RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
Thanks James. I was planning on closing the vote today. In the meantime, does anyone a quick way to clone/rename the wiki documentation for 3.2? --Pei -Original Message- From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] Sent: Monday, July 21, 2014 4:25 PM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Here's the additional I've done I ran mvn test with 0 Failures and 0 Errors. Ran the AggregateTemplateFiller.xml and received same output (except for internal UIMA identifiers) with rc2 as I did with 3.1.1. +1 to release -Original Message- From: Masanz, James J. Sent: Wednesday, July 16, 2014 3:59 PM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) FYI, so far I have done the following steps: downloaded the source archive compiled it using: maven compile downloaded the separately available resources set up classpath to include e.g. jars (from the bin distribution) set ctakes.umlsuser and ctakes.umlspw env vars run runctakesCVD.bat loaded AggregatePlaintextUMLSProcessor.xml ran against some simple text. verified did not through an exception. verified some EventMention and EntityMention annotations were produced. I will do more testing tomorrow. Just giving a status update. --James -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Saturday, July 12, 2014 6:24 AM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Agreed on that. I downloaded the new resources binary and was able to run my tests on the - bin version of the RC. +1 for making this the release. Tim From: Masanz, James J. [masanz.ja...@mayo.edu] Sent: Friday, July 11, 2014 7:27 PM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) I agree about keeping the thread open. -- James -Original Message- From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu] Sent: Friday, July 11, 2014 4:28 PM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Updated the lvg.properties file within ctakes-resources on sourceforge [1]. Since the Apache cTAKES artifacts didn't change, I would like to keep this VOTE thread open. Also renamed it to 3.2.0 (even though they technically do not have to follow each other, but probably nice to keep it consistent for users as James suggested.) [1] http://sourceforge.net/projects/ctakesresources/files/ctakes-resources- 3.2.0.zip/download -Original Message- From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] Sent: Thursday, July 10, 2014 5:53 PM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Can you also give ctakesresources the number 3.2 or 3.2.0 instead of 3.1.3 -Original Message- From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu] Sent: Thursday, July 10, 2014 2:12 PM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) I think this is due to the fact that the default lvg.properties also exits in the ctakes-resources project, so if you download and replace, it will override the ctakes configured one. I think it's a bug, but probably always been there... I'll fix up ctakes-resources on sourceforge nethertheless but it shouldn't require any changes to the release candidates. -Original Message- From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] Sent: Thursday, July 10, 2014 11:59 AM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Hi Tim, When you say that it didn't seem to affect the run, where you comparing output to last release or just checking if data seemed OK at a glance? -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Thursday, July 10, 2014 7:29 AM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) I was able to run the binary without issues this time. I also downloaded the resources from sourceforge and integrated into the bin release and ran with the ctakes dictionary. I did get some weird exceptions thrown that didn't seem to affect the run -- looks like some hardcoded file paths in LVG? (See below) Tim Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/stopWords.data (No such file or directory) ** Error: problem of opening/reading stop words file: '/export/home/lu/Development/LVG/lvg2008/data/misc/stopWords.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/nonInfoWords.data (No such file or directory) ** Error: problem of opening/reading non-Info words file: '/export/home/lu/Development/LVG
RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
When I asked Troy that question for 3.1.1, he didn't know of a way, and I don't either, which is why I had the 3.1.1 page mostly just reference the 3.2 documentation. -Original Message- From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu] Sent: Tuesday, July 22, 2014 10:00 AM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Thanks James. I was planning on closing the vote today. In the meantime, does anyone a quick way to clone/rename the wiki documentation for 3.2? --Pei -Original Message- From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] Sent: Monday, July 21, 2014 4:25 PM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Here's the additional I've done I ran mvn test with 0 Failures and 0 Errors. Ran the AggregateTemplateFiller.xml and received same output (except for internal UIMA identifiers) with rc2 as I did with 3.1.1. +1 to release -Original Message- From: Masanz, James J. Sent: Wednesday, July 16, 2014 3:59 PM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) FYI, so far I have done the following steps: downloaded the source archive compiled it using: maven compile downloaded the separately available resources set up classpath to include e.g. jars (from the bin distribution) set ctakes.umlsuser and ctakes.umlspw env vars run runctakesCVD.bat loaded AggregatePlaintextUMLSProcessor.xml ran against some simple text. verified did not through an exception. verified some EventMention and EntityMention annotations were produced. I will do more testing tomorrow. Just giving a status update. --James -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Saturday, July 12, 2014 6:24 AM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Agreed on that. I downloaded the new resources binary and was able to run my tests on the - bin version of the RC. +1 for making this the release. Tim From: Masanz, James J. [masanz.ja...@mayo.edu] Sent: Friday, July 11, 2014 7:27 PM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) I agree about keeping the thread open. -- James -Original Message- From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu] Sent: Friday, July 11, 2014 4:28 PM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Updated the lvg.properties file within ctakes-resources on sourceforge [1]. Since the Apache cTAKES artifacts didn't change, I would like to keep this VOTE thread open. Also renamed it to 3.2.0 (even though they technically do not have to follow each other, but probably nice to keep it consistent for users as James suggested.) [1] http://sourceforge.net/projects/ctakesresources/files/ctakes-resources- 3.2.0.zip/download -Original Message- From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] Sent: Thursday, July 10, 2014 5:53 PM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Can you also give ctakesresources the number 3.2 or 3.2.0 instead of 3.1.3 -Original Message- From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu] Sent: Thursday, July 10, 2014 2:12 PM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) I think this is due to the fact that the default lvg.properties also exits in the ctakes-resources project, so if you download and replace, it will override the ctakes configured one. I think it's a bug, but probably always been there... I'll fix up ctakes-resources on sourceforge nethertheless but it shouldn't require any changes to the release candidates. -Original Message- From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] Sent: Thursday, July 10, 2014 11:59 AM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Hi Tim, When you say that it didn't seem to affect the run, where you comparing output to last release or just checking if data seemed OK at a glance? -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Thursday, July 10, 2014 7:29 AM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) I was able to run the binary without issues this time. I also downloaded the resources from sourceforge and integrated into the bin release and ran with the ctakes dictionary. I did get some weird exceptions thrown that didn't seem to affect the run -- looks like some hardcoded file paths in LVG? (See below) Tim Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/stopWords.data (No such file or directory
RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
