Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-04-17

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All times shown according to UTC.

Time Nick Message
05:09 rojasm joined #bioclipse
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08:06 CIA-43 bioclipse: ospjuth * r5436 /bioclipse/trunk/plugins/net.bioclipse.jnanotube/: Initial import of plugin net.bioclipse.jnanotube for Bioclipse 1.2.x branch. Authors: Joe & Sam. Contact: wisarn151@hotmail.com.
08:07 CIA-43 bioclipse: ospjuth * r5437 /bioclipse/trunk/plugins/net.bioclipse.jnanotube/ (153 files in 31 dirs): Initial import of plugin net.bioclipse.jnanotube for Bioclipse 1.2.x branch. Authors: Joe & Sam. Contact: wisarn151@hotmail.com.
08:10 EskilA joined #bioclipse
08:42 olas FYI: http://bioclipse.blogspot.com/2008/04/jna​notube-nanotube-plugin-for-bioclipse.html
08:44 edrin joined #bioclipse
08:44 olas hi edrin
08:44 edrin hi
08:45 edrin servus ola
08:45 steinbeck joined #bioclipse
08:45 edrin hi ola
08:45 edrin hi steinbeck
08:45 steinbeck Hi edrin
08:46 edrin olas, did you notice this mail from Wael LABIDI about his current XMPP related research work
08:46 edrin ?
08:48 egonw joined #bioclipse
08:48 olas hi egonw
08:48 olas edrin: mom
08:49 olas egonw: http://bioclipse.blogspot.com/2008/04/jna​notube-nanotube-plugin-for-bioclipse.html
08:49 olas mailing the jmol list to announc eit :-)
08:50 olas edrin: reading the paper now
08:50 egonw olas: nice blog item
08:50 olas thx
08:50 olas edrin: seems interesting and very relevant
08:53 edrin relevant it is, yes
08:53 edrin but i think it is somehow a little bit hax0r
08:55 edrin egonw: this one: http://mail.jabber.org/pipermail​/ws-xmpp/2008-April/000013.html
08:57 edrin I got a date, I have the defense of my thesis thursday next week
08:59 edrin they use Jabber-RPC thus it can't be good ;)
09:01 olas haha
09:01 thomas_ku joined #bioclipse
09:02 olas hi stain
09:02 olas good to see you here :-)
09:02 stain hi, olas :)
09:02 egonw hi thomas_ku
09:02 egonw thomas_ku: did you see #taverna yet?
09:02 stain I'm really just lurking since I'm not really a bioclipse-dude..
09:03 egonw like I'm lurking #taverna? :)
09:03 egonw stain: or do you say you have not even tried olas taverna plugin for Bioclipse?
09:04 stain I have tried that one
09:04 edrin me is away
09:04 thomas_ku egonw:No didn't saw it
09:07 olas stain: it doesn't work anymore
09:07 olas but I'm in the process of trying agina for Bioclispe2
09:07 olas if I can get taverna to execute outside of the workbench
09:07 olas and package it into a plugin
09:08 olas last time it required headless mode
09:08 olas which was really limiting...
09:10 stain shouldn't be a problem with t2.. or you could use the execution service, although that might be a bit overkill
09:13 olas stain: is there a unit test that I can look at?
09:14 olas I realize we should keep this conv in #taverna
09:14 stain yes
09:14 stain speecially as we're trying to beef up the channel :)
09:15 olas hold on
09:19 CIA-43 bioclipse: ospjuth * r5438 /bioclipse/trunk/plugins/net.bioclipse.jnanotube/ (5 files in 2 dirs): Added doc to Bioclipse online help, and made stub for user guide, about, and license.
09:28 * jonalv off hunting for food
11:16 olas joined #bioclipse
12:11 jonalv joined #bioclipse
12:12 * jonalv placed a breakpoint at a bad position while debugging gui stuff and completely locked X :(
12:14 olas hahaha
12:14 olas remove all BPs?
12:14 jonalv huh no just the one making problemds :)
12:16 jonalv don't place breakpoints in validateDrop()was the lesson (once again...)
12:16 jonalv probably like the third time I did that...
12:18 edrin joined #bioclipse
12:45 edrin nice plugin screenshot about the nanontube ;)
12:49 olas thx
13:04 edrin really interesting what kind of people joined/interested the lest
13:05 jonalv huh?
13:05 edrin list
13:05 edrin sorry
13:06 edrin jonalv: the auto completion of the console rhino bc plugin, does it only show commands/functions/objects of rhino. or does it do this with every loaded class/object?
