RE: cTAKES user interface
Hi Pan, Fwd'ing to dev@ From: Pan Teng [mailto:teng...@udel.edu] Sent: Tuesday, October 29, 2013 4:37 PM To: user-ow...@ctakes.apache.org Subject: Fwd: cTAKES user interface Hi there, I'm trying to explore the cTAKES system. Just curious whether there is an way that I can use cTAKES system just in the terminal window by typing some command line including input and then the output data can be generated? Your kindly reply will be appreciated. Best, Pan
Re: cTAKES user interface
In my opinion, this user request is totally reasonable. Download time aside, it should take NO LONGER THAN 15 MINUTES to get started with cTakes. True, cTakes is massively powerful and UMLS is a license headache. Nonetheless! This keeps coming up, we should strongly consider an improved VM distribution option so folks can get online with "copy-paste" text ready applications on their local machine. IT WOULD BE A GAME CHANGER IN A GOOD WAY I'm strongly considering making an Ubuntu 13.10 cTakes distribution for my own work, would others want this as well? http://www.ubuntu.com/download/desktop Yes I know thats a tall order, but its true ! :) We dont have to provide the full UMLS instance, just the non-commercial dictionaries. Just get new users "hooked on cTakes" with ICD9 diagnoses, procedures, medications annotations. How do the other committers feel about this? PS: I'm back and with more vigor++ On Oct 29, 2013, at 2:02 PM, "Chen, Pei" wrote: > Hi Pan, > Fwd'ing to dev@ > > From: Pan Teng [mailto:teng...@udel.edu] > Sent: Tuesday, October 29, 2013 4:37 PM > To: user-ow...@ctakes.apache.org > Subject: Fwd: cTAKES user interface > > Hi there, > I'm trying to explore the cTAKES system. Just curious whether there is an way > that I can use cTAKES system just in the terminal window by typing some > command line including input and then the output data can be generated? Your > kindly reply will be appreciated. > Best, > Pan > >
RE: cTAKES user interface
+1 Pan, the short answer is yes- it can be done in CLI. The problem is that most of us who are already familiar with the nitty gritty are probably doing this with some sort of custom scripts or solution. Cc' the dev group to get a fresh perspective; not sure what the easiest would be-- run the CPE via command line with default input/output directories or running a Driver Main Class as part of examples. --Pei > -Original Message- > From: Andrew McMurry [mailto:mcmurry.a...@gmail.com] > Sent: Tuesday, October 29, 2013 5:41 PM > To: dev@ctakes.apache.org > Cc: Pan Teng; and...@apache.org > Subject: Re: cTAKES user interface > > In my opinion, this user request is totally reasonable. > > Download time aside, it should take NO LONGER THAN 15 MINUTES to get > started with cTakes. > True, cTakes is massively powerful and UMLS is a license headache. > Nonetheless! > > This keeps coming up, we should strongly consider an improved VM > distribution option so folks can get online with "copy-paste" text ready > applications on their local machine. > > IT WOULD BE A GAME CHANGER IN A GOOD WAY > > I'm strongly considering making an Ubuntu 13.10 cTakes distribution for my > own work, would others want this as well? > http://www.ubuntu.com/download/desktop > > Yes I know thats a tall order, but its true ! :) > > We dont have to provide the full UMLS instance, just the non-commercial > dictionaries. > Just get new users "hooked on cTakes" with ICD9 diagnoses, procedures, > medications annotations. > > How do the other committers feel about this? > > PS: I'm back and with more vigor++ > > On Oct 29, 2013, at 2:02 PM, "Chen, Pei" > wrote: > > > Hi Pan, > > Fwd'ing to dev@ > > > > From: Pan Teng [mailto:teng...@udel.edu] > > Sent: Tuesday, October 29, 2013 4:37 PM > > To: user-ow...@ctakes.apache.org > > Subject: Fwd: cTAKES user interface > > > > Hi there, > > I'm trying to explore the cTAKES system. Just curious whether there is an > way that I can use cTAKES system just in the terminal window by typing some > command line including input and then the output data can be generated? > Your kindly reply will be appreciated. > > Best, > > Pan > > > >
Re: cTAKES user interface
