Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-09-29

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All times shown according to UTC.

Time Nick Message
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06:37 olas hi
06:37 zarah hi olas
06:37 olas @msg
06:37 zarah olas: You have no new messages.
06:38 olas zarah: dz
06:38 zarah you're welcome, olas :)
07:39 jonalv joined #bioclipse
07:40 jonalv moin
07:40 zarah hi jonalv
07:42 olas moin jonalv
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08:13 olas @seen edrin
08:13 zarah edrin was last seen 2008-09-26T13:31:04 in #bioclipse saying 'have a nice weekend'
08:13 gilleain And so we did.
08:13 olas @tell edrin I'd like to talk about XWS when you have time
08:13 zarah Consider it noted.
08:14 jonalv yup :)
08:14 olas gilleain: indeed
08:23 gilleain Does anyone know why I get an ArrayIndexOutOfBounds exception when Bioclipse tries to online update?
08:24 gilleain Specfically, in ApplicationWorkbenchAdvisor.
08:24 gilleain line 179.
08:29 jonalv would someonw have anything against running Bioclipse with -server flag on the jvm?
08:30 olas why?
08:31 olas gilleain: that doesn't sound good
08:31 olas and could be my fault
08:31 olas mom
08:31 jonalv olas: are you talking to "me"?
08:31 olas jonalv: yes, and gilleain
08:31 olas gilleain: oh my bad
08:32 olas hmm well
08:32 olas that should not happen
08:33 olas vary strange
08:33 olas you always have a local installation site
08:33 olas but I guess I could catch that
08:33 olas gilleain: is it reproducible?
08:33 olas if you start from a new fresh build?
08:34 olas (set target platform, clean, new run config from bioclipse.product)
08:40 CIA-30 bioclipse: ospjuth * r7112 /bioclipse2/trunk/plugins/net.bioclipse.ui/src/ne​t/bioclipse/ui/ApplicationWorkbenchAdvisor.java: Catches if local installation does not have a site and throws exception in that case. No idea why this can occur.
08:40 olas ok, comitted a catch
08:41 olas gilleain: but please see if you can reproduce it
08:41 olas that should not happen
08:41 olas and might indicate your bioclispe installation is broken
08:41 olas or needs restart
08:41 olas do you run from within Eclipse?
08:41 olas then auto updates does not work anyway
08:42 olas only works if run from exported bioclipse
08:46 egonw joined #bioclipse
08:58 gilleain Ah. Hello. Went for coffee - didn't just lose the ability to type :)
08:58 gilleain I am running from eclipse, yes.
08:59 gilleain I will try the catch patch.
09:00 gilleain Ah yes. Caught.
09:00 gilleain "This should not happen." :)
09:02 egonw olas: reading material: doi:10.1093/bioinformatics/btn389
09:05 olas egonw: at work in new office?
09:05 egonw yes
09:05 olas nice
09:06 olas egonw: saw that
09:06 olas we should publish individual plugins as well
09:06 olas after Bioclipse2 comes out
09:06 egonw yes
09:06 olas egonw: will you be at work on tues of wed this week?
09:06 olas of=or
09:07 egonw not sure yet
09:07 olas I will
09:07 olas and Arvid will
09:07 egonw wed = 1st?
09:07 egonw so will I then
09:07 olas mom
09:07 olas yes
09:07 olas 1st
09:07 olas good
09:07 jonalv so no sushi tomorrow? :)
09:08 egonw huh?
09:08 jonalv we usually have sushi on tuesdays... :)
09:10 egonw ah, ok, will give that some thought
09:10 egonw depends a bit on how much I must do at home
09:11 jonalv but olas you will have sushi? :)
09:11 olas donät know
09:12 olas if I don't bring food, then maybe
09:12 jonalv and Gpox?
09:16 Gpox sushi++
09:17 egonw btw, I wrote a small library to keep a list of todo items, command line driven, git support for backup and sharing between machines
09:17 egonw in the end I hope to have a Bioclipse client
09:17 egonw but nothing fancy yet
09:18 egonw but it works
09:18 jonalv egonw: not sure I understand...
09:19 gilleain In java?
