Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-02-27

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All times shown according to UTC.

Time Nick Message
04:29 sneumann joined #bioclipse
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07:26 olass joined #bioclipse
07:27 olass moin
07:27 zarah privet olass
07:32 masak privet olass
07:32 olass dobar dan masak
07:32 masak ;)
08:00 egonw joined #bioclipse
08:02 egonw moin
08:02 zarah hello egonw, you fantastic person you
08:02 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
08:02 egonw @msg
08:02 zarah egonw: 17 h 59 m 13 s ago, masak said found a possible bug in org.openscience.cdk.smiles.​SmilesParser.parseString(). it throws a StringIndexOutOfBoundsException when given the empty string.
08:02 zarah egonw: 11 h 17 m 15 s ago, olass said can you confirm cdk plugins (org.openscience.*) have updated IDs for beta3?
08:02 olass hi egonw
08:03 egonw olass: please clarify with you mean with updated org.openscience.cdk.* plugin ids...
08:04 olass well
08:04 olass today is beta3
08:04 olass do all cdk plugins have correct id´s?
08:04 olass Re they 1.1.5?
08:04 egonw but those cdk plugins follow CDK versioning...
08:04 olass yes
08:04 egonw not bioclipse versioning
08:04 egonw yes, they have
08:04 olass are they up to date?
08:04 olass ok
08:04 olass seems people commit to them... renderer for example
08:05 egonw olass: there is one blocker bug...
08:05 egonw I really hope gilleain comes online
08:05 egonw he needs to fix it...
08:05 olass ok
08:05 egonw I tried, without success...
08:05 olass we have all day
08:05 olass well
08:05 olass until 15 I guess
08:05 olass but again egonw
08:05 olass every time someone commits to e.g. cdk.renderer
08:05 Gpox joined #bioclipse
08:06 olass is the version uåpdated then?
08:06 olass or stays at 1.1.5?
08:06 egonw mmm... for all but .control, .render, I think
08:06 olass how do you hanlde them?
08:07 egonw all others are only updated from CDK...
08:07 olass but these 2
08:07 egonw where the exports handles the new ID
08:07 olass need revision
08:07 egonw will bump these two manually
08:07 olass good
08:07 egonw the others are fine
08:07 olass we need to ensure this before every update
08:08 olass else we risk not getting fixes in these to go in online updates
08:08 olass I verify this manually for all bioclipse plugins every time
08:08 olass will try to remember control and renderer in cdk
08:11 CIA-55 bioclipse: egonw * r9116 /bioclipse2/trunk/cdk-externals/trunk/ (2 files in 2 dirs): Manually bumped versions
08:20 grandm44 joined #bioclipse
08:26 olass egonw: I ran the CDKManagerPlugintest again
08:26 olass 4 errors
08:26 olass I think it is the same thing
08:26 * egonw is booting eclipse...
08:26 egonw and will run it too...
08:26 olass NPE on: determineFormat(file.getContentD​escription().getContentType()),
08:27 olass file.getContentDescription() is null
08:27 olass line 567 in CDKManager
08:27 * egonw will see if it fails here too...
08:27 egonw and if so...
08:27 egonw which commit broke those 4 tests...
08:27 olass yup
08:28 egonw it better be me... because I am pissed...
08:28 egonw me -> my commit
08:28 * olass is scared
08:29 olass pretty sure it wasn't me
08:29 egonw let's hope it is just some platform incompatibility... :)
08:29 egonw would not be the first time
08:30 olass very true
08:30 olass but glad we found it in that case
08:33 egonw indeed
08:33 egonw still refreshing...
08:33 egonw btw... I found the cause why my laptop did not recover from suspend
08:33 egonw I was using the server kernel
08:33 egonw to have 4GB instead of 3.5GB
08:33 egonw but that kernel did not have proper suspend support :(
08:34 egonw actually knew that... but did not think of it at the time...
08:34 egonw because the next ubuntu server version 9.04 will have suspend support for servers :)
08:34 egonw and they asked last week for people to test it...
08:35 egonw so, I'll have to compile my own kernel next week ...
08:35 egonw should be fine... been a very long time since I have done that :)
08:37 egonw olass: good and bad news...
08:37 olass good first
08:37 egonw 58/58 working...
08:37 egonw meaning a platform problem
08:38 olass and bad?
08:39 egonw [09:37:10] <egonw> meaning a platform problem
08:39 egonw brb
08:39 olass egonw: where are the content types defined?
08:40 rojasm joined #bioclipse
08:41 olass hmm, net.bc.ui
08:41 olass not so logical
08:41 olass but I can live with that
08:47 CIA-55 bioclipse: goglepox * r9117 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.ui.sdfeditor/src/net/bioclipse/cdk/u​i/sdfeditor/editor/MoleculesEditor.java: Fixed focus
08:49 edrin joined #bioclipse
08:49 edrin hi
08:49 zarah hi edrin
08:57 egonw olass: there is a bug report for moving them...
08:57 egonw please file a bug report regarding the 4 failing tests, and make sure to include a stacktrace...
08:57 olass will do
09:04 olass egonw: bug #607
09:04 egonw @pz #607
09:04 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=607
09:05 egonw OK
09:09 CIA-55 bioclipse: egonw * r9118 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java: OK, reverted once more... while save() was working from an empty resource, it breaks save() a second time...
09:13 olass egonw: any idea about bug 607?
09:14 egonw no, not yet...
09:14 egonw will need to write an additional unit test, I think...
09:14 * olass is in bug report mode
09:14 shk3 joined #bioclipse
09:15 * olass will change to release mode at ~15 if no blocker
09:15 egonw shk3: is gilleain to be available today?
09:16 shk3 I don't know
09:16 shk3 he should
09:17 egonw ok
09:20 shk3 olass: there is this workspace problem
09:20 shk3 for me, the downloaded bioclipse starts
09:20 shk3 with my Eclipse development workspace
09:20 shk3 and there is no way to switch
09:20 shk3 this is not acceptable
09:20 olass shk3: you implemented theswitch, right?