I think this is also an area where Maven integration was a small step backwards (I greatly appreciate the steps forward it allowed). I used to run stuff from the command line and in scripts more often but it's slightly less straightforward setting up the classpath with maven -- before you could put a simple java -cp lib/*.jar in a script, now I'm not sure how to go about it using maven. I'm sure there's a way, but I am afraid of falling down the maven rabbit hole. Tim On Oct 29, 2013, at 5:53 PM, Chen, Pei wrote: > +1 > Pan, the short answer is yes- it can be done in CLI. > The problem is that most of us who are already familiar with the nitty gritty > are probably doing this with some sort of custom scripts or solution. > Cc' the dev group to get a fresh perspective; not sure what the easiest would > be-- run the CPE via command line with default input/output directories or > running a Driver Main Class as part of examples. > > --Pei > >> -Original Message- >> From: Andrew McMurry [mailto:mcmurry.a...@gmail.com] >> Sent: Tuesday, October 29, 2013 5:41 PM >> To: dev@ctakes.apache.org >> Cc: Pan Teng; and...@apache.org >> Subject: Re: cTAKES user interface >> >> In my opinion, this user request is totally reasonable. >> >> Download time aside, it should take NO LONGER THAN 15 MINUTES to get >> started with cTakes. >> True, cTakes is massively powerful and UMLS is a license headache. >> Nonetheless! >> >> This keeps coming up, we should strongly consider an improved VM >> distribution option so folks can get online with "copy-paste" text ready >> applications on their local machine. >> >> IT WOULD BE A GAME CHANGER IN A GOOD WAY >> >> I'm strongly considering making an Ubuntu 13.10 cTakes distribution for my >> own work, would others want this as well? >> http://www.ubuntu.com/download/desktop >> >> Yes I know thats a tall order, but its true ! :) >> >> We dont have to provide the full UMLS instance, just the non-commercial >> dictionaries. >> Just get new users "hooked on cTakes" with ICD9 diagnoses, procedures, >> medications annotations. >> >> How do the other committers feel about this? >> >> PS: I'm back and with more vigor++ >> >> On Oct 29, 2013, at 2:02 PM, "Chen, Pei" >> wrote: >> >>> Hi Pan, >>> Fwd'ing to dev@ >>> >>> From: Pan Teng [mailto:teng...@udel.edu] >>> Sent: Tuesday, October 29, 2013 4:37 PM >>> To: user-ow...@ctakes.apache.org >>> Subject: Fwd: cTAKES user interface >>> >>> Hi there, >>> I'm trying to explore the cTAKES system. Just curious whether there is an >> way that I can use cTAKES system just in the terminal window by typing some >> command line including input and then the output data can be generated? >> Your kindly reply will be appreciated. >>> Best, >>> Pan >>> >>> >
Re: cTAKES user interface
+1 to Andy's suggestion. Ease of initiation + community engagement = positive growth. On Tue, Oct 29, 2013 at 6:09 PM, Miller, Timothy < timothy.mil...@childrens.harvard.edu> wrote: > I think this is also an area where Maven integration was a small step > backwards (I greatly appreciate the steps forward it allowed). I used to > run stuff from the command line and in scripts more often but it's slightly > less straightforward setting up the classpath with maven -- before you > could put a simple java -cp lib/*.jar in a script, now I'm not > sure how to go about it using maven. I'm sure there's a way, but I am > afraid of falling down the maven rabbit hole. > Tim > > > On Oct 29, 2013, at 5:53 PM, Chen, Pei wrote: > > > +1 > > Pan, the short answer is yes- it can be done in CLI. > > The problem is that most of us who are already familiar with the nitty > gritty are probably doing this with some sort of custom scripts or solution. > > Cc' the dev group to get a fresh perspective; not sure what the easiest > would be-- run the CPE via command line with default input/output > directories or running a Driver Main Class as part of examples. > > > > --Pei > > > >> -Original Message- > >> From: Andrew McMurry [mailto:mcmurry.a...@gmail.com] > >> Sent: Tuesday, October 29, 2013 5:41 PM > >> To: dev@ctakes.apache.org > >> Cc: Pan Teng; and...