Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-06-03

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All times shown according to UTC.

Time Nick Message
06:31 Gpox joined #bioclipse
06:48 olass joined #bioclipse
06:48 olass moin
06:48 zarah hi olass
07:33 CIA-40 bioclipse: ospjuth * r10948 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Added a category "Scripting" and placed New Javascript file under this, with the jsfile icon. Solves 1172.
07:36 CIA-40 bioclipse: ospjuth * r10949 /bioclipse2/trunk/plugins/ne​t.bioclipse.gist/plugin.xml: Placed NewGistWizard in Scripting category.
07:46 CIA-40 bioclipse: ospjuth * r10950 /bioclipse2/trunk/plugins/net.bioclipse.jmol/ (2 files in 2 dirs): Set an icon for JmolModel. Solves #1173.
07:50 CIA-40 bioclipse: ospjuth * r10951 /bioclipse2/trunk/plugins/ne​t.bioclipse.jmol/plugin.xml:
07:50 CIA-40 bioclipse: After suggestions by beta testers, replaced the Jmol icon with a more general
07:50 CIA-40 bioclipse: icon of a 3D molecule. Motivation: Users should not have to know what Jmol is to
07:50 CIA-40 bioclipse: view structures in 3D, and the Icon did not make it clear what it was.
08:01 CIA-40 bioclipse: goglepox * r10952 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Fixed NPE when trying to set global properties.
08:11 shk3 joined #bioclipse
08:39 jonalv joined #bioclipse
08:46 sneumann Hi shk3
08:46 sneumann given the recent addition of the mzML plugin
08:46 sneumann and your previous work in BC1 on the mzData plugin
08:47 sneumann can you imagine hacking SpecMol view of mzML spectra ?
08:50 shk3 i can image
08:51 shk3 imagine
08:51 shk3 addition of the mzML plugin?
08:51 shk3 you added that?
08:55 CIA-40 bioclipse: ospjuth * r10953 /bioclipse2/trunk/plugins/net.bi​oclipse.ui/src/net/bioclipse/ui/ (5 files in 3 dirs): Changed UpdateDialog settings to be stored as plugin preferences and not DialogSettings. Solves #1120.
08:56 CIA-40 bioclipse: ospjuth * r10954 /bioclipse2/trunk/plugins/net.​bioclipse.ds/build.properties: Added all icons and contexts to build.props.
08:59 CIA-40 bioclipse: ospjuth * r10955 /bioclipse2/trunk/ (12 files in 12 dirs): Set version to 2.0.0.RC1 for release candidate 1.
08:59 CIA-40 bioclipse: ospjuth * r10956 /bioclipse2/trunk/plugins/net.bioclips​e.doc.developers/META-INF/MANIFEST.MF: Set version to 2.0.0.RC1 for release candidate 1.
09:01 CIA-40 bioclipse: ospjuth * r10957 /bioclipse2/trunk/plugins/ (4 files in 4 dirs): Set version to 2.0.0.RC1 for release candidate 1.
09:02 CIA-40 bioclipse: ospjuth * r10958 /bioclipse2/trunk/features/net.bioclip​se.platform_feature/bioclipse.product: Set version to 2.0.0.RC1 for release candidate 1.
09:02 CIA-40 bioclipse: ospjuth * r10959 /bioclipse2/trunk/features/net.bioc​lipse.platform_feature/feature.xml: Set correct features for RC1 export.
09:03 sneumann shk3: it is in the n.b.massbank_feature ;-)
09:03 sneumann shk3: it is in the n.b.massspec_feature ;-)
09:04 sneumann (Freud'scher Vertipper :-)
09:04 shk3 just checked out
09:04 masak joined #bioclipse
09:06 CIA-40 bioclipse: ospjuth * r10960 /bioclipse2/trunk/plugins/net.bioclipse.c​dk.ui.periodictable/META-INF/MANIFEST.MF: Set version to 2.0.0.RC1 for release candidate 1.
09:06 shk3 do you have sample data?
09:08 sneumann n.b.data.sample.massspec or so
09:08 sneumann also in the massspec_feature
09:08 sneumann ;-)
09:08 sneumann Only thing not working is the update site
09:08 sneumann because I can't export projects a.t.m.
09:08 sneumann because of build problems in the (unrelated ?!) chemoinformatics_feature
09:09 jonalv olass: STOP THE RELEASE!
09:09 jonalv olass: I found a blocker!
