Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-02-04

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All times shown according to UTC.

Time Nick Message
07:41 Gpox joined #bioclipse
07:41 Gpoks joined #bioclipse
07:42 Gpox joined #bioclipse
08:35 jonalv joined #bioclipse
08:42 jonalv oh hai
08:42 zarah hello jonalv, you fantastic person you
08:54 CIA-55 bioclipse: goglepox * r8570 /bioclipse2/trunk/plugins/net.bioclipse.ui/sr​c/net/bioclipse/ui/jobs/BioclipseUIJob.java:
08:54 CIA-55 bioclipse: Made getRetunrValue protected in BioclipseUIJob
08:54 CIA-55 bioclipse: so that users who override runInUI can get the
08:54 CIA-55 bioclipse: return value
08:54 CIA-55 bioclipse: goglepox * r8571 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MoleculeTableContentProvider.java:
08:54 CIA-55 bioclipse: Added support for SDFiles from Virtual to MoleculeTableContentProvider
08:54 CIA-55 bioclipse: It now checks if the file is in the Virtual project it then
08:54 CIA-55 bioclipse: load them as a list.
08:55 CIA-55 bioclipse: goglepox * r8572 /bioclipse2/trunk/plugins/ (5 files in 4 dirs): Added loadMolecules(IFile,BioclipseUIJob) to CDKManager
08:56 CIA-55 bioclipse: goglepox * r8573 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui.sdf​editor/src/net/bioclipse/cdk/ui/sdfeditor/editor/ (MoleculeTableContentProvider.java MoleculeTableViewer.java):
08:56 CIA-55 bioclipse: Added selection in MoleculesTable
08:56 CIA-55 bioclipse: Some drawing issues still exsists
08:56 CIA-55 bioclipse: goglepox * r8574 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MoleculeTableContentProvider.java: Added missing index in label for MoleculeTable
08:56 CIA-55 bioclipse: goglepox * r8575 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.ui.sdfeditor/plugin.xml: Menu for MoleculeViewer
08:57 CIA-55 bioclipse: goglepox * r8576 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MoleculeTableContentProvider.java: Removed no longer needed throws statement
08:57 CIA-55 bioclipse: goglepox * r8577 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.ui.sdfeditor/src/net/bioclipse/cdk/ui/sd​feditor/editor/MoleculeTableViewer.java: Fixed single selection. resolves bug 339 & 365
08:57 zarah bug #339 | http://tinyurl.com/c2ocku
08:58 CIA-55 bioclipse: goglepox * r8578 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.ui.sdfeditor/src/net/bioclipse/cdk/u​i/sdfeditor/editor/MoleculesEditor.java: Added popup menu fixed bug 332
08:58 zarah bug #332 | http://tinyurl.com/couztj
09:12 shk3 joined #bioclipse
11:09 edrin joined #bioclipse
11:15 maclean joined #bioclipse
11:52 masak joined #bioclipse
12:06 rojasm joined #bioclipse
12:27 egonw joined #bioclipse
12:34 jonalv joined #bioclipse
12:35 jonalv can we edit gists from within Bioclipse yet?
12:35 egonw no
12:35 egonw post 2.0
12:35 jonalv how do I find a gist?
12:35 egonw @gist search term
12:35 jonalv @gist structuredb
12:35 zarah http://tinyurl.com/b5merl
12:35 zarah http://tinyurl.com/dadn72
12:35 jonalv zarah: gist structredb
12:35 zarah http://tinyurl.com/as2a99
12:36 egonw @gist manager:structuredb
12:36 zarah http://tinyurl.com/b7eqjn
12:36 egonw in general:
12:36 egonw delicious.com/tag/bioclipse+gist
12:36 olass joined #bioclipse
12:37 olass egonw: you have bugs marked as NEW in pelezilla. http://pele.farmbio.uu.se/cgi-bin/bugzilla/buglis​t.cgi?query_format=advanced&short_desc_type=a​llwordssubstr&short_desc=&long_desc_type=​substring&long_desc=&bug_file_loc_type=al​lwordssubstr&bug_file_loc=&deadlinefrom=&​amp;deadlineto=&bug_status=NEW&emailassig​ned_to1=1&emailtype1=substring&email1=ego​n&emailassigned_to2=1&emailreporter2=1&am​p;emailcc2=1&emailtype2=substring&email2=​&bugidtype=include&bug_id=&vot
12:37 zarah olass's link is also http://tinyurl.com/aobm5s
12:37 egonw yes, I know
12:37 olass egonw: at least some of the should have Status Assigned
12:37 egonw anything in particular you want me to look at right now?