09:20 shk3 I tried to
09:21 olass shk3: you on windows?
09:21 shk3 no, linux
09:21 olass shk3: please test/set/change default workspace location to something more desireable
09:22 olass the default location must come from some place
09:22 olass maybe just set a better one there?
09:22 olass I agree that switch is important
09:22 shk3 I have no idea where it comes from
09:22 olass please search net.bioclipse.ui
09:23 olass hmm
09:23 olass could be logging plugin...
09:23 olass nah
09:24 olass sghk3: hold on, I'll give you a pointer
09:24 olass shk3 I mean
09:24 CIA-55 bioclipse: egonw * r9119 /bioclipse2/trunk/plugins/net.bioc​lipse.chemoinformatics/plugin.xml: Just one New Molecule wizard (see #604)
09:24 olass egonw++
09:25 * olass likey
09:27 shk3 I think we need the switch workspace in any case
09:27 egonw shk3: agreed
09:27 olass yes
09:27 olass but it should start somewhere good on all platforms
09:28 olass users should not have to switch workspace the first time
09:28 egonw my linux download actually did not boot with my eclipse WS
09:28 olass strange no one else has experienced this...
09:28 olass shk3: you might have set it once ther. Once you have set it, it will use it even after reinstallation
09:29 shk3 yeah, might be in some .eclipse file or so
09:29 shk3 egonw: which is the initial workspace for you?
09:29 olass shk3: the bioclispe product has this for Mac os X:
09:29 olass -data "@user.home/Library/Application Support/Bioclipse/Default Workspace/"
09:29 olass there is no such thing for linux or windows
09:30 olass I think this controls it in some way
09:30 shk3 yes
09:30 shk3 -data gives workspace
09:30 shk3 but not used on linux, as you said
09:30 egonw it was a runtime folder inside the zip
09:31 olass shk3: I said, there is no such line in the product
09:31 olass if we add it, it will be used on linux as default WS
09:31 olass but
09:32 olass on linux you have a user dir
09:32 olass makes more sense to put stuff there maybe?
09:32 olass hmm, I guess you have that on mac as well...
09:32 egonw yes, $HOME/.bioclipse
09:32 olass windows I know nothing of
09:32 olass is that default?
09:32 olass hmm
09:32 olass donät like a .bioclipse
09:32 egonw yes, quite common
09:32 olass dot is for metadata
09:32 olass this is actual data
09:32 shk3 should be for config, yes
09:33 egonw yes, $HOME/bioclipse then
09:33 olass shk3: ok, please set this up and try it
09:33 olass try an exported version and make sure to clean first
09:33 * olass has no time to work on that too
09:33 olass egonw: a general question
09:34 olass should generate2DCoordinates(mol) really return a new mol with 2D coordinates?
09:34 olass why not generate the new coords in mol?
09:34 olass is this logical?
09:34 olass to me it isn't...
09:36 egonw check who changed that behavior and bring it up on the mailing list...
09:37 egonw this is very much linked to the design of the scripting language...
09:37 egonw which is scheduled for 2.1
09:37 egonw it's not very logical to me either... but no aware of the reasons why it was made like that
09:38 olass can you change it?
09:38 olass seriaously, you decide
09:38 egonw not without discussion
09:38 olass :-(
09:38 egonw really...
09:38 olass takes too much time
09:38 egonw someone changed this...
09:39 egonw and must have had a good reason
09:39 olass it was me
09:39 olass and I have changed my mind
09:39 egonw it's not very productive to change it back...
09:39 egonw ah...
09:39 olass (I think...)
09:39 egonw check it
09:39 egonw svn annotate
09:39 olass ok
09:39 olass important for beta3
09:40 olass since affects generation in moltable
09:40 olass ok, checking
09:43 olass egonw: jonalv is listed everywhere because of his indentation fixing...
09:43 egonw annotate the version before that...
09:43 egonw mom, let me check syntax
09:44 CIA-55 bioclipse: goglepox * r9120 /bioclipse2/trunk/plugins/ (9 files in 7 dirs): Added generator extension to JCPEditor and JCPView
09:44 olass egonw: I'm using subclipse
09:44 olass just FYI
09:44 egonw ok, go to the command line...
09:44 egonw then type
09:44 egonw svn annotate /path/to/File.java@rev
09:44 CIA-55 bioclipse: goglepox * r9121 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui.sdf​editor/src/net/bioclipse/cdk/ui/sdfeditor/editor/ (3 files): Added get/set Renderer2DConfigurator to MoleculesEditor fixes bug #612
09:44 zarah bug #612 | http://tinyurl.com/cxkyxr
09:45 egonw owhere rev == the last revision of File.java before jonalv patch
09:45 egonw (or find the subclipse equivalent)
09:47 shk3 ok, I added the new default workspace
09:47 shk3 shall I commit this?
09:48 olass shk3: no
09:48 olass please export and verify
09:48 shk3 did so
09:48 olass works?
09:48 shk3 the syntax must be with @user.home
09:48 olass works?
09:48 shk3 $HOME creates a dir called $HOME in home
09:48 shk3 yes
09:49 egonw olass: didn't you commit something yesterday to properly set the resource upon save?
09:49 olass ok, please commit
09:49 olass egonw: yes
09:49 olass added one line in saveMolecules(...)
09:49 olass it was not there
09:49 olass it existsed in saveMolecule(...)
09:49 olass egonw: the null is not that the File is null, it is that the contentdescription is null
09:49 CIA-55 bioclipse: shk3 * r9122 /bioclipse2/trunk/plugins/net.b​ioclipse.ui/bioclipse.product: default workspace for linux now is home/bioclipse
09:50 egonw yes, yes, I know
09:51 egonw mmm...
09:51 egonw can't find what you added...
