Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-04-29

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All times shown according to UTC.

Time Nick Message
05:11 egonw joined #bioclipse
05:28 masak joined #bioclipse
06:11 rojasm joined #bioclipse
06:29 Gpox joined #bioclipse
07:00 olass joined #bioclipse
07:00 olass moin
07:00 zarah hi olass
07:15 edrin joined #bioclipse
07:16 edrin hi
07:16 zarah privet edrin
07:16 edrin olass: thanks for your mail
07:16 olass sure
07:16 * edrin reports: swine flue arrived in Bavaria
07:16 olass in Bavaria?
07:17 edrin yes, near munich
07:18 edrin Bavaria is a state in Germany, munich is capital
07:21 olass edrin: stay away from sweins
07:21 olass egonw: around?
07:22 edrin olass: it's distributed by humans i fear
07:22 olass yes
07:22 olass me too
07:22 edrin sorry, swine flu
07:22 olass bad naming
07:22 edrin yes
07:22 egonw yes
07:22 olass egonw: is this balloon change ok? "Number of conformations:" > "Number of conformations (target):"
07:23 egonw yes, perfect
07:23 olass ok
07:23 olass egonw: and the default value?
07:23 olass what do you suggest?
07:24 olass I agree we should have one
07:24 egonw 15?
07:24 olass why not?
07:24 * olass sets default to 15
07:25 olass we could ask John or rajarshi
07:25 olass they do this more than we do
07:25 egonw it depends very much on the number of atoms and rotatable bonds
07:25 egonw but 15 should be ok
07:25 olass ok
07:25 olass 15 it is
07:28 CIA-73 bioclipse: ospjuth * r9971 /bioclipse2/trunk/plugins/net.biocl​ipse.balloon.business/src/net/biocl​ipse/balloon/ui/BalloonDialog.java: Indicate that number of conformers is a target and set default value to 15. Solves bug #794.
07:28 zarah bug #794 | http://tinyurl.com/cpswm4
07:47 jonalv joined #bioclipse
07:53 jonalv o/
07:53 edrin http://xkcd.com/574/
07:56 masak *lol*
07:57 * masak searches for "swine flu" on twitter
07:57 egonw :)
08:00 masak http://tinyurl.com/c2a8fs # watch it spread -- nice
08:04 CIA-73 bioclipse: ospjuth * r9972 /bioclipse2/trunk/plugins/net.bioclips​e.balloon.business/src/net/bioclipse/b​alloon/business/BalloonManager.java: Added check for supported content types when running balloon from command line.
08:08 shk3 joined #bioclipse
08:12 jonalv egonw: can you see if you can get that branch running_
08:16 egonw ah... radio again...
08:16 egonw phew
08:16 egonw that saves the day
08:16 egonw jonalv: will try to boot it now
08:16 jonalv egonw: awesome
08:18 egonw still problems
08:18 egonw did you make new commits since yesterday?
08:18 jonalv egonw: not sure
08:18 jonalv egonw: where are you today?
08:19 egonw home
08:19 jonalv okey, I don't think there are any new changes yet but htere soon will be
08:19 egonw turns out I have a appointment at the vårdcentral early afternoon
08:20 jonalv I think I am gonna do svn rebase today as well
08:20 jonalv oki
08:20 jonalv could you try some more and get this started? I don't understand why it's not just working...
08:21 jonalv egonw: you made some progress yesterday... :)
08:21 egonw will try
08:22 jonalv wow I made some progress
08:22 jonalv egonw: was it complaining about net.bioclipse.recording? It turned out I wasn't even running that pluign...
08:23 egonw yeah, possibly
08:24 jonalv but that was while running tests
08:24 jonalv I can still not get it started... :(
08:28 egonw jonalv: this is my observation
08:28 egonw when it hits net.bioclipse.ui.Application it still has no workspace defined
08:29 jonalv egonw: hm how is that supposed to work? Is this related to that workspace switch thing made by shk3?
08:31 shk3 I can't run bioclipse since yesterday
08:31 shk3 nothing seems to help
08:31 jonalv this time I should be innocent. I haven't made any commtis to trunk the last couple of days :)
08:32 shk3 the odd thing is: it happened while I was working on the seneca plugin
08:32 shk3 no update or so
08:32 shk3 just changing code in a class
08:32 shk3 no restart
08:32 shk3 just in the middle of a session
08:32 shk3 it refused to start
08:32 CIA-73 bioclipse: ospjuth * r9973 /bioclipse2/trunk/plugins/​net.bioclipse.ui.business/ (3 files in 2 dirs):
08:32 CIA-73 bioclipse: Implemented ui.revealAndSelect for files since ResourcePathTransformer does not support folders.
08:32 CIA-73 bioclipse: Usage: ui.revealAndSelect("Sample Data/SDF/Fragments2.sdf")
08:32 CIA-73 bioclipse: Solves bug #981.
08:32 zarah bug #981 | http://tinyurl.com/cjm8hd
08:33 egonw shk3: any error message?
08:33 jonalv olass: I think masak was messing around with folders as well. Are you two fixing the same problem in two different ways?
08:34 masak I stopped trying to fix that problem.
