Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-05-14

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All times shown according to UTC.

Time Nick Message
01:06 ilogger2 joined #bioclipse
06:27 Gpox joined #bioclipse
07:11 olass joined #bioclipse
07:12 olass moin
07:12 zarah saluton olass
07:12 sneumann moin
07:12 zarah hello sneumann, you fantastic person you
07:12 CIA-40 bioclipse: ospjuth * r10361 /bioclipse2/trunk/plugins/net.bioclipse.cdk.smar​tsmatching/src/net/bioclipse/cdk/smartsmatching/ (7 files in 2 dirs): Fixed highlighting of hits in SmartsView. Also added a propertyysource for hits. Resolves #948.
07:25 egonw joined #bioclipse
07:27 sneumann Hi, After tonights commits I have a working bioclipse-medea ;-)
07:27 egonw ah, good
07:27 egonw I have not checked the feature yet
07:31 edrin joined #bioclipse
07:31 edrin hi
07:41 jonalv joined #bioclipse
07:41 jonalv egonw: ping
07:41 egonw pong
07:41 egonw we need to sit together in the same room
07:41 jonalv olass: wants you to come over
07:41 egonw ok
07:45 CIA-40 bioclipse: goglepox * r10362 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Cleand up dublicated painting code.
07:45 CIA-40 bioclipse: goglepox * r10363 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java: Fixed a NPE when moving atoms
07:46 rojasm joined #bioclipse
07:47 egonw_ joined #bioclipse
07:51 egonw_ shk3: ping
07:51 egonw_ rojasm: ping
07:51 egonw_ uppsala is ready for merging the NWO
07:51 egonw_ but this requires a freeze of trunk for a couple of hours
07:54 egonw_ so please no commits
07:54 egonw_ and later today we will have a NWO tutorial
07:56 egonw_ ola is suggesting skype..
07:56 egonw_ shk3: would that work for you at EBI?
07:56 sneumann NWO ?
07:57 egonw_ New World Order :)
07:57 egonw_ new design of the bioclipse manager architecture
07:57 egonw_ which provides scripting, recording, etc
07:57 sneumann Your problem, I guess ;-)
07:57 egonw_ yes
07:57 egonw_ nothing you need to worry about :)
08:05 rojasm hi egonw
08:05 egonw hi migue
08:05 egonw l
08:05 rojasm did you tested the data.medea script
08:06 egonw no, not yet
08:06 egonw will try later today
08:06 egonw but the NWO is priority right now
08:06 * egonw has cut off everyone from SVN write access for the time being
08:06 egonw awaiting finish of the merge
08:24 jonalv @ping
08:24 zarah jonalv: pong, dear
08:38 rojasm joined #bioclipse
08:40 olass @pong
08:40 olass zarah: did you not ping me?
08:40 zarah olass: please rephrase or stop trying to be witty :)
08:40 olass sry
08:41 sneumann rojasm: I have a running medea here, can I help testing data.medea script ?
08:42 steinbeck joined #bioclipse
08:42 olass hi steinbeck
08:42 steinbeck Hi olass
08:47 egonw hi steinbeck
08:48 steinbeck HI Egon
09:10 olass bye steinbeck :)
09:11 rojasm hi sneumman
09:12 rojasm you have to install the net.biioclipse.data.medea plugin
09:13 rojasm und than run the script inside
09:23 steinbeck joined #bioclipse
09:23 egonw rojasm: please blog about it :)
09:38 egonw git svn dcommit in progress
09:38 egonw 72 patches
09:39 CIA-40 bioclipse: egonw * r10364 /bioclipse2/trunk/plugins/net.bioclipse.gist/ (2 files in 2 dirs): started refactoring IGIstManager for my new way of doing manager implementations
09:40 CIA-40 bioclipse: egonw * r10365 /bioclipse2/trunk/plugins/ (9 files in 5 dirs): Decoupled Gist manager from Gist manager interface and started writing the Methodinterceptor that is to call the right method on the managers.
09:41 CIA-40 bioclipse: egonw * r10366 /bioclipse2/trunk/plugins/net.b​ioclipse.gist/META-INF/spring/ (context-osgi.xml context.xml): Merged Spring xml config files for net.bioclipse.gist into one file
09:41 CIA-40 bioclipse: egonw * r10367 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Removed the BioclipseUIJob methods from this manager. And created a BioclipseJobUpdateHook for possibilities to act upon partial results during job execution.
09:42 CIA-40 bioclipse: egonw * r10368 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Work on the IGIstManager interface. Added annotation telling which class contains the implementations and changed some method signatures.
09:44 CIA-40 bioclipse: egonw * r10369 /bioclipse2/trunk/plugins/ (6 files in 3 dirs): Created stubs for manager method dispatcher classes for Java and JavaScript and stub test classes for those
09:45 CIA-40 bioclipse: egonw * r10370 /bioclipse2/trunk/plugins/ (16 files in 6 dirs): Wrote first test trying to call with IFIle and BioclipseUpdateHook for the manager method dispatcher
09:46 CIA-40 bioclipse: egonw * r10371 /bioclipse2/trunk/plugins/net.bioclipse.co​re.tests/src/net/bioclipse/core/business/A​bstractManagerMethodDispatcherTest.java: added tests for the other two method signatures
09:47 CIA-40 bioclipse: egonw * r10372 /bioclipse2/trunk/plugins/ (4 files in 2 dirs): Created base class for the two manager method dispatchers that does the paramater translations and then will give it to the specific implemetnations to either just run them in the same thread or to create Jobs.
