Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-05-20

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All times shown according to UTC.

Time Nick Message
00:12 rojasm joined #bioclipse
00:34 CIA-40 bioclipse: miguelrojasch * r10585 /bioclipse2/trunk/plugins/net.biocl​ipse.reaction/META-INF/MANIFEST.MF: removed bundle manager
04:14 rednael [Planet Bioclipse] Eclipse-Spring Export problem: uses conflict for spring aop  http://chemicalrcp.blogspot.com/2009/05/​eclipse-spring-export-problem-uses.html
04:15 zarah rednael's link is also http://tinyurl.com/p2xppr
04:55 rojasm joined #bioclipse
05:29 egonw joined #bioclipse
05:54 rojasm moin
05:56 egonw hi rojasm
05:56 * egonw is about to have breakfast
05:57 egonw could you keep up yesterday
05:57 egonw what a disaster this spring/exporting problem was
05:57 rojasm uf
05:57 rojasm before I updated it was working!
05:57 egonw it should be working once more
05:58 egonw r10577
05:58 rojasm but today morning I have progress meeting with ABS
05:58 egonw ABS?
05:58 rojasm Division of Analytical BioSciences
05:58 egonw ah, right
05:58 rojasm with all statistical
05:58 egonw good
05:58 rojasm and I wanted to show what I did in Cambridge
05:59 egonw ic
05:59 egonw revision 10577 should be working
05:59 egonw it is here
05:59 rojasm can you test if for you works at least
05:59 egonw both running and using manager, and exporting
05:59 rojasm mmm
05:59 egonw sure
05:59 rojasm I have a error only to start
05:59 egonw first need to do breakfast now
05:59 egonw yes,
06:00 egonw one stacktrace on startup
06:00 rojasm sorry go ahead
06:00 egonw about something being locked
06:00 rojasm see you later
06:00 egonw does not seem to harm
06:00 egonw with jonathan and I will look at that today, I guess
06:00 egonw cu later
06:09 CIA-40 bioclipse: miguelrojasch * r10586 /bioclipse2/trunk/_playground_/net.bioclipse.medea​.test/src/net/bioclipse/medea/test/MedeaTest.java: Updated to new manager
06:13 rojasm error that I get
06:13 rojasm DEBUG - org.eclipse.core.internal.r​esources.ResourceException: The resource tree is locked for modifications.
06:15 rojasm some solutions
06:15 rojasm http://www.eclipsezone.com/​eclipse/forums/t114710.html
06:15 zarah rojasm's link is also http://tinyurl.com/q38nza
06:22 egonw rojasm: thanx for that link
06:22 egonw looks useful
06:27 olass joined #bioclipse
06:39 egonw Planet Eclipse: http://dev.eclipse.org/blogs/wayne/2009/0​5/19/calling-all-maceclipse-enthusiasts/
06:39 zarah egonw's link is also http://tinyurl.com/pune7l
06:41 rojasm egonw can I do some thing to solve the problem with the resource tree is locked error?
06:42 egonw no, not really
06:42 egonw we'll manage
06:42 egonw but thanx
06:42 rojasm ok let me know
06:48 CIA-40 bioclipse: egonw * r10587 /bioclipse2/trunk/plugins/net.bioclipse.ui/src/ne​t/bioclipse/ui/ApplicationWorkbenchAdvisor.java: Remove debug output to STDOUT
07:08 CIA-40 bioclipse: egonw * r10588 /bioclipse2/trunk/plugins/net.bioc​lipse.seneca/META-INF/MANIFEST.MF: Fixed MANIFEST.MF syntax: missing entry break ','
07:09 CIA-40 bioclipse: ospjuth * r10589 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.business/src/net/bioclip​se/cdk/domain/ISubStructure.java: Added method 'public Color getHighlightingColor(IAtom atom);' so that ISubStructure can supply a color for the highlighting.
07:09 CIA-40 bioclipse: ospjuth * r10590 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.smartsmatching/src/net/bioclipse/c​dk/smartsmatching/model/SmartsHit.java: SmartsHit should always be colored in same color.
07:10 egonw WTF??
07:10 CIA-40 bioclipse: ospjuth * r10591 /bioclipse2/trunk/plugins/net.bioclipse.ds/src/​net/bioclipse/ds/model/SubStructureMatch.java: Standards SubStructureMatches are colored in yellow. Subclasses may override.
07:10 egonw svn--
07:10 Gpox joined #bioclipse
07:12 olass egonw: what now?
07:12 CIA-40 bioclipse: ospjuth * r10592 /bioclipse2/trunk/plugins/net​.bioclipse.ds.signsig.bursi/ (3 files in 3 dirs): Cleaned up instantiation, added comments, and removed static declarations.
07:12 egonw dunno
07:12 olass egonw: why svn--?
07:13 egonw you and me commiting things at the same time messed up things
07:13 egonw at least git-svn is now seriously confused
07:13 egonw commits 10591 and 10588 are just missing here
07:13 egonw in my log
07:17 CIA-40 bioclipse: ospjuth * r10593 /bioclipse2/trunk/plugins/net.bioclip​se.ds.signsig.bursi/src/net/bioclipse​/ds/signsig/bursi/SignSIcRunner.java: Delete temp file upon completed prediction.
07:20 hadhadhadhadhadh joined #bioclipse
07:22 hadhadhadhadhadh joined #bioclipse
07:23 hadhadhadhadhadh [Bioclipse Twitter] glad that #bioclipse is exporting again... what a pain that was. @jonalv++  http://twitter.com/egonwill​ighagen/statuses/1857057532
07:23 hadhadhadhadhadh [Bioclipse Twitter] Upgraded #bioclipse to #jmol 11.6.21 and enjoying the new Jmol console, allowing me to type Jmol script directly, without jmol.run()  http://twitter.com/egonwill​ighagen/statuses/1677313855
07:23 zarah hadhadhadhadhadh's link is also http://tinyurl.com/q98y75
07:23 zarah hadhadhadhadhadh's link is also http://tinyurl.com/ptshto
07:23 egonw hadhadhadhadhadh: one item would have been enough, you know
07:24 hadhadhadhadhadh [Bioclipse Twitter] writing #bioclipse scripts to access #xmpp cloud services that use #cdk functionality, like XLogP  http://twitter.com/egonwill​ighagen/statuses/1715329066
07:24 zarah hadhadhadhadhadh's link is also http://tinyurl.com/odhv8r
07:24 egonw mmm...
07:25 hadhadhadhadhadh [Bioclipse Twitter] OK, #bioclipse / #xmpp cloud service calling scripts are online @ http://bit.ly/A8UHb  http://twitter.com/egonwill​ighagen/statuses/1715914718
07:29 olass egonw: very annoying name, hadhadhadhadhadh
07:30 egonw olass: that's masak's fault
07:30 egonw he made me do it
07:30 olass masak--
07:31 hadhadhadhadhadh joined #bioclipse
07:33 hadhadhadhadhadh [Bioclipse Twitter] /me wonders if the new #rednael is now properly working for #bioclipse twitter items  http://twitter.com/egonwill​ighagen/statuses/1857103416
07:33 zarah hadhadhadhadhadh's link is also http://tinyurl.com/pa4ct8
07:33 egonw rednael++
07:34 CIA-40 bioclipse: ospjuth * r10594 /bioclipse2/trunk/plugins/net.bioclipse.co​re/src/net/bioclipse/core/Activator.java: Commented out deleteVirtalProject since causing exception on startup. It was put there 'just to be sure' that virtual project would be empty on startup, but that should really be the case anyway.
