Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-02-05

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All times shown according to UTC.

Time Nick Message
07:36 Gpox joined #bioclipse
08:18 egonw joined #bioclipse
08:19 egonw moin
08:19 zarah oh hai egonw
08:19 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
08:19 egonw @msg
08:19 zarah egonw: 16 h 17 m 41 s ago, maclean said since the console will autocomplete functions, I guess having one for each is best (if a bit tiring to code)
08:55 jonalv joined #bioclipse
08:55 jonalv oh hai
08:55 zarah oh hai jonalv
08:58 egonw hej jonalv
08:58 egonw jonalv: there is a bug in the MF code
08:58 jonalv egonw: MF being what exactly?
08:58 egonw under certain conditions you can get C4H10H10H10O :)
08:59 egonw we had that yesterday when Ola demoed to Christoph
08:59 jonalv okey
08:59 jonalv egonw: so tht must be cdk?
08:59 egonw yes, likely
09:08 jonalv egonw: what should we do about it?
09:08 egonw fix it
09:08 jonalv egonw: how do I recreate the problem?
09:09 egonw have to think about that
09:09 egonw Ola created a molecule from SMILES
09:09 egonw then addeed 3d coord, I think
09:10 egonw Gpox: the maclean-jchempaint branch indeed looks fine for inclusion in jchempaint-primary
09:10 egonw doing so now
09:10 jonalv okey I will try around and see if I can get the problem...
09:10 egonw jonalv: not urgent, just wanted you to know
09:12 edrin joined #bioclipse
09:14 olass joined #bioclipse
09:14 egonw olass: quick sanity check
09:15 egonw +        writer.println("output.. = bin");
09:15 egonw writer.println("bin.includes = META-INF/,\\");
09:15 egonw -        writer.println("               bin/,\\");
09:15 egonw does that look like a proper patch?
09:15 egonw hi edrin
09:15 edrin hi egonw
09:15 olass egonw: for what?
09:15 egonw for build.properties
09:15 olass in what plugin?
09:16 olass all cdk plugins?
09:16 egonw yes
09:16 edrin olass: was the webservices plugin fixed?
09:16 olass edrin: we are looking into it
09:16 olass Gpox could not reproduce my bug
09:17 olass updating and will try to reproduce again
09:17 olass egonw: does it not work now?
09:17 jonalv egonw: seems we get that as soon as we have generated 3d coords...
09:17 olass egonw: I'm not so good at build.props text format
09:18 egonw problem was that all files were duplicated in the exported plugiuns jars
09:18 olass oh, not good
09:18 egonw umm... olass, didn't you file that bug report?
09:18 olass maybe :-)
09:19 olass but the dot must be there, right?
09:19 olass but should bin really be in props?
09:19 olass it's not there in net.bc.ui.build.props
09:19 egonw yes, the dot is still there
09:19 egonw mom
09:19 egonw right
09:20 egonw that's what that patch is doing
09:20 egonw remove bin/ from bin.includes
09:20 olass ok
09:20 egonw ok
09:21 jonalv isn't the first row in an sdf file the name of the molecule?
09:21 egonw google ctfile.pdf
09:21 zarah egonw: http://www.symyx.com/downloa​ds/public/ctfile/ctfile.jsp
09:22 egonw jonalv: follow that link
09:24 egonw everyone: updating cdk.control and cdk.render...
09:24 masak joined #bioclipse
09:24 egonw this *may* be a bumpu ride
09:25 egonw this *may* be a bumpy ride
09:25 jonalv it's going to be a bumpy ride!
09:26 * Gpox prepares to flatten the bumps
09:27 masak jonalv: do you know what "bump" is called in Esperanto?
09:27 zarah masak: You have new messages. Write '/msg zarah @messages' to read them.
09:27 masak @massage
09:27 zarah masak: 17 h 55 m 10 s ago, Dahlo said kolla in http://education.cmb.ki.se/tw​iki/bin/view/Main/TWikiUsers  kolla hur namnen inte �r sorterade in bokstavsordning. Verkar som om alla nyareggade hamnar under C. Inom C �r dock alla i bokstavsordning.. Id�er?
09:27 olass edrin: you there?
09:27 * jonalv is looking at the pubmed sdf file. WHy can't the stupid chemists follow their agreeements?
