
> . Who should I ask about that?
>
> Many thanks...
RE: cTAKES as a dependency
Posted by "Savova, Guergana" <Gu...@childrens.harvard.edu>.
We probably need to reach out to Sally Khudairi for guidance (copied).
Sally,
What would be your recommendation?
Thanks,
--Guergana
Guergana Savova, PhD, FACMI
Associate Professor
PI Natural Language Processing Lab
Boston Children's Hospital and Harvard Medical School
300 Longwood Avenue
Mailstop: BCH3092
Enders 144.1
Boston, MA 02115
Tel: (617) 919-2972
Fax: (617) 730-0817
Guergana.Savova@childrens.harvard.edu
Harvard Scholar: http://scholar.harvard.edu/guergana_k_savova/biocv
http://ctakes.apache.org
http://thyme.healthnlp.org
http://cancer.healthnlp.org
http://share.healthnlp.org
http://center.healthnlp.org
-----Original Message-----
From: Kean Kaufmann [mailto:kean@recordsone.com]
Sent: Monday, May 1, 2017 8:46 AM
To: dev@ctakes.apache.org
Subject: Re: cTAKES as a dependency
>
> On Fri, Apr 28, 2017 at 9:53 PM, Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
>
Hey Kean,
>
> It is great to know that your project is out there!
>
Hey Sean! Very kind of you. Speaking of which, our BizDevVeep would like to see RecordsOne listed under "Companies" on the "Users of cTAKES" page:
https://urldefense.proofpoint.com/v2/url?u=http-3A__ctakes.apache.org_usedby.html&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=SeLHlpmrGNnJ9mI2WCgf_wwQk9zL4aIrVmfBoSi-j0kfEcrO4yRGmRCJNAr-rCmP&m=L8s422nQDPgdtmXx1GSp0EjFwLprtxHkVqV02XoSOl8&s=bxgVB9OYUOWATh5aPUDwAscheOLC1vy_fj73rED16ZU&e= . Who should I ask about that?
Many thanks...
Re: cTAKES as a dependency
Posted by Kean Kaufmann <ke...@recordsone.com>.
>
> On Fri, Apr 28, 2017 at 9:53 PM, Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
>
Hey Kean,
>
> It is great to know that your project is out there!
>
Hey Sean! Very kind of you. Speaking of which, our BizDevVeep would like
to see RecordsOne listed under "Companies" on the "Users of cTAKES" page:
http://ctakes.apache.org/usedby.html . Who should I ask about that?
Many thanks...
RE: cTAKES as a dependency
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hey Kean,
It is great to know that your project is out there!
Cheers,
Sean
-----Original Message-----
From: Kean Kaufmann [mailto:kean@recordsone.com]
Sent: Friday, April 28, 2017 9:10 PM
To: dev@ctakes.apache.org
Subject: Re: cTAKES as a dependency
Sorry to be late to the thread!
Dima asks:
is it possible to set up a maven project that will use cTAKES as an
> external dependency?
Sean answers:
just add ctakes poms as dependencies.
I chime in: Yes, that's what we do. Don't know what's going on with the ctakes-the-api module, but here's a good starting point:
https://urldefense.proofpoint.com/v2/url?u=https-3A__libraries.io_github_acstevens_ctakes-2Dstandalone-2Dapplication&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=76EOuwGjH4TpgLdEkOLV_btVJOp25nBsLNBm6ir6rF0&s=o2jjVMiteD-kPkdek6YU2P7IPSF8VaY-FeZNqURVlkk&e=
I swapped in 4.0.0 for ctakes.version, removed my .m2 directory, and it compiled fine.
On Fri, Apr 14, 2017 at 11:04 AM, Finan, Sean < Sean.Finan@childrens.harvard.edu> wrote:
> Yes indeed. The chip-nlp and upmc Deep Phenome team uses ctakes as a
> maven dependency.
>
> If the project uses maven just add ctakes poms as dependencies. For
> instance, if you want to add everything necessary for the clinical pipeline:
> <dependency>
> <groupId>org.apache.ctakes</groupId>
> <artifactId>ctakes-clinical-pipeline</artifactId>
> <version>${ctakes.version}</version>
> </dependency>
>
> To add individual modules:
> <dependency>
> <groupId>org.apache.ctakes</groupId>
> <artifactId>ctakes-temporal</artifactId>
> <version>${ctakes.version}</version>
> </dependency>
>
> Either hardcode the version or use (with your desired version):
> <properties>
> <ctakes.version>3.2.3-SNAPSHOT</ctakes.version>
> ...
> </properties>
>
> You can find the available modules here:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mvnrepository.com
> _artifact_org.apache.ctakes&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZM
> SdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=76EOuwGjH
> 4TpgLdEkOLV_btVJOp25nBsLNBm6ir6rF0&s=Yggvxb1ODNONRa6xAbTktVeWdc22pwlaN
> Iiol6jZ71M&e=
>
> There is a tiny module in ctakes sandbox named ctakes-the-api. It
> consists of a simple pom.xml that can be used to do exactly what
> interests you. Download that pom and look at the comments inside. It
> should be pretty self-explanatory.
