Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-06-10

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Time Nick Message
05:06 sneumann_ joined #bioclipse
05:09 egonw joined #bioclipse
06:29 egonw joined #bioclipse
06:53 annzi joined #bioclipse
06:57 Gpox joined #bioclipse
07:02 egonw Gpox: I am making patches for the method name refactoring
07:13 sneumann_ joined #bioclipse
07:34 CIA-70 bioclipse.core: Arvid Berg 2.4.x * r2e3fa5d / net.bioclipse.target.platf​orm/target-platform.target :
07:34 CIA-70 bioclipse.core: Added org.eclipse.gef to target.platform
07:34 CIA-70 bioclipse.core: Should fix brunn build problem - http://bit.ly/ahhgHc
07:43 annzi egonw: I'm trying to run moss but get the following error : Error while reading JSON: Can not deserialize instance of
07:43 annzi net.bioclipse.moss.business.props.MossProperties out of START_ARRAY token
07:43 annzi at [Source: java.io.StringReader@1f69162; line: 1, column: 1]
07:44 annzi do you know why?
07:44 egonw can you put the script on gist.github.com ?
07:45 annzi egonw :http://gist.github.com/432683
07:56 egonw you got the {}'s in the wrong place
07:56 egonw what you pass is a string array
07:56 egonw not a JSON string
08:05 egonw Gpox: I'm now pushing CDK-JChemPaint 13 to org.openscience.cdk bioclipse branch
08:05 CIA-70 org.openscience.cdk: Egon Willighagen bioclipse2.4 * re30c939 / (2 files): Return two missing parameters - http://bit.ly/9V52IJ
08:05 CIA-70 org.openscience.cdk: Egon Willighagen bioclipse2.4 * r80060ee / (39 files in 22 dirs): Uploaded CDK-JChemPaint 13 - http://bit.ly/b71nNa
08:11 egonw Gpox: now going to refresh my bioclipse workspace
08:12 Gpox no get method?
08:13 egonw arghh...
08:13 egonw grmph...
08:13 egonw wanted to put that in a separate commit
08:13 egonw but I forgot to add that patch ...
08:13 egonw crap
08:14 patch14 here I come ...
08:17 * git pull patch14
08:21 egonw testing the release now
08:25 sneumann joined #bioclipse
08:34 egonw Gpox: making a new export for org.openscience.cdk now
08:36 CIA-70 org.openscience.cdk: Egon Willighagen bioclipse2.4 * r9d341dc / (12 files in 12 dirs): Uploaded CDK-JChemPaint 14 - http://bit.ly/cBywGG
08:41 CIA-70 bioclipse.cheminformatics: Egon Willighagen 2.4.x * rac2e290 / plugins/net.bioclipse.cdk.jchempaint​/src/net/bioclipse/cdk/jchempaint/pr​eferences/PreferenceInitializer.java : Use the getDefaultRenderingParameter method - http://bit.ly/b0jA1n
08:41 CIA-70 bioclipse.cheminformatics: Egon Willighagen 2.4.x * rb3f2be6 / (11 files in 7 dirs): Updated for new rendering parameter API in CDK-JChemPaint 14 - http://bit.ly/c649TG
08:45 jonalv joined #bioclipse
08:45 egonw jonalv: good morning
08:45 jonalv so RC2 today_
08:45 jonalv os everything working now? :)
08:48 annzi egonw: could you explain to me how it works. after createmossproperties what are you supposed to do next?
08:49 egonw annzi: please put somewhere online the full script...
08:49 egonw then I know the context...
08:49 egonw applying those props is yet to be implemented
08:49 egonw but I need to know the context, to decide how to do that
08:49 annzi that's the thing I don't have one I'm stuck
08:50 egonw then create one, with the bits you do know how to do...
08:50 egonw adding comments about the bits that are missing
08:50 annzi then I need to know what it is that you've done
08:50 egonw no, not to make the full workflow
08:50 egonw only to make the full workflow *work*
08:50 egonw not to create it
08:51 egonw this is called prototyping...
