Camelia, the Perl 6 bug

IRC log for #bioclipse, 2012-03-19

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All times shown according to UTC.

Time Nick Message
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10:30 CIA-137 bioclipse.core: Arvid Berg 2.5.x * r03dafc9 / net.bioclipse.target.platf​orm/target-platform.target : Re-aded missing bundles because of target platform editor behaviour - http://git.io/vrvJjA
10:30 CIA-137 bioclipse.core: Arvid Berg 2.5.x * r51b3f45 / (7 files): Moved to net.bioclipse.cml.tests - http://git.io/8iol0A
10:32 CIA-137 bioclipse.cheminformatics: Arvid Berg 2.5.x * re9b7476 / (8 files in 2 dirs): Moved missing tests files from net.bioclipse.ui.tests - http://git.io/TOlK3g
10:32 CIA-137 bioclipse.cheminformatics: Arvid Berg 2.5.x * rf246447 / (2 files in 2 dirs): Changed from cmlxom to net.bioclipse.comxom bundle - http://git.io/nVxsBQ
10:34 CIA-137 bioclipse.cheminformatics: Arvid Berg 2.5.x * rc266d3c / plugins/net.bioclipse.inchi.business.te​st/src/net/bioclipse/inchi/business/tes​t/AbstractInChIManagerPluginTest.java :
10:34 CIA-137 bioclipse.cheminformatics: Enabled InChI tests agin
10:34 CIA-137 bioclipse.cheminformatics: bug 3024 - http://git.io/z6q0mA
10:34 zarah bug #3024 | http://pele.farmbio.uu.se/bug​zilla36/show_bug.cgi?id=3024
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10:55 egonw Gpox++ (for the InChI fixing. Thanx!)
10:57 Gpox also fixed the cml error in the tests so now itis only 8 that fails
10:58 egonw good work!
11:03 Gpox Now to try and fix the jcp rendering...
11:04 egonw even better :)
11:04 egonw there are some glitches indeed
11:06 Gpox a little more that a glitch, the IRenderer hierarchy is totaly broken
11:06 egonw yeah, that might be it :)
11:06 egonw things are a bit more explicit now, indeed
11:07 egonw we did fix some propagation of properties, but not all indeed
11:09 Gpox AbstractRenderer is not nestable as it holds state about draw coordiantes and transforms
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12:28 olass egonw: about the InChI... what is the state now?
12:28 olass did you understand the hydrogen problem?
12:28 olass or managed to work around it?
13:15 olass egonw: ping
13:37 egonw pong: no, no progress
13:37 olass ok
13:37 egonw the deduce bond system tool patch by Kevin doesn't fix your problem
13:38 olass so right now we generate incorrect inchi in Bioclipse?
13:38 egonw and yesterday got filled with slides for my course in about an hour
13:38 egonw correct
13:38 olass in what cases do we do this?
13:38 olass all cases?
13:38 egonw release blocker, I'd say
13:38 egonw no, some cases
13:38 egonw in case when, no surprise, aromaticity is involved
13:38 egonw but
13:38 egonw not always when arom is involved
13:38 olass the cases with undefined aromaticity?
13:39 egonw no
13:39 olass ok, so what are the cases you'd say?
13:39 egonw if I knew...
13:39 olass do you think we can solve it?
13:40 egonw in time? dunno :(
13:40 olass I just don't know how deep the problem goes
13:40 egonw I'm putting more hope in the CS webservice
13:40 egonw then we just pass SMILES
13:40 egonw neither do I
13:40 olass for DS in chembl-rdf, yes
13:40 egonw I had hoped to explore that this weekend
13:40 olass do we need to remove inchi from Bioclipse for 2.6 release?
13:41 egonw depends on when the release is
13:41 olass we are talking weeks, not months...
13:42 olass would really be a shame if inchi had to be dropped...
13:42 olass but better drop than generate an incorrect inchi
13:42 egonw agreed
13:42 olass is we could pinpoint the problem we could output for these mols "could not generate inchi"
13:42 egonw we don't have to decide right now
13:42 olass true
13:42 olass ok, bbl
13:43 egonw I can think of a few workarounds
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14:15 olass o/
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