08:34 shk3 the usual ones:
08:34 shk3 org.osgi.framework.BundleException: Exception in net.bioclipse.core.Activator.start() of bundle net.bioclipse.core.
08:34 olass I have not fixed anything with folders so that is a distinct 'no'
08:34 masak as far as I remember, I reassigned it to olass.
08:34 shk3 Caused by: java.lang.ClassCastException: org.eclipse.core.internal.dtree.NoDataDeltaNode
08:34 olass I have no bug for fixing folders in resourcepathtransformer
08:34 shk3 but I found these messages don't tell anthing anyway
08:35 jonalv olass: I just read you last commit message...
08:35 olass jonalv: I wrote my last commit message
08:36 jonalv olass: I don't doubt that. Maybe I missunderstood...
08:36 olass jonalv: I have never written anything in the resourcepathtransformer
08:36 olass I try to stay away from it as it sems complex
08:36 jonalv olass: no I thought you were working around it...
08:36 olass nope
08:37 olass implemented for files as RPT does not support folders
08:37 jonalv olass: when running plugin tests based on a product. Should not all plugins defined in that product be added when I click add required plugins?
08:38 olass no
08:38 * jonalv is having problems with running plugin tests, (again)
08:38 olass it looks at the selection in the "select plugins" view
08:38 jonalv olass: no? How should I do it then?
08:38 olass and adds their dependencies
08:38 olass was that clear?
08:39 jonalv olass: maybe
08:39 olass remember to set target platform
08:39 jonalv must hionk a little
08:39 jonalv |think
08:42 egonw jonalv: ping
08:42 jonalv egonw: pong
08:43 egonw jonalv: the recurrent problem is that core.resources is booted before a workspace is defined
08:43 jonalv egonw: okey, do you know why as well?
08:43 egonw we need to set the workspace instance location as early as possible
08:43 jonalv egonw: definitly, where is it done now?
08:46 egonw jonalv: I have no clue
08:47 egonw who did the BC2 workspace stuff?
08:47 egonw olass?
08:47 jonalv egonw: I think shk3 added that a couple of weeks ago...
08:47 olass egonw: pong
08:47 olass yes
08:47 olass shk3 did that
08:47 shk3 yes
08:47 egonw ok
08:47 egonw so, please stay here
08:47 egonw all of you...
08:47 egonw don't run
08:48 shk3 can't say much since my bioclipse doesn't run
08:48 egonw shk3: no worries
08:48 egonw because this is in a branch you do not have anyway
08:48 egonw this is merely theoretical
08:48 egonw this is the deal
08:48 egonw the managers need
08:48 egonw the org.eclipse.core.resources plugin
08:49 egonw right now, that complains because the workspace is not instantiated yet
08:49 egonw so, I need info on:
08:49 egonw 1. which class boots BC2 at all?
08:49 egonw that is
08:49 egonw which net.bioclipse code is run as first net.bioclipse code
08:50 egonw 2. where are we currently setting up the workspace, and how does that work in general?
08:50 egonw that is
08:50 egonw how is the BC2 workspace defined (and in which bit of code)?
08:50 shk3 I found that net.bc.ui and net.bc.core
08:51 shk3 both need the workspace set in their activators
08:51 shk3 of these,
08:51 shk3 net.bc.core
08:51 shk3 is executed earlier
08:51 shk3 so in the activator of net.bc.core
08:51 shk3 the workspace is set
08:52 egonw ic...
08:52 shk3 look for code like
08:52 egonw ok, hang on
08:52 egonw jonalv: ping
08:52 shk3 Location instanceLoc = Platform.getInstanceLocation();
08:52 egonw shk3: yes, I see that code
08:52 jonalv egonw: yes
08:52 egonw it seems that nb.core.Activator is thus not called first anymore
08:53 egonw which makes sense if one considers that the Application is being run, which is in .ui ?
08:53 shk3 Jonathan said that net.bc.ui should be called first
08:53 egonw olass: does that make sense?
08:53 shk3 but I found this was not true when I tried
08:53 shk3 I didn't investigate which should run first and which runs first and why there is a difference
08:53 egonw shk3: yes, that depends on dependencies...
08:53 jonalv egonw: I would expect that ui is run first since that is where the product is. But I am not sure....
08:53 egonw which jonalv just cleaned up in this branch
08:53 olass jonalv knows best
08:54 egonw shk3: next time you find such a contradiction, please *do* report it...
08:54 egonw shk3: really, you are fairly observant with things that don't seem right...
08:54 olass I was not aware of that
08:54 egonw shk3: but you *must* report those
08:54 egonw otherwise they can't be fixed
08:54 shk3 it was all discussed on the mailing list
08:54 shk3 I didn't get much response
08:54 egonw ok, good
08:54 shk3 that's true
08:54 shk3 but not my fault
08:55 egonw should it have been?
08:55 egonw no need to make disclaimers
08:55 shk3 see my email "Sort of success with switch workspace"
08:55 shk3 and discussions following
08:55 egonw shk3: I know you did not write this BC2 boot code
08:55 shk3 from 2009-03-18
08:56 egonw shk3: may I request to bring those inconsistencies forward in a separate branch?
