Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-04-16

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Time Nick Message
04:14 rednael [Planet Bioclipse] Bioclipse2 Scripting #3: XLogP calculatation using a XMPP CDK cloud service  http://chemicalrcp.blogspot.com/2009/​04/bioclipse2-scripting-3-xlogp.html
04:14 zarah rednael's link is also http://tinyurl.com/cj5r2k
04:19 ilogger2 joined #bioclipse
04:59 egonw joined #bioclipse
06:27 Gpox joined #bioclipse
06:46 CIA-73 bioclipse: goglepox * r9833 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint/src/net/bioclipse/cdk/jch​empaint/business/JChemPaintManager.java:
06:46 CIA-73 bioclipse: Added updateView() to methods changeing rendering parameters
06:46 CIA-73 bioclipse: Fixes bug #909
06:46 zarah bug #909 | http://tinyurl.com/calj2l
07:14 CIA-73 bioclipse: goglepox * r9834 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java: fixed getCDKMoluecle to represent the current chem model
07:14 CIA-73 bioclipse: goglepox * r9835 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java:
07:14 CIA-73 bioclipse: Generates 2d coordinates and paint 'Generated' on screen.
07:14 CIA-73 bioclipse: This will generate all 2d coordinates if some atoms are missing 2d-coords.
07:14 CIA-73 bioclipse: goglepox * r9836 /bioclipse2/trunk/plugins/net.bioclipse.cdk.​jchempaint/src/net/bioclipse/cdk/jchempaint/ (2 files in 2 dirs):
07:14 CIA-73 bioclipse: Added syncronization of CDKMolecule.
07:14 CIA-73 bioclipse: It is only dont when JChemPaintEditor.getCDKMoleule() is called.
07:14 CIA-73 bioclipse: Resolves bug #648
07:14 zarah bug #648 | http://tinyurl.com/d5uexn
07:19 sneumann joined #bioclipse
07:21 egonw joined #bioclipse
07:26 CIA-73 bioclipse: goglepox * r9837 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.ui.sdfeditor/src/net/bioclipse/cdk/u​i/sdfeditor/editor/JCPCellPainter.java:
07:26 CIA-73 bioclipse: Generates coordinates if any atom is missing 2d-coords
07:26 CIA-73 bioclipse: Fixes bug #912
07:26 zarah bug #912 | http://tinyurl.com/chaugw
07:30 jonalv joined #bioclipse
07:30 jonalv o/
08:09 shk3 joined #bioclipse
08:47 olass joined #bioclipse
08:49 olass rednael: ping
09:16 edrin joined #bioclipse
09:17 egonw ha edrin
09:17 edrin hi egonw
09:17 egonw edrin: can you please check my patch on the XMPPManager?
09:17 egonw where I added a convenience method to convert a W3C Element to string
09:17 egonw see this gist:
09:17 egonw http://gist.github.com/95987
09:19 edrin sure, I must prepare some stuff first
09:20 egonw yes, no worries, thanx for looking at it...
09:21 egonw I tried using the JavaDOMTools but could not figure out how to instantiate it from the JS console in Bioclipse
09:23 edrin egonw: I think it's a static function, isn't it? you would then use it as Packages.net.bioclipse.xws.thepa​ckageof.JavaDOMTools.function();
09:24 olass hi edrin
09:24 egonw .function()
09:25 egonw oh
09:25 egonw s/function/toString/
09:25 egonw yes, tried that
09:25 egonw did not work
09:26 edrin egonw: no, I mean...
09:26 edrin give me a second
09:28 edrin egonw: JavaDOMTools = Packages.net.bioclipse.xws.JavaDOMTools;
09:29 edrin egonw: str = JavaDOMTools.w3cElementToString(result);
09:29 edrin egonw: but this only works in the editor and not in the console
09:29 egonw ah, ic
09:29 egonw I only tried the console
09:29 egonw why doesn't it work in both??
09:30 egonw the xmpp.connect() only seems to work in the console
09:30 egonw and gives a thread access error when run from the editor
09:30 edrin yes, ola sent this bug
09:30 edrin this is strange
09:30 edrin someone must have changed the editor plugin
09:34 jonalv egonw: do you have a moment. I want to have you oppinion...
09:37 egonw can you drop by?
09:37 jonalv oki
09:38 edrin jonalvsomething was changed/renamed in bc svn, what was this plugin?
09:41 CIA-73 bioclipse: ospjuth * r9838 /bioclipse2/trunk/plugins/net.b​ioclipse.jmol/build.properties: Added jmol documentation to build.props. I have no idea when this disappeared.