07:34 olass egonw: I fixed the stacktrace on startup
07:34 olass I was responsible for it
07:35 olass hence I can remove the line
07:35 egonw ah, ok
07:35 egonw olass++
07:35 olass egonw: I really want to make a new export today
07:35 egonw yes, beta
07:35 olass indeed
07:35 egonw sounds like a wise decision
07:35 egonw NWO needs good testing
07:37 hadhadhadhadhadh joined #bioclipse
07:42 hadhadhadhadhadh joined #bioclipse
07:44 hadhadhadhadhadh [Bioclipse Twitter] today's program: work on #metware: analyze it's OWL in #bioclipse, set up a manager  http://twitter.com/egonwill​ighagen/statuses/1857161676
07:44 zarah hadhadhadhadhadh's link is also http://tinyurl.com/r47c33
07:45 edrin joined #bioclipse
07:45 edrin morning
07:45 egonw hi edrin
07:45 edrin ok
07:45 jonalv joined #bioclipse
07:45 edrin time to test...?
07:45 * egonw is upgrading rednael with new code
07:45 egonw edrin: yes
07:45 edrin hello jonalv
07:45 egonw hi jonalv!
07:45 egonw jonalv++
07:46 jonalv egonw: are things working now?
07:46 zarah jonalv: You have new messages. Write '/msg zarah @messages' to read them.
07:46 egonw jonalv: yes
07:46 jonalv zarah: just tell me...
07:46 zarah jonalv: 12 h 11 m 58 s ago, olass said jonalv++ //for solving the exporting
07:46 zarah jonalv: 10 h 50 m 19 s ago, egonw said I applied his suggestions, and that they worked! jonalv++
07:46 jonalv woho :)
07:46 egonw @karma jonalv
07:46 zarah jonalv has a karma of 116
07:46 jonalv wow
07:47 jonalv karma egonw
07:47 zarah egonw has a karma of 91
07:47 olass jonalv: there was a big karma boost last night for you when we discovered you had fixed things
07:47 jonalv egonw++
07:47 olass yes, egonw++ //working hard on this too
07:47 olass karma olass
07:47 zarah olass has a karma of 47
07:47 olass :(
07:47 jonalv so egonw++ fixed it all for me
07:47 jonalv karma olas
07:47 zarah olas has a karma of 48
07:47 olass karma olas + olass
07:48 zarah olas + olass has a karma of 0
07:48 jonalv olass: you have your karma splitted on two names...
07:48 egonw olass: no
07:48 egonw masak would do:
07:48 egonw (karma olas) + (karma olass)
07:48 olass nope
07:48 olass did not work
07:48 egonw masak--
07:48 edrin karma
07:48 zarah edrin has a karma of 26
07:48 olass (@karma olas) + (@karma olass)
07:48 jonalv am I the only one on bmc today?
07:49 jonalv :(
07:49 olass jonalv: I'll be there tomorrow
07:49 egonw I'll be there tomorrow too
07:49 jonalv olass: I won't
07:49 jonalv :)
07:49 egonw and suggested a drink in the afternoon
07:49 egonw :(
07:49 egonw no jonalv
07:49 jonalv egonw: a drink?
07:49 jonalv :)
07:49 egonw to celebrate the New World Order
07:50 olass can I have jonalv's beer then?
07:50 jonalv I think masak and I ws planning a little perl6 hackaton tomorrow...
07:50 jonalv so I can definitly join in for a drink in the afternoon :)
07:50 olass jonalv: you could drop by for teh NWO celebration in the afternoon...
07:50 olass nice!
07:50 jonalv yup
07:50 olass today will be a release on SF
07:50 olass if things go well
07:50 jonalv okey
07:51 olass jonalv: I have some bugs that I need help with
07:51 jonalv egonw: what was this about a NPE in recording?
07:51 jonalv olass: okey
07:51 olass but wil make sure they are not solved by the new NWO first
07:51 egonw jonalv: see the bug report about it
07:52 jonalv egonw: that was justa stacktrace nothing about how to reproduce
07:53 olass @pz
07:53 zarah olass: Pelezilla is at http://bugs.bioclipse.net
07:56 egonw it refers to a commit
07:56 egonw check that commit too
07:56 egonw revert it
07:56 olass oh, about doc.developers
07:56 olass is that fixed?
07:58 egonw jonalv: you can revert a patch very simple:
07:58 egonw git revert HASH
08:01 jonalv egonw: yea I got merge problems when I tried that so I thought I was doing something wrong
08:03 CIA-40 bioclipse: ospjuth * r10595 /bioclipse2/trunk/ (36 files in 36 dirs): Set version to 2.0.0.B20090520.
08:04 CIA-40 bioclipse: ospjuth * r10596 /bioclipse2/trunk/plugins/ (4 files in 4 dirs): Set version to 2.0.0.B20090520.
08:06 rednael [Leander Git] Updated Leander:  http://github.com/egonw/rednael/commit/1​d63ef5344b2e38585367c90f0dde3f4ceb27862
08:07 zarah rednael's link is also http://tinyurl.com/p6b653
08:11 hadhadhadhadhadh joined #bioclipse
08:11 shk3 joined #bioclipse
08:12 rednael joined #bioclipse
08:14 jonalv egonw: can you run the AllStableManager plugin tests in net.bioclipse.tests?
08:14 rojasm joined #bioclipse
08:15 jonalv olass: can you run the AllStableManager plugin tests in net.bioclipse.tests?
08:15 olass have not that checked out
08:15 egonw jonalv: will try
08:16 olass testing stuff for edrin
08:16 rojasm egonw: let me know when you could solve the problem with lock
08:16 olass will check out and run test later
08:16 jonalv olass: I want that to run before I go in and make changes in that method in the dispatcher. Otherwise I might break a lot without realising...
08:16 egonw rojasm: olass already did
08:16 olass you could not run the javacdkmanager test?
08:17 olass oh, you want to run all tests?
08:17 jonalv olass: I haven't tried. I want to run all tests to see that I don't break something when I do changes
08:18 olass sounds good
08:18 jonalv olass: yes but I can't get it to work... :/
08:19 olass oh no :(
08:19 jonalv Failed to set up the Bioclipse workspace: Cannot change the location once it is set.
08:19 olass sounds logical
08:19 olass I think egonw was messing with that yesterday...
08:19 edrin oh no
08:19 olass no?
08:20 jonalv egonw: this seems like something you might be able to help with...
08:20 olass edrin: what is it?
08:21 edrin hm
08:21 edrin maybe not too severe
08:21 edrin i think the error you get if the password is wrong is not optimal...
08:22 egonw jonalv: AllStableManagerTest: 38 tests, 8 errors, 3 fails
08:22 egonw now running the PluginTest equiv
08:23 jonalv egonw: that can't be including cdk...
08:23 jonalv ah
08:23 egonw what cannot?
08:23 jonalv egonw: please run the plugin equivalent. I thought it was that you reported and it was way to few tests...
08:24 * jonalv can't run any plugin tests
08:26 egonw OK, I can reproduce the problem
08:27 egonw ha...
08:28 egonw we accidentally commited line 76 :)
08:28 egonw ApplicationWorkbenchAdvisor.java
08:28 egonw fix pending
08:30 CIA-40 bioclipse: egonw * r10597 /bioclipse2/trunk/plugins/net.bioclipse.ui/src/ne​t/bioclipse/ui/ApplicationWorkbenchAdvisor.java: Removed temporary test: again properly checks if instance location is set
08:31 egonw jonalv: it should work now
08:31 egonw ok, gonna grab coffee now
08:32 egonw and maybe some sleep too
08:32 egonw AllStableManagerPluginTests:
08:32 egonw 253, 8 ignores
08:32 rojasm oo
08:32 egonw 23 error, 8 fail
08:33 egonw seems about right, compared to what I had last time
08:33 egonw see wiki
08:33 egonw bbl
08:35 olass ef
08:36 CIA-40 bioclipse: ospjuth * r10598 /bioclipse2/trunk/features/ (14 files in 13 dirs): Set feature version to 2.0.0.B20090520 and update bioclipse.product version.
