Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-06-01

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All times shown according to UTC.

Time Nick Message
06:29 egonw joined #bioclipse
06:29 egonw moin
06:48 egonw relocating
06:54 egonw joined #bioclipse
07:08 Gpox joined #bioclipse
07:09 egonw hi Gpox
07:09 Gpox hi egonw
07:09 egonw the group is now listening to Ola mid-term presentation
07:11 Gpox mid-term isn't that a bit late? ;)
07:53 egonw ola is done
07:53 egonw now Martin's turn
08:13 egonw battery is running out
08:24 shk3 joined #bioclipse
08:30 CIA-40 bioclipse: goglepox * r10886 /bioclipse2/trunk/plugins/ (2 files in 2 dirs):
08:30 CIA-40 bioclipse: Made JCP toolbar visible when JCP context is visible.
08:30 CIA-40 bioclipse: Also made MultiPageMoleculesEditorPart set context
08:30 CIA-40 bioclipse: when switching to JCP.
08:30 CIA-40 bioclipse: Fixes bug #1049
08:30 zarah bug #1049 | http://tinyurl.com/nrqyeh
08:43 egonw joined #bioclipse
08:44 egonw shk3: at some point you were looking at a SaveAs dialog with drop down box for supported IO types
08:44 egonw did anything come out of that?
08:44 egonw or did you abondon that idea?
08:45 shk3 did not do anything
08:45 egonw OK
08:45 egonw I'll work on it
08:45 shk3 good
08:45 shk3 I am trying to sort out jobs etc. stuff
08:47 Gpox joined #bioclipse
08:58 masak joined #bioclipse
08:59 jonalv joined #bioclipse
09:31 jonalv Gpox: regardeing @pz 1029
09:32 jonalv zarah: you really should pick that up...
09:32 zarah jonalv: that was not so easy for a little bot to understand
09:35 Gpox @pz 1029
09:35 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1029
09:36 jonalv @pz 1049
09:36 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1049
09:36 jonalv Gpox: sry...
09:36 jonalv Gpox: I reopened that bug now...
09:37 CIA-40 bioclipse: goglepox * r10887 /bioclipse2/trunk/plugins/ (7 files in 4 dirs):
09:37 CIA-40 bioclipse: Chage Color from org.eclipse.swt to java.awt.Color
09:37 CIA-40 bioclipse: Because that is what the JCP renderer uses to pass
09:37 CIA-40 bioclipse: around a color.
09:38 CIA-40 bioclipse: goglepox * r10888 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/generators/SubStructureGenerator.java: New generator to visulize substructures
09:38 CIA-40 bioclipse: goglepox * r10889 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java:
09:38 CIA-40 bioclipse: Added use of SubStructureGenerator for visualization
09:38 CIA-40 bioclipse: of sub structures
09:38 CIA-40 bioclipse: Fixes bug #1088
09:38 zarah bug #1088 | http://tinyurl.com/le5fg5
09:42 maclean joined #bioclipse
09:42 CIA-40 bioclipse: goglepox * r10890 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.jchempaint/plugin.xml: Commented out closest to center of mass generator
11:00 CIA-40 bioclipse: goglepox * r10891 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jc​hempaint/src/net/bioclipse/cdk/jchempaint/busi​ness/JChemPaintGlobalPropertiesManager.java:
11:00 CIA-40 bioclipse: Made JChemPaintGlobalPropertiesManager pickup JCP in
11:00 CIA-40 bioclipse: MultiPartMoleculesEditorPage
11:00 CIA-40 bioclipse: goglepox * r10892 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jche​mpaint/src/net/bioclipse/cdk/jchempaint/widgets/ (GeneratorsView.java JChemPaintEditorWidget.java):
11:00 CIA-40 bioclipse: Added check for null
11:00 CIA-40 bioclipse: To allow JChemPaintEditorWidget.setInput() to take null as an argument
11:01 CIA-40 bioclipse: goglepox * r10893 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java:
11:01 CIA-40 bioclipse: Fixed ignore for same part selections
11:01 CIA-40 bioclipse: It no works for JCP embeded in MPMoleculeEditorPart
11:01 CIA-40 bioclipse: Resolves bug #1049
11:01 zarah bug #1049 | http://tinyurl.com/nrqyeh
11:10 CIA-40 bioclipse: jonalv * r10894 /bioclipse2/trunk/plugins/ (3 files in 3 dirs): Added DS tests to AllUnstableManagers plugins tests suite
11:11 maclean Gpox : interesting generator view, but it seems like it would be for 'expert' users (IE: developers) only...
