Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-01-14

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Time Nick Message
04:59 masak joined #bioclipse
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08:31 olass joined #bioclipse
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10:09 olass http://richclientplatform.blogspot.c​om/2008/04/dynamic-context-help.html
10:09 zarah olass's link is also http://tinyurl.com/7mtf7o
10:32 CIA-28 joined #bioclipse
10:34 CIA-28 bioclipse: jonalv * r8245 /bioclipse2/branches/jonalv-RunJSCommand​sAsJobs/plugins/net.bioclipse.ui/src/net​/bioclipse/ui/jobs/CreateJobAdvice.java: cleaned up a bit and made the solution a bit more backwards compatible
10:34 CIA-28 bioclipse: jonalv * r8246 /bioclipse2/branches/jonalv-RunJSCommandsAsJ​obs/plugins/net.bioclipse.cdk.business/src/n​et/bioclipse/cdk/business/CDKManager.java: added cancelability to numberOfentriesInSDF
10:37 * jonalv lunch!
10:37 masak lunch &
10:40 shk3 lunch?
10:41 shk3 at 10:40?
10:41 shk3 no thanks
10:47 gilleain joined #bioclipse
10:53 edrin joined #bioclipse
10:54 edrin hi
10:54 zarah hi edrin
10:54 edrin hi olass
10:54 gilleain hi
10:54 zarah hi gilleain
10:54 edrin got your mails
10:54 edrin hi gilleain
11:34 egonw joined #bioclipse
11:35 egonw moin
11:35 zarah hi egonw
11:35 egonw done with email backlog
11:39 * jonalv is back from lunch
11:40 * masak is back from sauna
11:40 masak er, lunch.
11:41 edrin hello egonw
11:42 egonw hi edrin
11:42 egonw my reply to you is pending...
11:42 egonw in case you wondered
11:42 egonw I'm done 'organizing' the backlog :)
11:42 edrin yes, sure
11:45 edrin joined #bioclipse
11:55 gilleain joined #bioclipse
11:59 edrin jonalv , masak: after checking out the whole platform again now even the old scripting console does not start anymore
11:59 edrin @gg pelezilla
11:59 zarah edrin: http://www.weddingbee.com/2008/06/01/o​ne-lucky-day-weekend-bonus-pele-zilla/
12:00 masak edrin: sorry to hear about your troubles.
12:00 masak @oz
12:00 edrin @gg pelezilla bioclipse
12:00 zarah edrin: http://wiki.bioclipse.net/index.p​hp%3Ftitle%3DContribute_feedback
12:00 masak @pz
12:00 zarah masak: Pelezilla is at http://pele.farmbio.uu.se/​cgi-bin/bugzilla/index.cgi
12:00 jonalv edrin: uhm that sounds bad, I don't really understnad what is going wrong for youi. It worked for me...
12:00 edrin http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=239
12:00 zarah edrin's link is also http://tinyurl.com/9o4nsg
12:00 masak edrin: I'm not putting much effort on the old console, because I want it to go away. I'd very much like feedback on the new console.
12:01 masak edrin: the latest edition of it resides in a branch.
12:01 edrin masak: for me the old console at least showed up for some time...
12:01 masak edrin: I know that. I'm removing it in a branch.
12:01 masak haven't actually removed it yet even there, but I will today.
12:01 edrin the new console crashs each time i try to show it with many many core exceptions in bioclipse.core
12:02 masak edrin: ok. that sounds bad. I don't know why. which exceptions?
12:02 edrin pls see this link: http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=239
12:02 zarah edrin's link is also http://tinyurl.com/9o4nsg
12:02 jonalv edrin: it does not find the Log4j
12:03 masak oh, a logger error.
12:03 jonalv edrin: could you try starting it thgough features instead?
12:03 masak jonalv++
12:03 edrin jonalv: why?
12:03 edrin it clicked set target platform?
