Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-04-07

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All times shown according to UTC.

Time Nick Message
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08:24 CIA-43 bioclipse: ospjuth * r5363 /bioclipse2/trunk/plugins/net.bioclipse.bioja​va.ui.test/src/net/bioclipse/biojava/ui/test/ (3 files in 2 dirs): Another attempt to create a test to catch bug 1934611.
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11:04 edrin olas: about the mail you sent me:
11:05 edrin if the server sends the result to the client within the COMPLETED packet i also fear that the data could get lost.
11:07 olas yes
11:07 olas that's what I fear
11:07 edrin on the other hand as far as I know the xmpp service will get an error notification from the routing server that the sent COMPLETE (with the data) did not arrive at the client. However it does not get a notification that the COMPLETED arrived ok...
11:07 olas so I guess I'd vote for option 2 then
11:08 edrin in option one the server could just say "ok, if i do not get an error notification in the next 5 minutes i guess the data arrived well and I am done and delete the process"
11:13 edrin about the chunk thing: i tend to not do this. the implementation is complicated ( no clear y = f(x) design in my opinion). if you want to have an option to access the data in chunks/meaning "the parts of the result that are already done" i would recommend to do it by splitting the job in pieces and make a single Web Service call for each piece. Or you do it in this "pseudo-RESTful" way the Fabio suggested
11:14 olas ok, sounds good
11:16 edrin but I agree, maybe Option 2 is the more save way to do the thing
11:17 edrin another thing, how do you like the presentation? is it simplified enough?
11:30 olas yes, I think so
11:30 olas the only thing I didn't get at first was the client/server interaction on the left
11:30 olas It was not clear why you had a duplicated client and duplicated server
11:31 olas but I got the point later on
11:31 olas otherwise it was great
11:35 CIA-43 bioclipse: ospjuth * r5364 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (CDKManager.java ICDKManager.java): Implemented trivial getSmiles as already on IMolecule. Fixed some warnings.
11:35 CIA-43 bioclipse: ospjuth * r5365 /bioclipse2/trunk/plugins/net.bioclipse.c​dk.business/src/net/bioclipse/cdk/domain/ (CDKMolecule.java ICDKMolecule.java): Implemented CDKMolecule.
11:40 CIA-43 bioclipse: ospjuth * r5366 /bioclipse2/trunk/plugins/net.bioclipse.cdk.​business.test/src/net/bioclipse/cdk/domain/ (. tests/ tests/TestCDKMolecule.java): Tests for CDKMolecule.
11:41 edrin ok:)
11:42 CIA-43 bioclipse: ospjuth * r5367 /bioclipse2/trunk/plugins/net.biocl​ipse.biomoby/src/net/bioclipse/biom​oby/business/BiomobyManager.java: Refactored out section for parsing molecule into List of BiojavaSequence.
12:16 CIA-43 bioclipse: jonalv * r5368 /bioclipse2/trunk/plugins/ (10 files in 7 dirs): Wrote tests for structuredb internal managers
12:27 CIA-43 bioclipse: jonalv * r5369 /bioclipse2/trunk/plugins/net.bioclipse.core/​src/net/bioclipse/core/domain/IMolecule.java: added throws to has3dcoordinates
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12:42 CIA-43 bioclipse: ospjuth * r5370 /bioclipse2/trunk/plugins/net.biocl​ipse.biomoby/src/net/bioclipse/biom​oby/business/BiomobyManager.java: Code cleanup.
12:43 CIA-43 bioclipse: ospjuth * r5371 /bioclipse2/trunk/plugins/n​et.bioclipse.biomoby.tests/ (5 files in 3 dirs): Managed to create a failing test for bug 1934611.
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12:56 CIA-43 bioclipse: ospjuth * r5372 /bioclipse2/trunk/plugins/net.bioclipse.biomoby.​tests/src/net/bioclipse/biomoby/tests/services/ (TestBiolistFromMoby.java TestDBServices.java): Refactored out failing test into its own class.
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13:26 olas egonw: any idea when you will work on the structure view/widget ?
13:26 egonw friday on the train home?
13:26 olas :-)
13:27 egonw I know how desparately you need it...
13:27 egonw can't route time at this moment, unfortunately...
13:27 olas yeah... actually very true
13:27 egonw :(
13:27 olas ack
13:27 egonw let me point you to the SWT code...
13:28 egonw maybe you found that inspiring
13:28 olas not really
13:29 egonw ack
13:29 egonw here's it anyway:
13:29 egonw http://bioclipse.svn.sourceforge.net/viewv​c/bioclipse/bioclipse/trunk/plugins/net.bi​oclipse.cdk.ui/src/net/bioclipse/plugins/s​wt/widgets/JChemPaintView.java?view=log
13:29 egonw that's the SWT widget for viewing 2D structures
13:30 egonw it auto-resizes etc
13:30 egonw useful for tables...
13:30 egonw but can easily be embedded as 'view' in a plain text editor...
13:30 egonw just like the old editor
13:30 olas what is the status of it?
13:31 egonw 'should work'
13:31 olas so the widget is operational??
13:31 egonw this is of rather late in the BC1 tree
13:31 egonw yes
13:31 egonw this one is
13:31 olas but not for bioclispe2 branch?
13:31 olas different CDK?
13:31 egonw depends if swt.Canvas has changed from Eclipse3.2 to 3.3
13:31 olas no idea
13:32 egonw yeah, this one might very well depend on the cdk10 plugin
13:32 egonw that's why I made that one...