08:44 CIA-40 bioclipse: jonalv * r10599 /bioclipse2/trunk/plugins/net.bioclipse.cdk​.business.test/src/net/bioclipse/cdk/busine​ss/test/AbstractCDKManagerPluginTest.java: indentation
08:45 CIA-40 bioclipse: jonalv * r10600 /bioclipse2/trunk/plugins/net.bioclipse.tests/ (3 files in 2 dirs): commented out and removed Structuredb references for now since structuredb is not compiling for the moment
08:46 CIA-40 bioclipse: goglepox * r10601 /bioclipse2/trunk/plugins/net.bioclipse.c​dk.ui.periodictable/src/net/bioclipse/cdk​/ui/periodictable/PeriodicTableView.java: Made inner class static and defined default color
08:46 jonalv egonw, olass: I still get build fail becasue of that perl script that should generate documentation...
08:46 CIA-40 bioclipse: goglepox * r10602 /bioclipse2/trunk/plugins/net.bioclipse.cdk.j​chempaint/src/net/bioclipse/cdk/jchempaint/ge​nerators/ClosestToCenterOfMassGenerator.java: Added alternative generate star method
08:47 egonw jonalv: did you install perl and xsltproc
08:47 egonw ?
08:47 jonalv egonw: this is a mac perl is installed from the beginning
08:47 CIA-40 bioclipse: goglepox * r10603 /bioclipse2/trunk/ (11 files in 11 dirs): Removed source.include
08:47 jonalv egonw: what is that other?
08:48 CIA-40 bioclipse: goglepox * r10604 /bioclipse2/trunk/cdk-externals/tr​unk/org.openscience.cdk.control/sr​c/org/openscience/cdk/controller/ (AddBondDragModule.java PhantomBondGenerator.java):
08:48 CIA-40 bioclipse: Added module to choose direction when adding bonds and a generator to show none commited changes
08:48 CIA-40 bioclipse: [jchempaint-primary] jchempaint-primary@14593
08:48 CIA-40 bioclipse: goglepox * r10605 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk.jchempaint/ (2 files in 2 dirs):
08:48 CIA-40 bioclipse: Changed Add bond toolbar button to use AddBondDragModule
08:48 CIA-40 bioclipse: Also added PhantomGenerator to show to be added bonds
08:48 CIA-40 bioclipse: Fixes bug #590
08:48 zarah bug #590 | http://tinyurl.com/dh6kcq
08:49 egonw xml processing tool
08:49 egonw Gpox++
08:49 jonalv egonw: I think the error I get is something like: "Can\t find perl"
08:50 egonw ant bug
08:50 egonw file me a bug report
08:50 egonw will try to think of a workaround
08:52 jonalv egonw: okey, how do I trigger that build so I can get the error message?
08:53 egonw Ctrl-B ?
08:53 egonw Meta-B in your case, I guess
08:53 jonalv egonw: where?
08:53 * jonalv tries a clean instead
08:54 jonalv that did it
08:54 olass jonalv: is perl really important for running the tests?
08:54 jonalv olass: I am multitasking :)
08:54 * olass does not have perl working
08:56 jonalv olass: I am rewrtiting you test into actually throwing that exception
09:00 CIA-40 bioclipse: jonalv * r10606 /bioclipse2/trunk/plugins/net.bioclipse.cdk​.business.test/src/net/bioclipse/cdk/busine​ss/test/AbstractCDKManagerPluginTest.java: rewrote testLoadATPInWorkspaceJob into rethrowing any exceptions thrown in the WorkSpaceJob
09:05 jonalv egonw: ping
09:06 jonalv olass: cdk.loadMolecules is a complete and utter mess... :(
09:06 edrin olass: i like this gist: http://gist.github.com/79822
09:06 edrin really cool
09:07 edrin its slow via the remote desctop but cool
09:08 edrin desktop
09:09 CIA-40 bioclipse: shk3 * r10607 /bioclipse2/trunk/plugins/net.b​ioclipse.data.seneca/data/hko1/ (. hko1.sjs mzdiv-762_c.cml mzdiv-762_c.jdx): added real-world seneca example
09:20 jonalv @pz cdk workspacejob
09:20 zarah jonalv: Zarro boogs found.
09:21 jonalv @pz 1079
09:21 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1079
09:28 CIA-40 bioclipse: jonalv * r10608 /bioclipse2/trunk/plugins/net.bioclipse.​core/src/net/bioclipse/managers/business​/AbstractManagerMethodDispatcher.java: abort to next method when run out of parameters to check in the method. fixes bug 1079 and most likely a bunch of other problems as well.
09:28 zarah bug #1079 | http://tinyurl.com/qmu6lf
09:30 egonw olass: ping
09:30 olass pong
09:30 egonw olass: what's the state of pcore in bc2?
09:30 egonw is that ready for a bioinfo programmer to work with?
09:30 olass no
09:30 egonw (a good one)
09:30 egonw ok
09:31 olass definitely not
09:31 olass let's talk next week IRL
09:31 olass hmm, please define "work with"
09:32 olass there is a stub for an EMF project started, but it requires much work
09:33 egonw ack
09:33 egonw all I need to know at this moment
09:33 olass what did you mean with "work with"
09:33 olass ?
09:34 jonalv egonw: have you found a student? :)
09:34 egonw I wish
09:34 * jonalv is at lunch
09:34 olass egonw: what did you mean with "work with"? Did you mean 'develop'?
09:35 olass egonw: and I think a cheminfo programemr is desirable...
09:36 olass egonw: let me know
09:36 olass @lunch
09:38 egonw work with -> use
09:38 egonw not 'work on'
09:47 CIA-40 bioclipse: shk3 * r10609 /bioclipse2/trunk/plugins/net.biocli​pse.seneca/src/net/bioclipse/seneca/ (business/SenecaManager.java judge/WCCNMRShiftDBJudge.java): now using dept and formula information
10:34 rojasm joined #bioclipse
10:53 jonalv am I the only one having to right click in the Bioclipse Navigaot in order to get the things there to show up after a restart?
10:54 egonw no, same here
10:54 egonw did not file a bug report
10:54 egonw but reported that last nite here on IRC
10:55 jonalv egonw: could it be related to the romval of that hack thingie?
10:57 olass jonalv: could we try bringing that back and see if it solves the problem?
10:57 olass I want to export today
10:57 olass but this must be resolved first
10:57 jonalv olass: I don't know how to. egonw can you?
10:58 jonalv olass: it was you and egonw who did that I think...
10:59 olass jonalv: I never did anything
10:59 olass I sat behind you for 2 minutes and have no idea what was committed
10:59 jonalv olass: well me neither...
10:59 olass egonw: can you please try to bring the hack back?
10:59 egonw what hack thingy?
11:00 olass jonalv: the wbadvisoryhack I assume?
11:00 egonw the fix ola made this morning?
11:00 jonalv it was something about resources and and navigator frameowrk
11:00 olass egonw: no, that was for the virual project
11:00 olass that was no hack
11:00 jonalv \egyou asked olass if it could be removed and olass said yes and then I think (but I am not sure) that egonw remvoed it...
