Camelia, the Perl 6 bug

IRC log for #bioclipse, 2013-08-21

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All times shown according to UTC.

Time Nick Message
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07:16 konditorn egonw_: ping
07:17 egonw pong
07:21 egonw what's up?
07:24 konditorn its a small question about downloading from pubChem to BC
07:25 egonw shoot
07:25 egonw but you have to be quick
07:25 konditorn In the dialog for that it's said that you can use an InChI as the query.
07:25 egonw almost in Maastricht (still on the train :)
07:26 egonw that doesn't work (anymore)?
07:26 konditorn oki =)
07:26 egonw let's get a unit tests running on Jenkins for that
07:26 konditorn I don't get anything from pubChem…
07:28 egonw > pubchem.search("acetic acid")
07:28 egonw List<Integer> of size 15
07:28 egonw so, at least that still works
07:28 konditorn it might be that I don't writhe the query right so I'm wondering if you can do a quick check and see if it works for you?
07:28 egonw > pubchem.search("InChI=1S/C2H​4O2/c1-2(3)4/h1H3,(H,3,4)")
07:28 egonw [176, 175]
07:29 egonw ok, so at a script level it works too
07:29 konditorn thats good, I think… =)
07:29 egonw ok, in the dialog searching on an InChI does not work...
07:30 egonw because it uses the search query as a file name, causing it to throw an exception :)
07:30 egonw (because there are slashes in "InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)" which suggests folders that don't exist :)
07:30 egonw idiot... who wrote this code?!
07:30 * egonw has a sneaking suspicion...
07:30 egonw I'll fix this later
07:31 konditorn that's fixed in the new RC… =)
07:31 egonw can you please file a bug report, copy/pasting this chat log?
07:31 egonw ah... good, good
07:31 egonw ok, train station
07:31 egonw ttl
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08:13 Topic for #bioclipse is now #bioclipse An open source workbench for chem- and bioinformatics - http://www.bioclipse.net/ | BioclipseWiki => http://wiki.bioclipse.net/ !! | logs => http://colabti.org/irclogge​r/irclogger_logs/bioclipse & http://moritz.faui2k3.org/irc​log/out.pl?channel=bioclipse
08:14 egonw joined #bioclipse
08:15 egonw konditorn: so, what is already fixed in the RC?
08:16 egonw what exactly...
08:16 egonw and what is still not working?
08:16 * egonw will update his workspace, meanwhile
08:17 konditorn yes, bug 3546
08:17 zarah bug #3546 | http://pele.farmbio.uu.se/bu​gzilla/show_bug.cgi?id=3546
08:18 egonw ah, got it
08:18 konditorn the download, i didn't get any thing 'cos I didn't know how to write the InChI in the query
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09:36 konditorn jonalv, Gpox matdax?
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10:53 Gpox egonw: have you had time to check on http://pele.farmbio.uu.se/jenkins/view/Tests​/job/Bioclipse.test.chemoinformatics/lastCom​pletedBuild/testReport/net.bioclipse.chemoin​formatics.test.feature.AllFeaturePluginTest$​net.bioclipse.cdk.AllCDKBusinessPluginTestSu​ite$net.bioclipse.cdk.business.test/JavaCDKM​anagerPluginTest/testTotalFormalCharge/ ?
10:53 zarah Gpox's link is also http://tinyurl.com/nkjrqe7
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11:31 egonw Gpox: no, and will not before the weekend, earliest
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