Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-01-09

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All times shown according to UTC.

Time Nick Message
08:00 Gpox joined #bioclipse
08:13 olass joined #bioclipse
08:13 olass moin
08:13 olass hi
08:13 olass @pz
08:13 olass zarah: are you there?
08:14 jonalv zarah: boo
08:14 jonalv zarah: booh
08:14 jonalv @restart
08:14 zarah joined #bioclipse
08:14 olass hi
08:14 zarah hi olass
08:15 olass @msg
08:15 zarah olass: You have no new messages.
08:44 edrin joined #bioclipse
08:44 edrin hi
08:44 zarah hi edrin
09:02 edrin hi olass
09:02 olass hi edrin
09:03 olass in the middle of a recatoring of the hivpred service
09:03 olass refactoring out the model into a separate plugin and building a GUI for the hivpred client
09:03 edrin i tried to throw an exception when the output was not valid, can you try the new io factory checkout??
09:04 edrin ah cool :)
09:21 olass edrin: will do as soon as it works again
09:22 edrin ok
09:30 CIA-54 bioclipse: carl_masak * r8168 /bioclipse2/trunk/plugins/net.bioclipse.ui.busine​ss/src/net/bioclipse/ui/business/IUIManager.java: [IUIManager.java] improved manager documentation
09:36 jonalv joined #bioclipse
10:08 jonalv Would anyone know how I make Eclipse not starting with gcj but with Sun java 6 instead?
10:21 jonalv uhm anyone in here running Eclipse 3.4.1 on Ubuntu? I just got told on #eclipse that it could not be done... :(
10:22 jonalv And I am having problems accepting that...
10:30 egonw joined #bioclipse
10:30 egonw moin
10:30 zarah hi egonw
10:30 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
10:31 egonw @msg
10:31 zarah egonw: 20 h 34 m 10 s ago, olass said Please make me admin on pelezilla
10:31 olass hi egonw
10:31 olass that is outdated
10:31 egonw ok, good
10:32 olass egonw: next time we meet, please show me some tips how to administer pelezilla
10:32 olass edirn: around?
10:32 olass adrin: around?
10:33 edrin hi egonw
10:33 edrin olass: yes
10:33 olass edrin: around?
10:33 egonw hi edrin
10:33 olass how do I, from script purely, set an XMPP acount?
10:33 olass I want not to be able to go via preferences
10:33 olass (this is to support unit testing of my client that tests the service)
10:34 edrin that's not possible with xws4j right now. but i can add this functionality
10:34 edrin ah
10:34 olass please do
10:34 edrin sorry, you mean not register a new account
10:34 olass no
10:34 olass just ad acount credentials to bioclipse
10:35 edrin sure, you can create an account...
10:35 olass xmpp.connect(olas@jabber.org/bioclient, pwd etc...)
10:35 edrin oh...
10:35 edrin hm... i would have to add this to the manager, but that's really easy
10:35 olass yes
10:35 edrin :)
10:35 olass I need it
10:35 olass in a unit test I start with a cleared runtime workspace
10:35 edrin can you write this me in an email?
10:36 olass sure
10:36 olass or I'll do it myself
10:36 olass now
10:36 olass because I need it :-)
10:36 edrin as you like
10:36 olass we'll see how it turns out
10:36 edrin it's quite easy...
10:36 edrin olass: to the manager, just add a function called:
10:38 edrin Client createClient(olas@jabber.org/bioclient, pwd etc...) { return net.bioclipse.xws.client.Client(...);}
10:38 edrin with the returned client you can then do client.connect();
10:39 olass edrin: that needs a mehod connect(Client client)
10:39 olass I'll do that too
10:39 olass hmm
10:39 edrin yes, can be done this way, too.
10:39 olass too?
10:39 egonw ok, enough for me again...
10:40 egonw back to bed
10:40 egonw bye
10:40 olass bye
10:40 edrin but why not use the created client (instanceof Client) .connect(); ?
10:40 olass edrin: maybe I'm missing something here...