08:56 egonw so that they are not hidden in a positive message?
08:56 egonw maybe as bug report or so...
08:56 egonw anyway...
08:57 egonw I will now try setting up the Location in net.bioclipse.ui
08:57 egonw and I expect that will solve the problems...
08:57 shk3 we can do it in both and check if it es already set
08:57 egonw shk3: thanx very much for the explanation! it was very useful
08:57 shk3 that shouldn't be a problem
08:57 shk3 I think
08:57 shk3 great I could help
08:57 egonw shk3: yes, was thinking about that too
08:58 * jonalv would be happier if we could figure out which bundle starts first. That is sort important to know...
08:59 egonw jonalv: I think:
08:59 egonw in BC2 in SVN:
08:59 egonw net.bioclipse.core
08:59 egonw in your branch:
08:59 egonw net.bioclipse.ui
08:59 jonalv oh
09:01 egonw jonalv: this makes BC2 boot in your branch
09:01 jonalv egonw: awesome
09:03 jonalv egonw: do you have a patch? or do you push? Or how can I get you code?
09:03 egonw yes, in your mail box shortly
09:04 olass_ joined #bioclipse
09:07 egonw shk3++ for pointing me to the right bit of code
09:07 shk3 glad I could help
09:08 jonalv egonw++ and shk3++ for making my brnahc start. ( I haven't seen it do it yet so it better... :)
09:09 masak wow, karma points and a threat, combined!
09:10 egonw masak: you make it sounds like diplomacy...
09:11 masak just saying what I saw.
09:11 * jonalv is waiting for that patch from egonw
09:11 jonalv :)
09:12 egonw sent
09:21 egonw jonalv: received?
09:22 jonalv egonw: yes
09:22 jonalv merging a rebase right now
09:22 jonalv will push new version after that
09:22 egonw ok
09:23 egonw 3 confirmed swine flue in DE now
09:32 CIA-73 bioclipse: goglepox * r9974 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint/src/net/bioclipse/cdk/jch​empaint/business/JChemPaintManager.java: This class can be static
09:32 CIA-73 bioclipse: goglepox * r9975 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jchem​paint/src/net/bioclipse/cdk/jchempaint/undoredo/ (SWTAddAtomsAndBondsEdit.java SWTUndoRedoFactory.java): Removed unused import
09:33 CIA-73 bioclipse: goglepox * r9976 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java: Fixed null check to check for all cases
09:33 CIA-73 bioclipse: goglepox * r9977 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jchem​paint.view/src/net/bioclipse/cdk/jchempaint/view/ (SWTFontManager.java SWTRenderer.java): Cleared up some warnings
09:34 CIA-73 bioclipse: goglepox * r9978 /bioclipse2/trunk/plugins/net.bioclipse.c​dk.ui.sdfeditor/src/net/bioclipse/cdk/ui/ (8 files in 4 dirs): Removed unused imports
09:34 CIA-73 bioclipse: goglepox * r9979 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.ui.sdfeditor/src/net/bioclipse/cdk/ui/sd​feditor/editor/AbstractSelectableRow.java: Replaces tabs with spaces
09:34 CIA-73 bioclipse: goglepox * r9980 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.ui.sdfeditor/src/net/bioclipse/cdk/u​i/sdfeditor/editor/MoleculesEditor.java: Removed unused method and cleaned up a if statement
09:35 CIA-73 bioclipse: goglepox * r9981 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MoleculesEditorContentProvider.java: Removed unused code
09:35 CIA-73 bioclipse: goglepox * r9982 /bioclipse2/trunk/plugins/net.bioclipse.c​dk.ui.sdfeditor/src/net/bioclipse/cdk/ui/​sdfeditor/editor/PropertySelector.java: Changed type of collection
09:36 CIA-73 bioclipse: goglepox * r9983 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MoleculeViewerContentProvider.java:
09:36 CIA-73 bioclipse: Deprecated class
09:36 CIA-73 bioclipse: I don't think it is used anywhere if it is this will make it show up.