09:19 egonw then you're not target audience :)
09:19 egonw yes
09:19 egonw with shell script wrapper..
09:19 egonw oh, and with BASH autocomplete :)
09:19 gilleain Ahh.
09:20 jonalv well I am not using git no. But I have been known to think about it. It\s jsut that I love being able to commit from within Eclipse... :)
09:20 egonw git is optional
09:20 gilleain There is /technically/ a git plugin for eclipse/
09:20 jonalv oh, but?
09:20 gilleain http://git.or.cz/gitwiki/EclipsePlugin
09:21 jonalv would I start hacking on that instead of Bioclipse if I tried it out? :)
09:21 gilleain I think it has a way to go.
09:22 gilleain So, yes, you might well get distracted :)
09:22 jonalv hehe
09:23 jonalv I will stay away then..
09:25 * egonw switches git branches all the time...
09:25 egonw with one project version in Eclipse...
09:25 * egonw just uses the Refresh button
09:26 gilleain Brachiation, eh?
09:37 egonw huh?
09:38 * egonw does not think he read that book
09:38 gilleain Sorry, rubbish joke - it means "swing from branch to branch".
09:38 egonw ah, Tarzanian :)
09:40 gilleain indeed.
09:50 egonw olas: did you switch BC2 n.b.jmol to point to the 11_v6 branch already?
09:50 egonw the new upcoming stable release?
09:56 * egonw is going to change network from eth1 to eth0
09:56 egonw brb
09:59 olas egonw: no
10:05 egonw joined #bioclipse
10:08 olas egonw: a quick question
10:09 olas what is the command line syntax to check out a specific revision in CVS?
10:09 egonw CVS?
10:10 egonw -r I think
10:10 egonw just like with SVN
10:10 egonw though that allows the @REV too
10:10 olas please be verbose
10:10 olas I have never done this before from CL
10:10 olas cvs checkout -d /opt/cvs -r 1234
10:10 olas is that correct?
10:11 egonw yes, something like that, IIRC
10:11 olas ok, so you donät klnow?
10:11 egonw it's been a really long while since I used CVS
10:11 egonw but that looks fine
10:11 egonw one thing...
10:11 egonw do you mean update or checkout?
10:12 egonw the above line should say cvs update, I think
10:12 olas checkout
10:12 egonw then I think it needs a path where the check out from
10:15 olas how do I see the latest revision number?
10:18 egonw that should just be HEAD
10:18 egonw checkout HEAD
10:18 egonw and then cvs log | more
10:18 egonw or so
10:45 egonw did it work?
10:53 shk3 I found the following behaviour of bioclipse:
10:53 shk3 if you have an anvalid file of a certain type in a directory,
10:53 shk3 the content describer gets disabled.
10:54 shk3 meaning all files of the same type in the same directory
10:54 shk3 or in a subdirectory are not detected.
10:54 shk3 is this a known feature?
10:54 shk3 is it intended?
10:54 shk3 I think it's not too great
11:02 shk3 ok, I find if you catch exceptions in the content describer, the problem is gone.
11:02 shk3 I think we should do this in all content describers.
11:02 shk3 just changed the MdlMolFileCoordinatesDescriber - shall I commit?
11:13 CIA-30 bioclipse: shk3 * r7113 /bioclipse2/trunk/plugins/net.bioclips​e.ui/src/net/bioclipse/ui/contenttypes​/MdlMolFileCoordinatesDescriber.java: catching exceptions makes sure the describer isn't disabled when it comes across a problem
11:28 egonw this is that todo tool I wrote yesterday: http://github.com/egonw/gtd/tree/master
11:28 egonw shk3: good fix
11:28 egonw a bad file should indeed not kill the describer
11:29 gilleain howeeeever. could it catch IOException, rather than Exception?
11:31 gilleain map(me, lunch)
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12:14 egonw olas, Gpox, jonalv: I won't make it tomorrow
12:14 egonw our personnummer's have arrived ! :)
12:15 jonalv w00t!
12:15 egonw so, we'll spend some good admin time downtown
12:15 jonalv yea
12:15 egonw this is excellent... now we can request broadband :)
12:16 jonalv sounds great!