09:09 * jonalv starts working on it now
09:09 shk3 doesn't sound too good
09:10 masak jonalv++
09:10 jonalv support for large sdf files has broken down. The maanger methods are not uding returners, shk3 I guess you know what effect that has... Ö=
09:11 shk3 sounds familiar
09:11 masak we should have tests for this...
09:11 jonalv masak: gui tests...
09:11 masak :(
09:12 olass jonalv: good you spotted it
09:13 olass the release will be at 15 if egonw manages to get internet today
09:13 olass if not, release will be at 09.00 tomorrow
09:13 olass since egonw holds blockers'
09:13 * olass is trying an export in the background anyway just to make sure
09:14 jonalv olass: oh okey good
09:14 jonalv olass: I should be able to fix this untill then...
09:14 olass soudns good
09:20 shk3 sneumann: How do i install the sample data? there is no new wizard, it seems
09:22 CIA-40 bioclipse: goglepox * r10961 /bioclipse2/trunk/plugins/net.bioclipse.cdk​.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfe​ditor/business/MoleculeTableManager.java: Added monitor.worked to parseProperties()
09:23 CIA-40 bioclipse: goglepox * r10962 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui​.sdfeditor/src/net/bioclipse/cdk/ui/sdfeditor/ (2 files in 2 dirs): Added setDirty to SDFIndexEditorModel
09:23 CIA-40 bioclipse: goglepox * r10963 /bioclipse2/trunk/plugins/net.bioclipse.cdk​.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfe​ditor/business/MoleculeTableManager.java: Make use of SubMonitor in molTable.saveSDF()
09:24 CIA-40 bioclipse: goglepox * r10964 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MultiPageMoleculesEditorPart.java: Made setDirty() public on MPMoleculeEditor
09:24 CIA-40 bioclipse: goglepox * r10965 /bioclipse2/trunk/plugins/net.bioclipse.cdk.​ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfedi​tor/handlers/CalculatePropertyHandler.java: Mark editor as dirty when calculating properties
09:25 sneumann Um, never did anything with a wizard,
09:25 sneumann but I tried to "install sample data" with the standard BC2 way
09:25 sneumann and the MS data turned up, just worked (tm) ;-)
09:29 shk3 mom
09:30 shk3 ah, it's part of the normal sample data
09:30 shk3 usually, we had separate wizards for specific data
09:31 shk3 like speclipse, medea etc
09:33 shk3 and the editor has no icon, it seems, which can easily be done and looks good
09:37 CIA-40 bioclipse: ospjuth * r10966 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Updated build.props to include all necessary resources for a build.
09:38 CIA-40 bioclipse: ospjuth * r10967 /bioclipse2/trunk/features/net.b​ioclipse.ds_feature/feature.xml: Unpack plugins with data resources upon installation.
09:38 CIA-40 bioclipse: goglepox * r10968 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui.sdfeditor/ (2 files in 2 dirs): Added handler for substructure search
09:39 CIA-40 bioclipse: jonalv * r10969 /bioclipse2/trunk/plugins/net.bioclipse.cdk​.ui.sdfeditor/src/net/bioclipse/cdk/ui/sdfe​ditor/business/MoleculeTableManager.java: Made moleuculeTable.createSDFIndex us a returner. It now runs as a job.
09:40 CIA-40 bioclipse: jonalv * r10970 /bioclipse2/trunk/plugins/net.biocl​ipse.structuredb/src/net/bioclipse/​structuredb/domain/DBMolecule.java: implemented getProperty on DBMolecule but only so that it compiles (throws UnsuppotedOperationException for now)
09:41 CIA-40 bioclipse: jonalv * r10971 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.jchempaint/src/net/bioclipse/cdk​/jchempaint/handlers/UndoHandler.java: Now at least an error message appears for the trouble described in bug: 1182
09:41 zarah bug #1182 | http://tinyurl.com/qefcfq
09:47 CIA-40 bioclipse: ospjuth * r10972 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk.jchempaint/ (icons/chem.png plugin.xml): A new draft for a 2D icon.
09:48 CIA-40 bioclipse: ospjuth * r10973 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui.sdfeditor/ (icons/table16.gif plugin.xml): A new draft for an SDF icon. Missing a chemistry piece in lower right corner.
09:52 jonalv is there an email adress for bugs?
09:52 olass what u mean?
09:53 * jonalv is redoing shk3++s LogUtils.handleException to make it look more like an Eclispe thing and I thought maybe we should add an amail adress of where to send the bug repport as welll...
09:54 jonalv olass: it's the dialog you can pop up when catching an exception that you think never should happend but that still happend. It tells the user that an unexcepted error has occured and tells the user where he can find the log file and I think it should give an email adress of where to send the log file as well...
