Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-04-04

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All times shown according to UTC.

Time Nick Message
05:29 rojasm joined #bioclipse
06:33 rojasm joined #bioclipse
07:36 olas joined #bioclipse
07:47 egonw joined #bioclipse
08:01 jonalv joined #bioclipse
08:33 CIA-22 bioclipse: jonalv * r5343 /bioclipse2/trunk/plugins/net.bioclipse.st​ructuredb.tests/tests/net/bioclipse/struct​uredb/persistency/dao/GenericDaoTest.java:
08:33 CIA-22 bioclipse: Moved applicationContext.xml back into root of the source folder. Structuredb
08:33 CIA-22 bioclipse: will have double layers of Spring managed classes. A standard Bioclipse manager
08:33 CIA-22 bioclipse: will wrap around many strucutredbInstancemanagers that will be created from
08:33 CIA-22 bioclipse: applicationContext.xml one for each created database instance.
08:34 CIA-22 bioclipse: jonalv * r5344 /bioclipse2/trunk/plugins/​net.bioclipse.structuredb/ (2 files in 2 dirs):
08:34 CIA-22 bioclipse: Moved applicationContext.xml back into root of the source folder. Structuredb
08:34 CIA-22 bioclipse: will have double layers of Spring managed classes. A standard Bioclipse manager
08:34 CIA-22 bioclipse: will wrap around many strucutredbInstancemanagers that will be created from
08:34 CIA-22 bioclipse: applicationContext.xml one for each created database instance.
08:43 CIA-22 bioclipse: jonalv * r5345 /bioclipse2/trunk/plugins/net.bioclipse.s​tructuredb/src/net/bioclipse/structuredb/ (5 files in 2 dirs): business -> privatebusiness
08:45 CIA-22 bioclipse: jonalv * r5346 /bioclipse2/trunk/plugins/net.bioclipse.structure​db/src/net/bioclipse/structuredb/privatebusiness/ (6 files): structuredbManager -> structuredbInstanceManager
08:48 rojasm joined #bioclipse
09:03 CIA-22 bioclipse: jonalv * r5347 /bioclipse2/trunk/plugins/net.bioclipse.structure​db/src/net/bioclipse/structuredb/privatebusiness/ (3 files): Started work on structuredbInstancemanagers
09:03 CIA-22 bioclipse: jonalv * r5348 /bioclipse2/trunk/plugins/net.bioclipse.stru​cturedb/src/net/bioclipse/structuredb/privat​ebusiness/StructuredbInstanceManager.java: Started work on structuredbInstancemanagers
09:07 de_maas joined #BIOCLIPSE
09:27 thomas_ku joined #bioclipse
10:02 CIA-22 bioclipse: jonalv * r5349 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/domain/ICDKMolecule.java: added getAtomcontainer to ICDKMolecule and a small TODO comment (question style)
10:02 CIA-22 bioclipse: jonalv * r5350 /bioclipse2/trunk/plugins/ (8 files in 5 dirs): Work with internal managers
10:03 * jonalv @ lunch
10:15 edrin joined #bioclipse
10:15 edrin hey olas
10:16 edrin available
10:16 edrin ?
10:20 edrin jonalv?
11:07 olas edrin: hi
11:10 edrin olas, I could really need some backing on the standards mailing list now
11:10 edrin http://mail.jabber.org/pipermail/​standards/2008-March/018403.html
11:12 edrin a very positive example, maybe you could write something similar from the once SOAP user point of view (and that you realized your long lasting web services are not easy to implement with SOAP or the not optimal "SOAP over XMPP" spec)
11:12 olas sure
11:12 olas I'll do that right now
11:13 olas do I need to join the ML or can I post anyway?
11:14 olas oh, I need to register.
11:14 olas ok, doing that now
11:15 jonalv edrin?
11:15 edrin :)
11:17 olas hmm
11:17 olas how can I reply to a mail that I never got?
11:17 olas I mean, t oget it in the correct thread?
11:18 olas edrin?
