Piper Submitter GUI missing?
Hello, cTakes newbie and big fan so far! I have installed and been using the user version (4.0.0) and the source code as per the developer install guide and have tried a few pipelines. I wanted to use the piper file submitter gui exposed by the developer version but I cannot locate an active profile in Maven for that. I checked the pom.xml (parent , ctakes-gui , ctakes-core etc.) but no profiles listed there either. I can locate the corresponding class in ctakes-gui but no launch folder etc. I could not locate specific instructions in the standard documentation either ... I am using Eclipse 4.16 , maven plugin (also installed Apache Maven separately and run command line from there) and it seems I have the latest trunk version so I am out of ideas at this point and very close to a deadline so any feedback, help comments will be greatly appreciated! Many thanks in advance, Kind Regards, Eugenia Disclaimer: This email and any attachments are sent in strictest confidence for the sole use of the addressee and may contain legally privileged, confidential, and proprietary data. If you are not the intended recipient, please advise the sender by replying promptly to this email and then delete and destroy this email and any attachments without any further use, copying or forwarding.
Re: Changes to UTS Authentication for Authorized Content Distributors [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
That link doesn't say anything there about incremental update releases, but even with the normal process I think we can get 4.0.1 out faster than usual because it is such a small change and there are unlikely to be multiple RCs to get one that works for everyone. Does anyone want to volunteer to be release manager? It needs to be someone on the PMC, so Sean, myself, Gandhi, or Chen probably. Tim On Tue, 2020-11-24 at 18:10 +, Finan, Sean wrote: > * External Email - Caution * > > > > > I haven't looked into whether or not Apache svn servers have a > > > locking mechanism ... > > I think it's worth checking -- if we're allowed to just branch off > > the > > 4.0.0 tag we can get a 4.0.1 distribution that just has this one > > change, and we could have it built and uploaded quickly so we're > > ready > > for the UMLS change. How would we find out? > > A 4.0.1 made directly from 4.0 with only the authentication update is > probably the way to go. > I suppose that for people with dependencies, downloads etc. fixed at > 4.0 would have to get their new umls key and change their ctakes > config anyway, so telling them to update any coded version numbers > doesn't involve too much extra effort. > > The main apache org how to release documentation is at > https://urldefense.proofpoint.com/v2/url?u=https-3A__infra.apache.org_release-2Dpublishing.html&d=DwIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=QVEto_k7Ovh16r4YjW7Uelv9_lDmvjxRwoI2r7_6qBk&s=fjMkpO1i2FXprtFbQ-XJ1cvVlSQ8-uz3gSOBojxNMI8&e= > > I am not sure of anything specifically regarding patches. > I don't know if we need to go through the full process for a point > release ... > > > > From: Miller, Timothy > Sent: Tuesday, November 24, 2020 12:45 PM > To: dev@ctakes.apache.org > Subject: Re: Changes to UTS Authentication for Authorized Content > Distributors [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] > > * External Email - Caution * > > > On Tue, 2020-11-24 at 16:29 +, Finan, Sean wrote: > > * External Email - Caution * > > > > > > Hi Tim and all, > > > > Peter kindly checked this into trunk last week. > > I tested that version and it seemed to work. > > > > Another question might be "how do we get this into the/a release? > > > > I haven't looked into whether or not Apache svn servers have a > > locking mechanism on release branches, but if not I think that a > > patch of 4.0 using the version that you and Greg tested should be a > > simple checkin. > > I think it's worth checking -- if we're allowed to just branch off > the > 4.0.0 tag we can get a 4.0.1 distribution that just has this one > change, and we could have it built and uploaded quickly so we're > ready > for the UMLS change. How would we find out? > > Tim > > > I am sure that everybody is tired of hearing me say this, but I > > would > > like to get out a version 5 asap