10:10 steinbeck__ joined #bioclipse
10:18 egonw fucking SVN
10:19 olass what up?
10:19 egonw just after we went for lunch
10:19 egonw an SSL connection error
10:19 olass bad luck
10:23 egonw OK, continuing now
10:30 olass egonw: Where are the commits?
10:32 egonw it's SVN
10:32 egonw it's in progress
10:38 jonalv @ping
10:38 zarah jonalv: pong
10:38 olass @ping
10:39 zarah olass: pong
10:39 jonalv hm seems my connection survived...
10:39 olass mine too
10:39 jonalv egonw: ETA on commit-flood?
10:40 jonalv SVN--
10:40 egonw svn--
10:40 egonw svn--
10:40 egonw svn--
10:40 zarah svn--
10:40 jonalv olass: can we switch to git now? :)
10:41 egonw no clue on ETA
10:41 egonw it seems stalled
10:41 egonw olass?
10:41 egonw please
10:45 olass left #bioclipse
10:46 olass joined #bioclipse
10:46 olass hi
10:46 zarah hi olass
10:50 egonw joined #bioclipse
10:53 egonw joined #bioclipse
10:59 masak joined #bioclipse
11:02 olass what is going on here?
11:03 egonw git svn dcommit is doin a large commit now
11:03 olass nice
11:04 CIA-40 bioclipse: egonw * r10373 /bioclipse2/trunk/ (157 files in 114 dirs): refactored out a plugin net.bioclipse.managers for manager stuff
11:06 egonw olass, steinbeck__: did you set a time?
11:06 olass no
11:06 egonw steinbeck__, shk3: when are you back from lunch?
11:07 olass egonw: you set the time please
11:07 egonw 14:00 CEST
11:07 olass when all commits are done
11:07 CIA-40 bioclipse: egonw * r10374 /bioclipse2/trunk/plugins/ (66 files in 21 dirs): refactored out the package net.bioclipse.recording from core to it's own plugin
11:07 egonw no, we don't need to wait for that really
11:07 shk3 back from lunch around 2pm CET
11:07 egonw CET or CEST?
11:07 egonw CEST irght
11:07 egonw ?
11:08 CIA-40 bioclipse: egonw * r10375 /bioclipse2/trunk/ (3 files in 3 dirs): Added missing dependencies Eclipse complains about
11:08 * egonw is bad at summer/winter time
11:08 egonw shk3: so 13:00 UK summer time?
11:08 jonalv could we please use relative times instead?
11:08 * egonw thought internet time by Swatch was a good idea
11:08 jonalv how long from now?
11:08 egonw it never picked up
11:09 shk3 ~ 1h
11:09 CIA-40 bioclipse: egonw * r10376 /bioclipse2/trunk/plugins/ (19 files in 11 dirs): created net.bioclipse.recording.tests and moved all recording tests there
11:09 shk3 2pm your time, 1pm our time
11:10 CIA-40 bioclipse: egonw * r10377 /bioclipse2/trunk/plugins/ (31 files in 11 dirs): create net.bioclipse.managers.tests and moved all related test in there
11:10 steinbeck we are not normally back from lunch at 1pm
11:11 CIA-40 bioclipse: egonw * r10378 /bioclipse2/trunk/plugins/ (6 files in 2 dirs): First passing test. It connects a method in the manager interface with an equal method in the manager class.
11:11 egonw steinbeck: so, later?
11:11 egonw 13:30 your time then?
11:11 steinbeck yes
11:11 steinbeck ok
11:11 egonw 14:30 our time
11:11 egonw OK
11:11 steinbeck yes
11:11 steinbeck how? Via Skype and video?
11:11 egonw jonalv: count down in 79 minutes
11:11 egonw yes
11:11 olass skype video
11:11 olass sounds good
11:11 steinbeck cool
11:12 olass steinbeck: you'll have to gather around one computer
11:12 olass on bigscreen maybe
11:12 olass can only do skype video between 2 comps, not more
11:12 jonalv I don't have that much to present you know... :)
11:13 Gpox jonalv: https://huckster.dev.java.net/
11:13 * jonalv hopes for interactive questions :)
11:13 CIA-40 bioclipse: egonw * r10379 /bioclipse2/trunk/plugins/ (30 files in 16 dirs): got some basic conversion from String to IFile to work. Lot's of shuffling around of code as well in order to avoid circular dependencies.
11:13 CIA-40 bioclipse: egonw * r10380 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Added code for the Job stuff. A bit unsure about how to continue. Also the String -> IFile conversions tests no longer pass
11:14 CIA-40 bioclipse: egonw * r10381 /bioclipse2/trunk/plugins/net.bioclip​se.core/META-INF/spring/context.xml: removed leftovers of the moleculemanager
11:14 CIA-40 bioclipse: egonw * r10382 /bioclipse2/trunk/plugins/net.bioclipse.​ui/src/net/bioclipse/ui/Activator.java: commented out call to method that seems to do nothign except using the workspace before has been initlaised
11:15 CIA-40 bioclipse: egonw * r10383 /bioclipse2/trunk/plugins/ (8 files in 5 dirs): Made the net.bioclipse.managers.tests to be run as plugin tests. Also removed the UglyHacker since it is not needed any longer becasue of this.