08:51 egonw in particularly, mocking up a solution
08:51 egonw a mock does not actually work, but look exactly like something that could have worked
08:51 egonw it helps you decide what is needed that does not exist yet
08:52 egonw like the hook up of that properties functionality with the MoSS manager methods to actually run MoSS
08:54 annzi that's the thing I thought that was set. So what you've done is basically that you created a class that sets properties but nothing further…
08:55 egonw indeed
08:56 annzi aha
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09:10 CIA-70 org.openscience.cdk: Egon Willighagen bioclipse2.4 * rb228bea / plugins/org.openscience.cdk.render/src/org/​openscience/cdk/renderer/RendererModel.java : Fixed the getDefault() method; this patch is filed upstream -
09:15 egonw Gpox: ping
09:15 egonw Gpox: I think we are good to go...
09:15 egonw there seems one issue left...
09:15 egonw the SWTRenderer asks for ShowImplicitHydrogens
09:15 egonw but...
09:16 Gpox no, still getting error from jchempaintglobalpropertiesmanager
09:16 egonw that param is not registered, being part of ExtendedAtomGenerator
09:16 Gpox Illegalaccesserror
09:16 egonw did you see this patch:
09:16 egonw [06/10/10 11:10] <CIA-70> org.openscience.cdk: Egon Willighagen bioclipse2.4 * rb228bea / plugins/org.openscience.cdk.render/src/org/​openscience/cdk/renderer/RendererModel.java : Fixed the getDefault() method; this patch is filed upstream -
09:16 egonw ?
09:16 egonw I think that will fix it
09:17 Gpox ah ok
09:18 egonw Gpox: so, what will we do...?
09:18 egonw add the ExtendedAtomGenerator?
09:19 Gpox if we want to render implicit hydrogens yes, they wont show up if we don't
09:19 Gpox thats the whole point the the parameters
09:19 egonw then we need to add the proper generator
09:19 Gpox I agree
09:20 egonw you know all the places where to put it?
09:20 Gpox yes
09:20 egonw the stacktrace I have is for JChemPaintWidget
09:21 egonw ok, different question...
09:21 egonw if I have an inner class... how do I get to see what the 'outer' class is?
09:22 jonalv egonw: how do you mean?
09:26 Gpox there is <outherclass>.this
09:27 Gpox egonw: can you open sd-files?
09:29 egonw Gpox: .this only works for Objects... not for Classes
09:30 * egonw is testing SD files...
09:30 Gpox yes. Isn't the outer class part of the class name BasicGenerator$BasicParameter
09:31 egonw true
09:31 egonw I could process the getName() output
09:31 egonw ah, right
09:34 egonw ok, will just give the full class name in the illegalAccessError then
09:34 egonw Gpox: I'd say the SDF editor is missing an important generator too
09:34 Gpox the generators are setup in different places for the different renderers jcp-editor, jcp-view, jcp-cellrenderer(Mol Table)
09:35 egonw hang on...
09:35 egonw will commit a patch that adds the renderingparameter name to the IAE error message
09:35 Gpox but jcpgloabproperties process all the hardcoded ones
09:36 Gpox it has access to the modle so it could filter out those that are not knownd by the renderermodel and not try to set them
09:37 egonw sounds like an idea...
09:37 egonw but then again...
09:38 egonw I guess your patch for autogenerating the props view would solve it too, not?
09:38 egonw java.lang.IllegalAccessError: You requested the active parameter of type org.openscience.cdk.renderer.generators.​AtomNumberGenerator$WillDrawAtomNumbers, but it has not been registered yet. Did you make sure the IGeneratorParameter is registered, by registring the appropriate IGenerator? Alternatively, you can use getDefault() to query the default value for any parameter on the classpath.
09:39 egonw RendererModel.isRegistered(C​lass<IRenderingParamater>)?
09:40 egonw I will apply your idea for now...
09:44 jonalv egonw: are you doing something that you want in RC2 now?
09:44 egonw yes
09:44 egonw fixing the SD opening
09:45 jonalv oh is that borken?
09:45 jonalv yiekes
09:56 egonw testing patch
09:58 * egonw finds another bug in the code
09:58 egonw Gpox: I'm closing in
10:00 egonw argh...