@apache.org > >> Subject: Re: cTAKES user interface > >> > >> In my opinion, this user request is totally reasonable. > >> > >> Download time aside, it should take NO LONGER THAN 15 MINUTES to get > >> started with cTakes. > >> True, cTakes is massively powerful and UMLS is a license headache. > >> Nonetheless! > >> > >> This keeps coming up, we should strongly consider an improved VM > >> distribution option so folks can get online with "copy-paste" text ready > >> applications on their local machine. > >> > >> IT WOULD BE A GAME CHANGER IN A GOOD WAY > >> > >> I'm strongly considering making an Ubuntu 13.10 cTakes distribution for > my > >> own work, would others want this as well? > >> http://www.ubuntu.com/download/desktop > >> > >> Yes I know thats a tall order, but its true ! :) > >> > >> We dont have to provide the full UMLS instance, just the non-commercial > >> dictionaries. > >> Just get new users "hooked on cTakes" with ICD9 diagnoses, procedures, > >> medications annotations. > >> > >> How do the other committers feel about this? > >> > >> PS: I'm back and with more vigor++ > >> > >> On Oct 29, 2013, at 2:02 PM, "Chen, Pei" < > pei.c...@childrens.harvard.edu> > >> wrote: > >> > >>> Hi Pan, > >>> Fwd'ing to dev@ > >>> > >>> From: Pan Teng [mailto:teng...@udel.edu] > >>> Sent: Tuesday, October 29, 2013 4:37 PM > >>> To: user-ow...@ctakes.apache.org > >>> Subject: Fwd: cTAKES user interface > >>> > >>> Hi there, > >>> I'm trying to explore the cTAKES system. Just curious whether there is > an > >> way that I can use cTAKES system just in the terminal window by typing > some > >> command line including input and then the output data can be generated? > >> Your kindly reply will be appreciated. > >>> Best, > >>> Pan > >>> > >>> > > > >
Re: cTAKES user interface
Maven allows to do marvelous things on the CLI, provided you throw in an additional component: Groovy. We did some amazing self-contained Groovy scripts with uimaFIT and DKPro Core which you might find interesting http://code.google.com/p/dkpro-core-asl/wiki/DKProGroovyCookbook -- Richard On 29.10.2013, at 23:09, "Miller, Timothy" wrote: > I think this is also an area where Maven integration was a small step > backwards (I greatly appreciate the steps forward it allowed). I used to run > stuff from the command line and in scripts more often but it's slightly less > straightforward setting up the classpath with maven -- before you could put a > simple java -cp lib/*.jar in a script, now I'm not sure how to > go about it using maven. I'm sure there's a way, but I am afraid of falling > down the maven rabbit hole. > Tim > > > On Oct 29, 2013, at 5:53 PM, Chen, Pei wrote: > >> +1 >> Pan, the short answer is yes- it can be done in CLI. >> The problem is that most of us who are already familiar with the nitty >> gritty are probably doing this with some sort of custom scripts or solution. >> Cc' the dev group to get a fresh perspective; not sure what the easiest >> would be-- run the CPE via command line with default input/output >> directories or running a Driver Main Class as part of examples. >> >> --Pei
Re: cTAKES user interface
Ricard: Groovy idea. Virtual Machine could benefit from that as well. *## IMHO: These are parallel tasks that I think are higher priority than new features. *It isn't as glamorous as playing Jeopardy, but deploy issues are keeping users out -- if I were to guess A LOT of the potential user base looks at ctakes and says "wow that amazing! " then they look at how complex it will be to do their simple "Hello Ctakes" example and the 15 minutes of attention -- we are one walk to the soda machine away from being either embraced or forgotten. It really is that basic -- if it takes to long to get started, chances are new users -- wont. The documentation is nicely done and this is absolutely no criticism of that. In fact, I apologize for being so out of touch (was thesis writing ). It just feels like 1992 all over again and your compiling linux just to find out you didn't tweak your VGA card settings right, and now your stuck. But you still think linux rocks. 