09:36 CIA-73 bioclipse: goglepox * r9984 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.ui.sdfeditor/src/net/bioclipse/cdk/u​i/sdfeditor/editor/JCPCellPainter.java: Fixed background color of 'Generated' message
09:36 CIA-73 bioclipse: goglepox * r9985 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint.view/src/net/bioclipse/cd​k/jchempaint/view/JChemPaintWidget.java: Take x,y of the client rectangle into account when drawing message
09:37 CIA-73 bioclipse: goglepox * r9986 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MultiPageMoleculesEditorPart.java:
09:37 CIA-73 bioclipse: If no noting is selected use the first
09:37 CIA-73 bioclipse: Fixes bug #978
09:37 zarah bug #978 | http://tinyurl.com/dcxj5a
09:37 CIA-73 bioclipse: goglepox * r9987 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java:
09:37 CIA-73 bioclipse: Save forwards to save as if resource is missing
09:37 CIA-73 bioclipse: Fixed bug #945
09:37 zarah bug #945 | http://tinyurl.com/c3zs5p
09:38 CIA-73 bioclipse: goglepox * r9988 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint.view/src/net/bioclipse/cd​k/jchempaint/view/JChemPaintWidget.java: Made Message's constructor public
09:38 CIA-73 bioclipse: goglepox * r9989 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java:
09:38 CIA-73 bioclipse: Added method on JCPEditor to set and clear a custom message
09:38 CIA-73 bioclipse: Message is displayed in the lower left corner
09:38 CIA-73 bioclipse: Fixes bug #670
09:38 zarah bug #670 | http://tinyurl.com/daf22h
09:38 CIA-73 bioclipse: goglepox * r9990 /bioclipse2/trunk/plugins/net.bioclipse.u​i.business/src/net/bioclipse/ui/business/ (IUIManager.java UIManager.java): Added refresh(path) method to manager
09:42 CIA-73 bioclipse: goglepox * r9991 /bioclipse2/trunk/plugins/net.bioclipse.core/src/​net/bioclipse/core/ResourcePathTransformer.java:
09:42 CIA-73 bioclipse: Do not create link in virtual if file exist in workspace
09:42 CIA-73 bioclipse: Fixes bug #983
09:42 zarah bug #983 | http://tinyurl.com/de8lw3
09:44 CIA-73 bioclipse: ospjuth * r9992 /bioclipse2/trunk/plugins/net.bioclip​se.ui.business/META-INF/MANIFEST.MF: Added loger to ui.business imports.
09:44 egonw oh goodies
09:44 egonw will break the 10000 commits today :)
09:44 * masak sincerely hates big red "you must determine a target milestone" message from Pelezilla
09:44 masak egonw: yup.
09:46 masak lunch &
09:47 CIA-73 bioclipse: ospjuth * r9993 /bioclipse2/trunk/plugins/net​.bioclipse.balloon.business/ (2 files in 2 dirs): Worked on select and reveal from Balloon. Pending bug #984.
09:47 zarah bug #984 | http://tinyurl.com/cb5cd6
09:47 olass_ also approaching bug 1000
09:48 egonw oh, who will win...
09:49 jonalv egonw: help
09:49 egonw sure, what's up?
09:49 jonalv egonw: I just made git svn rebase and the plugin net.bioclipse.recording is gone now
09:50 jonalv I must have done the wrong thing when merging. But I choose modified intead of removed so I thought it wouldn't remove anything... :(
09:52 jonalv egonw: but I can't undo a rebase so I don't know what to do now...
09:52 shk3 my eclipse is now complaining about
09:53 shk3 com.springsource.org.mozilla.javascript
09:53 shk3 not being found.
09:53 shk3 any idea?
09:53 shk3 never had that before
09:53 shk3 it must have been there
09:53 shk3 and probably still is
09:53 jonalv shk3: I added that to target platform so it should be there...
09:54 shk3 do i need to check that out or so?
09:55 * jonalv is going for lunch. He has just lost all his changes in that branch and might have to start over again... (git-svn)--
09:56 jonalv shk3: that was a long time ago so it should still be there. I ahven't changed anything in a couple of days....
09:56 * jonalv @lunch
09:56 egonw jonalv: no, you never loose patches
09:56 egonw jonalv: wait
09:56 egonw you'll have a better lunch
09:56 egonw after I explained
09:56 egonw assuming you commited things...
09:56 egonw did you?
09:57 jonalv egonw: but rebase changes the pathces...
09:57 egonw git has the concept of dangling commits
09:57 egonw no worries
09:57 egonw then your patches are not lost
09:57 egonw read that book Carl wanted you to read
09:57 egonw that explains about dangling commits
09:57 egonw they are still in the system
09:57 egonw but possible just not in your current history
09:57 jonalv egonw: okey but how do I find them?
09:57 egonw read that book
09:58 jonalv egonw: mhm
09:58 egonw I don't remember the commands
09:58 egonw do it after lunch
09:58 jonalv I am off now anyway
09:58 egonw but your work is likely not lost
09:58 egonw sure
09:58 egonw bon appetit
09:59 egonw shk3: you can check if your eclipse install has it in the plugins/ folder?
10:00 shk3 somehow it seems to be found now
10:01 egonw somehow++
10:15 maclean joined #bioclipse
10:25 egonw hi maclean
10:25 maclean hi
10:25 zarah oh hai maclean
10:44 CIA-73 bioclipse: ospjuth * r9994 /bioclipse2/trunk/plugins/net.bioclips​e.balloon.business/src/net/bioclipse/b​alloon/business/BalloonManager.java: Started working on balloon for cml files (bug 971) and realized this depends on bug #973 assigned to egonw.
10:44 zarah bug #971 | http://tinyurl.com/cuagf8
10:45 egonw olass: noted
10:45 olass egonw: ack
10:46 * egonw will be busy for a while: http://chem-bla-ics.blogspot.​com/2009/04/things-to-do.html
10:48 maclean haha! I love the last sentance.
10:48 maclean so enticing! "Here is a vast list of items...by the way - if you are not busy, anyone..."
10:49 egonw :)
10:51 maclean "learn to Swedish" is also an interesting one.