09:28 jonalv the first line is supposed to be the name
09:28 jonalv it's always a strange number only
09:28 masak jonalv: like '24601' :)
09:28 egonw pubchem cid?
09:28 CIA-55 bioclipse: goglepox * r8594 /bioclipse2/trunk/plugins/n​et.bioclipse.ui/plugin.xml: Changed priority for SMI contenttype
09:28 CIA-55 bioclipse: egonw * r8595 /bioclipse2/trunk/cdk-externals/trunk/ (56 files in 10 dirs): Updated from jchempaint-primary
09:28 edrin olass: yes
09:28 jonalv egonw: well it's like 156
09:28 egonw Gpox: back to you
09:29 egonw jonalv: mom, I'll drop by
09:29 jonalv I am wondering if it's just an index in the file
09:29 CIA-55 bioclipse: goglepox * r8596 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (CDKManager.java ICDKManager.java): Added BioclipseUIJob to loadSMILES
09:29 CIA-55 bioclipse: goglepox * r8597 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.business/src/net/bioclip​se/cdk/business/ICDKManager.java: Removed trailing spaces
09:29 CIA-55 bioclipse: goglepox * r8598 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MoleculeTableContentProvider.java: Refactored and added support for .SMI files
09:30 CIA-55 bioclipse: goglepox * r8599 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Added monitor.done() to CDKManager.createSDFIndex
09:30 CIA-55 bioclipse: goglepox * r8600 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Fix for when SD file has missing $$$$ at the end
09:32 masak Gpox, the channel flooder :)
09:32 olass Gpox++ //more flooding please!
09:43 edrin @ping
09:43 zarah edrin: pong
09:51 shk3 joined #bioclipse
10:00 jonalv @pz 407
10:00 zarah http://tinyurl.com/dxe4c9
10:03 CIA-55 bioclipse: egonw * r8601 /bioclipse2/trunk/cdk-externals/trunk/org.opensci​ence.cdk.render/src/org/openscience/cdk/renderer/ (generators/IReactionGenerator.java visitor/IDrawVisitor.java): Updated for missing cdk.module annotation
10:10 egonw Gpox: does that patch help?
10:10 Gpox yes egonw++
10:11 olass egonw: cdk.control does not compile here...
10:11 * olass is updating again
10:12 Gpox olass: wait for my fix
10:12 olass ah
10:18 maclean joined #bioclipse
10:18 maclean hi
10:18 zarah hello maclean, you fantastic person you
10:19 egonw hi maclean
10:19 egonw your branch looked fine for inclusion in jcp-prim
10:19 egonw so, I merged it
10:19 maclean ok cool
10:19 CIA-55 bioclipse: goglepox * r8602 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Removed unused classes
10:19 egonw BC2 is now being updated for the new code
10:19 maclean excellent
10:19 CIA-55 bioclipse: goglepox * r8603 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.ui.sdfeditor/.classpath: Removed org.eclipse.jdt.internal.de​bug.ui.launerStandarVMType from n.bc.cd.ui.sdfeditor's classpath
10:20 CIA-55 bioclipse: goglepox * r8604 /bioclipse2/trunk/plugins/ (6 files in 4 dirs): Integrated new Renderer class from cdk
10:21 CIA-55 bioclipse: goglepox * r8605 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint.view/src/net/bioclipse/cd​k/jchempaint/view/JChemPaintWidget.java: Fits atomContainer to screen
10:21 CIA-55 bioclipse: goglepox * r8606 /bioclipse2/trunk/ (2 files in 2 dirs): Changed from IJava2DRenderer to Renderer due to changes in ChemModelRelay
10:22 CIA-55 bioclipse: goglepox * r8607 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint.view/src/net/bioclipse/cd​k/jchempaint/view/SWTFontManager.java: Implemented new makeFonts() from AbstractFontManager
10:31 CIA-55 bioclipse: egonw * r8608 /bioclipse2/trunk/ (.gitignore makeHelpWebsite.pl): Added script to create the help website, with stuff from the TOC extension points
10:33 CIA-55 bioclipse: jonalv * r8609 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java:
10:33 CIA-55 bioclipse: Now tries PUBCHEM_IUPAC_TRADITIONAL_NAME as name when reading from sdf file
10:33 CIA-55 bioclipse: Also fixed reading of CDKConstants.TITLE which didn't work before because of name confusion between IMolecule interfaces...