13:32 olas does the new renderer not work for the latest cdk?
13:33 olas or is it the SWT portion of it that's outdated?
13:33 olas I mean, what needs to be done to get that vew to work in bc2?
13:33 olas was that the launchpad thingy?
13:33 egonw this is using the old renderer
13:33 egonw the new renderer's ETA is this summer
13:33 olas but the new renderer works, right?
13:33 egonw yes
13:33 olas now or this summer?
13:34 olas how can the ETA be this summer if it already works?
13:34 egonw now, but it's not overly functional...
13:34 olas oh
13:34 egonw bond orders, atom symbols etc work
13:34 egonw not sure about bond wedges
13:34 egonw likely needs some debugging... etc
13:34 olas is there a unit test for the renderer?
13:34 egonw that's tricky...
13:34 egonw (aka 'no')
13:36 olas any code snippet for me to start with?
13:36 olas the old gui code?
13:36 * olas wabt a structure view in bc2, even if it's not fully functional
13:38 egonw olas: will work on this asap (maybe this weekend, otherwise the weekend after that)
13:38 olas thanks egon
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14:38 edrin ola, did we apply for Summer of code this year?
14:39 edrin i think not
14:41 olas no :-(
14:41 olas I had nop time at that time
14:41 * olas is really really busy these days
14:42 edrin yes
14:42 edrin writing a paper?
14:43 egonw I submitted Bioclipse, IIRC
14:44 edrin ah
14:44 edrin also this year=?
14:44 egonw no
14:44 edrin ok
14:45 edrin we should try next year again ;)
14:48 olas yes, we really should
14:58 CIA-43 bioclipse: jonalv * r5373 /bioclipse2/trunk/plugins/net.bioclipse.​biomoby.tests/src/net/bioclipse/biomoby/​tests/services/TestBiolistFromMoby.java: read (and refactored) testParseItoBiolistOSGI. The problem seems to be with the biojava plugin.
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15:13 CIA-43 bioclipse: ospjuth * r5374 /bioclipse2/trunk/plugins/net.bioclipse.services/ (3 files in 2 dirs):
15:13 CIA-43 bioclipse: Added Drop support for ServiceView. Demonstrates the dropping of IBioObjects on
15:13 CIA-43 bioclipse: IServiceObjects. If an IFile is dropped, the ContentProvider of the Bioclipse
15:13 CIA-43 bioclipse: Navigator is used to parse the file into an array of IBioObjects that is
15:13 CIA-43 bioclipse: subsequently handed to the IServiceObject.
15:14 olas That was easy!
15:14 egonw_ I guess more work on typing the commit message ? :)
15:14 olas haha
15:14 egonw_ http://proteopedia.org/wiki/index.php/Main_Page
15:14 olas you like explicit commit messages, don't you?
15:14 egonw_ yes, I do
15:15 olas Will now start a moby service if dropped a sequence upon it, then a blog!
15:15 egonw_ cool
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15:40 CIA-43 bioclipse: jonalv * r5375 /bioclipse2/trunk/plugins/net.bioclipse.core/src​/net/bioclipse/recording/WrapInProxyAdvice.java:
15:40 CIA-43 bioclipse: Fix to bug #1934611
15:40 CIA-43 bioclipse: I wrongly thought that I could cache a proxyfactory in the wrap in proxy advice. Now it creates a new factory each time instead and that seems to work.
15:45 edrin indeed cool
15:45 edrin egonw_: do you manage this wiki?
15:45 edrin proteopedia
15:46 CIA-43 bioclipse: jonalv * r5376 /bioclipse2/trunk/plugins/net.bioclipse.​core.tests/net.bioclipse.recording/net/b​ioclipse/core/domain/BioListTest.java: removed testBug1934611 since it had absolutely nothing to to with the bug and turned out to test things that are more or less trivially true
15:46 egonw_ edrin: no
15:46 egonw_ but I found it cool
15:46 edrin yes
15:47 egonw_ would be nice if BC2 could scrape these wiki pages, and open 'it'
15:47 edrin yes
15:47 olas yes, scraping is on the todo
15:47 olas I call it "Rich browser"
15:47 edrin is there a current screenshot of bc?
15:47 edrin bc2
15:47 olas hmm, I think not
15:48 olas mom
15:48 olas not really
15:48 edrin ok
15:48 jonalv the "services" one is rather up to date isn't it oals?
15:48 olas will do one for the next blog
15:48 edrin jonalv: url?
15:49 jonalv http://bioclipse.blogspot.com/2008/03/​general-service-infrastructure-in.html
15:49 edrin I need holidays
15:51 jonalv so you can work? ;)
15:52 edrin :D
15:54 olas haha
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16:13 egonw_ olas: http://chem-bla-ics.blogspot.com/2008​/04/cdkmetabolomicschemometrics.html
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16:45 CIA-43 bioclipse: jonalv * r5377 /bioclipse2/trunk/plugins/ (15 files in 6 dirs): Implemented internal business methods. 0 tests passes for this at the moment because foreign key constraints forces me to get at least a mocked auditservice working before any tests will start to pass.
16:48 CIA-43 bioclipse: jonalv * r5378 /bioclipse2/trunk/plugins/net.bioclipse.core​/src/net/bioclipse/core/domain/BioList.java: Added constructor for Biolist taking a list and using a defensively copied copy as the internal list representation.
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