12:37 olass IMO
12:37 olass not really
12:38 olass just looking through my own list
12:38 egonw sure, I look at my Pelezilla inbox daily...
12:38 egonw but not this morning...
12:38 egonw sorry about that
12:38 olass :-)
12:38 egonw (not :)
12:38 egonw anyway
12:38 olass sorry to bother you
12:38 olass thought it might have slipped your queries
12:38 egonw I am moving the last reports on SF to pelezilla
12:38 egonw as others have not done so yet
12:38 olass excellent
12:38 egonw bugs were done
12:38 egonw feature requests not
12:39 olass hmm, thought I did all bugs yesterday?
12:39 olass ah
12:39 egonw some 12-ish left
12:39 olass egonw++
12:39 masak I think I did all mine... both bugs and feature requests...
12:39 olass I did only buigs
12:40 egonw no worries...
12:41 egonw just the type of work for a day where you cannot really think very properly...
12:42 olass indeed
12:43 olass in 30 mins it's perfect to review/update bug status
12:43 olass egonw: what is the status for bug #4?
12:44 egonw no improvement
12:44 jonalv egonw: how do I do the delicious tagging?
12:44 egonw FileDialog still does no allow excluding .svn
12:44 egonw so not really solving all problems
12:44 egonw and introduces the problem that is allows saving outside workspace
12:45 egonw which makes it more difficult for users
12:45 egonw jonalv: get a delicous account
12:45 egonw or kindly ask me
12:46 jonalv egonw: would you please tag this script: http://gist.github.com/58079
12:46 egonw what tags?
12:46 jonalv same as it's parent
12:47 egonw ha, a fork :)
12:48 egonw done
12:48 egonw jonalv: anyway, get a delicous account, and install the FF plugin
12:48 egonw really good stuff
12:48 jonalv it would be awesome to be bale to do that process from Bioclipse...
12:48 egonw yes
12:49 maclean olass : about the jmol image snapshot thing
12:49 maclean @bug 335
12:49 zarah http://tinyurl.com/cwgp69
12:50 maclean well, it is hooked to the gui, but the osx bug remains.
12:50 maclean :(
12:51 egonw ok, heading to the meeting room for Chris' talk
12:52 CIA-55 bioclipse: goglepox * r8579 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.ui.sdfeditor/src/net/bioclipse/cdk/ui/sd​feditor/editor/MoleculeTableViewer.java: Added check for empty selection in composittable
12:53 CIA-55 bioclipse: goglepox * r8580 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Fixed handling of newline characters when generating SDFile index. solves bug 341 & bug 180
12:53 zarah bug #341 | http://tinyurl.com/bdn3f3
12:53 CIA-55 bioclipse: goglepox * r8581 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Removed trailing spaces in CDKManager
13:01 olass_ joined #bioclipse
13:01 olass_ maclean: sorry
13:01 olass_ relocated to Christophs presentation :-)
13:01 maclean oh n/p
13:02 olass_ please go on
13:02 olass_ mom
13:02 olass_ will backlog
13:02 maclean oh, right. I think ...
13:02 maclean ...
13:02 olass_ ok
13:03 maclean ...that it's unfixable, sadly
13:03 maclean I have a gut feeling that it is some swt/awt bug that is osx specific
13:03 olass_ what does the snapshot feature do?
13:03 maclean takes a picture
13:03 olass_ isn't that what we want?
13:03 maclean you can use it like jmol.snapshot("/Sample Data/pic.png")
13:04 olass_ so what is not working?
13:04 * olass_ is confused
13:04 maclean the dialog
13:04 olass_ ok
13:05 olass_ so a general "Save as" dialog in SWT is not available on OS X?
13:05 maclean if you move the molecule (or interact with the jmol window) the dialog is unavailable
13:05 maclean no, I don't know about other save as dialogs
13:05 maclean that's why I suspect that this is a platform-dependent eclipse bug
13:05 olass_ I see
13:06 maclean shk3 asked if there should be a section (on the wiki?) for 'known bugs' - ie: difficult to fix ones...
13:06 olass_ there should be I guess...
13:06 olass_ please set one up
13:06 maclean oki
13:07 olass maybe you could ask about the SWT dialog issue on the eclipse newsgroup, in section SWT?