09:51 * egonw is issuing git log
09:51 olass line 407
09:51 olass //Associate molecule with the file it comes from
09:51 olass mol.setResource( file );
09:52 egonw ha, new lines with tabs :)
09:52 egonw don't let masak see commit a0e902aab78d3b30ffb8fb6cb23373bd91098a23
09:52 olass what!?
09:52 olass I am using his prop file
09:52 olass ssshhh!
09:52 olass donät tell masak
09:52 masak tsk, tsk.
09:52 olass *oops*
09:52 egonw oh no
09:52 * olass pads masak
09:52 olass pats
09:53 egonw now the beta3 has to be delayed
09:53 masak indeed.
09:53 olass because of me?
09:53 egonw we *have* *to* *check* tabs first
09:53 masak svn hook, anyone?
09:53 olass *aaargh*
09:53 olass ask CIA-55
09:54 olass egonw: I can't get svn.annotate to work
09:54 olass can you help me?
09:54 egonw what command did you use?
09:54 olass subclipse
09:54 egonw sorry, don't use subclipse
09:54 egonw no time to install it and all
09:54 olass can you please try?
09:54 olass use CL if you want
09:55 sneumann_ joined #bioclipse
09:55 egonw olass: I'm using git...
09:55 egonw checking how to annotate a particular version with git
09:56 egonw ok, that was easy
09:56 egonw git annotate file revision
09:57 egonw except that it doesn't work :(
09:57 olass git--
09:58 egonw oh, it did...
09:58 egonw jonalv has multiple tab fix commits :)
09:58 egonw was looking at the wrong rev :)
09:59 egonw 5ac50aa8 (ospjuth    2009-01-07 14:07:41 +0000  855)     public IMolecule generate2dCoordinates(IMolecule molecule) throws E
09:59 CIA-55 bioclipse: ospjuth * r9123 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.business.test/src/net/bioclipse/cdk/​business/test/CDKManagerPluginTest.java: Added Junit test to verify properties are stored on generate2D.
09:59 olass you see
09:59 olass it WAS me
10:00 olass and I've changed my mind completely
10:00 olass bug coming up
10:00 egonw no, not convinced yet
10:00 egonw I *should* be looking at ICDKManager
10:00 egonw instead
10:01 egonw it was stefan
10:01 egonw it was stefancommit 6392
10:01 egonw sorry, olass... no shortcut
10:02 CIA-55 bioclipse: goglepox * r9124 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui.sdf​editor/src/net/bioclipse/cdk/ui/sdfeditor/editor/ (MoleculeTableContentProvider.java MoleculeTableViewer.java): Added NatTable.reset() when changing model for MoleculesTable (resolves bug #610)
10:02 zarah bug #610 | http://tinyurl.com/bgbyxl
10:02 egonw -      <plugin id="org.eclipse.update.core.linux"/>
10:02 egonw +      <plugin id="org.eclipse.update.core.linux" fragment="true"/>
10:02 egonw olass: do those changes to .product files hurt?
10:02 egonw in either direction
10:02 jonalv joined #bioclipse
10:04 jonalv oh hai
10:04 zarah saluton jonalv
10:07 olass egonw: what do you mean?
10:07 egonw the @fragment attrib...
10:08 olass ?
10:08 egonw about generate2Dcoords... stefan made that API change, not you...
10:08 olass shk3: why did you do that?
10:08 olass to me it is unintuitive...
10:08 olass shk3: can we change it back?
10:10 shk3 sorry, which change?
10:11 olass void generate2DCoordinates(mol) --> IMolecule generate2DCoordinates(mol)
10:11 olass why return a new molecule?
10:12 olass it saams unintuitive
10:12 olass seems
10:12 shk3 mom
10:12 egonw shk3: commit 6392
10:12 olass then it should be named createNewMoleculeWith2dcoordin​atesFromExistingMolecule(mol)
10:13 olass at least I and egonw think it's unintuitive...
10:13 egonw no
10:13 egonw createNewMoleculeWith2dCoordin​atesFromExistingMolecule(mol)
10:13 egonw proper camel casing please :)
10:13 olass *murmel*
10:13 olass right
10:14 egonw btw, really nice weather outside
10:15 olass yeah, just change the subject :-)
10:15 olass but you are right
10:15 olass here in Stockholm too
10:16 shk3 I can't get this commit from the history
10:16 shk3 so I can't say why I did it
10:16 shk3 should both be possible, I think
10:16 shk3 do what you like
10:17 egonw shk3: look up the commit on SF's SVN web frontend
10:17 * olass wants more coffee
10:18 olass hmm, maybe lunch first?
10:19 olass shk3: please set a path on windows as well
10:19 olass in product
10:19 olass (if you have means to test it)
10:19 olass else file a bug to jonalv
10:20 olass he has parallells
10:20 olass this is not urgent for beta3
10:20 olass but for RC1 it is
10:20 egonw olass: the only things that is urgent is the fix by gilleain of save()
10:20 shk3 can't test it
10:20 egonw but when he is not around :(
10:20 shk3 jonalv needs to do it
10:21 olass where is gilleain?
10:21 shk3 don't knwo
10:21 olass shk3: can you get a hold of him?
10:21 olass call?
10:21 olass IM?
10:22 shk3 I don't have a phone number or so
10:22 shk3 no idea if somebody has
10:22 shk3 I can ask christohp
10:22 shk3 re the coordinates
10:22 shk3 the problem was:
10:23 shk3 if a structure has got 3d coordinates and you generate 2d and set these on the existing structure
10:23 shk3 it was still considered a 3d structure
10:23 shk3 remember, the conent types are either 3d or 2d
10:23 egonw OK, so this is a nice example for a workaround, not a fix
10:23 egonw the proper fix would be:
10:24 shk3 which meant the user got the impression, no 2d were created
10:24 egonw make a 5d data type
10:24 olass is there no 2d AND 3D?