13:07 jonalv for the moment it shows all loaded objects and all loaded objects methods annotated with @recorded
13:08 jonalv but the plan is taht it will show all objects annotated with  @publishedClass and all methods annotated with @publisehdMehod
13:09 jonalv so you can only tab complete on methods with help and there is only help for things you can tab complete on :)
13:10 edrin so you mean it is required that the source code has comments and this /* comment */ in the source code conatains @whatever, right?
13:11 jonalv uhm not comments annotations
13:11 jonalv it's those nifty java 5 things you know
13:11 edrin how do i annotate a function?
13:11 jonalv please have a look at the interface IUserManager in net.bioclipse.usermanager
13:12 edrin I have absolutely no clue
13:12 jonalv I think it's the only manager fully documented for this yet
13:12 edrin ah
13:12 jonalv It was the last thing I did before turning over to work with Brunn for some time
13:14 edrin ok, again, how do i annotate my function? do i have to do bioclipsesomeblahobject.annotate("@recorded"); or do i add this to the JavaDoc? or do i add the @recorded somewhere in the rhino plugin .xml ?
13:14 jonalv you do it between the javadoc and the method declaration
13:15 edrin can you give me a sample line in the http svn browser?
13:15 jonalv I should blog about this when I get back to working ob Bioclispe 2 next time
13:15 jonalv yep I was already working on that :)
13:16 jonalv edrin: <http://bioclipse.svn.sourceforge.net/viewvc/bioc​lipse/bioclipse2/trunk/plugins/net.bioclipse.use​rmanager/src/net/bioclipse/usermanager/business/​IUserManager.java?revision=5325&amp;view=markup>
13:17 * jonalv misses lambdabot...
13:17 edrin ah
13:17 edrin very cool
13:18 jonalv so the @recorded anootation has to do with the script generation (which we might not ever get to work fully but it's a cool thing fiddle with and I still whink it would be great if it woprked...)
13:18 edrin this "@Recorded", is this syntax/word defined in the Rhino plugin? are there othere words available, too? or is this a general java thing? (java 5 as you said)
13:19 jonalv @Recorded, @PublishedMethod and @PublishedClass are all annotaions we have created for Bioclipse 2
13:19 jonalv hang on and I will find one of them for you
13:20 jonalv edrin: <http://bioclipse.svn.sourceforge.net/vi​ewvc/bioclipse/bioclipse2/trunk/plugins​/net.bioclipse.core/src/net/bioclipse/c​ore/PublishedMethod.java?view=markup>
13:21 edrin perfect
13:21 edrin do you have experiences with JAXB ?
13:21 jonalv nope
13:21 jonalv what's taht? :)
13:21 edrin ok
13:22 edrin XML Schema 2 Java Class converter (and back)
13:22 jonalv hm cool
13:22 jonalv I think :)
13:22 jonalv not sure I fully understand what to use it for though...
13:23 edrin is the rhino execute javascript-file plugin already ported/available in BC2? is there a javascript editor with autocompletion available?
13:24 jonalv nope that's what we need next
13:25 edrin guck da! http://www.csg.is.titech.ac.jp/~chiba/javassist/
13:25 jonalv about running the scripts that need some fiddling in order to get in all managers into the environment but it's more or less the same as the environemnt for the console I guess...
13:25 edrin not in content with teh javascript console or editor, though
13:26 edrin jonalv: why not just copy the bc_rhino plugin to bc2?
13:27 olas edrin: so much has changed
13:27 olas most functionality is in bc2
13:27 jonalv hm this has been masaks field and I don't know that very much about it but would that mean gaining a nice editor=
13:28 olas there's no javascript editor in bc1
13:28 olas but there's an editor
13:28 jonalv If it's only for running scripts as I said it won't be enough since there are some more things needed when setting up the environment these days...
13:28 olas that can run javascript
13:28 olas so yes, that editor and actions could be ported easily
13:28 olas would need some changes for resource handling, but not complicated
13:29 olas If you file a bug and assign it to me then I'll do it next week
13:29 olas or, even better, do it you
13:29 * olas is talking to edrin
13:30 edrin heh :)
13:30 jonalv edrin: If you are planning on doing it we should also order up a thing with managers that I have been thinking about
13:31 jonalv that javascriptenvironemnt should use managers without the recording AOP stuff
13:31 jonalv No point in recording things from scripts alredy recorded so to say :)
13:31 jonalv as it is now those managers are not expprted from the plugins
13:31 jonalv only AOP wrapped versions are exported
13:32 jonalv btw olas: those non recorded managers should also be used by other managers for making calls to managers thus removing recording from those "happenings" to.
