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!
RE: [VOTE] Release Apache cTAKES 3.2.0
One other thing -- the User install guide says to download the -bin and the Dev install guide has you checking out from trunk. And the README in the -src distribution has instructions that only make sense for the -bin distribution. Are there instructions somewhere for how to install the -src version or are they basically the same as the dev install w/o the subversion checkout step? Tim From: Pei Chen [chen...@apache.org] Sent: Monday, July 07, 2014 12:06 PM To: dev@ctakes.apache.org Subject: Re: [VOTE] Release Apache cTAKES 3.2.0 Thanks for testing this Tim. I could recreate this on my mac now (worked previously on windows on luck because of the class load order). Essentially, the old mitre assertion module and LVG resources still need to be unpacked. We don't have access to modify the underlying lib to read from a stream, I'm just going to omit/exclude the redundant ctakes-assertion-res.jar from the distro (as the assertion module will be updated in the future release anyway). Let me know if you encounter anything else, otherwise will plan to create an RC-2. On Fri, Jul 4, 2014 at 12:01 PM, Miller, Timothy timothy.mil...@childrens.harvard.edu wrote: I get an error when I try to run the CVD following the README instructions for the binary release: 7/4/14 11:56:03 AM - 12: org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE: Initialization of annotator class org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine failed. (Descriptor: file:/home/tmill/Projects/sandbox/ctakes-rcs/apache-ctakes-3.2.0/desc/ctakes-assertion/desc/assertionAnalysisEngine.xml) org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine failed. (Descriptor: file:/home/tmill/Projects/sandbox/ctakes-rcs/apache-ctakes-3.2.0/desc/ctakes-assertion/desc/assertionAnalysisEngine.xml) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387) at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387) at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354) at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484) at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:477) at org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:52) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2018) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2341) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402
Re: [VOTE] Release Apache cTAKES 3.2.0
It's the latter: the -src is basically the same as the dev install w/o the subversion checkout step... On Tue, Jul 8, 2014 at 7:15 AM, Miller, Timothy timothy.mil...@childrens.harvard.edu wrote: One other thing -- the User install guide says to download the -bin and the Dev install guide has you checking out from trunk. And the README in the -src distribution has instructions that only make sense for the -bin distribution. Are there instructions somewhere for how to install the -src version or are they basically the same as the dev install w/o the subversion checkout step? Tim From: Pei Chen [chen...@apache.org] Sent: Monday, July 07, 2014 12:06 PM To: dev@ctakes.apache.org Subject: Re: [VOTE] Release Apache cTAKES 3.2.0 Thanks for testing this Tim. I could recreate this on my mac now (worked previously on windows on luck because of the class load order). Essentially, the old mitre assertion module and LVG resources still need to be unpacked. We don't have access to modify the underlying lib to read from a stream, I'm just going to omit/exclude the redundant ctakes-assertion-res.jar from the distro (as the assertion module will be updated in the future release anyway). Let me know if you encounter anything else, otherwise will plan to create an RC-2. On Fri, Jul 4, 2014 at 12:01 PM, Miller, Timothy timothy.mil...@childrens.harvard.edu wrote: I get an error when I try to run the CVD following the README instructions for the binary release: 7/4/14 11:56:03 AM - 12: org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE: Initialization of annotator class org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine failed. (Descriptor: file:/home/tmill/Projects/sandbox/ctakes-rcs/apache-ctakes-3.2.0/desc/ctakes-assertion/desc/assertionAnalysisEngine.xml) org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine failed. (Descriptor: file:/home/tmill/Projects/sandbox/ctakes-rcs/apache-ctakes-3.2.0/desc/ctakes-assertion/desc/assertionAnalysisEngine.xml) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387) at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387) at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354) at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484) at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:477) at org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed
[CANCELLED] [VOTE] Release Apache cTAKES 3.2.0