09:42 CIA-73 bioclipse: ospjuth * r9839 /bioclipse2/trunk/plugins/net.biocli​pse.cdk.jchempaint/build.properties: Added jcp documentation to build.props so it is added to exported versions.
09:44 olass egonw: around?
09:45 olass I get this error when compiling net.bc.doc
09:45 olass mbpro:net.bioclipse.doc ola$ ./run-the-whole-thing > html/index.htmlCan't locate YAML.pm in @INC (@INC contains: /System/Library/Perl/5.8.8/​darwin-thread-multi-2level /System/Library/Perl/5.8.8 /Library/Perl/5.8.8/darwin-thread-multi-2level /Library/Perl/5.8.8 /Library/Perl /Network/Library/Perl/5.8.8​/darwin-thread-multi-2level /Network/Library/Perl/5.8.8 /Network/Library/Perl /System/Library/Perl/Extras/5.​8.8/darwin-thread-multi-2level /System/Lib
09:45 olass BEGIN failed--compilation aborted at render-as-html line 4.
09:45 olass but it does do a lot
09:45 olass can I safely ignore this?
09:49 olass no, it did not work
10:14 CIA-73 bioclipse: goglepox * r9840 /bioclipse2/trunk/plugins/ (3 files in 2 dirs):
10:14 CIA-73 bioclipse: Changed jcp-widget to work on IChemModel
10:14 CIA-73 bioclipse: JCP now draws new bonds both for new molecules and old
11:16 olass egonw: could you please generate net.bioclipse.doc and net.bioclipse.doc.devel and commit this for the rescue pack?
11:17 olass did not succeed here :(
11:17 egonw ok
11:17 olass will wait for masak to teach me
11:17 olass installed all the stuff
11:17 olass but still have same errors
11:17 egonw hang on
11:27 edrin1 joined #bioclipse
11:29 edrin1 jonalv around?
11:37 olass egonw: how long does the run-the-whole-thing take?
11:38 egonw dunno
11:38 egonw not this long, AFAIK
11:39 egonw real    0m52.459s
11:39 egonw user    0m1.648s
11:39 egonw sys     0m3.844s
11:40 jonalv edrin1: I am now
11:45 edrin1 jonalv: it seems that objects are now generated in a different thread when created from a js thread
11:45 edrin1 right?
11:45 jonalv edrin1: uhm possibly, I can't asnwer that generally I am afraid
11:46 jonalv edrin1: no I don't think they should be.
11:46 jonalv edrin1: do you ahve an example?
11:48 edrin1 sorry
11:48 edrin1 must leave
11:48 edrin1 will write an email
11:48 jonalv oki
11:48 edrin1 cu later
11:50 CIA-73 bioclipse: egonw * r9841 /bioclipse2/trunk/plugins/net.​bioclipse.doc.developers/doc/ (13 files): Updated documentation for current SVN version
11:57 olass egonw: run_the_wholöe_thing is still running here...
11:57 egonw kill it
11:58 olass sure?
11:58 egonw yes
11:58 olass ok
11:58 olass you test
12:01 CIA-73 bioclipse: egonw * r9842 /bioclipse2/trunk/plugins/net.​bioclipse.doc/html/index.html: Added file, because script does not run on Ola's machine (worksaround for #923)
12:24 CIA-73 bioclipse: shk3 * r9843 /bioclipse2/trunk/plugins/net.biocli​pse.spectrum/src/net/bioclipse/spect​rum/wizards/NewSpectrumWizard.java: parent suggested as default if file is choosen in navigator
12:35 CIA-73 bioclipse: shk3 * r9844 /bioclipse2/trunk/plugins/n​et.bioclipse.data.seneca/: Initial import.
12:37 CIA-73 bioclipse: shk3 * r9845 /bioclipse2/trunk/plugins/​net.bioclipse.data.seneca/ (27 files in 13 dirs): the seneca examples
13:19 CIA-73 bioclipse: goglepox * r9846 /bioclipse2/trunk/plugins/net.bioclipse.co​re/src/net/bioclipse/core/Activator.java: Delete 'Virtual' before creating on startup
13:41 CIA-73 bioclipse: goglepox * r9847 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java:
13:41 CIA-73 bioclipse: Removed fit to screen from editor widget
13:41 CIA-73 bioclipse: and added setScale() when model is changed
13:41 CIA-73 bioclipse: Fixes bug #808
13:42 zarah bug #808 | http://tinyurl.com/cg2nww
14:34 egonw I hereby suggest we have a 2.0.0 release party at my place
14:35 egonw date to be agreed upon
14:35 egonw Gpox++
14:35 egonw Gpox++
14:35 egonw Gpox++
14:35 zarah Gpox++
14:35 egonw (three cheers for Gpox)
14:36 egonw for doing excellent bug fixing on JCP!
