Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-06-24

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All times shown according to UTC.

Time Nick Message
01:00 ilogger2 joined #bioclipse
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07:12 masak joined #bioclipse
07:13 olas joined #bioclipse
07:14 olas g'moin
07:15 malick joined #bioclipse
07:45 masak добый утро
07:52 olas hi masak
07:52 olas (I presume)
07:55 masak :)
08:09 jonalv joined #bioclipse
08:12 thomas_ku joined #bioclipse
08:26 CIA-34 bioclipse: ospjuth * r5901 /bioclipse2/trunk/plugins/net.biocl​ipse.pcore/src/net/bioclipse/pcore/ (editors/PcorePage.java model/MoleculeFile.java): Removed use of deprecated CDKMoleculeList.
08:26 EskilA joined #bioclipse
08:28 CIA-34 bioclipse: ospjuth * r5902 /bioclipse2/trunk/plugins/net.biocl​ipse.pcore/src/net/bioclipse/pcore/ (4 files in 2 dirs): Really removed use of deprecated CDKMoleculeList.
08:29 olas jonalv: hgo ahead with your commit
08:29 jonalv olas: thanks. Might be a little work left though. Is updating now :)
08:29 jonalv *am
08:30 jonalv *I am
08:30 * jonalv is restarting his english machinge...
08:39 shk3 joined #bioclipse
08:39 edrin joined #bioclipse
08:40 shk3 hi all
08:40 shk3 first question for today:
08:40 jonalv hi shk3
08:40 shk3 the execute method of the handler is supposed to return an object.
08:40 shk3 what is this object for?
08:40 shk3 i. e. what must it be?
08:41 * shk3 is away for hot chocolate for 5 minutes
08:42 * jonalv did not understand that. olas?
08:47 CIA-34 bioclipse: jonalv * r5903 /bioclipse2/trunk/plugins/ (8 files in 5 dirs): Removed CDKMoleculeList, code to the interface List<ICDKMolecule> instead. And use BioList<ICDKMolecule> as implementation (only needed when creating things in managers (it is for recording)).
08:57 CIA-34 bioclipse: jonalv * r5904 /bioclipse2/trunk/plugins/ (5 files in 3 dirs): renamed a few methods in structuredb manager
09:13 * shk3 is back
09:13 shk3 let me rephrase
09:14 shk3 Following the document How to add menus and actions I want to  Implement a handler class
09:14 shk3 it must have a method
09:14 shk3 public Object execute(ExecutionEvent arg0) throws ExecutionException {
09:14 shk3 So what is the Object about?
09:15 jonalv olas: Can you answer that? (me hasn't done that yet)
09:17 olas see eclipse docs
09:17 olas you are free to return null
09:17 olas and should, if you have nothing to report
09:17 olas got no better answer for you
09:17 olas my advice: return null
09:18 shk3 thanks
09:21 jonalv left #bioclipse
09:21 edrin imagine you have a server application. this server (java) must have the a ability to load user-defined function classes that implement IFunction from user-defined .jar(s)
09:21 edrin well
09:23 olas sounds like a plugin architecture, like OSGI
09:23 olas what are you after here?
09:23 olas edrin?
09:23 edrin currently i do it like this: the .jar must contain a certain package with a class that implements IFunctionLoader that offers a function that returns a Class[] of the classes in the jar that implement IFunction
09:24 jonalv` joined #bioclipse
09:24 edrin in fact it is already working very well, although i wonder if this is quite professional...
09:25 edrin Class[] net.bioclipse.xws.component.functi​ons.FunctionLoader.getFunctions();
09:27 olas edrin: you should have this discussion with jonalv
09:28 olas he is using Spring
09:28 * jonalv is fighting with emacs for the moment :/
09:28 olas let me paste:
09:28 olas jonalv: you got that?
09:28 jonalv no
09:29 * masak neither
09:29 olas (too large paste)
09:29 olas edrin (11:25:25 AM): imagine you have a server application. this server (java) must have the a ability to load user-defined function classes that implement IFunction from user-defined .jar(s)
09:29 olas that?
