Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-05-30

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Time Nick Message
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08:33 CIA-46 bioclipse: ospjuth * r5741 /bioclipse2/trunk/plugins/net.bioclipse.cdk​10.jchempaint/src/net/bioclipse/cdk10/jchem​paint/ui/editor/action/UndoableAction.java: Replaced NULL with NullProgressMonitor.
08:38 * egonw is debugging a clone() problem
08:39 egonw in CDK 1.0.x and trunk
08:57 thomas_ku_ joined #bioclipse
09:14 olas egonw: does the select box and lasso actions work?
09:15 olas I get an NPE
09:15 egonw not tried that in the SDF editor I think
09:15 egonw lasso at least works in MDLEditor
09:15 olas ok
09:15 egonw not sure about box
09:16 egonw never really used that anyway
09:16 olas I suspect there are still some bugs left in SDFEditor
09:16 egonw yeah, likely...
09:16 egonw so complex code...
09:16 olas will asko Gpox to look at that
09:16 egonw just JCP is rather complex already
09:16 egonw yes, good idea...
09:16 egonw our miracle worker
09:16 olas he solved the hardest problem in Bioclispe so far in just 2 days
09:16 olas yes :-)
09:16 olas Gpox: are you listening here?
09:17 egonw Gpox: thanx for that, btw...
09:17 olas Gpox: I will file some bugs for you
09:17 Gpox your welcome
09:18 olas are you subscribed to bioclispe-devel, and bioclipse-commit?
09:18 olas if not, please do
09:44 * egonw just noticed two subscribe notifications
09:48 olas yes
09:53 CIA-46 bioclipse: ospjuth * r5742 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk10.jchempaint/src/net/bio​clipse/cdk10/jchempaint/ui/editor/ (ToolBarMaker.java resources/small-bin/lasso_selected.gif): Fixed missing icons and removed unnecessry toolbar elements New, Open, SaveAs, Undo, Redo; these are all handled by the corresponding Eclispe actions.
09:54 olas Gpox: I get a lot of NullPOinterExceptions in JCP...
09:54 olas could you look at that?
09:54 olas They are there even if you open in MDLMolefileEditor
09:55 olas click some actions and then area, I get a lot of NPE thrown
09:55 olas Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
09:56 olas also, undo-redo is not tied into Eclipse undo-redo
09:56 * olas will file some bugs
09:56 egonw olas: the lasso worked...
09:56 egonw the box I am not sure abuot...
09:56 egonw but now you removed the lasso instead of the box
09:56 olas removed?
09:57 egonw ah, no
09:57 olas both are visible here
09:57 egonw yes
09:57 egonw sorry...
09:57 egonw I saw an icon removed from SVN
09:57 egonw and only one red box left...
09:57 olas oh?
09:57 olas no red box here
09:57 egonw overlooked the actual lasso icon, which is now visible :)
09:57 olas hmm
09:57 egonw ok, but lasso mode is now broken
09:57 egonw but used to work
09:58 olas Egonw: do you get NPEs when clicking actions and editing?
09:58 olas Gpox: Help!
09:58 egonw no, but I do get ArrayIndexOutOfBoundsExceptions...
09:58 egonw olas: anyway...
09:58 egonw might you remove the icon for select with box
09:59 olas what line?
09:59 olas remove entire action?
09:59 egonw Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: 0 >= 0
09:59 egonw at java.util.Vector.elementAt(Vector.java:432)
09:59 egonw at org.openscience.cdk.controller.AbstractController​2D.lassoSelection(AbstractController2D.java:700)
09:59 egonw at org.openscience.cdk.controller.AbstractControlle​r2D.mouseReleased(AbstractController2D.java:558)
09:59 egonw at org.openscience.cdk.controller.SimpleControlle​r2D.mouseReleased(SimpleController2D.java:59)
09:59 egonw at net.bioclipse.cdk10.jchempaint.ui.e​ditor.BCJCPPopupController.mouseRel​eased(BCJCPPopupController.java:73)
09:59 egonw yes, just remove the select-by-box
09:59 olas ok
09:59 egonw select with lasso is nicer anyway
09:59 egonw ok, got to run to pick up Lars from school now
09:59 olas ok
10:00 CIA-46 bioclipse: ospjuth * r5743 /bioclipse2/trunk/plugins/net.bioclipse.​cdk10.jchempaint/src/net/bioclipse/cdk10​/jchempaint/ui/editor/ToolBarMaker.java: Removed select-by-box action.