10:33 CIA-55 bioclipse: jonalv * r8610 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: removed a few tabs
10:43 CIA-55 bioclipse: goglepox * r8611 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Fixed font and SDF rendering fixes bug #402
10:43 zarah bug #402 | http://tinyurl.com/askhtc
10:45 CIA-55 bioclipse: shk3 * r8612 /bioclipse2/trunk/plugins/​net.bioclipse.nmrshiftdb/ (2 files in 2 dirs): using the newcmlfile wizard in the cheatsheet
10:56 CIA-55 bioclipse: goglepox * r8613 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui.sdfeditor/ (2 files in 2 dirs): Added vecmath dependency to net.bc.cdk.ui.sdfeditor
10:58 maclean_ joined #bioclipse
11:09 masak @pz 77
11:09 zarah http://tinyurl.com/578aen
11:11 maclean_ yaas?
11:11 CIA-55 bioclipse: goglepox * r8614 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MoleculesEditorLabelProvider.java: Changed how 2d coordinates are generated in MoleculeTable
11:11 maclean_ closed, huh, cool.
11:20 * jonalv food
11:21 * masak lunch
11:29 CIA-55 bioclipse: shk3 * r8615 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (CDKManager.java ICDKManager.java): bug #405, #406
11:29 zarah bug #405 | http://tinyurl.com/aprzzz
11:30 CIA-55 bioclipse: shk3 * r8616 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.business.test/src/net/bioclipse/cdk/ (3 files in 2 dirs): bug #405, #406
11:30 zarah bug #405 | http://tinyurl.com/aprzzz
11:43 shk3 olass?
11:47 ChanServ joined #bioclipse
12:15 shk3 olass?
12:19 shk3 olass?
12:19 zarah olass?
12:19 shk3 are you here?
12:20 egonw still at lunch?
12:20 shk3 still?
12:21 shk3 ah ok
12:21 olass sry
12:21 olass I am here
12:22 shk3 hi
12:22 zarah ni hao shk3
12:22 shk3 did you have a look at the cheat sheet problem?
12:22 shk3 you saw my comment in the bug report?
12:24 olass yes, been busy with other things
12:24 olass sort of working my way there
12:24 olass is this urgent?
12:24 shk3 not really
12:24 shk3 was just curious
12:24 olass ok, rest assured it is in my bug list
12:24 shk3 if it is a problem with my setup
12:24 olass :-)
12:25 shk3 or a real one
12:25 * jonalv thinks he suddenly got all bugs...
12:25 olass (which is very long at the moment)
12:25 shk3 anything particular I can help with?
12:25 olass let me look
12:27 maclean_ jonalv : congratulations! :)
12:29 egonw Gpox: when you're back... could you drop by?
12:35 olass shk3: one bug that I'd really appreciate you looking at is bug #364
12:35 olass I can comment on it to get you started
12:36 olass when we ran latest build of bioclispe it complained on some computers that it detected the flag -noUpdate
12:36 olass which definetely was not in the config.ini
12:36 olass so we need to test and see what is wrong
12:37 olass I fear I will not have time for this
12:37 olass shk3: another thing is to write general Bioclipse2 documentation: Help, CheatSheet, intro pages
12:37 maclean_ @bug 364
12:37 zarah http://tinyurl.com/abhapb
12:37 shk3 it's hard to do that for plugins by other people
12:38 shk3 but I will try to improve it
12:38 shk3 btw, I wrote parts of the bioclipse tutorial.
12:38 shk3 have a look please
12:38 shk3 if I missed major things
12:40 olass shk3: sure!
12:40 olass jonalv: maybe shk3 can assist you with some bug?
12:40 * shk3 having lunch first
12:41 jonalv I am not sure...
12:47 CIA-55 bioclipse: ospjuth * r8617 /bioclipse2/trunk/plugins/net.bioc​lipse.data/src/net/bioclipse/data/​wizards/NewDataProjectWizard.java: Fixed bug #337: Install sample data should have a progress bar
12:47 zarah bug #337 | http://tinyurl.com/abvx3t
13:03 CIA-55 bioclipse: egonw * r8618 /bioclipse2/trunk/cdk-externals/trunk/org​.openscience.cdk.control/src/org/openscie​nce/cdk/controller/HighlightModule.java: Take into account the hightlight radius when deciding which atom or bond to hightight: if far away from atoms and bonds, do not highlight anything (needs porting upstream)
13:05 maclean_ egonw: I tried implementing jcp.getRenderingOptions() and it seems to work - did you see the bug commet?