11:15 CIA-40 bioclipse: egonw * r10384 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Not net.bioclipse.core but net.bioclipse.ui is booted first (BC2 boots again)
11:16 CIA-40 bioclipse: egonw * r10385 /bioclipse2/trunk/plugins/net.bioclipse.man​agers.tests/src/net/bioclipse/managers/test​s/AbstractManagerMethodDispatcherTest.java: switched from using a mock implementation of IFile to using a real Eclipse file
11:16 CIA-40 bioclipse: egonw * r10386 /bioclipse2/trunk/plugins/ (5 files in 3 dirs): Refactored out an interface IPartialReturner containing the method used for partial return callbacks. Also implemented a way to circumvent and do all when runnign from JavaScript.
11:17 CIA-40 bioclipse: egonw * r10387 /bioclipse2/trunk/plugins/ (4 files in 2 dirs): Added a couple of tests for String -> IFile conversions in different situations like when not running as a Job.
11:17 CIA-40 bioclipse: egonw * r10388 /bioclipse2/trunk/plugins/net.biocl​ipse.managers.tests/src/net/bioclip​se/managers/tests/TestManager.java: switched from file.getLocation() to file.getFullPath() which works for virtual files
11:18 CIA-40 bioclipse: egonw * r10389 /bioclipse2/trunk/plugins/ (6 files in 3 dirs): Added functionlaity to AbstractManagerMethodDispatcherTest.java to see that the method is actually called. And worked on getting things to run as jobs.
11:19 egonw olass: alternatively, skype for video
11:19 egonw regular conference call for voice
11:19 olass if not good audio, yes
11:19 CIA-40 bioclipse: egonw * r10390 /bioclipse2/trunk/ (23 files in 13 dirs): All tests except the one for callbacks in JavaScript now passes. Just hope they are testing somewhat the right things now...
11:20 egonw a second laptop webcam for a second connection if needed
11:20 egonw but I don't see rojasm around anymore
11:20 CIA-40 bioclipse: egonw * r10391 /bioclipse2/trunk/plugins/net.bioclip​se.ui.business/META-INF/MANIFEST.MF: added "," that should have been added in merge step...
11:20 egonw so it will be two locations, I guess
11:20 egonw ok, commiting seems to be back in action
11:20 egonw not sure how many commits done yet
11:21 egonw I count some 15
11:21 egonw I count some 25
11:21 egonw so, at about 30%
11:21 egonw well, 35%
11:21 CIA-40 bioclipse: egonw * r10392 /bioclipse2/trunk/plugins/ (9 files in 8 dirs): fixed a bunch of compile error caused during reshuffling of code between plugins
11:22 CIA-40 bioclipse: egonw * r10393 /bioclipse2/trunk/plugins/ (6 files in 2 dirs): Added test and code for converting from IFile to String for return values
11:28 egonw OK, another SSL fail
11:29 egonw recovering
11:31 egonw and comitting again
11:31 egonw svn--
11:31 egonw did I say this already?
11:32 CIA-40 bioclipse: egonw * r10394 /bioclipse2/trunk/plugins/ (23 files in 8 dirs): Started to refactor the Gist manager. Ran into some problems with the manager design and changed that. (removed annotation for ManagerImplementation and had to wrap dispatchers in Advisors)
11:32 olass @tell egonw YES
11:32 zarah Consider it noted.
11:32 egonw :)
11:32 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
11:33 CIA-40 bioclipse: egonw * r10395 /bioclipse2/trunk/plugins/ (6 files in 2 dirs): Wrote tests for the gist manager. ( 1 actually passes :-)
11:34 CIA-40 bioclipse: egonw * r10396 /bioclipse2/trunk/plugins/ (25 files in 8 dirs): Converted the InChI manager to NWO
11:35 CIA-40 bioclipse: egonw * r10397 /bioclipse2/trunk/plugins/net.bioclipse.​managers/src/net/bioclipse/managers/busi​ness/JavaManagerMethodDispatcher.java: Made method that are not void into not being run as jobs
11:35 egonw http://www.generationrescue.o​rg/media/Biomedical-101.html
11:35 zarah egonw's link is also http://tinyurl.com/c62bb5
11:35 CIA-40 bioclipse: egonw * r10398 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (CDKManager.java CDKManager.java.orig): added stub for method delcared in the cdk interface. (just to get things to compile, needs to be changed)
11:35 jonalv karma svn
11:35 zarah svn has a karma of -2
11:35 jonalv karma SVN
11:35 zarah SVN has a karma of -4
11:35 CIA-40 bioclipse: egonw * r10399 /bioclipse2/trunk/plugins/net.bioclipse.gist/src​/net/bioclipse/gist/business/IGistManager.java: cleanup after merge (when will I learn to do it correct from the start?)
