Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-03-16

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All times shown according to UTC.

Time Nick Message
06:25 sneumann joined #bioclipse
07:45 annzi joined #bioclipse
07:46 Gpox joined #bioclipse
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07:56 sneumann joined #bioclipse
08:46 egonw joined #bioclipse
08:46 egonw moin
08:46 zarah oh hai egonw
08:46 jpansanel moin
08:46 zarah oh hai jpansanel
08:47 egonw jpansanel: any luck on bioclipse.net ?
08:47 jpansanel works agin
08:47 egonw good
08:48 jpansanel egonw: Do you known if Bioclipse is usable for SAR studies ?
08:50 egonw yes it is very much
08:51 jpansanel good
08:51 egonw check my blog post of yesterday
08:51 jpansanel I've written a short article (in french) about FOSS for molecular screening
08:51 egonw it has some relevant links
08:51 jpansanel thx
08:51 egonw ah, cool
08:52 egonw there are three relevant bioclipse features: QSAR, MetaPrint2D, and DS (decision support)
08:52 egonw make sure you check the matching wiki.bioclipse.net pages
08:52 jpansanel very nice
08:52 egonw jpansanel: btw, to what extend are you still working on MyChem?
08:52 egonw actively?
08:52 jpansanel porting to mysql 5.1
08:52 egonw I think jonalv is exploring making a Bioclipse frontend to it...
08:52 egonw as part of his StructureDB project
08:52 jpansanel mysql 5.1 has a new plugin structure
08:53 jpansanel and many security lock
08:53 jpansanel it is hard to write a big plugin like mychem with the new security framework :(
08:53 annzi joined #bioclipse
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10:18 annzi joined #bioclipse
10:24 egonw joined #bioclipse
10:26 egonw Gpox: ping
10:26 Gpox egonw: pong
10:26 egonw throw new IllegalArgumentException("modle must have a resource.");
10:26 egonw patch 3f432b2b118aafa671f10255c080b7e606e7eabf
10:26 egonw 1. Model
10:27 egonw 2. perhaps be a bit more descriptive so that developers getting that Exception get a clue how to fix the problem
10:28 egonw about patch 3103b312562957a41a7f5567a9aa58e3e6a1d887
10:28 egonw calculateCoordianates -> please fix typo
10:29 egonw /FIXME work-around for bug 613 -> please file a new bug ticket for that indicating that that needs to be fixed when 613 is fixed, and mention that new ticket in the source code please
10:29 annzi joined #bioclipse
10:29 CIA-60 bioclipse.cheminformatics: Arvid Berg master * rca436f3 / plugins/net.bioclipse.cdk.ui.sdfeditor​/src/net/bioclipse/cdk/ui/sdfeditor/ed​itor/MoleculeTableContentProvider.java : Increased cache size to 50 - http://bit.ly/driwyN
10:41 CIA-60 bioclipse.rdf: annzi master * r15a4328 / (3 files in 2 dirs): Added convenient methods to the chembl plug-in - http://bit.ly/bmuDky
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11:01 Gpox egonw: fixed
11:02 * egonw is pulling
11:02 egonw fetching, really .)
11:02 egonw :)
11:03 egonw Gpox: almost fixed :)
11:03 egonw model.getResource().getLocationURI()+"dose not exist ");
11:03 egonw missing space + dOEs :)
11:04 CIA-60 bioclipse.cheminformatics: Arvid Berg master * rd368371 / (2 files in 2 dirs): Put 2D-coordiante generation in moltable lookup code instead of in the renderer. - http://bit.ly/9KBmV1
11:04 egonw (you forgot the same typo fix in the commit message I now notice)
11:07 CIA-60 bioclipse.cheminformatics: Arvid Berg master * rc6d2d2b / plugins/net.bioclipse.cdk.ui.sdfeditor​/src/net/bioclipse/cdk/ui/sdfeditor/ed​itor/MoleculeTableContentProvider.java : Cancel task when item is removed from cache. - http://bit.ly/dchSKS
11:24 Gpox egonw: fixed the ' does' too
11:25 CIA-60 bioclipse.cheminformatics: Arvid Berg master * rf662f87 / plugins/net.bioclipse.cdk.ui.sdfedit​or/src/net/bioclipse/cdk/ui/sdfedito​r/business/MoleculeTableManager.java :
11:25 CIA-60 bioclipse.cheminformatics: Added check that file exsists before parsing properties.