14:47 olass egonw: I have already said release party is at my place in STockholm :)
14:56 olass but we can have many parties
15:00 egonw olass: ah, right
15:00 egonw good!
15:09 egonw olass, jonalv: https://circle.ubc.ca//handle/2429/7115
15:09 egonw e-Science stuff
15:09 egonw metadata, bioinformatics
15:09 egonw of Benjamin Good
15:18 rajarshi joined #bioclipse
15:20 jonalv @pz 887
15:20 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=887
15:37 CIA-73 bioclipse: egonw * r9849 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java: Fixed getting of the active model using getCDKMolecule(): fixes saving a new file
15:54 edrin1 jonalv: i get thread access errors when i run a js command. for example in the js console xmpp.connect()
15:54 edrin1 jonalv: why is this?
15:55 edrin1 it wasn't like this in the past
16:05 CIA-73 bioclipse: shk3 * r9850 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java: Changed a misleading error message
16:08 egonw bbl
16:09 jonalv edrin1: I have no idea. I would suggest you to debug... I am going a way a couple of days so I will have a hard time giving you more help...
16:09 CIA-73 bioclipse: ospjuth * r9851 /bioclipse2/trunk/plugins/net.bioclipse.r/src​/net/bioclipse/r/ui/views/RConsoleView.java: Set R working dir to bioclipse-workspace on R console initialization.
16:19 edrin1 jonalv: when will you leave?
16:23 maclean joined #bioclipse
16:23 maclean hmmm. Arvid not around, eh?
16:25 olass nope
16:25 olass he's gone home
16:25 olass he fixed some major bugs today :)
16:27 maclean not necessarily...
16:29 maclean I'm not sure how he is testing after making changes, but things are broken - albeit in a different way.
16:29 olass oh no
16:29 olass send him bugs
16:30 olass and great spotting :)
16:31 maclean it wasn't difficult - have you updated?
16:37 shk3 joined #bioclipse
16:40 olass @tell egonw I filed bug 928 for the thread access problem
16:40 zarah Consider it noted.
16:47 maclean olass : If I find and fix a bug at the same time, do I still submit a bug report?
16:47 olass nope
16:47 maclean And then mark it as fixed?
16:47 olass I don't
16:47 olass seems like waste of time
16:47 maclean but it would leave a record of why the change was made.
16:47 olass the commit message?
16:48 maclean better than a commit message
16:48 olass if you feel like it, please do
16:48 maclean well, maybe.
16:48 maclean hmmm I'm not sure.
16:48 olass I have absolutely no objections for it
16:48 olass it's just that I am lazy
16:48 maclean :)
16:48 maclean I wasn't asking YOU to do it...
16:48 olass indeed
16:49 olass and just because I am lazy does not mean you are
16:49 maclean Anyway, you mostly like re-opening bug reports ;)
16:49 olass lol
16:49 maclean Oh I am lazy.
16:49 olass you donät seem lazy to me...
16:49 olass ä and ' sit very close...
16:50 maclean I guess the benefit of filing a bug report is that I can get it to mail itself to Arvid.
16:50 olass right
16:50 olass you can say he may close it after testing it
16:50 olass if you want a tester
16:52 maclean aha! that is a good reason, and yes I do, as I am changing his code (again) which can be annoying (especially if I did it wrong! :)
16:54 jonalv joined #bioclipse
17:06 CIA-73 bioclipse: gilleain * r9852 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java: Fixes a bug (#929) introduced by r9847, where molecules in JCP would not appear on screen by resetting the renderer when the chem model is set.
17:09 olass @tell egonw see gist 96528
17:09 zarah Consider it noted.
17:09 olass I'm very proud of it
17:13 CIA-73 bioclipse: ospjuth * r9853 /bioclipse2/trunk/plugins/net.bioclip​se.data/data/Javascripts/buildmol.js: Added a JS to show iterative building of a molecule in JCP.