09:54 shk3 bioclipse-devel?
09:54 jonalv shk3: yea I guess that's the best way...
09:57 CIA-40 bioclipse: carl_masak * r10974 /bioclipse2/trunk/plugins/net.bioc​lipse.biojava.ui/src/net/bioclipse​/biojava/ui/editors/Aligner.java:
09:57 CIA-40 bioclipse: [Aligner] whitespace therapy
09:57 CIA-40 bioclipse: Shortened a couple of hyper-80 lines. There's more work that can be done
09:57 CIA-40 bioclipse: here. The indentation is too extreme and the variable names are quite long.
09:58 olass bioclipse-devel is good enough IMO
09:58 olass will probably not be overly much trafic
09:58 * olass is on lunch
10:08 * olass is back from a quick lunch
10:15 stain lunch munching
10:17 CIA-40 bioclipse: jonalv * r10975 /bioclipse2/trunk/plugins/net.bioclipse.core​/src/net/bioclipse/core/util/LogUtils.java:
10:17 CIA-40 bioclipse: Made LogUtils.handleException pop up an ErrorDialog instead of a MessageDialog
10:17 CIA-40 bioclipse: and added bioclipse-devel@lists.sourceforge.net as email adress where to send an
10:17 CIA-40 bioclipse: error raport. Also made a variant of LogUtils.handleException taking a String
10:17 CIA-40 bioclipse: pluginId of in what plugin the error occured and deprecated the old one.
10:21 olass jonalv: how should these new log-error-methods be used?
10:21 olass could that be written on a wiki page?
10:21 jonalv olass: just as before. HAven't you seen this method before? I am writing a mail to bioclipse devel about it now...
10:22 olass great
10:22 olass no, never seen it
10:22 olass a wiki page would be een better than an email to devel
10:22 olass then email devel with a link to the wiki page
10:23 olass jonalv++
10:41 shk3 great to see you appreciate my code ;-)
10:46 olass jonalv: I get this output
10:46 olass WARN - molTable.createSDFIndex is not void or returning a BioclipseJob. But implementation takes a progress monitor.  Can not run as Job. Running in same thread.
10:46 olass WARN - The MonitorContainer could not find a monitor connected to current thread so returning a NullProgressMonitor
10:46 olass is this fixed in a late commit?
10:47 * olass is running an exported version
10:50 CIA-40 bioclipse: ospjuth * r10976 /bioclipse2/trunk/plugins/net.bioclipse.ds.sm​arts/src/net/bioclipse/ds/smarts/model/impl/ (SmartsInclusiveExclusiveTest.java SmartsMatchingTest.java): Verbose logging when locating native data files.
11:27 jonalv olass: I think so yes
11:27 olass ok
11:27 * olass has now updated
11:27 olass egonw will not get internet today
11:28 olass telia messed up (surprised?)
11:28 olass so RC1 will be tomorrow
11:28 olass early
11:28 olass but eginw is fixing his blockers
11:28 jonalv olass: Gpox and I discussed how to develop substracutresearch over lunch
11:28 olass luckily ge runs git
11:28 olass cool
11:28 jonalv olass: we don't want to break the release...
11:28 olass substracutresearch soudns funny
11:29 olass jonalv: the sooner the better
11:29 jonalv olass: and since we don't run git yet we find that to be a bit unpleasant...
11:51 edrin joined #bioclipse
11:52 masak is net.bioclipse.core.jobs a goner?
11:52 edrin hi
11:52 zarah hello edrin, you fantastic person you
11:52 masak hi edrin.
11:55 masak ah, core.jobs replaced by core.ui.jobs.
11:55 masak in February! :)
11:55 CIA-40 bioclipse: goglepox * r10977 /bioclipse2/trunk/plugins/net.bioclipse.core/src/​net/bioclipse/core/ResourcePathTransformer.java:
11:55 CIA-40 bioclipse: Changed exception handling to give better error message
11:55 CIA-40 bioclipse: parsePath() now throws URIException to get better error message
11:55 CIA-40 bioclipse: The other parse...() methods shoulb probably do the same
11:56 masak olass: ping.
11:56 olass masak: pong
11:57 masak olass: two classes in net.bioclipse.biojava.ui.actions fail to compile.
11:57 olass ok?
11:57 masak olass: FailingLongRunningAction and LongRunningAction.
11:57 * olass does not have biojava checked out
11:57 masak olass: they fail due to a change by you in n.b.core in February.
