Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-10-27

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All times shown according to UTC.

Time Nick Message
00:08 CIA-52 bioclipse: edrin_t * r7452 /xws/trunk/xws4j-binding/src/net/biocl​ipse/xws/binding/BindingManager.java: added missing function
00:10 CIA-52 bioclipse: edrin_t * r7453 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/ (7 files in 3 dirs): updated file
08:09 olass joined #bioclipse
08:09 olass moin
08:09 zarah hi olass
08:09 Gpox joined #bioclipse
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12:59 edrin joined #bioclipse
12:59 edrin hi
12:59 zarah hi edrin
13:10 olass hi edrin
13:10 edrin hi
13:10 zarah hi edrin
13:11 olass great progress with xws4j
13:11 olass will try my service today I hope
13:11 olass sooo many things to fix before holidays
13:11 edrin yeaa, was getting good progress with xml binding this weekend
13:12 olass really nice
13:12 olass It'd be great if I could get it working with EMF binding too
13:12 olass I feel like I am really close
13:12 shk3 hi to uppsala
13:12 olass that would make UI generation more simple
13:12 olass hi UK
13:12 edrin olass: you may try the batchbinder to generate a binding for your sample java client
13:12 shk3 some questions
13:13 shk3 what does the @Recorded in a manager interface do?
13:13 olass edrin: if I have time...
13:13 olass shk3: It makes the recorder record the command in the AcitonHistory
13:13 olass which can be seen in ActionHistoryView
13:13 olass a first step towards auditing
13:13 olass and replay of evenst
13:14 olass you can select multiple steps in the ActionHistoryView, right-click and say "create javascript"
13:14 olass and replay what you just have done
13:14 olass regardless if from GUI or console
13:14 olass at least that is the plan
13:14 shk3 ah  ok, didn't have this view open
13:14 olass it's in early alpha-status
13:14 olass and sort of works in some occasions
13:14 shk3 ok
13:14 olass jonalv's doing
13:15 shk3 and what is spring used for?
13:15 olass email devel if ou have more detailed questions
13:15 olass spring is for AOP
13:15 olass amongst others
13:15 shk3 but it's not for making managers available on the console, is it?
13:15 olass AOP recognizes the @job annotation and runs a method before that call to record what we are doing
13:15 shk3 that via an extension point, irght?
13:15 olass not sure
13:15 olass maybe a bit of both
13:16 olass ask jonalv on devel
13:16 olass not my boat
13:16 shk3 ok
13:20 CIA-52 bioclipse: shk3 * r7455 /bioclipse2/trunk/plugins/net.bioclipse.​webservices/src/net/bioclipse/plugins/: removed empty folder
13:20 olass is SF slow for you too?
13:22 olass it's unbearable
13:22 olass edrin: any new plugins to check out?
13:22 olass or just update xws4j, sample client, and coffee-machine?
13:28 CIA-52 bioclipse: ospjuth * r7456 /bioclipse2/trunk/cdk-externals/trunk/ (21 files in 21 dirs): Removed execution environment J2SE-1.5 as this is problematic on Mac OS X.
13:28 CIA-52 bioclipse: shk3 * r7457 /bioclipse2/trunk/plugins/net.biocli​pse.webservices/doc/wsdbfetch.html: adopeted the help
14:31 CIA-52 bioclipse: ospjuth * r7458 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.business.test/src/net/bioclipse/cdk/​business/test/CDKManagerPluginTest.java: Added CDKManagerPluginTest for testing CDKManager from a Plugin-junit-test.
14:53 edrin olass: i also updated xws4j bc2 plugin. however currently the binding loading does not work...
14:53 edrin the rest in bc2 plugin are just bugfixes...
14:55 edrin maybe i did a mistake...
14:56 edrin the class loading functions might not work properly... i will try another idea today...
14:58 edrin olass: but maybe you can add something to the plugin:
15:01 edrin in http://bioclipse.svn.sourceforge.net/viewvc/bi​oclipse/bioclipse2/trunk/plugins/net.bioclipse​.xws4j/src/net/bioclipse/xws4j/DefaultBindingD​efinitions.java?revision=7441&view=markup
15:01 edrin in function private static String getTargetDirectory(BundleContext context)
15:01 edrin can you add code there that returns a directory in the current (bioclipse) workspace where bc2 could dumb the autogenerated files/classes?
15:01 zarah edrin's link is also http://tinyurl.com/5td8yl
15:12 CIA-52 bioclipse: shk3 * r7459 /bioclipse2/trunk/plugins/net.bioclipse.webse​rvices/src/net/bioclipse/webservices/scripts/ (IWebservicesManager.java WebservicesManager.java): changed the method in the manager so it is actually usefull