11:35 jonalv SVN--, svn--
11:36 jonalv SVN--, svn--
11:36 jonalv SVN--, svn--
11:36 egonw that's the McCarthy that is killing people by convincing people to not have vaccines against deadly diseases because she feels they cause autism
11:36 zarah SVN--, svn--
11:36 CIA-40 bioclipse: egonw * r10400 /bioclipse2/trunk/plugins/net.bioclipse.gist/sr​c/net/bioclipse/gist/business/GistManager.java: made the methods taking an IFile in returning an IFile as well
11:36 sneumann karma git
11:36 zarah git has a karma of 19
11:36 sneumann wow
11:36 jonalv git++
11:36 CIA-40 bioclipse: egonw * r10401 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Made conversion for returnvalues from IFile to String happen both for JavaScript and Java (but only when aplicable)
11:36 jonalv :)
11:36 egonw to speak with the music
11:36 egonw this girl is dangerous
11:37 CIA-40 bioclipse: egonw * r10402 /bioclipse2/trunk/plugins/net.bioclipse.tests/ (2 files in 2 dirs): Added test suite for all new world order plugin tests
11:37 jonalv karma git-svn
11:37 zarah git-svn has a karma of 3
11:37 CIA-40 bioclipse: egonw * r10403 /bioclipse2/trunk/plugins/net.bioclipse.m​anagers/src/net/bioclipse/managers/busine​ss/AbstractManagerMethodDispatcher.java: ignore IPartialReturner when finding method to run
11:38 CIA-40 bioclipse: egonw * r10404 /bioclipse2/trunk/plugins/ (11 files in 4 dirs): Converted CDKDebugManager to the New World Order
11:38 CIA-40 bioclipse: egonw * r10405 /bioclipse2/trunk/plugins/net.bioclipse.tests/src​/net/bioclipse/tests/AllStableManagerTests.java: Removed reference to class which I deleted in a previous patch
11:38 CIA-40 bioclipse: egonw * r10406 /bioclipse2/trunk/plugins/net.bioclip​se.tests/src/net/bioclipse/tests/AllN​ewWorldOrderManagerPluginTests.java: Added the new NWO test suites for the CDKDebugManager
11:43 CIA-40 bioclipse: egonw * r10407 /bioclipse2/trunk/plugins/ (59 files in 35 dirs): changed names on cdkmanagerplugin test files to better correspond to the names in other plugins
11:43 CIA-40 bioclipse: egonw * r10408 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (bioclipse.product bioclipse.product.orig): bioclipse.product.... :)
11:44 CIA-40 bioclipse: egonw * r10409 /bioclipse2/trunk/plugins/net.bioclipse.cdk.bus​iness.test/src/net/bioclipse/cdk/business/test/ (6 files): Fixed test classes so that they compile again
11:45 CIA-40 bioclipse: egonw * r10410 /bioclipse2/trunk/plugins/ (4 files in 3 dirs): Start of refactoring CDKManager
11:45 CIA-40 bioclipse: egonw * r10411 /bioclipse2/trunk/plugins/n​et.bioclipse.cdk.business/ (6 files in 2 dirs): now the cdk manager is built using the New World order
11:46 CIA-40 bioclipse: egonw * r10412 /bioclipse2/trunk/plugins/ (3 files in 3 dirs): added cdk plugin tests to suite in net.bioclipse.tests
11:46 CIA-40 bioclipse: egonw * r10413 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business.test/src/net/bioclipse/​cdk/domain/tests/TestCDKMolecule.java: @BeforeClass annotated Junit methods need to be static
11:46 CIA-40 bioclipse: egonw * r10414 /bioclipse2/trunk/plugins/net.bioclipse.cdk​.debug.test/src/net/bioclipse/cdk/debug/tes​t/AbstractCDKDebugManagerPluginTest.java: Correct call to cdk.loadMolecule()
11:47 CIA-40 bioclipse: egonw * r10415 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (CDKManager.java CDKManager.java.orig): started to refactor the CDKManager class
11:47 CIA-40 bioclipse: egonw * r10416 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Completed first iteration of going through the CDKManager
11:48 CIA-40 bioclipse: egonw * r10417 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (3 files): Redid layout of ICDKManager
11:48 jonalv www.teamviewer.com
11:48 CIA-40 bioclipse: egonw * r10418 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.business/src/net/bioclip​se/cdk/business/ICDKManager.java: removed all method containing a progress monitor from ICDKManager
11:48 jonalv anyone up for a test? :)
11:49 CIA-40 bioclipse: egonw * r10419 /bioclipse2/trunk/plugins/ (3 files in 3 dirs): wrote tests for both testNumberOfEntriesInSDF methods
11:49 CIA-40 bioclipse: egonw * r10420 /bioclipse2/trunk/plugins/ (7 files in 4 dirs): Made sure the callbacks to BioclipseUIJobs are performed
11:50 CIA-40 bioclipse: egonw * r10421 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Can't test BioclipseUIJob stuff. Don't know how to do it.
11:50 CIA-40 bioclipse: egonw * r10422 /bioclipse2/trunk/plugins/net.bioclipse.m​anagers/src/net/bioclipse/managers/busine​ss/AbstractManagerMethodDispatcher.java: only try to index the array if it is big enough
11:51 CIA-40 bioclipse: egonw * r10423 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/domain/CDKConformer.java: need an empty constructor in order to be able to create a proxy (used for recording)
11:51 CIA-40 bioclipse: egonw * r10424 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Fixed tests to use a unique file name, because each unit test is now run twice (Java + JavaScript version)
11:52 CIA-40 bioclipse: egonw * r10425 /bioclipse2/trunk/plugins/net.bioclipse.man​agers/src/net/bioclipse/managers/business/ (2 files): rethrow those BioclipseException at any cost. Managers methods claiming to throw BioclipseExceptions should actually do throw them...
11:58 olass egonw: how many left?