13:33 jonalv olas: Did you understand that last sentence? It felt strange... :)
13:34 olas no
13:34 jonalv You used the biojava manager from the services manager right?
13:35 olas but I assume you mean that if a manager calls another manager, that call should not be recorded?
13:35 jonalv exactly
13:36 jonalv and if calls a manager that doesn't have those aspects it won't be recorded and that's how we should do it
13:36 jonalv + that would also mean that you could put that biojava manger into the servicemanager declaratively
13:36 edrin sorry, I can't comment, I don't know the bc2-plugin-design
13:37 jonalv in the applicationcontext.xml for the service plugin
13:37 jonalv or context.xml or whatever yu might call it...
13:38 jonalv edrin: It's okey. Think of it as an extended bc1 design. All that could be done in bc1 can still be done but there is also a bunch of Spring things that can be used by those who wants to
13:39 jonalv (like me)   =)
13:39 edrin ok
13:39 edrin I still dont know what spring is...
13:40 jonalv I would highly recommend that you read up on it a bit. It it cool. Mosly the AOP stuff
13:40 edrin can you say in one word?
13:40 jonalv no
13:40 jonalv :)
13:41 edrin like "y=f(x)"
13:41 edrin and now you have z, this is cool because
13:41 edrin ...
13:41 jonalv I spent almost a week trying to figure out what it was. Read about 100-200 pages in one of the spring books in order to understand what it was...
13:42 jonalv so no I am afraid I can't explain in one word what it is and why it's so good
13:42 steinbeck joined #bioclipse
13:43 jonalv Maybe someone on the web has managed to describe Spring good in a few words I don't know...
13:43 edrin wikipedia is my friend
13:45 edrin it seems it is something like mfc, qt or wxwidgets for c++ + some optional tools to manage/configure the processes in the java runtime...
13:47 jonalv okey, I am not familiar with those :)
13:47 edrin it's a framework to make programing more easy
13:48 jonalv yea
14:10 CIA-43 bioclipse: ospjuth * r5439 /bioclipse2/trunk/plugins/net.bioclip​se.biomart/src/net/bioclipse/biomart/ (7 files in 3 dirs): Added a preference page for biomart servers.
14:11 CIA-43 bioclipse: ospjuth * r5440 /bioclipse2/trunk/plugins/net.bioclipse.b​iomart/src/net/bioclipse/biomart/wizards/ (. AttributesPage.java BiomartWizard.java tmp.txt): Started working on a wizard for Biomart queries.
14:11 CIA-43 bioclipse: ospjuth * r5441 /bioclipse2/trunk/plugins/net.bioclipse.biomart/ (META-INF/MANIFEST.MF plugin.xml): Added prefs page to manifest.
14:13 CIA-43 bioclipse: ospjuth * r5442 /bioclipse2/trunk/plugins/net.bioclipse.biomart/ (8 files in 4 dirs): Added a biomart editor as a form-based multipage editor. Started linking in filters into filtersPage.
14:15 masak joined #bioclipse
14:15 masak edrin: hullo
14:15 masak I heard you're interested in enabling js file execution in bc2
14:16 masak we could discuss it a little and see if we arrive at something
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14:41 CIA-43 bioclipse: ospjuth * r5443 /bioclipse2/trunk/plugins/net.bioclipse.biomart/ (6 files in 5 dirs): Double-click on dataset now opens empty editor for query construction.
14:58 egonw steinbeck: has the NMRShiftDB plugin for Bioclipse 1.2.x been update for the server move?
14:59 egonw he, the submit interface has changed ! :)
15:00 egonw "Add literature Items" :)
15:03 steinbeck egonw: I don't thing so
15:03 egonw steinbeck: and hit a bug just now
15:03 egonw and a typo, I think
15:04 egonw Submit Data
15:04 egonw Klö
15:04 egonw the second line is the page content :)
15:06 masak things that people, if they don't know them, are doomed to repeat/reinvent: history, lisp, unix, prolog
15:07 masak source: google search for "know * are doomed to * it"
15:51 CIA-43 bioclipse: carl_masak * r5444 /bioclipse2/trunk/plugins/net.biocli​pse.biomart/src/net/bioclipse/biomar​t/editors/BiomartQueryEditor.java:
15:51 CIA-43 bioclipse: [BiomartQueryEditor.java]
15:51 CIA-43 bioclipse: * whitespace nit-picking
15:51 CIA-43 bioclipse: * reconfigured constructors
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