11:00 egonw olass: right (my point too :)
11:01 olass egonw: did you remove the WorkbenchAdvisoryHack?
11:01 egonw no
11:01 olass jonalv: then what are you talking about?
11:01 jonalv oh it's still there. then that can't be it...
11:02 olass egonw: but you did comment out getDefaultPageInput()...
11:02 olass did you not?
11:02 olass did this cause problems?
11:02 egonw possibly
11:02 egonw if only I knew what commit we were talking about
11:02 egonw which hack thingy we are talking about
11:03 olass [13:04] < olass> egonw: did you remove the WorkbenchAdvisoryHack?
11:03 egonw the hack thingy is still used
11:03 olass but there are things commented out
11:04 olass what has happened with the Navigator!?
11:04 olass when did this happen?
11:04 jonalv what is jcpprop? Is that a manager? Why is it not in the chemoinformatics feature? Why does jcpcustom.js in sample data use it even though it's not around in standard installation?
11:05 egonw jcpprop now is jcpglobal
11:05 egonw per request
11:05 egonw yes, a manager
11:05 * olass dislikes having a separate manager for that
11:05 egonw in the cheminfo feature it is
11:05 jonalv egonw: filing bug for you then...
11:05 egonw ack
11:05 olass anyway, we need to solve the Navigator now
11:05 olass we cannot release as it is
11:06 olass it is a blocker
11:06 egonw I think it merely needs to be an 'update call' at some convenient place
11:06 olass egonw: it used to work fine
11:06 olass what has changd?
11:06 egonw we fixed exporting
11:06 jonalv olass: is there a container bug for todays release which I can add blcoker bugs as deps to?
11:06 olass no
11:07 olass make one if you like
11:07 jonalv olass: would you mind creating one?
11:07 olass sure...
11:07 jonalv olass++: dz
11:07 olass @pz 1090
11:07 egonw for minding creating one?
11:07 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1090
11:08 olass egonw: where do you suggest we call update? I am not up to date when resources are loaded...
11:08 * jonalv is testing things now and rporting bugs...
11:08 olass postStartup() in wbadvisor would be my bet
11:08 olass egonw: what do you think?
11:08 egonw sounds good
11:09 olass will you do it?
11:09 egonw but me has little knowledge about how the Bioclipe boot process works
11:09 * olass neither nowadays
11:09 egonw not sure what method to use to give the navigator a kick
11:09 olass me neither
11:09 * egonw thinks we need some good graphcs in the boot order
11:09 * olass too
11:09 jonalv what egonw said
11:10 egonw if only the stupid idiots who designed this Bioclipse2 thingy wrote a book
11:10 egonw oh... wait, we are
11:10 egonw I was thinking last nite to put in some logging messages
11:11 egonw in all those pre and post hooks
11:11 olass sounds good
11:11 egonw and use the output to automagically create a graphviz graph
11:11 * olass is testing an update in postStartup()
11:11 jonalv yea... about that... MAybe we should have a book-writing-hack-session sometime....
11:14 egonw yes, sounds like a good idea
11:15 olass nope, refresh in postStartup() did not solve problem
11:15 egonw just after the move-to-git, autobuilds-on-pele, move-to-Eclipse3.5, and have-a-release-party sesssions ?
11:15 olass egonw: a bit later I guess
11:15 egonw oh yes...
11:15 olass but in that region probably
11:15 egonw I forgot the sell-357-licenses session
11:15 olass anyway
11:15 olass I need help
11:16 olass the navigator is killing us now
11:16 CIA-40 bioclipse: shk3 * r10610 /bioclipse2/trunk/plugins/net.bioclipse.reaction/ (2 files in 2 dirs): added missing dependency, editor title is file name
11:16 jonalv don't look at me...
11:16 olass have you any idea when this may have happened?
11:17 jonalv olass: it must have been during the startup changes after the merging of managers and recording
11:17 olass ok, can we look at what was changed there?
11:17 olass I have no idea what was changed...
11:17 olass egonw: can git give us a picture of teh changes that could be shared in a pastebin or gist?
11:18 egonw svn log
11:18 egonw svn diff
11:18 egonw or use the SF web interface
11:19 olass how?
11:19 egonw see the changes of a commit with:
11:19 egonw http://bioclipse.svn.sourceforge.net/view​vc/bioclipse?view=rev&amp;revision=10610
11:19 zarah egonw's link is also http://tinyurl.com/qp9wvt
11:19 egonw update the last 5 digits to match the commit you are interested in
11:20 olass ok, so which commits are important here?
11:20 jonalv olass: on a different topic. IS the qsar feature goign to be in the export?
11:20 egonw use svn log
11:20 olass jonalv: no, never
11:20 olass it is not 2.0
11:20 olass it will be on the update site
11:20 olass expoerimental
11:20 jonalv olass: why is qsar.js and qsar-multi.js in standard sample data then?
11:20 olass as it always has
11:20 olass ?
11:20 olass jonalv: good question
11:20 olass oh
11:21 olass a remnant from the workshop
11:21 olass sorry about that
11:21 jonalv olass: filing a bug to you about that then...
11:21 egonw "git log" at http://gist.github.com/114756
11:21 egonw it's one of these commits that broke the refresh of the Navigator
11:25 olass I see no commit whose message indicates that anything in the startup is changed
11:25 olass jonalv: you need to assist here
11:25 jonalv olass: okey what should I do?
11:26 egonw olass: it's one of the manager merge commits
11:26 olass find out what commit affected the startup
11:26 egonw that changed the order in which plugins are started...
11:26 egonw but neither me or jonalv understand it in detail
11:26 jonalv egonw: sounds like git intersect...
11:26 egonw otherwise we would not have broken it in the first place
11:27 egonw rojasm gave this link this morning:
11:27 egonw http://gist.github.com/114756
11:27 egonw crap
11:27 egonw ask rojasm
11:27 egonw for the correct one
11:27 egonw or check the logs
11:27 olass egonw: I thought this was due to updated workspace initialization
11:27 egonw about delayed running of ws updates
11:27 egonw olass: perhaps
11:28 egonw need to run now
11:28 egonw bbl
11:28 olass so what commit is that?
11:28 olass jonalv: about commit http://bioclipse.svn.sourceforge.net/view​vc/bioclipse?view=rev&amp;revision=10575
11:28 zarah olass's link is also http://tinyurl.com/p7b4w9
11:28 olass that affects the workbenchadvisor
11:30 olass rojasm: about that link for delayed WS updates
11:30 olass could you post link?
11:31 jonalv hm not intersect but bisect. oh well...
11:32 CIA-40 bioclipse: shk3 * r10611 /bioclipse2/trunk/plugins/net.bioclipse.compute/: net.bioclipse.computee is a legacy plugin no longer needed, therefore I delete it.
11:35 rojasm I am looking for one moment
11:37 rojasm http://www.eclipsezone.com/​eclipse/forums/t114710.html
11:37 zarah rojasm's link is also http://tinyurl.com/q38nza
11:46 rojasm egonw, olass
11:46 olass egonw is gone
11:46 olass sry rojasm, this was not what I was looing for
11:47 olass another topic
11:47 olass jonalv: just calling refresh on Navigator does not solve the problem
11:47 maclean joined #bioclipse
11:47 jonalv olass: I anm doing some time travellign here trying to figure out when it stopped working...
11:47 olass nice
11:48 jonalv it's a bit complicated becasue _very_ much has chagned altely...
11:48 jonalv so it's gonna take a while...
11:48 olass it seems teh viewer does not get any input
11:48 olass wil ltry to force it some...
11:49 jonalv olass: I am back at Mon 11 May now and still same problem. It feels strange...
