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: Sundry
Hi John, I was away for a little bit and finally got a chance to catch up on emails... > 2) I work for the DoD and have latched on to several IRB approved projects > within that community where Ill be using cTakes, though minimally at first. > This is just a statement, a bug in the ear of the community of what people > are up to. This is really news! Looking forward to hearing more... > has anyone considered (and maybe the components already do this in some way I > haven't explored yet - time is ever limited) adding an OPQRST classifier? I'm not too familiar on how OPQRST would be determined from the patient's record. Just curious, how is it currently determined manually now? Is it a single score determined by a formula/rule(s)? Seems like another good use case for cTAKES output-- clinically focused. --Pei
Re: Sundry
Thanks for bumping this Pei, it reminds me I meant to respond to it. The OPQRST does sound like a great ML project. At a glance I might think a sequence model over sentences (like a CRF) would be a good model. But I'm wondering what the end use case is? Is it for teaching OPQRST to new clinicians? Or maybe as a sort of middleware for other projects where it might be a useful feature? Without a physician's intuition I sometimes suffer from a failure of imagination on these things. Tim On 10/30/2013 09:59 AM, Chen, Pei wrote: Hi John, I was away for a little bit and finally got a chance to catch up on emails... 2) I work for the DoD and have latched on to several IRB approved projects within that community where Ill be using cTakes, though minimally at first. This is just a statement, a bug in the ear of the community of what people are up to. This is really news! Looking forward to hearing more... has anyone considered (and maybe the components already do this in some way I haven't explored yet - time is ever limited) adding an OPQRST classifier? I'm not too familiar on how OPQRST would be determined from the patient's record. Just curious, how is it currently determined manually now? Is it a single score determined by a formula/rule(s)? Seems like another good use case for cTAKES output-- clinically focused. --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
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
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
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
> 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
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
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
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
>>
>
>
apache maven errors
Anyone else getting maven central errors recently? I was trying a fresh checkout and build of ctakes trunk... If using the apache parent pom 13: [INFO] Scanning for projects... Downloading: http://repo.maven.apache.org/maven2/org/apache/apache/13/apache-13.pom [ERROR] The build could not read 1 project -> [Help 1] [ERROR] [ERROR] Non-resolvable parent POM: Could not find artifact org.apache:apache:pom:13 in central (http://repo.maven.apache.org/maven2) and 'parent.relativePath' points at wrong local POM @ line 85, column 10 -> [Help 2] If using parent pom 11: [ERROR] Failed to execute goal on project ctakes-utils: Could not resolve dependencies for project org.apache.ctakes:ctakes-utils:jar:3.2.0-SNAPSHOT: The following artifacts could not be resolved: log4j:log4j:jar:1.2.16, org.apache.lucene:lucene-core:jar:4.0.0, org.apache.lucene:lucene-queries:jar:4 .0.0, org.apache.lucene:lucene-queryparser:jar:4.0.0, org.apache.lucene:lucene-analyzers-common:jar:4.0.0: Failure to find log4j:log4j:jar:1.2.16 in http://repo.maven.apache.org/maven2 was cached in the local repository, resolution will not be reattempted until the update interval of central has elapsed or updates are forced -> [Help 1] Wonder if there's just something weird going on with the env... --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 >> >>