09:29 edrin yes
09:29 masak olas: nopaste
09:29 olas edrin (11:27:30 AM): currently i do it like this: the .jar must contain a certain package with a class that implements IFunctionLoader that offers a function that returns a Class[] of the classes in the jar that implement IFunction
09:29 olas I know
09:29 edrin Class[] net.bioclipse.xws.component.functi​ons.FunctionLoader.getFunctions();
09:30 olas in bc2 we use managers to constribute functionality
09:30 olas managers are contributed by Spring
09:30 olas so we define them in a context.xml
09:30 olas jonalv can tell you more about this
09:31 olas another possibility is to have an Extension point that requires you to implement an Interface
09:31 edrin and in the .cfg file of the service application you can specify the .jar(s) to load... then the application loads these .jar(s) and adds all IFunction it got to the xmpp service ;=
09:31 edrin maybe i will just keep it as it is
09:31 olas ok
09:31 edrin because it is working well
09:31 olas or use plugin.xml
09:31 olas and an extension point
09:31 olas your decision
09:31 edrin :)
09:32 olas if it is working well, why bother changing?
09:32 olas :-)
09:32 edrin yeah
09:32 olas edrin: you should move to bc2 soon
09:32 olas if we set up a JS editor with run capabilities, would that be enough?
09:32 edrin will do so
09:32 edrin well, first i have to finish the xws lib
09:32 olas ok
09:33 edrin i will merge the component and client lib in one lib...
09:33 edrin well,
09:34 edrin dont want to promise any stuff now but lets see
09:34 jonalv edrin: if you do it by managers you can publish them to the scripting console :)
09:34 edrin jonalv: the service will not run in eclipse
09:34 edrin it will be standalone
09:35 edrin ...
09:35 edrin have to work
09:35 edrin cu
11:03 shk3 did anybody use the command/handler stuff?
11:04 olas yes
11:05 shk3 great
11:05 shk3 it doesn't work for me
11:05 shk3 I get
11:05 shk3 There is no handler to execute for command
11:05 shk3 but the ids match
11:05 shk3 I have a command with id x
11:05 shk3 and a handler with commandId x
11:06 shk3 anything else needed?
11:07 olas mom
11:07 olas see plugin.xml in net.bioclipse.services
11:08 shk3 hm, looks similar
11:09 olas eclipse help has some good tips and examples
11:09 olas and the bioclipse wiki
11:09 shk3 I don't have the enabledWhen
11:09 olas sorry, can't help much more
11:09 shk3 thanks nevertheless
11:09 olas that's just a filter
11:09 shk3 there must be some difference I can't spot right now
11:09 olas if you don't have it, it will always be enabled
11:09 shk3 thought so
11:10 shk3 the rest seems to be the same
11:10 shk3 hm
11:11 CIA-34 bioclipse: ospjuth * r5905 /bioclipse2/trunk/plugins/net.bioclipse.c​dk10.jchempaint/src/net/bioclipse/cdk10/j​chempaint/views/Java2DRendererView.java: Removed unused debug out.
11:30 CIA-34 bioclipse: ospjuth * r5906 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Do not display explicit hydrogens in 2DView and SDFTable.
11:35 EskilA joined #bioclipse
12:44 jonalv How do I add drag and drop behavior to the service view? It's something to do with xml right?
12:56 CIA-34 bioclipse: goglepox * r5907 /bioclipse2/trunk/plugins/net.bioclipse.core/ (2 files in 2 dirs): Enabeled expand on zip-files
13:04 olas goglepox: nice
13:38 shk3 me again
13:38 shk3 I got things working so far
13:38 jonalv w00t
13:38 shk3 seems the activator (which I need to use for calling the manager, right?) is not initialized
13:39 shk3 the plugin variable in there is null
13:39 shk3 and it is supposed to be set in start
13:39 jonalv and the plugin is started?
13:39 shk3 Do I need to activate/register or whatever the activator?
13:39 shk3 well, the menu item is in the menu, so I guess yes
13:46 shk3 for some reason I am now getting a bunch of other exeptions. Perhaps these help...
