Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-01-05

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Time Nick Message
08:29 olass joined #bioclipse
08:29 olass moin
08:29 zarah hi olass
08:31 olass egonw: how is the tag for cdk coming along?
08:32 olass were the atom typing problems a walk in the park?
08:35 egonw hi olass
08:35 olass hi
08:35 zarah hi olass
08:35 olass hi zarah
08:35 egonw no, did no get around to that yet
08:36 olass today?
08:36 egonw maybe
08:36 olass at least, please place a tag and update the cdk plugins in bioclipse
08:36 olass I really need that
08:36 olass for the AZ work
08:36 egonw ok
08:37 olass we can add a new tags and update again later when things are in better shape
08:37 olass but need to synch now with Sam
08:37 olass and you will be away for some time :-)
08:38 * olass finds himself constantly dependent on egonw's work ;-)
08:38 olass not my intention to stress you
08:38 olass but you said ETA was today :-)
08:39 olass about the WS1...
08:39 olass will test it today again
08:39 olass could not get my service to run on WS1 last friday
08:39 olass could run it from home, which is starnge
08:39 olass Anders opened up some more ports to play with so I can test today
08:40 olass if not, I will go to Anders on wednesday (when in Uppsala) and sort this out.
08:42 egonw yeah, I did Expect that...
08:42 egonw OK, the CDK is up and running
08:49 olass yup
08:49 olass egonw: do you run the service on ws1?
08:49 egonw yes
08:50 olass I can see your service
08:50 olass damn :-(
08:50 egonw good :)
08:50 olass somehow I cannot run the service on ws1
08:50 egonw added a new function yesterday...
09:11 olass @seen masak
09:11 zarah masak was last seen 16 h 44 m 6 s ago in #farmbio saying 'jonalv: jo.'
09:13 olass @tell masak What is the current status of the biojava plugin regarding I/O of sequences?
09:13 zarah Consider it noted.
09:28 egonw joined #bioclipse
09:29 egonw OK, missed the bus :(
10:15 atom joined #bioclipse
10:16 atom hi
10:16 zarah hi atom
10:16 edrin hi
10:16 zarah hi edrin
10:16 edrin hi olass
10:16 olass hi edrin
10:22 edrin olass: availble?
10:23 olass quite busy
10:23 olass short?
10:24 edrin the discovery view is almost complete, wanna try?
10:25 edrin olass: but you would have to get currentl svn
10:26 olass will try in afternoon
10:26 edrin ok
10:26 edrin i think it looks good
10:26 edrin but it was more complicated then expected... i added some *lazy* discovery...
10:27 edrin that's a lot of code...
10:28 edrin olass: everything ok?
10:28 olass will try in afternoon
10:28 olass cannot say now
10:29 olass without trying
10:29 edrin question to be just in general
10:40 edrin no egon today?
10:42 CIA-53 bioclipse: edrin_t * r8126 /xws/trunk/xws4j-sample-client/src​/sample/client/SampleClient.java: minor updates to xws4j
11:03 egonw joined #bioclipse
11:03 edrin hi egonw
11:04 egonw hi edrin
11:11 egonw olass: https://cdk.svn.sourceforge.net/svnr​oot/cdk/cdk/tags/cdk-1.1.4.20090105
11:11 egonw olass: http://cdk.svn.sourceforge.net/svnr​oot/cdk/cdk/tags/cdk-1.1.4.20090105
11:11 zarah egonw's link is also http://tinyurl.com/76hfcn
11:41 CIA-53 bioclipse: egonw * r8127 /bioclipse2/trunk/cdk-externals/trunk/ (189 files in 124 dirs): Synchronized with CDK rev 13803, aka 1.1.4.20080105
11:42 CIA-53 bioclipse: egonw * r8128 /bioclipse2/trunk/cdk-externals/trunk/​org.openscience.cdk.inchi/src/org/open​science/cdk/inchi/InChIGenerator.java: Manually applied CDK patch #2405759
11:42 CIA-53 bioclipse: egonw * r8129 /bioclipse2/trunk/cdk-externals/trunk/org​.openscience.cdk.extra/src/org/openscienc​e/cdk/io/random/RandomAccessReader.java: Throw IOException, not Exception
11:42 masak joined #bioclipse
11:44 egonw hi masak
11:44 masak olass: (biojava plugin, sequences I/O) it sounds like something which is fairly easy to implement. what exactly do you need?
11:44 masak egonw: y0
11:44 edrin hi masak
11:44 egonw masak: check BC1
11:44 egonw fasta support
11:44 egonw and visualization
11:44 egonw basic BLAST
11:45 masak egonw: ok.