12:03 edrin and have no features installed
12:04 jonalv edrin: because that's what I would try...
12:04 edrin what feature are you talking about
12:04 jonalv net.bioclipse_feature
12:04 edrin why is this required?
12:05 jonalv edrin: I am not sure that is required but I want to explore that way. If that works then we know that some thing works at least...
12:05 jonalv besides that's how Bioclipse is run when we export it...
12:06 edrin i cant do this now because i am not at home
12:06 jonalv okey
12:06 edrin but the error shows only when i try to show one of the consoles...
12:06 edrin if i do not use the scripting stuff: no problems
12:07 edrin but they show also up if i try to get the managers from the core
12:07 jonalv edrin: probably because the plugins needing Log4j is not started until you do
12:07 edrin this means there is probably code in scripting that should be in core and, that this code is buggy
12:07 * jonalv is detail studying the log now...
12:08 jonalv edrin: I think it means that the list of required plugins might not be correctly updated but I don't know yet...
12:08 edrin ERROR - Failed to get a service: Plug-in "net.bioclipse.scripting.ui" was
12:08 edrin unable to execute setInitializationData on an instance of
12:08 edrin "net.bioclipse.scripting.ui.bus​iness.JsConsoleManagerFactory".
12:08 edrin org.eclipse.core.runtime.CoreException: Plug-in "net.bioclipse.scripting.ui"
12:08 edrin was unable to execute setInitializationData on an instance of
12:08 edrin "net.bioclipse.scripting.ui.bus​iness.JsConsoleManagerFactory".
12:08 edrin at
12:09 edrin these are the same errors I see when i try to get collect managers from my plugin
12:09 jonalv yea and that error means that the manager has not been built
12:09 edrin yes
12:09 jonalv there are many possible reasons for that
12:09 edrin what file is responsible for this?
12:10 jonalv edrin: how do you mean?
12:10 olass joined #bioclipse
12:10 edrin there should in core be some file that is responsible for delivering the managers to the api. if they do nto exist they would have to create them
12:11 jonalv org.springframework.osgi.extender is responisble for building the managers if that is what you mean...
12:11 jonalv edrin: no, that is not how it works
12:11 jonalv each pugin "delivers" it's manager to the api
12:12 edrin jonalv: another: i saw man Exception.printStackTrace() in core they should go into log4j thoug
12:12 edrin jonalv: but what API is responsible for *lazy* loading the plugins when the managers are requested?
12:12 jonalv they indded should (given that it is not before the logger framework has started but it probably isn't)
12:12 jonalv edrin: That sounds like OSGi
12:13 jonalv edrin: or the Eclipse plugin management system ontop of OSGi to be more precise I guess
12:14 edrin i thought OSGI is just a *debug* hook you put into the eclipse opjects? they should not overtake eclipse?
12:14 edrin yeah
12:15 edrin jonalv: could it be that some class in core is extending an eclipse platform class and "should" overload a "plug+in" start function?
12:15 jonalv edrin: Eclipse is built ontop of OSGi. What do you mean "debug hook"?
12:16 edrin joined #bioclipse
12:16 olass hi
12:16 zarah hi olass
12:17 jonalv f
12:17 jonalv edrin: Eclipse is built ontop of OSGi. What do you mean "debug hook"?
12:17 edrin sorry, i messed up with Sprng
12:17 edrin soring
12:28 jonalv structuredb.addMoleculesFromSDF("db2", "/MyProject/small.sdf")
12:31 CIA-28 bioclipse: goglepox * r8247 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.ui.sdfeditor/plugin.xml: Removed JCP-toolbar form sdf editor fixes bugs #159 #162
12:31 gilleain hmmm. It occurs to me that I could actually do with using bioclipse with what I'm doing...
12:34 jonalv gilleain: oooh
12:34 jonalv Our first user?
12:34 jonalv :)
12:35 jonalv or is that edrin?