11:19 edrin :/ dunno, maybe just set the correct "subject" ? most of the important readers read the mail in chronological order anyway
11:19 olas ok
11:22 rojasm joined #bioclipse
11:23 CIA-22 bioclipse: jonalv * r5351 /bioclipse2/trunk/plugins/net.bioclipse.s​tructuredb/src/net/bioclipse/structuredb/ (8 files in 2 dirs): changed privatebusiness -> internalbusiness since it doesn't imply as much which masak suggested the first one did...
11:24 olas edrin: about SOAP ofver XMPP
11:24 olas what is the downside of that? A workaround?
11:25 rojasm left #bioclipse
11:27 edrin 1.) it implements SOAP again, this depends the submission of WSDL files again. there is not spec for this in XMPP. in addition to that there is no session based asynchronous notification system... and this is very bad:
11:27 edrin there is a reply to my mail from the original author of SOAP over XMPP where he states this:
11:27 edrin http://mail.jabber.org/pipermail/​standards/2008-March/018397.html
11:27 edrin (quote: " While it's true that in SOAP+XMPP specs there is no asynchronous message exchange pattern (and that was a mistake, though I think it's possible to add a new MEP")
11:29 edrin in my opinion xmpp comes with enough abstraction already, no need for additional SOAP specs. all that is required is a namespace where you can transmit any xml data (representing a data object). my xep proposal even suggests how the schema of this input/output XMLencoded data can be dynamically discovered by the client
11:32 olas edrin: how about soething like this:
11:33 olas anything else I should mention?
11:34 olas In my opinion, Bioclipse will be an excellent showcase for XMPP-based Web services, and we will continue to support this technology in the future.
11:35 edrin <olas> edrin: how about soething like this:
11:35 edrin [13:33:16] <olas> anything else I should mention?
11:35 edrin [13:34:21] <olas>  In my opinion, Bioclipse will be an excellent showcase for XMPP-based Web services, and we will continue to support this technology in the future.
11:35 edrin did i miss something in between?
11:35 olas hmm
11:35 olas w8 for pastebin
11:36 olas http://paste2.org/p/18792
11:37 edrin olas:  looks great,
11:38 edrin i hope this will push it :)
11:38 olas ok, then I'll send it as soon as i get permissions
11:39 edrin great :)
11:49 egonw joined #bioclipse
11:49 olas hi egonw
11:49 egonw hi olas
11:50 olas don't think I congratulated you enough yesterday
11:50 edrin heh :)
11:50 olas Congratulationd Dr. Willighagen!
11:50 egonw thanx guys
11:51 olas Wish I could have been there
11:51 egonw edrin: saw the second +1 from someone on the list... it's going in the right direction :)
11:51 egonw yeah, would have been nice
11:51 olas Are you back at work now?
11:51 egonw no
11:51 egonw at home
11:51 egonw relaxing...
11:52 olas a well deserved vacation... always nice
11:52 egonw yesterday we had a small unconference thingy, and did a bit of QSPR work using R and CDK
11:52 egonw but without Bioclipse
11:52 olas why without?
11:52 egonw not familiar enough with the R interface in R
11:52 olas haha
11:52 egonw ... in Bioclipse
11:52 olas right
11:52 olas what did you do?
11:52 egonw yeah, it would be very much appreciate if some demo presentations can be placed online...
11:53 olas what did you do?
11:53 egonw maybe blogging some cheat sheets or so...
11:53 olas could we have that as a Use-case and try to reproduce it in Bioclispe?
11:53 egonw model chromatographic retention indices...
11:53 egonw will ask the data provider...
11:53 olas If you documented it on the bioclispe wiki as a use-case, that'd be great
11:54 olas we need a good showcase
11:54 egonw well, would have to figure out how to do it in Bioclipse first...
11:54 olas but I fear I need to work on the bioclipse-descriptor thingy in biolcipse2
11:54 egonw no idea at this moment how to get it to read a SDF file of 200 molecules properly...
11:54 olas is that the input?
11:54 egonw then calculate QSAR descriptors and pass this to R...
11:54 olas egonw: that's why I need the use-case!
11:54 egonw actually, we used Rajarshi's rcdk package
11:54 egonw ah, ok :)
11:55 egonw so, a theorical one...