11:45 masak I'll gladly do all that, but it's possible I need more input than just BC1
11:47 edrin masak: i guess they want some nice representations of sequence files (various formats exist, and biojava supports them all (or almost all))...
11:48 edrin masak: i think biojava has also support to render sequence overview pictures of a sequence in color...
11:48 egonw yes, graphical sequence visualization  and alignment visualization
11:48 egonw those are two primary bioinfo stuff thingies BC2 sucks at
11:49 masak aye
11:49 edrin as long as it does not support this it is questioanle calling it "bioinformatic workbench" ;)
11:50 egonw but please ask ola if the console should not have priority first... olass?
11:51 masak edrin: full ack.
11:51 masak egonw: I suspect it should.
11:51 edrin masak: but console is more important ;)
11:51 masak on the bright side, that work won't take long.
11:51 masak edrin: aye. will look at it now.
12:13 masak edrin: are you committing from inside Eclipse? if so, there's a simple way to select previous commit comments by means of a pull-down menu under the comment text field. better than leaving the comments blank.
12:13 masak edrin: the rest of us, who like to review commits, will have a much easier job if the intent behind the commit is explained through a commit comment.
12:14 masak kthxbai.
12:17 edrin masak: ok
12:19 edrin masak: as i was just working on a text control: it seems the best way to listen for "enter" key presses is to addKeyListener of a KeyAdapter where you capture the KeyEvent.character "SWT.CR", thus the small "enter button" will work, too
12:19 edrin i think this was not working in the old version of the console
12:19 edrin only for the big enter button
12:20 masak I almost understood that.
12:20 masak I think I listen to SWT.CR in ScriptingConsoleView, yes?
12:20 edrin do you? ok, then it should be fine
12:20 masak I think so.
12:20 masak I'll check.
12:20 CIA-53 bioclipse: edrin_t * r8130 /bioclipse2/trunk/plugins/net.bioclipse.​xws4j/src/net/bioclipse/xws4j/views/serv​icediscovery/ServiceDiscoveryView.java: now enter on text address control works to start discovery
12:22 masak yes, I capture SWT.CR
12:22 edrin ok
12:25 masak heh, the new Javascrip console works, but it prints things to the old one. :)
12:25 edrin oh
12:25 masak plus it gives the old one focus, which is pretty evil.
12:28 olass masak: regarding biojava, it would be nice to just be able to load a sequence from console, and to identify it as a sequence based on contenttype in the navigator
12:28 masak @tell olass we need to make it extremely clear to people that the Sample Data plugin contains a lot of good stuff, and that they probably want it on a first install. without it, the Bioclipse Explorer is a bit boring.
12:28 zarah Consider it noted.
12:28 olass @tell me
12:28 zarah olass: 11 s ago, masak said we need to make it extremely clear to people that the Sample Data plugin contains a lot of good stuff, and that they probably want it on a first install. without it, the Bioclipse Explorer is a bit boring.
12:28 olass masak: I agree
12:29 olass I have a proposal
12:29 olass we do a small sample data plugin that goes with bioclipse
12:29 edrin kick zarah?
12:29 masak olass: re loading of sequences: aye, let's start with that.
12:29 olass and a larger one that can be installed optionally (loike it is now)
12:29 olass masak: it might work, donät know the status with the Biojava manager
12:29 olass but we should have tests as ell
12:30 masak indeed.
12:30 olass but please, focus on the console first
12:30 olass that is more important
12:30 masak olass: that's what I'm looking at right now.
12:30 olass nice
12:30 masak edrin: she's just doing her job.
12:30 olass edrin: will test service discovery now
12:31 egonw olass: ping
12:31 olass pong
12:31 egonw CDK tagged
12:31 olass egonw: saw the tag
12:31 olass thx
12:31 egonw ok, good
12:31 masak 乒乓
12:31 olass masak: ?
12:32 masak olass: that' ping-pong in Chinese.
12:32 masak s/'/'s/
12:33 masak @plan bc2 old
12:33 zarah masak: bc2/console-egonw-single-line-refactor: 2 h planned, 1 h 38 m elapsed
12:33 zarah masak: bc2/managerdocs-finder: 1 h 30 m planned, 1 h 37 m elapsed
12:33 zarah masak: bc2/managerdocs-finder-html-skin: 1 h 15 m planned, 1 h 10 m elapsed
12:33 zarah masak: bc2/scriptconsole-backspace-bug: 30 m planned, 2 m elapsed
12:33 zarah masak: bc2/scriptconsole-literal-tab-bug: 30 m planned, 15 m elapsed
12:33 masak @start console-egonw..
12:33 zarah masak: Starting task 'bc2/console-egonw-single-line-refactor'.
