Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-03-10

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All times shown according to UTC.

Time Nick Message
02:23 CIA-22 bioclipse: rklancer * r5061 /bioclipse2/trunk/ (27 files in 21 dirs): Logging fixup: fixed manifests to strictly use import-package to get logging packages; removed redundant export of logging packages; removed redundant logging jars
02:24 CIA-22 bioclipse: rklancer * r5062 /bioclipse2/trunk/net.bioclipse​.target.platform/required-libs/ (8 files): logging fixup: updating to SLF4J version 1.5.0
02:31 CIA-22 bioclipse: rklancer * r5063 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (3 files in 2 dirs): logging fixup: changes needed to configure logging on startup
03:07 CIA-22 bioclipse: rklancer * r5064 /bioclipse2/trunk/net.bioclipse.targ​et.platform/target-platform.target: general/logging fixup: fixed target-platform.target to specify exactly which plugins can contribute to Bioclipse. See http://wiki.bioclipse.net/ind​ex.php?title=Target_Platform
03:11 CIA-22 bioclipse: rklancer * r5065 /bioclipse2/trunk/plugins/net.b​ioclipse.ui/bioclipse.product: logging fixup: Made product configuration list of plugins conform to fixed-up list of plugins in the target platform. Linked SLF4J's commons-logging implementation to Log4J.
07:04 rojasm joined #bioclipse
07:12 rojasm moin
08:06 olas joined #bioclipse
08:06 olas good morning
08:08 rojasm moin olas!
08:08 rojasm I try to update bioclipse again
08:09 rojasm do I need to have installed the spring IDE, isn't it?
08:09 olas no
08:10 olas mom
08:10 olas everything you need to know is listed on http://wiki.bioclipse.net/index.p​hp?title=Checking_out_Bioclipse_2
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08:21 egonw moin
08:21 olas moin egonw
08:23 EskilA joined #bioclipse
08:25 egonw hi olas
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09:15 CIA-22 bioclipse: miguelrojasch * r5066 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): update from CDK the MFAnalyser to MolecularFormulaManipulator to extract the elemental composition. MFAnalyser does't exist anymore.
09:18 CIA-22 bioclipse: ospjuth * r5067 /bioclipse2/trunk/plugins/net.bioclipse​.biojava.ui/src/net/bioclipse/biojava/u​i/views/SequenceContentProvider.java: Working on viewer updates when resources changes.
09:19 olas miguelrojasch: Good to see you working on CDK in Bioclipse!
09:21 * egonw will go to a BioMoby/Metabolomics meeting in Cologne this week
09:21 rojasm :)
09:22 rojasm not exactly I wanted to update Bioclipse to play some bit
09:23 rojasm And I was a aesy touch up
09:23 olas We have some compilation errors in Bioclipse2 in net.bioclipse.cdk.ui
09:23 olas did you fix them?
09:24 rojasm what you mean with compilation
09:24 olas red crosses in Eclipse :-)
09:24 rojasm I don't see any errors
09:24 olas ok, good
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09:25 olas hi masak
09:27 masak y0 olas
09:28 olas rojasm: I get error on import in JChemPaintModel: cannot find IMolecularFormula and MolecularFormulaManipulator
09:28 olas in net.bioclipse.cdk.ui
09:29 rojasm you have to update other one
09:29 olas which one?
09:29 rojasm cdk
09:29 olas hmm, thought I did that...
09:29 rojasm META-INF of net.bioclipse.cdk
09:30 olas ok, thx
09:30 rojasm which gives the packages free, isn't it?
09:30 olas problem goes away
09:30 rojasm :)
09:31 rojasm question I want to implement some thing I have to do in bioclipse2 or bioclipse or both
09:31 CIA-22 bioclipse: ospjuth * r5068 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: cdk.business compiles again.
09:31 olas rojasm: yes
09:31 rojasm that mean both!
09:32 olas ok
09:33 olas we will mostly support only bioclipse2 from now on
09:33 rojasm but the idea is that bioclipse2 substitutes bioclipse, isn't it?
09:33 olas yes
09:33 olas superseeds
09:33 olas but Bioclispe2 will not be released for some time...
09:33 olas this time we will get it right :-)
09:36 egonw TM
09:37 olas Trade Mark ?
09:37 masak olas: yes, as in "this time we'll get it right(TM)"
09:38 olas sounds like a movie line
09:41 * masak thinks he likes the spelling "superseeds" in favor of the more conventional "supercedes"
09:43 rojasm Sorry again! when I run Bioclipse I can see it has all necessary plugins to create a molecule in Help>About Bioclipse>Plug-ing Details but I can not see the views or Perpespetive of Chemoinformatics or JCP? I am doing some thing wrong?
09:45 olas you running bioclispe1 or 2?