2013 is here and linux now runs out of the box. The OS itself has changed less in features and more in ease of use. I know its not Jeopardy but we gotta do it. *## I'm going to make a VM (Ubuntu 13.10) for myself and let everyone kick it around. **I strongly encourage the Groovy deploy targets as Richard suggested. * This really isn't an either | OR. We need to be able to have easier turn around on cTakes so we can get back to Jeopardy. *## Who agrees, and are there any counter proposals? * AndyMC On Tue, Oct 29, 2013 at 3:49 PM, Richard Eckart de Castilho wrote: > Maven allows to do marvelous things on the CLI, provided you throw in an > additional component: Groovy. > > We did some amazing self-contained Groovy scripts with uimaFIT and DKPro > Core which you might find interesting > > http://code.google.com/p/dkpro-core-asl/wiki/DKProGroovyCookbook > > -- Richard > > On 29.10.2013, at 23:09, "Miller, Timothy" < > timothy.mil...@childrens.harvard.edu> wrote: > > > I think this is also an area where Maven integration was a small step > backwards (I greatly appreciate the steps forward it allowed). I used to > run stuff from the command line and in scripts more often but it's slightly > less straightforward setting up the classpath with maven -- before you > could put a simple java -cp lib/*.jar in a script, now I'm not > sure how to go about it using maven. I'm sure there's a way, but I am > afraid of falling down the maven rabbit hole. > > Tim > > > > > > On Oct 29, 2013, at 5:53 PM, Chen, Pei wrote: > > > >> +1 > >> Pan, the short answer is yes- it can be done in CLI. > >> The problem is that most of us who are already familiar with the nitty > gritty are probably doing this with some sort of custom scripts or solution. > >> Cc' the dev group to get a fresh perspective; not sure what the easiest > would be-- run the CPE via command line with default input/output > directories or running a Driver Main Class as part of examples. > >> > >> --Pei > >
RE: cTAKES user interface
Hi Tim, I've had a related issue, where I wanted all of the resources and libraries for a cTAKES application bundled into a single jar file. The Maven solution that works for me is to add the following to your pom's plugins section: maven-assembly-plugin your.class.Here jar-with-dependencies I then call Maven with the following goals: clean compile assembly:single This generates a single jar file with all of your dependencies. -Will -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Tuesday, October 29, 2013 5:09 PM To: Subject: Re: cTAKES user interface I think this is also an area where Maven integration was a small step backwards (I greatly appreciate the steps forward it allowed). I used to run stuff from the command line and in scripts more often but it's slightly less straightforward setting up the classpath with maven -- before you could put a simple java -cp lib/*.jar in a script, now I'm not sure how to go about it using maven. I'm sure there's a way, but I am afraid of falling down the maven rabbit hole. Tim On Oct 29, 2013, at 5:53 PM, Chen, Pei wrote: > +1 > Pan, the short answer is yes- it can be done in CLI. > The problem is that most of us who are already familiar with the nitty gritty > are probably doing this with some sort of custom scripts or solution. > Cc' the dev group to get a fresh perspective; not sure what the easiest would > be-- run the CPE via command line with default input/output directories or > running a Driver Main Class as part of examples. > > --Pei > >> -Original Message- >> From: Andrew McMurry [mailto:mcmurry.a...@gmail.com] >> Sent: Tuesday, October 29, 2013 5:41 PM >> To: dev@ctakes.apache.org >> Cc: Pan Teng; and...@apache.org >> Subject: Re: cTAKES user interface >> >> In my opinion, this user request is totally reasonable. >> >> Download time aside, it should take NO LONGER THAN 15 MINUTES to get >> started with cTakes. >> True, cTakes is massively powerful and UMLS is a license headache. >> Nonetheless! >> >> This keeps coming up, we should strongly consider an improved VM >> distribution option so folks can get online with "copy-paste" text >> ready applications on their local machine. >> >> IT WOULD BE A GAME CHANGER IN A GOOD WAY >> >> I'm strongly considering making an Ubuntu 13.10 cTakes distribution >> for my own work, would others want this as well? >> http://www.ubuntu.com/download/desktop >> >> Yes I know thats a tall order, but its true ! :) >> >> We dont have to provide the full UMLS instance, just the >> non-commercial dictionaries. >> Just get new users "hooked on cTakes" with ICD9 diagnoses, >> procedures, medications annotations. >> >> How do the other committers feel about this? >> >> PS: I'm back and with more vigor++ >> >> On Oct 29, 2013, at 2:02 PM, "Chen, Pei" >> >> wrote: >> >>> Hi Pan, >>> Fwd'ing to dev@ >>> >>> From: Pan Teng [mailto:teng...