12:36 gilleain well, it's just that I am working with large sdf files, and it's a bit foolish not to use bioclipse to take a look at them :)
12:36 jonalv :)
12:38 gilleain hmmm. NPException at MoleculeTableContentProvider line 321
12:41 CIA-28 bioclipse: ospjuth * r8248 /bioclipse2/trunk/plugins/se.uu.farmbio.h​ivpred.client/src/net/bioclipse/xmpp/hivp​red/views/HIVPredictionResultView.java: Round results to 2 decimals.
12:45 edrin joined #bioclipse
12:45 Gpox gilleain: do you have the latest form svn?
12:49 gilleain yup, just updated n.bc.cdk.ui.sdfeditor
12:51 gilleain the stack trace indicates that it is the jFile that is null
12:52 gilleain which may not be so surprising given that the line above is:
12:52 gilleain java.io.File jFile = (location!=null?location.toFile():null);
12:53 gilleain the file still opens and displays, though, so it's not a huge deal
12:53 Gpox yeah that is handled wrong
12:54 Gpox it dose that is a little odd
12:55 gilleain I'm writing it up as a bug report, worry about it later :)
12:56 edrin jonalv: did the error log tell you something?
12:56 jonalv edrin: no not really
12:57 edrin what do you conclude from it?
12:57 jonalv edrin: I still would like you to test running from features but it seems that you are missing the Log4j pluign
12:58 edrin no, the bioclipse.logger is in
12:58 jonalv edrin: sry I mean the Log4j bundle
12:59 jonalv I am 100% sure which one it is though
13:00 jonalv but are you running: slf4j.log4j12, org.springframework.osgi.log4j.osgi, and org.apache.commons.logging?
13:07 edrin i have no clue
13:07 edrin i am just using the plugins and set target platform
13:07 edrin shouldn't the plugins take care of this?
13:11 grandm44 joined #bioclipse
13:12 egonw grandm44: welcome back
13:12 grandm44 hello all
13:12 zarah hi grandm44
13:12 egonw de__maas: hey, you're back online too? :)
13:15 de__maas Hi egonw, just for a quick look how's around.
13:15 egonw sure, no problem :)
13:15 egonw de__maas: did you hear about the improved SD support in Bioclipse2 ?
13:16 de__maas it Lookes like the number of developers increased
13:16 egonw you can now browse 1GB sized files
13:16 de__maas Yes, I'm really looking forward to the new release.
13:16 jonalv uhm well currently yoiu can't. Right Gpox?
13:17 egonw jonalv: huh?
13:17 jonalv or did gilleain have a broken file?
13:17 egonw jonalv: what happened?
13:17 de__maas Oeps, just started calculating on a small part of my libary being larger then 1GB
13:17 * gilleain sets molgen at work on generating isomers of c30h60 to test the limit
13:17 egonw gilleain++
13:18 grandm44 Still in the place place : i can launch bioclipse, despite a few errors. But i can't play with jchempaint. I wiped out all projects, checked out all plugins in bioclipse2/plugins, all cdk-externals, all features, and net.bioclipse.target.platform. I set target platform, then went to the run config, deselected all plugins, added the workspace, added required plugins. What else can I do ?
13:18 gilleain egonw : actually, it would take 10,000 years, so probably I won't trty c30 :)
13:18 egonw grandm44: put your stacktrace online, so that we can suggest something...
13:19 egonw e.g. at http://bioclipse.pastebin.com/
13:19 zarah egonw's link is also http://tinyurl.com/7ckm92
13:19 gilleain jonalv : it wasn't a size issue with the file.
13:19 egonw gilleain: yeah, I can imagine...
13:20 gilleain it was only 4Mb
13:20 grandm44 egonw: here it is http://paste2.org/p/129716
13:20 gilleain Also, I can only get sdf files to open properly from /Virtual, not /Sample Data...
13:21 shk3 not the other way round?