10:24 olass yes
10:24 shk3 no
10:24 egonw olass: no not yet
10:24 shk3 at least there was none
10:24 egonw please file a bug report
10:24 olass will do
10:24 egonw will do that next week
10:24 olass shk3: can you fix this today?
10:24 olass oh
10:24 olass egonw do it?
10:24 olass ok
10:24 olass I filw to egonw then
10:25 egonw shk3: next time... please file a bug report when you find you cannot do something with current stuff
10:26 egonw I mean... creating 2D coordinates should not be solving the problem that one cannot visualize files with both 2D and 3D coordinates
10:28 * egonw is fetching lunch
10:29 CIA-55 bioclipse: ospjuth * r9125 /bioclipse2/trunk/plugins/net.b​ioclipse.ui/bioclipse.product: Updated to use new core feature ID.
10:29 olass shk3: I seriously doubt you have updated features/plugins before that commit to the product
10:30 olass shk3: please update from SVN on a regular basis, at least before making commits to core plugins
10:30 shk3 problem is updating requires an hour of work to get things running again
10:31 olass what!?
10:31 olass incorrect
10:31 olass then you do thins wrong
10:32 CIA-55 bioclipse: goglepox * r9126 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk.jchempaint/ (2 files in 2 dirs): Added CDK(Atom/Bond)ChemObject to fix popupmenu visibility. bug #445
10:32 olass always run from the product
10:32 zarah bug #445 | http://tinyurl.com/bddfwo
10:32 olass not eclipse run config
10:32 olass that solves all my problems
10:38 egonw shk3: how come updating takes so long?
10:38 egonw it SF that slow at the EBI?
10:38 egonw that's not good...
10:38 egonw Gpox: ping...
10:38 Gpox egonw: pong
10:39 egonw do you think you have time to look at that save() problem?
10:39 egonw since I have no hope maclean will show up today
10:40 egonw olass: ping
10:41 olass pong
10:41 egonw commiting two patches
10:41 egonw all unit tests...
10:41 egonw two questions:
10:41 egonw 1. please see if the tests from the first patch run for you
10:42 egonw 2. please check the second patch, and see if those assertions make sense to you
10:42 egonw (they fail for me)
10:42 Gpox egonw: is there a bug for the save problem?
10:42 egonw yes, mom
10:42 egonw @pz save
10:42 CIA-55 bioclipse: goglepox * r9127 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MoleculeTableContentProvider.java: Fixed null check and SMI files now get scrollbar
10:42 zarah [597] New CML files do not save content  http://tinyurl.com/b8rd5s
10:42 zarah [604] Create NewWizard named "New Mol... http://tinyurl.com/bp3fnf
10:42 zarah [607] CDKManagerPluginTest has errors... http://tinyurl.com/bw5ton
10:42 zarah [573] Inconsistent white space for Ja... http://tinyurl.com/cyrecq
10:42 zarah [565] Add this JS-script to example d... http://tinyurl.com/c8tsey
10:42 zarah Entire list (25) at http://tinyurl.com/aepojw
10:43 egonw Gpox: the first one, 597
10:43 egonw I'm around to explain what fails in detail...
10:43 egonw but that bug report has the basic steps to reproduce
10:43 egonw Gpox: also, I tried a patch, but that did not solve it adequately
10:44 egonw rev number should be given in the report
10:46 egonw olass: patches pending... got a merge conflict
10:47 Gpox egonw: there seams to be a problem with adding only rings to the file, it works ok when i use 'Add Bond' and then a ring
10:47 olass egonw: ack
10:47 egonw ah, excellent catch!
10:48 egonw Gpox: so, a problem with adding rings...
10:54 Gpox egonw: yes
10:54 egonw Gpox: can you debug?
10:54 egonw do you have time for that?
10:56 Gpox egonw: I don't know much about the AtomContainer structure 371-378 & 660-663 in ControllerHub
10:57 egonw hang on
10:59 Gpox it adds a ring to a IMoleculeSet but no atoms/bond?
11:00 egonw that should be OK
11:00 egonw a ring is an IAtomContainer...
11:02 Gpox yes but in addRing(IAtom,int) there is some looping over atoms in ring adding them to antoher container
11:02 CIA-55 bioclipse: egonw * r9128 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.business.test/src/net/bioclipse/cdk/​business/test/CDKManagerPluginTest.java: Added unit for testing determining format for files from the workspace
11:02 CIA-55 bioclipse: egonw * r9129 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.business.test/src/net/bioclipse/cdk/​business/test/CDKManagerPluginTest.java: Checks that saveXX() sets the resource
11:04 Gpox egonw: The rings are rendered corectly so it might be in how they are savd, a IMoleculeSet that only contains a IRingSet
11:04 Gpox or IRing
11:04 egonw the latter... yes
11:04 egonw let's try a patch...
11:04 egonw mom
11:04 egonw 664 should read like:
11:05 egonw set.addAtomContainer(ring.getBu​ilder().newAtomContainer(ring))
11:06 egonw olass: ping
11:06 egonw olass: the patches are in SVN now: 9128 and 9129
11:07 egonw Gpox: booting bc
11:08 Gpox egonw: same with 643
11:08 egonw yes, think so...
11:10 egonw no, that does not solve the bug
11:12 egonw Gpox: how is the first bond added?
11:13 egonw btw, I think is should add just a single atom, not a bond
11:15 Gpox 372 in ControllerHub when there is no MoleculeSet
11:16 maclean joined #bioclipse
11:16 maclean egonw : ping
11:16 egonw pon
11:16 egonw +g
11:16 egonw maclean: happy to see you online
11:16 egonw do you have time for debugging, is in *now* ?
11:17 maclean I'm not really meant to be working on bioclipse, you know...
11:17 egonw I know
11:17 egonw then you don't have time...
11:17 egonw I can live with that :)
11:17 egonw this is why I ask
11:18 maclean is it the jchempainteditor.save thing?
11:18 egonw yes
11:18 egonw Gpox and I are looking at it now...
