RE: cTAKES user interface
I agree that we got new users to a certain point. Much better than years back, but not as fast as could be. If you go down the VM route you have to make some choices. They don't all play in the same sand box. Would you do a VMWare VM or would you do an AWS cloud RC2 instance or something else. Which one is best for the community. Going back and forth with one image can be done but I've never seen it be straight forward. No matter the choice would, you leave out more people than if you chose to write deploy scripts because they don't use a particular virtual machine world? For these reasons I think would be better to focus on a deploy script: - Easier to maintain and download - Can be checked into the code repository - Can support more than one OS - VMs make decisions for users that could be choices in a script - (weak argument) One could argue that given a VM a user might not learn enough to be successful doing a deploy once thy like cTAKES and want to use it in their enterprise after having only known the VM - everything you said about DEPLOY and scripts Arguments against deploy scripts: - Which framework do most people use Puppet, Capistrano, Chef? They don't play nice together either, so going from one to the other is a pain - Needs documentation on how to use the deploy script as a user could be new to the deploy framework Thanks Troy -Original Message- From: dev-return-2179-Bleeker.Troy=mayo@ctakes.apache.org [mailto:dev-return-2179-Bleeker.Troy=mayo@ctakes.apache.org] On Behalf Of Andrew McMurry Sent: Tuesday, October 29, 2013 6:15 PM To: dev@ctakes.apache.org Cc: Pan Teng; and...@apache.org Subject: Re: cTAKES user interface Summary: Maven is great. Not going away. VM still highly desirable for first time users and even developers. Maven solves the dependency problem. VM solves an installation problem. OK So I should put my money where my mouth is. :) OK I'll make a cTakes VM (Ubuntu 13.10). I basically have to do this anyway. We must admit it is pretty tough to setup cTakes even with all the nicely written docs. NLP is complicated. CTAKES is a powerful and configurable engine. Nonetheless, the user request is completely well warranted. " How do I just make it work for the simplest case of copy pasting text into a console window ? " In my experiences Maven is great for dependancies of code (jars, wars, zips) but really struggles with DEPLOY and INSTALLATION tasks, especially across OS systems. Most of the FOSS community has moved past maven for DEPLOY tasks. Puppet, Capistrano, and custom shell scripts are far more frequently used than Maven for DEPLOY targets. How does everyone feel about having trying a VM distribution and see how it goes? Volunteers thus far: AndyMC (me) On Oct 29, 2013, at 2:52 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
Re: cTAKES user interface
Summary: Maven is great. Not going away. VM still highly desirable for first time users and even developers. Maven solves the dependency problem. VM solves an installation problem. OK So I should put my money where my mouth is. :) OK I'll make a cTakes VM (Ubuntu 13.10). I basically have to do this anyway. We must admit it is pretty tough to setup cTakes even with all the nicely written docs. NLP is complicated. CTAKES is a powerful and configurable engine. Nonetheless, the user request is completely well warranted. " How do I just make it work for the simplest case of copy pasting text into a console window ? " In my experiences Maven is great for dependancies of code (jars, wars, zips) but really struggles with DEPLOY and INSTALLATION tasks, especially across OS systems. Most of the FOSS community has moved past maven for DEPLOY tasks. Puppet, Capistrano, and custom shell scripts are far more frequently used than Maven for DEPLOY targets. How does everyone feel about having trying a VM distribution and see how it goes? Volunteers thus far: AndyMC (me) On Oct 29, 2013, at 2:52 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
This is a very good point. I can attest as a new user, these hurdles mentioned by Andy seem paramount to broader adoption. Just by-the-by I loved the Linux analogy Andy. At least, to a greater or lesser degree, it survived! JG On Tue, Oct 29, 2013 at 7:33 PM, andy mcmurry wrote: > 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
James: EXCELLENT suggestion. Last time I checked CTAKES was way out of date. Makes sense that one of us should play "red rover" and keep cTakes up to date. I just this moment sent a message to iDASH to start the update conversation. --Andy On Oct 30, 2013, at 8:04 AM, "Masanz, James J." wrote: > Andy, > > You might want to talk with the folks at iDASH. > They have an image with a number of NLP tools installed, but it doesn't have > the latest version of cTAKES. > > http://idash.ucsd.edu/nlp/natural-language-processing-nlp-ecosystem > > Perhaps they would be open to your help with upgrading to a later version of > cTAKES. > > -- James > > -Original Message- > From: dev-return-2151-Masanz.James=mayo@ctakes.apache.org > [mailto:dev-return-2151-Masanz.James=mayo@ctakes.apache.org] On Behalf Of > andy mcmurry > Sent: Tuesday, October 29, 2013 6:34 PM > To: dev@ctakes.apache.org > Subject: 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
Fwiw, I've had trouble with runctakesCPE.sh classpath for projects that
are not ctakes-clinical-pipeline. The most reliable ways I know are to get
the runtime classpath are:
1. Add it programmatically: System.getProperty("java.class.path")... Then
recompile and run.