11:00 stain_ just say 'hejdå' no matter if you are arriving or leaving
11:06 CIA-73 bioclipse: ospjuth * r9995 /bioclipse2/trunk/plugins/net.bioclipse​.balloon.business/META-INF/MANIFEST.MF: Added missing dep.
11:07 olass 5 to go
11:07 olass no git cheating with many commits now!
11:08 egonw shk3: ping
11:08 shk3 egonw: ping
11:09 egonw shk3: you wrote makeReactantInExistingReaction() in ControllerHub?
11:09 egonw line 1595
11:09 shk3 I am afraid I did
11:09 egonw can you explain the purpose of the first param String s ?
11:09 shk3 mom
11:09 egonw e.g. maybe add JavaDoc ?
11:09 CIA-73 bioclipse: ospjuth * r9996 /bioclipse2/trunk/plugins/net.bi​oclipse.ui/intro/firststeps.xml: Removed install features as already exists. Solves bug #866.
11:10 zarah bug #866 | http://tinyurl.com/crw6dy
11:22 CIA-73 bioclipse: ospjuth * r9997 /bioclipse2/trunk/plugins/net.bioclipse.c​dk.jchempaint/src/net/bioclipse/cdk/jchem​paint/describer/JCPEditorDescriber.java: ICDKMolecules without 3D are opened in JCP with ui.open(mol). Solves bug #908.
11:22 zarah bug #908 | http://tinyurl.com/d55aag
11:23 * olass is going for 10.000
11:23 olass must be a real bug closed to count
11:24 olass jonalv: around?
11:25 shk3 just tried a new bc checkout,
11:25 shk3 but the wiki page seems out of date.
11:25 olass What manager should the command: assertFeatureInstalled("net.bioclipse.qsar") recide in?
11:25 Gpox olass: soon
11:25 shk3 it seems the net.bioclipse_feature is gone
11:25 olass shk3: that has been since 2 months approx
11:25 shk3 please update the wiki page
11:25 olass and was aanounced on ML
11:26 olass shk3: what wiki page?
11:26 shk3 Checking out Bioclipse 2
11:26 olass @tell jonalv please backlog
11:26 zarah Consider it noted.
11:26 olass shk3: URL?
11:26 shk3 http://wiki.bioclipse.net/index.php?title=Instruc​tion_for_how_to_check_out_and_compile_Bioclipse_2
11:26 zarah shk3's link is also http://tinyurl.com/6nh6qk
11:26 olass @gg Checking out Bioclipse 2
11:26 zarah olass: http://wiki.bioclipse.net/in​dex.php%3Ftitle%3DBioclipse2
11:27 olass fixed
11:27 jonalv zarah: just tell me...
11:27 zarah jonalv: 1 m 2 s ago, olass said please backlog
11:27 jonalv olass: I am back
11:27 olass What manager should the command: assertFeatureInstalled("net.bioclipse.qsar") recide in?
11:28 jonalv olass: as of right now I would say ui. But in the best of worlds some new one...
11:28 olass ok
11:29 olass jonalv: is the best of worlds perhaps another new world order away?
11:29 * jonalv depserately grabs the "Git MAgic" text and hopes to find the solution to all his problems
11:29 jonalv olass: you don't need a new world order to create a new manager. Just please put it in a plugin of it's own iof you do
11:30 * olass will wait a few new world orders
11:30 olass ;)
11:38 shk3 tried a new checkout with the minimum requirements:
11:38 shk3 net.bc.scripting requires net.bioclipse.jsexecution
11:39 shk3 and net.bc.ui.business requires  org.eclipse.ui.navigator;bundle-version="3.3.102"
11:48 olass shk3: please update the wiki accordingly
11:48 olass jsexecution is required now
11:49 olass remove teh bundle version
11:49 olass or wait
11:49 olass let me remove the bundle version
11:51 CIA-73 bioclipse: ospjuth * r9998 /bioclipse2/trunk/plugins/net.bi​oclipse.ui/META-INF/MANIFEST.MF: Removed required Eclipse bundle versions.
11:51 olass shk3: please update and verify commit 9998 solves this
11:51 CIA-73 bioclipse: goglepox * r9999 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk.jchempaint/ (2 files in 2 dirs):
11:51 CIA-73 bioclipse: Added key binding for delete key
11:51 CIA-73 bioclipse: To get key bindings to work a new context for JChemPaint is necessary.
11:51 CIA-73 bioclipse: Resolves bug #853
11:51 zarah bug #853 | http://tinyurl.com/dnyjbo
11:52 CIA-73 bioclipse: goglepox * r10000 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.jchempaint/plugin.xml:
11:52 CIA-73 bioclipse: Added key bindings for changing atom type
11:52 CIA-73 bioclipse: C, I, O, N, P, S, F
11:52 CIA-73 bioclipse: Resolves bug #927
11:52 zarah bug #927 | http://tinyurl.com/cfgy87
11:52 Gpox :)
11:53 Gpox git++
11:53 jonalv git++ (git reflog)++
11:54 jonalv (git reflog)++
11:55 olass Gpox: you beat me!
11:55 olass but I must admit that you really solved bugs
11:56 olass right, this calls for a prize
11:56 olass will be delivered at the release party in my place after 2.0 release
11:58 olass maclean: no need to get angry, you are invited too!
