Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-01-27

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All times shown according to UTC.

Time Nick Message
05:21 ilbot2 joined #bioclipse
05:21 Topic for #bioclipseis now An open source workbench for chem- and bioinformatics - http://www.bioclipse.net/ | BioclipseWiki => http://wiki.bioclipse.net/ !! | logs => http://colabti.org/irclogge​r/irclogger_logs/bioclipse & http://moritz.faui2k3.org/irc​log/out.pl?channel=bioclipse || Bioclipse2 beta released! See http://bioclipse.blogspot.com/
05:31 ChanServ joined #bioclipse
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05:31 Topic for #bioclipseis now An open source workbench for chem- and bioinformatics - http://www.bioclipse.net/ | BioclipseWiki => http://wiki.bioclipse.net/ !! | logs => http://colabti.org/irclogge​r/irclogger_logs/bioclipse & http://moritz.faui2k3.org/irc​log/out.pl?channel=bioclipse || Bioclipse2 beta released! See http://bioclipse.blogspot.com/
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07:40 Topic for #bioclipseis now An open source workbench for chem- and bioinformatics - http://www.bioclipse.net/ | BioclipseWiki => http://wiki.bioclipse.net/ !! | logs => http://colabti.org/irclogge​r/irclogger_logs/bioclipse & http://moritz.faui2k3.org/irc​log/out.pl?channel=bioclipse || Bioclipse2 beta released! See http://bioclipse.blogspot.com/
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09:39 edrin @ping
09:39 zarah edrin: pong
09:46 CIA-55 bioclipse: carl_masak * r8500 /bot/trunk/zarah.pl: [zarah] now reports the official pelezilla url
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09:51 edrin hi#
09:51 masak yallo
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10:35 olass joined #bioclipse
10:35 olass moin
10:35 zarah privet olass
10:35 zarah olass: You have new messages. Write '/msg zarah @messages' to read them.
10:35 olass @msg
10:35 zarah olass: 43 m 17 s ago, masak said http://www.artima.com/weblog​s/viewpost.jsp?thread=203994
10:36 olass yummy
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11:01 egonw joined #bioclipse
11:01 egonw moin
11:01 zarah hi egonw
11:13 egonw sneumann: hi! where are you know?
11:13 * egonw is with Stefan @ EBI
11:17 egonw shk3: http://dx.doi.org/10.1021/ci8002123
11:17 zarah egonw's link is also http://tinyurl.com/cozx3v
11:47 egonw leaving for lunch
12:32 de__maas joined #bioclipse
12:34 de__maas Hi All, just a very question about bioclipse 2 (great work) . Is it true that most of the CDK features (like qsar) are only accessible via the javascript console?
12:50 olass de__maas: not really
12:50 olass qsar for example is not added yet
12:50 olass but the general idea is
12:50 olass all functionality should be available from scripting
12:51 olass and then guild nice GUIs on top of it
12:51 olass naturally, having it as scripting is the first step
12:51 olass but there will also be cases when the GUI will preceed the scripting
12:51 olass qsar is one such example
12:52 olass but generally I'd say that actions are first available from console, and then it is straightforward to build a GUI upon it
12:52 olass de__maas: hope this sheds some light on the development procedure
12:52 olass all important funct SHOULD have a GUI
12:52 olass that is the objective
12:58 de__maas olass: thanks that explains it :)
12:58 de__maas Actually I was looking for the qsar stuff but indeed I could not find it.
12:59 olass sorry, I have not yet put it up
12:59 olass so many tasks, so little time :-)
12:59 olass really focusing on Bioclipse 2.0 now
12:59 de__maas Noworries, you sound like Rajarshi now.
12:59 olass haha
13:00 olass after 2.0, it will be QSAR and pharmacophores in bioclipse
13:00 de__maas BTW, I like the reading of big SF-files , I used it on mine which are about 300,000 records
13:00 olass did it work?
13:00 de__maas Yes, pretty fast as well.
13:00 olass we now process 200 at a time
13:00 olass could be changed for best user experience
13:01 olass we are experimenting with this
13:01 de__maas Well if you need big files I can help you :-D
13:01 olass haha, good to know
13:01 olass well
13:01 de__maas Would be nice if there is a way to see the additional fields.
13:01 olass how big do you generally work with?
13:01 olass yes
13:01 olass in the pipe
13:02 olass (a high prio bug)
13:02 olass I know people work with bug sdfiles, but in what magnitude are we talking?
13:02 olass >1Gb?
13:02 de__maas good to know, our stock database is about 300.000
13:02 olass ~500Mb?
13:02 de__maas Oh, in size . give me a second.
13:03 olass do you use it as an SDF generally?