10:40 olass oh, ok
10:40 olass hmm
10:40 olass will that work with isConnected?
10:41 edrin yes, i think so
10:41 olass that just checks defaultClient
10:41 edrin n
10:41 edrin no
10:41 olass public boolean isConnected() throws Xws4jException {
10:41 olass Client client;
10:41 olass client = Activator.getDefaultClientCu​rator().getDefaultClient();
10:41 olass return client.isConnected();
10:41 olass }
10:41 edrin but you can do client.isConnected()
10:41 edrin from the created client
10:41 olass no, I naturally want to use the manager calls
10:42 olass the manager should not be restricted to a default client IMO
10:42 olass that sounds like a large limitation
10:43 olass IMO the manager shoule keep track of the active client, but a user should be able to switch client in a script
10:50 edrin then we have to add a list or array with create clients...
10:50 olass yes
10:50 edrin then you can pick one: xmpp.getClient(1);
10:50 olass something like that
10:50 edrin but there should be a default client
10:51 olass or just have one active
10:51 olass Activator.getDefaultClientC​urator().setDefaultClient()
10:51 edrin nene
10:51 edrin no
10:51 olass that would be enough for me now
10:51 edrin do not do this
10:51 olass Activator.getDefaultClientCurator​().setDefaultClient(myNewClient)
10:51 olass why not?
10:52 edrin it *is* possible, but let me do this thing... this is not trivial...
10:52 edrin i dont think that is a good idea
10:53 olass se priv msg
10:53 olass pasted there
10:53 olass edrin: OK, I'll lte you do this
10:53 olass willemail you now
10:53 olass and do a workaround for me
10:53 edrin please also tell me, why you need this...#
10:54 edrin but i agree that it might make sense to have multiple clients...
10:55 olass ok
10:56 edrin olass: priv msg
11:54 olass edrin: sent you an email
12:08 olass edrin: How can I validate that a function is online?
12:09 olass right now all I get is an exception "invalid response" is my service is down
12:10 olass IMO it should throw excpetion "could not locate function"
12:11 edrin that's the same
12:11 edrin :)
12:11 edrin me in course
12:11 edrin cu l8
12:19 olass edrin: IMO, invalid response means it returned something unexpected
12:19 olass edrin: IMO, error messages are important
12:20 olass @tell edrin xmpp.isAvailable(IFunction f) is requested
12:20 zarah Consider it noted.
13:23 olass joined #bioclipse
13:23 olass edrin: HELP
13:23 olass my service suddenly doesn't work
13:23 olass I fear it has something to do with your xws updates
13:34 olass @tell edrin I have emailed you my error
13:34 zarah Consider it noted.
14:27 edrin olass: i did not understand the second mail with the "binding" comment
14:27 zarah edrin: You have new messages. Write '/msg zarah @messages' to read them.
14:28 olass edrin: ok
14:28 olass working on it here
14:28 olass it seems it is just my SampleClient that does not work
14:28 olass but
14:28 olass what does this mean?
14:28 olass XWS4J: xmpp: ProcPipes.processMessage() - this command element was not expected.
14:30 edrin this means xws client does not remember that this session was started by him... does not sound good :/
14:31 edrin what means "When using the binding in xwsj, it works" ?
14:35 edrin olass: `?
14:36 olass well
14:36 olass when calling from script in Bioclipse, it works
14:36 olass when calling from my SampleClientHivpred it does not
14:36 olass and that used to work
14:37 edrin did you clean the workspace ?
14:37 edrin maybe some compiled classes are left?
14:38 edrin theoretically this could be a multithreading problem, but i thought i considered all circumstances
14:39 edrin when running the sample client against the samle /coffeemachine functions with the current checkout, does this fail?
14:39 edrin back in 2 h... student course continues
14:54 CIA-54 bioclipse: ospjuth * r8169 /bioclipse2/trunk/plugins/se​.uu.farmbio.hivpred.model/: Initial import.