and disclaim that it is required > > for > > the new umls authentication. That would make patching v4 a non- > > issue. > > > > Regardless of repository inclusion, the documentation (also written > > by Peter) needs to get to the ctakes wiki - and probably the main > > ctakes web site. On that note, the web site needs to be redone > > asap. > > > > Anyway, cheers to Peter for taking upon himself this update! > > We do still have a few things left to do. > > Volunteers? > > > > Sean > > > > > > From: Miller, Timothy > > Sent: Tuesday, November 24, 2020 11:07 AM > > To: dev@ctakes.apache.org > > Subject: Re: Changes to UTS Authentication for Authorized Content > > Distributors [EXTERNAL] [SUSPICIOUS] > > > > * External Email - Caution * > > > > > > Peter, > > I was able to try your changes and get this new authentication > > mechanism to work in the default pipeline. Peter, Sean, et al, what > > are > > the next steps for getting this in to trunk? If you're not > > comfortable > > checking in directly maybe you can share the patch for review. > > Tim > > > > On Sun, 2020-11-15 at 20:54 +0100, Peter Abramowitsch wrote: > > > * External Email - Caution * > > > > > > > > > Hi Greg > > > > > > I've got the modifications finished for the new UMLS > > > authentication > > > method > > > using API keys. If you're game, I'd like you to be next to test > > > it. > > > Contact me at pabramowit...@gmail.com and I'll get you a new > > > ctakes-dictionary-lookup-fast.4.0,1,x,jar and Readme. > > > > > > If it's smooth for you, I'll talk with Sean about checking it in > > > and > > > what > > > wiki locations need to be updated. > > > > > > To get your key you'll need to log into UMLS, If you've not > > > been > > > there > > > recently you'll need to go through their profile upgrade process > > > where user > > > details will be rerouted through one of the public > > > authentication > > > mechanisms. > > > Once in, go to your profile
Re: Piper Submitter GUI missing? [EXTERNAL]
Hi Eugenia,
I am glad that you are a fan!
The trunk version has a profile to start the piper file submitter gui defined
in the ctakes-examples pom.
However, the 4.0 release does not have a profile to do so.
If you want to use a pfs gui profile in 4.0 then you will need to edit a
downstream (like ctakes-clinical-pipeline) pom.xml and add the following
(snippet from ctakes-examples 4.0.1-SNAPSHOT pom.xml) in :
runPiperGui
runPiperGui
org.codehaus.mojo
exec-maven-plugin
exec
java
true
true
${project.parent.basedir}
-classpath
-Xmx3G
org.apache.ctakes.gui.pipeline.PiperRunnerGui
Sean
From: Monogyiou, Eugenia
Sent: Wednesday, November 25, 2020 8:49 AM
To: dev@ctakes.apache.org
Subject: Piper Submitter GUI missing? [EXTERNAL]
* External Email - Caution *
Hello,
cTakes newbie and big fan so far!
I have installed and been using the user version (4.0.0) and the source code as
per the developer install guide and have tried a few pipelines. I wanted to use
the piper file submitter gui exposed by the developer version but I cannot
locate an active profile in Maven for that. I checked the pom.xml (parent ,
ctakes-gui , ctakes-core etc.) but no profiles listed there either. I can
locate the corresponding class in ctakes-gui but no launch folder etc. I could
not locate specific instructions in the standard documentation either ... I am
using Eclipse 4.16 , maven plugin (also installed Apache Maven separately and
run command line from there) and it seems I have the latest trunk version so I
am out of ideas at this point and very close to a deadline so any feedback,
help comments will be greatly appreciated!
Many thanks in advance,
Kind Regards,
Eugenia
Disclaimer: This email and any attachments are sent in strictest confidence for
the sole use of the addressee and may contain legally privileged, confidential,
and proprietary data. If you are not the intended recipient, please advise the
sender by replying promptly to this email and then delete and destroy this
email and any attachments without any further use, copying or forwarding.
Re: Piper Submitter GUI missing? [EXTERNAL] [SUSPICIOUS]
Oh -- ctakes-clinical-pipeline does not have ctakes-gui as a dependency. So if
you want to put the profile in that pom then you will also need to add
ctakes-gui as a dependency in that pom.