11:59 * olass gets even more coffee
12:13 jonalv has someone removed all the bundleversion numbers in net.bioclispe.ui?
12:13 jonalv olass: why?
12:13 * jonalv is trying to merge here...
12:13 olass I did
12:13 olass why could I not?
12:13 jonalv olass: why? Isn't that a bit evil?
12:14 olass what for?
12:14 Gpox how can you remove them if they are required?
12:14 olass we use 3.4 now
12:14 olass I removed the versions
12:14 jonalv so they should be updated then?
12:14 olass that gets the latest version
12:14 olass no version = use currently installed
12:14 jonalv ah okey
12:15 jonalv that can be dangerous if the currently installed is not compatible with the expected...
12:15 olass eliminates problems with different eclipse cersions
12:15 olass sure
12:15 shk3 i can't run even a new checkout in a new workspace
12:15 olass in that case we should have versions
12:15 jonalv I will make sure to keep the version without the numbers then... :)
12:15 olass but have not experienced this yet
12:15 olass jonalv: please do for now
12:15 * jonalv redoes the merge..
12:16 * olass redoes the coffee
12:19 shk3 anybody any suggestion on how to run bioclipse?
12:20 shk3 i get the normal org.osgi.framework.BundleException: Exception in net.bioclipse.core.Activator.start() of bundle net.bioclipse.core. messages
12:20 shk3 which don't tell anything
12:20 olass bioclipse.product
12:20 olass open product
12:20 olass click run
12:20 olass well, set target platform first
12:21 shk3 doesn't help
12:21 shk3 I tried all sort of clean set target platform update classpath
12:21 olass paste error in pastebin
12:23 CIA-73 bioclipse: ospjuth * r10001 /bioclipse2/trunk/plugins/​net.bioclipse.ui.business/ (3 files in 2 dirs): Added commands: assertInstalled(feature) and getInstalledFeatures(). Only works in exported version. Solves bug #956 and bug #986.
12:23 zarah bug #956 | http://tinyurl.com/d56y9p
12:24 shk3 http://pastebin.com/d5c0157bf
12:25 maclean joined #bioclipse
12:26 maclean Gpox++ (for 10,000th commit). :)
12:29 maclean hmmm. who changed net.bc.ui.buisiness.UIManager?
12:30 maclean AS stefan and I get an error on the import for ...wait
12:31 maclean ok, fixed. there was a bundle version dependency in the manifest that was causing problems.
12:32 shk3 anybody an idea what that "The System Bundle's start level can not be modified." means?
12:37 shk3 ok, it seems the problem was my bioclipse workspace was somehow write protected
12:41 * olass hates to debug stuff that requires exporting to test
12:42 * jonalv hates merging
12:43 * jonalv is still mergine... :(
12:43 jonalv but now finally maybe I managed to do things right
12:50 jonalv egonw: new rebased and merged version on pele. :)
13:06 egonw shk3: did you reply on the 'String s' question?
13:06 egonw don't see it in the IRC logs, but there was much, and may have overlooked it...
13:06 shk3 commited
13:08 egonw shk3: which commit?
13:09 shk3 r14577
13:09 egonw ah, to jcp-prim, ok
13:09 egonw not bc2, ok
13:11 egonw OK, will updated jcp-prim in bc2 too then
13:40 jonalv egonw: I need to talk to you...
13:40 jonalv olass: or maybe you
13:40 jonalv egonw, olass:  or maybe both of yoyu
13:40 egonw IRC, skype?
13:40 jonalv IRC maybe
13:41 * olass is in tel
13:41 egonw ok
13:41 jonalv It's about calling methods that does partial return from JavaScript
13:42 jonalv that is when they are used from Java they take a BioclipseJobUpdateHook and returns a job
13:42 jonalv how should we do when using them from JavaScript?
13:43 jonalv Doing it the old way and returning a List has the danger that this list may become too big resulting in a OutOfMemory Exception...
13:44 jonalv but on the other hand. Implementing a BioclipseJobUpdateHook might not be the best way to do it from JavaScript
13:44 jonalv (not consdiern g trying to record and generate JAvaScript for that call)
13:44 jonalv egonw, olass: How would one want to work?
13:45 egonw restrict BioclipseJobUpdateHook to not be callable from JS?
13:45 olass sounds good with me
13:45 jonalv egonw: no
13:45 olass JS should be as easy as posible
13:45 jonalv no we can't restrict it. Then we need double implementations of those methods
13:46 jonalv I don't want code duplication
13:46 olass jonalv: what do you suggest?
13:46 jonalv olass: hm
13:47 jonalv or maybe we could jsut throw an excpetion if they are called...
13:47 jonalv from JAvaScript that is
13:47 jonalv but when doing recording
13:47 jonalv it won't work
13:48 jonalv If I do a substructuresearch in this 2 gig file and find 1 gig of hits then I will run out of memery when running the corresponding JavaScript script for that operation
13:49 jonalv that is the JavaScript script gnerated from the recording
13:49 jonalv egonw, olass: Do you follow? :)
13:49 egonw why does not not happen outside JS?