11:49 olass yes...
11:50 maclean Be sure to refill the Mr. Fusion, and don't run out of gas.
11:50 jonalv :)
11:53 olass haha
11:53 olass jonalv: I solved it
11:53 olass or at least I was ableto work around it
11:53 jonalv olass: okey please explain
11:53 olass explain?
11:53 olass no idea
11:53 olass but this commit helps:
11:53 jonalv olass: how did you work around it?
11:53 olass CommonNavigator nav = (CommonNavigator) PlatformUI.getWorkbench().getActiveWork​benchWindow().getActivePage().findView( "net.bioclipse.navigator" );
11:53 olass nav.getCommonViewer().setInput( getDefaultPageInput() );
11:53 olass in postStartup()
11:53 olass so forcing the root into the navigator
11:53 jonalv okey
11:54 olass at least it seems to work
11:54 * jonalv refuels his time machine and returns to the future then..
11:54 olass jonalv: what bug nr was this?
11:54 jonalv olass: I am not sure this one even got a ticket... :)
11:55 olass oh, will create onw then
11:55 olass I want to comment on the solution
11:57 jonalv olass: you could comment on the commit...
11:58 olass doin that too
11:58 jonalv good
11:59 sneumann morning
11:59 sneumann What kind of bot is raednel ?
12:00 maclean it's egon's creation - a java bot.
12:00 jonalv sneumann: he/she (?) uhm I think it reads git commits and blog posts and such
12:01 sneumann Why is zarah not doing this job ?!
12:01 CIA-40 bioclipse: ospjuth * r10612 /bioclipse2/trunk/plugins/net.bi​oclipse.ui/src/net/bioclipse/ui/ (ApplicationWorkbenchAdvisor.java WorkbenchAdvisorHack.java): Explicitly populate Navigator in ApplicationWorkbenchAdvisor.postStartup() with root defined in WorkbenchAdvisorHack. Solves bug #1093.
12:01 zarah bug #1093 | http://tinyurl.com/qwp84p
12:01 jonalv sneumann: good question. probably because egonw wanted this functionality and not masak...
12:01 olass jonalv: can you confirm the fix in r10612?
12:02 jonalv olass: as soon as I get some order on my Eclipse workspace again
12:02 olass yes
12:02 olass let me know
12:04 jonalv olass++ //it works now
12:04 olass :)
12:20 jonalv short update on status of plugin tests in Bioclipse:
12:20 jonalv I have found 289
12:20 jonalv 8 of them are marek to be ignored
12:20 jonalv 22 errors and 9 failures when I run them
12:21 jonalv s0 250 of 289 passes
12:21 jonalv Bioclipse++
12:23 CIA-40 bioclipse: shk3 * r10613 /bioclipse2/trunk/plugins/net.biocl​ipse.reaction/META-INF/MANIFEST.MF: net.bioclipse.managers has been removed, so dependency not needed
12:23 maclean 87% pass rate, pretty good.
12:25 jonalv timne to write more tests :)
12:25 jonalv ...but first I am gonna clean up the tests uites a bit more...
12:26 edrin egonw: ping
12:29 olass egonw is on a meeting at school
12:31 edrin oh
12:33 rojasm hi stefan (shk3)
12:33 rojasm I have committed. But I am checking again
12:34 shk3 no problem
12:34 shk3 It should be all in the reaction plugin, right?
12:34 shk3 no other plugin involved I need to update?
12:35 rojasm Revision: 10579
12:36 shk3 I have 10609
12:37 * olass is exporting beta5
12:40 CIA-40 bioclipse: jonalv * r10614 /bioclipse2/trunk/ (42 files in 16 dirs): cleaned up among tests suites. Removed net.bioclipse.managers.tests and net.bioclipse.recording.tests
12:50 rojasm shk3 you are right!
12:50 rojasm it is not working either
12:50 rojasm I have a look
12:53 CIA-40 bioclipse: ospjuth * r10615 /bioclipse2/trunk/plugins/ (5 files in 3 dirs): Added a SignSicHit object to allow for custom coloring in substructures.
12:55 rojasm sorry It works but it is a bit tricky! The activation is only when you click in the center! At the same time you should be able to see how the box changes the color of the box to white
12:56 shk3 ok
12:56 shk3 trying
12:56 shk3 just updating bioclipse
12:56 maclean "how the box changes the color of the box to white"??
12:56 shk3 might take a while
12:56 rojasm becouse it tries to change the name inside of the box
12:58 rojasm It is not ideal. Looking how to improve the activation
13:10 rojasm The main class detecting the activation is MyAbstractObjectEditPart.performRequest
13:10 rojasm I set the two options
13:10 rojasm one-click -> introduce text and show molecule
13:11 rojasm double-click -> opening JCP. Now not working
13:11 CIA-40 bioclipse: ospjuth * r10616 /bioclipse2/trunk/plugins/net.biocli​pse.ds.signsig.bursi/src/net/bioclip​se/ds/signsig/bursi/SignSicHit.java: Create and cache colors for hits in a better way.
13:16 CIA-40 bioclipse: ospjuth * r10617 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.smartsmatching/src/net/bioclipse/c​dk/smartsmatching/model/SmartsHit.java: Create and cache colors for hits in a better way.
13:45 maclean rojasm : I've got the medea_feature, and all its dependent plugins, but the reaction plugin is not started. Do you know of any fixes for this?
13:47 maclean oh, wait - I don't have the medea plugin! d'oh.
13:47 * maclean mutters bloody features...
13:50 rojasm sorry I have not idea how works the feature staff
13:51 maclean rojasm : no problem
13:52 egonw rojasm: I'll look at it...
13:52 egonw mom
13:52 rojasm oh thanks egonw
13:52 egonw maclean: I see the medea plugin be part of the medea feature
13:53 egonw olass: ping
13:53 olass pong
13:53 maclean egonw : I know. that's why I said "oh, wait - I don't have the medea plugin! "
13:53 egonw olass: what should a copy of net.bioclipse.platform_feature with a media.product be called?
13:53 egonw maclean: ah... sorry... read that as 'no medea plugin in the feature'
13:53 egonw as opposed to
13:54 egonw no medea plugin in my workspace
13:54 egonw because you were talking about the feature in the sentence before
13:54 olass egonw: how about net.bioclipse.medea.wrapper_feature?
13:54 olass medea is not a platform
13:54 olass bioclipse is the platform
13:55 olass medea can be a targetted release
13:55 olass and thus might benefit from a wrapper feature
13:55 egonw nb.medea.product_feature ?
13:55 egonw perhaps?
13:55 olass I guess that could work too?
13:55 egonw likewise, nb.speclipse.product_feature
13:56 egonw wrapper is so non-informative
13:56 olass well, we now use product a lot, it might be confusing
13:56 olass there is the product defined in plugin.xml in net.bc.ui
13:56 olass there is the product file bioclipse.product
13:56 olass and if we add a feature called product, this adds complexity
13:56 egonw mmm...
13:56 olass but I agree that wrapper is not informative
13:57 olass so if you like product better, then use that
13:57 maclean application?
13:57 egonw as in
13:57 egonw nb.medea.application_feature?
13:57 olass maclean: there is a bioclispe application declared in plugin.xml of net.bioclipse.ui as well..
13:57 olass I guess I like product best
13:58 olass n.b.medea.product_feature
14:00 egonw ok, will do that
14:01 maclean hmmm. now I get "medea plugin can't find LearnAction"...