11:25 CIA-60 bioclipse.cheminformatics: Solves bug #1612 - http://bit.ly/9o8J1a
11:25 egonw thanx!
11:26 zarah bug #1612 | http://tinyurl.com/y9dn3wy
12:03 egonw jonalv: ping
12:03 egonw jonalv: d'you got a sec?
12:03 egonw if so, can you drop by?
12:27 CIA-60 bioclipse.cheminformatics: Egon Willighagen master * r5c6745b / (2 files in 2 dirs): Fixed copying of properties (fixes #613) - http://bit.ly/c5Cs8x
12:27 zarah bug #0613 | http://tinyurl.com/cm84ht
12:37 CIA-60 bioclipse.cheminformatics: Egon Willighagen master * r40a1f40 / plugins/net.bioclipse.cdk.business.te​st/src/net/bioclipse/cdk/business/tes​t/AbstractCDKManagerPluginTest.java : Updated test; SMILES are not unique or canonical. Instead test for a substring that always be present - http://bit.ly/9TYJH0
12:57 olass joined #bioclipse
13:21 egonw jonalv: ping
13:21 egonw jonalv: another question
13:21 jonalv egonw: shoot
13:21 egonw did the proxy start wrapping bioclipse excepotions in runtime exception?
13:22 jonalv egonw: hm exceptions is a bit of a mess...
13:22 jonalv I think the asnwer is that it depends
13:22 jonalv if you are running as a job then exception handling is done by the proxy yes
13:23 jonalv if not then I have a feeling that there was a special case which hasn\t been fully explored and solved yet
13:27 samuell joined #bioclipse
13:30 jpansanel hi jonalv
13:30 egonw jpansanel: he's a away for fika (:= coffee + cake)
13:46 jpansanel ok
13:51 edrin joined #bioclipse
13:51 edrin hi again
13:56 edrin I will be in Stockholm next week, maybe someone of you will have time for a meeting :) ?
14:08 egonw in stockholm or uppsala?
14:08 egonw around what time?
14:09 egonw btw, still going to the ice hotel?
14:12 edrin egonw: yes
14:12 jonalv edrin: cool
14:12 jonalv :)
14:13 egonw jonalv: jpansanel pinged you earlier
14:13 jonalv egonw: oh. jpansanel: uhm, pong?
14:14 edrin I will fly to Stockholm on Monday and will fly to Kiruna on Thursday
14:14 edrin That means I will be in or around Stockholm on Tuesday and Wednesday
14:14 olass edrin: oh no, I'd love to meet up but I will be in California :(
14:14 jonalv edrin: Kiruna, that\s probably even cooler >(
14:14 jonalv hm wrong layout
14:15 jonalv olass: you going to California next week?
14:15 edrin olass: oh, that's really too bad.
14:15 olass EclipseCon
14:15 jonalv olass: ah right is that already next week.
14:16 olass yes
14:16 olass http://bioclipse.blogspot.com/2010/03/​bioclipse-is-finalist-for-eclipse.html
14:16 zarah olass's link is also http://tinyurl.com/yldwett
14:16 olass edrin: bad timing :(
14:17 egonw edrin: yeah, can't you ask the move the wedding?
14:17 egonw theY move
14:18 edrin I can try, maybe it's too late...
14:18 egonw :)
14:18 edrin heh
14:18 egonw meeting in Uppsala then?
14:18 olass edrin: are you getting married again?
14:18 olass :)
14:19 egonw olass++
14:19 olass in the ice hotel
14:19 edrin yes, however I have to arrange this with my wife
14:19 olass cool
14:19 olass very cool
14:19 edrin olass: .. no it's a friend of my wife who is getting married with a Swedish guy
14:19 edrin ?
14:19 olass ah
14:20 olass cold I guess..
14:20 edrin probably
14:20 olass egonw: pingeling
14:20 egonw wassup?
14:20 edrin otherwise it will be very wet
14:21 edrin yes, however I have to arrange this with my wife <- this was directed to egonw, and not to ola
14:21 egonw edrin: ack
14:22 edrin ;)
14:23 samuell egonw: JFYI: Have asked on smw-devel now about ARC vs RAP
14:23 egonw ack
14:28 * egonw finds himself writing yet another save method in the CDKManager ...
14:29 jonalv &me guesses he is supposed to ask egonw: 'Why? How is this one different?'