One page at a time. At least there's that. Thanks Troy -Original Message- From: Masanz, James J. Sent: Tuesday, July 22, 2014 10:38 AM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) When I asked Troy that question for 3.1.1, he didn't know of a way, and I don't either, which is why I had the 3.1.1 page mostly just reference the 3.2 documentation. -Original Message- From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu] Sent: Tuesday, July 22, 2014 10:00 AM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Thanks James. I was planning on closing the vote today. In the meantime, does anyone a quick way to clone/rename the wiki documentation for 3.2? --Pei -Original Message- From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] Sent: Monday, July 21, 2014 4:25 PM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Here's the additional I've done I ran mvn test with 0 Failures and 0 Errors. Ran the AggregateTemplateFiller.xml and received same output (except for internal UIMA identifiers) with rc2 as I did with 3.1.1. +1 to release -Original Message- From: Masanz, James J. Sent: Wednesday, July 16, 2014 3:59 PM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) FYI, so far I have done the following steps: downloaded the source archive compiled it using: maven compile downloaded the separately available resources set up classpath to include e.g. jars (from the bin distribution) set ctakes.umlsuser and ctakes.umlspw env vars run runctakesCVD.bat loaded AggregatePlaintextUMLSProcessor.xml ran against some simple text. verified did not through an exception. verified some EventMention and EntityMention annotations were produced. I will do more testing tomorrow. Just giving a status update. --James -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Saturday, July 12, 2014 6:24 AM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Agreed on that. I downloaded the new resources binary and was able to run my tests on the - bin version of the RC. +1 for making this the release. Tim From: Masanz, James J. [masanz.ja...@mayo.edu] Sent: Friday, July 11, 2014 7:27 PM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) I agree about keeping the thread open. -- James -Original Message- From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu] Sent: Friday, July 11, 2014 4:28 PM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Updated the lvg.properties file within ctakes-resources on sourceforge [1]. Since the Apache cTAKES artifacts didn't change, I would like to keep this VOTE thread open. Also renamed it to 3.2.0 (even though they technically do not have to follow each other, but probably nice to keep it consistent for users as James suggested.) [1] http://sourceforge.net/projects/ctakesresources/files/ctakes-resources - 3.2.0.zip/download -Original Message- From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] Sent: Thursday, July 10, 2014 5:53 PM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Can you also give ctakesresources the number 3.2 or 3.2.0 instead of 3.1.3 -Original Message- From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu] Sent: Thursday, July 10, 2014 2:12 PM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) I think this is due to the fact that the default lvg.properties also exits in the ctakes-resources project, so if you download and replace, it will override the ctakes configured one. I think it's a bug, but probably always been there... I'll fix up ctakes-resources on sourceforge nethertheless but it shouldn't require any changes to the release candidates. -Original Message- From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] Sent: Thursday, July 10, 2014 11:59 AM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Hi Tim, When you say that it didn't seem to affect the run, where you comparing output to last release or just checking if data seemed OK at a glance? -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Thursday, July 10, 2014 7:29 AM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) I was able to run the binary without issues this time. I also downloaded the resources from sourceforge and integrated into the bin release and ran with the ctakes dictionary. I did get some weird exceptions thrown that didn't seem
RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
There is currently no guides on the confluence wiki for cTAKES 3.2.0... I was thinking of just cloning 3.1.1 https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1.1 And just add the YTEX and/or any new changes to it... Would be grateful for any help here... -Original Message- From: John Green [mailto:john.travis.gr...@gmail.com] Sent: Tuesday, July 22, 2014 2:37 PM To: dev@ctakes.apache.org Subject: Re: [VOTE] Release Apache cTAKES 3.2.0 (rc2) What exactly needs updated? I have not had the time (unfortunately) to help with this project very much because of the steep learning curve on the technology. I'm currently on some protected research time working with cTakes as of this week and would be happy to help with some grunt work. JG On Tue, Jul 22, 2014 at 11:39 AM, Bleeker, Troy C. bleeker.t...@mayo.edu wrote: One page at a time. At least there's that. Thanks Troy -Original Message- From: Masanz, James J. Sent: Tuesday, July 22, 2014 10:38 AM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) When I asked Troy that question for 3.1.1, he didn't know of a way, and I don't either, which is why I had the 3.1.1 page mostly just reference the 3.2 documentation. -Original Message- From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu] Sent: Tuesday, July 22, 2014 10:00 AM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Thanks James. I was planning on closing the vote today. In the meantime, does anyone a quick way to clone/rename the wiki documentation for 3.2? --Pei -Original Message- From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] Sent: Monday, July 21, 2014 4:25 PM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Here's the additional I've done I ran mvn test with 0 Failures and 0 Errors. Ran the AggregateTemplateFiller.xml and received same output (except for internal UIMA identifiers) with rc2 as I did with 3.1.1. +1 to release -Original Message- From: Masanz, James J. Sent: Wednesday, July 16, 2014 3:59 PM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) FYI, so far I have done the following steps: downloaded the source archive compiled it using: maven compile downloaded the separately available resources set up classpath to include e.g. jars (from the bin distribution) set ctakes.umlsuser and ctakes.umlspw env vars run runctakesCVD.bat loaded AggregatePlaintextUMLSProcessor.xml ran against some simple text. verified did not through an exception. verified some EventMention and EntityMention annotations were produced. I will do more testing tomorrow. Just giving a status update. --James -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Saturday, July 12, 2014 6:24 AM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Agreed on that. I downloaded the new resources binary and was able to run my tests on the - bin version of the RC. +1 for making this the release. Tim From: Masanz, James J. [masanz.ja...@mayo.edu] Sent: Friday, July 11, 2014 7:27 PM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) I agree about keeping the thread open. -- James -Original Message- From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu] Sent: Friday, July 11, 2014 4:28 PM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Updated the lvg.properties file within ctakes-resources on sourceforge [1]. Since the Apache cTAKES artifacts didn't change, I would like to keep this VOTE thread open. Also renamed it to 3.2.0 (even though they technically do not have to follow each other, but probably nice to keep it consistent for users as James suggested.) [1] http://sourceforge.net/projects/ctakesresources/files/ctakes-resourc es - 3.2.0.zip/download -Original Message- From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] Sent: Thursday, July 10, 2014 5:53 PM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Can you also give ctakesresources the number 3.2 or 3.2.0 instead of 3.1.3 -Original Message- From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu] Sent: Thursday, July 10, 2014 2:12 PM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) I think this is due to the fact that the default lvg.properties also exits in the ctakes-resources project, so if you download and replace, it will override
RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
Ill play with it tonight or tomorrow night. JG — Sent from Mailbox for iPhone On Tue, Jul 22, 2014 at 4:27 PM, Chen, Pei pei.c...@childrens.harvard.edu wrote: There is currently no guides on the confluence wiki for cTAKES 3.2.0... I was thinking of just cloning 3.1.1 https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1.1 And just add the YTEX and/or any new changes to it... Would be grateful for any help here... -Original Message- From: John Green [mailto:john.travis.gr...@gmail.com] Sent: Tuesday, July 22, 2014 2:37 PM To: dev@ctakes.apache.org Subject: Re: [VOTE] Release Apache cTAKES 3.2.0 (rc2) What exactly needs updated? I have not had the time (unfortunately) to help with this project very much because of the steep learning curve on the technology. I'm currently on some protected research time working with cTakes as of this week and would be happy to help with some grunt work. JG On Tue, Jul 22, 2014 at 11:39 AM, Bleeker, Troy C. bleeker.t...@mayo.edu wrote: One page at a time. At least there's that. Thanks Troy -Original Message- From: Masanz, James J. Sent: Tuesday, July 22, 2014 10:38 AM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) When I asked Troy that question for 3.1.1, he didn't know of a way, and I don't either, which is why I had the 3.1.1 page mostly just reference the 3.2 documentation. -Original Message- From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu] Sent: Tuesday, July 22, 2014 10:00 AM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Thanks James. I was planning on closing the vote today. In the meantime, does anyone a quick way to clone/rename the wiki documentation for 3.2? --Pei -Original Message- From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] Sent: Monday, July 21, 2014 4:25 PM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Here's the additional I've done I ran mvn test with 0 Failures and 0 Errors. Ran the AggregateTemplateFiller.xml and received same output (except for internal UIMA identifiers) with rc2 as I did with 3.1.1. +1 to release -Original Message- From: Masanz, James J. Sent: Wednesday, July 16, 2014 3:59 PM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) FYI, so far I have done the following steps: downloaded the source archive compiled it using: maven compile downloaded the separately available resources set up classpath to include e.g. jars (from the bin distribution) set ctakes.umlsuser and ctakes.umlspw env vars run runctakesCVD.bat loaded AggregatePlaintextUMLSProcessor.xml ran against some simple text. verified did not through an exception. verified some EventMention and EntityMention annotations were produced. I will do more testing tomorrow. Just giving a status update. --James -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Saturday, July 12, 2014 6:24 AM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Agreed on that. I downloaded the new resources binary and was able to run my tests on the - bin version of the RC. +1 for making this the release. Tim From: Masanz, James J. [masanz.ja...