11:18 maclean ok, cool
11:18 egonw Gpox gave some good insight
11:18 maclean I'm sorry, but I don't really understand eclipse save/load stuff anywat
11:18 maclean y
11:19 egonw well, the problem is not there
11:19 maclean oh?
11:19 egonw it's inconsistent models between the hub and the JChempaint editor
11:19 maclean do feel free (of course :) to revert any changes I may have made to the editorwidget that broke things..
11:20 maclean when tidying the class up, I may have changed something
11:21 maclean ah, no, from backlogging, it seems like some problem to do with IRings not being IAtomContainers.
11:22 egonw yes, something like that...
11:22 egonw cdx.debug(jcp.getModel())
11:22 egonw very useful right now :)
11:22 egonw adding a new bond fills the ICDKMOlecule
11:22 egonw but adding a ring on an empty canvas does not
11:23 maclean makes sense - we had problems with this before
11:26 maclean right, so egonw : you and Arvid are handling this, eh?
11:27 egonw yes
11:27 * maclean is going offline in a second...
11:27 maclean okay, cool
11:30 Gpox egonw: CDKMolecule holds one atom container which is saved, when adding a ring not connected to any exisitng atoms it is just added as a new AtomContainer to the set, not to the container that will be saved
11:31 egonw right
11:31 egonw my previous patch synched the CDKMolecule IAtomContainer with the hub
11:31 egonw but that was not so successful
11:31 egonw I now have a patch in the ControllerHub...
11:31 egonw but, I notice that we will be bitten by this again...
11:32 egonw as the hub can create new atomcontainers at various locations...
11:32 egonw e.g. after a zap()...
11:32 egonw but at least saving of rings works now, I think
11:33 egonw yes, seems to work
11:33 egonw I'll commit... please test too
11:34 charlgren joined #bioclipse
11:35 CIA-55 bioclipse: egonw * r9130 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.business.test/src/net/bioclipse/cdk/​business/test/CDKManagerPluginTest.java: Removed duplicate method
11:35 CIA-55 bioclipse: egonw * r9131 /bioclipse2/trunk/cdk-externals/trunk/or​g.openscience.cdk.control/src/org/opensc​ience/cdk/controller/ControllerHub.java: Preferably, add the ring to the already existing first IAtomContainer... it's a bit bad practice, but need right now for Bioclipse... the introduced behavior is consistent with addAtom, which does this too...
11:43 Gpox egonw: Adding unconnected rings works for me
11:43 egonw ok, good
11:44 egonw olass: ping
11:44 egonw Gpox: many thanx for that crucial observation that adding an Atom first did work!
11:44 egonw Gpox++
11:55 olass egonw: pong
11:56 * olass is back from lunch
11:56 egonw olass: please run those unit tests...
11:56 olass ok
12:02 Gpox olass: in testGenerated2D you only check atom properties
12:05 egonw Gpox: something funny just happened...
12:05 egonw in JCPEditor, atom popup
12:05 egonw I could apply a pathc :)
12:05 egonw apparently... some Team contributions sneaked in...
12:05 egonw Compare To -> Local History .. :)
12:06 egonw Gpox: and please teach me how I can attach keys to the editor...
12:06 egonw so that hitting the 'F' while an atom is highlighted changes the symbol...
12:06 egonw like in the JCP applet
12:10 shk3 glad you noticed that
12:10 shk3 it's nice, I think
12:11 egonw yes, Rich' applet has that too...
12:11 egonw I like it very much
12:11 egonw shk3: did you do that perspective yet? if not, I should have it done in a few minutes...
12:11 CIA-55 bioclipse: egonw * r9132 /bioclipse2/trunk/plugins/net.b​ioclipse.nmrshiftdb/plugin.xml: Typo fixed
12:11 egonw will make Bioclipse2 look better
12:12 egonw (as platform)
12:12 shk3 no, not yet done
12:12 shk3 please go ahead
12:12 egonw ok
12:13 olass egonw: I have 4 errors and 4 failures in test now
12:13 egonw good
12:13 egonw that means that my suspicion is right...
12:13 egonw please file the stacktraces...
12:13 olass is null:        Assert.assertNotNull(mol.getResource());
12:13 olass ok
12:13 egonw I need those for gettin further
12:13 olass bug no?
12:14 egonw going to pick up kids from school...
12:14 olass what bug number is it?
12:14 egonw olass: same as before
12:14 egonw just add the stacktraces
12:14 olass which is?
12:14 egonw check IRC log
12:14 olass ok
12:14 egonw you filed it...
12:14 olass I know
12:14 egonw I'll be back in 15 minutes
12:15 olass drive safely
12:15 olass MOHAHAHAHA
12:16 * olass is well aware that egonw has no drivers license
12:35 egonw back
13:00 CIA-55 bioclipse: goglepox * r9133 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.ui.sdfeditor/src/net/bioclipse/cdk/u​i/sdfeditor/editor/JCPCellPainter.java: Default margin in MoleculeTable to 30
13:01 CIA-55 bioclipse: goglepox * r9134 /bioclipse2/trunk/cdk-externals/trunk/​org.openscience.cdk.render/src/org/ope​nscience/cdk/renderer/Renderer.java: Replaced over complicated code to figure out zoom
13:04 CIA-55 bioclipse: goglepox * r9135 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint.view/src/net/bioclipse/cd​k/jchempaint/view/JChemPaintWidget.java: Added SWT.DOUBLE_BUFFERED to JCPWidget
13:07 egonw that sounds like a good patch
13:07 egonw Gpox: can you check that for Jmol too?
13:10 Gpox egonw: done
13:10 egonw thanx!
13:10 CIA-55 bioclipse: goglepox * r9136 /bioclipse2/trunk/plugins/net.bioclipse.jmol/s​rc/net/bioclipse/jmol/editors/JmolEditor.java: Added SWT.DOUBLE_BUFFERED
13:21 CIA-55 bioclipse: egonw * r9137 /bioclipse2/trunk/plugins/ (4 files in 4 dirs): Added a Speclipse perspective and made 'New Spectrum' and 'New SpecMol' show up in the navigator
13:27 egonw shk3: please disable the specmol clone facility...