09:45 rojasm bioclipse2
09:45 olas JCP does not work in BC2
09:45 rojasm ach so
09:45 rojasm ok
09:45 olas no one has fixed it
09:45 rojasm ups
09:45 olas we have no CDK-experienced person with us for the moment
09:45 olas egon does not have time
09:46 olas and all else have left
09:46 olas so currently, Bioclisp2 has very limited CDK capabilities
09:46 rojasm ok
09:46 rojasm I see
09:46 olas that is unfortunately the status
09:46 olas so if you need these things, use Bioclipse2
09:47 olas Bioclispe1 I mean
09:47 rojasm ok!
09:47 jonalv anyone more than me having problems using the new target.platform for bioclipse 2?
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11:17 CIA-22 bioclipse: jonalv * r5069 /bioclipse2/trunk/plugins/net.bioclipse.core​/src/net/bioclipse/core/domain/BioList.java: Fixes concurrent modification exception problem which was due to wrong use of iterators and maps
11:22 egonw lunch time
11:56 CIA-22 bioclipse: ospjuth * r5070 /bioclipse2/trunk/plugins/ne​t.bioclipse.biojava.ui.test/ (2 files in 2 dirs): Proper setup of tests.
11:58 CIA-22 bioclipse: ospjuth * r5071 /bioclipse2/trunk/plugins/net.bioclipse​.biojava.ui/src/net/bioclipse/biojava/u​i/views/SequenceContentProvider.java: Updates to resources regarding sequences propagate to viewer.
12:02 CIA-22 bioclipse: ospjuth * r5072 /bioclipse2/trunk/plugins/net.bioclipse.services/ (9 files in 6 dirs): Implemented run on services according to command "service.run("clustalw@EBI");
13:14 egonw bbl
13:27 olas cya egonw
13:32 jonalv <http://bioclipse.blogspot.com/2​008/03/recording-progress.html>
13:47 egonw jonalv: you forgot to exit the type writer mode
13:48 jonalv oh okey
13:48 rklancer joined #bioclipse
13:48 jonalv I will have alook at that
13:49 jonalv egonw, I can't even see it :)
13:49 egonw :)
13:49 egonw windows, I assume?
13:49 jonalv ubuntu
13:49 jonalv firefox
13:50 jonalv hi rklancer
13:50 rklancer hi there
13:51 egonw well, the text after the code example (which I don't get), has the same font as the code example
13:51 egonw assuming that that text is actually *not* part of the example :)
13:51 jonalv I think I removed it now
13:51 egonw hi rklancer
13:51 egonw ok, you remove all now...
13:51 jonalv huh?
13:52 egonw now, the code is no longer in <pre> any more
13:52 * jonalv is not very good with html. prefers tex...
13:52 egonw heheheh
13:53 rklancer recording-progress: looks exciting
13:53 jonalv yup that's the idea :)
13:54 egonw btw, maybe mention the file extension of that example file?
13:54 jonalv good point
13:54 egonw looks very nice indeed
13:56 rklancer btw, do you know how the spring bundle extender gets started when you fire up bioclipse?
13:56 rklancer i noticed it seems to set itself to autostart
13:56 rklancer but i'm not sure of the mechanism
13:57 jonalv it's started from the ui activator
13:57 rklancer actually
13:57 jonalv it was the only way I could figure out
13:57 rklancer i found that, after the first time you run bioclipse, the bundle extender gets autostarted by the framework
13:58 jonalv huh?
13:58 rklancer yeah
13:58 jonalv only after the first time?
13:58 jonalv I have no idea about that...
13:58 rklancer well, the first time, you have to start it, right?
13:59 jonalv well the UI activator always starts it...
14:00 rklancer but i found that after that it gets started by the Start Level Manager (or something like that) every time the framework starts up
14:00 jonalv okey so it would already be started when ui tries to start it?
14:00 rklancer it seems to be a race
14:01 jonalv okey, that's a bit strange... :)
14:02 rklancer i stepped through the framework startup and both bundle activators (ui and extender) get called right when the framework goes to startlevel 4
14:02 rklancer not totally strange, in that you want the bundle extender ACTIVE before your the bundles you want to extend get to STARTING
14:02 jonalv alright, I added that code because it didn't start without it... Have yout tried to remvoe it?
14:03 rklancer no, because you still need to load it 'manually' on the first startup
14:03 rklancer the only reason it's an issue is that it creates a race condition wrt logging
14:04 jonalv how come?
14:04 rklancer because I put logging config in ui.activator
14:04 rklancer but sometimes the bundle extender will start before n.b.ui
14:04 rklancer and because it tries to log when it starts up, log4j complains that there are no appenders
14:05 rklancer the handful of log messages that get lost before log4j gets configured in ui.activator probably aren't a big deal
14:05 jonalv I see
14:05 rklancer but I worry that the message will be unnecessarily confusing
14:05 jonalv No idea of what is going on though...
14:05 rklancer so I'm trying to figure out how the bundle extender tells the framework to autostart it
14:05 rklancer ok
14:06 jonalv so it changes it' settings after it have ben runned once?