@mayo.edu] Sent: Friday, July 11, 2014 7:27 PM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) I agree about keeping the thread open. -- James -Original Message- From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu] Sent: Friday, July 11, 2014 4:28 PM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Updated the lvg.properties file within ctakes-resources on sourceforge [1]. Since the Apache cTAKES artifacts didn't change, I would like to keep this VOTE thread open. Also renamed it to 3.2.0 (even though they technically do not have to follow each other, but probably nice to keep it consistent for users as James suggested.) [1] http://sourceforge.net/projects/ctakesresources/files/ctakes-resourc es - 3.2.0.zip/download -Original Message- From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] Sent: Thursday, July 10, 2014 5:53 PM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Can you also give ctakesresources the number 3.2 or 3.2.0 instead of 3.1.3 -Original Message- From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu] Sent: Thursday, July 10, 2014 2:12 PM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) I
RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
Here's the additional I've done I ran mvn test with 0 Failures and 0 Errors. Ran the AggregateTemplateFiller.xml and received same output (except for internal UIMA identifiers) with rc2 as I did with 3.1.1. +1 to release -Original Message- From: Masanz, James J. Sent: Wednesday, July 16, 2014 3:59 PM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) FYI, so far I have done the following steps: downloaded the source archive compiled it using: maven compile downloaded the separately available resources set up classpath to include e.g. jars (from the bin distribution) set ctakes.umlsuser and ctakes.umlspw env vars run runctakesCVD.bat loaded AggregatePlaintextUMLSProcessor.xml ran against some simple text. verified did not through an exception. verified some EventMention and EntityMention annotations were produced. I will do more testing tomorrow. Just giving a status update. --James -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Saturday, July 12, 2014 6:24 AM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Agreed on that. I downloaded the new resources binary and was able to run my tests on the -bin version of the RC. +1 for making this the release. Tim From: Masanz, James J. [masanz.ja...@mayo.edu] Sent: Friday, July 11, 2014 7:27 PM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) I agree about keeping the thread open. -- James -Original Message- From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu] Sent: Friday, July 11, 2014 4:28 PM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Updated the lvg.properties file within ctakes-resources on sourceforge [1]. Since the Apache cTAKES artifacts didn't change, I would like to keep this VOTE thread open. Also renamed it to 3.2.0 (even though they technically do not have to follow each other, but probably nice to keep it consistent for users as James suggested.) [1] http://sourceforge.net/projects/ctakesresources/files/ctakes-resources-3.2.0.zip/download -Original Message- From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] Sent: Thursday, July 10, 2014 5:53 PM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Can you also give ctakesresources the number 3.2 or 3.2.0 instead of 3.1.3 -Original Message- From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu] Sent: Thursday, July 10, 2014 2:12 PM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) I think this is due to the fact that the default lvg.properties also exits in the ctakes-resources project, so if you download and replace, it will override the ctakes configured one. I think it's a bug, but probably always been there... I'll fix up ctakes-resources on sourceforge nethertheless but it shouldn't require any changes to the release candidates. -Original Message- From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] Sent: Thursday, July 10, 2014 11:59 AM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Hi Tim, When you say that it didn't seem to affect the run, where you comparing output to last release or just checking if data seemed OK at a glance? -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Thursday, July 10, 2014 7:29 AM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) I was able to run the binary without issues this time. I also downloaded the resources from sourceforge and integrated into the bin release and ran with the ctakes dictionary. I did get some weird exceptions thrown that didn't seem to affect the run -- looks like some hardcoded file paths in LVG? (See below) Tim Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/stopWords.data (No such file or directory) ** Error: problem of opening/reading stop words file: '/export/home/lu/Development/LVG/lvg2008/data/misc/stopWords.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/nonInfoWords.data (No such file or directory) ** Error: problem of opening/reading non-Info words file: '/export/home/lu/Development/LVG/lvg2008/data/misc/nonInfoWords.dat a'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/conjunctionWord.d ata (No such file or directory) ** Error: problem of opening/reading conjunction words file: '/export/home/lu/Development/LVG/lvg2008/data/misc/conjunctionWord. data'. ** ERR: problem of opening/reading diacritics file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/diacriticMap.da ta'. Exception
RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
Updated the lvg.properties file within ctakes-resources on sourceforge [1]. Since the Apache cTAKES artifacts didn't change, I would like to keep this VOTE thread open. Also renamed it to 3.2.0 (even though they technically do not have to follow each other, but probably nice to keep it consistent for users as James suggested.) [1] http://sourceforge.net/projects/ctakesresources/files/ctakes-resources-3.2.0.zip/download -Original Message- From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] Sent: Thursday, July 10, 2014 5:53 PM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Can you also give ctakesresources the number 3.2 or 3.2.0 instead of 3.1.3 -Original Message- From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu] Sent: Thursday, July 10, 2014 2:12 PM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) I think this is due to the fact that the default lvg.properties also exits in the ctakes-resources project, so if you download and replace, it will override the ctakes configured one. I think it's a bug, but probably always been there... I'll fix up ctakes-resources on sourceforge nethertheless but it shouldn't require any changes to the release candidates. -Original Message- From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] Sent: Thursday, July 10, 2014 11:59 AM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Hi Tim, When you say that it didn't seem to affect the run, where you comparing output to last release or just checking if data seemed OK at a glance? -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Thursday, July 10, 2014 7:29 AM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) I was able to run the binary without issues this time. I also downloaded the resources from sourceforge and integrated into the bin release and ran with the ctakes dictionary. I did get some weird exceptions thrown that didn't seem to affect the run -- looks like some hardcoded file paths in LVG? (See below) Tim Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/stopWords.data (No such file or directory) ** Error: problem of opening/reading stop words file: '/export/home/lu/Development/LVG/lvg2008/data/misc/stopWords.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/nonInfoWords.data (No such file or directory) ** Error: problem of opening/reading non-Info words file: '/export/home/lu/Development/LVG/lvg2008/data/misc/nonInfoWords.dat a'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/conjunctionWord.d ata (No such file or directory) ** Error: problem of opening/reading conjunction words file: '/export/home/lu/Development/LVG/lvg2008/data/misc/conjunctionWord. data'. ** ERR: problem of opening/reading diacritics file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/diacriticMap.da ta'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/diacriticMap.da ta (No such file or directory) Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/ligatureMap.da ta (No such file or directory) ** Error: problem of opening/reading ligature file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/ligatureMap.da ta'. ** Error: problem of opening/reading symbol synonym file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/synonymMap. data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/synonymMap.d ata (No such file or directory) **Error: problem of opening/reading file '/export/home/lu/Development/LVG/lvg2008/data/misc/removeS.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/removeS.data (No such file or directory) ** Error: problem of opening/reading Unicode symbol file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/symbolMap.da ta'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/symbolMap.dat a (No such file or directory) ** Error: problem of opening/reading Unicode file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/unicodeMap.d ata'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/unicodeMap.da ta (No such file or directory) ** Error: problem of opening/reading nonStripMap file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/nonStripMap.d ata'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/nonStripMap.d ata
RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
I agree about keeping the thread open. -- James -Original Message- From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu] Sent: Friday, July 11, 2014 4:28 PM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Updated the lvg.properties file within ctakes-resources on sourceforge [1]. Since the Apache cTAKES artifacts didn't change, I would like to keep this VOTE thread open. Also renamed it to 3.2.0 (even though they technically do not have to follow each other, but probably nice to keep it consistent for users as James suggested.) [1] http://sourceforge.net/projects/ctakesresources/files/ctakes-resources-3.2.0.zip/download -Original Message- From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] Sent: Thursday, July 10, 2014 5:53 PM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Can you also give ctakesresources the number 3.2 or 3.2.0 instead of 3.1.3 -Original Message- From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu] Sent: Thursday, July 10, 2014 2:12 PM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) I think this is due to the fact that the default lvg.properties also exits in the ctakes-resources project, so if you download and replace, it will override the ctakes configured one. I think it's a bug, but probably always been there... I'll fix up ctakes-resources on sourceforge nethertheless but it shouldn't require any changes to the release candidates. -Original Message- From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] Sent: Thursday, July 10, 2014 11:59 AM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Hi Tim, When you say that it didn't seem to affect the run, where you comparing output to last release or just checking if data seemed OK at a glance? -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Thursday, July 10, 2014 7:29 AM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) I was able to run the binary without issues this time. I also downloaded the resources from sourceforge and integrated into the bin release and ran with the ctakes dictionary. I did get some weird exceptions thrown that didn't seem to affect the run -- looks like some hardcoded file paths in LVG? (See below) Tim Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/stopWords.data (No such file or directory) ** Error: problem of opening/reading stop words file: '/export/home/lu/Development/LVG/lvg2008/data/misc/stopWords.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/nonInfoWords.data (No such file or directory) ** Error: problem of opening/reading non-Info words file: '/export/home/lu/Development/LVG/lvg2008/data/misc/nonInfoWords.dat a'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/conjunctionWord.d ata (No such file or directory) ** Error: problem of opening/reading conjunction words file: '/export/home/lu/Development/LVG/lvg2008/data/misc/conjunctionWord. data'. ** ERR: problem of opening/reading diacritics file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/diacriticMap.da ta'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/diacriticMap.da ta (No such file or directory) Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/ligatureMap.da ta (No such file or directory) ** Error: problem of opening/reading ligature file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/ligatureMap.da ta'. ** Error: problem of opening/reading symbol synonym file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/synonymMap. data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/synonymMap.d ata (No such file or directory) **Error: problem of opening/reading file '/export/home/lu/Development/LVG/lvg2008/data/misc/removeS.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/removeS.data (No such file or directory) ** Error: problem of opening/reading Unicode symbol file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/symbolMap.da ta'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/symbolMap.dat a (No such file or directory) ** Error: problem of opening/reading Unicode file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/unicodeMap.d ata'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/unicodeMap.da ta (No such file or directory) ** Error
RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
I was able to run the binary without issues this time. I also downloaded the resources from sourceforge and integrated into the bin release and ran with the ctakes dictionary. I did get some weird exceptions thrown that didn't seem to affect the run -- looks like some hardcoded file paths in LVG? (See below) Tim Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/stopWords.data (No such file or directory) ** Error: problem of opening/reading stop words file: '/export/home/lu/Development/LVG/lvg2008/data/misc/stopWords.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/nonInfoWords.data (No such file or directory) ** Error: problem of opening/reading non-Info words file: '/export/home/lu/Development/LVG/lvg2008/data/misc/nonInfoWords.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/conjunctionWord.data (No such file or directory) ** Error: problem of opening/reading conjunction words file: '/export/home/lu/Development/LVG/lvg2008/data/misc/conjunctionWord.data'. ** ERR: problem of opening/reading diacritics file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/diacriticMap.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/diacriticMap.data (No such file or directory) Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/ligatureMap.data (No such file or directory) ** Error: problem of opening/reading ligature file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/ligatureMap.data'. ** Error: problem of opening/reading symbol synonym file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/synonymMap.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/synonymMap.data (No such file or directory) **Error: problem of opening/reading file '/export/home/lu/Development/LVG/lvg2008/data/misc/removeS.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/removeS.data (No such file or directory) ** Error: problem of opening/reading Unicode symbol file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/symbolMap.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/symbolMap.data (No such file or directory) ** Error: problem of opening/reading Unicode file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/unicodeMap.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/unicodeMap.data (No such file or directory) ** Error: problem of opening/reading nonStripMap file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/nonStripMap.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/nonStripMap.data (No such file or directory) java.sql.SQLException: File input/output error /export/home/lu/Development/LVG/lvg2008/data/HSqlDb/lvg2008.properties java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/HSqlDb/lvg2008.properties.new (No such file or directory) From: Masanz, James J. [masanz.ja...@mayo.edu] Sent: Wednesday, July 09, 2014 2:26 PM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) So far for rc2, I've Verified MD5 and signatures of .zip archives Verified that source at tag matches source in.zip Imported source from archive into eclipse as maven project(s) and compiled without any Errors. -- James -Original Message- From: Pei Chen [mailto:chen...@apache.org] Sent: Tuesday, July 08, 2014 5:11 PM To: dev@ctakes.apache.org Subject: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Hi all, The main difference between rc1 and rc2 is that we removed the lvg-res and assertion-res.jar from the distro. They still need to be unpacked. This is a call for a vote on releasing the following candidate (rc2) as Apache cTAKES 3.2.0. The major changes include: - New optional YTEX component(s) (Yale Extensions to cTAKES) - New optional improved/faster dictionary lookup (dictionary-lookup-fast) - New optional Temporal component (Time + Event extraction. Relations will be including in a future release.) - Other bug fixes/enhancements from Jira [TODO: Online documentation still needs to be updated on wiki] For more detailed information on the changes/release notes, please visit: https://issues.apache.org/jira/secure/ReleaseNote.jspa?projectId=12313621version=12324066 The release was made using the cTAKES release process documented here: http://ctakes.apache.org/ctakes-release-guide.html The candidate is available at: http://people.apache.org/~chenpei/RCs/ctakes-3.2.0-rc2/apache-ctakes-3.2.0-src.tar.gz /.zip The tag to be voted on: http://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.2.0-rc2 The MD5
RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