2. Run Eclipse in Debug mode, right click on running process, look under
Properties (don't remember exactly).
3. Export an Ant buildfile.
Dunno if that's helpful to anyone.
stephen
On 10/30/13 11:13 AM, "Finan, Sean"
wrote:
>Well, thanks to my not checking the utils pom (or building trunk since
>I'm currently still in incubator), I made Jenkins angry. Instead of
>adding uima as a dependency to ctakes-utils, I moved the cpe cli to
>ctakes-core. I hope that works. My apologies to anybody that checked
>out in the last hour.
>
>-Original Message-
>From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu]
>Sent: Wednesday, October 30, 2013 11:20 AM
>To: Lingren, Todd; dev@ctakes.apache.org
>Subject: RE: cTAKES user interface
>
>> Sean Finan (I think is on this group) already wrote a command line CPE
>>runner like Pei described.
>I am in this group, and I have written a very simple cli cpe runner. As
>Pei mentioned:
>
>>>> 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.
>The class that I have is probably not doing anything that others are not
>- in fact, I'm sure that I used somebody else's code as a template as I
>am not that familiar with Senior Nitty Gritty.
>
>I committed (Trunk, 1537124) a class named CmdLineCpeRunner.java to
>ctakes-utils in package ...utils.cpe It was so quick 'n dirty that
>there isn't any documentation, no logging, etc. but it gets the job done.
> It takes a path to a cpe.xml file as an argument and simply runs the
>pipeline specified therein.
>
>I suggest that James has the correct startup approach:
>> However you need to have a classpath set properly. To accomplish that,
>>you could try copying runctakesCPE.bat or runctakesCPE.sh and within
>>the script file, replacing org.apache.uima.tools.cpm.CpmFrame with
>>[CLASS TO CALL]
>
>To the best of my knowledge the easiest way to create the cpe.xml file is
>probably to run through the gui once, setting up the pipeline and saving
>the xml - but run through at least once to make certain that the pipeline
>works.
>
>Enjoy,
>Sean
>
>-Original Message-
>From: Lingren, Todd [mailto:todd.ling...@cchmc.org]
>Sent: Wednesday, October 30, 2013 9:52 AM
>To: dev@ctakes.apache.org
>Cc: Finan, Sean
>Subject: RE: cTAKES user interface
>
>Hi all,
>Sean Finan (I think is on this group) already wrote a command line CPE
>runner like Pei described. I've been using it and would be happy to
>provide some user guides if he provides the class,etc.
>
>Todd Lingren
>Biomedical Informatics
>Cincinnati Children's Hospital
>todd.ling...@cchmc.org
>513-803-9032
>
>
>-Original Message-
>From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu]
>Sent: Tuesday, October 29, 2013 9:56 PM
>To: dev@ctakes.apache.org
>Subject: 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
>>
>
>
RE: cTAKES user interface
Well, thanks to my not checking the utils pom (or building trunk since I'm currently still in incubator), I made Jenkins angry. Instead of adding uima as a dependency to ctakes-utils, I moved the cpe cli to ctakes-core. I hope that works. My apologies to anybody that checked out in the last hour. -Original Message- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Wednesday, October 30, 2013 11:20 AM To: Lingren, Todd; dev@ctakes.apache.org Subject: RE: cTAKES user interface > Sean Finan (I think is on this group) already wrote a command line CPE runner > like Pei described. I am in this group, and I have written a very simple cli cpe runner. As Pei mentioned: >>> 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. The class that I have is probably not doing anything that others are not - in fact, I'm sure that I used somebody else's code as a template as I am not that familiar with Senior Nitty Gritty. I committed (Trunk, 1537124) a class named CmdLineCpeRunner.java to ctakes-utils in package ...utils.cpe It was so quick 'n dirty that there isn't any documentation, no logging, etc. but it gets the job done. It takes a path to a cpe.xml file as an argument and simply runs the pipeline specified therein. I suggest that James has the correct startup approach: > However you need to have a classpath set properly. To accomplish that, >you could try copying runctakesCPE.bat or runctakesCPE.sh and within >the script file, replacing org.apache.uima.tools.cpm.CpmFrame with >[CLASS TO CALL] To the best of my knowledge the easiest way to create the cpe.xml file is probably to run through the gui once, setting up the pipeline and saving the xml - but run through at least once to make certain that the pipeline works. Enjoy, Sean -Original Message- From: Lingren, Todd [mailto:todd.ling...@cchmc.org] Sent: Wednesday, October 30, 2013 9:52 AM To: dev@ctakes.apache.org Cc: Finan, Sean Subject: RE: cTAKES user interface Hi all, Sean Finan (I think is on this group) already wrote a command line CPE runner like Pei described. I've been using it and would be happy to provide some user guides if he provides the class,etc. Todd Lingren Biomedical Informatics Cincinnati Children's Hospital todd.ling...@cchmc.org 513-803-9032 -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Tuesday, October 29, 2013 9:56 PM To: dev@ctakes.apache.org Subject: 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 >