11:12 Gpox yeah, it is mostly for me to check what generators are rendered and in what order
11:12 maclean ah, right.
11:12 maclean in which order...hmmm
11:12 maclean perhaps altering the order using the view? :)
11:13 Gpox one could clean it up a bit, and allow to toggle the visibility of the contributed extensionpoint generators
11:14 maclean that's true.
11:14 Gpox maybe it would requier that either the list from Renderer is not a copy or that there is a set generators on Renderer
11:15 maclean currently the renderer method returns a new list wrapping the generator list - does this make it immutable?
11:15 maclean a setGenerators method seems reasonable.
11:16 maclean there had not been a use-case for this before, so I hadn't included such a method, but I don't object to it.
11:16 maclean anyway..
11:16 * maclean goes back to backtracking
11:19 CIA-40 bioclipse: goglepox * r10895 /bioclipse2/trunk/plugins/net.bioclipse.cdk​.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfe​ditor/business/IMoleculeTableManager.java: Added uiJob to calculateProperty(...)
11:19 CIA-40 bioclipse: goglepox * r10896 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui​.sdfeditor/src/net/bioclipse/cdk/ui/sdfeditor/ (2 files in 2 dirs):
11:19 CIA-40 bioclipse: Use uiJob to update moleculesTable when property is calculated
11:19 CIA-40 bioclipse: CalculatePropertyHandler now inserts the calculated
11:19 CIA-40 bioclipse: coulmn as the first column in the table.
11:19 CIA-40 bioclipse: Fixes bug #1144
11:19 zarah bug #1144 | http://tinyurl.com/krv9e7
11:20 Gpox Might be cleander just to return the real list, it becomes a litle bit more like a hack to replace the generators but atleast you are aware you are changing how the renderer renders thing
11:20 Gpox with setGenerators() you just change it poof. when onnly you wanted to modify one
11:23 maclean true. so like : renderer.getGenerators().add(new MyGenerator());
11:24 Gpox yes
11:25 maclean I guess a truly generic way of doing things would be for generators to know what type of ChemObject they handle
11:25 maclean so there could be a renderer method .getGeneratorFor(IChemObject object);
11:26 maclean which would require a method in the IGenerator interface 'boolean canHandle(IChemObject object)'
11:27 maclean although that gets complex for generators that handle more than one chemobject at a time, or things that are not chemobjects.
11:28 Gpox exactly, getGenerators() is an easy to implement and powerfull way to modify what generators are used
11:29 Gpox some of my generators don't even use the atomcontainer that is passed to it
11:29 maclean indeed. I saw the SubStructureGenerator.
11:31 Gpox overriding the createGenerator method on JCPWidget is the only way right now to insert generators in bioclipse
11:48 jonalv joined #bioclipse
11:59 CIA-40 bioclipse: carl_masak * r10897 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java:
11:59 CIA-40 bioclipse: [JsConsoleView] reviewed r10869
11:59 CIA-40 bioclipse: - replaced testing membership in a List with unconditional adding to a Set
11:59 CIA-40 bioclipse: - small whitespace and braces changes
11:59 CIA-40 bioclipse: Resolves #1146.
12:02 CIA-40 bioclipse: carl_masak * r10898 /bot/trunk/zarah.pl: [zarah] now recognizes 'resolves' as a bug keyword
12:03 masak @reboot
12:03 zarah joined #bioclipse
12:07 maclean resolves #100
12:07 maclean curses.