+1 for the ytex method of handling a umls login before download of the umls resources. While this also doesn't truly prevent people from sharing files (data) without a umls account, it is a little bit of a nicer mechanism. Aside ... Does anybody out there have experience with izpack? (izpack.org) Creation of an InstallAnywhere style module is under consideration ... -Original Message- From: vijay garla [mailto:vnga...@gmail.com] Sent: Wednesday, July 09, 2014 10:30 AM To: dev@ctakes.apache.org Subject: Re: [VOTE] Release Apache cTAKES 3.2.0 (rc2) ctakes-ytex-lib-3.1.2-SNAPSHOT.zip https://ytex.googlecode.com/files/ctakes-ytex-lib-3.1.2-SNAPSHOT.zip - this contains non-asf compliant ytex libs. I would like to add it to the sourceforge site / or add it to the ctakes resources directly (that way users simply have to unzip a single zip file) ctakes-ytex-resources-3.1.2-SNAPSHOT.zip http://www.ytex-nlp.org/umls.download/secure/3.1/ctakes-ytex-resources- 3.1.2-SNAPSHOT.zip - this contains data derived from the UMLS - concept graphs and dictionary lookup tables. downloading this requires a UTS login. It is conceptually no different from the ctakes resources, so I believe it would be OK to add it to that zip file, but I'm not a lawyer. On another note: I think forcing users to specify the UTS username/password and contacting NIH every time you run cTAKES is problematic, and doesn't prevent users who don't have a valid UTS login from viewing the data contained in the lucene index dictionary. I personally believe requiring a UTS login to download would be the best way to make resources derived from the UMLS available to users (this is what I'm doing for ytex-resources). to summarize: for now, I would like to add the ytex libs to the ctakes resources zip. -vj On Wed, Jul 9, 2014 at 4:04 PM, Chen, Pei pei.c...@childrens.harvard.edu wrote: The maven artifacts are also available in the staging area: https://repository.apache.org/content/repositories/orgapachectakes-100 1 VJ: Just curious- how did you envision ytex users downloading the jars/war? From the distro bin.zip or from maven central? --Pei -Original Message- From: Pei Chen [mailto:chen...@apache.org] Sent: Tuesday, July 08, 2014 6:11 PM To: dev@ctakes.apache.org Subject: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Hi all, The main difference between rc1 and rc2 is that we removed the lvg-res and assertion-res.jar from the distro. They still need to be unpacked. This is a call for a vote on releasing the following candidate (rc2) as Apache cTAKES 3.2.0. The major changes include: - New optional YTEX component(s) (Yale Extensions to cTAKES) - New optional improved/faster dictionary lookup (dictionary-lookup-fast) - New optional Temporal component (Time + Event extraction. Relations will be including in a future release.) - Other bug fixes/enhancements from Jira [TODO: Online documentation still needs to be updated on wiki] For more detailed information on the changes/release notes, please visit: https://issues.apache.org/jira/secure/ReleaseNote.jspa?projectId=12313 621 version=12324066 The release was made using the cTAKES release process documented here: http://ctakes.apache.org/ctakes-release-guide.html The candidate is available at: http://people.apache.org/~chenpei/RCs/ctakes-3.2.0-rc2/apache-ctakes - 3.2.0-src.tar.gz /.zip The tag to be voted on: http://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.2.0-rc2 The MD5 checksum of the tarball can be found at: http://people.apache.org/~chenpei/RCs/ctakes-3.2.0-rc2/apache-ctakes - 3.2.0-src.tar.gz.md5 /.zip.md5 The signature of the tarball can be found at: http://people.apache.org/~chenpei/RCs/ctakes-3.2.0-rc2/apache-ctakes - 3.2.0-src.tar.gz.asc /.zip.asc Apache cTAKES' KEYS file, containing the PGP keys used to sign the release: https://dist.apache.org/repos/dist/release/ctakes/KEYS Please vote on releasing these packages as Apache cTAKES 3.2.0. The vote is open for at least the next 72 hours. Only votes from the cTAKES PMC are binding, but folks are welcome to check the release candidate and voice their approval or disapproval. The vote passes if at least three binding +1 votes are cast. [ ] +1 Release the packages as Apache cTAKES 3.2.0 [ ] -1 Do not release the packages because... Also, the convenience binary can be found at: http://people.apache.org/~chenpei/RCs/ctakes-3.2.0-rc2/apache-ctakes - 3.2.0-bin.tar.gz /.zip Note: It's temporarily on people.a.o because the artifacts were too large for https://dist.apache.org/repos/dist/dev/ctakes (Working with infra on increasing the limit). Thanks!
RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
Hi Tim, When you say that it didn't seem to affect the run, where you comparing output to last release or just checking if data seemed OK at a glance? -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Thursday, July 10, 2014 7:29 AM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) I was able to run the binary without issues this time. I also downloaded the resources from sourceforge and integrated into the bin release and ran with the ctakes dictionary. I did get some weird exceptions thrown that didn't seem to affect the run -- looks like some hardcoded file paths in LVG? (See below) Tim Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/stopWords.data (No such file or directory) ** Error: problem of opening/reading stop words file: '/export/home/lu/Development/LVG/lvg2008/data/misc/stopWords.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/nonInfoWords.data (No such file or directory) ** Error: problem of opening/reading non-Info words file: '/export/home/lu/Development/LVG/lvg2008/data/misc/nonInfoWords.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/conjunctionWord.data (No such file or directory) ** Error: problem of opening/reading conjunction words file: '/export/home/lu/Development/LVG/lvg2008/data/misc/conjunctionWord.data'. ** ERR: problem of opening/reading diacritics file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/diacriticMap.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/diacriticMap.data (No such file or directory) Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/ligatureMap.data (No such file or directory) ** Error: problem of opening/reading ligature file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/ligatureMap.data'. ** Error: problem of opening/reading symbol synonym file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/synonymMap.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/synonymMap.data (No such file or directory) **Error: problem of opening/reading file '/export/home/lu/Development/LVG/lvg2008/data/misc/removeS.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/removeS.data (No such file or directory) ** Error: problem of opening/reading Unicode symbol file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/symbolMap.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/symbolMap.data (No such file or directory) ** Error: problem of opening/reading Unicode file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/unicodeMap.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/unicodeMap.data (No such file or directory) ** Error: problem of opening/reading nonStripMap file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/nonStripMap.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/nonStripMap.data (No such file or directory) java.sql.SQLException: File input/output error /export/home/lu/Development/LVG/lvg2008/data/HSqlDb/lvg2008.properties java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/HSqlDb/lvg2008.properties.new (No such file or directory) From: Masanz, James J. [masanz.ja...@mayo.edu] Sent: Wednesday, July 09, 2014 2:26 PM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) So far for rc2, I've Verified MD5 and signatures of .zip archives Verified that source at tag matches source in.zip Imported source from archive into eclipse as maven project(s) and compiled without any Errors. -- James -Original Message- From: Pei Chen [mailto:chen...@apache.org] Sent: Tuesday, July 08, 2014 5:11 PM To: dev@ctakes.apache.org Subject: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Hi all, The main difference between rc1 and rc2 is that we removed the lvg-res and assertion-res.jar from the distro. They still need to be unpacked. This is a call for a vote on releasing the following candidate (rc2) as Apache cTAKES 3.2.0. The major changes include: - New optional YTEX component(s) (Yale Extensions to cTAKES) - New optional improved/faster dictionary lookup (dictionary-lookup-fast) - New optional Temporal component (Time + Event extraction. Relations will be including in a future release.) - Other bug fixes/enhancements from Jira [TODO: Online documentation still needs to be updated on wiki] For more detailed information on the changes/release notes, please visit: https://issues.apache.org/jira/secure/ReleaseNote.jspa?projectId
Re: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