11:55 egonw yeah sure
11:55 olas for a start
11:55 olas step 1: start with an SDFile
11:55 olas step 2 calculate these descriptors...
11:55 egonw right...
11:55 olas and so on
11:55 egonw 1a view the molecules as 2D
11:55 egonw and browse them
11:55 olas damn
11:55 egonw 1b: calculate 3D structures
11:55 olas no JCP
11:56 egonw JCP is an editor
11:56 egonw we don't need editing functionality for this...
11:56 olas we have no viewer either
11:56 egonw sure we do!
11:56 olas not in bc2
11:56 egonw there is the SWT widget based on the new rendere
11:56 olas dows it work?
11:56 egonw that should be trivial to port to BC2
11:56 egonw as it does not depend on any BC1 code
11:56 egonw last time I cheked...
11:57 olas would be really great!
11:57 olas Will you do that?
11:57 egonw BC2 currently has no 2D viewing at all?
11:57 olas no
11:57 olas nothing
11:57 egonw oh...
11:57 olas no chemoinformatics at all
11:57 egonw I thought the 2Dviewing was already in there...
11:57 olas no
11:57 egonw and that just the editor was lacking...
11:57 olas there is no one working on cdk in bioclipse
11:58 olas I hope steinbeck will provide someone soon...
11:58 olas but for now: nothing
11:58 olas 2d viewing is MUCH better than nothing
11:58 egonw yeah, was briefly getting Christoph up to speed with JCP state in trunk/ yesterday
11:58 egonw yes, abosolutely
11:58 edrin egon the second backing +1 comes from a guy i contacted some weeks/month ago after his post to JDEV mailing list
11:58 edrin http://mail.jabber.org/pipermail​/jdev/2007-December/025874.html
12:00 olas egonw: if you can make the 2Dviewer to work, I'll assist with getting it properly into Bioclipse
12:01 olas it will also encourage me to add more chemoinfo stuff
12:01 olas from bc1
12:01 olas right now it fells kinda fruitless :-)
12:01 olas haha
12:01 olas fruitless
12:02 egonw will try...
12:02 egonw too tired now...
12:02 egonw the exhausting is now slowly getting released
12:03 olas take your time to enjoy victory
12:10 CIA-22 bioclipse: ospjuth * r5352 /bioclipse2/trunk/plugins/net.bioclipse.bio​moby.tests/src/net/bioclipse/biomoby/tests/ (old/testBiomoby.java services/TestDBServices.java): Added tests for multiple Biomoby downloads.
12:12 CIA-22 bioclipse: ospjuth * r5353 /bioclipse2/trunk/plugins/net.biocli​pse.biomoby/src/net/bioclipse/biomob​y/services/DownloadGenbankMoby.java: Removed unused class
12:12 CIA-22 bioclipse: ospjuth * r5354 /bioclipse2/trunk/plugins/net.bioclipse.biomoby/ (10 files in 3 dirs): Implemented multiple MobyService calls wrapped in a job. DownloadFromGenbank fully operational.
12:13 egonw cool
12:13 CIA-22 bioclipse: ospjuth * r5355 /bioclipse2/trunk/plugins/net.​bioclipse.services/plugin.xml: Added serviceType for downloadGenbank.
12:20 edrin olas: thanks for your posting :)
12:22 olas hope it helps
12:23 olas and happy I can support your suggestion
12:23 olas REALLY looking forward to doing more XMPP in bioclipse, just so busy with infrastructure now
12:23 olas core stuff in bc2
12:41 CIA-22 bioclipse: jonalv * r5356 /bioclipse2/trunk/plugins/ (10 files in 6 dirs):
12:41 CIA-22 bioclipse: Fixed cascades on delete. Currently I am leaning towards the behavior that a
12:41 CIA-22 bioclipse: structure can be in a library or not in a library and if a library is removed
12:41 CIA-22 bioclipse: the structures in it aren't deleted but merely not in a library any longer. But
12:41 CIA-22 bioclipse: maybe this behavior is more what's expected if a structure could be in many
12:41 CIA-22 bioclipse: libraries? I am a bit uncertain...
16:17 olas left #bioclipse
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21:34 edrin left #bioclipse

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