11:59 egonw thanx for the ping
11:59 egonw another SSL fail
11:59 egonw svn--
11:59 egonw counting
11:59 egonw anmd recovering
12:02 egonw OK, 10 left
12:02 masak egonw++
12:02 masak soon the SVN nightmare will be over for the Bioclipse project.
12:03 gilleain joined #bioclipse
12:04 gilleain egonw : ping
12:04 CIA-40 bioclipse: egonw * r10426 /bioclipse2/trunk/plugins/ (9 files in 8 dirs): Compile fixes for new and here and there older code, towards using the new NWO API. The new code just brought in by the rebase on master
12:04 CIA-40 bioclipse: egonw * r10427 /bioclipse2/trunk/plugins/net.bioclipse.ma​nagers/src/net/bioclipse/managers/business​/JavaScriptManagerMethodDispatcher.java: Rethrow BioclipseExceptions so that manager methods that are declared as throwing BioclipseExceptions actually do that
12:04 CIA-40 bioclipse: egonw * r10428 /bioclipse2/trunk/plugins/net.bioclipse.m​anagers/src/net/bioclipse/managers/busine​ss/AbstractManagerMethodDispatcher.java: the right method should now be found in Java version when the method takes a BioclipseJobUpdateHook
12:05 CIA-40 bioclipse: egonw * r10429 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): no progressmonitors on the public manager methods
12:05 gilleain er. well, anyone : I'm doing a bioclipse update and I'm getting files  like "SomeClassOrOther.java.LOCAL.9352.java" and "SomeClassOrOther.java.REMOTE.9352.java" !!
12:05 CIA-40 bioclipse: egonw * r10430 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.business.test/src/net/bioclipse/cdk/ (2 files in 2 dirs): "normal" manager tests are run against the class so progress monitors are needed
12:05 gilleain eg GenerateInChI.java
12:06 jonalv gilleain: are you gonan participate in this presentation thingie?
12:06 gilleain I spose so.
12:06 CIA-40 bioclipse: egonw * r10431 /bioclipse2/trunk/plugins/ (4 files in 4 dirs): fixed cdk.loadmolecule(IFIle, BioclipseUIJob) used when opening jcp
12:07 CIA-40 bioclipse: egonw * r10432 /bioclipse2/trunk/plugins/net.biocl​ipse.cdk.qsar.test/src/net/bioclips​e/cdk/qsar/test/TestCDKQsar.java: no progressmonitor to the method in the interface
12:07 CIA-40 bioclipse: egonw * r10433 /bioclipse2/trunk/plugins/net.bioclipse.mana​gers.tests/src/net/bioclipse/managers/tests/ (ITestManager.java TestManager.java): Moved methods around for pedagogical purpose
12:07 jonalv gilleain: if so, could you install www.teamviewer.com on your computer? :)
12:08 gilleain I followed that link, and the answer is : categorically no.
12:08 gilleain I am happy to use someone else's computer that has been zombified in this way, but not mine.
12:08 jonalv gilleain: uhm why not?
12:08 CIA-40 bioclipse: egonw * r10434 /bioclipse2/trunk/plugins/ (20 files in 7 dirs): Removed files which I added in a stupid (git add .) action
12:09 gilleain also, I can't install things on this windows machine.
12:09 jonalv gilleain: you only need to install the variant for looking at my computer...
12:09 gilleain hmmmm.
12:09 jonalv gilleain: I thought it would help us to see the same thing...
12:09 gilleain perhaps.
12:09 jonalv means to and end...
12:09 jonalv |an end
12:09 jonalv :)
12:09 egonw gilleain: pong
12:10 CIA-40 bioclipse: egonw * r10435 /bioclipse2/trunk/plugins/ (8 files in 7 dirs): Fixed compile errors and added updated for the NWO
12:10 egonw yeah
12:10 gilleain egonw : things are fucked.
12:10 egonw that was number 72!
12:10 egonw dead animals?
12:10 gilleain no : my workspace.
12:10 gilleain oh, no wait.
12:10 egonw OK, after what commit?
12:11 egonw OK, all NWO patches are in...
12:11 gilleain well, I am trying to update again. I'll keep you updated.
12:11 egonw OK
12:11 egonw all: please update now
12:11 egonw all NWO patches are in SVN on SF now
12:11 egonw you will need to import new plugins
12:12 egonw jonalv: can you please explain which?
12:12 shk3 back from lunch
12:12 egonw jonalv: or will we see that in the presentation?
12:12 jonalv egonw: sry, which what?
12:12 * egonw is enabling SVN write access for everyone again
12:12 egonw the new plugins
12:12 jonalv oh, I don't know
12:12 egonw all: after updating, add those new plugins, and don't forget the Set target Platform thingy
12:13 egonw net.bioclipse.managers
12:13 egonw and
12:13 egonw net.bioclipse.recording, right?
12:13 jonalv yes at least those two
12:13 egonw more?
12:13 jonalv might be something more as well
12:13 jonalv I am not sure
12:13 egonw :)
12:14 egonw ok, please do make sure
12:14 egonw I'll add the above two to the wiki now
12:14 jonalv okey
12:14 jonalv but someone using subclipse (olass?) could see which plugins they need to add. The deps should be there...
12:14 egonw olass:  can you please reply to your email on bc-devel ?