13:47 masak nopaste
13:47 shk3 ?
13:47 masak http://www.rafb.net/paste/
13:48 shk3 ah, the activator is defined in the MANIFEST.MF - looks like I am making progress
13:49 shk3 oh, I had no intention to paste
13:56 jonalv joined #bioclipse
14:13 jonalv olas is the class javadoc for net.bioclipse.services.views​.model.AbstractServiceObject ?
14:13 jonalv correct
14:13 jonalv ? :)
14:16 olas what do you mean?
14:16 olas aha
14:16 olas author olas
14:16 olas yup
14:17 olas correct
14:17 jonalv "An abstract base class for objects in the JmolContentOutline"
14:21 jonalv olas: Is this really connected to JMol? I am feeling a bit confused now...
14:24 olas no
14:24 olas its an artifact
14:25 olas as I told you before, things are not carved in stone, code is neither finished nor beautiful nor well documented
14:25 olas please keep this in mind
14:25 * jonalv will try to :)
14:25 olas and please try to make it better
14:29 EskilA joined #bioclipse
14:29 CIA-34 bioclipse: biocoder * r5908 /bioclipse2/trunk/plugins/net​.bioclipse.statistics.jama/: Initial import of port.
14:30 CIA-34 bioclipse: biocoder * r5909 /bioclipse2/trunk/plugins/ne​t.bioclipse.statistics.jama/ (17 files in 9 dirs): Initial import of port.
14:33 CIA-34 bioclipse: ospjuth * r5910 /bioclipse2/trunk/plugins/net.bioclipse.c​dk10.jchempaint/src/net/bioclipse/cdk10/j​chempaint/views/Java2DRendererView.java: Do not react on null in selection.
14:33 CIA-34 bioclipse: biocoder * r5911 /bioclipse2/trunk/plugins/​net.bioclipse.statistics/ (9 files in 5 dirs): You should now be able to open csv files in the MatrixEditor, however save is currently not working.
14:46 CIA-34 bioclipse: ospjuth * r5912 /bioclipse2/trunk/plugins/net.biocl​ipse.pcore/src/net/bioclipse/pcore/ (10 files in 2 dirs): Added interface and updated model to support management of HitSets. Also added a Hits page in MPE.
14:48 CIA-34 bioclipse: ospjuth * r5913 /bioclipse2/trunk/plugins/net.biocl​ipse.pcore/src/net/bioclipse/pcore/ (18 files in 3 dirs): Refactored classes to package providers.
14:51 CIA-34 bioclipse: ospjuth * r5914 /bioclipse2/trunk/plugins/net.bioclipse​.pcore/src/net/bioclipse/pcore/editors/ (PcoreEditorModel.java providers/HitsContentProvider.java): HitsCOntentProvider now provides elements.
14:51 * olas is afk
15:02 EskilA How would you check that a file is synchronized with the workspace before writing to it?
15:27 CIA-34 bioclipse: jonalv * r5915 /bioclipse2/trunk/plugins/ (7 files in 4 dirs): Started work on gui for structuredb. It lists local databases at startup but doesn't update on changes yet
15:33 CIA-34 bioclipse: biocoder * r5916 /bioclipse2/trunk/plugins/net.bioclipse.​statistics/src/net/bioclipse/statistics/ (editors/MatrixEditor.java model/MatrixResource.java): Implemented matrix saving.
15:52 CIA-34 bioclipse: carl_masak * r5917 /bot/trunk/zarah.pl: [zarah] karma is now persisted over sessions
15:56 CIA-34 bioclipse: jonalv * r5918 /bioclipse2/trunk/plugins/ (6 files in 6 dirs): Fixed logging related porting from bc1 stuff
16:45 shk3 hm, getting the manager doesn't work: Could not get validate CML manager
16:46 shk3 I suppose it's a problem with the spring configuration
16:46 shk3 is there a way to check this?
16:49 edrin left #bioclipse
16:49 shk3 the call "(IValidateCMLManager) finderTracker.waitForService(1000*30);" returns null. Not much usefull information given.
16:49 shk3 any way to locate the problem?

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