11:57 jonalv masak: those are so old that they are past deprecation :)
11:57 olass you can safely remove these
11:57 masak jonalv: that was my question. :)
11:57 masak good. removing.
11:57 olass NWO should handle that
11:57 olass in the future
11:58 masak in... *gasp* ...the FUTURE?!
11:58 jonalv masak: I think you might want to rwerite instead of removing though. but I have not looked at it...
11:58 masak jonalv: I'll remove them and see which other things complain. :)
11:58 * jonalv rolls over to masaks screen...
11:59 masak they removed cleanly.
11:59 * masak commits
12:02 jonalv guys, could we add a "new from inchi" wizard as well?
12:02 CIA-40 bioclipse: carl_masak * r10978 /bioclipse2/trunk/plugins/net.bioclipse.bioj​ava.ui/src/net/bioclipse/biojava/ui/actions/ (FailingLongRunningAction.java LongRunningAction.java):
12:02 CIA-40 bioclipse: [n.b.biojava.ui.actions] removed two old classes
12:02 CIA-40 bioclipse: http://irclog.perlgeek.de/bi​oclipse/2009-06-03#i_1205863
12:02 CIA-40 bioclipse: <jonalv> masak: those are so old that they are past deprecation :)
12:02 CIA-40 bioclipse: <olass> you can safely remove these
12:02 zarah CIA-40's link is also http://tinyurl.com/qn7enf
12:03 olass jonalv: is that possible?
12:04 olass does cdk support it?
12:04 olass file a bug for egonw anyway
12:05 maclean joined #bioclipse
12:06 masak maclean: oh hai
12:06 maclean o.h.i
12:06 CIA-40 bioclipse: carl_masak * r10979 /bioclipse2/trunk/plugins/net.bioclipse.script​ing/src/net/bioclipse/scripting/JsThread.java:
12:06 CIA-40 bioclipse: [JsThread] suppressed deprecation warning
12:06 CIA-40 bioclipse: It's the JsThread.this.stop() that's causing it. We should really try to
12:06 CIA-40 bioclipse: find a non-deprecated way to do what we're doing there.
12:08 maclean_ joined #bioclipse
12:09 CIA-40 bioclipse: ospjuth * r10980 /bioclipse2/trunk/plugins/net.bioclipse.ds/s​rc/net/bioclipse/ds/ui/views/TestsView.java: Removed a deprecated method and an unused static variable.
12:12 maclean joined #bioclipse
12:17 CIA-40 bioclipse: goglepox * r10981 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java:
12:17 CIA-40 bioclipse: Added firestructureChagned when undoing and redoing
12:17 CIA-40 bioclipse: Fixes bug #1155
12:17 zarah bug #1155 | http://tinyurl.com/ptb4cr
12:19 CIA-40 bioclipse: ospjuth * r10982 /bioclipse2/trunk/plugins/net.bioclipse.ds.sm​arts/src/net/bioclipse/ds/smarts/model/impl/ (SmartsInclusiveExclusiveTest.java SmartsMatchingTest.java): Major cleanup of error reporting and debugging.
12:19 CIA-40 bioclipse: ospjuth * r10983 /bioclipse2/trunk/plugins/net.biocl​ipse.ds/src/net/bioclipse/ds/model/ (AbstractWarningTest.java IDSTest.java): Added field for errorMessage on initialization of DStests
12:20 CIA-40 bioclipse: ospjuth * r10984 /bioclipse2/trunk/plugins/net.bioclipse.ds/src/ne​t/bioclipse/ds/ui/views/TestsViewDecorator.java: Decorate DSTests and TestRuns if TestErrorMessage exists.
12:21 CIA-40 bioclipse: ospjuth * r10985 /bioclipse2/trunk/plugins/net.bioclipse.ds/s​rc/net/bioclipse/ds/ui/views/TestsView.java: Do not run tests that have TestErrorMessage.
12:22 shk3 olass: what are release plans?
12:22 shk3 I just need to know for speclipse planning
12:22 olass RC1 tomorrow early
12:23 olass RC2 monday next week
12:23 shk3 ok, tomorrow
12:23 olass 2.0 thursday next week
12:23 olass yes, since egonw does not have internet
12:23 olass at home
12:23 olass awaiting his blocker commits
12:24 shk3 ok, no problem
12:24 shk3 just need to do some planning
12:24 shk3 sneumann: around
12:24 shk3 ?
12:24 olass updated http://wiki.bioclipse.net/index.p​hp?title=Bioclipse2_release_plan
12:24 zarah olass's link is also http://tinyurl.com/5guree
12:28 shk3 jonalv: i would try to make the tanimoto calculation a background job (bug #1040)
12:28 shk3 would you be around to help out if I get stuck?