From: Finan, Sean
Sent: Wednesday, November 25, 2020 9:30 AM
To: dev@ctakes.apache.org
Subject: Re: Piper Submitter GUI missing? [EXTERNAL] [SUSPICIOUS]
* External Email - Caution *
Hi Eugenia,
I am glad that you are a fan!
The trunk version has a profile to start the piper file submitter gui defined
in the ctakes-examples pom.
However, the 4.0 release does not have a profile to do so.
If you want to use a pfs gui profile in 4.0 then you will need to edit a
downstream (like ctakes-clinical-pipeline) pom.xml and add the following
(snippet from ctakes-examples 4.0.1-SNAPSHOT pom.xml) in :
runPiperGui
runPiperGui
org.codehaus.mojo
exec-maven-plugin
exec
java
true
true
${project.parent.basedir}
-classpath
-Xmx3G
org.apache.ctakes.gui.pipeline.PiperRunnerGui
Sean
From: Monogyiou, Eugenia
Sent: Wednesday, November 25, 2020 8:49 AM
To: dev@ctakes.apache.org
Subject: Piper Submitter GUI missing? [EXTERNAL]
* External Email - Caution *
Hello,
cTakes newbie and big fan so far!
I have installed and been using the user version (4.0.0) and the source code as
per the developer install guide and have tried a few pipelines. I wanted to use
the piper file submitter gui exposed by the developer version but I cannot
locate an active profile in Maven for that. I checked the pom.xml (parent ,
ctakes-gui , ctakes-core etc.) but no profiles listed there either. I can
locate the corresponding class in ctakes-gui but no launch folder etc. I could
not locate specific instructions in the standard documentation either ... I am
using Eclipse 4.16 , maven plugin (also installed Apache Maven separately and
run command line from there) and it seems I have the latest trunk version so I
am out of ideas at this point and very close to a deadline so any feedback,
help comments will be greatly appreciated!
Many thanks in advance,
Kind Regards,
Eugenia
Disclaimer: This email and any attachments are sent in strictest confidence for
the sole use of the addressee and may contain legally privileged, confidential,
and proprietary data. If you are not the intended recipient, please advise the
sender by replying promptly to this email and then delete and destroy this
email and any attachments without any further use, copying or forwarding.
RE: Piper Submitter GUI missing? [EXTERNAL] [SUSPICIOUS]
So many thanks for a prompt response Sean - I have used previous responses of
yours to other requests and it always helped when I was changing source code!
(Examples is the only place I never checked and the obvious one -why is it
called examples , Eugenia ?).
Also can I please ask - I thought I saw somewhere that I can only run a piper
file once this way unlike user version- so if I make any changes I can simply
rename the file and run it again same way correct?
Thank you!
Kind Regards,
Eugenia Monogyiou | NTT Data UK
Consulting & IT Solutions Ltd. 1 Royal Exchange, London EC3V 3DG
Mob: +44 (0)7971623683 Email: eugenia.monogy...@nttdata.com
-Original Message-
From: Finan, Sean
Sent: 25 November 2020 14:33
To: dev@ctakes.apache.org
Subject: Re: Piper Submitter GUI missing? [EXTERNAL] [SUSPICIOUS]
Oh -- ctakes-clinical-pipeline does not have ctakes-gui as a dependency. So if
you want to put the profile in that pom then you will also need to add
ctakes-gui as a dependency in that pom.
From: Finan, Sean
Sent: Wednesday, November 25, 2020 9:30 AM
To: dev@ctakes.apache.org
Subject: Re: Piper Submitter GUI missing? [EXTERNAL] [SUSPICIOUS]
* External Email - Caution *
Hi Eugenia,
I am glad that you are a fan!
The trunk version has a profile to start the piper file submitter gui defined
in the ctakes-examples pom.
However, the 4.0 release does not have a profile to do so.