12:15 olass jonalv, egonw: ok
12:15 jonalv egonw: BUILD FAILED
12:15 jonalv /Users/jonathan/Work/git/bioclipse2/plugins​/net.bioclipse.doc.developers/build.xml:4: Execute failed: java.io.IOException: perl: not found
12:15 jonalv
12:17 egonw jonalv: that would be accurate
12:17 shk3 pleae tell us if the new worls order tutorial is starting
12:17 olass shk3: we decided 14.30
12:18 olass for us
12:18 olass that is in 10 minutes
12:18 egonw shk3: are all of you set?
12:18 olass jonalv: that will take me more than 10 minutes however
12:18 olass so will do that after the presentation
12:19 shk3 I think so
12:19 shk3 Christoph will do the skype stuff
12:19 shk3 I rely on him to handle that
12:20 olass shk3: let me know when you are set to go and I'll call christoph on skype
12:20 gilleain egonw : checking out those plugins improved things
12:20 shk3 i am ready
12:20 * egonw is pushing NewWorldOrder3 to git@pele
12:20 egonw gilleain: ack
12:20 egonw gilleain: yes, the patch is disruptive
12:20 egonw gilleain: and we will likely have some stuff to do to get all 100% again
12:21 gilleain I should coco!
12:21 egonw but we can run unit tests again
12:21 egonw (plugin unit tests)
12:21 olass ok, I'll set up my laptop for the conference call now
12:22 egonw OK, will join in Jarls room
12:24 * masak -> Jarl's room
12:28 rojasm joined #bioclipse
12:29 olass_ joined #bioclipse
12:29 olass_ steinbeck: skype?
12:30 gilleain what username?
12:31 gilleain olass_ or phone
12:32 Gpoks joined #bioclipse
12:32 steinbeck I can go to Gilleain's computer
12:32 olass_ steinbeck, gilleain: yes, that would be good
12:33 jonalv` joined #bioclipse
12:33 olass_ we can only do one comp to one comp
12:33 gilleain my username is gilleain.torrance
12:33 jonalv` @ping
12:33 zarah jonalv`: pong
12:33 jonalv` gilleain: do you want to try an share scrren?
12:34 olass_ gilleain: skype for video?
12:34 rojasm can I participate too?
12:39 Gpox http://www.teamviewer.com/
13:12 jonalv` "ping
13:12 jonalv` @ping
13:12 zarah jonalv`: pong
13:12 shk3 question: shouldn't I be able to commit?
13:12 olass_ oh
13:12 shk3 oh?
13:13 olass_ egonw was too optimistic :)
13:13 jonalv` (git-svn)--
13:13 olass_ it's not done yet
13:13 olass_ will see to it asap
13:13 shk3 ah
13:13 shk3 thanks
13:17 Gpoks joined #bioclipse
13:20 jonalv joined #bioclipse
13:20 jonalv o/
13:21 gilleain \o
13:23 gilleain or \..&*$..o..$%^..
13:23 gilleain (with added noise)
13:23 masak whoa.
13:23 masak my first reaction was to parse that as a Perl regex.
13:23 gilleain no masak, it wasn't perl
13:23 masak it didn't go very well. :/
13:24 gilleain :)
13:24 jonalv masak: my first reactions was: "Bah that is a Perl regexp, and it looks complicated too. I won't even bother"
13:24 masak this inverted-screen-colors thing is awesome!
13:24 jonalv *lol*
13:24 egonw joined #bioclipse
13:25 jonalv egonw: why do I get: "BUILD FAILED
13:25 jonalv /Users/jonathan/Work/git/bioclipse2/plugins​/net.bioclipse.doc.developers/build.xml:4: Execute failed: java.io.IOException: perl: not found
13:25 jonalv "
13:25 gilleain you don't have perl?
13:25 jonalv or masak?
13:25 gilleain well if you don't have masak, that might be a problem, too.
13:25 masak jonalv: you must have perl. Mac OS X comes with it.
13:26 masak jonalv: however, Eclipse might look for it in the wrong place.
13:26 masak jonalv: check where it's looking for it.
13:26 jonalv masak: uhm how do I do that?
13:27 masak jonalv: this is part of the build, right?
13:28 rojasm joined #bioclipse
13:28 gilleain I have a /usr/bin/perl, an /opt/local/perl, and a /System/Library/Perl/.../perl
13:29 egonw masak: yes
13:29 egonw ant might look in the wrong place
13:29 egonw I have 'perl' as executable
13:29 egonw so assume it takes the default paths for execs
13:30 egonw that reminds me... need to remove the now autogenerated .xml and .html files...
13:32 * gilleain only has two errors now - both in structure db (due to changes in cdk.business)
13:34 egonw gilleain: yes, same here
13:43 * egonw refreshing his workspace
13:43 olass joined #bioclipse
13:45 egonw jonalv: for doc.devel
13:45 egonw you will also need xsltproc
13:46 jonalv egonw: I changed from perl to the exactl ocation of my perl library. It ran. Then I reverted and now I don't get any error any longer. Does it check if it needs to rebuild somehow before rebuilding?
13:46 egonw yes
13:47 jonalv okey so I guess I will get problem next time those files are changed then...
13:49 CIA-40 bioclipse: egonw * r10436 /bioclipse2/trunk/plugins/net.​bioclipse.doc.developers/doc/ (15 files): Remove XML and HTML documentation files which are now autogenrated with Ant/Perl/xsltproc when Eclipse builds the project
13:49 rojasm I realize that Bioclipse in sourceforge has not integrated git yet. egonw How do you were using it? from github?