12:33 masak just need to make it look nice, then people can start using it.
12:35 egonw OK, going offline for the afternoon
12:35 egonw downtown, and home later
12:35 egonw bye
12:35 masak egonw: see you
12:44 masak @stop
12:44 zarah masak: Stopping task 'bc2/console-egonw-single-line-refactor' after 11 m at 1 h 49 m out of 2 h (90%).
12:47 CIA-53 bioclipse: carl_masak * r8131 /bioclipse2/trunk/plugins/net.bioclipse.​scripting.ui/src/net/bioclipse/scripting​/ui/views/NewScriptingConsoleView.java:
12:47 CIA-53 bioclipse: [NewScriptingConsoleView] got the controls to line up like
12:47 CIA-53 bioclipse: they should: one on top of the other
12:49 masak edrin: though the New Js Console is still very primitive, you are welcome to try it out and comment.
12:49 CIA-53 bioclipse: carl_masak * r8132 /bioclipse2/trunk/plugins/net.bioclipse.​scripting.ui/src/net/bioclipse/scripting​/ui/views/NewScriptingConsoleView.java:
12:49 CIA-53 bioclipse: [NewScriptingConsole] sets focus to the input box
12:49 CIA-53 bioclipse: this doesn't always seem to work, though -- needs more experimenting
13:00 CIA-53 bioclipse: edrin_t * r8133 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/ (2 files in 2 dirs): added nicer icon
13:04 masak lunch &
15:23 olass joined #bioclipse
15:23 edrin hi
15:23 olass hi
15:23 zarah hi olass
15:23 olass @msg
15:23 zarah olass: You have no new messages.
15:23 olass zarah: z
15:23 zarah olass: I'm just a bot, you expect me to understand that?
15:23 olass zarah: dz
15:23 zarah you're welcome, olass :)
15:37 olass edrin: how's progress?
15:37 olass edrin: a short question for you
15:37 olass mom
15:53 egonw joined #bioclipse
15:55 egonw olass: ping
15:55 olass egon: pong
15:55 egonw permission to merge in RDF plugins
15:56 egonw asked
15:56 olass sure
15:56 olass what do they contain?
15:57 egonw RDF stuff
15:59 olass any functionality in bioclipse yet or just libs?
15:59 egonw mom
15:59 egonw functionality
16:00 egonw let me check if I have a screenshot
16:00 olass great
16:00 olass or a blog item?
16:00 egonw http://chem-bla-ics.blogspot.com/2008/​11/solubility-data-in-bioclipse-1.html
16:00 olass ;-)
16:00 zarah egonw's link is also http://tinyurl.com/5zcv9x
16:00 olass edrin: do you have an account on the pelezilla?
16:01 olass I want to be able to report bugs to you there
16:01 olass @google pelezilla
16:01 zarah olass: http://www.weddingbee.com/2008/06/01/o​ne-lucky-day-weekend-bonus-pele-zilla/
16:01 olass what!?
16:01 egonw huh?
16:02 olass http://pele.farmbio.uu.se/​cgi-bin/bugzilla/index.cgi
16:02 zarah olass's link is also http://tinyurl.com/6c9nzh
16:02 edrin no account there
16:03 olass edrin: please create one
16:03 olass and see http://wiki.bioclipse.net/index.php?title=Mylyn
16:03 zarah olass's link is also http://tinyurl.com/5qp5rl
16:03 olass pelezilla is so great
16:04 olass bug handling just got so much easier
16:11 egonw olass: btw -> http://chemicalrcp.blogspot.com/
16:11 zarah egonw's link is also http://tinyurl.com/8w5lmo
16:11 egonw I requested adding that to Planet Eclipse
16:11 egonw it only contains copies of stuff in chem-bla-ics
16:11 egonw but bioclipse/rcp only
16:12 olass why not write on bioclipse.blogspot.com?
16:12 olass so that we all write on same place?
16:13 egonw because we decided only to blog about released stuff there
16:16 egonw mom, I'll install planet-venus :)
16:25 egonw olass: http://pele.farmbio.uu.se/planetbioclipse/
16:25 zarah egonw's link is also http://tinyurl.com/a8pzmt
16:28 olass nice
16:28 olass can't see your rcp post here though...
16:28 olass only bioclipseblog
16:29 egonw ok, reload
16:29 egonw had not added that one yet :)
16:30 olass indeed :-)
16:31 egonw now, we do need to add the Bioclipse log, etc, etc...
16:33 egonw of course, there also is: http://friendfeed.com/rooms/bioclipse
16:33 zarah egonw's link is also http://tinyurl.com/6bbxz5
16:35 olass Bioclipse log?
16:35 olass what is that?
16:35 egonw huh?