12:09 maclean a 'resolve' keyword would be great : "@resolve bug 100"
12:09 maclean (or solve, perhaps)
12:12 masak maclean: zarah only triggers on those keywords when they're uttered by other bots.
12:12 maclean ohhh.
12:12 maclean @kill-all-humans
12:12 masak maclean: she now has qw<bug fixes addresses resolves>
12:18 Gpox dose she have a becomeSkynetCost yet?
12:23 masak Gpox: oh noes, I forgot that one! o_O
12:24 Gpox it necessary especially with all the @kill-all-humans lately
12:25 CIA-40 bioclipse: carl_masak * r10899 /bot/trunk/zarah.pl: [zarah] added becomeSkynetCost
12:25 masak phew.
12:29 Gpox masak++ <!-- for preventing Skynet -->
12:29 masak Gpox++ -- XML comments! :)
12:41 olass joined #bioclipse
12:41 olass hi
12:41 zarah oh hai olass
12:42 * olass has been doing boring administrative stuff today
12:43 jonalv olass: http://wiki.bioclipse.net/i​ndex.php?title=Architecture
12:43 zarah jonalv's link is also http://tinyurl.com/la8u8v
12:43 jonalv olass: I am not so good at writing longtexts on this subject it seems
12:43 olass jonalv: great start
12:43 jonalv olass: maybe you can add soemthing? :)
12:43 olass sure
12:43 olass will do some
12:43 olass and send the link back for completion
12:43 olass ok?
12:43 jonalv perfect
12:45 edrin joined #bioclipse
12:47 maclean architecture, eh? olass : would you like some sort of diagram to illustrate?
12:47 olass maclean: yes please
12:47 * maclean is a keen systems architecture drawer...
12:47 olass that would be a great addition
12:48 olass jonalv: and please add the image from the german magazine
12:48 jonalv olass: will do
12:48 jonalv (now where did I put that one? ;)
12:49 olass jonalv: ball is back with you, http://wiki.bioclipse.net/i​ndex.php?title=Architecture
12:49 zarah olass's link is also http://tinyurl.com/la8u8v
12:52 masak olass: I found some things I'd like to change when you're done editing.
12:53 * olass is not editing, the ball is back with jonalv
12:53 masak olass: OSGi is spelled with a small 'i'.
12:53 jonalv masak: go ahead
12:53 olass good point
12:53 olass did not know that
12:56 masak jonalv: done. lock released.
13:03 CIA-40 bioclipse: carl_masak * r10900 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java: [JsConsoleView] fixed error message (fixes #1147)
13:04 zarah bug #1147 | http://tinyurl.com/ndzso2
13:11 shk3 does this tell somebody something:
13:11 shk3 loader constraints violated when linking org/apache/log4j/Logger class
13:11 shk3 ?
13:13 CIA-40 bioclipse: ospjuth * r10901 /bioclipse2/trunk/plugins/net.bioclipse.ds/ (2 files in 2 dirs): Return empty atomcontainer instead of null when implementing ISubStructure. Solves #1151.
13:43 CIA-40 bioclipse: shk3 * r10902 /bioclipse2/trunk/plugins/net​.bioclipse.data.seneca/data/ (7 files in 2 dirs): more examples
14:04 jonalv olass: I think we are nearing perfection: http://wiki.bioclipse.net/i​ndex.php?title=Architecture
14:04 zarah jonalv's link is also http://tinyurl.com/la8u8v
14:05 olass sweet
14:06 maclean nice. what did you use?
14:06 shk3 you are nearing perfection?
14:06 shk3 both of you?
14:07 shk3 I am looking forward to meet you again and see what changed
14:07 jonalv maclean: sry? Oh the image? It's an old inkscape illustration
14:07 maclean ohh.
14:07 jonalv (I lost the bitmaps though...)
14:07 jonalv so it will be a bit trixy to redo it...
14:10 shk3 can I ask a question about this bioclipseuijob stuff?
14:12 jonalv shk3: okey?