14:01 shk3 not sure about net.bc.product_feature
14:02 shk3 i though about putting the speclipse.product file in net.bc.speclipse_feature
14:02 shk3 it would mean to have a feature just for one file, if I understand it correctly
14:02 shk3 first line should read "not sure about net.bc.speclipse.product_feature"
14:11 egonw that's an option...
14:11 egonw olass: that would not give trouble on the update site, or would it?
14:12 olass no idea
14:13 egonw well, there is only one way to find out...
14:13 maclean fiiiiiiight!
14:13 maclean :) (sorry)
14:13 egonw oh, action at the EBI?
14:13 egonw Chris against Paula ?
14:14 maclean no, no, just a UK tv meme :"Which is better? There's only one way to find out..."
14:14 egonw over who gets to use the stapler first
14:14 egonw ah, ic
14:17 maclean these bundle-version constraints are a real pain.
14:17 CIA-40 bioclipse: ospjuth * r10618 /bioclipse2/trunk/plugins/net.biocli​pse.ds/src/net/bioclipse/ds/model/Su​bStructureMatchPropertySource.java: Show the correct matching atoms in properties view.
14:18 maclean the reaction plugin is not starting because I remove the bundle-version (because of a compile error).
14:19 maclean and Validation in the run configuration says that the plugin has a missing constraint (version='0.0.0'). grrr.
14:19 maclean hmmm. add required plugins works.
14:19 * egonw is about to commit medea.product
14:20 maclean well, what a surprise. running as plugins is yet again superior to running as features...
14:20 egonw maclean: because the medea_feature configuration is broken...
14:20 egonw does not mean running via features is
14:21 maclean oh
14:21 maclean sez u
14:21 egonw well, maybe your eclipse installation is broken
14:21 egonw that's of course possible too...
14:21 maclean perhaps local gravitational forces are to blame, also.
14:21 egonw oh, and timezone of course
14:21 egonw but actually... really...
14:22 * olass thinks the rain is to blame
14:22 egonw I think it the driving on the left side
14:22 egonw I mean...
14:22 egonw perfect correlation
14:22 egonw everywhere where they drive on the left side, running by features is not working
14:25 masak joined #bioclipse
14:30 olass egonw: 1091 would be a 20 sec fix for you
14:32 CIA-40 bioclipse: ospjuth * r10619 /bioclipse2/trunk/plugins/net.b​ioclipse.data/data/Javascripts/ (qsar-multi.js qsar.js): Removed qsar files from sampledata. Solves bug #1092.
14:32 zarah bug #1092 | http://tinyurl.com/oqtkz3
14:34 egonw @pz 1091
14:34 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1091
14:35 * maclean chuckles at this line : "b = ([0], [1])[x & 1] + b"
14:37 CIA-40 bioclipse: egonw * r10620 /bioclipse2/trunk/features/net.bioc​lipse.medea_feature/medea.product: Added 'Bioclipse MEDEA' product, with the platform and medea features
14:38 CIA-40 bioclipse: jonalv * r10621 /bioclipse2/trunk/plugins/net.bioclip​se.ds/src/net/bioclipse/ds/business/ (DSManager.java IDSManager.java): Layout. 80 cols.
14:40 CIA-40 bioclipse: jonalv * r10622 /bioclipse2/trunk/plugins/ (13 files in 6 dirs): refactored ds manager into NWO.
14:46 olass ok, be back in 1 hour
14:54 jonalv jonalv-- // writes borken code
14:55 maclean lol-o-lol. an adjacency matrix generator in 21 lines of python? http://gist.github.com/114856
14:56 maclean unfortunately, for n = (3, 4, 5, 6), |X| = (84, 3060, 324,632, 109,453,344)...
14:57 CIA-40 bioclipse: jonalv * r10623 /bioclipse2/trunk/plugins/net.bioclips​e.core/src/net/bioclipse/managers/busi​ness/JavaManagerMethodDispatcher.java: don't remove null from the list if there is no uiJob. oops...
15:02 CIA-40 bioclipse: egonw * r10624 /bioclipse2/trunk/features/net.bio​clipse.medea_feature/feature.xml: Added MEDEA example data
15:02 CIA-40 bioclipse: miguelrojasch * r10625 /bioclipse2/trunk/plugins/net.bioclipse.​reaction/src/net/bioclipse/reaction/dnd/ (4 files): Added preliminary drag and drop functionality. Not usefull at the moment until the BiclipseNavigator implement the functionality.
15:02 rojasm Is some intention to implement drag and drop functionality in bioclipse?
15:04 maclean For what?
15:04 maclean Oh, right, sorry. Just read your commit comment...
15:04 CIA-40 bioclipse: egonw * r10626 /bioclipse2/trunk/features/net.bioc​lipse.medea_feature/medea.product: Exclude Balloon and include speclipse features
15:04 maclean I thought that the qsar interface used D&D?
15:05 rojasm e.g. copy some molecules file into other places. Editor reactions
15:05 maclean Ah, so drag from folder to folder, within the navigator?
15:05 rojasm not. From folder to editor
15:06 maclean "No" not "not"!
15:06 maclean :)
15:06 maclean well, like I say, try the D&D in the qsar stuff.
15:07 shk3 i did similar thing in seneca, works nicely
15:07 shk3 but needs to be implemented by each editor
15:07 shk3 obviously
15:07 rojasm ok. I will take a look!
15:07 shk3 if the editor wants it, that is
15:08 rojasm shk3, did it worked for you showing the single structure in the reaction viewer?
15:08 rojasm worked == work
15:08 egonw maclean: ok, finally managed to commit all thre medea.product patches
15:08 maclean egonw : cool.
15:08 shk3 sorry, still updating
15:08 rojasm thanks egonw
15:09 shk3 net.bc.seneca.editor.JudgePage in net.bc.seneca has d&d
15:09 shk3 starting l 132
15:09 shk3 was easy to implement
15:10 maclean no. not working.
15:11 maclean log4j.
15:11 maclean resetting target platform
15:11 egonw maclean: the medea.product?
15:11 rojasm the same error
15:12 maclean haven't tried the medea.product
15:12 maclean but running bioclipse as features is now giving all sorts of errors (it does start, though)
15:13 egonw can you gave an example error?
15:13 maclean well, I just removed all features except platform and medea, and now seems fine.
15:14 maclean except that reaction files are not working
15:14 egonw ah, yes
15:15 maclean the reaction plugin is probably not being loaded.
15:15 egonw you do have to typically remove all features, save, and add them again, save again
15:15 rojasm cdk.pastebin.com/m33304c2c
15:15 egonw OK, thanx
15:15 egonw maclean: what reaction file are you trying?
15:15 maclean any.
15:16 egonw from the reaction data samepl I assume
15:16 maclean they are not showing the icons in the navigator which indicates to me that things are not working
15:16 maclean egonw : yes, from there.
15:16 egonw ok, will look into that
15:17 maclean I did the remove-save-add-save cycle, too.
15:17 egonw ok, good
15:17 egonw than that is ruled out
15:18 maclean when I run using the run configuration (as plugins) the validate has some problem with the reaction plugin, unless I "add required plugins"
15:18 maclean which may be to do with this bundle-version thing on the GEF plugin.
15:18 egonw possibly
15:18 egonw and the feature one does not have a validate, does it...
15:19 maclean is there something in the feature that asks its plugins to look for dependencies?
15:19 * maclean launches the medea.product
15:20 maclean nope, no reactions there either
15:21 egonw mmm...
15:21 egonw just to make sure...
15:21 egonw you do have the GEF feature installed, right?
15:21 egonw in your eclipse?
15:21 egonw sure you do
15:21 egonw (I don't)
15:21 maclean yeeess
15:21 maclean of course.