16:36 olass the log file?
16:36 olass why add that?
16:36 olass and where?
16:36 egonw ah... sorry. .. logO
16:36 olass oh
16:36 egonw missing O
16:36 olass :-)
16:36 egonw indeed :)
16:37 egonw hahaha
16:39 edrin olass: you can try the scripting console with a cdk service, too
16:39 edrin egonw: do your service work with the console/IoFactory binding?
16:40 egonw have not tried
16:40 egonw edrin: can you please try?
16:40 egonw I need to get some RDF stuff implemented tonite
16:41 edrin egonw: only with help of olass
16:41 edrin console is not working for me
16:42 egonw ok, tell me what to type
16:42 edrin f = xws.getFunction("cdk.ws1.bmc.uu.se");
16:43 edrin ioschemata = f.getIoSchemataSync(30000);
16:43 edrin sorry
16:43 edrin again
16:43 olass edrin: can try
16:43 edrin f = xws.getFunction("cdk.ws1.bmc.uu.se", _one_of_your_functions_);
16:43 edrin ioschemata = f.getIoSchemataSync(30000);
16:44 edrin iofactory = xws.getIoFactory(ioschemata);
16:44 olass sorry, must run now :-(
16:44 olass hope you get it to work
16:44 edrin input = iofactory._TAB_COMPLETE_HERE;
16:44 edrin ...#
16:44 olass (you seem to be well on the way)
16:45 olass cu on wednesday
16:45 egonw how did I log in again?
16:45 olass (will be in Uppsala then)
16:45 egonw olass: bye!
16:45 olass xws.connect()
16:45 olass bye!
16:45 edrin bye
16:46 egonw ok, connected
16:47 egonw and have the XMPP SD view open :)
16:47 edrin cool
16:47 edrin egonw: try to discover home ;)
16:47 egonw home?
16:47 egonw ok
16:47 edrin note: binding does not work yet
16:47 egonw already discoverd cdk.ws1 :)
16:47 edrin there is a "home" button
16:47 edrin ok
16:48 egonw yes, got it... nice
16:48 edrin do you see the Ping command ;) that's the problem i was talking about
16:48 egonw mmm... me thinks drag-and-drop to JavaScript console of functions in the Service Discover view :)
16:48 edrin and did you notice the nice recursive discovery?
16:48 egonw yes
16:49 edrin you can even browse into chat rooms and see users in chat rooms: jabber.ccc.de there is a conference component...
16:49 edrin will need some time to discover them...
16:50 egonw console works fine
16:50 egonw including the autogeneration of the data model :)
16:51 edrin and can you create valid input in the console and invoke the service with it?
16:52 egonw checking
16:53 egonw http://gist.github.com/22185
16:53 edrin ah cool
16:53 edrin can you send this link to ola?
16:55 egonw yes, invokation still works fine
16:55 edrin cool
16:55 edrin because olas did not work
16:55 egonw ah, ic
16:57 edrin put probably a xml parsing problem
16:58 edrin btw: i will rename xws manager to xmpp manager
16:59 egonw ok
17:01 egonw ok, have to go for dinner now
17:01 edrin ok, cu later
17:49 egonw back for some minutes
17:49 egonw edrin: did you get a pelezilla account?
17:50 edrin not yet
17:51 edrin wont have time for this today
17:51 edrin and i do not really know what this is
18:00 egonw pelezilla is just bugzilla
18:00 egonw for bioclipse
18:00 egonw bbl
18:00 egonw hivpred seems to work somewhat
18:00 egonw maybe except building data structure...
18:00 egonw would be nice to have the schema open as XML resource
18:00 egonw or in the XML Schema editor :)
18:01 egonw cu later
18:46 edrin egonw:
18:49 CIA-53 bioclipse: edrin_t * r8134 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/s​rc/net/bioclipse/xws4j/views/servicediscovery/ (BindingGenerator.java ServiceDiscoveryView.java): added action create binding
19:11 CIA-53 bioclipse: edrin_t * r8135 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/sr​c/net/bioclipse/xws4j/DefaultClientCurator.java: on reconnect and account data was the same the xmpp items stay valid, same client session is used again
19:12 CIA-53 bioclipse: edrin_t * r8136 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/sr​c/net/bioclipse/xws4j/business/XwsManager.java: the xws manager is now called xmpp manager!
22:23 CIA-53 bioclipse: edrin_t * r8137 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/ (5 files in 3 dirs):
22:30 CIA-53 bioclipse: edrin_t * r8138 /xws/trunk/xws4j-binding/src/net/biocl​ipse/xws/binding/BindingManager.java: now always the latest version of autogenerated bindings is returned on getIoFactory()

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