RE: cTAKES user interface
Cool -Original Message- From: Lingren, Todd [mailto:todd.ling...@cchmc.org] Sent: Wednesday, October 30, 2013 11:50 AM To: dev@ctakes.apache.org Subject: RE: cTAKES user interface I would add that in our environment we use this command line cpe runner in on a large cluster over many folders. I have a small shell script that I've written to write a new cpe.xml for each folder in a parent folder. In this method we are able to achieve a pretty efficient pseudo-parallelization of ctakes. Todd Lingren Biomedical Informatics Cincinnati Children's Hospital todd.ling...@cchmc.org 513-803-9032 -Original Message- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Wednesday, October 30, 2013 11:15 AM To: Lingren, Todd; dev@ctakes.apache.org Subject: RE: cTAKES user interface > Sean Finan (I think is on this group) already wrote a command line CPE runner > like Pei described. I am in this group, and I have written a very simple cli cpe runner. As Pei mentioned: >>> 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. The class that I have is probably not doing anything that others are not - in fact, I'm sure that I used somebody else's code as a template as I am not that familiar with Senior Nitty Gritty. I committed (Trunk, 1537124) a class named CmdLineCpeRunner.java to ctakes-utils in package ...utils.cpe It was so quick 'n dirty that there isn't any documentation, no logging, etc. but it gets the job done. It takes a path to a cpe.xml file as an argument and simply runs the pipeline specified therein. I suggest that James has the correct startup approach: > However you need to have a classpath set properly. To accomplish that, >you could try copying runctakesCPE.bat or runctakesCPE.sh and within >the script file, replacing org.apache.uima.tools.cpm.CpmFrame with >[CLASS TO CALL] To the best of my knowledge the easiest way to create the cpe.xml file is probably to run through the gui once, setting up the pipeline and saving the xml - but run through at least once to make certain that the pipeline works. Enjoy, Sean -Original Message- From: Lingren, Todd [mailto:todd.ling...@cchmc.org] Sent: Wednesday, October 30, 2013 9:52 AM To: dev@ctakes.apache.org Cc: Finan, Sean Subject: RE: cTAKES user interface Hi all, Sean Finan (I think is on this group) already wrote a command line CPE runner like Pei described. I've been using it and would be happy to provide some user guides if he provides the class,etc. Todd Lingren Biomedical Informatics Cincinnati Children's Hospital todd.ling...@cchmc.org 513-803-9032 -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Tuesday, October 29, 2013 9:56 PM To: dev@ctakes.apache.org Subject: 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 >
RE: cTAKES user interface
I would add that in our environment we use this command line cpe runner in on a large cluster over many folders. I have a small shell script that I've written to write a new cpe.xml for each folder in a parent folder. In this method we are able to achieve a pretty efficient pseudo-parallelization of ctakes. Todd Lingren Biomedical Informatics Cincinnati Children's Hospital todd.ling...@cchmc.org 513-803-9032 -Original Message- From: Finan, Sean [mailto:sean.fi...@childrens.harvard.edu] Sent: Wednesday, October 30, 2013 11:15 AM To: Lingren, Todd; dev@ctakes.apache.org Subject: RE: cTAKES user interface > Sean Finan (I think is on this group) already wrote a command line CPE runner > like Pei described. I am in this group, and I have written a very simple cli cpe runner. As Pei mentioned: >>> 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. The class that I have is probably not doing anything that others are not - in fact, I'm sure that I used somebody else's code as a template as I am not that familiar with Senior Nitty Gritty. I committed (Trunk, 1537124) a class named CmdLineCpeRunner.java to ctakes-utils in package ...utils.cpe It was so quick 'n dirty that there isn't any documentation, no logging, etc. but it gets the job done. It takes a path to a cpe.xml file as an argument and simply runs the pipeline specified therein. I suggest that James has the correct startup approach: > However you need to have a classpath set properly. To accomplish that, >you could try copying runctakesCPE.bat or runctakesCPE.sh and within >the script file, replacing org.apache.uima.tools.cpm.CpmFrame with >[CLASS TO CALL] To the best of my knowledge the easiest way to create the cpe.xml file is probably to run through the gui once, setting up the pipeline and saving the xml - but run through at least once to make certain that the pipeline works. Enjoy, Sean -Original Message- From: Lingren, Todd [mailto:todd.ling...@cchmc.org] Sent: Wednesday, October 30, 2013 9:52 AM To: dev@ctakes.apache.org Cc: Finan, Sean Subject: RE: cTAKES user interface Hi all, Sean Finan (I think is on this group) already wrote a command line CPE runner like Pei described. I've been using it and would be happy to provide some user guides if he provides the class,etc. Todd Lingren Biomedical Informatics Cincinnati Children's Hospital todd.ling...@cchmc.org 513-803-9032 -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Tuesday, October 29, 2013 9:56 PM To: dev@ctakes.apache.org Subject: 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 >