15:21 egonw :)
15:22 maclean well, I did think to check that...
15:29 egonw maclean, rojasm: please file all problems you have, and I'll fix them one by one, OK?
15:29 egonw now installing GEF and will check reactions here
15:29 rojasm I have the same like maclean
15:29 rojasm It doesn't show the icons for the reaction
15:30 rojasm and the error is what I pasted
15:30 rojasm I try again all
15:31 edrin Guanine Nucleotide Exchange Factor
15:31 maclean GNEF?
15:31 edrin no
15:32 maclean GEF := "Graph Editing Framework"
15:32 edrin http://en.wikipedia.org/wiki/Gua​nine_nucleotide_exchange_factor
15:32 zarah edrin's link is also http://tinyurl.com/pc99o9
15:32 edrin ah#
15:32 egonw rojasm: please copy that snippet into a bug report
15:32 egonw need to make dinner now
15:32 egonw and eclipse is downloading...
15:32 edrin :)
15:32 edrin mhm dinner
15:33 egonw maclean: please let me, next time we meet, help you get running with features working for you too
15:33 rojasm ok!
15:33 maclean egonw : I say again : it just fails sometimes. There is no magical fix that you can provide.
15:35 maclean i think the 'remove-save-add-save' and target-platform incantations are clear indications that all this dynamic stuff is very fragile...
15:35 maclean I'm not saying don't use it, just don't blame me if it breaks for no diagnosable reason :)
15:41 jonalv maclean: yes I agree but since this is what is used by Eclipse during export we have to make sure that it works or the export will fail.
15:43 jonalv @pz 1038
15:43 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1038
15:43 jonalv anyone?
15:47 egonw sure
15:47 egonw assign to me...
15:48 egonw but do we want four spaces?
15:48 egonw I use 2
15:48 egonw 2 should be enough for everyone
15:55 masak egonw++
15:56 masak egonw: I use 4 spaces for indentation, and 2 spaces for some other things.
15:56 masak egonw: jonalv has been nagging me about it creating inconsistencies, but he's apparently too lazy to go change it himself.
15:56 masak egonw: now, it seems, it's a matter of principle rather than anything else.
15:57 masak maybe we should make a vote about it. :P
15:57 egonw actually... I am using 4 in Eclipse
15:57 egonw but 2 with normal editors
15:57 egonw anyway...
15:57 jonalv egonw: are you using 2 steps????
15:57 egonw does not matter what I think
15:57 egonw what is the concensus
15:57 egonw the report is not clear about it
15:57 masak I like having it at 2 because it makes me see tab chars easier in Eclipse.
15:57 egonw change from 2 to 4 spaces, irght?
15:57 masak egonw: the consensus is 4, at least between me and jonalv.
15:57 masak egonw: the style guide says 4.
15:57 egonw :)
15:58 maclean 4
15:58 egonw OK, good
16:02 jonalv egonw: have you patched DBMolecule for the SMILES sutff?
16:03 egonw I thought so
16:03 jonalv okey that explains it
16:04 egonw not good?
16:05 jonalv egonw: I added it to DBMoleucle only. It's a quick fix...
16:06 egonw shk3: seneca was *not* the last plugin to use net.bioclipse.compute
16:06 shk3 maclean
16:06 shk3 ?
16:06 egonw shk3: did I forget to ask about checking if something else was using it?
16:07 rojasm shk3. the drag and drop that you commented was in the same panel. And I wanted to refer between Bioclispe Explorer in ReactionEditor. Do you know some example in Bioclipse?
16:07 egonw rojasm: can you please check if MEDEA's use of the compute plugin can be removed and/or replaced?
16:07 shk3 medea seems to have a dependency only
16:07 rojasm I don't think it is used
16:07 shk3 we found that as well
16:08 rojasm I check it
16:08 egonw it's used by the net.bioclipse.medea/src/net/bioclipse/p​lugins/wizards/NewAquisitionWizard.java
16:08 rojasm oh yes
16:08 CIA-40 bioclipse: jonalv * r10627 /bioclipse2/trunk/plugins/ (7 files in 5 dirs): Made structuredb compile again. And now the tests run as well. (not all passing of course)
16:08 rojasm but now they are uncommented
16:08 egonw shk3: it is also still a dependency for the speclipse feature
16:08 shk3 sorry ola wrote compute was only used by seneca
16:08 shk3 i trusted that
16:08 shk3 oh, missed that
16:08 shk3 that can be removed
16:08 shk3 mom
16:10 CIA-40 bioclipse: shk3 * r10628 /bioclipse2/trunk/features/net.biocl​ipse.speclipse_feature/feature.xml: removed dependency on net.bioclipse.compute
16:10 egonw ok, one less problem for the MEDEA .product
16:10 edrin edrin gone
16:10 edrin good luck
16:10 edrin cu
16:10 edrin left #bioclipse
16:10 egonw rojasm: please let me know what to do about that Wizard later
16:11 shk3 the wizard is not in build path for me
16:11 rojasm I am checking what it was the intention. I don't remember anymore
16:11 shk3 looks like it needs updating anyway
16:11 shk3 so I suggest to comment out its use in plugin.xml
16:11 shk3 but we can bring back the compute plugin as well
16:11 shk3 I don't mind
16:12 maclean I think it is for running the learning and prediction actions
16:12 shk3 just wanted to avoid the accumulation of outdated stuff
16:12 maclean which were n.bc.compute jobs
16:12 * egonw is waiting for rojasm's view on this, being the likely author of the code
16:13 shk3 net.bioclipse.medea.case seems to just depend on compute
16:13 shk3 yes, miguel can decide
16:13 egonw OK, gone for dinner now
16:13 rojasm :(
16:13 shk3 as I said, no problem with re-adding it
16:13 egonw will be back later
16:13 egonw rojasm: please email
16:13 rojasm yes egonw
16:14 rojasm yes The compute was to run the prediction and learning process!
16:17 rojasm yes we can comment out its use in plugin
16:17 rojasm I will guess to use the scripts function first
16:18 rojasm and when it is all fixed came back to the wizards
16:20 shk3 that would have been my suggestion as well
16:20 shk3 but don't feel pressed
16:20 rojasm :)
16:20 shk3 we can keep the plugin
16:21 shk3 but the wizard need a rework anyway
16:21 shk3 and that can be done without compute, so its reasonable to take it out now.
16:21 rojasm yes
16:23 rojasm I am commenting out all what have to do with compute
16:24 rojasm is it enoght? or should I eliminate ?
16:26 maclean well,  I guess that depends on who will be fixing it again :) You?
16:27 CIA-40 bioclipse: miguelrojasch * r10629 /bioclipse2/trunk/_playgro​und_/net.bioclipse.medea/ (2 files in 2 dirs): Comment out dependences with Compute jobs
16:27 maclean As in, the job stuff that needs to be migrated to the nwo.
16:29 maclean heh heh heh. a function returning a range object. nice.