10:03 CIA-46 bioclipse: ospjuth * r5744 /bioclipse2/trunk/plugins/net.bioclipse.​cdk10.jchempaint/src/net/bioclipse/cdk10​/jchempaint/ui/editor/ToolBarMaker.java: Removed debug outs for unused actions.
10:09 olas Gpox: see bug 1979114
10:10 olas this is very important
10:10 olas we need to have editing resolved until monday
10:10 olas if you could look at this today I'd appreciate it
10:10 olas ask me if you need more information about the bug
10:11 olas I'll also try to look into this after lunch
10:11 * olas is off for lunch
10:16 egonw ok, the bug fix for the cloning seems to have fixed the too many rings problem
10:16 egonw (or some other patch did)
10:16 egonw ah, no, it does not
10:44 egonw ah, upon an edit action, any action is performed twice...
11:19 egonw seems the model at some point gets too listeners
11:19 egonw but got no idea which patch caused that
11:19 egonw olas: need your help
11:25 olas egonw: pong
11:25 olas Gpox: are you here?
11:26 egonw one of the recent patches caused a duplication of listeners, I think...
11:26 egonw causing actions to be performed twice or more
11:27 olas that could be me, but I'm guessing Gpox can make some sense from this
11:27 olas he's experienced with this stuff
11:27 olas but he seems away for the moment
11:31 Topic for #bioclipseis now An open source workbench for chemo- and bioinformatics - http://www.bioclipse.net/ | BioclipseWiki => http://wiki.bioclipse.net/ !! | logs => http://colabti.org/irclogge​r/irclogger_logs/bioclipse & http://moritz.faui2k3.org/irc​log/out.pl?channel=bioclipse
11:33 olas left #bioclipse
11:35 olas joined #bioclipse
12:09 olas jonalv: around?
12:09 olas I will make an API change to IMolecule
12:09 olas according to egonw's instructions
12:10 olas will add public String getCML()
12:10 olas that's what CDK-Taverna does
12:10 olas and makes sense in my opinion
12:10 olas but
12:10 olas you have created Molecule and SmilesMolecule
12:10 olas which are almost identical
12:10 olas jonalv: around?
12:13 CIA-46 bioclipse: ospjuth * r5745 /bioclipse2/trunk/plugins/net.bioclips​e.core/src/net/bioclipse/core/domain/ (IMolecule.java Molecule.java SmilesMolecule.java): API change in IMolecule: added getCML(), updated Molecule and SmilesMolecule accordingly to return null in this method.
12:16 CIA-46 bioclipse: ospjuth * r5746 /bioclipse2/trunk/plugins/net.bioclips​e.core/src/net/bioclipse/core/domain/ (IMolecule.java Molecule.java SmilesMolecule.java): Updated to throw Exception instead of returning NULL.
12:16 jonalv olas: yea a little while longer
12:16 jonalv olas: I am heading to Masaks presentation soon...
12:17 olas ok
12:17 olas the changes I made will break structureDB
12:17 olas FYI
12:17 olas but will be easy to fix
12:17 jonalv which changes? :)
12:17 olas please backlog
12:18 CIA-46 bioclipse: ospjuth * r5747 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/domain/CDKChemFile.java: Removed unused class.
12:18 jonalv getCML on IMolecule?
12:18 olas yes
12:18 jonalv hm we really need that?
12:18 olas yes
12:18 CIA-46 bioclipse: ospjuth * r5748 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/domain/ICDKMolecule.java: Removed getCML() on ICDKMolecule, as pushed on IMolecule.
12:19 olas to be able to have a format that serializes between molecule reprs
12:19 olas SMILES is not good enough
12:19 olas so, yes we do
12:19 olas makes sense in every way
12:19 jonalv if you say so :)
12:19 olas egonw says so too
12:19 egonw well, SMILES cannot do coordinates
12:19 olas :-)
12:20 jonalv aha
12:20 egonw nor crystal structures
12:20 egonw not proteins
12:20 egonw etc, etc
12:20 jonalv okey it's not a problem so :)
12:20 olas adding stuff seldom is
12:51 jonalv joined #bioclipse
13:19 CIA-46 bioclipse: ospjuth * r5749 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (CDKManager.java ICDKManager.java): Updated ICDKManager and CDKManager to work with interfaces, added method fromString(String).
13:30 CIA-46 bioclipse: ospjuth * r5750 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.business.test/src/net/bioclipse/cdk/ (2 files in 2 dirs): Updated to use interface ICDKMolecule.