17:15 CIA-73 bioclipse: ospjuth * r9854 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jchem​paint/src/net/bioclipse/cdk/jchempaint/business/ (IJChemPaintManager.java JChemPaintManager.java):
17:15 CIA-73 bioclipse: Wrapped some JCP Manager methods in Display.getDefault().asyncExec( ... ) to
17:15 CIA-73 bioclipse: make them run when called from Javascript. It seems the @GuiAction did not work
17:15 CIA-73 bioclipse: here, possibly to to NWO not implemented on JCPManager (see bug 928).
17:15 zarah bug #928 | http://tinyurl.com/c6lspp
17:16 CIA-73 bioclipse: ospjuth * r9855 /bioclipse2/trunk/plugins/net.bioclipse.scripti​ng.ui/src/net/bioclipse/scripting/ui/business/ (IJsConsoleManager.java JsConsoleManager.java): Implemented the command 'js.delay(int seconds)' to be able to delay a script at some points. Used in gist 96528.
17:17 egonw joined #bioclipse
17:19 olass hi egonw
17:19 olass watch my cool gist
17:19 olass 96528
17:19 olass (you need to update)
17:22 egonw ah, you fixed the threading issue?
17:22 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
17:22 egonw @msg
17:23 zarah egonw: 1 d 6 h 25 m 53 s ago, olass said STOP SINGING
17:23 zarah egonw: 42 m 3 s ago, olass said I filed bug 928 for the thread access problem
17:23 zarah egonw: 13 m 50 s ago, olass said see gist 96528
17:23 olass lol
17:23 olass it works very nicely
17:23 * olass is proud
17:23 olass egonw: how do you calculate center of mass on a molecule?
17:24 olass and the closest molecule to that?
17:24 olass and the closest atom to that?
17:24 maclean in 2D?
17:24 olass yes
17:25 maclean don't think you can do this from scripting.
17:25 olass no but from cdk?
17:25 maclean oh in java code?
17:25 egonw GeometryToold
17:25 egonw GeometryTools
17:25 egonw in cdk.geometry
17:25 olass and then?
17:25 egonw getCenterOfMass
17:25 egonw or so
17:25 egonw and pass it an atom container
17:25 olass and closest atom?
17:26 egonw jcp.closestAtom(Point2d)
17:26 olass thx
17:28 maclean if you want to do a lot of distance calculations, you might want to use the cdk.graph.rebond.Bspt class (the binary space partioning tree)
17:28 maclean or any such thing : quadtree, etc
17:29 egonw bbl
17:32 egonw olass: quicky
17:32 olass yes?
17:32 egonw I think jcp.addAtom() returns the added atom
17:32 egonw should clean up your script quite some
17:32 maclean it does
17:32 olass no
17:32 olass I would like ity to
17:32 maclean no?
17:32 olass but donät think so
17:33 maclean I thought for adding bonds, it did.
17:33 olass was gonna file a bug report about it :)
17:33 maclean hmmm.
17:33 olass public void addAtom(String atomType, Point2d worldcoord) {
17:33 egonw I'm pretty sure it did
17:33 olass ah
17:33 olass not that
17:33 olass public void addAtom(final String elementSymbol, final IAtom atom) {
17:34 olass void
17:34 egonw OK, will check later to see what changed that API
17:34 egonw bbl
17:34 maclean I think one of the addAtom methods do, and one doesn't
17:34 olass sure
17:34 egonw egonw: I'll fix the API otherwise
17:34 egonw oh, maybe the controller does
17:34 egonw but not the manager yet
17:34 egonw will check
17:34 egonw olass: please do file a bug report
17:34 olass should I file a bug?
17:34 olass :)
17:36 olass @bug 932
17:36 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=932
17:37 olass @tell Gpox bug 931 can also be that JCP changed in other ways that make M2D not visualize, but 930 would be diserable anyway.
17:37 zarah Consider it noted.
17:39 maclean Cross in 4 lines? Why not 2? :)
17:39 maclean Line extravagance!
17:40 olass well, two lines is a plus
17:40 olass might go unnoticed
17:40 olass 4 lines are two plus, one rotated 45 deg
17:41 maclean Oh. A star. I guess I should have looked at it...
17:41 maclean *
17:41 olass something like that :)
17:41 maclean No, that's five-membered.
17:41 maclean
17:48 egonw hahaha
17:50 egonw olass: patch to have jcp.addAtom return IAtom coming up
17:50 olass thx
17:51 olass will make my gist more clearer
17:51 olass did you like it?
17:51 maclean hmmm. I tried your script, olass, and everything is at the top of the screen ( which is not your fault, but it looks terrible :(
17:51 olass yes
17:51 olass but it works
17:51 maclean true.