RE: cTAKES user interface
> Sean Finan (I think is on this group) already wrote a command line CPE runner > like Pei described. I am in this group, and I have written a very simple cli cpe runner. As Pei mentioned: >>> 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. The class that I have is probably not doing anything that others are not - in fact, I'm sure that I used somebody else's code as a template as I am not that familiar with Senior Nitty Gritty. I committed (Trunk, 1537124) a class named CmdLineCpeRunner.java to ctakes-utils in package ...utils.cpe It was so quick 'n dirty that there isn't any documentation, no logging, etc. but it gets the job done. It takes a path to a cpe.xml file as an argument and simply runs the pipeline specified therein. I suggest that James has the correct startup approach: > However you need to have a classpath set properly. To accomplish that, you > could try copying runctakesCPE.bat or runctakesCPE.sh and within the script >file, replacing org.apache.uima.tools.cpm.CpmFrame with [CLASS TO CALL] To the best of my knowledge the easiest way to create the cpe.xml file is probably to run through the gui once, setting up the pipeline and saving the xml - but run through at least once to make certain that the pipeline works. Enjoy, Sean -Original Message- From: Lingren, Todd [mailto:todd.ling...@cchmc.org] Sent: Wednesday, October 30, 2013 9:52 AM To: dev@ctakes.apache.org Cc: Finan, Sean Subject: RE: cTAKES user interface Hi all, Sean Finan (I think is on this group) already wrote a command line CPE runner like Pei described. I've been using it and would be happy to provide some user guides if he provides the class,etc. Todd Lingren Biomedical Informatics Cincinnati Children's Hospital todd.ling...@cchmc.org 513-803-9032 -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Tuesday, October 29, 2013 9:56 PM To: dev@ctakes.apache.org Subject: 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 >
Re: cTAKES user interface
Hi all, Thank you so much for your reply. Yes I was trying to start it faster when I run it repeatedly. Your emails help me a lot. I really appreciate it. Thanks. Best, Pan On Wed, Oct 30, 2013 at 11:02 AM, Pan Teng wrote: > Hi all, > > Thank you so much for your reply. Yes I was trying to start it faster when > I run it repeatedly. Your emails help me a lot. I really appreciate it. > Thanks. > > Best, > Pan > > > On Wed, Oct 30, 2013 at 10:28 AM, Masanz, James J. > wrote: > >> >> Hi Pan, >> >> Is your interest in a command line because you are unable to open a GUI >> on your display, or is it for other reason, such as able to start it faster >> when you run repeatedly? Understanding why you are asking for a command >> line interface might help us make sure we address the root of the question. >> >> There is a class that will run one of the pipelines from the command line >> without a gui and put the xml output into a directory. However you need to >> have a classpath set properly. To accomplish that, you could try copying >> runctakesCPE.bat or runctakesCPE.sh >> and within the script file, replacing >> org.apache.uima.tools.cpm.CpmFrame >> with >> org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls >> >> For now that might be a start. >> >> >> All, >> I don't think the class I mentioned above is documented anywhere other >> than some brief comments at the start of the class. Maybe it could be a >> start of something simple that is command line driven until we get >> something with groovy written. Otherwise if a simpler interface (GUI) is >> needed than the UIMA-provided CPE/CVD GUIs (rather than strictly command >> line), perhaps our own GUI with some defaults would do a better job address >> new users. >> >> -- James >> >> -Original Message- >> From: dev-return-2154-Masanz.James=mayo@ctakes.apache.org [mailto: >> dev-return-2154-Masanz.James=mayo@ctakes.apache.org] On Behalf Of >> Miller, Timothy >> Sent: Tuesday, October 29, 2013 8:56 PM >> To: dev@ctakes.apache.org >> Subject: 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" < >> 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