14:56 CIA-54 bioclipse: ospjuth * r8170 /bioclipse2/trunk/plugins/s​e.uu.farmbio.hivpred.model/ (65 files in 25 dirs): Upload of model plugin for HIVPredictions containing schema, generated model, and utility classes.
14:57 CIA-54 bioclipse: ospjuth * r8171 /bioclipse2/trunk/plugins/se​.uu.farmbio.hivpred.client/: Initial import.
15:00 CIA-54 bioclipse: ospjuth * r8172 /bioclipse2/trunk/plugins/se​.uu.farmbio.hivpred.client/ (53 files in 18 dirs): Upload of a client for a HivPred XMPP service. Adds namespace 'hivpred' with functions to predict from sequence and file from console. No GUI yet.
15:00 CIA-54 bioclipse: ospjuth * r8173 /bioclipse2/trunk/plugins/se.uu​.farmbio.hivpred.client.tests/: Initial import.
15:02 CIA-54 bioclipse: ospjuth * r8174 /bioclipse2/trunk/plugins/se.uu​.farmbio.hivpred.client.tests/ (19 files in 11 dirs): Upload of test classes for hivpred.client. Contains a PluginTestHivpredManager.
15:10 CIA-54 bioclipse: ospjuth * r8175 /bioclipse2/trunk/features/se​.uu.farmbio.hivpred-feature/: Initial import.
15:11 CIA-54 bioclipse: ospjuth * r8176 /bioclipse2/trunk/features/se​.uu.farmbio.hivpred-feature/ (.project build.properties feature.xml): A feature for Hivpred client.
15:35 CIA-54 bioclipse: ospjuth * r8177 /bioclipse2/trunk/plugins/se.uu.farmbi​o.hivpred.client/META-INF/MANIFEST.MF: Removed redundant xws4j jar.
15:40 CIA-54 bioclipse: ospjuth * r8178 /bioclipse2/trunk/plugins/net.bioc​lipse.xws4j/META-INF/MANIFEST.MF: Made a lot of packages public.
15:44 olass edrin: around?
15:44 olass have you updated xws4j.jar in net.bc.xws4j?
15:45 olass is it up to date?
15:45 olass @tell edrin is the xws4j.jar up to date in plugin net.bioclipse.xws4j?
15:45 zarah Consider it noted.
16:05 olass edrin: have a look at http://wiki.bioclipse.net/index​.php?title=HIVpred_XMPP_service
16:05 zarah olass's link is also http://tinyurl.com/7ph7wo
16:05 olass @tell edrin: http://wiki.bioclipse.net/index​.php?title=HIVpred_XMPP_service
16:05 zarah olass's link is also http://tinyurl.com/7ph7wo
16:05 zarah Consider it noted.
16:05 olass gotta run now
16:06 olass this will be a blog item later ;-)
16:06 olass (with a screenshot)
16:06 olass also will add a GUI
16:06 olass bye for now!
16:06 olass see you on monday
16:06 jonalv bye
16:07 stain joined #bioclipse
16:31 edrin tell olass xws4j.jar in plugin net.bioclipse.xws4j should be up-to-date
16:31 zarah edrin: You have new messages. Write '/msg zarah @messages' to read them.
16:31 edrin zarah: tell olass xws4j.jar in plugin net.bioclipse.xws4j should be up-to-date
16:31 zarah Consider it noted.
17:21 CIA-54 bioclipse: goglepox * r8179 /bioclipse2/branches/gpox-newMoleculeTable/plugi​ns/net.bioclipse.cdk.ui.sdfeditor/src/net/biocli​pse/cdk/ui/sdfeditor/editor/MoleculeTable.java: Refactoring CompositTable
17:21 CIA-54 bioclipse: goglepox * r8180 /bioclipse2/branches/gpox-newMoleculeTable​/plugins/net.bioclipse.cdk.ui.sdfeditor/sr​c/net/bioclipse/cdk/ui/sdfeditor/editor/ (3 files): Moved code from MoleculesEditor to MoleculeTable and MoleculeTableContentProvider
19:17 edrin left #bioclipse
20:42 edrin joined #bioclipse
21:56 edrin stain available?

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