Camelia, the Perl 6 bug

IRC log for #bioclipse, 2012-01-18

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All times shown according to UTC.

Time Nick Message
05:29 egonw joined #bioclipse
07:09 sneumann_ joined #bioclipse
07:19 Bagarn joined #bioclipse
08:05 zaetnick joined #bioclipse
08:20 Gpox joined #bioclipse
08:48 olass joined #bioclipse
08:58 jonalv joined #bioclipse
09:09 egonw joined #bioclipse
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09:39 egonw joined #bioclipse
12:13 CIA-104 bioclipse.core: jonalv 2.5.x * r7d9a228 / plugins/net.bioclipse.usermanager/src/net/bio​clipse/usermanager/business/UserManager.java :
12:13 CIA-104 bioclipse.core: added missing persist() in switchUserContainer
12:13 CIA-104 bioclipse.core: fixes bug: 3038 - http://git.io/DbFchQ
12:13 zarah bug #3038 | http://tinyurl.com/6lojjde
12:26 zaetnick joined #bioclipse
12:26 CIA-104 bioclipse.cheminformatics: jonalv 2.5.x * rbda22ab / plugins/net.bioclipse.cdk.ui/c​heatsheets/editrunscripts.xml :
12:26 CIA-104 bioclipse.cheminformatics: fixed name for JavaScript scripts folder
12:26 CIA-104 bioclipse.cheminformatics: fixes bug: 3112
12:26 CIA-104 bioclipse.cheminformatics: Seems it had changed... Maybe we should have tests for cheat sheets somehow? I wonder if that is feasible though. - http://git.io/bhje_w
12:26 zarah bug #3112 | http://tinyurl.com/7o5h8wn
12:38 egonw @pelezilla gist
12:38 egonw @bug gist
12:38 egonw @help !
12:38 zarah [3059] Can not start Bioclipse 2.6 32... http://tinyurl.com/7s5wdla
12:38 zarah [3043] opentox.registerDataset(ontolo... http://tinyurl.com/7mumg7c
12:38 zarah [3113] Bioclipse can't find Gist         http://tinyurl.com/7vupbqz
12:38 zarah [3109] The "Scripting CDK" cheat sheet   http://tinyurl.com/6wwqw6e
12:38 zarah Entire list at http://tinyurl.com/7msu4fa
12:38 zarah [3059] Can not start Bioclipse 2.6 32... http://tinyurl.com/7s5wdla
12:38 zarah [3043] opentox.registerDataset(ontolo... http://tinyurl.com/7mumg7c
12:38 zarah [3113] Bioclipse can't find Gist         http://tinyurl.com/7gb5lqu
12:39 zarah [3109] The "Scripting CDK" cheat sheet   http://tinyurl.com/6wwqw6e
12:39 zarah Entire list at http://tinyurl.com/7msu4fa
12:39 zarah egonw: avaliable commands are ask bcwiki botsnack clear-messages gist google help hi hug karma messages pelezilla ping plan planet pong ps replan restart seen slap start stop tell thank thanks tutorial unplan welcome
12:39 egonw :)
12:49 jonalv "pz 3113
12:49 jonalv @pz 3113
12:49 zarah http://pele.farmbio.uu.se/bug​zilla36/show_bug.cgi?id=3113
12:50 jonalv egonw: is that the one you were looking for?
12:50 egonw yes
12:51 jonalv I am gonna look at it now I think
12:51 jonalv or do you want it? :)
12:53 jonalv egonw: _
12:54 egonw I was just looking at it...
12:54 egonw I think it
12:54 egonw I think it's just URLs that have changed on Gist
12:55 egonw but, if you feel like hacking... why not use their new Java libary for Gist interaction?
12:55 jonalv egonw: I only feel like fixing it as easy as possible... :)
13:00 jonalv egonw: uhm, are you parsing html?
13:00 egonw yes
13:00 egonw check line 112
13:00 egonw that line needs fixing
13:00 egonw they changes the site
13:00 egonw and you can now have multiple files in one gist
13:00 egonw so /gistfile1.txt no longer works
13:01 jonalv hm
13:02 jonalv this seems not se simple :(
13:05 jonalv egonw: do we need to support multiple files for the moment?
13:05 egonw probably...
13:06 egonw I'm hacking...
13:06 jonalv okicool, I will look at something else then...
13:06 jonalv egonw: do you want the bug as well?
13:07 egonw yes
13:10 olass joined #bioclipse
14:47 egonw jonalv: no idea :)
14:48 jonalv hm the Matrix Editor tab does not show the file name but it says: "Matrix editor" is that still so I wonder...
14:48 jonalv (in Olas OpenTox / QSAR presenation that is...)
14:51 jonalv egonw: question
14:52 jonalv egonw: it seems olass in that presentation has two Open tox servers
14:52 jonalv Ambit2 and TUM
14:52 jonalv do they have some sort of joint sign in?