13:21 shk3 sdf does not work from virtual
13:21 shk3 that's a feature
13:21 gilleain shk3: oh
13:22 shk3 I have been told
13:22 gilleain 'feature' eh? :)
13:22 gilleain No, I can import a file into /Virtual, and it opens.
13:22 egonw jonalv: can you check that pastebin too, please?
13:22 gilleain If I import into /Sample Data, I only get the first two entries.
13:22 egonw grandm44: I think you are missing the plugin for log4j...
13:23 egonw jonalv: what are those one needs again?
13:24 grandm44 egonw: can i find it in the repository ?
13:24 egonw no
13:24 egonw that one is part of your eclipse 3.4 installation
13:26 egonw blah... my network is being rather slow :(
13:31 grandm44 installed Apache Jakarta log4j, reset target platform etc... nothing seems to change http://bioclipse.pastebin.com/m70cba68c
13:31 zarah grandm44's link is also http://tinyurl.com/7nxw55
13:32 egonw grandm44: no, that's not the solution
13:32 egonw connections are being slow here...
13:32 egonw looking for the correct fix
13:32 egonw should be on wiki.bioclipse.net
13:33 egonw jonalv: ping
13:33 egonw Gpox: ping
13:33 egonw jonalv, olass, Gpox: what's the plugin needed for BC2 to provid log4j again...
13:33 egonw the one with that weird name
13:34 olass import org.apache.log4j
13:34 olass that should be enough
13:34 egonw no, not for in the META-INF, but for running BC2
13:34 olass no required dep to net.bioclipse.logging
13:34 egonw see the stacktrace from grandm44
13:35 egonw grandm44: btw, did you try running using the features?
13:35 olass grandm44: did you add impor
13:35 olass grandm44: do you import org.apache.log4j?
13:35 olass run the bioclipse.product is my advice
13:35 olass it should work
13:35 olass first: set target platform
13:36 * jonalv backslogs
13:38 jonalv grandm44: congratulations it seems you have managed to reproduce the problems edrin has. Are you using Windows perhaps?
13:38 jonalv grandm44: Could you try starting from features?
13:39 grandm44 olass: I installed log4j from eclipse software update, did set target platform, then run bioclipse.product. I'm using linux. I'll try to start it from features right now
13:40 jonalv this is intresting
13:40 olass product is using features
13:40 edrin no, that's not the only problem
13:40 edrin my first and still sever problem is that i cannot instantiate the managers
13:41 * masak comes flying in through the window
13:41 masak someone needs help here?
13:42 masak I thought I heard the suffering of a citizen.
13:42 grandm44 when i try to add a new feature from bioclipse, i get this error http://bioclipse.pastebin.com/m138fa060
13:42 zarah grandm44's link is also http://tinyurl.com/a56mxt
13:42 grandm44 I do have checked out net.bioclipse_feature
13:42 egonw grandm44: do you have red crosses in your workspace
13:43 egonw on any project?
13:43 grandm44 yes, on several
13:43 masak grandm44: we think you need to add the bioclipse feature.
13:43 masak (actually, it's jonalv++ who thinks that.)
13:43 jonalv grandm44: have you added the Bioclipse feature to the product?
13:43 egonw grandm44: ah, I think we need to resolve those first
13:43 egonw which projects have red crosses?
13:43 edrin who is grandm44?
13:43 egonw edrin: try /whois
13:44 grandm44 edrin: a new guy
13:44 masak who is that edrin guy? :)
13:44 edrin ah
13:44 edrin grandm44: you jist started?
13:44 grandm44 yes
13:44 edrin what are your intentions to do with bc2?
13:44 egonw get it running :)
13:44 masak haha
13:45 masak edrin: he's running it, not marrying it. :)
13:47 grandm44 red crosses with: cdk.libiomd, cdk.pdbcml, cdk.qsarcml, nmrshiftdb, specmol, seneca, spectrum.test, cml, cdk.libiocml, spectrum, cdk.inchi, qsar.ui
13:50 grandm44 edrin: first, I would like to use the generated molecules from jchempaint in our software, which doesn't have a gui. Then do some more stuff.