14:13 shk3 i had a look at loadMolecule in cdkmanager
14:13 shk3 ICDKManager has
14:13 shk3 public void loadMolecule( IFile file,
14:13 shk3 BioclipseUIJob<ICDKMolecule> bioclipseUIJob );
14:13 shk3 which method in CKDManager is this mapped to?
14:14 shk3 public void loadMolecule( IFile file,
14:14 shk3 BioclipseUIJob<ICDKMolecule> bioclipseUIJob );
14:14 shk3 ?
14:14 shk3 perhaps?
14:14 shk3 sorry, wrong paste
14:14 shk3 I meant:
14:14 shk3 public List<ICDKMolecule> loadMolecules( IFile file,
14:14 shk3 IProgressMonitor monitor )
14:14 masak shk3: please don't paste in-channel. :/
14:15 jonalv shk3: the loadMolecules method is a mess... IT should be rewritten for sanity but I sort of think it works right now.
14:15 shk3 hm, ok
14:15 shk3 bad example then
14:16 jonalv &me takes a deep breatch and heads in to the mess to try and answer shk3s question
14:16 shk3 my real question is what to do in seneca
14:16 shk3 and I thought this could be an example
14:16 shk3 I need to run something with a monitor which returns a value
14:17 Gpox in IMoleculeTableManager there is createSDFIndex(IFile file, IBioclipseUIJob uiJob) and in MoleculeTableManager there is only createSDFIndex(IFile, IProgressMonitor)
14:17 jonalv shk3: Hm I think you should have a look at the BioclipseUIJob approach
14:17 jonalv that sounds like a good example to look at
14:18 shk3 ok, I will look at this
14:19 shk3 question:
14:19 shk3 createSDFIndex in the IMoleculeTableManager has a return value,
14:20 shk3 but his seems to be ignored when called.
14:20 shk3 it is done via
14:20 shk3 the runinui method of the job and getReturnValue, right?
14:21 Gpox Row 238 in MoleculesEditor is the important one sdfIndex = getReturnValue() in runInUI() on the  BioclipseUIJob
14:21 Gpox yes
14:21 shk3 ok, then I think I got it
14:21 shk3 will try to use this in seneca
14:21 shk3 and I will come back to you if there are problems
14:21 shk3 thanks
15:03 masak olass: http://wiki.bioclipse.net/index.p​hp?title=Bioclipse2_release_plan looks like it might need some updating.
15:03 zarah masak's link is also http://tinyurl.com/5guree
15:04 olass indeed
15:04 olass masak: updated
15:04 masak olass++
15:04 olass :) that was easy karma
15:05 shk3 jonalv: no success
15:05 shk3 still blocking and the runInUI is never executed
15:05 masak easy karma is the best.
15:05 shk3 I get
15:05 shk3 WARN - The MonitorContainer could not find a monitor connected to current thread so returning a NullProgressMonitor
15:05 shk3 could that be a hint to the problem?
15:06 jonalv shk3: yes it at least sounds like something you don't want...
15:07 jonalv shk3: have you commited? What method is this? How do I reproduce?
15:08 shk3 would be greate if you can have a look
15:08 shk3 committing
15:08 shk3 mom
15:08 shk3 you need the seneca examples
15:09 shk3 I think you already got these?
15:09 CIA-40 bioclipse: shk3 * r10903 /bioclipse2/trunk/plugins/net.biocli​pse.seneca/src/net/bioclipse/seneca/ (7 files in 5 dirs): tried to use a bioclispeuijob for executing jobs
15:11 shk3 open the hko2 folder and hko2.sjs file
15:11 shk3 hit the start button in tool bar
15:11 shk3 the method is executeJob in the managers in net.bioclipse.seneca.business
15:12 jonalv shk3: I need seneca nad what else?
15:12 jonalv speclipse only?
15:12 maclean seneca plugin, seneca sample data plugin, speclipse...
15:13 maclean cheminformatics plugin er..
15:13 maclean feature, rather.
15:13 shk3 if you run by features, the seneca feature should do it
15:13 jonalv but the sample data ahs not changed or has it?