10:00 egonw another bug
10:01 * jonalv does a test run of RC2 export
10:28 egonw ok, SD file opening works again...
10:28 jonalv egonw++
10:28 jonalv oh Gpox++
10:28 jonalv you guys rock!
10:42 egonw Gpox: ping
10:43 egonw Gpox: is there an rendering parameter to control the placement and/or offset of the atom number?
10:43 egonw that is... do you know if there is ...
10:43 Gpox dont think so
10:43 egonw ack... I did not think so either...
10:44 Gpox if it did id should be a Vector2d
10:47 egonw indeed :)
10:47 CIA-70 org.openscience.cdk: Egon Willighagen bioclipse2.4 * rc27eb5a / (4 files in 3 dirs): Two backported patches from CDK-JChemPaint 15 (or so): return parameters from super generators; more informative IllegalAccessError message - http://bit.ly/cDznsv
10:51 CIA-70 bioclipse.cheminformatics: Egon Willighagen 2.4.x * r6e46b35 / plugins/net.bioclipse.cdk.ui.sdfeditor/src/net/bio​clipse/cdk/ui/sdfeditor/editor/JCPCellPainter.java : Fixed a IllegalAccessError: since the AtomNumberGenerator is not registered, the matching boolean cannot be set to false either - http://bit.ly/clU8Pm
10:51 CIA-70 bioclipse.cheminformatics: Egon Willighagen 2.4.x * rd834c28 / plugins/net.bioclipse.cdk.jchempaint/sr​c/net/bioclipse/cdk/jchempaint/business​/JChemPaintGlobalPropertiesManager.java : Fixed IllegalAccessParameters: there are several generator combinations used throughout Bioclipse; we cannot define a definate list of parameters we need to set - http://bit.ly/alzs1E
11:19 * jonalv is back from lunch :)
11:24 jonalv egonw: those commits... Are you ready for RC2 now or how much do you have left?
11:25 egonw I think I am ready
11:26 egonw_ joined #bioclipse
11:26 jonalv cool
11:26 egonw_ am I back?
11:27 masak joined #bioclipse
11:28 jonalv egonw: how do you mean?
11:29 egonw I think I had a network split
11:30 jonalv ah
11:30 * jonalv usually use:
11:30 jonalv @ping
11:30 zarah jonalv: pong
11:30 jonalv when wondering
11:31 * jonalv pulls in all his repos one last time now
11:32 jonalv oh I just realised, Gpox the placement of the version number on the splash screen, we should probably do something about it?
11:33 egonw jonalv: no
11:34 egonw that will be solved when you remove the .RCx
11:34 jonalv egonw: yea but don't we want the .RCx to readable?
11:34 jonalv |to be
11:36 egonw not with priority
11:36 egonw there are worse 'bugs'
11:36 Gpox net.bioclipse.ui/plugin.xml line 90
11:37 jonalv egonw: yea but it is the _very_ first thign you see of Bioclispe...
11:37 egonw yeah, but this is just the RC...
11:37 egonw it will not apply to the real release
11:37 egonw and as such, fix itself automatically
11:38 egonw anyway... no more words about it...
11:38 * jonalv has a feeling Gpox might already be on it. If so please speak up now. Otherwise we will just let it be...
11:38 egonw because in the same time we could likely have made the bloody thing just right align :)
11:51 Gpox it is set in net.bioclipse.ui/plugin.xml on line 90, I am not sure where it should be, feel free to tweek it
11:54 egonw Gpox: I think jonalv is refering to the splash screen
11:54 egonw where the version number is only half shown
11:54 Gpox yes and so am I
11:55 jonalv les't jsut ignore that shall we?
11:55 * jonalv is already building...
11:56 Gpox having it in the current location is problematic if we want versions like 2.5.0.20100915
11:58 jonalv true
11:58 jonalv + we might want that
11:59 jonalv let's remember to fix that for the 2.4.0 release
11:59 jonalv that one will have a date wont it?