13:51 CIA-28 bioclipse: jonalv * r8249 /bioclipse2/branches/jonalv-RunJSCommandsAsJobs​/plugins/net.bioclipse.scripting/src/net/biocli​pse/scripting/business/JSJobCreatorAdvice.java: Fixed the advice creating jobs from JavaScript methods
13:51 jonalv grandm44: any progress with starting Bioclipse from features?
13:52 egonw grandm44: that would typically mean you do not have enough plugins checked out
13:52 egonw grandm44: it seems you lack the XOM plugin
13:53 jonalv grandm44: are you familiar with running SVN from the terminal?
13:53 egonw grandm44: http://bioclipse.svn.sourceforge.net/view​vc/bioclipse/bioclipse2/trunk/externals/
13:53 zarah egonw's link is also http://tinyurl.com/99y8yc
13:53 egonw grandm44: from that SVN location
13:53 egonw checkout : org.xmlcml.cmlxom
13:53 egonw that should solve a few problems, I think
13:53 egonw problems == red crosses == missing dependencies
13:54 grandm44 jonalv: i can't add any features : "current configuration problems", the box says
13:54 grandm44 egonw: thanks, i try this
13:55 jonalv grandm44: strange. Have you tried removing all to sort of "restart"?
13:55 egonw grandm44: it's my mistake...
13:55 egonw you're just following the wiki...
13:55 egonw the wiki is outdated...
13:55 egonw will fix that now...
13:55 egonw sorry about that :(
13:56 grandm44 Yes, just blindly following the wiki...
13:57 egonw well, RTFM is what they say...
13:57 egonw but the never add to that the the FM is often outdated :(
13:57 grandm44 jonalv: yes, wiped out all the project this morning, then did all the steps again
13:58 masak I always forget how to do a fresh install, and then I follow the steps on the wiki.
13:58 masak but I get it working that way, so I don't know what could be the problem. :/
14:00 grandm44 egonw: i have trouble adding the repository http://bioclipse.svn.sourceforge.net/view​vc/bioclipse/bioclipse2/trunk/externals/
14:00 zarah grandm44's link is also http://tinyurl.com/99y8yc
14:01 egonw yeah... that's the HTML interface URL...
14:02 egonw replace viewvc with svnroot
14:02 egonw I think
14:02 egonw and maybe http -> https
14:03 egonw not sure about anynomous read-only access...
14:03 egonw grandm44: use the same SVN commands you used earlier this week
14:07 grandm44 That's better ! there is only errors with spectrum.test and qsar.ui. Do I really need these ?
14:08 egonw no, not at this moment
14:08 egonw grandm44: I've updated the wiki
14:08 egonw thanx for reporting your problems!
14:09 grandm44 You're welcome, thanks for solving mine :)
14:13 egonw grandm44: so, it runs now?
14:18 grandm44 Yes, it runs, I'm playing with it, creating a cml file :) I look for the chemoinformatics view with jchempaint
14:18 egonw excellent
14:18 egonw grandm44: note that things are still under heavy development
14:18 egonw so expect bugs...
14:19 egonw you are free to report them, if you think they should be fixed before release
14:19 grandm44 I am aware of this, anyway thank you for your efficient support :)
14:19 egonw we are likely already aware of them, so check the current bug list...
14:20 grandm44 do u have a bug tracker somewhere ?
14:20 egonw btw, also feel free to request feature request
14:20 egonw @pz
14:20 zarah egonw: Pelezilla is at http://pele.farmbio.uu.se/​cgi-bin/bugzilla/index.cgi
14:20 egonw it uses bugzilla, and requires you to register with an email account...
14:20 egonw so that we can follow up
14:21 grandm44 ok, i'll register. And maybe my nick on nickserv too.