17:51 olass I hope Gpox can fix the location tomorrow...
17:51 egonw ola, why did you make those fields static?
17:51 olass he will give it a go anyway
17:51 olass which ones?
17:51 olass what fields?
17:52 egonw of addAtom
17:52 olass ?
17:52 olass I made them final?
17:52 egonw yes
17:52 egonw not needed?
17:52 egonw ok, good
17:52 olass but not static?
17:52 olass what did I make static?
17:53 maclean final is only necessary for certain situations. like inner classes, or extreme memory use, I think.
17:53 olass final is to be reachable inside the SWT thread
17:54 maclean ahh.
17:54 olass but egonw has made up that I did anything static
17:54 olass (I hope)
17:54 olass yes
17:54 egonw I never said static
17:54 olass no match for static in JCPManager
17:54 olass [19:54] < egonw> ola, why did you make those fields static?
17:55 egonw ah...
17:55 egonw amazing...
17:55 egonw who says I am not dyslectic...
17:55 * olass feels a bit insulted
17:55 maclean an american might say "you mis-spoke" :)
17:55 olass egonw: several more occasions probably need         Display.getDefault().asyncExec( new Runnable() {
17:55 olass while you are at it I mean...
17:56 egonw not sure this is the right place to do this
17:56 egonw should be in updateView()
17:56 olass no
17:56 egonw and it is
17:57 olass it's the relay call that gives the error
17:57 olass it calls setDirty()
17:57 egonw so, the relay is doing things it should not be
17:57 olass which eclispe reacts on
17:57 olass I think
17:57 egonw ok, so going to revert your patch
17:57 olass do as you like, just donät break my gist!
17:57 egonw :)
17:58 olass IMO this should be solved with the @GuiAction annotation
17:58 olass but that does not seem to work yet...
17:58 olass NWO is not here yet
17:59 egonw no, that was really bad timing
17:59 egonw but fortunately there are enough JCP bugs
17:59 egonw to make it so much not a problem
18:00 olass indeed
18:00 olass tomorrow will be a patch on update site
18:02 maclean hmmm. that was almost a fix.
18:02 egonw what was?
18:03 maclean this change I made locally.
18:03 egonw ah, ic
18:03 maclean it makes olass script work nicely
18:03 egonw how so almost?
18:03 maclean but it breaks opening a new structure :(
18:03 egonw ah...
18:03 olass maclean: maybe not ready for commit yet?
18:04 egonw olass: where was this setDirty() call
18:04 maclean well not if it breaks things, no!
18:05 olass egonw: I remember it from a stacktrace
18:05 olass bug 928?
18:05 egonw ok
18:05 olass @bug 928
18:05 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=928
18:06 olass yes, that's it
18:06 maclean setDirty(boolean) is in JChemPaintEditorWidget
18:06 olass hmm
18:06 maclean it used to be setDitry... :)
18:06 olass something is listening
18:06 olass controllerhub
18:07 olass ok, so an easy fix is to wrap the setdirty in the JCPWidget
18:07 olass then if this is correct, I don't know
18:13 maclean dammit! it's like you can have centering, or scroll-zooming, but not both.
18:14 maclean why did I  make the renderer so hard to use?
18:16 egonw so that Chris could not fire you?
18:16 egonw :)
18:19 maclean but I tried to make it easy to use, not hard! :((
18:19 egonw yeah, same here...
18:29 * egonw loves git
18:29 egonw git++
18:29 CIA-73 bioclipse: egonw * r9856 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jchem​paint/src/net/bioclipse/cdk/jchempaint/business/ (IJChemPaintManager.java JChemPaintManager.java):
18:29 CIA-73 bioclipse: Revert "Wrapped some JCP Manager methods in Display.getDefault().asyncExec( ...
18:29 CIA-73 bioclipse: ) to make them run when called from Javascript. It seems the @GuiAction did not
18:29 CIA-73 bioclipse: work here, possibly to to NWO not implemented on JCPManager (see bug 928)."
18:29 CIA-73 bioclipse: This reverts commit d748b0808d702563acb5ffa82ec6de8c669b3d11.
18:29 CIA-73 bioclipse: Reason: this is not the right place to fix this. The setDirty should be done differently instead.