13:08 olass maclean: only do so if you feel comfortable
13:08 olass else we let it be
13:08 maclean I googled it, but found nothing, but the newsgroup might e better
13:08 maclean the only hope that I can think of is that there is something to do with setting up the jmol panel that needs to be done
13:08 maclean threading issues, or so
13:09 olass yes, would be great to follow it up
13:09 maclean but I'll ask...
13:09 olass maclean++
13:21 olass edrin: I have commented on bug #372
13:22 olass @pz #372
13:22 zarah http://tinyurl.com/c98bn5
13:22 olass @tell edrin Testing of webservices failed, see bug #372
13:22 zarah Consider it noted.
13:22 edrin '/Virtual' is
13:22 edrin not open.
13:22 zarah edrin: You have new messages. Write '/msg zarah @messages' to read them.
13:23 edrin @msg
13:23 zarah edrin: 12 s ago, olass said Testing of webservices failed, see bug #372
13:23 edrin yes
13:23 olass what do you mean?
13:23 edrin hm
13:23 edrin why can't it access the virtual folder?
13:23 edrin Resource '/Virtual' is not open
13:24 edrin olass: in your workspace, is there the virtual folder?
13:25 olass yes
13:25 olass hmm
13:25 olass I think Gpox mentioned something about renaming it...
13:25 olass will talk to him
13:25 edrin ah
13:25 olass did this work at your place?
13:25 edrin ok, maybe this is the reason
13:25 edrin olass: yes, i think so
13:26 edrin but did this on sunday
13:26 olass ok
13:26 olass I will assign the bug to Gpox
13:26 edrin me was ill, maybe i did mistakes
13:27 edrin ok
13:32 edrin olass: when discovery of an xmpp item fails, it will show this with a small icon: yellow exclamation mark!
13:32 edrin olass: you can try by trying to discover a JID that does not exist
13:33 olass ok
13:36 maclean http://wiki.bioclipse.net/ind​ex.php?title=Intractable_Bugs
13:36 zarah maclean's link is also http://tinyurl.com/bfhd57
13:41 olass maclean: thanks
13:41 maclean n/p
13:46 olass maclean: linked to it from http://wiki.bioclipse.net/index.p​hp?title=Bioclipse2_release_plan
13:46 zarah olass's link is also http://tinyurl.com/5guree
13:46 maclean ah, good.
13:47 maclean I also put it on: http://wiki.bioclipse.net/​index.php?title=Bioclipse2 under 'Development Tidbits'
13:47 zarah maclean's link is also http://tinyurl.com/6h4zlk
13:52 maclean ack! CoreGraphics crash.
13:54 maclean left #bioclipse
14:18 masak @stop
14:18 zarah masak: There's nothing to stop.
14:19 masak thank heavens for that.
14:19 heavens masak: you are welcome
14:19 masak lol
14:19 masak @thank heavens
14:19 zarah heavens: masak says thank you
14:27 masak jonalv: http://pele.farmbio.uu.se/manager-docs/
14:27 jonalv masak: I can has adrees?
14:27 zarah masak's link is also http://tinyurl.com/aqykgf
14:28 masak actually, that's not the latest version.
14:28 masak hold on.
14:30 masak there: http://pele.farmbio.uu.se/manager-docs/
14:30 zarah masak's link is also http://tinyurl.com/aqykgf
14:31 masak jonalv: plz check: http://bioclipse.svn.sourceforge.net/v​iewvc/bioclipse/bioclipse2/trunk/manag​er-apidocs/render-as-html?view=markup
14:31 zarah masak's link is also http://tinyurl.com/aofsda
14:51 CIA-55 bioclipse: carl_masak * r8582 /bioclipse2/trunk/manager-apidocs/render-as-html: [managerdocs] a bit more civilized line length
14:51 maclean joined #bioclipse
15:04 CIA-55 bioclipse: gilleain * r8583 /bioclipse2/trunk/plugins/net.bioclipse.ui/src/net​/bioclipse/ui/contenttypes/CmlFileDescriber.java: Removed rogue System.err output.
15:09 masak maclean++ # 'rogue'
15:09 maclean It was my code, but was still annoying me
15:22 egonw joined #bioclipse
15:52 CIA-55 bioclipse: ospjuth * r8584 /bioclipse2/trunk/plugins/net.bioclip​se.scripting/src/net/bioclipse/script​ing/business/JSJobCreatorAdvice.java: jonalv++ fixed a bug relating to number of arguments when executing scripts.
15:53 maclean egonw : how would bug 369 work?
15:53 olass joined #bioclipse
15:54 maclean like : jcp.set("bondLength", "10")
15:54 maclean ?