If you want to use a pfs gui profile in 4.0 then you will need to edit a
downstream (like ctakes-clinical-pipeline) pom.xml and add the following
(snippet from ctakes-examples 4.0.1-SNAPSHOT pom.xml) in :
runPiperGui
runPiperGui
org.codehaus.mojo
exec-maven-plugin
exec
java
true
true
${project.parent.basedir}
-classpath
-Xmx3G
org.apache.ctakes.gui.pipeline.PiperRunnerGui
Sean
From: Monogyiou, Eugenia
Sent: Wednesday, November 25, 2020 8:49 AM
To: dev@ctakes.apache.org
Subject: Piper Submitter GUI missing? [EXTERNAL]
* External Email - Caution *
Hello,
cTakes newbie and big fan so far!
I have installed and been using the user version (4.0.0) and the source code as
per the developer install guide and have tried a few pipelines. I wanted to use
the piper file submitter gui exposed by the developer version but I cannot
locate an active profile in Maven for that. I checked the pom.xml (parent ,
ctakes-gui , ctakes-core etc.) but no profiles listed there either. I can
locate the corresponding class in ctakes-gui but no launch folder etc. I could
not locate specific instructions in the standard documentation either ... I am
using Eclipse 4.16 , maven plugin (also installed Apache Maven separately and
run command line from there) and it seems I have the latest trunk version so I
am out of ideas at this point and very close to a deadline so any feedback,
help comments will be greatly appreciated!
Many thanks in advance,
Kind Regards,
Eugenia
Disclaimer: This email and any attachments are sent in strictest confidence for
the sole use of the addressee and may contain legally privileged, confidential,
and proprietary data. If you are not the intended recipient, please advise the
sender by replying promptly to this email and then delete and destroy this
email and any attachments without any further use, copying or forwarding.
Disclaimer: This email and any attachments are sent in strictest confidence for
the sole use of the addressee and may contain legally privileged, confidential,
and proprietary data. If you are not the intended recipient, please advise the
sender by replying promptly to this email and then delete and destroy this
email and any attachments without any further use, copying or forwarding.
Re: Changes to UTS Authentication for Authorized Content Distributors [EXTERNAL] [SUSPICIOUS]
Hi Sean, Can pick up wiki update if I could get some guidance on what exactly need to be updated and will proceed from there. On Tue, Nov 24, 2020 at 11:53 PM Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Hi Gandhi, > > That would be great! > > I think that an additional test would be useful and putting Peter's > documentation on the wiki is important. > Can you take one of those tasks? > Or would you like to handle something else like point release prep, web > site disclaimer, web site link update (to 4.1), etc.? > > Peter, is your documentation available only on your private (web) > directory or do you have it someplace publicly available? > > Many thanks, > Sean > > > > From: gandhi rajan > Sent: Tuesday, November 24, 2020 1:06 PM > To: dev@ctakes.apache.org > Subject: Re: Changes to UTS Authentication for Authorized Content > Distributors [EXTERNAL] [SUSPICIOUS] > > * External Email - Caution * > > > Hi Sean, > > I can take up a few things if you can guide me on the same. > > On Tue, Nov 24, 2020 at 9:59 PM Finan, Sean < > sean.fi...@childrens.harvard.edu> wrote: > > > Hi Tim and all, > > > > Peter kindly checked this into trunk last week. > > I tested that version and it seemed to work. > > > > Another question might be "how do we get this into the/a release? > > > > I haven't looked into whether or not Apache svn servers have a locking > > mechanism on release branches, but if not I think that a patch of 4.0 > using > > the version that you and Greg tested should be a simple checkin. > > > > I am sure that everybody is tired of hearing me say this, but I would > like > > to get out a version 5 asap and disclaim that it is required for the new > > umls authentication. That would make patching