12:01 egonw Gpox: ah, ok :) sorry
12:18 egonw Gpox: did you have a patch for the missing ExtendedAtomGenerator ?
12:19 Gpox no
12:20 ice9 joined #bioclipse
12:20 egonw hi ice9
12:20 ice9 hi egon
12:20 CIA-70 bioclipse.cheminformatics: Egon Willighagen 2.4.x * r6440436 / plugins/net.bioclipse.cdk.jchempaint​/src/net/bioclipse/cdk/jchempaint/pr​eferences/PreferenceInitializer.java : The default is to not show atom numbers - http://bit.ly/cVonEG
12:20 egonw Gpox: what are the places where it should be added?
12:21 egonw Gpox: or shall I just fix this one stacktrace?
12:21 Gpox you got a stacktrace?
12:22 egonw no longer I hope :)
12:22 egonw testing
12:23 egonw fixed pushed:
12:24 CIA-70 bioclipse.cheminformatics: Egon Willighagen 2.4.x * r102e636 / plugins/net.bioclipse.cdk.jchempai​nt.view/src/net/bioclipse/cdk/jche​mpaint/view/JChemPaintWidget.java : We want to draw implicit hydrogens, so we need the ExtendedAtomGenerator - http://bit.ly/bM8G9Z
12:58 jonalv Bioclipse 2.4.0.RC2 has been built and is ready for testing :)
12:58 * jonalv is gonna do commits and taggings now
13:11 CIA-70 bioclipse.core: jonalv 2.4.x * re6f2601 / (4 files in 3 dirs): Set version to 2.4.0.RC2 - http://bit.ly/9udP1g
13:20 egonw Gpox: http://chem-bla-ics.blogspot.com/2010/06/cd​k-jchempaint-6-rendering-atom-numbers.html
13:20 zarah egonw's link is also http://tinyurl.com/2bnf9go
13:33 CIA-70 bioclipse.structuredb: jonalv master * r75fcfe2 / (3 files in 3 dirs): fix for inchi changes - http://bit.ly/aSkpv0
13:55 CIA-70 bioclipse.rdf: jonalv 2.4.x * r8f3452c / (2 files in 2 dirs): Set version to 2.4.0.RC2 - http://bit.ly/9Agcs3
13:58 egonw jonalv: ping
13:59 egonw jonalv: ola had the practice of versioning all plugins too...
13:59 egonw not just the features
13:59 egonw just FYI :)
14:01 egonw jonalv: you missed a patch for the RC2
14:01 egonw an important one
14:01 egonw two important patches, actually
14:04 egonw jonalv: I'll hold off a merge for bioclipse.cheminformatics until we talked
14:04 jonalv egonw: but you said you didn't have any more when I asked you... :(
14:05 jonalv egonw: oh versioning the plugins too? Yiekes, didn't think of that
14:05 jonalv hm
14:05 jonalv is that really needed?
14:05 egonw there is always RC3 :)
14:05 jonalv maybe it is
14:05 egonw no, don't think it is really important
14:05 egonw we'll see
14:05 jonalv I don't know
14:06 egonw yes, at 13:25 I did say I thought I was done...
14:06 jonalv what patches was that?
14:06 egonw but I was wrong :)
14:06 egonw [06/10/10 14:20] <CIA-70> bioclipse.cheminformatics: Egon Willighagen 2.4.x * r6440436 / plugins/net.bioclipse.cdk.jchempaint​/src/net/bioclipse/cdk/jchempaint/pr​eferences/PreferenceInitializer.java : The default is to not show atom numbers - http://bit.ly/cVonEG
14:06 egonw [06/10/10 14:24] <CIA-70> bioclipse.cheminformatics: Egon Willighagen 2.4.x * r102e636 / plugins/net.bioclipse.cdk.jchempai​nt.view/src/net/bioclipse/cdk/jche​mpaint/view/JChemPaintWidget.java : We want to draw implicit hydrogens, so we need the ExtendedAtomGenerator - http://bit.ly/bM8G9Z
14:07 CIA-70 bioclipse.joelib: jonalv 2.4.x * rc02f952 / features/net.bioclipse.joelib_feature/feature.xml : Set version to 2.4.0.RC2 - http://bit.ly/cS0Fnb
14:08 jonalv egonw: so was it features or bug fixes or what was it? :)
14:08 egonw important bug fixes
14:08 jonalv oh what bug?
