Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-04-01

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All times shown according to UTC.

Time Nick Message
05:11 CIA-58 bioclipse: egonw * r9525 /bioclipse2/trunk/plugins/ (3 files in 3 dirs): Added 2D/3D SDF content types (fixes #776)
05:11 zarah bug #776 | http://tinyurl.com/d5khaw
06:14 rojasm joined #bioclipse
06:48 Gpox joined #bioclipse
07:16 egonw joined #bioclipse
07:23 olass joined #bioclipse
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08:10 jonalv joined #bioclipse
08:26 CIA-58 bioclipse: ospjuth * r9526 /bioclipse2/trunk/plugins/net.bioclipse.bibtexml/ (18 files in 5 dirs): Updated generated EMF model after egonws entrytype fix.
08:27 CIA-58 bioclipse: ospjuth * r9527 /bioclipse2/trunk/plugins/n​et.bioclipse.bibtexml.edit/ (11 files in 5 dirs): Updated generated EMF edit code following model update.
08:27 CIA-58 bioclipse: ospjuth * r9528 /bioclipse2/trunk/plugins/ne​t.bioclipse.bibtexml.tests/ (6 files in 3 dirs): Updated generated EMF test code following model update.
08:31 jonalv I hates our wiki. I get lost in it
08:31 jonalv it brings me back to the main page when I log in
08:31 olass jonalv: is that too hard for you?
08:31 olass poor jonalv
08:31 jonalv olass: everything that is not working correctly makes me sad and angry
08:32 jonalv olass: I thought you knew that I am a perfictionist
08:32 olass not when it comes to spelling
08:32 olass smacka
08:32 jonalv touche
08:32 olass :)
08:35 jonalv but I would actually want to say: Not when it comes to spelliong on irc
08:35 jonalv olass: when I am not here I try to spel coretcly
08:35 olass sure
08:36 CIA-58 bioclipse: ospjuth * r9529 /bioclipse2/trunk/plugins/​net.bioclipse.qsar.model/ (42 files in 9 dirs): Removed generated bibtexml code here and import bibtexml plugin instead. Also updated model and generated code after egonw's fix to entrytype in bibtexml schema.
08:37 CIA-58 bioclipse: ospjuth * r9530 /bioclipse2/trunk/plugins/ne​t.bioclipse.qsar.model.edit/ (22 files in 5 dirs): Removed generated bibtexml edit code here and import bibtexml edit plugin instead. Also updated generated edit code.
08:37 CIA-58 bioclipse: ospjuth * r9531 /bioclipse2/trunk/plugins/net.bioclipse.qsar.test/ (5 files in 4 dirs): New model requires updated tests.
08:37 CIA-58 bioclipse: ospjuth * r9532 /bioclipse2/trunk/features/net.bi​oclipse.qsar_feature/feature.xml: Updated feature to comprise required plugins.
08:38 CIA-58 bioclipse: ospjuth * r9533 /bioclipse2/trunk/plugins/net.biocl​ipse.cdk.qsar.test/src/net/bioclips​e/cdk/qsar/test/TestCDKQsar.java: Cleanup of cdk qsar tests.
08:42 olass jonalv: could you look at bug 781 today?
08:42 olass egonw: could you look at bug 780 today?
08:42 olass ballon on win/linux
08:42 jonalv olass: I am writing documentation on managers today
08:42 olass I know, and that's good
08:42 jonalv olass: you told me to do so yesterday...
08:43 jonalv is 781 more important?
08:43 olass testing balloon is fast
08:43 jonalv @pz 781
08:43 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=781
08:43 olass check out, test run
08:43 olass on windows
08:43 jonalv olass: what should I do?
08:43 olass check out baloon feature and required plugins, test run
08:44 olass jonalv: commented in bug 781
08:44 olass how to test
08:45 olass I'd like this to work for the next beta
08:45 olass so we can test multi-platform deployment
08:45 jonalv oki
08:45 olass hmm, will just be an updated update-site but anyway...