13:04 de__maas No, i try to get in a database (symyx) as fast as possible.
13:04 de__maas Our last release to customers is 610Mb
13:05 de__maas Not all our customers have tools to access databases or have chemical software at all. Mostly they request excell files :P
13:06 de__maas So I like to point them to a non-commercial package which can handle that and BioClipse could be it.
13:20 de__maas olass: is there any docs on the js or just the help which is included in js?
13:20 olass hmm
13:20 olass good question
13:21 olass we are generating the inline help as HTML, but I donät think this is up yet
13:21 olass masak: can you confirm this?
13:21 olass the thing is, we generate HTML from all manager methods (lik a simple API documentation)
13:22 olass to be used as a basis for a scripting documnetation
13:22 olass (or at least a reference)
13:23 masak olass: how do I confirm it?
13:23 olass the HTML is not up?
13:23 olass as we talked about earlier
13:23 olass generated HTML not on pele?
13:24 masak oh, that HTML.
13:24 masak I'll have a look.
13:24 olass great
13:27 masak no, it's not up on pele.
13:27 masak seems I put a version here: http://masak.org/carl/managers.html
13:27 zarah masak's link is also http://tinyurl.com/5887bk
13:28 masak I'll put one on pele instead.
13:32 de__maas masak: what's pele?
13:32 masak de__maas: it's our development server.
13:32 masak @pz
13:32 zarah masak: Pelezilla is at http://pele.farmbio.uu.se/​cgi-bin/bugzilla/index.cgi
13:32 olass masak++ //I like the generated manager doc a lot!
13:33 de__maas Cool, thanks.
13:33 masak olass: thank you :) made it while you were on vacation.
13:33 masak it was a breeze to make with Perl.
13:33 olass Perl++
13:33 masak the source is in bioclipse/managerdocs/
13:33 olass edrin: around?
13:33 edrin yes
13:34 olass I am setting up the xmpp/xws wiki on pele
13:34 edrin ok :)
13:34 olass for suppl info and docu etc
13:34 edrin yes
13:34 olass what should we call it?
13:34 olass xmpp?
13:34 olass xws?
13:34 olass XMPP-XWS?
13:34 olass cloudcomp
13:34 edrin xmpp services
13:34 edrin ?
13:34 masak sorry, bioclipse2/manager-apidocs/
13:40 masak hm, I'm not really sure where to put it on pele so that it'll be publicly visible.
13:42 de__maas Aha, I thought it was just me
13:47 olass masak: put it under /var/www/
13:48 olass well, a subdir
13:48 olass placed there
13:50 masak oki
13:56 masak hm, running through tidy, I see I'm not quite done yet. :)
13:56 masak @plan old bc2
13:56 zarah masak: bc2/console-egonw-single-line-refactor: 2 h planned, 21 h 53 m elapsed
13:56 zarah masak: bc2/managerdocs-finder: 1 h 30 m planned, 1 h 37 m elapsed
13:56 zarah masak: bc2/managerdocs-finder-html-skin: 1 h 15 m planned, 1 h 10 m elapsed
13:56 zarah masak: bc2/scriptconsole-backspace-bug: 30 m planned, 2 m elapsed
13:56 zarah masak: bc2/scriptconsole-literal-tab-bug: 30 m planned, 15 m elapsed
13:57 masak @start managerdocs-finder-html..
13:57 zarah masak: Starting task 'bc2/managerdocs-finder-html-skin'.
14:02 masak @stop
14:02 zarah masak: Stopping task 'bc2/managerdocs-finder-html-skin' after 5 m at 1 h 15 m out of 1 h 15 m (100%).
14:02 masak phew.
14:07 CIA-55 bioclipse: carl_masak * r8501 /bioclipse2/trunk/manager-apidocs/render-as-html: [managerdocs] added HTML escaping to handle rogue characters
14:21 CIA-55 bioclipse: carl_masak * r8502 /bioclipse2/trunk/manager-apidocs/render-as-html: [managerdocs] added an empty-string default to silence warnings
14:21 CIA-55 bioclipse: carl_masak * r8503 /bioclipse2/trunk/manager-a​pidocs/run-the-whole-thing: [managerdocs] run-the-whole-thing now also runs tidy as a last step
14:26 olass masak: please write to bioclispe-devel when the new manager-apidocs is up on pele
14:26 masak olass: aye.
14:40 grandm44 joined #bioclipse
14:40 grandm44 hello
14:40 zarah privet grandm44
14:40 olass hi grandm44
14:41 grandm44 i prepared something, but it's a bit long to paste it in the channel, do you have some mailing list I can send it to ?