15:21 olass edrin: the workspace?
15:21 olass the workspace contains molecules and sequences etc
15:21 olass code should not go ther IMO
15:21 olass hmm
15:21 olass you mean install dir or something like that?
15:22 olass isa temp file not enough?
15:26 CIA-52 bioclipse: shk3 * r7460 /bioclipse2/trunk/plugins/net.bioclipse​.webservices/src/net/bioclipse/webservi​ces/scripts/IWebservicesManager.java: changed the method in the manager so it is actually usefull
15:29 olass edrin: please paste some examples in respond to jonalv's mail
15:29 olass se devel ML
15:36 edrin olass: there will be a function called public static IoFactory = BindingManager.getIoFactory(Function fun); this will search the binding in the local target dir
15:36 olass sorry, I'm not good at this
15:36 olass at all
15:41 edrin k
15:41 edrin no problem :)
15:46 edrin olass: well, my idea was that a user "stores" the binding of discovered functions in the resources (next to proteinsequences and stuff). user can then rightclick such a service and use it with something...
15:47 olass I think it should appear in teh ServiceView
15:47 edrin for example as a service target for a workflow view
15:47 edrin ok
15:47 olass http://wiki.bioclipse.net/index.​php?title=Service_infrastructure
15:47 zarah olass's link is also http://tinyurl.com/6qoupu
15:47 edrin well, in any case user would need some kind of "service library view" ;)
15:47 olass jonalv will work on that
15:48 olass after christmas and bioclispe 2.0.0 release
15:48 olass if you want it more urgent, feel free to write it up :-)
15:48 edrin yes, that's what I was thinking about
15:49 edrin btw. you can try this with the xws4j-binding lib on your service:
15:49 edrin java SampleClient user@server.example.com/home secret server.example.com 5222 xws.server.example.com testFunction c:/myBindingFiles true c:/xmlbeans/jsr173_1.0_api.jar;c:/xmlbeans/resolve​r.jar;c:/xmlbeans/xbean.jar;c:/xmlbeans/xbean_xpat​h.jar;c:/xmlbeans/xmlbeans-qname.jar;c:/xmlbeans/x​mlpublic.jar;c:/xws4j-binding-test.jar;c:/xws4j-te​st.jar;c:/Programme/Java/jre1.6.0_07/lib/rt.jar
15:49 edrin uhm... sorry, not SampleClient but BatchBinder
15:50 edrin this will autogenerate a client stub against your service ;)
16:24 CIA-52 bioclipse: shk3 * r7461 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: cleaned up a bit
16:25 CIA-52 bioclipse: shk3 * r7462 /bioclipse2/trunk/plugins/ (6 files in 4 dirs): more methods in managers
16:32 olass edrin: At least I solved my serialization problem that made the validation fail!
16:34 edrin olass: ah :)
16:34 olass it was just me who didn't understand the EMF way of working
16:34 olass will test with validation now
16:35 olass hope the client works with mine as well...
16:35 edrin means the component accepts it now?
16:36 olass not tested yet
17:02 olass edrin: seems to work now
17:02 olass nice!
17:03 olass will test async as well
17:03 olass YES!
17:03 olass edrin: nice work
17:04 olass I now have a working HivPrediction client and server
17:04 olass with EMF binding
19:27 edrin olass: cool :)
19:27 olass yes
19:27 olass hope to get it on ws1.bmc.uu.se tomorrow
19:27 olass and plugin for bioclipse as well
19:27 olass should be fast
19:27 edrin hehe
19:27 edrin yes
19:28 olass you worked on the article?
19:28 edrin not at this time, i was working in the lab whole weekend and day, no i mean
19:29 edrin on weekend i was working on this binding tools
19:29 edrin and today in bench experiments
19:29 edrin will go home now. cu then - if you are still on-line
19:30 edrin left #bioclipse
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23:09 CIA-52 bioclipse: edrin_t * r7463 /xws/trunk/xws4j-binding/src/net/bio​clipse/xws/binding/BatchBinder.java: fixed spelling error
23:10 CIA-52 bioclipse: edrin_t * r7464 /xws/trunk/xws4j-binding/src​/net/bioclipse/xws/binding/ (BindingManager.java tools/JarClasspathLoader.java): can now load thing within eclipse, too
23:35 CIA-52 bioclipse: edrin_t * r7465 /xws/trunk/xws4j-binding/src/net/bioclipse​/xws/binding/tools/IoFactoryBuilder.java: spelling error
23:45 CIA-52 bioclipse: edrin_t * r7466 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/ (7 files in 3 dirs): updated to current libs of xws4j

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