12:18 olas egonw: nice
12:31 gilleain joined #bioclipse
12:37 shk3 egonw: the problem is the exception which actually brought up the problem isn't an ioexception,
12:37 shk3 but an ArrayOutOfBoundsException, so catching IO doesn't help
12:37 gilleain Well, catch the array out of bounds exception then?
12:38 shk3 well, but there might be others with other sorts of corruptions
12:38 shk3 I thought it might  be best to prepare for everything
12:38 gilleain hmmm. maybe.
12:38 gilleain I see the point.
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13:46 CIA-30 bioclipse: goglepox * r7114 /bioclipse2/trunk/plugins/net.b​ioclipse.ui/bioclipse.product: Removed metaprint2d feature from product definition
13:59 edrin joined #bioclipse
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14:15 edrin hi
14:15 zarah hi edrin
14:15 zarah edrin: You have new messages. Write '@messages' to read them.
14:15 edrin @messages
14:15 zarah edrin: olas said I'd like to talk about XWS when you have time
14:16 edrin masak, jonalv: is there something like the empty_plugin for bc2 ?
14:17 jonalv edrin: there is an example plugin for Spring stuff
14:17 edrin location?
14:17 jonalv _playground_
14:17 edrin if you write a new plugin, how do you start?
14:17 jonalv is the plugin gonna contribute a mangaer?
14:18 edrin yes
14:20 jonalv then I suggest starting from that example plugin
14:23 gilleain ooh. what is the plugin?
14:26 edrin nothing special, just a plugin to have the xws library available
14:27 gilleain oh well. still interesting. I'm a keen tryer-out of plugins.
14:28 * jonalv and me is still trying to have some sort of overview of all plugins. Which reminds me that I must look at shk3 spectrum things... :)
14:28 jonalv lol
14:28 * jonalv and me :)
14:29 gilleain Do try them. Especially the specmol one on cml files with a spectrum and a molecule (different icon). You can click on atoms to highlight the peak...
14:32 edrin shk3: is the problem with web service plugin manager solved?
14:32 shk3 yes
14:33 jonalv gilleain: I will but not today
14:33 shk3 Bundle-ActivationPolicy: lazy
14:33 shk3 missing in MANIFEST.MF
14:33 edrin and that's a problem?
14:34 edrin because spring must be initialized first?
14:34 jonalv edrin: The plugin must be activated when the manager class get's loaded
14:34 jonalv otherwise the mangaer can't get published to the console...
14:34 jonalv uhm to JavaScript
14:34 jonalv :)
14:34 edrin ok
14:38 shk3 jonalv: Spectrum stuff is mainly a port from bc1, although I applied quite a few fixes and small improvments
14:39 jonalv yea sounds exciting :)
14:39 jonalv If I only knew more about spectrums... :)
14:39 masak jonalv: spectra.
14:39 masak :)
14:39 jonalv that was the first lesson I guess...
14:39 masak aye
14:39 shk3 i had a look at the feature stuff
14:40 shk3 should we make a spectrum feature?
14:40 shk3 later on, a speclipse product based on that would follow
14:53 malick left #bioclipse
14:53 masak "speclipse" :)
15:18 CIA-30 bioclipse: carl_masak * r7116 /bioclipse2/trunk/plugins/net.bioclipse.scrip​ting.ui/src/net/bioclipse/scripting/ui/views/ (JsConsoleView.java ScriptingConsoleView.java):
15:18 CIA-30 bioclipse: [JsConsoleView, ScriptingConsoleView]
15:18 CIA-30 bioclipse: * renamed q() into interceptDroppedString()
15:18 CIA-30 bioclipse: [ScriptingConsoleView]
15:18 CIA-30 bioclipse: * made command history remember the command being typed
15:18 CIA-30 bioclipse: * this fixes bug 2124749
15:18 masak CIA-30: oh, so you're back now?
16:36 CIA-30 bioclipse: shk3 * r7117 /bioclipse2/trunk/plugins/net.biocl​ipse.data.sampledata/data/specmol/ (5 files): added some specmol sample data
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