v4 a non-issue. > > > > Regardless of repository inclusion, the documentation (also written by > > Peter) needs to get to the ctakes wiki - and probably the main ctakes > web > > site. On that note, the web site needs to be redone asap. > > > > Anyway, cheers to Peter for taking upon himself this update! > > We do still have a few things left to do. > > Volunteers? > > > > Sean > > > > > > From: Miller, Timothy > > Sent: Tuesday, November 24, 2020 11:07 AM > > To: dev@ctakes.apache.org > > Subject: Re: Changes to UTS Authentication for Authorized Content > > Distributors [EXTERNAL] [SUSPICIOUS] > > > > * External Email - Caution * > > > > > > Peter, > > I was able to try your changes and get this new authentication > > mechanism to work in the default pipeline. Peter, Sean, et al, what are > > the next steps for getting this in to trunk? If you're not comfortable > > checking in directly maybe you can share the patch for review. > > Tim > > > > On Sun, 2020-11-15 at 20:54 +0100, Peter Abramowitsch wrote: > > > * External Email - Caution * > > > > > > > > > Hi Greg > > > > > > I've got the modifications finished for the new UMLS authentication > > > method > > > using API keys. If you're game, I'd like you to be next to test it. > > > Contact me at pabramowit...@gmail.com and I'll get you a new > > > ctakes-dictionary-lookup-fast.4.0,1,x,jar and Readme. > > > > > > If it's smooth for you, I'll talk with Sean about checking it in and > > > what > > > wiki locations need to be updated. > > > > > > To get your key you'll need to log into UMLS, If you've not been > > > there > > > recently you'll need to go through their profile upgrade process > > > where user > > > details will be rerouted through one of the public authentication > > > mechanisms. > > > Once in, go to your profile section and you'll find the API_KEY. > > > > > > All of you will need to do this eventually. > > > > > > Regards > > > Peter > > > > > > Regards, Peter > > > > > > On Wed, Nov 11, 2020 at 10:13 PM Greg Silverman > > > wrote: > > > > > > > Hi Peter, > > > > Thanks, that would be great. I like the backwards compatible > > > > method. Our > > > > issue is that we have custom configurations for use in Docker and > > > > Kubernetes with UIMA-AS, so this would be ideal. > > > > > > > > Greg-- > > > > > > > > > > > > On Wed, Nov 11, 2020 at 3:07 PM Peter Abramowitsch < > > > > pabramowit...@gmail.com> > > > > wrote: > > > > > > > > > Hi Greg > > > > > It's actually extremely simple for current UMLS licensees. > > > > > The new API uses an API_KEY instead of user/password.Just > > > > > login to > > > > the > > > > > UTS site, go to your profile area and check on your key > > > > > I or someone else will make changes to the cTAKES validator to > > > > > accept > > > > this > > > > > key in lieu of name and password > > > > > > > > > > For new UMLS users, they will need a couple of extra > > > > > steps. They will > > > > get > > > > > an identity from one of the authentication providers like > > > > > Login.gov as a > > > > > part of the UTS registration process. But having completed > > > > > that, they > > > > > will have a profil
Re: Changes to UTS Authentication for Authorized Content Distributors [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
I will be done with the UmlsUserApprover 4.0.0 backport by tomorrow. It's working already but I need to try all the ways of setting the auth params. A bit of the infrastructure around CLI and Envvars in the UimaContext is different. Peter On Wed, Nov 25, 2020 at 3:08 PM Miller, Timothy < timothy.mil...