13:50 jonalv because in Java it would be solved by partial callbacks after each result. a bit like iterating..
13:50 jonalv that is what the BioclipseJobUpdateHook is for
13:50 egonw if the method has an iterating aspect
13:50 olass jonalv: if a user is stupid he can always end up in a situation with out of memory
13:50 egonw would that not have ot be used as such from JS too?
13:50 olass egonw: that is the point
13:50 olass we don't want that
13:51 olass it makes it very complicated to write scripts
13:51 olass we must make scripting easy, with the downside of some reduced features
13:51 jonalv egonw: it would have to in the sence that if we don't then we might run out of memory. It would not have to because of recording. The recording can change to a corresponding method call better suited for JavaScript
13:53 egonw then we basically define two APIs
13:53 jonalv olass: the problem is that with this approach we totally remove the possibility to write a JavaScript that handles more data than can fit in memory...
13:53 egonw one which does iteration, one which does not
13:53 egonw so , two methods
13:53 olass sounds ok with me to have 2 methods
13:53 jonalv egonw: yes I have 3 methods already on the interface but they should all use one method implemetnation.
13:54 jonalv however, this does not help the day I am recording an action using the iterative solution and tries to run that JavaScript which totally lack the iterative variant...
13:54 jonalv egonw, olass: do you follow?
13:55 olass jonalv: yes
13:55 olass should we worry about recording now?
13:55 olass you usually say it's broken
13:56 olass brb
13:56 jonalv olass: if we want it then we should worry about designing so that it is theorethically possible
13:56 olass jonalv: agreed
13:56 olass if we can solve it, yes
13:57 jonalv olass: Since I am redoing things quite thorugly here we can basically do it in whatever fashion we want. Question is just: How do one do partial returns in Javascript?
13:57 jonalv callbacks seem a bit to wordy and complicated...
13:57 egonw no callback == memory limitations
13:58 egonw that's an inherit problem
13:58 jonalv yes
13:58 jonalv so we want it some way
14:02 maclean joined #bioclipse
14:05 shk3 joined #bioclipse
14:14 rojasm joined #bioclipse
14:36 * jonalv seems to need a reboot
14:36 jonalv brb
14:42 shk3 joined #bioclipse
14:47 CIA-73 bioclipse: egonw * r10002 /bioclipse2/trunk/cdk-externals/trunk/ (99 files in 76 dirs): Upgraded to CDK 1.2.1
14:48 CIA-73 bioclipse: egonw * r10003 /bioclipse2/trunk/cdk-externals/trunk/org.open​science.cdk.standard/src/org/openscience/cdk/ (event/ICDKChangeListener.java geometry/GeometryTools.java):
14:48 CIA-73 bioclipse: Patching GeometryTools and ICDKChangeEvent from jchempaint-primary
14:48 CIA-73 bioclipse: Was git-svn-id:
14:48 CIA-73 bioclipse:  https://bioclipse.svn.sourceforge.net/s​vnroot/bioclipse/bioclipse2/trunk@9295 fcb5ba71-d80d-0410-8237-ba3920747fcc
14:48 CIA-73 bioclipse: Author: goglepox <goglepox@fcb5ba71-d80d-0410-8237-ba3920747fcc>
14:48 masak joined #bioclipse
14:49 CIA-73 bioclipse: egonw * r10004 /bioclipse2/trunk/cdk-externals/trunk/ (33 files in 9 dirs): Updated from jchempaint-primary svn rev 14577
14:50 CIA-73 bioclipse: egonw * r10005 /bioclipse2/trunk/cdk-externals/trunk/or​g.openscience.cdk.standard/src/org/opens​cience/cdk/geometry/GeometryTools.java: Applied jchempaint-primary commit 14507
14:50 CIA-73 bioclipse: egonw * r10006 /bioclipse2/trunk/cdk-externals/trunk/or​g.openscience.cdk.standard/src/org/opens​cience/cdk/geometry/GeometryTools.java: Applied jchempaint-primary commit 14534
14:50 jonalv joined #bioclipse
14:51 CIA-73 bioclipse: egonw * r10007 /bioclipse2/trunk/cdk-externals/trunk/or​g.openscience.cdk.standard/src/org/opens​cience/cdk/geometry/GeometryTools.java: Applied jchempaint-primary commit 14542
14:52 CIA-73 bioclipse: egonw * r10008 /bioclipse2/trunk/cdk-externals/trunk/or​g.openscience.cdk.standard/src/org/opens​cience/cdk/geometry/GeometryTools.java: Applied jchempaint-primary commit 14552
14:52 olass egonw: you've been busy :)
14:53 egonw well, took time to work out some jcp-prim, cdk-1.2.x incompatabilities
14:55 maclean_ joined #bioclipse
15:07 maclean_ joined #bioclipse
15:07 masak maclean_: hello, goodbye, hello.
15:07 maclean_ (hello|goodbye)*
15:08 egonw (hello|goodbye)+
15:09 masak [ hello | goodbye ]+ # perl 6
15:10 egonw who cares for a full EBNF grammar?
15:10 maclean_ I can't parse that sentance.
