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Posted to dev@ctakes.apache.org by Thomas W Loehfelm <tw...@ucdavis.edu> on 2017/04/26 22:21:30 UTC
ctakes 4.0.1 - Install experience
First off, thank you all and congratulations on this major release milestone.
I went through the dev install on a clean Ubuntu 17.04 desktop VM and while things went pretty smoothly I had a few comments to add in case others are going through the same process:
1. I received an error message when trying to runCVD due to a missing dependency version in the clinical pipeline pom.xml file
* Error message:
"The project org.apache.ctakes:ctakes-clinical-pipeline:4.0.1-SNAPSHOT (<my ctakes dir>) has 1 error
'build.plugins.plugin[org.codehaus.mojo:exec-maven-plugin].dependencies.dependency.version' for gov.nih.nlm.nls.lvg:lvgdist:jar is missing. @ org.apache.ctakes:ctakes-clinical-pipeline:[unknown-version], <my ctakes dir>/ctakes-clinical-pipeline/pom.xml, line 174, column 20
* Fix:
Add "<version>2016.0</version>" for that dependency in pom.xml (line 177)
2. I had to uncheck the box "Use command line client: [svn]" at File>Settings>Version Control>Subversion before I could checkout the project. I don't know Subversion or IntelliJ well enough to know whether this is idiosyncratic to my environment. Consider adding is as Step 2 for IntelliJ install instructions under "Perform a fresh checkout from SVN" right after "1. Start IntelliJ IDEA" in case it is a more global issue.
3. I decided to switch from Eclipse to IntelliJ for this fresh install and wasn't sure where to add my umlsuser and pw in IntelliJ. I ended up finding File>Settings>Build,Execution,Deployment>Build Tools>Maven>Runner>VM Options and put them there: -Dctakes.umlsuser=<> -Dctakes.umlspw=<>
Those were the only minor stumbles along the way.
Tom
RE: ctakes 4.0.1 - Install experience
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Tom,
A thousand thanks for the testing and problem report. I will (at some point today) update the documentation based upon your information. I never noticed that lvg version error. Poor/incomplete testing on my part - we may need to create an immediate patch for that one.
Sean
p.s. congrats on the switch to intellij ...
In the "run configuration" panel there is an "environment variables" area where you can enter a table of names and values. That is possibly the easiest place to set ctakes.umlsuser etc. Otherwise, you can use the "command options" (or similar) box in that same panel to list them as you would on a command line. You can also set "vm options" -Xmx3G in that same dialog. When I run/test different classes, I open run configurations and copy an existing one, then just change the starting class or i/o or whatever. Another useful item in that panel is the option to pipe logging to a file. In some longer runs that really comes in handy.
The svn built-in vs. external (command line) is up to the user/env. I have an external client that I use. I will document the difference on the dev setup page.
-----Original Message-----
From: Thomas W Loehfelm [mailto:twloehfelm@ucdavis.edu]
Sent: Wednesday, April 26, 2017 6:22 PM
To: dev@ctakes.apache.org
Subject: ctakes 4.0.1 - Install experience
First off, thank you all and congratulations on this major release milestone.
I went through the dev install on a clean Ubuntu 17.04 desktop VM and while things went pretty smoothly I had a few comments to add in case others are going through the same process:
1. I received an error message when trying to runCVD due to a missing dependency version in the clinical pipeline pom.xml file
* Error message:
"The project org.apache.ctakes:ctakes-clinical-pipeline:4.0.1-SNAPSHOT (<my ctakes dir>) has 1 error 'build.plugins.plugin[org.codehaus.mojo:exec-maven-plugin].dependencies.dependency.version' for gov.nih.nlm.nls.lvg:lvgdist:jar is missing. @ org.apache.ctakes:ctakes-clinical-pipeline:[unknown-version], <my ctakes dir>/ctakes-clinical-pipeline/pom.xml, line 174, column 20
* Fix:
Add "<version>2016.0</version>" for that dependency in pom.xml (line 177)
2. I had to uncheck the box "Use command line client: [svn]" at File>Settings>Version Control>Subversion before I could checkout the project. I don't know Subversion or IntelliJ well enough to know whether this is idiosyncratic to my environment. Consider adding is as Step 2 for IntelliJ install instructions under "Perform a fresh checkout from SVN" right after "1. Start IntelliJ IDEA" in case it is a more global issue.