16:31 CIA-40 bioclipse: jonalv * r10630 /bioclipse2/trunk/plugins/ (3 files in 3 dirs): added net.bioclipse.structuredb tests to AllBioclipseTestsSuites in net.bioclipse.tests (and made them run in that environment as well)
16:31 CIA-40 bioclipse: jonalv * r10631 /bioclipse2/trunk/.gitignore: .gitignore log files
16:32 shk3 the functions would need to become manager methods
16:32 shk3 but that's needed anyway
16:32 shk3 or it should be done to proper port to bc2
16:35 CIA-40 bioclipse: jonalv * r10632 /bioclipse2/trunk/ (.gitignore plugins/net.bioclipse.tests/filename): removed and .gitignored net.bioclipse.tests/filename
16:49 * jonalv gives up for today, cya
17:13 CIA-40 bioclipse: miguelrojasch * r10633 /bioclipse2/trunk/_playground_/net​.bioclipse.medea/src/net/bioclipse​/medea/business/MedeaManager.java: Added JAVADOC for some methods
17:45 CIA-40 bioclipse: egonw * r10634 /bioclipse2/trunk/features/net.bio​clipse.medea_feature/feature.xml: Removed unimportant, possibly harmful micro version
18:00 CIA-40 bioclipse: egonw * r10635 /bioclipse2/trunk/_playground_/​net.bioclipse.medea/plugin.xml: Commented out plugin entry for disabled NewAquisitionWizard (see also commit 10629 and comment in .xml
18:03 CIA-40 bioclipse: egonw * r10636 /bioclipse2/trunk/_playground_/net.bioc​lipse.medea.case/META-INF/MANIFEST.MF: Removed another reference to the unused and remove net.bioclipse.compute plugin
18:36 rojasm shk3. why is SpectrumContentProvider not accessible from other plugins? Some specific reason?
18:37 rojasm I would like to use it for selecting in the wizard only spectra
18:38 rojasm shk3 ping
18:40 maclean joined #bioclipse
18:41 maclean hey rojasm : shk3 is off somewhere (food perhaps).
18:43 CIA-40 bioclipse: ospjuth * r10637 /bioclipse2/trunk/plugins/net.bioclips​e.ds.smarts/src/net/bioclipse/ds/smart​s/model/impl/SmartsMatchingTest.java: Try to catch illegalarg exception thrown by CDK when running smarts query on a non-connected molecule.
18:43 rojasm oo
18:43 rojasm ok. I send him a email
18:44 egonw rojasm: perhaps the package is not exported
18:44 egonw rojasm: which plugin is it in?
18:44 CIA-40 bioclipse: ospjuth * r10638 /bioclipse2/trunk/plugins/n​et.bioclipse.qsar.ui/data/ (. qsar-multi.js qsar.js): Added sample QSAR scripts for later inclusion in a cheat sheet.
18:45 rojasm Spectrum plugin
18:47 egonw ok, the package is not exported
18:47 egonw patch pending
18:47 rojasm thanks
18:49 CIA-40 bioclipse: egonw * r10639 /bioclipse2/trunk/plugins/net.biocl​ipse.spectrum/META-INF/MANIFEST.MF: Exported more packages so that classes in it can be used by, for example, MEDEA (per Miguel's request)
18:49 rojasm thanks egonw
19:01 CIA-40 bioclipse: egonw * r10640 /bioclipse2/trunk/features/net.bioc​lipse.medea_feature/medea.product: No special name, which seems to modify the net.bioclipse.ui/plugin.xml all the time
19:01 CIA-40 bioclipse: egonw * r10641 /bioclipse2/trunk/_playground_/​net.bioclipse.medea/plugin.xml: Added missing entry in the plugin.xml for the scripting contribution
19:06 rojasm It doesn't work with the SpectrumContentProvider to show in the wizard the spectra in the different directories. Strange
19:09 egonw yeah, seeing something strange too
19:10 egonw too bad jonalv is not around
19:20 egonw ok, found that problem
19:20 egonw and I think that might lso be a problem for the reaction stuff...
19:20 egonw but that is next
19:24 CIA-40 bioclipse: miguelrojasch * r10642 /bioclipse2/trunk/plugins/ne​t.bioclipse.data.medea/data/ (molecule/5-Hexen-3-one.mol spectra/5-Hexen-3-one.jdx): Added more examples for data medea (molecule with its corresponding spectrum in jdx format)
19:26 egonw rojasm: ping
19:26 rojasm yes egonw
19:26 egonw can you add to the demo medea script
19:26 egonw at the first line
19:26 egonw a comment that the filename of the structure loaded
19:26 egonw may need tuning...
19:26 egonw e.g. I had a different name for the 'MEDEA Sample Data'
19:28 rojasm oh yes!
19:29 egonw there are tons of problems with the MEDEA feature :)
19:29 rojasm :(
19:29 egonw it amazes me that maclean and you actual can run it from within eclipse :)
19:29 egonw no worries...
19:30 egonw I can fix them
19:30 egonw just takes some effort :)
19:51 egonw OK, two more fixes being commited
19:51 CIA-40 bioclipse: egonw * r10643 /bioclipse2/trunk/plugins/net.biocl​ipse.spectrum/META-INF/MANIFEST.MF: Added dependencies on a few Spring related plugins because Spectrum extends IBioObject so that the Bioclipse recording framework will try to use a proxy
19:52 CIA-40 bioclipse: egonw * r10644 /bioclipse2/trunk/_playground_/net​.bioclipse.medea/src/net/bioclipse​/medea/business/MedeaManager.java: The manager should no longer extend the interface (in the NWO)
19:54 egonw OK, now trying a reaction
19:57 egonw OK, reaction stuff is definately not working yet
20:05 CIA-40 bioclipse: ospjuth * r10645 /bioclipse2/trunk/plugins/net.bioclipse.ds/ (4 files in 3 dirs): Adapted running of tests to NWO and to use BioclipseUIJob. Seeems not to work 100% yet; it does not run in a separate thread.
20:06 CIA-40 bioclipse: ospjuth * r10646 /bioclipse2/trunk/plugins/net.bioclipse.ds.tests/ (2 files in 2 dirs): Wrote tests for running DS tests using BioclipseUIJob calls. Works, but seems to be queued and not run in parallel.
20:10 * egonw is going offline
20:10 * olass too
20:10 egonw and will fix the reaction part later
20:11 egonw rojasm: the reaction stuff is pretty borken for me
20:11 egonw .rxn files are not recognized
20:11 egonw the example .cml files are attempted to be opened
20:11 egonw but
20:11 rojasm mmm. Stranges because for me yes!
20:11 rojasm I will checke. maybe I missed some commit
20:11 egonw each entry goes into MDL molfile parsing...
20:11 egonw while it is a CML file!
20:12 egonw well... maybe some depedencies again...
20:12 egonw who knows
20:12 egonw this is why running with features is so important !
20:13 egonw anyway
20:13 egonw olass: ping
20:13 olass pong
20:13 egonw olass: you will be at BMC tomorrow?
20:13 olass yes
20:13 egonw ok, then I will too
20:13 egonw cu tomorrow then
20:13 egonw bye
20:16 olass bye
20:16 rojasm bye
20:16 zarah bye
20:24 CIA-40 bioclipse: miguelrojasch * r10647 /bioclipse2/trunk/plugins/​net.bioclipse.data.medea/ (8 files in 6 dirs): Added comment in the js file indicating required medea data installation. Restructuring the medea data
20:28 CIA-40 bioclipse: miguelrojasch * r10648 /bioclipse2/trunk/_playgro​und_/net.bioclipse.medea/ (7 files in 3 dirs): Added wizards for learning process.
20:31 CIA-40 bioclipse: miguelrojasch * r10649 /bioclipse2/trunk/plugins/net.bioclipse.d​ata.medea/data/Javascripts/prediction.js: correction of the patch loading the molecule
21:02 CIA-40 bioclipse: miguelrojasch * r10650 /bioclipse2/trunk/plugins/net.biocl​ipse.reaction/src/net/bioclipse/rea​ction/editor/ReactionEditor.java: Align code.
21:13 CIA-40 bioclipse: miguelrojasch * r10651 /bioclipse2/trunk/plugins/n​et.bioclipse.data.reaction/ (17 files in 4 dirs): Restructuring reaction sample data

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