15:14 maclean some new sample data, yes
15:14 jonalv hm why don't I get the sample data?
15:14 maclean when you run?
15:14 jonalv is that a sinlge feature of it's own?
15:14 maclean no
15:14 maclean it's in the seneca_feature...
15:14 jonalv okey I didn't have it under seneca
15:15 jonalv ah it's under data
15:17 jonalv hm that seemed broken indeed...
15:17 shk3 sorry, i don't understand this
15:17 shk3 what do you mean with "it's under data"?
15:18 jonalv the new wizard is under data not uinder seneca. I don't know which is best. Can it be in both?
15:18 shk3 ok
15:18 shk3 well, it seems to be a pattern to have it under data
15:19 shk3 I once tried putting things in two places, but didn't succeed
15:19 jonalv okey
15:20 jonalv what is the name of the interface method? I can't find any executeJob method in the interface...
15:20 shk3 I put it in IJavaSenecaManager
15:21 shk3 and IJavascriptSenecaManager
15:21 jonalv shk3: oh, intresting
15:21 shk3 well, I couldn't execute it on javascript
15:21 shk3 when only having the method with BioclipseUIJob
15:21 jonalv so you can't execute a job from AJvaScript?
15:21 shk3 in the interace
15:21 shk3 no, go some error
15:21 shk3 sort of method not found
15:22 shk3 but would need to reproduce this
15:22 jonalv mhm
15:22 jonalv shk3: well it's still not void...
15:23 shk3 no, but createSDFIndex isn't as well
15:23 shk3 I followed that
15:24 jonalv shk3: yes it is
15:25 jonalv row 32 in IMoleculeTableManager
15:25 shk3 ah hm, perhaps i didn't update
15:26 jonalv :)
15:26 shk3 in my workspace, it is not void
15:26 shk3 btw, you can have a new wizard in two categories, but it seems you need to repeat the whole <wizard> entry.
15:26 shk3 not too nice
15:26 jonalv okey well try with having it void. If it's not void it can't be run as a job since it must return...
15:27 shk3 ok, i will upate
15:27 jonalv shk3: might be wroth it though...
15:27 jonalv brb
15:27 shk3 and compare again with moleculetablemanager and retry
15:27 shk3 yes, think so
15:27 shk3 other data wizards should use that as well
15:36 shk3 jonalv: i am still struggling to understand how things are supposed to work in js
15:37 shk3 when the method is void
15:38 jonalv shk3: you define another method which is not coid that you publish
15:39 jonalv so one method for Java and one for JavaScript. (Both can be called from both though) and they both will get redirected to the same implementation
15:40 shk3 ok
15:41 shk3 i wait for the update
15:41 jonalv shk3: oh and these classes are wider than 80 cols I am having to scroll horizontally... :(
15:42 jonalv shk3: sry ar eyou waiting for me?
15:42 shk3 no
15:42 shk3 waiting for svn
15:43 jonalv ah
15:44 shk3 which revision of net.sf.cdk.ui.sdfeditor should I have?
15:44 jonalv uhm beats me. The latest?
15:45 shk3 which one do you have?
15:45 jonalv shk3: uhm how do I find that out?
15:45 jonalv hang on...
15:45 shk3 right click, properties, svn
15:45 shk3 or so
15:46 jonalv shk3: git-svn...
15:46 jonalv 10903 but that's the root
15:46 jonalv I hope thats the same all the way...
15:46 shk3 well, i wait for the update to be done
15:46 jonalv yea
15:47 jonalv svn--?
15:49 shk3 ok, got latest sdfeditor
15:50 shk3 I will try to make seneca manager the same style
15:50 jonalv good
15:52 shk3 ok, so the implementation has return value and bioclipseuijob
15:52 shk3 and it is used for both methods in the interface, right?
15:52 jonalv yea
15:52 jonalv (sure hope so)
15:52 jonalv :)
15:53 shk3 shouldn't/couldn't we put the one with return value in js interface
15:53 shk3 and the other one in java interface?