3. I decided to switch from Eclipse to IntelliJ for this fresh install and wasn't sure where to add my umlsuser and pw in IntelliJ. I ended up finding File>Settings>Build,Execution,Deployment>Build Tools>Maven>Runner>VM Options and put them there: -Dctakes.umlsuser=<> -Dctakes.umlspw=<>
Those were the only minor stumbles along the way.
Tom
RE: ctakes 4.0.1 - Install experience
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
I ran a one xmi cvd test and an old desc cpe test. That isn't exactly thorough for removing a dependency declaration.
How does everybody feel about removing the lvg-dist in trunk? We can release an "immediate" patch with v.2016 declared just in case it is needed.
Sean
-----Original Message-----
From: James Masanz [mailto:masanz.james@gmail.com]
Sent: Thursday, April 27, 2017 2:26 PM
To: dev@ctakes.apache.org
Subject: Re: ctakes 4.0.1 - Install experience
Looks like it's a left over from when we switched from using a local copy of LVG jar in a local lib directory to using a maven dependency several years ago.
When I updated the artifactId and version of lvg for cTAKES 4.0, I didn't consider whether the explicit reference could be removed from that profile.
On Thu, Apr 27, 2017 at 2:09 PM, Finan, Sean < Sean.Finan@childrens.harvard.edu> wrote:
> Dear ctakers:
>
> Does anybody know why the CVD profile (and CPE) in the
> clinical-pipeline pom.xml has an explicit dependency on lvg-dist? It
> doesn't make sense to me and I can run through a typical workflow without it.
>
> Thanks,
> Sean
>
> -----Original Message-----
> From: Thomas W Loehfelm [mailto:twloehfelm@ucdavis.edu]
> Sent: Wednesday, April 26, 2017 6:22 PM
> To: dev@ctakes.apache.org
> Subject: ctakes 4.0.1 - Install experience
>
> First off, thank you all and congratulations on this major release
> milestone.
>
> I went through the dev install on a clean Ubuntu 17.04 desktop VM and
> while things went pretty smoothly I had a few comments to add in case
> others are going through the same process:
>
> 1. I received an error message when trying to runCVD due to a
> missing dependency version in the clinical pipeline pom.xml file
> * Error message:
> "The project org.apache.ctakes:ctakes-clinical-pipeline:4.0.1-SNAPSHOT
> (<my ctakes dir>) has 1 error 'build.plugins.plugin[org.
> codehaus.mojo:exec-maven-plugin].dependencies.dependency.version' for
> gov.nih.nlm.nls.lvg:lvgdist:jar is missing. @
> org.apache.ctakes:ctakes- clinical-pipeline:[unknown-version], <my
> ctakes
> dir>/ctakes-clinical-pipeline/pom.xml, line 174, column 20
> * Fix:
> Add "<version>2016.0</version>" for that dependency in pom.xml (line 177)
> 2. I had to uncheck the box "Use command line client: [svn]" at
> File>Settings>Version Control>Subversion before I could checkout the
> project. I don't know Subversion or IntelliJ well enough to know
> whether this is idiosyncratic to my environment. Consider adding is as
> Step 2 for IntelliJ install instructions under "Perform a fresh checkout from SVN"
> right after "1. Start IntelliJ IDEA" in case it is a more global issue.
> 3. I decided to switch from Eclipse to IntelliJ for this fresh
> install and wasn't sure where to add my umlsuser and pw in IntelliJ. I
> ended up finding File>Settings>Build,Execution,Deployment>Build
> Tools>Maven>Runner>VM Options and put them there: -Dctakes.umlsuser=<>
> -Dctakes.umlspw=<>
>
> Those were the only minor stumbles along the way.
>
> Tom
>
Re: ctakes 4.0.1 - Install experience
Posted by James Masanz <ma...@gmail.com>.
Looks like it's a left over from when we switched from using a local copy
of LVG jar in a local lib directory to using a maven dependency several
years ago.
When I updated the artifactId and version of lvg for cTAKES 4.0, I didn't
consider whether the explicit reference could be removed from that profile.
On Thu, Apr 27, 2017 at 2:09 PM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:
> Dear ctakers:
>
> Does anybody know why the CVD profile (and CPE) in the clinical-pipeline
> pom.xml has an explicit dependency on lvg-dist? It doesn't make sense to
> me and I can run through a typical workflow without it.