Sorry, I should've been more specific. I just meant that it didn't prevent the pipeline from running and that it recognized the named entities in the small examples I gave it. It could be that it is causing the LVG annotator to operate incorrectly in a way that didn't obviously affect downstream components at a glance. Tim On 07/10/2014 11:59 AM, Masanz, James J. wrote: Hi Tim, When you say that it didn't seem to affect the run, where you comparing output to last release or just checking if data seemed OK at a glance? -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Thursday, July 10, 2014 7:29 AM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) I was able to run the binary without issues this time. I also downloaded the resources from sourceforge and integrated into the bin release and ran with the ctakes dictionary. I did get some weird exceptions thrown that didn't seem to affect the run -- looks like some hardcoded file paths in LVG? (See below) Tim Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/stopWords.data (No such file or directory) ** Error: problem of opening/reading stop words file: '/export/home/lu/Development/LVG/lvg2008/data/misc/stopWords.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/nonInfoWords.data (No such file or directory) ** Error: problem of opening/reading non-Info words file: '/export/home/lu/Development/LVG/lvg2008/data/misc/nonInfoWords.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/conjunctionWord.data (No such file or directory) ** Error: problem of opening/reading conjunction words file: '/export/home/lu/Development/LVG/lvg2008/data/misc/conjunctionWord.data'. ** ERR: problem of opening/reading diacritics file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/diacriticMap.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/diacriticMap.data (No such file or directory) Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/ligatureMap.data (No such file or directory) ** Error: problem of opening/reading ligature file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/ligatureMap.data'. ** Error: problem of opening/reading symbol synonym file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/synonymMap.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/synonymMap.data (No such file or directory) **Error: problem of opening/reading file '/export/home/lu/Development/LVG/lvg2008/data/misc/removeS.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/removeS.data (No such file or directory) ** Error: problem of opening/reading Unicode symbol file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/symbolMap.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/symbolMap.data (No such file or directory) ** Error: problem of opening/reading Unicode file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/unicodeMap.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/unicodeMap.data (No such file or directory) ** Error: problem of opening/reading nonStripMap file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/nonStripMap.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/nonStripMap.data (No such file or directory) java.sql.SQLException: File input/output error /export/home/lu/Development/LVG/lvg2008/data/HSqlDb/lvg2008.properties java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/HSqlDb/lvg2008.properties.new (No such file or directory) From: Masanz, James J. [masanz.ja...@mayo.edu] Sent: Wednesday, July 09, 2014 2:26 PM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) So far for rc2, I've Verified MD5 and signatures of .zip archives Verified that source at tag matches source in.zip Imported source from archive into eclipse as maven project(s) and compiled without any Errors. -- James -Original Message- From: Pei Chen [mailto:chen...@apache.org] Sent: Tuesday, July 08, 2014 5:11 PM To: dev@ctakes.apache.org Subject: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Hi all, The main difference between rc1 and rc2 is that we removed the lvg-res and assertion-res.jar from the distro. They still need to be unpacked. This is a call for a vote on releasing the following candidate (rc2) as Apache cTAKES 3.2.0. The major changes include: - New optional YTEX
RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
I think this is due to the fact that the default lvg.properties also exits in the ctakes-resources project, so if you download and replace, it will override the ctakes configured one. I think it's a bug, but probably always been there... I'll fix up ctakes-resources on sourceforge nethertheless but it shouldn't require any changes to the release candidates. -Original Message- From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] Sent: Thursday, July 10, 2014 11:59 AM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Hi Tim, When you say that it didn't seem to affect the run, where you comparing output to last release or just checking if data seemed OK at a glance? -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Thursday, July 10, 2014 7:29 AM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) I was able to run the binary without issues this time. I also downloaded the resources from sourceforge and integrated into the bin release and ran with the ctakes dictionary. I did get some weird exceptions thrown that didn't seem to affect the run -- looks like some hardcoded file paths in LVG? (See below) Tim Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/stopWords.data (No such file or directory) ** Error: problem of opening/reading stop words file: '/export/home/lu/Development/LVG/lvg2008/data/misc/stopWords.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/nonInfoWords.data (No such file or directory) ** Error: problem of opening/reading non-Info words file: '/export/home/lu/Development/LVG/lvg2008/data/misc/nonInfoWords.dat a'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/conjunctionWord.d ata (No such file or directory) ** Error: problem of opening/reading conjunction words file: '/export/home/lu/Development/LVG/lvg2008/data/misc/conjunctionWord. data'. ** ERR: problem of opening/reading diacritics file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/diacriticMap.da ta'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/diacriticMap.da ta (No such file or directory) Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/ligatureMap.da ta (No such file or directory) ** Error: problem of opening/reading ligature file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/ligatureMap.da ta'. ** Error: problem of opening/reading symbol synonym file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/synonymMap. data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/synonymMap.d ata (No such file or directory) **Error: problem of opening/reading file '/export/home/lu/Development/LVG/lvg2008/data/misc/removeS.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/removeS.data (No such file or directory) ** Error: problem of opening/reading Unicode symbol file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/symbolMap.da ta'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/symbolMap.dat a (No such file or directory) ** Error: problem of opening/reading Unicode file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/unicodeMap.d ata'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/unicodeMap.da ta (No such file or directory) ** Error: problem of opening/reading nonStripMap file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/nonStripMap.d ata'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/nonStripMap.d ata (No such file or directory) java.sql.SQLException: File input/output error /export/home/lu/Development/LVG/lvg2008/data/HSqlDb/lvg2008.properti es java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/HSqlDb/lvg2008.properti es.new (No such file or directory) From: Masanz, James J. [masanz.ja...@mayo.edu] Sent: Wednesday, July 09, 2014 2:26 PM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) So far for rc2, I've Verified MD5 and signatures of .zip archives Verified that source at tag matches source in.zip Imported source from archive into eclipse as maven project(s) and compiled without any Errors. -- James -Original Message- From: Pei Chen [mailto:chen...@apache.org] Sent: Tuesday, July 08, 2014 5:11 PM To: dev@ctakes.apache.org Subject: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Hi all, The main difference between rc1 and rc2 is that we removed the lvg-res and assertion
RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
Can you also give ctakesresources the number 3.2 or 3.2.0 instead of 3.1.3 -Original Message- From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu] Sent: Thursday, July 10, 2014 2:12 PM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) I think this is due to the fact that the default lvg.properties also exits in the ctakes-resources project, so if you download and replace, it will override the ctakes configured one. I think it's a bug, but probably always been there... I'll fix up ctakes-resources on sourceforge nethertheless but it shouldn't require any changes to the release candidates. -Original Message- From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] Sent: Thursday, July 10, 2014 11:59 AM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Hi Tim, When you say that it didn't seem to affect the run, where you comparing output to last release or just checking if data seemed OK at a glance? -Original Message- From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu] Sent: Thursday, July 10, 2014 7:29 AM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) I was able to run the binary without issues this time. I also downloaded the resources from sourceforge and integrated into the bin release and ran with the ctakes dictionary. I did get some weird exceptions thrown that didn't seem to affect the run -- looks like some hardcoded file paths in LVG? (See below) Tim Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/stopWords.data (No such file or directory) ** Error: problem of opening/reading stop words file: '/export/home/lu/Development/LVG/lvg2008/data/misc/stopWords.