14:52 olass yes
14:52 olass opentox has a federated authentication system
14:52 olass so you use same credentials
14:53 jonalv okey so you sign in to one and are signed in to all?
14:53 jonalv I see
14:53 jonalv have I asked this before?
14:53 olass egonw: can you confirm this?
14:53 jonalv I am having a feeling of deja vu
14:53 egonw jonalv: I got one gist method working :)
14:53 egonw huh?
14:53 egonw yes, think so
14:53 olass egonw: sign in to one place, access all opentox servers
14:53 * olass thinks so too
15:01 jonalv okey, now I understand how OpenTox is used from Bioclipse
15:01 jonalv olass++
15:02 jonalv there is definitly no editor/view to put the "Create Open Tox" account action in
15:03 jonalv it needs to be File +> New... -> something
15:03 olass yes, I think this would be best
15:03 jonalv should it go under Bioclipse core?
15:03 olass is it a genera lwizard?
15:03 olass then core is good
15:04 olass if a specific OpenTox NewWizard, then create an OpenTox category in the New... dialog
15:04 jonalv I am thinking maybe a general wizard where the first page provides a choice to more pages provided by an extension point
15:04 jonalv isn't that what you were talking about olass ??
15:04 olass yes, this sounds like a plan
15:04 jonalv I just seemed to recall something about that
15:04 olass it sounds good
15:04 jonalv it was so long ago that I had almost forgotten all again... :(
15:04 olass it's just that so many projects will only require username and password
15:05 olass so tha basic variant will suffice in that case
15:05 olass but yes, I agree with you on the general wizard complemented with an EP
15:05 olass jonalv++
15:06 jonalv I will scetch some dialog mock up and get back to you?
15:06 jonalv olass: is that ok?
15:07 olass sure thing!
15:07 jonalv olass: could you perhaps file me a bug about this? :)
15:07 jonalv or feature request even
15:07 olass ok, coming right up
15:07 olass @pz opentox
15:07 zarah [3068] Error calculating CPDB Signatu... http://tinyurl.com/82g29fx
15:07 zarah [3069] Server prefs not persisted if ... http://tinyurl.com/8yvcnsd
15:07 zarah [3043] opentox.registerDataset(ontolo... http://tinyurl.com/7mumg7c
15:07 zarah [3080] support  curl -X DELETE /task/id  http://tinyurl.com/7oxlxvy
15:07 zarah [3040] Adding a new OT server does no... http://tinyurl.com/88jluxu
15:07 zarah Entire list (10) at http://tinyurl.com/6vxw6kl
15:07 olass just checking...
15:08 olass @pz 3093
15:08 zarah http://pele.farmbio.uu.se/bug​zilla36/show_bug.cgi?id=3093
15:08 jonalv wow olass++
15:08 olass jonalv: is it OK if I comment on this bug?
15:09 jonalv olass: With regards to this or in general? In general I always think it's okey if you comment on bugs
15:09 olass with respect to this
15:09 olass I think this bug is about the same thing...
15:10 olass or would you like a new bug?
15:10 jonalv ah
15:10 jonalv I think this one is very general
15:10 jonalv maybe a child to this one?
15:10 olass ok, I will file a new bug
15:11 olass should the bug be a general account wizard or specific for the OpenTox use case?
15:11 jonalv go for general account wizard
15:12 olass ok
15:12 olass hold on...
15:12 jonalv I could use some help if we are to implement all things in this wish list
15:16 olass jonalv: see bug #3115
15:16 jonalv @pz 3115
15:16 zarah http://pele.farmbio.uu.se/bug​zilla36/show_bug.cgi?id=3115
15:17 jonalv zarah: remind me to fix you so you handle that correctly
15:17 zarah jonalv: are you making fun of me?
15:17 jonalv zno, itäs just that I think you should give the link when ola says things like that
15:18 jonalv zarah:  itäs just that I think you should give the link when ola says things like that
15:18 zarah jonalv: Hokay. You provide the commits, I provide the "should"-ing
15:18 jonalv zyes, my point axactly
15:18 jonalv grr
15:18 jonalv zaetnick: you are messing with my tab complete :)
15:19 zaetnick jonalv: how so?
15:19 jonalv you and zarah have so many letters in common in the beginning :)
15:20 zaetnick jonalv: thank you anyway - I didn't know  there's tab complete in Colloquy
15:21 jonalv oh :)
15:21 zaetnick now it's much easier to to type your nick - see jonalv
15:21 jonalv yea :)
15:21 zaetnick jonalv:
15:21 zaetnick hih
15:29 egonw argh.... this is painful
15:31 jonalv egonw: how is it going?
15:31 egonw not good :)
15:32 jonalv egonw: okey, that's too bad :(
15:32 jonalv egonw: This is not exactly an easy thing we are doing here though...
15:32 egonw indeed
15:33 egonw I'm removing functionality
15:33 egonw one could select a file before
15:33 egonw but that no longer makes sense
15:34 egonw but closing in
15:36 jonalv on a side note
15:36 jonalv How do we explain complicated things like the UserManager to the user who just wants to get going?