08:53 CIA-58 bioclipse: ospjuth * r9534 /bioclipse2/trunk/plugins/net.biocl​ipse.cdk.qsar.test/src/net/bioclips​e/cdk/qsar/test/TestCDKQsar.java: Yup, Gpox++ chnage from loadMolecule(str) to loadMolecule(new MockIFile(str), new NullProgressMonitor()) was needed.
08:59 CIA-58 bioclipse: ospjuth * r9535 /bioclipse2/trunk/plugins/net.bioclipse​.qsar.test/src/net/bioclipse/qsar/test/ (TestRead.java TestWrite.java): Added validation in tests and made test write produce a valid model.
09:01 CIA-58 bioclipse: ospjuth * r9536 /bioclipse2/trunk/plugins/net.b​ioclipse.qsar.test/myQSAR2.xml: Updated produced test qsar.xml.
09:02 egonw jonalv: preposition ?
09:03 jonalv egonw: yes that was the word I suggested so it sounds reasonable...
09:08 Gpox olass: i did not change from 'loadMolecule(str)' i changed form 'loadMolecule( new MockIFile(str), null)'
09:09 olass ok
09:20 * jonalv is working on http://wiki.bioclipse.net/index.​php?title=How_to_make_a_manager
09:20 jonalv feel free to stop by and come with critical comments!
09:20 grandm44 joined #bioclipse
09:24 grandm44 hello all
09:24 zarah hello grandm44, you fantastic person you
09:24 jonalv grandm44: hi
09:25 grandm44 does jmol resquire a new library since today ?
09:25 grandm44 com.sun.j3d
09:25 grandm44 i can't find it on the svn
09:25 * jonalv has no idea...
09:25 jonalv olass: do you know anything about this?
09:26 grandm44 it says the import cannot be resolved :(
09:26 jonalv grandm44: what system are you on?
09:26 grandm44 linux
09:26 olass no idea
09:26 jonalv grandm44: what file uses that class?
09:26 grandm44 The import com.sun.j3d cannot be resolvedJmolEditor.javanet.bioclipse.j​mol/src/net/bioclipse/jmol/editorsline 78Java Problem
09:26 egonw com.sun classes should in general not be used
09:26 jonalv egonw: could I ask you to see if you ahve the same problem on your linux machine?
09:27 egonw have not tried
09:27 egonw but better to only use stuff in java.*
09:27 * jonalv hopes he has not messed up...
09:27 egonw or from a plugin
09:28 jonalv just removed that linbe, it's not being used...
09:32 CIA-58 bioclipse: jonalv * r9537 /bioclipse2/trunk/plugins/net.bioclipse.jmol/s​rc/net/bioclipse/jmol/editors/JmolEditor.java: cleaned up imports
09:32 grandm44 ok thanks it works :)
09:33 jonalv I guess I made that... :)
09:33 jonalv sry...
09:44 CIA-58 bioclipse: ospjuth * r9538 /bioclipse2/trunk/plugins/net.bioclipse.qs​ar.ui/src/net/bioclipse/qsar/ui/editors/: Removed old editor package.
09:45 egonw error: Untracked working tree file 'plugins/net.bioclipse.qsar.model/.s​ettings/org.eclipse.jdt.core.prefs' would be overwritten by merge.
09:46 CIA-58 bioclipse: ospjuth * r9539 /bioclipse2/trunk/plugins/net.bioclipse.qsar.ui/ (24 files in 5 dirs): Updated editor and parsing for new model. This breaks QSAR auto build, needs to be fixed asap.
09:46 egonw olass: please remove the .settings folder from SVN
09:47 egonw jonalv: what's the URL of your new blog?
09:48 olass [10:45] < olass> egonw: could you look at bug 780 today?
09:48 egonw yes, was trying too...