12:28 jonalv shk3: yes
12:28 shk3 thanks
12:28 shk3 i will try and ask if anything is unclear
12:28 olass all: please update http://wiki.bioclipse.net/ind​ex.php?title=Intractable_Bugs if you stumble upon intractable bugs
12:28 zarah olass's link is also http://tinyurl.com/bfhd57
12:29 jonalv I am spending the day hunting for bugs
12:29 olass jonalv++
12:29 jonalv right now I am cleaning up more error messages...
12:29 sneumann shk3: pong
12:29 shk3 pin
12:29 shk3 g
12:29 shk3 I would add mzparsing to spectrum plugin/editor
12:30 shk3 but the speclipse feature needs to depend on massspec for that
12:30 CIA-40 bioclipse: ospjuth * r10986 /bioclipse2/trunk/plugins/net.bioclip​se.ds.dblookup/src/net/bioclipse/ds/d​blookup/impl/DBExactMatchTest.java: Set TestErrorMessage if initialization fails.
12:30 shk3 will you do an update site?
12:30 sneumann I'd say massspec_feature is planned for BC2.1
12:31 shk3 ok
12:31 sneumann Yes, as soon as I can "Build all" on my msbiSite I will
12:31 shk3 then I will leave it out from spectrum till bc2.0 release
12:31 sneumann yes. Get that out of the door,
12:31 sneumann and then add all the cool stuff for 2.1
12:31 shk3 ok
12:31 sneumann That might include some integration between medea et al as well
12:32 sneumann egon has some cool plans
12:32 sneumann I can also (re-)do the mzData plugins
12:32 sneumann but I wanted to get the mzML in shape first
12:32 sneumann becuas I am pretty new to BC2 world
12:33 shk3 sounds good
12:33 shk3 then full steam for bc2.0
12:36 shk3 did you read my comment on the sample data?
12:36 CIA-40 bioclipse: shk3 * r10987 /bioclipse2/trunk/plugins/net.bio​clipse.spectrum/doc/formats.html: removed mzdata related stuff for 2.0
12:37 jonalv shk3: do we really need to print the stack trace to both logger.debug and logger.error in LogUtils.handleException?
12:38 jonalv shk3: logger.error should be enough I think...
12:38 jonalv shk3: do you agree?
12:38 shk3 yes i do
12:38 shk3 no idea why it's on both
12:38 jonalv oki
12:38 CIA-40 bioclipse: carl_masak * r10988 /bioclipse2/trunk/plugins/net.bioc​lipse.biojava.ui/src/net/bioclipse​/biojava/ui/editors/Aligner.java:
12:38 CIA-40 bioclipse: [Aligner] removed some duplication
12:38 CIA-40 bioclipse: This also solved the problem with deep indentation and long variable names.
12:39 maclean olass : could the smarts matcher work on moltables (sdf viewer, whatever it's called)?
12:39 olass in theory, yes
12:39 olass but not implemented yet
12:39 shk3 the cdkmanager is already in nwo, right?
12:39 maclean ah right.
12:40 shk3 i can just transoform the calculatetanimoto using returner etc.?
12:40 maclean I like the new interface/buttons, by the way. I'm slightly hampered by having no idea how to use smarts, though...
12:55 CIA-40 bioclipse: jonalv * r10989 /bioclipse2/trunk/plugins/net.bi​oclipse.core/src/net/bioclipse/ (2 files in 2 dirs): used LogUtils.handleException in the JavaManagerMethodDispatcher class by creating a handleException method taking an already created status
12:55 jonalv shk3: I should hope so yes... :)
12:55 sneumann [14:36] <shk3> did you read my comment on the sample data?
12:55 sneumann which one ?
12:56 shk3 we used to have a new wizard/project per feature (at least that was my undestanding)
12:56 shk3 like medea, speclipse etc.
12:57 shk3 right now, expecting that, one will not necessarily find the mzdata sample data
12:57 sneumann I think I copied the smaple data stuff from one of the other plugins
12:57 sneumann that might be why it ends up with unrelated stuff
12:58 shk3 i will try
12:58 shk3 to add a wizard
12:58 shk3 mom
12:58 masak icons2/ ? wtf?