13:27 egonw as you cannot change the spectrum or molecule anyway
13:28 grandm44 hello
13:28 zarah saluton grandm44
13:29 grandm44 hi bot and others
13:31 egonw hi grandm44
13:32 grandm44 I have a problem (again)
13:32 grandm44 I can't boot Bioclipse anymore
13:32 egonw grandm44: no worries...
13:32 egonw that happens to us all the time too
13:33 grandm44 I had to reinstall eclipse, I updated to 3.4.2 and installed Eclipse SDK and Platform SDK
13:33 egonw oh...
13:33 egonw what happened?
13:33 grandm44 http://bioclipse.pastebin.com/m7ef1291c
13:33 zarah grandm44's link is also http://tinyurl.com/bmxrkc
13:33 grandm44 An update broke eclipse
13:34 egonw ah, ic
13:34 egonw the eclipse update was too slow for me to download any update...
13:34 grandm44 it did not want to start anymore, now it's done but maybe I forgot to reinstall something
13:35 grandm44 Yes ! For me too...
13:35 egonw make sure you have .jsexucate (or so) instead of the .rhino it was named earlier
13:35 grandm44 yes, that's ok
13:36 egonw did you rerun that 'set target platform' ?
13:36 egonw (sure)
13:37 grandm44 i did clean, set target platform, removed all plugin in the run config, saved and add them again.
13:37 egonw please try running it with features
13:37 egonw that works best
13:37 egonw (or is that what you meant?)
13:37 grandm44 yes ;)
13:38 grandm44 i did it via features in bioclipse.product/Configuration
13:38 egonw ok
13:38 egonw any exception trace we can have a look at?
13:39 grandm44 http://bioclipse.pastebin.com/m7ef1291c
13:39 zarah grandm44's link is also http://tinyurl.com/bmxrkc
13:42 egonw ok, I had that one once too...
13:42 egonw try clean, refresh, update, etc... once more
13:42 egonw then another 'set target platform'
13:42 egonw then another removal of all features from bioclipse.product, *save*, adding them again, another save
13:42 egonw after a while it worked again
13:42 egonw without fixes in SVN...
13:43 egonw it's some internal Eclipse thing...
13:43 egonw which makes some config thingy somewhere outdated...
13:43 egonw and make sure you have zero compile errors...
13:43 egonw which you would have noted already...
13:43 egonw oh...
13:43 egonw and make sure you do not have local changes...
13:44 egonw with 'svn update' or so...
13:44 egonw sometimes, one of the config files get emptied here...
13:44 egonw which cause an exception like yours too
13:44 egonw forgot which files it was, though...
13:44 egonw but restoring the one from SVN fixed it in those cases
13:45 grandm44 I think this has nothing to with my problem but I do not use sublipse anymore, only svn from command line and a script I wrote
13:46 grandm44 Maybe it's better to check out all plugins
13:46 grandm44 and erase everything
13:46 egonw grandm44++
13:46 * egonw is not using speclipse either :)
13:46 egonw svn from the command line is easier to monitor
13:46 egonw (via git-svn in my case, btw)
13:48 grandm44 I try to update a very last time, then do all the clean-set target-clean config stuff.
13:48 grandm44 Revision check: all at 9137
13:48 egonw ok
13:49 egonw bioclipse development is a bit of a pain
13:49 egonw we all run into these issues every now and then
13:49 olass it will be much better after we do the Eclipse-plugin to set up the workspace
13:49 egonw twice a month, on average, I'd say...
13:49 egonw but at some point you get a feeling for which action to do to get it working again
13:51 grandm44 like Haitian Vodou for example
13:51 egonw :)
13:52 grandm44 still not working. Wipe mode on.
13:52 olass egonw: are we ready for beta3?
13:53 egonw think so
13:53 olass can we take 15 mins to test the basic stuff?
13:53 egonw only those unit tests for you are failing...
13:53 olass ok, so no luck there?
13:53 olass ok
13:53 egonw not finished yet, no
13:54 egonw let me test one last thing...
13:54 egonw 5 minutes...
13:54 olass it will take me an hour or so to build so we still have time to test things
13:54 egonw who knows...
13:54 egonw ok
13:55 egonw olass: please check the testStoresResource_* unit tests...
13:55 egonw are those assertions correct?
13:55 egonw I really need that info
13:56 olass mom
13:58 olass egonw: looks ok
13:58 olass but do you set the resource in saveMolecule()?
13:58 egonw no, clearly not
13:59 olass that is probably a flaw
14:00 egonw fixing that
14:05 egonw olass: please test this patch
14:05 egonw ...
14:05 olass r?
14:05 CIA-55 bioclipse: egonw * r9138 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Store the resource as property of the CDKMolecule
14:05 olass ah
14:05 egonw :)
14:06 olass that makes the four last tests to pass
14:06 olass but still 4 errors
14:07 olass are you on to something?
14:07 egonw dunno
14:07 egonw at least fixing some things...
14:07 egonw but apparently not the solution to your mac problem...
14:08 egonw ok, which tests still fail?
14:08 olass testSaveMolecule_IMolecule
14:08 olass testSaveMolecule_IMolecule_boolean
14:08 olass testSaveMolecule_IMolecule_String_boolean
14:09 olass testSaveMolecule_IMolecule_IFile_boolean
14:09 olass these 4
14:09 olass boolean seems to be common...
14:09 egonw still the same stacktrace?
14:10 olass yes
14:10 olass file.getContentDescription() is null
14:10 olass 567 in CDKManager
14:10 egonw ok
14:14 * egonw is testing a new unit test
14:14 egonw closing in...