>
> If you aren't using maven you can download the jar files that you want
> from the same site
> (https://urldefense.proofpoint.com/v2/url?u=https-3A__mvnrepository.co
> m_artifact_org.apache.ctakes&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZ
> MSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=76EOuwGj
> H4TpgLdEkOLV_btVJOp25nBsLNBm6ir6rF0&s=Yggvxb1ODNONRa6xAbTktVeWdc22pwla
> NIiol6jZ71M&e= ). Click on a module then a version. There will be
> -code- for various build systems.
> If your build is manual, click "Download (JAR)". If you go the jar
> route you will also need to download all of the "compile dependencies" below.
>
> Sean
>
>
> -----Original Message-----
> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
> Sent: Friday, April 14, 2017 10:48 AM
> To: cTAKES Developer list
> Subject: cTAKES as a dependency
>
> Hello,
>
> Has anybody tried to run a cTAKES pipeline without having a local
> cTAKES installation? In other words, is it possible to set up a maven
> project that will use cTAKES as an external dependency?
>
> Dima
>
>
>
>
--
_____________________________________________________
*Kean Kaufmann*
NLP Developer
RecordsOne
nSight Driven | *Priority. Clarity. Integrity. *
*mobile* |
240-401-6131
*Twitter: **@R1_RecordsOne*
*See us in Vegas @ ACDIS 2017 *
*See us in Los Angeles @ AHIMA 2017*
---------------------------------------------------------------------------------------------------
*Confidentiality Notice: *This email, including any attachments is the property of RecordsOne, LLC and is intended for the sole use of the intended recipient(s). It may contain information that is privileged and confidential. Any unauthorized review, use, disclosure, or distribution is prohibited. If you are not the intended recipient, please reply to the sender that you have received the message in error, then delete this message.
---------------------------------------------------------------------------------------------------
*Mailing*: 10641 Airport Pulling Road, Suite 30 | Naples, FL 34109
*Main*: 239.451.6112
*Please consider the environmental impact before printing this email. *
Re: cTAKES as a dependency
Posted by Kean Kaufmann <ke...@recordsone.com>.
Sorry to be late to the thread!
Dima asks:
is it possible to set up a maven project that will use cTAKES as an
> external dependency?
Sean answers:
just add ctakes poms as dependencies.
I chime in: Yes, that's what we do. Don't know what's going on with the
ctakes-the-api module, but here's a good starting point:
https://libraries.io/github/acstevens/ctakes-standalone-application
I swapped in 4.0.0 for ctakes.version, removed my .m2 directory, and it
compiled fine.
On Fri, Apr 14, 2017 at 11:04 AM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:
> Yes indeed. The chip-nlp and upmc Deep Phenome team uses ctakes as a
> maven dependency.
>
> If the project uses maven just add ctakes poms as dependencies. For
> instance, if you want to add everything necessary for the clinical pipeline:
> <dependency>
> <groupId>org.apache.ctakes</groupId>
> <artifactId>ctakes-clinical-pipeline</artifactId>
> <version>${ctakes.version}</version>
> </dependency>
>
> To add individual modules:
> <dependency>
> <groupId>org.apache.ctakes</groupId>
> <artifactId>ctakes-temporal</artifactId>
> <version>${ctakes.version}</version>
> </dependency>
>
> Either hardcode the version or use (with your desired version):
> <properties>
> <ctakes.version>3.2.3-SNAPSHOT</ctakes.version>
> ...
> </properties>
>
> You can find the available modules here:
> https://mvnrepository.com/artifact/org.apache.ctakes
>
> There is a tiny module in ctakes sandbox named ctakes-the-api. It
> consists of a simple pom.xml that can be used to do exactly what interests
> you. Download that pom and look at the comments inside. It should be
> pretty self-explanatory.
>
> If you aren't using maven you can download the jar files that you want
> from the same site (https://mvnrepository.com/artifact/org.apache.ctakes
> ). Click on a module then a version. There will be -code- for various
> build systems.
> If your build is manual, click "Download (JAR)". If you go the jar route
> you will also need to download all of the "compile dependencies" below.
>
> Sean
>
>
> -----Original Message-----
> From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
> Sent: Friday, April 14, 2017 10:48 AM
> To: cTAKES Developer list
> Subject: cTAKES as a dependency
>
> Hello,
>
> Has anybody tried to run a cTAKES pipeline without having a local cTAKES
> installation? In other words, is it possible to set up a maven project that
> will use cTAKES as an external dependency?