12:59 CIA-40 bioclipse: shk3 * r10990 /bioclipse2/trunk/plugins/net.bio​clipse.data.speclipse/plugin.xml: better formatting
13:00 CIA-40 bioclipse: goglepox * r10991 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui.sdfeditor/ (2 files in 2 dirs): Created CDKFingerprintPropertyCalculator
13:01 CIA-40 bioclipse: goglepox * r10992 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.ui.sdfeditor/plugin.xml: Added fingerprint calculator to calculated properties and menu molTable menu
13:08 jonalv @pz 1189
13:08 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1189
13:08 jonalv olass: http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1189
13:08 zarah jonalv's link is also http://tinyurl.com/recf62
13:09 CIA-40 bioclipse: shk3 * r10993 /bioclipse2/trunk/plugins/net.bio​clipse.data.massspec/plugin.xml: added a separate wizard for new massspec sample data project
13:10 shk3 btw, I just saw the "general" sample data project is still called "New sample data project"
13:10 shk3 shouldn't we call that "Chemoinformatics sample data project" or so?
13:10 olass please file bugs with clear refs
13:10 shk3 because that's what it is and there are now many other sample data
13:11 olass shk3: please file a bug then
13:11 olass jonalv: must be due to NWO
13:11 olass this needs fixing
13:11 olass jonalv: do you have much to do?
13:11 jonalv olass: also found it threw another exception when having it in Virtual...
13:12 * olass needs help with NWO
13:12 olass jonalv: a bug exists for that already
13:12 jonalv olass: aha good
13:12 * olass needs help with NWO
13:12 jonalv olass: I will take a look at the non-virtual case then..
13:12 olass getting balloon to NWO is important then
13:12 olass jonalv: that is the only case we have
13:12 olass so that sounds good
13:13 olass regarding balloon on virtual: Will do that if I have time
13:13 jonalv olass: uhm it would be nice if it worked from the Virtual folder as well...
13:13 olass regarding balloon on virtual: Will do that if I have time
13:13 jonalv :)
13:13 olass jonalv: there are many things that would be good to have
13:13 olass StructureDB would be good to have
13:14 maclean joined #bioclipse
13:14 jonalv olass: well yes but this is something that is there but does not work. Structuredb is something that is not there at all...
13:14 olass but since Virtual is scheduled for removal, I am not overly eager to spend a lot of time on this
13:14 shk3 jonalv: I need help with nwo as well :-(
13:14 jonalv shk3: what is it now?
13:15 shk3 wrong number of arguments
13:15 shk3 I tried to change the calculatetanimoto in cdk manager
13:15 shk3 to background in line with seneca
13:15 olass shk3: write a unit test
13:15 olass that fails
13:15 shk3 well, i may be doing something wrong
13:15 olass this is how we improve quality of stuff
13:15 jonalv yes that would be really nice if you could do that
13:16 olass shk3: then the unit test will tell
13:16 shk3 sure I can do that
13:16 olass good
13:16 olass the more unit tests the more stable BC2 will be
13:16 shk3 but that means I need to commit my stuff, right?
13:17 jonalv shk3: hm yea but did it work before you changed things?
13:17 shk3 yes
13:17 shk3 that's what worries me :-)
13:17 shk3 but it was not background job stuff
13:19 jonalv aha, if we only had git and branchs... Taht would really help with release job...
13:19 jonalv as it is now we don't dare to fix things that breaks things in the meantime...
13:19 shk3 well, my change would fix a bug report if it would work
13:20 shk3 I suggest I do the test and commit
13:20 shk3 jonalv can have then a look
13:20 shk3 might be easy for him, after all
13:20 shk3 if not, we can revert
13:20 shk3 I can revert
13:20 jonalv well it's not ideal since we are releasing, tomorrow morning was it?
13:21 shk3 yeah
13:21 shk3 well, I suggest we wait till after the release
13:22 jonalv olass: please advice, as things are now we are sort of beginning to not do things and just wait for the release instead...
13:22 olass what is the problem?
13:23 olass if shk3 writes a unit test, what is wrong with that?
13:23 olass balloon must be fixed, as it is in the release
13:23 olass put on SF
13:23 olass that has prio
13:24 olass jonalv: please look at NWO for that manager
13:24 jonalv olass: Tanimoto is also in the release
13:24 olass is there a failing unit test?
13:24 olass jonalv: can you reproduce the error?
13:25 olass outside of seneca?
13:25 jonalv olass: no because if he were to write a failing Unit test he would have to brke the bad implemenation that is there now.
13:25 shk3 brke?
13:25 olass then I cannot advice on that
13:25 olass RC1 is allowed to have bugs
13:26 jonalv olass: there is somthing there now which is sort of working but appharnelty not runnign as a job. shk3 tried to make that work better but failed. If he commits that so I can work on it after I ahve done the balloon manager then he breaks what we have there now.