14:17 egonw olass: another test in the next commit, please test
14:17 egonw testStoresResource_ContentType()
14:17 olass ok
14:17 egonw I think that one will fail for you
14:17 CIA-55 bioclipse: egonw * r9139 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.business.test/src/net/bioclipse/cdk/​business/test/CDKManagerPluginTest.java: Added another unit test: make sure getContentType is set...
14:18 olass that passes
14:18 egonw it passes ?
14:18 olass testStoresResource_ContentType
14:18 egonw mmm...
14:18 olass yes
14:18 egonw not good
14:25 jonalv @pz
14:25 zarah jonalv: Pelezilla is at http://bugs.bioclipse.net
14:29 egonw olass: another test
14:29 egonw ...
14:29 egonw commit on its way
14:30 olass sure
14:30 CIA-55 bioclipse: egonw * r9140 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.business.test/src/net/bioclipse/cdk/​business/test/CDKManagerPluginTest.java: OK, another test...
14:30 egonw let's hope this one fails for you
14:31 olass :)
14:31 olass no, passes
14:31 egonw shit
14:33 CIA-55 bioclipse: ospjuth * r9141 /bioclipse2/trunk/plugins/ (5 files in 5 dirs): Set version to 2.0.0.B20090227
14:34 egonw stupid OS/X
14:35 CIA-55 bioclipse: ospjuth * r9142 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui.sdf​editor/src/net/bioclipse/cdk/ui/sdfeditor/editor/ (IRenderer2DConfigurator.java JCPCellPainter.java): RendererConfigurator now operates on AtomContainer.
14:35 CIA-55 bioclipse: ospjuth * r9143 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Set version to 2.0.0.B20090227
14:37 CIA-55 bioclipse: goglepox * r9144 /bioclipse2/trunk/plugins/ (6 files in 5 dirs): Changed to only one generator extension point
14:37 CIA-55 bioclipse: goglepox * r9145 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui.sdf​editor/src/net/bioclipse/cdk/ui/sdfeditor/editor/ (5 files): Enable/disable usaged of extension point generator
14:38 CIA-55 bioclipse: goglepox * r9146 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Made MoleucleTable update when show generator property changed
14:41 egonw olass: testing a workaround here...
14:41 olass ack
14:41 egonw if it does not break anything here, I'll ask you to test
14:41 olass sure
14:41 CIA-55 bioclipse: goglepox * r9147 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.ui.sdfeditor/src/net/bioclipse/cdk/ui/sd​feditor/editor/MoleculeTableViewer.java: Made property columns in MolTable a little larger
14:43 egonw olass: here comes
14:43 CIA-55 bioclipse: egonw * r9148 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Workaround for OS/X which has a stupid bug somewhere... see ERROR send to logger
14:44 egonw please try and let me know if the tests now still fail
14:45 olass ok
14:46 CIA-55 bioclipse: ospjuth * r9149 /bioclipse2/trunk/plugins/ (12 files in 12 dirs): Set version to 2.0.0.B20090227
14:48 olass one step further
14:48 olass assertion failed
14:49 olass expected O(C)C   actual COC
14:49 olass for the two topmost
14:49 egonw ah, that one :)
14:49 olass 2 still get errors
14:49 egonw shk3: do you see that?
14:49 egonw shk3: CDK's canonical SMILES in action :)
14:49 egonw olass: which two tests?
14:50 olass hold on
14:50 olass testSaveMolecule_IMolecule fails (see above)
14:50 olass testSaveMolecule_IMolecule_boolean fails (see above)
14:50 olass testSaveMolecule_IMolecule_String_boolean error
14:50 shk3 well, one smiles was typed by the programer, I suppose, so don't blame CDK ;-)
14:51 egonw 4?
14:51 olass testSaveMolecule_IMolecule_IFIle_boolean error
14:51 olass error is:
14:51 egonw shk3: no, the actual smiles produces as platform dependent
14:51 egonw olass: so, still 4 fails?
14:51 olass NPE 604 CDKManager oldFile.getContentDescription().getContentType()
14:51 olass no
14:51 olass 2 fails, 2 errors
14:51 egonw oh, ic
14:51 olass not same error
14:52 olass previously there were 4 errors
14:52 olass you are progressing!
14:52 egonw ic
14:52 egonw OS/X sucks
14:52 shk3 ah, platform-dependent smiles
14:52 shk3 that's nice
14:52 egonw ah... now I understand what OS/X means
14:52 egonw OS/X SuX
14:53 egonw it's one of those recursive acronyms...
14:53 egonw how cool :)
14:53 egonw olass: I give up
14:53 olass :-(
14:53 olass ok
14:54 olass you have worked hard
14:54 olass egonw++
14:59 egonw olass:
14:59 egonw one more try
14:59 olass sure
14:59 egonw two commits
14:59 egonw use both
14:59 olass ok
15:00 CIA-55 bioclipse: egonw * r9150 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.business.test/src/net/bioclipse/cdk/​business/test/CDKManagerPluginTest.java: Either 'canonical' SMILES is fine
15:00 CIA-55 bioclipse: egonw * r9151 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: OK, same workaround as r9148
15:03 egonw olass: and?
15:04 olass mom
15:05 olass egonw: ALL PASSES!
15:05 olass success
15:05 egonw good
15:11 CIA-55 bioclipse: goglepox * r9152 /bioclipse2/trunk/plugins/ (5 files in 4 dirs): Refactored out ChoiceGenerator to net.bioclipse.cd.jchempaint.view
15:12 CIA-55 bioclipse: goglepox * r9153 /bioclipse2/trunk/plugins/ (4 files in 3 dirs): Moved extension point generator to net.bc.cdk.jcp.view
15:12 CIA-55 bioclipse: goglepox * r9154 /bioclipse2/trunk/plugins/net.biocli​pse.cdk.jchempaint.view/plugin.xml: Changed id on generator extension point
15:33 CIA-55 bioclipse: goglepox * r9155 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jchem​paint.view/src/net/bioclipse/cdk/jchempaint/view/ (ChoiceGenerator.java JChemPaintView.java): Fixed NPE in view and added method for showing extension generators
15:35 olass egonw: does atom numbering start on 0?