13:50 jonalv rojasm: git-svn? (/me is not sure he understnds the question)
13:50 masak rojasm: we tend to use git-svn here.
13:50 rojasm oh ok
13:50 masak rojasm: it hurts a lot less than pure svn, but it still hurts.
13:51 rojasm ok. I see
13:51 jonalv yea git++ svn--
13:52 masak @karma svn
13:52 zarah svn has a karma of -4
13:52 masak svn--
13:52 olass karma git
13:52 zarah git has a karma of 21
13:52 masak git++
13:52 olass not bad
13:52 olass karma rojasm
13:52 masak @karma olass
13:52 zarah rojasm has a karma of 2
13:52 zarah olass has a karma of 49
13:53 jonalv @karma masak
13:53 zarah masak has a karma of 85
13:53 masak @karma jonalv
13:53 olass :(
13:53 zarah jonalv has a karma of 97
13:53 olass there was a time...
13:53 masak olass-- # I knew it!
13:53 gilleain if you could sum up all the karma from all irc rooms, you could have a sort of voting system
13:53 masak jonalv++
13:53 olass are you stealing karma again masak?
13:53 masak olass: yup.
13:53 olass last time you stole 50 points!
13:54 olass I remeber that time...
13:54 masak olass--
13:54 olass *morrr*
13:54 olass *MORRRR*
13:54 masak :P
13:54 masak olass: it's completely your fault.
13:54 olass :(
13:54 olass no
13:54 jonalv olass: I would keep silent if I where you...
13:54 olass you have no proof whatsoever
13:54 jonalv karma egonw
13:54 zarah egonw has a karma of 88
13:54 masak olass: you're right, I don't.
13:54 olass you just stole 50 p
13:54 jonalv egonw++
13:55 masak olass: no, I restored the points after they were inexplicably boosted.
13:55 jonalv olass: you admited it. That's good enough for me in that case
13:55 olass they were NOT
13:55 olass I di not!
13:55 masak olass--
13:55 olass for what?
13:55 masak for being wrong _and_ stubborn.
13:55 olass left #bioclipse
13:56 masak I like olass, but I don't want people to jury-rig the karma system.
13:57 gilleain you'll have the U.N. on the case.
13:59 olass joined #bioclipse
13:59 olass @morr
13:59 masak gilleain: it was after olass did this that I introduced global logging.
14:00 olass did what?
14:00 masak it does actually have parallels to the UK.
14:00 masak olass: sorry, we were talking about a few things here while you were away...
14:00 * olass were hiding from the karma-thief
14:00 masak olass: you know, being off the channel doesn't help.
14:01 olass hmm
14:04 CIA-40 bioclipse: egonw * r10437 /bioclipse2/trunk/_playground_/ (4 files in 4 dirs): Updated the MEDEA plugins for the NWO: IBioclipse manager moved from net.bioclipse.core to net.bioclipse.managers
14:06 egonw olass: ping
14:06 egonw are you fixing the .ds plugins for NWO?
14:08 olass yes
14:14 egonw good
14:24 CIA-40 bioclipse: ospjuth * r10438 /bioclipse2/trunk/plugins/net.bioclipse.ds/ (2 files in 2 dirs): IBioclipse manager moved from net.bioclipse.core to net.bioclipse.managers
14:28 CIA-40 bioclipse: ospjuth * r10439 /bioclipse2/trunk/plugins/​net.bioclipse.ds.dblookup/ (3 files in 2 dirs): Adapted for NWO and new API to get cached properties on IMolecule.
14:30 jonalv olass: is it okey if I redo the UIManager while I write that new page?
14:30 jonalv masak: is it okey if I redo the UIManager?
14:30 masak jonalv: yes, more than OK.
14:30 olass jonalv: I'm fine with that
14:30 CIA-40 bioclipse: ospjuth * r10440 /bioclipse2/trunk/plugins/net.biocl​ipse.ds.dblookup.bursi/plugin.xml: Set desired tanimoto difference to 0.7.
14:31 jonalv olass: that might take some longer but it will be better with a real example and me actually doing it as I write it...
14:31 olass jonalv++ //Sounds like an excellent idea
14:31 masak jonalv++ # you're so diligent!
14:32 CIA-40 bioclipse: ospjuth * r10441 /bioclipse2/trunk/plugins/net​.bioclipse.ds.signsig.bursi/ (4 files in 4 dirs): Adapted for NWO API.
14:32 CIA-40 bioclipse: ospjuth * r10442 /bioclipse2/trunk/plugins/net.bioclipse.ds.sm​arts/src/net/bioclipse/ds/smarts/model/impl/ (SmartsInclusiveExclusiveTest.java SmartsMatchingTest.java): Adapted for NWO API and deps.
14:34 egonw jonalv: in for a test?
14:34 egonw can you boot TeamViewer?
14:34 CIA-40 bioclipse: ospjuth * r10443 /bioclipse2/trunk/plugins/net.bioclipse.ds.tests/ (4 files in 2 dirs): Adapted for NWO API and deps.
14:34 jonalv egonw: define "test"
14:38 * masak doesn't seem to be able to get Bioclipse running again after the Big Merge
14:39 egonw masak: no problem here
14:39 masak I think I'm missing some plugins.
14:39 egonw and I now have TeamViewer to prove it :)
14:40 masak :P
14:40 masak even screen dumps can be forged. :)
14:43 egonw true
14:44 masak egonw: I can see your desktop from here! :)
14:44 egonw me has MEDEA in action
14:44 egonw right
14:44 egonw who else wants?