13:26 jonalv |brake
13:26 olass ok, if you look at balloon first we see how much time is left
13:26 olass shk3: what is the bug number?
13:27 shk3 1040
13:27 olass ok
13:27 olass jonalv: does that sound liek a good idea?
13:27 shk3 @pz 1040
13:27 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1040
13:27 olass ballon first, then new decision?
13:27 olass balloon
13:28 olass damn, we need git for these occasions
13:28 * olass is really starting to see the advantages of git
13:28 jonalv olass: yes...
13:29 olass jonalv: let me know if I can help with balloon to NWO
13:29 jonalv olass: maybe we could make the shift after RC1? :)
13:29 olass right
13:29 jonalv olass: is balloon supposed to be NWO or not?
13:29 olass eh... NO
13:29 olass it is not
13:29 olass jonalv: bug 806
13:30 jonalv olass: hm intresting, maybe better to not move it into NWO right now but just try to fix this buig then?
13:30 olass jonalv: indeed, if it can be solved
13:30 jonalv olass: are you sure it's not NWO?
13:30 olass jonalv: can you not tell?
13:30 * jonalv does not understand what he is looking at right now...
13:30 * olass is not sure
13:31 jonalv the error is in NWO code in the BioclispeJob...
13:31 shk3 ok guys, I leave you to sort this out
13:31 olass quite sure not newest NWO
13:31 shk3 sounds like you need some time
13:31 olass shk3: yes
13:31 jonalv olass: true, it is not in NWO but somehow it stumbles into NWo code. bad
13:32 olass indeed
13:32 jonalv I guess the best I can do is debug it...
13:33 jonalv hm the status of this manager is not very good...
13:39 olass jonalv: how much work to move to NWO? can we do it together today?
13:39 * olass has run into more CDK threading problems...
13:39 jonalv olass: I am beginnign to think that might be a good idea...
13:39 jonalv olass: in balloon?
13:39 olass no
13:39 olass in smartsmatching
13:39 jonalv okey
13:39 jonalv olass: I will try to get it into NWO
13:40 olass great
13:40 jonalv olass: are there any balloon tests?
13:40 olass I'll assist as much as I can
13:40 olass think so
13:40 olass yes
13:40 jonalv plugin tets?
13:40 olass net.bioclipse.balloon.tests
13:40 olass always
13:40 jonalv olass: if you could port them that would be very good...
13:40 olass how do I do that?
13:41 olass will do that after you commit, right?
13:41 jonalv olass: http://wiki.bioclipse.net/index.php?title=H​ow_to_make_a_manager_2#Testing_the_manager
13:41 zarah jonalv's link is also http://tinyurl.com/ouun2r
13:41 jonalv olass: egonw++ wrote that...
13:42 olass looks complicated...
13:42 jonalv olass: it does?
13:42 jonalv good
13:43 * jonalv is happy he is not the only one around here making complicated instructioons...
13:43 jonalv :)
13:45 masak that's not a goal to strive towards! :/
13:46 maclean indeed.
13:47 CIA-40 bioclipse: ospjuth * r10994 /bioclipse2/trunk/plugins/net.bioclip​se.ds/src/net/bioclipse/ds/ui/views/ (TestsViewDecorator.java TestsViewLabelProvider.java): Decorate Tests with errors accordingly.
13:48 CIA-40 bioclipse: ospjuth * r10995 /bioclipse2/trunk/plugins/net.bioclipse.ds.d​blookup/src/net/bioclipse/ds/dblookup/impl/ (DBExactMatchTest.java DBNearestNeighborTest.java): Throw errors on initialization according to new API.
13:48 CIA-40 bioclipse: ospjuth * r10996 /bioclipse2/trunk/plugins/ (4 files in 3 dirs): Fixed error reporting and commented out 2 smarts tests. Until CDK threading is resolved, we can only run one SMARTS test at a time. Sad.
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13:54 jonalv olass: why are not all methods in the IBallonMnager interface public?
13:54 masak olass: r10997
13:55 olass dunno
13:55 masak uh, hold on... conflict. :/
13:55 jonalv olass: so no good reason? Do I make em public?
13:55 ilogger2 joined #bioclipse
13:55 masak here we go. :)
13:55 CIA-40 bioclipse: carl_masak * r10997 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui.sdfeditor/ (3 files in 2 dirs):
13:55 CIA-40 bioclipse: [n.b.cdk.ui.sdfeditor] added table icon with small molecule
13:55 CIA-40 bioclipse: Also set this as the default for SD files in plugin.xml.