13:05 maclean_ ^comment
13:06 maclean_ (although you have to say jcp.updateView() after each change...)
13:07 maclean_ @bug 369 that is
13:07 zarah http://tinyurl.com/arm5kx
13:07 maclean_ thing is, I can't seem to get fitToScreen to register properly
13:28 maclean_ it occurs to me that the renderer should be listening to changes on the renderer model...
13:42 CIA-55 bioclipse: shk3 * r8619 /bioclipse2/trunk/plugins/net.bioclip​se.ui/html/tutorials/using_help.html: typo
13:54 maclean joined #bioclipse
13:55 shk3 all: is it possible to change workspace in Bioclipse?
13:59 shk3 olass?
13:59 shk3 jonalv?
13:59 shk3 Gpox?
14:09 shk3 anybody?
14:12 shk3 :-(
14:15 maclean huh. shk3 : remember that problem with maaronilide.xml where you couldn't highlight?
14:15 maclean it happens with cyclooctan.mol from the cdk test date
14:15 maclean ^data
14:16 maclean so src/test/data/mdl/cyclooctan.mol
14:16 maclean no highlighting, no mouse clicks...
14:16 shk3 hm
14:17 maclean it just seems to be a molfile, so I can't see why
14:18 maclean also, you can select bonds in the outline pane, but not atoms.
14:18 shk3 strange
14:20 shk3 can't see whats's particular with that file
14:21 maclean I'll file a bug report
14:22 egonw shk3: changing workspace in BC would indeed be nice
14:22 shk3 so it's not possible?
14:23 shk3 how is the workspace determined if bioclipse is run for the first time?
14:24 egonw shk3: I never tried, so don't know if it is possible or note
14:24 egonw shk3: I never tried, so don't know if it is possible or not
14:24 shk3 ok, I will get a coke and then I will ask olass... this is an important issue, it seems
14:25 olass don't know if you can
14:25 olass never tried
14:25 olass never wanted to try
14:25 olass shopuld naturally be possible out of the box
14:26 olass probably just add an action to menu
14:26 egonw right... there is none at this moment
14:27 * maclean has an inkling of a germ of an idea what the problem is
14:28 maclean hmmm okay probably not
14:31 shk3 olass: if i start the download,
14:31 shk3 bc uses the workspace used by eclipse
14:31 shk3 ie the one with the bc checkout in it
14:31 shk3 don't know why
14:32 shk3 but this is bad, especially if there is no way to change it
14:32 shk3 shall I investigate how to enable switching?
14:43 egonw might be nice
14:43 egonw what about this failing unit test?
14:46 shk3 no idea
14:48 maclean dammit dammit dammit
14:49 olass shk3: please do
14:54 CIA-55 bioclipse: shk3 * r8620 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (2 files in 2 dirs): added the switch workspace item (this is supposed to work in exported software only, so can't test right now), some improvements in help.
15:00 egonw olass: ping...
15:01 olass pong
15:01 egonw I would like to do an update of the CDK code
15:01 olass is this the last before 2.0?
15:01 egonw 1.1.4.20090105 -> 1.1.4.100900205
15:01 egonw yes, think so
15:02 olass ok
15:02 egonw we found a possible problem with the DrugBank SDF
15:02 egonw reading in CDK...
15:02 olass oh
15:02 olass yes, that's important
15:02 olass I mean
15:02 egonw which causes the second and third item to not be read properly
15:02 olass I am never against updating cdk
15:02 egonw it will require a db rebuild for metaprint
15:02 olass just donät want to bother sam too much with updating new databases
15:03 egonw right
15:03 olass it takes quite some hours
15:03 olass but on the other hand, it's his job
15:03 olass just send me+him an email with a tag for him to check out in cdk
15:03 egonw ok
15:03 * olass is reading eclipse source
15:13 maclean sounds fun
15:15 * maclean is investigating a severe flaw in the rendering architecture
15:16 * egonw doesn't like the sound of that
15:17 maclean I don't like the sound of it either :(
15:18 maclean it's fine for molecules laid out by the structure diagram generator, but totally not fine for molecules in a larger model coordinate space
15:19 maclean I am making a diagram to illustrate the problem...