@childrens.harvard.edu> wrote: > That link doesn't say anything there about incremental update releases, > but even with the normal process I think we can get 4.0.1 out faster > than usual because it is such a small change and there are unlikely to > be multiple RCs to get one that works for everyone. > Does anyone want to volunteer to be release manager? It needs to be > someone on the PMC, so Sean, myself, Gandhi, or Chen probably. > > Tim > > > On Tue, 2020-11-24 at 18:10 +, Finan, Sean wrote: > > * External Email - Caution * > > > > > > > > I haven't looked into whether or not Apache svn servers have a > > > > locking mechanism ... > > > I think it's worth checking -- if we're allowed to just branch off > > > the > > > 4.0.0 tag we can get a 4.0.1 distribution that just has this one > > > change, and we could have it built and uploaded quickly so we're > > > ready > > > for the UMLS change. How would we find out? > > > > A 4.0.1 made directly from 4.0 with only the authentication update is > > probably the way to go. > > I suppose that for people with dependencies, downloads etc. fixed at > > 4.0 would have to get their new umls key and change their ctakes > > config anyway, so telling them to update any coded version numbers > > doesn't involve too much extra effort. > > > > The main apache org how to release documentation is at > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__infra.apache.org_release-2Dpublishing.html&d=DwIF-g&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=QVEto_k7Ovh16r4YjW7Uelv9_lDmvjxRwoI2r7_6qBk&s=fjMkpO1i2FXprtFbQ-XJ1cvVlSQ8-uz3gSOBojxNMI8&e= > > I am not sure of anything specifically regarding patches. > > I don't know if we need to go through the full process for a point > > release ... > > > > > > > > From: Miller, Timothy > > Sent: Tuesday, November 24, 2020 12:45 PM > > To: dev@ctakes.apache.org > > Subject: Re: Changes to UTS Authentication for Authorized Content > > Distributors [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] > > > > * External Email - Caution * > > > > > > On Tue, 2020-11-24 at 16:29 +, Finan, Sean wrote: > > > * External Email - Caution * > > > > > > > > > Hi Tim and all, > > > > > > Peter kindly checked this into trunk last week. > > > I tested that version and it seemed to work. > > > > > > Another question might be "how do we get this into the/a release? > > > > > > I haven't looked into whether or not Apache svn servers have a > > > locking mechanism on release branches, but if not I think that a > > > patch of 4.0 using the version that you and Greg tested should be a > > > simple checkin. > > > > I think it's worth checking -- if we're allowed to just branch off > > the > > 4.0.0 tag we can get a 4.0.1 distribution that just has this one > > change, and we could have it built and uploaded quickly so we're > > ready > > for the UMLS change. How would we find out? > > > > Tim > > > > > I am sure that everybody is tired of hearing me say this, but I > > > would > > > like to get out a version 5 asap and disclaim that it is required > > > for > > > the new umls authentication. That would make patching v4 a non- > > > issue. > > > > > > Regardless of repository inclusion, the documentation (also written > > > by Peter) needs to get to the ctakes wiki - and probably the main > > > ctakes web site. On that note, the web site needs to be redone > > > asap. > > > > > > Anyway, cheers to Peter for taking upon himself this update! > > > We do still have a few things left to do. > > > Volunteers? > > > > > > Sean > > > > > > > > > From: Miller, Timothy > > > Sent: Tuesday, November 24, 2020 11:07 AM > > > To: dev@ctakes.apache.org > > > Subject: Re: Changes to UTS Authentication for Authorized Content > > > Distributors [EXTERNAL] [SUSPICIOUS] > > > > > > * External Email - Caution * > > > > > > > > > Peter, > > > I was able to try your changes and get this new authentication > > > mechanism to work in the default pipeline. Peter, Sean, et al, what > > > are > > > the next steps for getting this in to trunk? If you're not > > > comfortable > > > checking in directly maybe you can share the patch for review. > > > Tim > > > > > > On Sun, 2020-11-15 at 20:54 +0100, Peter Abramowitsch wrote: > > > > * External Email - Caution * > > > > > > > > > > > > Hi Greg > > > > > > > > I've got the modifications finished for the new UMLS > > > > authentication > > > > method > > > > using API keys. If you're game, I'd like you to be next to test > > > > it. > > > > Contact me at pabramowit...@gmail.