15:54 jonalv olass: thanks
15:54 egonw maclean: jcp.setDefaultBondColor(x)
15:54 egonw maclean: yes, maybe like that
15:54 maclean oh
15:54 maclean because otherwise, it's reflection
15:54 egonw I will have to expose those things in the Hub, I guess
15:54 maclean or risk missing out on options
15:54 egonw maclean: quick question... have you started a case manager for bioclipse yet?
15:54 egonw maclean: yes, indeed
15:55 jonalv what's a case manager?
15:55 maclean egonw: hmm, no I havent
15:55 edrin hi egonw
15:55 egonw jcp.setOption("key", "value") is a good idea
15:55 egonw hi edrin
15:55 egonw maclean: ack
15:55 maclean jonalv: CASE is "Computer Assisted (Aided) Structure Elucidation"
15:55 olass anyone who knows about the /virtual has affected scripts etc?
15:56 jonalv maclean: oh
15:56 egonw I filed a bug report about making /Virtual a temporary alias to /Temp
15:56 jonalv olass: I did not undestand that
15:56 edrin egonw: could you think about how to put the xws/taverna stuff into the texts? for example to link to the source/how to install...?
15:56 olass Gpox said he fixed that, right?
15:56 egonw maclean: on the other hand, hard coded methods would not require me to map strings to methods
15:56 jonalv browsing of sdf files from virtual?
15:56 maclean true
15:57 egonw edrin: yes, I will
15:57 olass well, that and others
15:57 egonw edrin: I actually wrote up a bit...
15:57 egonw edrin: please think about where you want to put that stuff...
15:57 egonw edrin: right now it's duplicate in methods and results...
15:57 edrin ok
15:57 maclean egonw: it's a tradeoff, either you have the mapping code, and throw some kind of "option not found" error
15:57 egonw edrin: it should only be in the latter, IMHO
15:57 egonw maclean: yes... so, I think I go for hardcoded
15:57 edrin the taverna plugin? or the things it does?
15:58 egonw also, because I need to put these things in a preference page
15:58 egonw edrin: both
15:58 * egonw is afk for a conference call
16:02 maclean zarah: tell egonw since the console will autocomplete functions, I guess having one for each is best (if a bit tiring to code)
16:02 zarah Consider it noted.
16:02 maclean takk
16:21 CIA-55 bioclipse: ospjuth * r8585 /bioclipse2/trunk/plugins/net.bioclipse.cml/src/ne​t/bioclipse/cml/managers/IValidateCMLManager.java: Removed @Job annotation since this is deprecated.
16:22 CIA-55 bioclipse: ospjuth * r8586 /bioclipse2/trunk/plugins/net.bioclipse.jmol/src​/net/bioclipse/jmol/business/IJmolManager.java: Removed @Job annotation since this is deprecated.
16:23 CIA-55 bioclipse: ospjuth * r8587 /bioclipse2/trunk/plugins/net.bioclipse​.structuredb/src/net/bioclipse/structur​edb/business/IStructuredbManager.java: Removed @Job annotation since this is deprecated.
16:25 CIA-55 bioclipse: ospjuth * r8588 /bioclipse2/trunk/plugins/net.bioclip​se.core/src/net/bioclipse/core/jobs/: Removed core.jobs package since replaced with core.ui.jobs.
16:27 CIA-55 bioclipse: ospjuth * r8589 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Removed @Job annotation since this is deprecated.
16:28 CIA-55 bioclipse: ospjuth * r8590 /bioclipse2/trunk/plugins/net.bio​clipse.core/META-INF/MANIFEST.MF: Removed exporting core.jobs package since replaced with core.ui.jobs.
16:28 CIA-55 bioclipse: ospjuth * r8591 /bioclipse2/trunk/plugins/net.bioc​lipse.chemoinformatics/plugin.xml: Moved chemoinformatics context to correct plugin.
16:29 CIA-55 bioclipse: ospjuth * r8592 /bioclipse2/trunk/plugins/n​et.bioclipse.data.drugbank/ (4 files in 3 dirs): New icon for drugbank plugin.
16:50 CIA-55 bioclipse: gilleain * r8593 /bioclipse2/trunk/plugins/net.bioclipse.jmol/src​/net/bioclipse/jmol/actions/ExportHandler.java: Fixes bug #335 by using the eclipse SaveAsDialog rather than the platform-native dialog, which was causing problems on osx.
16:50 zarah bug #335 | http://tinyurl.com/cwgp69
18:11 edrin left #bioclipse

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