I'll paste Pan's reply to my email here so it shows within the same thread: Hi all, Thank you so much for your reply. Yes I was trying to start it faster when I run it repeatedly. Your emails help me a lot. I really appreciate it. Thanks. Best, Pan -Original Message- From: dev-return-2158-Masanz.James=mayo@ctakes.apache.org [mailto:dev-return-2158-Masanz.James=mayo@ctakes.apache.org] On Behalf Of Masanz, James J. Sent: Wednesday, October 30, 2013 9:28 AM To: 'dev@ctakes.apache.org'; Pan Teng Subject: RE: cTAKES user interface Hi Pan, Is your interest in a command line because you are unable to open a GUI on your display, or is it for other reason, such as able to start it faster when you run repeatedly? Understanding why you are asking for a command line interface might help us make sure we address the root of the question. There is a class that will run one of the pipelines from the command line without a gui and put the xml output into a directory. However you need to have a classpath set properly. To accomplish that, you could try copying runctakesCPE.bat or runctakesCPE.sh and within the script file, replacing org.apache.uima.tools.cpm.CpmFrame with org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls For now that might be a start. All, I don't think the class I mentioned above is documented anywhere other than some brief comments at the start of the class. Maybe it could be a start of something simple that is command line driven until we get something with groovy written. Otherwise if a simpler interface (GUI) is needed than the UIMA-provided CPE/CVD GUIs (rather than strictly command line), perhaps our own GUI with some defaults would do a better job address new users. -- James -Original Message- From: dev-return-2154-Masanz.James=mayo@ctakes.apache.org [mailto:dev-return-2154-Masanz.James=mayo@ctakes.apache.org] On Behalf Of Miller, Timothy Sent: Tuesday, October 29, 2013 8:56 PM To: dev@ctakes.apache.org Subject: 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 >
RE: cTAKES user interface
Andy, You might want to talk with the folks at iDASH. They have an image with a number of NLP tools installed, but it doesn't have the latest version of cTAKES. http://idash.ucsd.edu/nlp/natural-language-processing-nlp-ecosystem Perhaps they would be open to your help with upgrading to a later version of cTAKES. -- James -Original Message- From: dev-return-2151-Masanz.James=mayo@ctakes.apache.org [mailto:dev-return-2151-Masanz.James=mayo@ctakes.apache.org] On Behalf Of andy mcmurry Sent: Tuesday, October 29, 2013 6:34 PM To: dev@ctakes.apache.org Subject: 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 Pan, Is your interest in a command line because you are unable to open a GUI on your display, or is it for other reason, such as able to start it faster when you run repeatedly? Understanding why you are asking for a command line interface might help us make sure we address the root of the question. There is a class that will run one of the pipelines from the command line without a gui and put the xml output into a directory. However you need to have a classpath set properly. To accomplish that, you could try copying runctakesCPE.bat or runctakesCPE.sh and within the script file, replacing org.apache.uima.tools.cpm.CpmFrame with org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls For now that might be a start. All, I don't think the class I mentioned above is documented anywhere other than some brief comments at the start of the class. Maybe it could be a start of something simple that is command line driven until we get something with groovy written. Otherwise if a simpler interface (GUI) is needed than the UIMA-provided CPE/CVD GUIs (rather than strictly command line), perhaps our own GUI with some defaults would do a better job address new users. -- James -Original Message- From: dev-return-2154-Masanz.James=mayo@ctakes.apache.org [mailto:dev-return-2154-Masanz.James=mayo@ctakes.apache.org] On Behalf Of Miller, Timothy Sent: Tuesday, October 29, 2013 8:56 PM To: dev@ctakes.apache.org Subject: 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 >
RE: cTAKES user interface
Hi all, Sean Finan (I think is on this group) already wrote a command line CPE runner like Pei described. I've been using it and would be happy to provide some user guides if he provides the class,etc. Todd Lingren Biomedical Informatics Cincinnati Children's Hospital todd.ling...@cchmc.org 513-803-9032 -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Tuesday, October 29, 2013 9:56 PM To: dev@ctakes.apache.org Subject: 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 >
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 >
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
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
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
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
+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
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 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
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
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