Re: Changes to UTS Authentication for Authorized Content Distributors [EXTERNAL] [SUSPICIOUS]
Hi Gandhi If you hang on a bit for some of it, it will save you having to revise. Yesterday I attached the instructions I had given for using the new code in the trunk environment and that will give you a good overview. But there may be some minor differences in the backport. This is because the infrastructure for exposing environment vs system vs desc*xml variables is a bit different and I'm still in testing mode. The bit that you could start with is about how to obtain your API key. Peter On Wed, Nov 25, 2020 at 3:47 PM gandhi rajan wrote: > Hi Sean, > > Can pick up wiki update if I could get some guidance on what exactly need > to be updated and will proceed from there. > > On Tue, Nov 24, 2020 at 11:53 PM Finan, Sean < > sean.fi...@childrens.harvard.edu> wrote: > > > Hi Gandhi, > > > > That would be great! > > > > I think that an additional test would be useful and putting Peter's > > documentation on the wiki is important. > > Can you take one of those tasks? > > Or would you like to handle something else like point release prep, web > > site disclaimer, web site link update (to 4.1), etc.? > > > > Peter, is your documentation available only on your private (web) > > directory or do you have it someplace publicly available? > > > > Many thanks, > > Sean > > > > > > > > From: gandhi rajan > > Sent: Tuesday, November 24, 2020 1:06 PM > > To: dev@ctakes.apache.org > > Subject: Re: Changes to UTS Authentication for Authorized Content > > Distributors [EXTERNAL] [SUSPICIOUS] > > > > * External Email - Caution * > > > > > > Hi Sean, > > > > I can take up a few things if you can guide me on the same. > > > > On Tue, Nov 24, 2020 at 9:59 PM Finan, Sean < > > sean.fi...@childrens.harvard.edu> wrote: > > > > > Hi Tim and all, > > > > > > Peter kindly checked this into trunk last week. > > > I tested that version and it seemed to work. > > > > > > Another question might be "how do we get this into the/a release? > > > > > > I haven't looked into whether or not Apache svn servers have a locking > > > mechanism on release branches, but if not I think that a patch of 4.0 > > using > > > the version that you and Greg tested should be a simple checkin. > > > > > > I am sure that everybody is tired of hearing me say this, but I would > > like > > > to get out a version 5 asap and disclaim that it is required for the > new > > > umls authentication. That would make patching v4 a non-issue. > > > > > > Regardless of repository inclusion, the documentation (also written by > > > Peter) needs to get to the ctakes wiki - and probably the main ctakes > > web > > > site. On that note, the web site needs to be redone asap. > > > > > > Anyway, cheers to Peter for taking upon himself this update! > > > We do still have a few things left to do. > > > Volunteers? > > > > > > Sean > > > > > > > > > From: Miller, Timothy > > > Sent: Tuesday, November 24, 2020 11:07 AM > > > To: dev@ctakes.apache.org > > > Subject: Re: Changes to UTS Authentication for Authorized Content > > > Distributors [EXTERNAL] [SUSPICIOUS] > > > > > > * External Email - Caution * > > > > > > > > > Peter, > > > I was able to try your changes and get this new authentication > > > mechanism to work in the default pipeline. Peter, Sean, et al, what are > > > the next steps for getting this in to trunk? If you're not comfortable > > > checking in directly maybe you can share the patch for review. > > > Tim > > > > > > On Sun, 2020-11-15 at 20:54 +0100, Peter Abramowitsch wrote: > > > > * External Email - Caution * > > > > > > > > > > > > Hi Greg > > > > > > > > I've got the modifications finished for the new UMLS authentication > > > > method > > > > using API keys. If you're game, I'd like you to be next to test it. > > > > Contact me at pabramowit...@gmail.com and I'll get you a new > > > > ctakes-dictionary-lookup-fast.4.0,1,x,jar and Readme. > > > > > > > > If it's smooth for you, I'll talk with Sean about checking it in and > > > > what > > > > wiki locations need to be updated. > > > > > > > > To get your key you'll need to log into UMLS, If you've not been > > > > there > > > > recently you'll need to go through their profile upgrade process > > > > where user > > > > details will be rerouted through one of the public authentication > > > > mechanisms. > > > > Once in, go to your profile section and you'll find the API_KEY. > > > > > > > > All of you will need to do this eventually. > > > > > > > > Regards > > > > Peter > > > > > > > > Regards, Peter > > > > > > > > On Wed, Nov 11, 2020 at 10:13 PM Greg Silverman > > > > > wrote: > > > > > > > > > Hi Peter, > > > > > Thanks, that would be great. I like the backwards compatible > > > > > method. Our > > > > > issue is that we have custom configurations for use in Docker and > > > > > Kubernetes with UIMA-AS, so this would be ideal. > > > > > > > > > > Greg-- > > > > > > > > > > > > > > > On Wed, Nov 11,
Re: Piper Submitter GUI missing? [EXTERNAL] [SUSPICIOUS]
>if I make any changes I can simply rename the file and run it again
I haven't tried that and it is an interesting idea.