14:09 egonw regressions due to the new CDK-JChemPaint
14:09 egonw older bugs that now became shallow
14:09 jonalv sounds like an RC3 tomorrow then...
14:09 egonw or early next week
14:09 egonw so that a few more bug reports can flow in
14:13 jonalv yea probably an even better idea
14:24 CIA-70 bioclipse.social: jonalv 2.4.x * r0aa98c3 / features/net.bioclipse.social_feature/feature.xml : Set version to 2.4.0.RC2 - http://bit.ly/bkQMQj
14:51 jonalv joined #bioclipse
14:51 jonalv I iz back
14:56 egonw_ joined #bioclipse
14:57 * egonw_ is downloading RC2
14:57 egonw_ and will test booting on Ubuntu L 64bit
14:59 jonalv cool, egonw_++
15:22 egonw jonalv: rc2 does not work on Ubuntu L64
15:23 jonalv :(
15:23 jonalv egonw: what are the symptoms?
15:23 egonw Bioclipse.2.4.0.RC2$ ./bioclipse
15:23 egonw Running a 32-bit JVM is not supported on this platform.
15:23 egonw it seems the 64bit release is just a 32bit in diguish
15:23 jonalv hm
15:23 * jonalv has a bad feeling about this
15:24 jonalv oops
15:24 jonalv I fumbled
15:24 jonalv none of the 64 bit versions will work unless they can be run in 32 bit
15:24 jonalv the -d32 flag has snuck in
15:24 egonw ah, ic
15:25 egonw don't feel bad...
15:25 egonw it's your first steps as release manager :)
15:25 egonw these are difficult steps
15:25 jonalv I think I will rebuild and put up new versions
15:25 egonw hej, I just made 5 CDK-JChemPaint releases in the past two days ...
15:25 jonalv wow
15:26 jonalv yea I guess that's the way it is
15:26 jonalv question is if I should make a new release today? RC2.1_ :)
15:27 egonw depends on how much time you have...
15:27 jonalv I have time
15:27 egonw but, given the disastrous state of RC2 :)
15:27 egonw alternatively...
15:27 jonalv or hm
15:27 egonw you pull the release from the web page
15:27 jonalv maybe not the update sites too
15:28 jonalv that takes a bit too long for my taste
15:28 egonw because anyone now routed to RC1 will see RC2 and download that one
15:29 jonalv egonw: but your changes are only in chminformatics?
15:29 jonalv egonw: and only in stuff that are in the core release?
15:29 jonalv egonw: or?
15:30 egonw yes, I think so
15:30 jonalv egonw: becuase if so then I can make an RC2.1 build and leave the update sites untouched
15:32 * jonalv goes for that
15:44 jonalv hm JVM terminated Exit code=13
15:44 jonalv wtf?
16:02 masak a very Unlucky Termination.
16:03 jonalv strange error message but I think I got passed it
16:05 * egonw is leaving for dinner
16:06 egonw jonalv: please remove RC2 from the bioclipse-devel/ webpage
16:06 egonw to ensure no one is downloading it
16:06 jonalv egonw: it's only the 64 bit ubuntu version and the 64 bit windows version that is goign to be borken
16:06 jonalv egonw: new version is pending
16:06 egonw so, remove those two then
16:06 egonw ok
16:07 egonw ok, cu later
16:07 jonalv cu
16:24 jonalv zarah: tell egonw okey feel free to try again now. I sure hope it works. I don't have a 64 bit linux machine myself so I can't test that build
16:24 zarah Consider it noted.
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20:24 sneumann Found a very nice tool on the web http://bioweb.ucr.edu/ChemMineV2
20:24 zarah sneumann's link is also http://tinyurl.com/38flm5q
20:24 sneumann which is great for quick&dirty jobs.
20:25 sneumann calculating similarities, clustering etc
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