>
> Thanks,
> Sean
>
> -----Original Message-----
> From: Thomas W Loehfelm [mailto:twloehfelm@ucdavis.edu]
> Sent: Wednesday, April 26, 2017 6:22 PM
> To: dev@ctakes.apache.org
> Subject: ctakes 4.0.1 - Install experience
>
> First off, thank you all and congratulations on this major release
> milestone.
>
> I went through the dev install on a clean Ubuntu 17.04 desktop VM and
> while things went pretty smoothly I had a few comments to add in case
> others are going through the same process:
>
> 1. I received an error message when trying to runCVD due to a missing
> dependency version in the clinical pipeline pom.xml file
> * Error message:
> "The project org.apache.ctakes:ctakes-clinical-pipeline:4.0.1-SNAPSHOT
> (<my ctakes dir>) has 1 error 'build.plugins.plugin[org.
> codehaus.mojo:exec-maven-plugin].dependencies.dependency.version' for
> gov.nih.nlm.nls.lvg:lvgdist:jar is missing. @ org.apache.ctakes:ctakes-
> clinical-pipeline:[unknown-version], <my ctakes
> dir>/ctakes-clinical-pipeline/pom.xml, line 174, column 20
> * Fix:
> Add "<version>2016.0</version>" for that dependency in pom.xml (line 177)
> 2. I had to uncheck the box "Use command line client: [svn]" at
> File>Settings>Version Control>Subversion before I could checkout the
> project. I don't know Subversion or IntelliJ well enough to know whether
> this is idiosyncratic to my environment. Consider adding is as Step 2 for
> IntelliJ install instructions under "Perform a fresh checkout from SVN"
> right after "1. Start IntelliJ IDEA" in case it is a more global issue.
> 3. I decided to switch from Eclipse to IntelliJ for this fresh install
> and wasn't sure where to add my umlsuser and pw in IntelliJ. I ended up
> finding File>Settings>Build,Execution,Deployment>Build
> Tools>Maven>Runner>VM Options and put them there: -Dctakes.umlsuser=<>
> -Dctakes.umlspw=<>
>
> Those were the only minor stumbles along the way.
>
> Tom
>
RE: ctakes 4.0.1 - Install experience
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Dear ctakers:
Does anybody know why the CVD profile (and CPE) in the clinical-pipeline pom.xml has an explicit dependency on lvg-dist? It doesn't make sense to me and I can run through a typical workflow without it.
Thanks,
Sean
-----Original Message-----
From: Thomas W Loehfelm [mailto:twloehfelm@ucdavis.edu]
Sent: Wednesday, April 26, 2017 6:22 PM
To: dev@ctakes.apache.org
Subject: ctakes 4.0.1 - Install experience
First off, thank you all and congratulations on this major release milestone.
I went through the dev install on a clean Ubuntu 17.04 desktop VM and while things went pretty smoothly I had a few comments to add in case others are going through the same process:
1. I received an error message when trying to runCVD due to a missing dependency version in the clinical pipeline pom.xml file
* Error message:
"The project org.apache.ctakes:ctakes-clinical-pipeline:4.0.1-SNAPSHOT (<my ctakes dir>) has 1 error 'build.plugins.plugin[org.codehaus.mojo:exec-maven-plugin].dependencies.dependency.version' for gov.nih.nlm.nls.lvg:lvgdist:jar is missing. @ org.apache.ctakes:ctakes-clinical-pipeline:[unknown-version], <my ctakes dir>/ctakes-clinical-pipeline/pom.xml, line 174, column 20
* Fix:
Add "<version>2016.0</version>" for that dependency in pom.xml (line 177)
2. I had to uncheck the box "Use command line client: [svn]" at File>Settings>Version Control>Subversion before I could checkout the project. I don't know Subversion or IntelliJ well enough to know whether this is idiosyncratic to my environment. Consider adding is as Step 2 for IntelliJ install instructions under "Perform a fresh checkout from SVN" right after "1. Start IntelliJ IDEA" in case it is a more global issue.
3. I decided to switch from Eclipse to IntelliJ for this fresh install and wasn't sure where to add my umlsuser and pw in IntelliJ. I ended up finding File>Settings>Build,Execution,Deployment>Build Tools>Maven>Runner>VM Options and put them there: -Dctakes.umlsuser=<> -Dctakes.umlspw=<>
Those were the only minor stumbles along the way.
Tom