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/nonInfoWords.data (No such file or directory) ** Error: problem of opening/reading non-Info words file: '/export/home/lu/Development/LVG/lvg2008/data/misc/nonInfoWords.dat a'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/conjunctionWord.d ata (No such file or directory) ** Error: problem of opening/reading conjunction words file: '/export/home/lu/Development/LVG/lvg2008/data/misc/conjunctionWord. data'. ** ERR: problem of opening/reading diacritics file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/diacriticMap.da ta'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/diacriticMap.da ta (No such file or directory) Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/ligatureMap.da ta (No such file or directory) ** Error: problem of opening/reading ligature file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/ligatureMap.da ta'. ** Error: problem of opening/reading symbol synonym file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/synonymMap. data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/synonymMap.d ata (No such file or directory) **Error: problem of opening/reading file '/export/home/lu/Development/LVG/lvg2008/data/misc/removeS.data'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/misc/removeS.data (No such file or directory) ** Error: problem of opening/reading Unicode symbol file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/symbolMap.da ta'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/symbolMap.dat a (No such file or directory) ** Error: problem of opening/reading Unicode file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/unicodeMap.d ata'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/unicodeMap.da ta (No such file or directory) ** Error: problem of opening/reading nonStripMap file: '/export/home/lu/Development/LVG/lvg2008/data/Unicode/nonStripMap.d ata'. Exception: java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/Unicode/nonStripMap.d ata (No such file or directory) java.sql.SQLException: File input/output error /export/home/lu/Development/LVG/lvg2008/data/HSqlDb/lvg2008.properti es java.io.FileNotFoundException: /export/home/lu/Development/LVG/lvg2008/data/HSqlDb/lvg2008.properti es.new (No such file or directory) From: Masanz, James J. [masanz.ja...@mayo.edu] Sent: Wednesday, July 09, 2014 2:26 PM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2) So far for rc2, I've Verified MD5 and signatures of .zip archives Verified that source at tag matches source in.zip Imported source from archive into eclipse as maven project(s) and compiled without any Errors. -- James -Original
RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
The maven artifacts are also available in the staging area: https://repository.apache.org/content/repositories/orgapachectakes-1001 VJ: Just curious- how did you envision ytex users downloading the jars/war? From the distro bin.zip or from maven central? --Pei -Original Message- From: Pei Chen [mailto:chen...@apache.org] Sent: Tuesday, July 08, 2014 6:11 PM To: dev@ctakes.apache.org Subject: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Hi all, The main difference between rc1 and rc2 is that we removed the lvg-res and assertion-res.jar from the distro. They still need to be unpacked. This is a call for a vote on releasing the following candidate (rc2) as Apache cTAKES 3.2.0. The major changes include: - New optional YTEX component(s) (Yale Extensions to cTAKES) - New optional improved/faster dictionary lookup (dictionary-lookup-fast) - New optional Temporal component (Time + Event extraction. Relations will be including in a future release.) - Other bug fixes/enhancements from Jira [TODO: Online documentation still needs to be updated on wiki] For more detailed information on the changes/release notes, please visit: https://issues.apache.org/jira/secure/ReleaseNote.jspa?projectId=12313621 version=12324066 The release was made using the cTAKES release process documented here: http://ctakes.apache.org/ctakes-release-guide.html The candidate is available at: http://people.apache.org/~chenpei/RCs/ctakes-3.2.0-rc2/apache-ctakes- 3.2.0-src.tar.gz /.zip The tag to be voted on: http://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.2.0-rc2 The MD5 checksum of the tarball can be found at: http://people.apache.org/~chenpei/RCs/ctakes-3.2.0-rc2/apache-ctakes- 3.2.0-src.tar.gz.md5 /.zip.md5 The signature of the tarball can be found at: http://people.apache.org/~chenpei/RCs/ctakes-3.2.0-rc2/apache-ctakes- 3.2.0-src.tar.gz.asc /.zip.asc Apache cTAKES' KEYS file, containing the PGP keys used to sign the release: https://dist.apache.org/repos/dist/release/ctakes/KEYS Please vote on releasing these packages as Apache cTAKES 3.2.0. The vote is open for at least the next 72 hours. Only votes from the cTAKES PMC are binding, but folks are welcome to check the release candidate and voice their approval or disapproval. The vote passes if at least three binding +1 votes are cast. [ ] +1 Release the packages as Apache cTAKES 3.2.0 [ ] -1 Do not release the packages because... Also, the convenience binary can be found at: http://people.apache.org/~chenpei/RCs/ctakes-3.2.0-rc2/apache-ctakes- 3.2.0-bin.tar.gz /.zip Note: It's temporarily on people.a.o because the artifacts were too large for https://dist.apache.org/repos/dist/dev/ctakes (Working with infra on increasing the limit). Thanks!
RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
I believe the only dictionaries shipped with Apache cTAKES in lucene indexes contain just the Orange Book, RxNorm, and some made-up terms, not SNOMED-CT or the other sources taken from UMLS. If that is not correct, then I agree there is a problem with what is being shipped in lucene indexes. -- James -Original Message- From: vijay garla [mailto:vnga...@gmail.com] Sent: Wednesday, July 09, 2014 9:30 AM To: dev@ctakes.apache.org Subject: Re: [VOTE] Release Apache cTAKES 3.2.0 (rc2) ctakes-ytex-lib-3.1.2-SNAPSHOT.zip https://ytex.googlecode.com/files/ctakes-ytex-lib-3.1.2-SNAPSHOT.zip - this contains non-asf compliant ytex libs. I would like to add it to the sourceforge site / or add it to the ctakes resources directly (that way users simply have to unzip a single zip file) ctakes-ytex-resources-3.1.2-SNAPSHOT.zip http://www.ytex-nlp.org/umls.download/secure/3.1/ctakes-ytex-resources-3.1.2-SNAPSHOT.zip - this contains data derived from the UMLS - concept graphs and dictionary lookup tables. downloading this requires a UTS login. It is conceptually no different from the ctakes resources, so I believe it would be OK to add it to that zip file, but I'm not a lawyer. On another note: I think forcing users to specify the UTS username/password and contacting NIH every time you run cTAKES is problematic, and doesn't prevent users who don't have a valid UTS login from viewing the data contained in the lucene index dictionary. I personally believe requiring a UTS login to download would be the best way to make resources derived from the UMLS available to users (this is what I'm doing for ytex-resources). to summarize: for now, I would like to add the ytex libs to the ctakes resources zip. -vj On Wed, Jul 9, 2014 at 4:04 PM, Chen, Pei pei.c...@childrens.harvard.edu wrote: The maven artifacts are also available in the staging area: https://repository.apache.org/content/repositories/orgapachectakes-1001 VJ: Just curious- how did you envision ytex users downloading the jars/war? From the distro bin.zip or from maven central? --Pei -Original Message- From: Pei Chen [mailto:chen...@apache.org] Sent: Tuesday, July 08, 2014 6:11 PM To: dev@ctakes.apache.org Subject: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Hi all, The main difference between rc1 and rc2 is that we removed the lvg-res and assertion-res.jar from the distro. They still need to be unpacked. This is a call for a vote on releasing the following candidate (rc2) as Apache cTAKES 3.2.0. The major changes include: - New optional YTEX component(s) (Yale Extensions to cTAKES) - New optional improved/faster dictionary lookup (dictionary-lookup-fast) - New optional Temporal component (Time + Event extraction. Relations will be including in a future release.) - Other bug fixes/enhancements from Jira [TODO: Online documentation still needs to be updated on wiki] For more detailed information on the changes/release notes, please visit: https://issues.apache.org/jira/secure/ReleaseNote.jspa?projectId=12313621 version=12324066 The release was made using the cTAKES release process documented here: http://ctakes.apache.org/ctakes-release-guide.html The candidate is available at: http://people.apache.org/~chenpei/RCs/ctakes-3.2.0-rc2/apache-ctakes- 3.2.0-src.tar.gz /.zip The tag to be voted on: http://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.2.0-rc2 The MD5 checksum of the tarball can be found at: http://people.apache.org/~chenpei/RCs/ctakes-3.2.0-rc2/apache-ctakes- 3.2.0-src.tar.gz.md5 /.zip.md5 The signature of the tarball can be found at: http://people.apache.org/~chenpei/RCs/ctakes-3.2.0-rc2/apache-ctakes- 3.2.0-src.tar.gz.asc /.zip.asc Apache cTAKES' KEYS file, containing the PGP keys used to sign the release: https://dist.apache.org/repos/dist/release/ctakes/KEYS Please vote on releasing these packages as Apache cTAKES 3.2.0. The vote is open for at least the next 72 hours. Only votes from the cTAKES PMC are binding, but folks are welcome to check the release candidate and voice their approval or disapproval. The vote passes if at least three binding +1 votes are cast. [ ] +1 Release the packages as Apache cTAKES 3.2.0 [ ] -1 Do not release the packages because... Also, the convenience binary can be found at: http://people.apache.org/~chenpei/RCs/ctakes-3.2.0-rc2/apache-ctakes- 3.2.0-bin.tar.gz /.zip Note: It's temporarily on people.a.o because the artifacts were too large for https://dist.apache.org/repos/dist/dev/ctakes (Working with infra on increasing the limit). Thanks!