Cancelling the rc-1. Will send out another vote thread for RC2 shortly. --Pei On Tue, Jul 8, 2014 at 10:53 AM, Pei Chen chen...@apache.org wrote: It's the latter: the -src is basically the same as the dev install w/o the subversion checkout step... On Tue, Jul 8, 2014 at 7:15 AM, Miller, Timothy timothy.mil...@childrens.harvard.edu wrote: One other thing -- the User install guide says to download the -bin and the Dev install guide has you checking out from trunk. And the README in the -src distribution has instructions that only make sense for the -bin distribution. Are there instructions somewhere for how to install the -src version or are they basically the same as the dev install w/o the subversion checkout step? Tim From: Pei Chen [chen...@apache.org] Sent: Monday, July 07, 2014 12:06 PM To: dev@ctakes.apache.org Subject: Re: [VOTE] Release Apache cTAKES 3.2.0 Thanks for testing this Tim. I could recreate this on my mac now (worked previously on windows on luck because of the class load order). Essentially, the old mitre assertion module and LVG resources still need to be unpacked. We don't have access to modify the underlying lib to read from a stream, I'm just going to omit/exclude the redundant ctakes-assertion-res.jar from the distro (as the assertion module will be updated in the future release anyway). Let me know if you encounter anything else, otherwise will plan to create an RC-2. On Fri, Jul 4, 2014 at 12:01 PM, Miller, Timothy timothy.mil...@childrens.harvard.edu wrote: I get an error when I try to run the CVD following the README instructions for the binary release: 7/4/14 11:56:03 AM - 12: org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE: Initialization of annotator class org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine failed. (Descriptor: file:/home/tmill/Projects/sandbox/ctakes-rcs/apache-ctakes-3.2.0/desc/ctakes-assertion/desc/assertionAnalysisEngine.xml) org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine failed. (Descriptor: file:/home/tmill/Projects/sandbox/ctakes-rcs/apache-ctakes-3.2.0/desc/ctakes-assertion/desc/assertionAnalysisEngine.xml) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387) at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387) at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185) at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94) at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62) at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354) at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484
[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!
Re: [VOTE] Release Apache cTAKES 3.2.0
) at java.awt.Container.processEvent(Container.java:2229) at java.awt.Component.dispatchEventImpl(Component.java:4861) at java.awt.Container.dispatchEventImpl(Container.java:2287) at java.awt.Component.dispatchEvent(Component.java:4687) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422) at java.awt.Container.dispatchEventImpl(Container.java:2273) at java.awt.Window.dispatchEventImpl(Window.java:2719) at java.awt.Component.dispatchEvent(Component.java:4687) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:735) at java.awt.EventQueue.access$200(EventQueue.java:103) at java.awt.EventQueue$3.run(EventQueue.java:694) at java.awt.EventQueue$3.run(EventQueue.java:692) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87) at java.awt.EventQueue$4.run(EventQueue.java:708) at java.awt.EventQueue$4.run(EventQueue.java:706) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:705) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138) at java.awt.EventDispatchThread.run(EventDispatchThread.java:91) Caused by: java.lang.RuntimeException: problem accessing resource at org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine.initialize(AssertionAnalysisEngine.java:114) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250) ... 62 more Caused by: org.apache.uima.resource.ResourceAccessException at org.apache.uima.impl.UimaContext_ImplBase.getResourceFilePath(UimaContext_ImplBase.java:253) at org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine.initialize(AssertionAnalysisEngine.java:93) ... 63 more From: Finan, Sean [sean.fi...@childrens.harvard.edu] Sent: Wednesday, July 02, 2014 3:49 PM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 +1 Pulled fresh candidate, built, and ran Clinical using CPE without problem. Other than that, no testing. SVN gave me a problem initially (checked out as anonymous) asking for a password then flunking the checkout, but an update completed it. I blame the heat. From: Masanz, James J. [masanz.ja...@mayo.edu] Sent: Monday, June 30, 2014 10:24 PM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 This is pretty obvious, but since this is a record of what was voted upon, note that some of the URLs contain an extra ctakes-3.2.0/ For example http://people.apache.org/~chenpei/RCs/ctakes-3.2.0/ctakes-3.2.0/apache-ctakes-3.2.0-src.tar.gz should be just http://people.apache.org/~chenpei/RCs/ctakes-3.2.0/apache-ctakes-3.2.0-src.tar.gz -- James From: Pei Chen [chen...@apache.org] Sent: Friday, June 27, 2014 5:15 PM To: dev@ctakes.apache.org Subject: [VOTE] Release Apache cTAKES 3.2.0 Hi all, This is a call for a vote on releasing the following candidate (rc1) 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 the abo] 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/ctakes-3.2.0/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-rc1