15:37 jonalv that is my problem
15:38 jonalv Gpox: are you comming to Uppsala tomorrow?
15:39 Gpox jonalv: yes
15:39 jonalv Gpox: Maybe I can test some ideas with you regarding UserManager then?
15:39 Gpox sure
15:41 egonw > gist.download(1139002)
15:41 egonw List<File> of size 3
15:42 egonw that should be expanded for recording, I guess?
15:43 jonalv egonw: recording is a dream
15:44 egonw one that you will make come true :)
15:44 jonalv egonw: but how do you mean?
15:45 egonw ok, bug fixes
15:45 egonw sort of...
15:45 egonw I can download gists again
15:45 egonw but the script will have to change
15:46 jonalv egonw: cause we are now handling multiple files?
15:46 egonw sure
15:47 jonalv I hate installing things in Eclispe btw
15:47 jonalv they have this fancy Marketplace thing but why can I not install things from it?
15:52 jonalv zaetnick: are you handling the matrix editor these days?
15:52 jonalv @pz matrixeditor
15:52 zarah jonalv: Zarro boogs found.
15:52 jonalv @pz matrix editor
15:52 zarah jonalv: Zarro boogs found.
15:52 jonalv @pz statistics
15:52 zarah [3083] Installation of Bioclipse-R In... http://tinyurl.com/7cw4tjd
15:52 zarah [3052] Libraries loading fails in loa... http://tinyurl.com/7nyjtbq
15:52 zarah [3053] Newlines lost when routing R c... http://tinyurl.com/75ye56e
15:52 zarah Entire list at http://tinyurl.com/7rp7864
15:53 zaetnick jonalv: not really
15:53 jonalv zaetnick: I just found a bug, wondering if you would wanna fix it or if I should do it...
15:53 CIA-104 bioclipse.core: Egon Willighagen 2.5.x * rd6ec026 / plugins/net.bioclipse.scripting/src/net​/bioclipse/scripting/GroovyThread.java : No JS top level commands for the Groovy console - http://git.io/ex2uvQ
15:53 CIA-104 bioclipse.core: Egon Willighagen 2.5.x * rc98ee9e / plugins/net.bioclipse.scripting.ui/src/net/bioc​lipse/scripting/ui/views/GroovyConsoleView.java : Commented out tab complete from an empty command line, as I have yet to figure out how to implement listing all active variables, and pull that into the Bioclipse console code - http://git.io/wt9jlg
15:53 CIA-104 bioclipse.core: Egon Willighagen 2.5.x * r67b3ed5 / (4 files in 3 dirs): Fixed the code to support the current Gist with multifile support (adresses #3113) - http://git.io/UttOtA
15:54 jonalv The matrix editor tab does not show the file name but gladly says: "Matrix Editor"
15:55 zaetnick jonalv: this shouldn't be a lot of work… but I think I better concentrate on R
15:55 jonalv k
15:55 jonalv I will file a bug for it for now
15:56 zaetnick and I know nothing about the Matrix Editor, so I'll have to spend some time with it
15:57 zaetnick jonalv: yes, do it and I'll take a look, hoping that it'll be a quick fix
15:58 mioukyyy joined #bioclipse
15:58 jonalv hi mioukyyy
15:59 mioukyyy hi everyone
16:00 mioukyyy what's happen here?
16:00 jonalv mioukyyy: the building of Bioclipse?
16:00 jonalv :)
16:01 zaetnick @pz Matrix editor
16:01 zarah [3116] The Matrix editor tab should s... http://tinyurl.com/6qysbcx
16:01 zarah Entire list at http://tinyurl.com/89bp6xp
16:03 mioukyyy cool!
16:05 jonalv mioukyyy: so, how did you end up here? :)
16:37 Bagarn left #bioclipse
16:44 CIA-104 bioclipse.core: jonalv bug3115 * r84c7bad / plugins/net.bioclipse.usermanager/src/net/biocl​ipse/usermanager/dialogs/CreateUserDialog.java : added explanation about why another account - http://git.io/W4yxQA
17:04 zaetnick joined #bioclipse
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20:23 CIA-104 chembl.rdf: Egon Willighagen master * r474768f / activities.php : Only cite literature, when the data was published (+15 more commits...) - http://git.io/p4jU-A
20:29 CIA-104 bioclipse.bridgedb: Egon Willighagen master * rd51aa76 / (15 files in 4 dirs): Added the testing framework - http://git.io/duIL4w
20:33 zaetnick joined #bioclipse
20:43 sneumann_ joined #bioclipse
20:50 CIA-104 bioclipse.bridgedb: Egon Willighagen master * rfe50b75 / features/net.bioclipse.bridgedb.te​sts_feature/AllPluginTests.launch : Added a launch file for Hudson testing - http://git.io/z8SZ6g
21:10 Gpox joined #bioclipse
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