15:20 egonw ok
15:52 jonalv joined #bioclipse
16:04 jonalv oh be nice oh bi one
16:04 jonalv oh hai
16:04 zarah hello jonalv, you fantastic person you
16:04 olass hi
16:04 jonalv @thank zarah
16:04 zarah oh hai olass
16:04 zarah zarah: jonalv says thank you
16:04 olass hi
16:04 zarah oh hai olass
16:05 masak oh hai olass
16:05 olass hi
16:05 zarah ni hao olass
16:05 olass hi
16:05 zarah privet olass
16:05 masak :)
16:05 jonalv privet
16:05 olass aaah that's it
16:05 olass I really feel like a privet today
16:05 masak :)
16:05 masak who doesn't?
16:05 maclean a type of hedge?
16:05 masak but you only get them once in a while.
16:05 masak no need to wear the privets out.
16:06 jonalv they don't handle sunlight very good?
16:07 masak they're very warm, even in the winter.
16:20 egonw joined #bioclipse
16:23 * maclean is now moving on to explanatory diagram number 3
16:24 maclean but you'll be glad to know that zooming works in jcp
16:24 maclean (again)
16:35 * masak and jonalv just debugged a statement that finished } } } ); } }));
16:35 masak bit frightening.
16:43 CIA-55 bioclipse: ospjuth * r8621 /bioclipse2/trunk/plugins/net.bioclipse.data/ (9 files in 5 dirs): Working on action to install sample data from intro page. Implemented IIntro action in net.bc.data plugin.
16:43 CIA-55 bioclipse: ospjuth * r8622 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (intro/samples.xml plugin.xml): Refactored samples intro contribution to net.bc.data plugin.
16:43 maclean Attack of the brackets!
16:44 olass gotta run to train
16:44 olass tomorrow I'll be really focused on bugs
16:44 olass bye for now
17:01 maclean ackackack
17:26 masak Popeye, is that you?
17:27 CIA-55 bioclipse: carl_masak * r8623 /bioclipse2/trunk/plugins/net.bioclipse​.scripting/src/net/bioclipse/scripting/ (JsEnvironment.java JsThread.java ScriptingEnvironment.java): [scripting] factored the JsEnv to return Object instead of String
17:27 CIA-55 bioclipse: carl_masak * r8624 /bioclipse2/trunk/plugins/ (7 files in 4 dirs):
17:27 CIA-55 bioclipse: [scripting, scripting.ui] moved stringification to js console
17:27 CIA-55 bioclipse: This involved exporting the js jar from n.b.scripting to n.b.scripting.ui,
17:27 CIA-55 bioclipse: since the stringification involves recognizing and converting from a
17:27 CIA-55 bioclipse: NativeJsObject.
17:28 CIA-55 bioclipse: carl_masak * r8625 /bioclipse2/trunk/plugins/net.bioclipse.scrip​ting.ui/src/net/bioclipse/scripting/ui/views/ (JsConsoleView.java ScriptingConsoleView.java):
17:28 CIA-55 bioclipse: [scripting.ui] started on making molecule list output nicer
17:28 CIA-55 bioclipse: Didn't come all the way yet; trouble with the obligatory splitIntoSeveralLines
17:28 CIA-55 bioclipse: call before actual output.
17:33 egonw_ joined #bioclipse
17:43 edrin egonw_: do you think you have some time to read the current state of the doc?
17:43 edrin There is some text for the taverna plugin missing
17:47 edrin and I would be happy about some comments anyway
17:51 edrin left #bioclipse
18:40 edrin joined #bioclipse
18:57 edrin zarah tell olass pls try webservices plugin/manager again, this works for me
18:57 zarah Consider it noted.
21:22 CIA-55 bioclipse: ospjuth * r8626 /bioclipse2/trunk/plugins/net.bioclipse.data/ (5 files in 3 dirs): Added code to install sample data from welcome page. Also added functionality to downlaod and install extended sample data from welcome page. Closes bug #345.
21:22 zarah bug #345 | http://tinyurl.com/alrqq6

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