Re: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
Sorry, I meant the snomed dictionary lookup database - I think it is hsql, not lucene. -vj On Wed, Jul 9, 2014 at 5:30 PM, Masanz, James J. masanz.ja...@mayo.edu wrote: I believe the only dictionaries shipped with Apache cTAKES in lucene indexes contain just the Orange Book, RxNorm, and some made-up terms, not SNOMED-CT or the other sources taken from UMLS. If that is not correct, then I agree there is a problem with what is being shipped in lucene indexes. -- James -Original Message- From: vijay garla [mailto:vnga...@gmail.com] Sent: Wednesday, July 09, 2014 9:30 AM To: dev@ctakes.apache.org Subject: Re: [VOTE] Release Apache cTAKES 3.2.0 (rc2) ctakes-ytex-lib-3.1.2-SNAPSHOT.zip https://ytex.googlecode.com/files/ctakes-ytex-lib-3.1.2-SNAPSHOT.zip - this contains non-asf compliant ytex libs. I would like to add it to the sourceforge site / or add it to the ctakes resources directly (that way users simply have to unzip a single zip file) ctakes-ytex-resources-3.1.2-SNAPSHOT.zip http://www.ytex-nlp.org/umls.download/secure/3.1/ctakes-ytex-resources-3.1.2-SNAPSHOT.zip - this contains data derived from the UMLS - concept graphs and dictionary lookup tables. downloading this requires a UTS login. It is conceptually no different from the ctakes resources, so I believe it would be OK to add it to that zip file, but I'm not a lawyer. On another note: I think forcing users to specify the UTS username/password and contacting NIH every time you run cTAKES is problematic, and doesn't prevent users who don't have a valid UTS login from viewing the data contained in the lucene index dictionary. I personally believe requiring a UTS login to download would be the best way to make resources derived from the UMLS available to users (this is what I'm doing for ytex-resources). to summarize: for now, I would like to add the ytex libs to the ctakes resources zip. -vj On Wed, Jul 9, 2014 at 4:04 PM, Chen, Pei pei.c...@childrens.harvard.edu wrote: The maven artifacts are also available in the staging area: https://repository.apache.org/content/repositories/orgapachectakes-1001 VJ: Just curious- how did you envision ytex users downloading the jars/war? From the distro bin.zip or from maven central? --Pei -Original Message- From: Pei Chen [mailto:chen...@apache.org] Sent: Tuesday, July 08, 2014 6:11 PM To: dev@ctakes.apache.org Subject: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Hi all, The main difference between rc1 and rc2 is that we removed the lvg-res and assertion-res.jar from the distro. They still need to be unpacked. This is a call for a vote on releasing the following candidate (rc2) as Apache cTAKES 3.2.0. The major changes include: - New optional YTEX component(s) (Yale Extensions to cTAKES) - New optional improved/faster dictionary lookup (dictionary-lookup-fast) - New optional Temporal component (Time + Event extraction. Relations will be including in a future release.) - Other bug fixes/enhancements from Jira [TODO: Online documentation still needs to be updated on wiki] For more detailed information on the changes/release notes, please visit: https://issues.apache.org/jira/secure/ReleaseNote.jspa?projectId=12313621 version=12324066 The release was made using the cTAKES release process documented here: http://ctakes.apache.org/ctakes-release-guide.html The candidate is available at: http://people.apache.org/~chenpei/RCs/ctakes-3.2.0-rc2/apache-ctakes- 3.2.0-src.tar.gz /.zip The tag to be voted on: http://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.2.0-rc2 The MD5 checksum of the tarball can be found at: http://people.apache.org/~chenpei/RCs/ctakes-3.2.0-rc2/apache-ctakes- 3.2.0-src.tar.gz.md5 /.zip.md5 The signature of the tarball can be found at: http://people.apache.org/~chenpei/RCs/ctakes-3.2.0-rc2/apache-ctakes- 3.2.0-src.tar.gz.asc /.zip.asc Apache cTAKES' KEYS file, containing the PGP keys used to sign the release: https://dist.apache.org/repos/dist/release/ctakes/KEYS Please vote on releasing these packages as Apache cTAKES 3.2.0. The vote is open for at least the next 72 hours. Only votes from the cTAKES PMC are binding, but folks are welcome to check the release candidate and voice their approval or disapproval. The vote passes if at least three binding +1 votes are cast. [ ] +1 Release the packages as Apache cTAKES 3.2.0 [ ] -1 Do not release the packages because... Also, the convenience binary can be found at: http://people.apache.org/~chenpei/RCs/ctakes-3.2.0-rc2/apache-ctakes- 3.2.0-bin.tar.gz /.zip Note: It's temporarily on people.a.o because the artifacts were too large for https://dist.apache.org/repos/dist/dev/ctakes (Working with infra on increasing the limit). Thanks!
RE: [VOTE] Release Apache cTAKES 3.2.0 (rc2)
So far for rc2, I've Verified MD5 and signatures of .zip archives Verified that source at tag matches source in.zip Imported source from archive into eclipse as maven project(s) and compiled without any Errors. -- James -Original Message- From: Pei Chen [mailto:chen...@apache.org] Sent: Tuesday, July 08, 2014 5:11 PM To: dev@ctakes.apache.org Subject: [VOTE] Release Apache cTAKES 3.2.0 (rc2) Hi all, The main difference between rc1 and rc2 is that we removed the lvg-res and assertion-res.jar from the distro. They still need to be unpacked. This is a call for a vote on releasing the following candidate (rc2) as Apache cTAKES 3.2.0. The major changes include: - New optional YTEX component(s) (Yale Extensions to cTAKES) - New optional improved/faster dictionary lookup (dictionary-lookup-fast) - New optional Temporal component (Time + Event extraction. Relations will be including in a future release.) - Other bug fixes/enhancements from Jira [TODO: Online documentation still needs to be updated on wiki] For more detailed information on the changes/release notes, please visit: https://issues.apache.org/jira/secure/ReleaseNote.jspa?projectId=12313621version=12324066 The release was made using the cTAKES release process documented here: http://ctakes.apache.org/ctakes-release-guide.html The candidate is available at: http://people.apache.org/~chenpei/RCs/ctakes-3.2.0-rc2/apache-ctakes-3.2.0-src.tar.gz /.zip The tag to be voted on: http://svn.apache.org/repos/asf/ctakes/tags/ctakes-3.2.0-rc2 The MD5 checksum of the tarball can be found at: http://people.apache.org/~chenpei/RCs/ctakes-3.2.0-rc2/apache-ctakes-3.2.0-src.tar.gz.md5 /.zip.md5 The signature of the tarball can be found at: http://people.apache.org/~chenpei/RCs/ctakes-3.2.0-rc2/apache-ctakes-3.2.0-src.tar.gz.asc /.zip.asc Apache cTAKES' KEYS file, containing the PGP keys used to sign the release: https://dist.apache.org/repos/dist/release/ctakes/KEYS Please vote on releasing these packages as Apache cTAKES 3.2.0. The vote is open for at least the next 72 hours. Only votes from the cTAKES PMC are binding, but folks are welcome to check the release candidate and voice their approval or disapproval. The vote passes if at least three binding +1 votes are cast. [ ] +1 Release the packages as Apache cTAKES 3.2.0 [ ] -1 Do not release the packages because... Also, the convenience binary can be found at: http://people.apache.org/~chenpei/RCs/ctakes-3.2.0-rc2/apache-ctakes-3.2.0-bin.tar.gz /.zip Note: It's temporarily on people.a.o because the artifacts were too large for https://dist.apache.org/repos/dist/dev/ctakes (Working with infra on increasing the limit). Thanks!