I think that you can run multiple times as long as there aren't any annotators
that try to persist something immutable through a complete run and throw
exceptions if the next run tries to reset the information.
In reality, I just need to remember to fix the code ...
Sean
From: Monogyiou, Eugenia
Sent: Wednesday, November 25, 2020 9:39 AM
To: dev@ctakes.apache.org
Subject: RE: Piper Submitter GUI missing? [EXTERNAL] [SUSPICIOUS]
* External Email - Caution *
So many thanks for a prompt response Sean - I have used previous responses of
yours to other requests and it always helped when I was changing source code!
(Examples is the only place I never checked and the obvious one -why is it
called examples , Eugenia ?).
Also can I please ask - I thought I saw somewhere that I can only run a piper
file once this way unlike user version- so if I make any changes I can simply
rename the file and run it again same way correct?
Thank you!
Kind Regards,
Eugenia Monogyiou | NTT Data UK
Consulting & IT Solutions Ltd. 1 Royal Exchange, London EC3V 3DG
Mob: +44 (0)7971623683 Email: eugenia.monogy...@nttdata.com
-Original Message-
From: Finan, Sean
Sent: 25 November 2020 14:33
To: dev@ctakes.apache.org
Subject: Re: Piper Submitter GUI missing? [EXTERNAL] [SUSPICIOUS]
Oh -- ctakes-clinical-pipeline does not have ctakes-gui as a dependency. So if
you want to put the profile in that pom then you will also need to add
ctakes-gui as a dependency in that pom.
From: Finan, Sean
Sent: Wednesday, November 25, 2020 9:30 AM
To: dev@ctakes.apache.org
Subject: Re: Piper Submitter GUI missing? [EXTERNAL] [SUSPICIOUS]
* External Email - Caution *
Hi Eugenia,
I am glad that you are a fan!
The trunk version has a profile to start the piper file submitter gui defined
in the ctakes-examples pom.
However, the 4.0 release does not have a profile to do so.
If you want to use a pfs gui profile in 4.0 then you will need to edit a
downstream (like ctakes-clinical-pipeline) pom.xml and add the following
(snippet from ctakes-examples 4.0.1-SNAPSHOT pom.xml) in :
runPiperGui
runPiperGui
org.codehaus.mojo
exec-maven-plugin
exec
java
true
true
${project.parent.basedir}
-classpath
-Xmx3G
org.apache.ctakes.gui.pipeline.PiperRunnerGui
Sean
From: Monogyiou, Eugenia
Sent: Wednesday, November 25, 2020 8:49 AM
To: dev@ctakes.apache.org
Subject: Piper Submitter GUI missing? [EXTERNAL]
* External Email - Caution *
Hello,
cTakes newbie and big fan so far!
I have installed and been using the user version (4.0.0) and the source code as
per the developer install guide and have tried a few pipelines. I wanted to use
the piper file submitter gui exposed by the developer version but I cannot
locate an active profile in Maven for that. I checked the pom.xml (parent ,
ctakes-gui , ctakes-core etc.) but no profiles listed there either. I can
locate the corresponding class in ctakes-gui but no launch folder etc. I could
not locate specific instructions in the standard documentation either ... I am
using Eclipse 4.16 , maven plugin (also installed Apache Maven separately and
run command line from there) and it seems I have the latest trunk version so I
am out of ideas at this point and very close to a deadline so any feedback,
help comments will be greatly appreciated!
Many thanks in advance,
Kind Regards,
Eugenia
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and pr
Small hitch in Authentication backport
Hi All It turns out that the code to approve UMLS usage is duplicated and exists in two different jars. My upgrade was only in the class UmlsUserApprover, but after some head scratching to explain what I was seeing, I discovered that there's an earlier version of the same code still buried in ./ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsDictionaryLookupAnnotator.java It is a problem even in the trunk, but only affects the old UMLS Lookup annotator I'll modify it to pont back to the distinct Approver class - unless doing that causes a cyclic dependency between projects. Does anyone have other thoughts? Peter