09:48 jonalv egonw: blogspot
09:48 egonw but svn update does not work because of that .settings
09:48 jonalv egonw: http://jonalv.blogspot.com/
09:49 egonw tack
09:49 olass tada
09:49 olass en ny blog
09:50 egonw jonalv: are all your blog items going to start with 'I just'... that would rock ... :)
09:50 jonalv egonw: uhm I don\t know...
09:51 jonalv egonw: it\s a new thing for me. I am trying it out...
09:54 CIA-58 bioclipse: ospjuth * r9540 /bioclipse2/trunk/plugins/net.b​ioclipse.qsar.model/.settings/: Removed per egonw's request
09:54 egonw jonalv: added you to planet.bioclipse.net
09:54 jonalv woho :)
09:56 CIA-58 bioclipse: ospjuth * r9541 /bioclipse2/trunk/plugins/net.b​ioclipse.qsar.model/plugin.xml: Changed extension from qsar to xml.
09:56 olass @planet
09:56 olass nope
09:57 jonalv zarah: tell masak zarah should give a link the the Bioclipse planet on the commando @planet
09:57 zarah Consider it noted.
09:57 egonw http://planet.bioclipse.net
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10:17 olass egonw: What is the easiest way to determine if a file is xml-based?
10:17 egonw dunno
10:17 egonw there is a eclipse xml contenttype
10:17 egonw and a XML root element detector
10:17 olass no, from java
10:17 olass not eclipse
10:17 egonw try reading it with a XML parser
10:18 olass hmm, ok...
10:18 olass thx
10:18 olass lunch
10:36 egonw jonalv: I get a compile error in jmol.cdk
10:36 egonw new JmolListener(part) not defined
10:36 egonw at line 73 of Jmol panel
10:56 edrin joined #bioclipse
10:59 jonalv egonw: yes I have heard about this. It seems to me like that code is not used...
11:05 jonalv egonw: it also seems to like this is an ugly code duplication of the jmol stuff. Do you know what his code is?
11:06 CIA-58 bioclipse: goglepox * r9542 /bioclipse2/trunk/plugins/net.bioclipse.jmol.cdk/​src/net/bioclipse/jmol/cdk/views/JmolPanel.java: Changed from JmolListener(part) to JmolListener(part,viewer) fixes compile error
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11:10 CIA-58 bioclipse: jonalv * r9543 /bioclipse2/trunk/plugins/net.bioclipse.ui.busine​ss/src/net/bioclipse/ui/business/IUIManager.java: method ordering in interface
12:01 CIA-58 bioclipse: ospjuth * r9544 /bioclipse2/trunk/plugins/net.bioclipse.qsar/ (3 files in 2 dirs): Implemented manager methods to add resources to QsarModel and to calulcate transient properties.
12:02 CIA-58 bioclipse: ospjuth * r9545 /bioclipse2/trunk/plugins/net.bioclipse.q​sar.ui/src/net/bioclipse/qsar/ui/editors/ (MoleculesPage.java QsarEditor.java): Fixed MoleculesPage in QsarEditor.
12:05 egonw rojasm1: ping
12:11 egonw edrin: http://xmpp.org/extensions/xep-0263.html
12:11 zarah egonw's link is also http://tinyurl.com/cd9jgs
12:26 edrin egonw: yeah
12:26 edrin indeed a important xep today
12:26 egonw yes, huge step forward in the acceptance of XMPP
12:27 egonw happy to see the finally made this fundamental change
12:28 jonalv w00t! (I think, it soudns like that at least...)
12:47 maclean joined #bioclipse
12:49 egonw hi maclean
12:49 maclean hi egonw
12:50 maclean egonw : do you know anything about jiinchi on 64-bit macs?
12:50 egonw not so much
12:50 maclean ah, right. apparently there's some problem with it - I should test it, I guess.
