Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-04-11

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All times shown according to UTC.

Time Nick Message
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12:12 dbolser hello bioperl
12:14 dbolser here is a question... how come when I load GFF via a Bio::DB::SeqFeature::Store, the ID attribute ends up under $f->{attributes}->{load_id}, yet the Name attribute ends up under $f->{name}?
12:14 dbolser is there any consistent way to predict where my standard GFF attributes will turn up, or how to get them out?
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12:59 pyrimidine dbolser: That's likely b/c 'Name' is one of the predefined attributes, along with 'Target', 'ID', etc
13:00 pyrimidine they have a special connotation
13:00 pyrimidine I think 'Name' is analagous to display_name IIRC
13:05 dbolser pyrimidine: seems so
13:06 dbolser but if Name goes to {name}, why does ID go to {attributes}{load_id}
13:06 dbolser just a minor gripe, so ignore me
13:07 dbolser I fixed the documention issue that I mentioned previously to do with Bio/DB/SeqFeature/Store/DBI/mysql.pm
13:07 dbolser s/to do with/to do with the 'update' command desribed in/
13:13 pyrimidine dbolser: I know there were some issues at one point with how ID was stored, which is why there is a load_id and a primary_id, but I can't recall
13:15 pyrimidine dbolser: personally, I wouldn't worry about the internals of SF::Store unless you are running into specific problems
13:33 dbolser ok
13:35 pyrimidine never know when Lincoln will make major changes for a release
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15:53 pyrimidine for anyone here, announcement sent to the mail list: https://gist.github.com/913745
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16:46 dbolser rbuels: thanks for pull comments, I'll look into it soon
16:47 rbuels dbolser: np
16:49 pyrimidine rbuels: any comments on my bioperl-l post (beyond 'hurry your ass up')?
16:50 rbuels pyrimidine: eh, since you ask, seems like the release branch could have been just another branch, you probably didn't have to tell people to lay off master
16:50 rbuels but if it's done quickly, not a big deal
16:50 pyrimidine right
16:51 rbuels pyrimidine: there might be a bit of a missed opportunity here though
16:51 pyrimidine rbuels: the problem I had in the past was, if I indicated I was about to make a release, I had everyone rushing to push their code into master w/o testing.  became a PITA
16:51 rbuels pyrimidine: we could probably have used this issue to make lincoln and scott split out the thing they needed fixes on
16:52 rbuels but oh well
16:52 pyrimidine right, but I think (b/c the code is already part of 1.6 anyway) we have to keep it in for now
16:52 rbuels that makes sense.
16:53 pyrimidine my intent is to not have anything but bug fixes now, and everything else wait for the split up
16:53 pyrimidine (which I'm kinda thinking should be v2)
16:54 rbuels sure, could call it that
16:54 rbuels cause it might start developing some back-incompat
16:54 * deafferret waves
16:54 rbuels well, probably not
16:54 pyrimidine o/
16:54 * dbolser needs to get his dna day order in with 23andme
16:54 * rbuels waves
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17:18 pyrimidine dukeleto must live in a flood plain
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17:20 svaksha heh
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17:21 rbuels wtf
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17:22 rbuels pyrimidine: could you kick duk
17:22 rbuels e
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17:22 rbuels well, ban i guess
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17:22 rbuels pyrimidine: and also could you msg chanserv to give me ops
17:23 rbuels ah, well i'll do it myself then
17:23 rbuels heh
17:24 CIA-119 bioperl-live: Scott Cain master * re6c5916 / Bio/DB/SeqFeature/Store/DBI/Pg.pm :
17:24 CIA-119 bioperl-live: subtle bug fixed: when a type is supplied with a trailing colon (like "repeat:")
17:24 CIA-119 bioperl-live: the Pg adaptor checked whether the $source that resulted was defined (which it
17:24 CIA-119 bioperl-live: was) not whether it was true. As a result, the wrong sql would get generated. -
17:24 CIA-119 bioperl-live: http://bit.ly/eJgsMp
17:24 CIA-119 bioperl-live: Scott Cain master * r47439fb / (4 files in 4 dirs): Merge branch 'master' of github.com:bioperl/bioperl-live - http://bit.ly/ia7uN3
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17:27 pyrimidine poor dukeleto
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17:40 pyrimidine dukeleto: glad to see you above water :)
17:42 dukeleto i had dueling irc clients
17:42 dukeleto sorry, peeps
17:56 pyrimidine np
18:06 CIA-119 bioperl-live: Scott Cain master * r550862b / t/LocalDB/SeqFeature.t : making the "search for something that isn't there" test a little more reasonable. - http://bit.ly/ftKXwh
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18:35 CIA-119 bioperl-live: Chris Fields topic/bug_3196 * r0ed6182 / Bio/Root/Build.pm :
18:35 CIA-119 bioperl-live: Remove process_metadata override, which is bitrotting away from the
18:35 CIA-119 bioperl-live: Module::Build version - http://bit.ly/dVnFRq
18:35 CIA-119 bioperl-live: Chris Fields topic/bug_3196 * r00197fb / MANIFEST : upate MANIFEST - http://bit.ly/f8meL9
18:35 CIA-119 bioperl-live: Chris Fields topic/bug_3196 * red51e5d / Build.PL :
18:35 CIA-119 bioperl-live: Pull out the 'recommends' table and refactor to make a bit more
18:35 CIA-119 bioperl-live: Module::Build friendly - http://bit.ly/eouuSu
18:53 CIA-119 bioperl-live: Chris Fields topic/bug_3196 * r1b74610 / Bio/Root/Build.pm : fix typo; simplify, comment out prereq check methods and use Module::Build default methods - http://bit.ly/iiLACM
19:18 CIA-119 bioperl-live: Lincoln Stein master * r7aaaad4 / Bio/DB/GFF/Adaptor/dbi/mysql.pm : mysql adaptor now checks version of mysql and uses TYPE=MyISAM or ENGINE=MyISAM as appropriate - http://bit.ly/eJTVAK
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21:03 CIA-119 bioperl-live: Chris Fields topic/bug_3196 * r1073f38 / t/LocalDB/BioDBGFF.t : make the test script check for OS, not leave it up to the Build.PL - http://bit.ly/eLUfg2
21:03 CIA-119 bioperl-live: Chris Fields topic/bug_3196 * r37ab41e / (Bio/Root/Build.pm Build.PL): dismantle a little more Bio::Root::Build, get it in line more with Module::Build API - http://bit.ly/eZxegP
21:10 rbuels hurray for standard stuff
21:10 * rbuels has the bioperl backtrace on his shit list also
21:11 rbuels confess is a lot better.
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