13:31 CIA-46 bioclipse: ospjuth * r5751 /bioclipse2/trunk/plugins/net.bioclipse.c​dk10.jchempaint/src/net/bioclipse/cdk10/ (5 files in 2 dirs): Created CDK10Molecule and updated CDK10Manager accordingly.
13:34 CIA-46 bioclipse: ospjuth * r5752 /bioclipse2/trunk/plugins/net.bioclipse.cdk10.​jchempaint/src/net/bioclipse/cdk10/business/: Removed duplicate CDK10Manager.
13:40 CIA-46 bioclipse: ospjuth * r5753 /bioclipse2/trunk/plugins/net​.bioclipse.cdk10.jchempaint/ (6 files in 2 dirs): Refactored resources into cdk10.jcp plugin from sdfeditor.
13:41 CIA-46 bioclipse: ospjuth * r5754 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk10.sdfeditor/ (10 files in 4 dirs): Refactored resources from sdfeditor into JCP and changed Activator package.
13:41 CIA-46 bioclipse: ospjuth * r5755 /bioclipse2/trunk/plugins/net.bioclipse.cd​k10.ui/src/net/bioclipse/cdk10/ui/content/ (MoleculeContentProvider.java MoleculeLabelProvider.java): Updated imports after CDK10Molecule move
13:42 olas All: please update cdk10.*
13:42 olas I have made major updates there
13:42 olas much needed refactoring of cdk10molecule
13:45 CIA-46 bioclipse: ospjuth * r5756 /bioclipse2/trunk/plugins/net.bioclipse​.cdk10.sdfeditor/META-INF/MANIFEST.MF: Updated manifest after Activator move.
13:49 * egonw is updating
13:49 egonw no Gpox yet?
13:52 olas Gpox said he's on the JCP bug
13:53 egonw the duplication of actions, right?
13:55 olas well, there are many related bugs
13:55 olas Gpox: you listening to this?
13:56 * egonw has the feeling that the lassoing no longer working is caused by this action problem too
13:57 Gpox yes, there is 4 instances of BCJCPPopupController created when starting up with an editor open
14:00 olas woops
14:17 CIA-46 bioclipse: ospjuth * r5757 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/domain/CDKMolecule.java: Added getAdapter for 2Dview.
14:21 CIA-46 bioclipse: goglepox * r5758 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk10.jchempaint/src/net/bio​clipse/cdk10/jchempaint/ui/editor/ (JCPMultiPageEditorContributor.java JCPPage.java):
14:21 CIA-46 bioclipse: Fix for bug [ 1979114 ] JCP actions throws exceptions
14:21 CIA-46 bioclipse: removed creation of multiple BCJCPPopupController instances
14:22 * egonw will test
14:25 * olas will test too
14:25 * olas will test later
14:28 CIA-46 bioclipse: ospjuth * r5759 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.business.test/ (2 files in 2 dirs): Added test to fromString() and create(Imolecule) methods. Passes.
14:32 olas egonw: does it work for you?
14:32 * olas hasn't tested
14:32 egonw no
14:32 egonw sort of...
14:32 egonw but not really...
14:32 egonw Gpox: I just opened a second MDLEditor
14:33 egonw and then it happens again
14:33 egonw though upon fresh BC2 boot it's fine...
14:33 egonw Gpox: I assume it requires some close down of stuff when the editor is closed...
14:34 egonw it seems that active page switching still registers a new listener...
14:35 olas egonw: could you help me with one thing
14:36 egonw I hope so
14:36 olas I nkow you can
14:36 olas this is your area :-)
14:36 olas Please await my commit
14:36 olas the thing is
14:37 olas Open an sdf
14:37 olas have the 2DView open
14:37 olas click on an entry in the table
14:37 olas the 2DView should display it
14:37 olas but the conversion via CML seems to mess things up
14:37 olas but it should not
14:37 * egonw is waiting for the commit
14:37 olas so
14:38 CIA-46 bioclipse: ospjuth * r5760 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.ui/src/net/bioclipse/cdk​/ui/views/Java2DRendererView.java: Updated to use getAdapter and convert via CDKManager.create(IMolecule).
14:39 CIA-46 bioclipse: ospjuth * r5761 /bioclipse2/trunk/plugins/net.bioclipse.c​dk10.sdfeditor/src/net/bioclipse/cdk10/sd​feditor/editor/StructureTableEntry.java: Implemneted getAdapter() to present 2dView with IMolecule.