12:56 * jonalv is beginning to make some progress on http://wiki.bioclipse.net/index.​php?title=How_to_make_a_manager
12:57 egonw http://www.springerlink.com​/content/kt430778npr45t48/
12:57 zarah egonw's link is also http://tinyurl.com/cwwh3y
12:57 egonw Interview with Overington
13:25 maclean okay, so who made the net.bioclipse.jnati or net.sf.jniiinchi plugins? olass?
13:26 egonw I integrated the inchi stuff
13:27 maclean oh, ok
13:29 maclean because I seem to remember testing it. it's weird that it doesn't work from the command line.
13:30 edrin left #bioclipse
13:31 egonw can you file a bug report, so I can test the same on Linux 32bit?
13:31 maclean http://wiki.bioclipse.net/inde​x.php?title=Inchi_in_Bioclipse
13:31 maclean heh
13:31 zarah maclean's link is also http://tinyurl.com/dherce
13:32 maclean well, it probably works on linux 32 bit. it's all down to not finding an executable for the mac 64 bit architecture.
13:35 CIA-58 bioclipse: ospjuth * r9546 /bioclipse2/trunk/plugins/net.bioclipse.q​sar.ui/src/net/bioclipse/qsar/ui/editors/ (DescriptorLabelProvider.java DescriptorsPage.java): Fixed the descriptors page.
13:41 maclean ah, right, it works in bioclipse because that is using java 5.
13:42 maclean or something.
13:55 CIA-58 bioclipse: jonalv * r9547 /bioclipse2/trunk/plugins/net.b​ioclipse.jmol/META-INF/spring/ (context-osgi.xml context.xml): Merged the Spring config XML into one file. No reason to seperate them.
14:16 CIA-58 bioclipse: ospjuth * r9548 /bioclipse2/trunk/plugins/net.bioclipse.​qsar/ontology/descriptor-algorithms.owl: Misspelled protein category.
15:02 rajarshi joined #bioclipse
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15:26 CIA-58 bioclipse: ospjuth * r9549 /bioclipse2/trunk/plugins/net.bioc​lipse.qsar.ui/src/net/bioclipse/qs​ar/ui/editors/ResponsesPage.java: Fixed ResponsesPage.
15:26 CIA-58 bioclipse: ospjuth * r9550 /bioclipse2/trunk/plugins/net.bioc​lipse.qsar.ui/src/net/bioclipse/qs​ar/ui/editors/MoleculesPage.java: Fixed removal of molecules from QsarModel.
15:26 CIA-58 bioclipse: ospjuth * r9551 /bioclipse2/trunk/plugins/net.bioclipse​.qsar/src/net/bioclipse/qsar/business/ (IQsarManager.java QsarManager.java): Added method to remove molecules from qsarmodel in QsarManager.
15:28 olass egonw: around?
15:36 egonw yes
16:48 CIA-58 bioclipse: ospjuth * r9552 /bioclipse2/trunk/plugins/ (9 files in 5 dirs): Set changed to "true" by default for descriptors and structures.
16:58 edrin joined #bioclipse
17:04 CIA-58 bioclipse: ospjuth * r9553 /bioclipse2/trunk/plugins/net.bioclipse.qsar.ui/sr​c/net/bioclipse/qsar/ui/builder/QSARBuilder.java: Advanced Builder to calculate changed combos of mol/descriptor.
17:20 edrin egonw: available?
18:05 egonw hi edrin
18:06 egonw just had a teleconf presentation on:
18:09 edrin egonw: I have now not much time
18:09 egonw neither do I
18:09 egonw so that's a nice match
18:09 egonw :)
18:09 egonw what's up?
18:10 edrin I commmented several things in the current manuscript, is it possible that you check comments and fix where they concern your text?
18:11 egonw yes, will do so as soon as possible...
18:11 edrin (i.e. the cdk/qsar service thing and the taverna abstract)
18:11 egonw VR grant application writing season is alsmost over... (just two weeks left)
18:11 egonw will read your comments tomorrow, OK?
18:12 edrin ok

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