14:29 jonalv hm wrong layout again
14:30 egonw sharing code, fixing bugs
14:36 olass egonw: sorry, was interrupted by 2 phone calls
14:36 olass (at the same time)
14:37 olass egonw: you know that bug about QSAR should accept SMILES as input?
14:37 egonw the DnD one?
14:37 olass well... the Add... did not show smiles files
14:37 olass the dialog
14:37 egonw yes, I remember that one too
14:38 olass well, this dialog is from cheminformatics plugin
14:38 olass and teh ChemoinformaticUtils class
14:38 olass isMolecule(...)
14:38 * egonw has a bad feeling about where this is going
14:38 olass so, in order to solve it I need to add smiles content type there
14:38 olass is that ok?
14:39 olass I could send you a patch
14:39 olass and confirm it works
14:40 olass but wanted to clear things out before sending the patch
14:40 olass egonw: what do you think?
14:40 egonw mom
14:40 olass ok
14:40 egonw ok, extending the SUPPORTED_CONTENT_TYPES list, right?
14:41 olass yes, adding the smi content types
14:41 olass smi single and smi multi
14:41 olass since we open them in MoleculesEditor it feels accurate
14:41 egonw yeah, sounds good
14:42 olass ok, pul lrequest coming up
14:42 olass sent
14:44 CIA-60 bioclipse.qsar: Ola Spjuth master * r878ff5c / (15 files in 7 dirs): Added has2d and has3d as attributes on StructureType. - http://bit.ly/cchNPH
14:44 CIA-60 bioclipse.qsar: Ola Spjuth master * rb159dad / (3 files in 3 dirs):
14:44 CIA-60 bioclipse.qsar: Override getNo2D. getNo3D, getNoStructures in ResourceTypeImpl.
14:44 CIA-60 bioclipse.qsar: Also, deprecate addCalculatedProps() method. - http://bit.ly/cR2IpD
14:44 CIA-60 bioclipse.qsar: Ola Spjuth master * r27bebcc / (3 files in 3 dirs): Override getNoMols and adap to overridden model methods has2d and has3d and getNoMols. - http://bit.ly/9l7c7G
14:48 egonw who wrote this CDKManager ?!?!
14:50 jonalv egonw: lot's of people...
14:50 egonw each time I look at it I find a mess
14:51 jonalv egonw: I am afraid it's become too big. There was a time when I read through it and looked at things in it.  Ihave given that up :)
14:52 egonw just spend two hours fixing failing unit tests, and bugs
14:52 jonalv egonw++
14:52 olass egonw++
14:53 CIA-60 bioclipse.cheminformatics: Ola Spjuth master * r4e41b42 / plugins/net.bioclipse.chemoinformat​ics/src/net/bioclipse/chemoinformat​ics/util/ChemoinformaticUtils.java :
14:53 CIA-60 bioclipse.cheminformatics: Added smiles extension for QsarEditor Add... dialog
14:53 CIA-60 bioclipse.cheminformatics: (bug 1883). - http://bit.ly/cYg7Dx
14:53 zarah bug #1883 | http://tinyurl.com/yfzbn6y
14:53 egonw I wish people would just run those bloody test suites :(
14:54 egonw yeah, I am looking at you
14:54 olass me?
14:54 olass *gulp*
14:55 egonw :)
14:55 * jonalv whishes we had nightly run of the test suites
14:55 masak *gulp*
14:55 egonw jonalv: the test run for the CDK manager takes less than a minute
14:55 * jonalv looks at that sentence and feels that he can write better english than that
14:55 jonalv egonw: still
14:56 jonalv it's not so much the time though...
14:56 egonw true
14:56 egonw it's mostly Eclipse not wanting to run the tests at all
14:56 egonw I know
14:58 * egonw notes that Gpox's patch make the mol table performance nice again
14:58 egonw Gpox++ (for fixing it)
14:58 egonw Gpox-- (for breaking it in the first place)
14:58 egonw (just to discourage people intentionally breaking things, to fix it then again, and gain free karma)
14:58 egonw yes, I am looking at you
15:01 olass *gulp*
15:01 * olass hides
15:04 annzi joined #bioclipse
15:51 jonalv zarah: seen jpansanel ?
15:51 zarah I have not seen jpansanel
15:52 jonalv egonw: didn't you say that jpansanel pinged me?
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