15:53 jonalv shk3: I guess you might...
15:53 shk3 ok, but more important is that it works at all
15:53 shk3 ...
15:53 jonalv yea
15:54 shk3 going to test now
16:00 jonalv shk3: iz it woeking?
16:00 maclean no lolspeak
16:01 masak maclean: what u mean?
16:01 maclean oh, right, just erratic typing. never mind.
16:02 masak kthx.
16:02 maclean -_-
16:03 shk3 not really
16:03 shk3 just trying to figure out what's going on
16:03 shk3 shall I commit so that you can have a look as well?
16:03 jonalv I MITE HAS SPENT 2 MUTCH TIEM ON I CAN HAS CHEEZBURGER
16:03 jonalv shk3: oki
16:03 maclean I blame mofaha
16:04 shk3 jonalv:
16:04 shk3 I see the following problems
16:04 shk3 - still blocking, no monitor shown in java
16:04 shk3 - monitor shown in js
16:05 CIA-40 bioclipse: shk3 * r10904 /bioclipse2/trunk/plugins/net.bioclipse.s​eneca/src/net/bioclipse/seneca/business/ (3 files): upated the manager stuff to run in jobs
16:05 shk3 in java, saving of the result fails
16:05 shk3 with odd error
16:05 shk3 - an in java, it's way to fast
16:05 shk3 I don't think an elucidation is actually done
16:05 shk3 but I will look at this later
16:05 masak \⚉/
16:06 jonalv shk3: hm I guess I should have a look at what you are doing..
16:06 jonalv \⚉/++
16:06 jonalv karma \⚉/
16:06 zarah \⚉/ has a karma of 0
16:06 masak (\⚉/)++
16:06 masak karma \⚉/
16:07 zarah \⚉/ has a karma of 1
16:07 masak jonalv: that's how you do it. :)
16:07 jonalv masak: yea I keep forgetting...
16:07 masak yes. :)
16:07 jonalv masak: we need to leave soon...
16:07 Gpox karma /
16:07 masak jonalv: good idea.
16:07 zarah / has a karma of 0
16:07 masak (/)++
16:07 masak karma /
16:07 zarah / has a karma of 1
16:08 masak Gpox: non-word characters simply don't register.
16:08 jonalv masak: what is the reason for this?
16:09 masak jonalv: I don't want random ASCII patterns to screw with karma ratings.
16:09 masak so there are two mechanisms:
16:09 masak one word++
16:09 masak and one (complicated arbitrary expression)++
16:10 jonalv hm but if the work is L337?
16:11 masak then you do (L337)++
16:11 masak or you change the regular expression in zarah...
16:11 jonalv masak: but would something bad happend if I changed the reg exp?
16:12 masak who knows? :)
16:12 masak but I don't think so.
16:14 CIA-40 bioclipse: shk3 * r10905 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): adde sample data wizard to the speclipse/seneca categories as well, apart from sample data
16:18 CIA-40 bioclipse: shk3 * r10906 /bioclipse2/trunk/plugins/​net.bioclipse.cml.tests/: ignoring bin
16:28 shk3 jonalv: could you have a look at the problem with that job?
16:28 shk3 I got 10 bugs or so assigned related to this.
16:28 shk3 I am happy to help, but as long as I don't understand the whole thing,
16:29 shk3 I can't do much.
19:59 olass joined #bioclipse
20:05 CIA-40 bioclipse: ospjuth * r10907 /bioclipse2/trunk/plugins/net.bioclipse.ds/ (11 files in 4 dirs): Updated to use java.awt.color (bug 1150).
20:05 zarah bug #1150 | http://tinyurl.com/ngezw5
20:06 CIA-40 bioclipse: ospjuth * r10908 /bioclipse2/trunk/plugins/net.biocli​pse.ds.signsig.bursi/src/net/bioclip​se/ds/signsig/bursi/SignSicHit.java: Updated to use java.awt.color (bug 1150).
20:06 zarah bug #1150 | http://tinyurl.com/ngezw5

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