13:55 olass jonalv: if you like
13:56 jonalv olass: I will
13:57 olass ok
13:58 masak feedback welcome on that new icon.
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14:10 jonalv olass: it seems to me that the balloonmanager is not working with IFIles at all, Can you comment?
14:16 CIA-40 bioclipse: goglepox * r10998 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MultiPageMoleculesEditorPart.java:
14:16 CIA-40 bioclipse: MultiPageMoleculesEditor derives dirty from jcp
14:16 CIA-40 bioclipse: Fixes bug # 1152
14:20 olass jonalv: no
14:21 olass no comments
14:21 jonalv olass: well this is going to take some time. Much needs to be rewritten...
14:22 * olass thought NWO was optional
14:22 jonalv olass: oh it is but you jsut told me to make this manager into NWO didn't you?
14:22 olass yes?
14:22 jonalv it's going to take a while...
14:23 olass it was an explanation why this has showed up so late..
14:35 jonalv masak: https://bugs.eclipse.org/b​ugs/show_bug.cgi?id=46297
14:36 jonalv oh and everyone else, vote on that bug! :)
14:40 * masak voted
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15:10 maclean masak : icon - I like it.
15:11 masak thanks.
15:26 CIA-40 bioclipse: jonalv * r10999 /bioclipse2/trunk/plugins/net.bioclips​e.balloon.business/src/net/bioclipse/b​alloon/business/IBalloonManager.java: layout
15:27 CIA-40 bioclipse: jonalv * r11000 /bioclipse2/trunk/plugins/net.bioclips​e.balloon.business/src/net/bioclipse/b​alloon/business/BalloonManager.java: layout
15:27 CIA-40 bioclipse: jonalv * r11001 /bioclipse2/trunk/plugins/net.bioclipse​.balloon.tests/src/net/bioclipse/balloo​n/tests/BalloonManagerPluginTests.java: layout
15:28 CIA-40 bioclipse: jonalv * r11002 /bioclipse2/trunk/plugins/ (7 files in 4 dirs): made the balloon manager into NWO. Nothing worked before and nothing works now so I guess I am safe...
15:30 jonalv wtf
15:30 * jonalv verkar inte ha fattat hur git stash funkar
15:30 jonalv oh and that was proabbly the wrong language or the wrong channel, pick one
15:31 maclean something about the git stash not working...
15:31 jonalv maclean: yes it seems like it does not do what I want
15:32 maclean git in not doing what you want it to shock....
15:33 jonalv maclean: sry?
15:35 maclean I just meant that git never seems to do what I want :)
15:35 jonalv oh
15:36 jonalv well I have been agreing with it lately, sort of at least
15:36 jonalv up to right now that is...
15:37 CIA-40 bioclipse: ospjuth * r11003 /bioclipse2/trunk/plugins/net.bioc​lipse.ds.smarts.bursi/plugin.xml: Changed the SMARTS test being run to bursiapprovedCDKcorrected.
15:38 CIA-40 bioclipse: ospjuth * r11004 /bioclipse2/trunk/plugins/net.bioclipse.ds.sm​arts/src/net/bioclipse/ds/smarts/model/impl/ (SmartsInclusiveExclusiveTest.java SmartsMatchingTest.java): Better reporting of invalid SMARTS.
15:43 CIA-40 bioclipse: jonalv * r11005 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): made the balloon manager into NWO. Nothing worked before and nothing works now so I guess I am safe...
15:46 CIA-40 bioclipse: shk3 * r11006 /bioclipse2/trunk/plugins/net.bioclipse​.seneca/src/net/bioclipse/seneca/judge/ (WCCHOSECodeJudge.java WCCNMRShiftDBJudge.java): files do not get overwritten when dropping on judge
15:48 CIA-40 bioclipse: carl_masak * r11007 /bioclipse2/trunk/plugins/net.bi​oclipse.cdk.ui.sdfeditor/icons/ (table16-with-molecule.png table16-with-molecule.xcf):
15:48 CIA-40 bioclipse: [table16-with-molecule] moved mol to southwest corner
15:48 CIA-40 bioclipse: Turned out the VirtualView 'V' obscured it when it was in the southeast one.
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16:14 de__maas1 left #bioclipse
16:25 maclean joined #bioclipse
17:19 CIA-40 bioclipse: ospjuth * r11008 /bioclipse2/trunk/plugins/net.bioclip​se.ds.signsig.bursi/src/net/bioclipse​/ds/signsig/bursi/SignSIcRunner.java: Removed a lot of debugging statements, kept the important ones.
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