14:39 olas one more
14:39 olas no
14:39 olas thats it
14:39 olas please update
14:39 olas Gpox: how are things going?
14:40 olas Gpox: don't forget to update cdk10.*
14:40 olas not that it has anything to do with your bug, but anyway :-)
14:42 olas egonw: can you reproduce my error?
14:42 egonw mom
14:44 * olas is waiting
14:45 egonw yeah, booting BC2 is slow... because it has some logger config stuff failing...
14:45 olas it has!?!
14:45 egonw yeah. sorry about that
14:45 egonw ok, regarding the 2D view:
14:45 egonw java.lang.IllegalStateException: Could not get the CDK manager
14:45 egonw at net.bioclipse.cdk.business.Activato​r.getCDKManager(Activator.java:83)
14:46 olas ??
14:46 olas please ste target platform
14:46 olas create a new run config
14:46 egonw ok, will try
14:46 olas and try again
14:46 olas you have not the CDK plugin loaded
14:46 olas /I think)
14:48 egonw ko, that solved some issues
14:48 olas and?
14:48 egonw though still got a race condition:
14:48 egonw java.lang.RuntimeException: Widget disposed too early!
14:48 egonw at org.eclipse.ui.internal.WorkbenchPartReference$1​.widgetDisposed(WorkbenchPartReference.java:171)
14:49 egonw and
14:49 egonw ERROR - Failed to get a service: org.eclipse.core.runtime.CoreException: Plug-in "net.bioclipse.core" was unable to execute setInitializationData on an instance of "net.bioclipse.core.busines​s.MoleculeManagerFactory".
14:49 olas yes
14:49 olas the last is known
14:49 egonw ERROR - Failed to get a service: org.eclipse.core.runtime.CoreException: Plug-in "net.bioclipse.core" was unable to execute setInitializationData on an instance of "net.bioclipse.core.busines​s.MoleculeManagerFactory".
14:49 egonw how about that one?
14:49 olas that is bad
14:49 olas but should only affect scripting
14:49 olas does it start?
14:50 egonw not sure
14:50 egonw while copy/pasting errors...
14:50 egonw it seems to have closed automatically
14:50 egonw no BC2 window
14:51 olas did you set target platform
14:51 olas removed all plugins
14:51 olas addded cdk.ui and cdk10.* and clicked add req plugins
14:51 olas run
14:51 olas is that what you did?
14:52 olas that procedure never fails me
14:52 egonw yes, sort of...
14:52 egonw added cdk10.sdfeditor + required
14:52 olas you need cdk.ui as well
14:52 olas otherwise you will not get the 2DView
14:53 egonw nope
14:53 egonw can't get it to boot anymore...
14:53 olas wtf
14:53 olas have you updated?
14:54 olas pastebin a complete stacktrace of startup
14:54 egonw yeah, working no that already :)
14:54 egonw on
14:54 rojasm joined #bioclipse
14:55 egonw http://pastebin.com/me09f70a
14:55 egonw got to pick up son
14:55 egonw bbl
14:56 egonw Eclipse 3.4.0
14:56 egonw in case you wonder
14:56 egonw particularly that XPCOM error on the Mozilla browser seems nasty
14:56 egonw ok, gone now
14:57 olas never tried Eclipse 3.4
14:57 olas using 3.3.1.1
15:11 CIA-46 bioclipse: goglepox * r5762 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk10.jchempaint/src/net/bio​clipse/cdk10/jchempaint/ui/editor/ (JCPMultiPageEditorContributor.java JCPPage.java): Moved BCJCPPopupControll instance form JCPMultipageEditorContributor to JCPPage
15:46 CIA-46 bioclipse: ospjuth * r5763 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business.test/src/net/bioclipse/​cdk/domain/tests/TestCDKMolecule.java: Updates to ConvertTest to test for isIsomorph()
15:57 CIA-46 bioclipse: jonalv * r5764 /bioclipse2/trunk/plugins/ne​t.bioclipse.structuredb/src/ (net/bioclipse/structuredb/domain/Structure.java sqlMap.xml): adapted the structuredb domain class Structure to the new IMolecule interface
16:09 * egonw will go offline for dinner
16:09 egonw bbl later tonite
16:19 CIA-46 bioclipse: jonalv * r5765 /bioclipse2/trunk/plugins/ (9 files in 5 dirs): Wrote a test while trying to fix the last failing structuredb test. The new test fails in yet another way. :(
16:29 * jonalv takes weekend. Leaves the failing tests for next week. (Better leave before I find more things that doesn't work) :)
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