14:06 rklancer seems to
14:06 rklancer but i can't figure out where
14:06 rklancer that's the problem with stuff like spring
14:06 rklancer it works great if you know how it works
14:06 jonalv you should ask the spring-dm people
14:06 jonalv they are very nice
14:06 rklancer but if you don't know where the magic config files are and how they work, it seems like magic when you look at the code :)
14:07 jonalv rklancer, <http://groups.google.com/group/spring-osgi>
14:07 olas hi rklancer
14:07 rklancer great idea, i'll take like an hour or two to figure it out then i'll ask
14:08 rklancer btw, I think the spring stuff is/will be great, everyone seems to like it...I'm just in that stage where I have yet to figure out how it works :)
14:09 rklancer hi olas
14:09 jonalv btw if you are in doing stuff with spring. we are still running verison 1.0rc1 I think the latest is 1.2 or something like that. maybe you could look at what is needed to upgrade?
14:09 rklancer yup, thinking the same thing
14:15 rklancer btw, jonalv, target platform works ok? you're getting logging output?
14:15 jonalv yes
14:15 rklancer awesome :)
14:15 jonalv I had some problemds but now it works
14:15 jonalv keep up the good work! :)
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15:09 CIA-22 bioclipse: ospjuth * r5073 /bioclipse2/trunk/plugins/net.bioclipse.services/ (20 files in 7 dirs): Added a ServiceView with its own model.
16:13 jonalv egonw, is there a bioclipse 1.2 tag in the repo?
16:15 egonw would have been in bioclipse/tags
16:16 olas I have never done tags
16:16 olas donät know how
16:16 olas 1.2 is currently in trunk IMO
16:16 olas ASAIK
16:16 olas AFAIK
16:17 jonalv a lot has happend to trunk since 1.2, right?
16:17 egonw not too much, I think
16:18 egonw for example.... SDF has not
16:18 jonalv I have problems running Brunn out of Eclipse
16:18 jonalv it works great from within Eclipse but not very well after I ahve exported it out of eclipse so I am looking for reasons.
16:19 jonalv It would have helped to be able to riun bioclispe 1.2 from within eclipse safe harbour...
16:19 olas I'd say that almost nothing has happended to 1.2 since release
16:19 olas apart from a fix by me for proxy settings
16:19 jonalv "almost nothing" might not be good enough since I am having problems...
16:19 egonw stefan commited something...
16:20 jonalv I wanted to be able to absolutely sure that they are not related to changes in trunk
16:20 olas I cannot help much I'm afraid
16:20 jonalv An irritating fact is that I get exceptions but no logged stacktraces
16:21 olas logging is not perfect in 1.2
16:21 jonalv I ahve to figure out where the excetiption might have happend and catch them and manually print them
16:21 olas add -consoleLog
16:21 jonalv where?
16:21 olas start from console
16:21 jonalv of course I am starting from console
16:21 olas add -vmargs -consolelog
16:22 jonalv oh
16:22 jonalv testing
16:22 olas or create a file config.ini with this line
16:22 olas should be possible
16:22 olas but not 100% sure about syntax
16:22 jonalv still no exception and it has not printed everything that it should
16:23 olas not good
16:23 jonalv so I think it should have thrown an exception
18:13 CIA-22 bioclipse: ospjuth * r5074 /bioclipse2/trunk/plugins/net.bioclipse.services/ (24 files in 6 dirs): A lot of work on the ServiceView. See wiki page http://wiki.bioclipse.net/index.​php?title=Service_infrastructure for screenshot.
18:13 CIA-22 bioclipse: ospjuth * r5075 /bioclipse2/trunk/plugins/net.bioclipse.core/ (3 files in 2 dirs): Added a convenience class to cache images.
18:14 CIA-22 bioclipse: ospjuth * r5076 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (3 files in 2 dirs): Updated icon and category for Bioclipse Navigator.
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18:57 CIA-22 bioclipse: ospjuth * r5077 /bioclipse2/trunk/plugins/net.bioclipse.s​ervices/src/net/bioclipse/services/model/ (ServiceImpl.java ServiceImplementation.java ServiceType.java): New model for ServiceTypes and ServiceImplementations that initializes from Extension Points.
18:58 CIA-22 bioclipse: ospjuth * r5078 /bioclipse2/trunk/plugins/net.biocl​ipse.services/src/net/bioclipse/ser​vices/business/ServiceManager.java: Updated ServiceManager to work on new model objects.
19:45 olas bye for today
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23:09 CIA-22 bioclipse: rklancer * r5079 /bioclipse2/trunk/plugins/net.bioclipse.​ui/src/net/bioclipse/ui/Activator.java: fixed race condition between logging configuration and Spring bundle extender startup
23:19 CIA-22 bioclipse: rklancer * r5080 /bioclipse2/trunk/net.bioclipse.targ​et.platform/target-platform.target: Removed slf4j.simple from target. Having both slf4j.simple and slf4j.log4j12 seemed to confuse PDE too much.
23:33 CIA-22 bioclipse: rklancer * r5081 /bioclipse2/trunk/plugins/net.bioclipse.​ui/src/net/bioclipse/ui/Activator.java: trivial formatting cleanup

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