15:36 olass I mean in CDK and in chemoinformatics in general?
15:36 egonw in many informatics, yes
15:36 egonw and as in container.getAtom(), yes
15:36 egonw as in Java array, yes
15:38 olass just wondering
15:59 CIA-55 bioclipse: goglepox * r9156 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint.view/src/net/bioclipse/cd​k/jchempaint/view/ChoiceGenerator.java: Corrected name for generator extension point
16:15 egonw shk3: ping
16:25 shk3 hi egonw
16:25 egonw hej
16:25 * egonw is having fun with speclipse :)
16:25 shk3 saw that
16:25 egonw was wondering about bibtex
16:25 egonw can't seem to figure out how to add a reference
16:26 shk3 if you have a smr open, there should be a menu item
16:26 egonw mmm... I just wondered why I did not check the cheat sheet
16:26 egonw sorry about that
16:27 shk3 no problem
16:28 egonw ok, submitted :)
16:28 CIA-55 bioclipse: goglepox * r9157 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Renerer2DConfigurator is now called on generated atomcontainers aswell
16:29 CIA-55 bioclipse: goglepox * r9158 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Changed loadSMILESFile to preserve the order
16:30 egonw shk3: OK, checking my home page, the bib ref showed up nicely :)
16:30 shk3 good to hear
16:30 egonw one glitch
16:31 egonw the bibtex to bibtexml conversion does not convert the latex ~ for no-break-space to a real space in bibtexml
16:32 * egonw loves 19F NMR spectra :)
16:32 egonw ok, dinner time
16:32 egonw bbl
16:33 grandm44 it works again, thx
16:33 grandm44 have a good week-end
16:35 CIA-55 bioclipse: goglepox * r9159 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.ui.sdfeditor/src/net/bioclipse/cdk/u​i/sdfeditor/editor/JCPCellPainter.java: Work around for bug #613
16:35 zarah bug #613 | http://tinyurl.com/cm84ht
16:46 CIA-55 bioclipse: goglepox * r9160 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java: Work around for bug #613 in JCP
16:46 zarah bug #613 | http://tinyurl.com/cm84ht
17:06 CIA-55 bioclipse: goglepox * r9161 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.jchempaint/src/net/bioclipse/cdk/jchempa​int/widgets/JChemPaintEditorWidget.java: added getter for atomContainer,
17:06 CIA-55 bioclipse: ospjuth * r9162 /bioclipse2/trunk/ (8 files in 8 dirs): Set version to 2.0.0.B20090227
17:32 CIA-55 bioclipse: ospjuth * r9163 /bioclipse2/trunk/plugins/net.bioc​lipse.logger/META-INF/MANIFEST.MF: Set version to 2.0.0.B20090227
17:34 CIA-55 bioclipse: ospjuth * r9164 /bioclipse2/trunk/plugins/net.bi​oclipse.logger/log4j.properties: Set default logging level to WARN
17:34 CIA-55 bioclipse: ospjuth * r9165 /bioclipse2/trunk/plugins/net.bi​oclipse.ui/META-INF/MANIFEST.MF: Set version to 2.0.0.B20090227
17:43 CIA-55 bioclipse: ospjuth * r9166 /bioclipse2/trunk/features/net.bio​clipse.xws4j_feature/feature.xml: Set version to 2.0.0.B20090227
17:44 CIA-55 bioclipse: ospjuth * r9167 /bioclipse2/trunk/features/ (4 files in 4 dirs): Set version to 2.0.0.B20090227
17:44 CIA-55 bioclipse: ospjuth * r9168 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/ (.settings/org.eclipse.jdt.core.prefs META-INF/MANIFEST.MF): Set version to 2.0.0.B20090227
17:49 shk3 how are things going twith the release?
17:49 olass quite bad
17:49 olass dunno if I have time to finish it
17:49 olass trying
17:49 olass now exporting
17:50 olass but still quite some things to do
17:50 egonw what's the problem?
17:50 olass no problem
17:50 olass time
17:50 olass testing
17:50 olass more testing
17:50 olass exporting
17:50 olass packaging
17:50 olass uploading
17:51 olass blogging
17:51 olass mailing
17:51 olass etc
17:51 olass etc
17:51 olass might need to finish this tomorrow
17:51 olass btw, the generate 2D recreate2D etc is not working properly
17:51 olass have not had time to file a proper bug
17:51 egonw yeah, there is some sense if a freeze/branch week
17:52 egonw ok
17:52 olass dunno about branch
17:52 olass but a freeze sounds like a good idea
17:53 egonw that's the same
17:54 egonw but it remains a lot of work indeed...
17:55 olass yes
17:55 olass but this week has been a big step forward
17:56 egonw yes, indeed
18:01 olass ok, weekend for me
18:01 olass have a nice weekend all of you
18:01 olass might be online tomorrow for release
18:01 olass bye
20:00 CIA-55 bioclipse: egonw * r9169 /bioclipse2/trunk/plugins/net.bio​clipse.rdf/src/net/bioclipse/rdf/ (5 files in 2 dirs): Made the manager stateless
20:01 CIA-55 bioclipse: egonw * r9170 /bioclipse2/trunk/plugins/net.bioclipse.rdf/s​rc/net/bioclipse/rdf/business/JenaModel.java: Better output to console: number of triples
20:02 CIA-55 bioclipse: egonw * r9171 /bioclipse2/trunk/plugins/net.bioclips​e.rdf/src/net/bioclipse/rdf/business/ (IRDFManager.java RDFManager.java): Return the model again, so that the JavaScript reports the number of triples
22:06 CIA-55 bioclipse: egonw * r9172 /bioclipse2/trunk/ (3 files in 2 dirs): Return a list of lists so that we can process the sparql results (see for example http://gist.github.com/71677)

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