Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-12-31

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All times shown according to UTC.

Time Nick Message
04:14 CIA-57 joined #bioclipse
04:44 CIA-53 joined #bioclipse
08:56 egonw joined #bioclipse
09:07 edrin joined #bioclipse
09:07 edrin hi
09:07 zarah hi edrin
09:07 edrin good morning egon
09:32 egonw hi edrin
09:36 edrin egonw: i installed taverna 2 and played a little bit with it
09:36 edrin it looks much better then1 in my opinion
09:37 edrin but i could not find any information about how to write plugins
09:38 edrin i think to remember that you have a "plugin" from stain to work on(start with)
09:39 egonw right
09:39 egonw I'll work on this today
09:40 egonw I'll upload stuff to GitHub
09:42 edrin egonw: can you send me a copy of the sample plugin, too?
09:42 edrin it would be really good if we have also a xmpp service discovery view in taverna
09:43 edrin because this way it would be really cool to discover and use such services...
09:46 egonw the code stain send me does not cover discovery, I think
09:47 edrin egonw: ok. what can plugins do?
09:47 edrin are they similar to eclipse plugins and can they add windows + menu items?
09:48 egonw they add workers
09:48 edrin ah ok
09:48 egonw so, I'd add a worker that would run a specific service
09:48 edrin can they add also activities?
09:49 egonw I guess so...
09:49 egonw they have logic to discover BioMoby services... so, that should be possible too
09:49 edrin for example when clicking on the Activities menu and choos BioMoby a window pops up that
09:49 edrin does not look like being part of taverna itself
09:50 edrin and: depending on the worker, the configure window looks different...
09:50 egonw edrin: yes, that would be rather interesting indeed...
09:50 egonw talk to stain...
09:51 egonw stain: ping
09:51 edrin a simplified version of something like the PSI disco browser would be very helpful.�.
09:52 egonw indeed
09:53 edrin and then you click the function of a service and a worker is generated: creating java binding and some wrap to make it a worker
09:54 edrin and a window to setup the xmpp account is required, too
09:56 egonw edrin: no idea if Taverna2 has dynamic worker detection/addition
09:57 edrin oh
09:57 egonw no idea...
09:57 egonw not saying it is impossible
09:58 edrin well... at least the local workers seem to allowe code execution
09:59 edrin The LocalWorkers seem to be essentially some kind of scripts... you can edit them pressing configure...
09:59 edrin what scripting engine is this?
09:59 edrin or what script language? it looks like plain java
10:00 edrin or is it javascript?
10:02 edrin i dont see an option to add a local worker
10:03 edrin ah local workers seem to be been shells
10:07 egonw beanshell
10:07 egonw right
10:07 edrin hm
10:07 egonw yes, that would be an option too
10:08 edrin but it seems that i cannot save my personal/modified beanshell in the workers view
10:08 egonw but I rather have a worker which I configure by setting jabber account info, service to run and input
10:08 egonw never tried beanshell serialization
10:08 egonw should work, AFAIK
10:09 edrin for example i wonder why it is not possible to create a new beanshell, and then add it to the localworker list
10:09 edrin to reuse it in another workflow...
10:10 egonw ah, in that sense...
10:10 egonw yes, that would be useful
10:10 edrin egonw: i think it should be possible to just create/write a beanshell script, in the taverna config editor one can add external .jars to the classpath of the script... and just add xws4j code
10:11 edrin it seems one could already use xws4j from taverna right now...
10:11 egonw yes, does not sounds unreasonable
10:11 edrin but for each service one would need to write a new beanshell
10:11 edrin not so good
10:12 edrin at least a "create a beanshell for this service" wizard would be required....
10:18 edrin egonw: it seems that when running the Activities->New Activity->WSDL... and specifying a new wsdl it adds these workers to the worker view!
10:20 egonw right
10:20 egonw so, it should be possible indeed
10:20 edrin yes
10:20 edrin i successfully added a wsdl for protein prediction
10:20 edrin cool
10:20 edrin it seems i can even use this...
10:21 edrin ok
10:22 edrin that means: when clicking Activities->New Activity in the menu, a "XMPP Service..." must be shown
10:22 edrin when clicking it a service discovery window must show up... and then
10:22 edrin one can browse through the xmpp services