15:11 masak maclean_: it can mean 'who would like...? (I have one at home)" or "who gives a damn about...? (I don't)"
15:12 egonw OK, bioclipse workspace backed up to external drive
15:12 egonw ready to boot BC2
15:13 egonw bring on the data-loss bugs
15:13 egonw cool... I broke JCP
15:14 egonw :(
15:15 egonw I hate it when Eclipse Refresh does not work :(
15:15 egonw eclipse--
15:16 jonalv egonw: yea it depends on what one selects... (Eclipse Refresh)--
15:20 masak egonw: Free Tip of the Day: to make Eclipse Refresh refresh everything, select one thing, and then deselect it again with Ctrl+click. that way, you'll be sure that nothing is selected, and everything will be refreshed.
15:20 egonw huh??
15:21 masak egonw: having nothing selected means it'll refresh the whole workspace.
15:21 egonw ah... ic
15:21 egonw I typically select all
15:21 masak egonw: problem is, there's no obvious way to select nothing. the above method is the best one I've found.
15:22 egonw but that does not seem to work
15:22 masak egonw: select all works too, but then the problem comes (at least on Mac) that it's pretty inconvenient to deselect things again. :)
15:23 CIA-73 bioclipse: egonw * r10009 /bioclipse2/trunk/plugins/net.bioclipse.c​dk.jchempaint/src/net/bioclipse/cdk/jchem​paint/undoredo/SWTUndoRedoFactory.java: Missing implemented method, that came with the new interface with the upgrade to jchempaint-primary (see #987)
15:25 egonw maclean_: ping
15:25 maclean_ oh, I'm underscored
15:25 egonw yeah, that sounds bad
15:25 egonw mexican flue in UK I heard...
15:26 egonw scottland, england too now?
15:26 maclean_ guess so.
15:26 maclean_ media panic, is what I call it.
15:26 masak egonw: really? a mexican FLUE? :)
15:26 * masak hides
15:26 egonw you better
15:27 maclean_ Attack of the foreign chimneys
15:27 masak :)
15:27 egonw otherwise I'll cough in your face next week
15:27 * jonalv smiles and nods
15:27 masak egonw: you can cough on me through one of your chimneys.
15:28 egonw maclean_: anyways...
15:28 maclean_ yess
15:28 egonw maclean_: do you happen to know anything about SelectionGenerator.java ?
15:28 egonw we need that in BC2?
15:28 maclean_ Ummm.
15:28 maclean_ mom
15:29 egonw I would have asked Gpox, but in his absense...
15:29 egonw well, if you don't know... no worries
15:29 maclean_ No, I was just looking back at it.
15:29 egonw I have it around... so can reinstate it...
15:30 maclean_ Yes, you probably need it in bc2. For selections. For generating displays of selections.
15:30 maclean_ Reinstate? Where did it go?
15:30 egonw got lost upon the update from jchempaint-primary
15:31 maclean_ oops.
15:31 egonw apparently another patch that did not make upstream
15:31 maclean_ it is an essential generator. please reinstate, yes.
15:31 egonw :)
15:35 jonalv what do I run an a Virtual file to get the string representing it's path?
15:36 olass jonalv: can you really do that?
15:36 jonalv olass: I very much hope so.
15:36 jonalv olass: why not?
15:37 jonalv the toString contains that inforamtion + some other stuff
15:37 olass wel... you can get the workspace path
15:37 olass but not the rawLocation
15:37 olass so an IFile but not a File
15:37 jonalv no I want the workspace path
15:37 olass IFile.getFullPath()
15:37 jonalv I want /Virtual/test.file
15:37 olass IFile.getFullPath()
15:38 egonw IFile.getFullPath() ?
15:38 egonw sure?
15:38 egonw nvm
15:38 jonalv it worked, olass++
15:39 olass :)
15:43 jonalv masak: http://gist.github.com/103850
15:44 CIA-73 bioclipse: egonw * r10010 /bioclipse2/trunk/cdk-externals/trunk/org.ope​nscience.cdk.render/src/org/openscience/cdk/r​enderer/generators/SelectionGenerator.java: Reinstated SelectionGenerator which got lost with the update from jchempaint-primary, to which the generator has not yet been added (see #988)
15:47 jonalv masak: http://gist.github.com/103856
15:48 jonalv masak: http://gist.github.com/103857
16:18 olass egonw: are you doing heavy testing of jcp after cdk update?
16:18 olass I noticed at least one gist broken
16:19 olass filed a bug about that
16:21 CIA-73 bioclipse: ospjuth * r10011 /bioclipse2/trunk/plugins/net.bioclipse.r/ (5 files in 3 dirs): Fixed file permissions for native pty. Required renaming of pty to not contain spaces, hardcoded this for "mac os x". R-console now runs in exported versions. Solves bug #967.
16:21 zarah bug #967 | http://tinyurl.com/ccfegm
17:10 egonw olass: I asked stefan and arvid that all local patches where applied upstream
17:11 egonw stefan indicated one patch, which I applied
17:11 egonw arvid said he had nothing only in bc2 svn
17:11 egonw that was incorrect
17:13 egonw but I'll i sort it out with arvid...
19:40 olass joined #bioclipse

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