14:43 olass bioclipse-devel is fine
14:43 olass @gg bioclipse-devel
14:43 zarah olass: http://sourceforge.net/mail/%3Fgroup_id%3D150681
14:43 olass hmm
14:43 olass nope
14:44 grandm44 http://sourceforge.net/mailarchive/f​orum.php?forum_name=bioclipse-users ?
14:44 zarah grandm44's link is also http://tinyurl.com/akuus2
14:44 olass bioclipse-devel is better
14:44 grandm44 ok
14:44 olass https://sourceforge.net/mail/?group_id=150681
14:48 masak http://pele.farmbio.uu.se/manager-docs/
14:48 zarah masak's link is also http://tinyurl.com/aqykgf
14:48 * masak sends to list
15:02 olass masak: bug 296
15:02 masak @bug 296
15:02 zarah http://tinyurl.com/c4lue7
15:02 masak :)
15:02 masak olass: consider it done.
15:03 olass aah
15:03 olass masak++ //effektivare än en tysk
15:03 olass woops, swedish :-)
15:03 masak olass: http://steve-yegge.blogspot.com/2008​/06/done-and-gets-things-smart.html
15:03 zarah masak's link is also http://tinyurl.com/5pgqco
15:04 masak (not implying that I'm one of them, only that it's a nice ideal)
15:05 olass Gpox: do we have any general manager method for file manipulation (create project, create folder, copy file)?
15:05 olass if not, I'll file a bug
15:05 Gpox no
15:05 olass ok
15:06 masak olass: also, it's not me, it's Perl. :)
15:06 olass masak: would it be possible if zarah listened to pelezilla and reported when someone submitted a bug?
15:06 olass like the commit hook in SVN on SF...
15:06 masak olass: I'm sure. it's probably just a question of RSS.
15:07 olass masak: Iäll file a bug
15:07 * olass likes filing bugs
15:07 masak olass: :)
15:09 masak olass: http://pele.farmbio.uu.se/manager-docs/
15:09 zarah masak's link is also http://tinyurl.com/aqykgf
15:10 masak I'll have to think some about the layout, but I guess that's good for now.
15:10 olass nice!
15:10 masak hm, I'll have them sorted alphabetically, while am at it.
15:10 olass ok
15:11 masak olass: an index was a 4-line addition. :)
15:11 olass :)
15:12 olass masak: @bug 298
15:12 olass no rush :-)
15:12 masak zarah: @bug 298
15:12 zarah masak: that was not so easy for a little bot to understand
15:12 masak zarah: bug 298
15:13 zarah http://tinyurl.com/dc926e
15:14 masak olass: I like the idea. been trying to add RSS support to zarah before, and failing. I don't know enough about POE to pull it off yet.
15:14 olass no worries
15:15 CIA-55 bioclipse: carl_masak * r8504 /bioclipse2/trunk/manager-apidocs/render-as-html: [managerdocs] now prints an index at the top of the file
15:16 CIA-55 bioclipse: carl_masak * r8505 /bioclipse2/trunk/manager-apidocs/render-as-html: [managerdocs] now sorts managers alphabetically
15:45 * olass will run off to meet eclipse usergroup sweden in Stockholm and hear about Eclipse P2
15:45 olass cu tomorrow
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17:52 CIA-55 bioclipse: shk3 * r8506 /bioclipse2/trunk/plugins/ne​t.bioclipse.cml/plugin.xml: solves bug #273
17:52 zarah bug #273 | http://tinyurl.com/cfvur5
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21:33 CIA-55 bioclipse: edrin_t * r8507 /bioclipse2/trunk/plugins/net.b​ioclipse.webservices/src-axis1/ (4 files in 4 dirs): removed empty directories
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21:40 CIA-55 bioclipse: edrin_t * r8508 /bioclipse2/trunk/plugins/net.bioclipse.webse​rvices/src-axis1/net/bioclipse/webservices/: removed empty dir
21:41 CIA-55 bioclipse: edrin_t * r8509 /bioclipse2/trunk/plugins/net.bioclipse.webs​ervices/src-axis1/com/themindelectric/www/: removed empty dir
21:43 CIA-55 bioclipse: edrin_t * r8510 /bioclipse2/trunk/plugins/net.b​ioclipse.webservices/src-axis1/ (com/themindelectric/ net/bioclipse/): removed empty dir
22:46 CIA-55 bioclipse: edrin_t * r8511 /bioclipse2/trunk/plugins/net.b​ioclipse.webservices/src-axis1/ (com/ net/): removed empty dir
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23:50 CIA-55 bioclipse: edrin_t * r8512 /bioclipse2/trunk/plugins/net.bioclipse.w​ebservices/src/net/bioclipse/webservices/ (5 files in 3 dirs): optimized code. manager still not working, client stub probably invalid atm

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