14:44 jonalv this is cool :)
14:44 egonw this is Bioclipse showing MEDEA in action
14:44 egonw it calculated the MS spectrum of the test compound of earlier this weeken
14:45 egonw an alphapinone thingy
14:45 egonw who wants to shout a SMILES?
14:45 egonw :)
14:45 egonw steinbeck: TeamViewer is working for me...
14:46 egonw this will work very nicely for virtual CDK workshops too
14:46 jonalv egonw: C(C1C(C(C(C(O1)O)O)O)O)O
14:46 masak o_O
14:46 gilleain that looks like your sugar example, yes
14:47 egonw this is the fragmentation modeling in action
14:47 egonw it is testing what reactions are possible
14:47 egonw and calculating which are likely
14:47 jonalv cool
14:47 egonw who wants to look up the real MS in NIST?
14:48 egonw mmm
14:48 jonalv what are we gonna get from it when it's done?
14:48 egonw maybe we should have a NIST manager :)
14:48 egonw the mass spectrum (EI)
14:48 * jonalv doesn't really know what NIST is but sure why not?
14:48 egonw google for NIST webbook
14:48 zarah egonw: http://webbook.nist.gov/chemistry/
14:49 jonalv zarah++
14:49 egonw indeed
14:49 egonw zarah++
14:49 egonw mostly silent... but when she speaks ...
14:49 egonw jonalv: thanx for this SMILES :(
14:50 jonalv egonw: is it failing? :)
14:50 egonw no
14:50 egonw it just takes very long :)
14:50 jonalv is it because it's a ring?
14:50 egonw perhaps
14:51 egonw also, many lone pairs
14:51 egonw aha... something happened
14:51 jonalv egonw: you got an exception
14:51 egonw arg...
14:51 jonalv lolo
14:51 egonw forgot to give it a new name :(
14:51 egonw stupid me
14:51 jonalv lolol
14:52 jonalv here we go again...
14:52 egonw :)
14:52 egonw you took the words right out of my mouth
14:53 egonw brb
14:53 jonalv I can see what egonw is about to say before he has said it :)
14:58 jonalv jmol++
15:00 egonw ha, secretly reading my mail are you?
15:01 gilleain that jmol-svg graph stuff is very cool
15:01 egonw yes, need to look at that
15:01 gilleain http://chemapps.stolaf.edu/jmol/doc​s/examples-11/jmol-flot-energy.htm
15:01 zarah gilleain's link is also http://tinyurl.com/rbgpp8
15:05 egonw OK, me is going home
15:06 jonalv gilleain: what is that on the right? :)
15:06 gilleain a graph?
15:06 gilleain click on the points of the graph, and the jmol should change state
15:06 jonalv of what? The axis doesn't say...
15:06 gilleain oh, right. I have no idea. Energy or something.
15:07 gilleain "Degree of chemical magic vs conformation", perhaps.
15:07 jonalv okey
15:08 jonalv gilleain: yea cool indeed
15:24 jonalv does anyone except egonw know anythign about the ui.save method takinga Runnable callBackFunction?
15:51 jonalv karma
15:51 zarah jonalv has a karma of 99
15:52 jonalv soo cloose...
15:52 jonalv :)
15:52 masak jonalv++
15:52 jonalv karma
15:52 zarah jonalv has a karma of 100
15:52 masak that one's one me. :)
15:52 masak jonalv--
15:52 masak oops.
15:53 jonalv oh I remember a time when I had... :)
15:53 masak jonalv++ # :)
15:53 gilleain it took me ages to parse "that one's one me".
15:54 gilleain I guess it was "on me", like milkybars.
15:54 masak aye...
15:55 masak s:2nd/one/on/
15:56 * gilleain is tired of the automatic updater nagging me to restart my machine, so is going off line. bye
15:57 * masak shouts "bye!" after gilleain
16:20 edrin left #bioclipse
16:25 steinbeck joined #bioclipse
16:51 CIA-40 bioclipse: ospjuth * r10444 /bioclipse2/trunk/plugins/net.biocli​pse.xws4j/cheatsheets/xmppgists.xml: Replaced hivpred gist with bioschemata gist in xmppscripts cheatsheet.
16:51 CIA-40 bioclipse: ospjuth * r10445 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.smartsmatching/src/net/bioclipse/cdk/sma​rtsmatching/views/SmartsMatchingView.java: Clear SMARTS matches on structure changes in JCP. Solves #1067.
18:35 edrin joined #bioclipse
18:36 edrin hi
18:36 zarah hi edrin
18:37 CIA-40 bioclipse: ospjuth * r10446 /bioclipse2/trunk/plugins/net.bioclipse.ds.tests/​src/net/bioclipse/ds/tests/TestBursiSmarts.java: We now have 6 tests, updated list size assertion.
19:18 olass joined #bioclipse
21:29 edrin1 joined #bioclipse
22:02 CIA-40 bioclipse: edrin_t * r10447 /bioclipse2/trunk/plugins/net.bioclips​e.jseditor/src/net/bioclipse/jseditor/ (RhinoConsole.java actions/RunRhinoScriptAsJobAction.java): nowthe js editor console is shown when a script is run
23:22 CIA-40 bioclipse: edrin_t * r10448 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/ (4 files in 3 dirs): removed .jar that is not needed...

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