>
> Dima
>
>
>
>
--
_____________________________________________________
*Kean Kaufmann*
NLP Developer
RecordsOne
nSight Driven | *Priority. Clarity. Integrity. *
*mobile* |
240-401-6131
*Twitter: **@R1_RecordsOne*
*See us in Vegas @ ACDIS 2017 *
*See us in Los Angeles @ AHIMA 2017*
---------------------------------------------------------------------------------------------------
*Confidentiality Notice: *This email, including any attachments is the
property of RecordsOne, LLC and is intended for the sole use of the
intended recipient(s). It may contain information that is privileged and
confidential. Any unauthorized review, use, disclosure, or distribution is
prohibited. If you are not the intended recipient, please reply to the
sender that you have received the message in error, then delete this
message.
---------------------------------------------------------------------------------------------------
*Mailing*: 10641 Airport Pulling Road, Suite 30 | Naples, FL 34109
*Main*: 239.451.6112
*Please consider the environmental impact before printing this email. *
RE: cTAKES as a dependency
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Yes indeed. The chip-nlp and upmc Deep Phenome team uses ctakes as a maven dependency.
If the project uses maven just add ctakes poms as dependencies. For instance, if you want to add everything necessary for the clinical pipeline:
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-clinical-pipeline</artifactId>
<version>${ctakes.version}</version>
</dependency>
To add individual modules:
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-temporal</artifactId>
<version>${ctakes.version}</version>
</dependency>
Either hardcode the version or use (with your desired version):
<properties>
<ctakes.version>3.2.3-SNAPSHOT</ctakes.version>
...
</properties>
You can find the available modules here:
https://mvnrepository.com/artifact/org.apache.ctakes
There is a tiny module in ctakes sandbox named ctakes-the-api. It consists of a simple pom.xml that can be used to do exactly what interests you. Download that pom and look at the comments inside. It should be pretty self-explanatory.
If you aren't using maven you can download the jar files that you want from the same site (https://mvnrepository.com/artifact/org.apache.ctakes ). Click on a module then a version. There will be -code- for various build systems.
If your build is manual, click "Download (JAR)". If you go the jar route you will also need to download all of the "compile dependencies" below.
Sean
-----Original Message-----
From: Dligach, Dmitriy [mailto:ddligach@luc.edu]
Sent: Friday, April 14, 2017 10:48 AM
To: cTAKES Developer list
Subject: cTAKES as a dependency
Hello,
Has anybody tried to run a cTAKES pipeline without having a local cTAKES installation? In other words, is it possible to set up a maven project that will use cTAKES as an external dependency?
Dima
Re: cTAKES as a dependency
Posted by James Masanz <ma...@gmail.com>.
Prior to 4.0 there was a problem with some dependencies not being in maven
- there were in local lib directory instead. Those dependencies were
removed for 4.0 and there are no "system" dependencies in 4.0
I haven't tested it yet, but if you are using the fast dictionary
lookup, setting
up a maven project that will use cTAKES as an external dependency should
work for 4.0.0 rc2.
For rc2, I noticed some poms for the original dictionary lookup had not
been updated yet, and the original dictionary won't run using maven
dependencies for rc2 because the resources it points to are using hsqldb
1.8. This morning I made a change to some POMs that will be needed for
using the original dictionary lookup. And those resources need to be
pushed to maven central.
The system dependencies needed prior to 4.0 are
<dependency>
<groupId>org.mitre.medfacts</groupId>
<artifactId>medfacts-i2b2</artifactId>
<version>1.2</version>
<scope>system</scope>
<systemPath>
${project.basedir}/lib/med-facts-i2b2-1.2-SNAPSHOT.jar
</systemPath>
</dependency>
<dependency>
<groupId>org.mitre.medfacts</groupId>
<artifactId>medfacts-zoner</artifactId>
<version>1.1</version>
<scope>system</scope>
<systemPath>${project.basedir}/lib/med-facts-zoner-1.1.jar</systemPath>
</dependency>
<dependency>
<groupId>org.mitre.jcarafe.core</groupId>
<artifactId>jcarafe.core</artifactId>
<version>2.9.1</version>
<scope>system</scope>
<systemPath>
${project.basedir}/lib/jcarafe-core_2.9.1-0.9.8.3.RC4.jar
</systemPath>
</dependency>
<dependency>
<groupId>org.mitre.jcarafe.ext</groupId>
<artifactId>jcarafe.ext</artifactId>
<version>2.9.1</version>
<scope>system</scope>
<systemPath>
${project.basedir}/lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar
</systemPath>
</dependency>
That was taken from:
https://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.2.2-rc2/ctakes-assertion/pom.xml
Hope this helps,
James
On Fri, Apr 14, 2017 at 10:48 AM, Dligach, Dmitriy <dd...@luc.edu> wrote:
> Hello,
>
> Has anybody tried to run a cTAKES pipeline without having a local cTAKES
> installation? In other words, is it possible to set up a maven project that
> will use cTAKES as an external dependency?
>
> Dima
>
>
>
>