RE: [VOTE] Release Apache cTAKES 3.2.0
) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:735) at java.awt.EventQueue.access$200(EventQueue.java:103) at java.awt.EventQueue$3.run(EventQueue.java:694) at java.awt.EventQueue$3.run(EventQueue.java:692) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87) at java.awt.EventQueue$4.run(EventQueue.java:708) at java.awt.EventQueue$4.run(EventQueue.java:706) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:705) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138) at java.awt.EventDispatchThread.run(EventDispatchThread.java:91) Caused by: java.lang.RuntimeException: problem accessing resource at org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine.initialize(AssertionAnalysisEngine.java:114) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250) ... 62 more Caused by: org.apache.uima.resource.ResourceAccessException at org.apache.uima.impl.UimaContext_ImplBase.getResourceFilePath(UimaContext_ImplBase.java:253) at org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine.initialize(AssertionAnalysisEngine.java:93) ... 63 more From: Finan, Sean [sean.fi...@childrens.harvard.edu] Sent: Wednesday, July 02, 2014 3:49 PM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 +1 Pulled fresh candidate, built, and ran Clinical using CPE without problem. Other than that, no testing. SVN gave me a problem initially (checked out as anonymous) asking for a password then flunking the checkout, but an update completed it. I blame the heat. From: Masanz, James J. [masanz.ja...@mayo.edu] Sent: Monday, June 30, 2014 10:24 PM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 This is pretty obvious, but since this is a record of what was voted upon, note that some of the URLs contain an extra ctakes-3.2.0/ For example http://people.apache.org/~chenpei/RCs/ctakes-3.2.0/ctakes-3.2.0/apache-ctakes-3.2.0-src.tar.gz should be just http://people.apache.org/~chenpei/RCs/ctakes-3.2.0/apache-ctakes-3.2.0-src.tar.gz -- James From: Pei Chen [chen...@apache.org] Sent: Friday, June 27, 2014 5:15 PM To: dev@ctakes.apache.org Subject: [VOTE] Release Apache cTAKES 3.2.0 Hi all, This is a call for a vote on releasing the following candidate (rc1) 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 the abo] 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/ctakes-3.2.0/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-rc1/ The MD5 checksum of the tarball can be found at: http://people.apache.org/~chenpei/RCs/ctakes-3.2.0/ctakes-3.2.0/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/ctakes-3.2.0/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
RE: [VOTE] Release Apache cTAKES 3.2.0
+1 Pulled fresh candidate, built, and ran Clinical using CPE without problem. Other than that, no testing. SVN gave me a problem initially (checked out as anonymous) asking for a password then flunking the checkout, but an update completed it. I blame the heat. From: Masanz, James J. [masanz.ja...@mayo.edu] Sent: Monday, June 30, 2014 10:24 PM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 This is pretty obvious, but since this is a record of what was voted upon, note that some of the URLs contain an extra ctakes-3.2.0/ For example http://people.apache.org/~chenpei/RCs/ctakes-3.2.0/ctakes-3.2.0/apache-ctakes-3.2.0-src.tar.gz should be just http://people.apache.org/~chenpei/RCs/ctakes-3.2.0/apache-ctakes-3.2.0-src.tar.gz -- James From: Pei Chen [chen...@apache.org] Sent: Friday, June 27, 2014 5:15 PM To: dev@ctakes.apache.org Subject: [VOTE] Release Apache cTAKES 3.2.0 Hi all, This is a call for a vote on releasing the following candidate (rc1) 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 the abo] 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/ctakes-3.2.0/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-rc1/ The MD5 checksum of the tarball can be found at: http://people.apache.org/~chenpei/RCs/ctakes-3.2.0/ctakes-3.2.0/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/ctakes-3.2.0/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/ctakes-3.2.0/apache-ctakes-3.2.0-bin.tar.gz /.zip Note: It's tempoarily 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