18:29 zarah bug #928 | http://tinyurl.com/c6lspp
18:30 CIA-73 bioclipse: egonw * r9857 /bioclipse2/trunk/plugins/net.bioclipse.cdk.​jchempaint/src/net/bioclipse/cdk/jchempaint/ (2 files in 2 dirs): Wrap in runnable to avoid threading issues when this is indirectly called from addAtom from the JCP manager
18:30 CIA-73 bioclipse: egonw * r9858 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jchem​paint/src/net/bioclipse/cdk/jchempaint/business/ (IJChemPaintManager.java JChemPaintManager.java): Follow the ControllerHub API and return the Created IAtom (Jonathan is going to love this :)
18:34 maclean wtf? if I run from features, I get no toolbar in jcp.
18:39 maclean right I see the problem. I was using features with overlapping plugin sets.
18:39 egonw what is wrong with that?
18:40 maclean well, clearly it breaks things...
18:40 egonw :)
18:40 maclean (on osx, at least)
18:43 olass egonw: does my gist still run?
18:43 * olass need to take the train back to stockholm really soon
18:43 olass actually quite happy with my presentation now
18:44 olass need to make Cheat Sheets
18:44 edrin when is release?
18:44 olass and verify everything
18:44 egonw yes, it does
18:44 edrin what presentation?
18:44 olass Bioclipse 2,0 is in mid May
18:44 egonw and the JCP manager returns IAtom now
18:44 edrin ok
18:44 egonw but the console disagrees
18:44 olass thx
18:44 olass wil update the gist
18:44 olass egonw: what do you mean?
18:44 olass console disagrees?
18:45 olass egonw?
18:46 egonw ah... wait
18:46 olass please commit fast..
18:46 egonw it now seems to work
18:46 olass need to run...
18:46 egonw not sure why
18:46 egonw run
18:46 olass so no new commit?
18:46 egonw I'll send an updated script
18:46 egonw no new commit
18:46 olass thx
18:46 egonw your script was running anyway
18:46 olass I'll fix the gist
18:47 olass no prob
18:47 olass bye!
19:19 CIA-73 bioclipse: edrin_t * r9859 /bioclipse2/trunk/plugins/net.bioclipse.xws​4j/src/net/bioclipse/xws4j/XwsConsole.java: Fixed the bug that reported a thread access error when printing to console from different thread
19:23 egonw edrin: and sneaked in colors too
19:27 CIA-73 bioclipse: edrin_t * r9860 /bioclipse2/trunk/plugins/net.bioclipse.xws​4j/src/net/bioclipse/xws4j/XwsConsole.java: added check to avoid potential null pointer exception
19:31 CIA-73 bioclipse: edrin_t * r9861 /bioclipse2/trunk/plugins/net.bioclipse.jsedito​r/src/net/bioclipse/jseditor/RhinoConsole.java:
19:31 CIA-73 bioclipse: Although the previous code seemed to work I moved the SWT code into the runnable
19:31 CIA-73 bioclipse: that runs in GUI thread. This was done because the Console used in the xws4j
19:31 CIA-73 bioclipse: plugin from now to then complained about a thread access caused by this SWT
19:31 CIA-73 bioclipse: code. As the xws4j console is very similar and changed accordingly.
19:53 CIA-73 bioclipse: edrin_t * r9862 /bioclipse2/trunk/plugins/net.biocli​pse.xws4j/src/net/bioclipse/xws4j/ac​tions/ToggleConnectionAction.java: The connect action when called from GUI shows an error box if connecting to xmpp server is not possible because no account data was set in preferences.
20:10 CIA-73 bioclipse: edrin_t * r9863 /bioclipse2/trunk/plugins/net.biocl​ipse.xws4j/src/net/bioclipse/xws4j/ (2 files in 2 dirs): A GUI msg error box is shown if connecting failed on GUI connect because of an error (e.g. unknown host...).
20:35 maclean_ joined #bioclipse
21:21 charlgren joined #bioclipse
21:23 egonw joined #bioclipse
21:25 egonw ok, that was 15 minutes waisted
21:25 egonw more keyboard trouble
21:25 egonw had to reboot
21:25 egonw to get things functioning normally again :(
21:33 edrin uhm?
21:33 egonw yes?
21:33 edrin what was wasted?
21:33 egonw the time
21:33 edrin ah
21:33 edrin sorry, was confused
22:10 edrin egonw, did rajarshi manage to create/connect his service to the xws server?
22:10 egonw not yet
22:10 egonw I think
22:10 egonw I said at some point:
22:11 egonw [23:06:33] <rajarshi> off for the day, goodnight
22:11 edrin ah ok
22:16 edrin I am off now too
22:16 edrin cu

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