@udel.edu] >>> Sent: Tuesday, October 29, 2013 4:37 PM >>> To: user-ow...@ctakes.apache.org >>> Subject: Fwd: cTAKES user interface >>> >>> Hi there, >>> I'm trying to explore the cTAKES system. Just curious whether there >>> is an >> way that I can use cTAKES system just in the terminal window by >> typing some command line including input and then the output data can be >> generated? >> Your kindly reply will be appreciated. >>> Best, >>> Pan >>> >>> >
RE: cTAKES user interface
Nice! +1 for Groovy. It's like being able to program in Python again. -Original Message- From: Richard Eckart de Castilho [mailto:r...@apache.org] Sent: Tuesday, October 29, 2013 5:49 PM To: dev@ctakes.apache.org Subject: Re: cTAKES user interface Maven allows to do marvelous things on the CLI, provided you throw in an additional component: Groovy. We did some amazing self-contained Groovy scripts with uimaFIT and DKPro Core which you might find interesting http://code.google.com/p/dkpro-core-asl/wiki/DKProGroovyCookbook -- Richard On 29.10.2013, at 23:09, "Miller, Timothy" wrote: > I think this is also an area where Maven integration was a small step > backwards (I greatly appreciate the steps forward it allowed). I used to run > stuff from the command line and in scripts more often but it's slightly less > straightforward setting up the classpath with maven -- before you could put a > simple java -cp lib/*.jar in a script, now I'm not sure how to > go about it using maven. I'm sure there's a way, but I am afraid of falling > down the maven rabbit hole. > Tim > > > On Oct 29, 2013, at 5:53 PM, Chen, Pei wrote: > >> +1 >> Pan, the short answer is yes- it can be done in CLI. >> The problem is that most of us who are already familiar with the nitty >> gritty are probably doing this with some sort of custom scripts or solution. >> Cc' the dev group to get a fresh perspective; not sure what the easiest >> would be-- run the CPE via command line with default input/output >> directories or running a Driver Main Class as part of examples. >> >> --Pei
Re: cTAKES user interface
Thanks William and Richard, those are both really excellent pointers. Tim On 10/29/2013 07:58 PM, William Karl Thompson wrote: > Nice! > > +1 for Groovy. It's like being able to program in Python again. > > -Original Message- > From: Richard Eckart de Castilho [mailto:r...@apache.org] > Sent: Tuesday, October 29, 2013 5:49 PM > To: dev@ctakes.apache.org > Subject: Re: cTAKES user interface > > Maven allows to do marvelous things on the CLI, provided you throw in an > additional component: Groovy. > > We did some amazing self-contained Groovy scripts with uimaFIT and DKPro Core > which you might find interesting > > http://code.google.com/p/dkpro-core-asl/wiki/DKProGroovyCookbook > > -- Richard > > On 29.10.2013, at 23:09, "Miller, Timothy" > wrote: > >> I think this is also an area where Maven integration was a small step >> backwards (I greatly appreciate the steps forward it allowed). I used to run >> stuff from the command line and in scripts more often but it's slightly less >> straightforward setting up the classpath with maven -- before you could put >> a simple java -cp lib/*.jar in a script, now I'm not sure how >> to go about it using maven. I'm sure there's a way, but I am afraid of >> falling down the maven rabbit hole. >> Tim >> >> >> On Oct 29, 2013, at 5:53 PM, Chen, Pei wrote: >> >>> +1 >>> Pan, the short answer is yes- it can be done in CLI. >>> The problem is that most of us who are already familiar with the nitty >>> gritty are probably doing this with some sort of custom scripts or solution. >>> Cc' the dev group to get a fresh perspective; not sure what the easiest >>> would be-- run the CPE via command line with default input/output >>> directories or running a Driver Main Class as part of examples. >>> >>> --Pei >