The LVG is particularly important, users are most likely to compare cTAKES and MetaMap (or other) performance on the NER task and the LVG clearly helps. Requiring a new user to understand LVG is the hard part, the download isn't a tough requirement but I wonder how many new users would even know to do that. Even with clear instructions . On Sat, Jun 28, 2014 at 7:25 PM, Masanz, James J. masanz.ja...@mayo.edu wrote: The release notes include some JIRA issues that are open (and I think some that have not had any changes done for them) Example of one that has not been implemented as far as I know: https://issues.apache.org/jira/i#browse/CTAKES-122 Example of one that has status=open and Resolution=Unresolved https://issues.apache.org/jira/i#browse/CTAKES-224 There are others -- James -Original Message- From: Pei Chen [mailto:chen...@apache.org] Sent: Friday, June 27, 2014 5:16 PM To: dev@ctakes.apache.org Subject: [VOTE] Release Apache cTAKES 3.2.0 Hi all, This is a call for a vote on releasing the following candidate (rc1) 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 the abo] 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/ctakes-3.2.0/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-rc1/ The MD5 checksum of the tarball can be found at: http://people.apache.org/~chenpei/RCs/ctakes-3.2.0/ctakes-3.2.0/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/ctakes-3.2.0/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/ctakes-3.2.0/apache-ctakes-3.2.0-bin.tar.gz /.zip Note: It's tempoarily 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
Thanks James. I just did a Jira review for 3.2. There are just 2 remaining items that are pending some clarification from respective dev. Otherwise, it should be up to date now- any items that didn't make it to 3.2 have been updated to 3.2.1 instead now. --Pei -Original Message- From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] Sent: Saturday, June 28, 2014 10:26 PM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 The release notes include some JIRA issues that are open (and I think some that have not had any changes done for them) Example of one that has not been implemented as far as I know: https://issues.apache.org/jira/i#browse/CTAKES-122 Example of one that has status=open and Resolution=Unresolved https://issues.apache.org/jira/i#browse/CTAKES-224 There are others -- James -Original Message- From: Pei Chen [mailto:chen...@apache.org] Sent: Friday, June 27, 2014 5:16 PM To: dev@ctakes.apache.org Subject: [VOTE] Release Apache cTAKES 3.2.0 Hi all, This is a call for a vote on releasing the following candidate (rc1) 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 the abo] 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/ctakes-3.2.0/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-rc1/ The MD5 checksum of the tarball can be found at: http://people.apache.org/~chenpei/RCs/ctakes-3.2.0/ctakes-3.2.0/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/ctakes-3.2.0/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/ctakes-3.2.0/apache- ctakes-3.2.0-bin.tar.gz /.zip Note: It's tempoarily 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
Thanks! I haven't downloaded and reviewed the packages themselves yet but I do plan to at least start on that today. -- James -Original Message- From: Chen, Pei [mailto:pei.c...@childrens.harvard.edu] Sent: Monday, June 30, 2014 1:47 PM To: dev@ctakes.apache.org Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 Thanks James. I just did a Jira review for 3.2. There are just 2 remaining items that are pending some clarification from respective dev. Otherwise, it should be up to date now- any items that didn't make it to 3.2 have been updated to 3.2.1 instead now. --Pei -Original Message- From: Masanz, James J. [mailto:masanz.ja...@mayo.edu] Sent: Saturday, June 28, 2014 10:26 PM To: 'dev@ctakes.apache.org' Subject: RE: [VOTE] Release Apache cTAKES 3.2.0 The release notes include some JIRA issues that are open (and I think some that have not had any changes done for them) Example of one that has not been implemented as far as I know: https://issues.apache.org/jira/i#browse/CTAKES-122 Example of one that has status=open and Resolution=Unresolved https://issues.apache.org/jira/i#browse/CTAKES-224 There are others -- James -Original Message- From: Pei Chen [mailto:chen...@apache.org] Sent: Friday, June 27, 2014 5:16 PM To: dev@ctakes.apache.org Subject: [VOTE] Release Apache cTAKES 3.2.0 Hi all, This is a call for a vote on releasing the following candidate (rc1) 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 the abo] 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/ctakes-3.2.0/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-rc1/ The MD5 checksum of the tarball can be found at: http://people.apache.org/~chenpei/RCs/ctakes-3.2.0/ctakes-3.2.0/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/ctakes-3.2.0/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/ctakes-3.2.0/apache- ctakes-3.2.0-bin.tar.gz /.zip Note: It's tempoarily 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!
[VOTE] Release Apache cTAKES 3.2.0
Hi all, This is a call for a vote on releasing the following candidate (rc1) 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 the abo] 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/ctakes-3.2.0/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-rc1/ The MD5 checksum of the tarball can be found at: http://people.apache.org/~chenpei/RCs/ctakes-3.2.0/ctakes-3.2.0/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/ctakes-3.2.0/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/ctakes-3.2.0/apache-ctakes-3.2.0-bin.tar.gz /.zip Note: It's tempoarily 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!