10:25 edrin then click one, some magic happens-> autogenerating binding for xmpp service...
10:26 edrin and the binding is then added to the worker view...
10:26 edrin should be possible
10:27 edrin but it seems that one cannot edit/modify/delete workers in the worker view... that's maybe todo for Taverner programmers
10:28 edrin egonw: ok, must buy some fruits now, will be back later
10:28 edrin egonw: the worker sample thing stain gave u, may I see a copy?
10:29 edrin egonw: do you know what GUI API they are using in taverna?
10:30 edrin stain?
11:46 edrin egonw?
11:47 egonw sorry.... had to do some things offline
11:47 egonw I'm trying to find how to build the whole of Taverna2
11:47 egonw as I cannot find the things stain emailed me yet
11:48 edrin i think the whole project wouldn't be too complicated
11:49 edrin there are these .pom files, they seem to define what .ajr to be loaded where in the Taverna
11:51 egonw yes
11:55 egonw joined #bioclipse
11:55 edrin egonw: i found this: http://www.mygrid.org.uk/us​ermanual1.7/dev_guide.html
11:55 zarah edrin's link is also http://tinyurl.com/6uz7zh
11:56 egonw ah, that looks updated
11:56 edrin egonw: do you know what GUI they use? is it the same
11:56 edrin eclipse uses?
11:56 egonw no, I think Taverna is Swing based
11:56 edrin thus we could write one service discovery browser and reuse it
11:57 edrin but swing works in eclipse, right=
11:57 edrin ?
11:58 edrin we can use SWTSwing
11:59 edrin hm.. but in fact here on windows the taverna does not look as the usual uggly Swing stuff
12:01 edrin heh
12:01 edrin i just found a mail of Ola to the taverna mailing list where he asked this question ;)
12:01 edrin "What is the status and intentions for a new graphical editor for T2? Has it been decided what windowing system will be used (Swing)? "
12:02 edrin and it is swing
12:10 egonw edrin: that was not the right usermanual
12:10 egonw that was for 1.7
12:10 egonw not 2.0
12:11 edrin maybe there is non yet?
12:11 egonw guess so
12:11 edrin maybe it is very similiar anyway
12:16 egonw http://sourceforge.net/mailarchive/forum.php?threa​d_name=a20e6fb10811100900w6f722084te11c7b68abd7694​5%40mail.gmail.com&forum_name=taverna-hackers
12:16 zarah egonw's link is also http://tinyurl.com/a93l4h
12:21 CIA-53 bioclipse: edrin_t * r8105 /bioclipse2/trunk/plugins/net.bio​clipse.xws4j/jars/xws4j-current/ (4 files):
12:21 CIA-53 bioclipse: edrin_t * r8106 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/ (META-INF/MANIFEST.MF build.properties):
13:28 CIA-53 joined #bioclipse
14:33 shk3 joined #bioclipse
14:37 edrin hi shk3
14:39 shk3 hi edrin
14:40 egonw hi shk3
14:41 shk3 hi egonw
14:47 egonw edrin: http://github.com/egonw/xws-taverna/tree/master
14:47 zarah egonw's link is also http://tinyurl.com/72ewnz
14:48 edrin great :)
14:48 egonw edrin: no code there yet...
14:48 egonw but it's a start :)
14:48 edrin yes, true
14:49 egonw at least, I'll continue posting there my log for getting a local source copy of T2
14:49 egonw from their, I'll set up a plugin project
14:49 egonw and maybe we can add code for your ideas later too there...
14:50 edrin ok, sure
14:51 edrin how should we call GUI items associated with xws4j? XMPP Services, XMPP Web Services, XMPP Cloud Services, xws4j, just XMPP, ... ?
14:51 edrin (for bioclipse...)
14:52 edrin shk3: what do you think?
14:52 edrin egonw?
14:52 shk3 sorry, no idea what you are talking about
14:53 egonw XMPP Services
14:53 edrin for example a menu item to connect
14:53 egonw maybe even: XMPP IO-DATA Services
14:53 edrin ok, so call it XMPP or "XMPP Services"
14:54 shk3 ah
14:54 shk3 is this a generic service?
14:54 edrin yes
14:54 shk3 i. e. the  user can decide which service to  use?
14:55 edrin shk3 it is the middleware
14:55 edrin like soap
14:55 shk3 yes
14:55 edrin so
14:55 shk3 and the user needs to know an xmpp server
14:55 edrin maybe just XMPP ?
14:55 edrin yes
14:55 shk3 then "connect to xmpp service" or so
14:55 shk3 I would think
14:55 edrin ok
15:38 egonw_ joined #bioclipse
15:39 * egonw found a new IRC client for Ubuntu: quassel
15:39 egonw quite nice
15:40 egonw quassel++
15:45 egonw j taverna
15:45 egonw j #taverna
15:46 egonw edrin: seems building Taverna2 form CVS is broken
15:46 egonw missing module ;(
16:09 egonw ok, enough toying around...
16:09 egonw a shame that it did not lead to new code...
16:09 egonw but did learn a lot
16:09 egonw bye

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