14:21 egonw :)
14:23 jonalv egonw: git sucks btw
14:23 jonalv egonw: I am merging now and I have to hand merge every little freaking commit...
14:24 egonw how? why?
14:24 jonalv I am trying to merge back my branch
14:24 egonw you must be doing something wron...
14:24 egonw try a rebase from master first...
14:24 jonalv I have merged it with trunk earlier
14:24 egonw ah...
14:24 egonw there's the mistake
14:24 CIA-28 bioclipse: goglepox * r8250 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Moved 2D structure view to n.bc.cdk.jchempiant.view bug #184
14:24 zarah bug #184 | http://tinyurl.com/77sfzt
14:24 egonw I made that one in the paste too...
14:25 jonalv egonw: what?
14:25 egonw if you make a branch
14:25 jonalv egonw: what should I do then?
14:25 egonw then you do not merge from the one you branched from
14:25 egonw but rebase
14:25 egonw so, say:
14:25 egonw git checkout -b newBranch master
14:25 egonw commit, commit, commit
14:25 egonw then, you should do:
14:25 jonalv egonw: Gpox and I tried that but we got conflicts...
14:26 egonw git checkout newBranch; git rebase master
14:26 jonalv egonw: and what can I do right now?
14:27 egonw manually apply patches I guess...
14:27 egonw I have about 600 left from cdk1.2.x to merge with cdk trunk :(
14:27 egonw so, I feel your pain
14:27 jonalv it's just that I thought you said that it worked...
14:27 jonalv when it appharently don't
14:28 egonw well, if two branches are very much diverged... you can always have conflicts...
14:28 jonalv yea but I haven't even touched these plugins...
14:28 egonw well... that's likely caused by the merge with trunk you did earlier...
14:29 egonw I've had such problems too...
14:29 jonalv yea that must be it...
14:29 egonw being a relative git novice too...
14:29 jonalv could I undo that merge?
14:29 egonw yes, should be possible...
14:29 egonw but not sure if that will make things easier...
14:29 egonw try this:
14:29 jonalv do you think that is a better way?
14:29 egonw create a branch from the current branch...
14:29 egonw but not from HEAD
14:30 egonw but from the last version just before that merge with trunk
14:30 egonw then do a rebase from trunk with that new branch...
14:30 jonalv how do I find that one?
14:30 egonw git log?
14:31 egonw or...
14:31 egonw maybe better even:
14:31 egonw make a branch from the master version you branched from before
14:31 egonw then apply all patches from your current branch except the merge with trunk
14:31 jonalv how do I abort this merge then?
14:31 egonw depends I think...
14:32 egonw question:
14:32 egonw did you commit the merge with trunk to SVN already?
14:32 egonw or is that just local?
14:32 jonalv egonw: everything is on svn
14:32 egonw if the latter
14:32 egonw :(
14:32 jonalv why does that matter?
14:33 egonw well, you can remove (aka delete) local git commits
14:33 egonw when you have not shared them yet
14:33 egonw but since you already uploaded the trunk-merge to SVN
14:33 jonalv but how do I get rid of this merge branch which I am in now?
14:33 jonalv I can' switch branch and I cant stash
14:34 egonw git merge --abort
14:34 egonw or something like that
14:34 egonw man git
14:34 jonalv git merge --abort
14:34 jonalv fatal: You are in the middle of a conflicted merge.
14:34 jonalv
14:34 egonw @gg git merge abort
14:34 zarah egonw: http://www.kernel.org/pub/softwa​re/scm/git/docs/git-rerere.html
14:34 egonw jonalv: then resolve that one first :)
14:35 jonalv egonw: but that will take forever and once I have done that I will be done anyways...
14:35 egonw yeah, sorry about that...
14:36 egonw I learned about the difference between 'git merge' and 'git rebase' the hard way too
14:37 egonw olass, others: when learning git... when you are typing 'git merge', make sure to think "should I not be using git rebase instead?"
14:40 gilleain joined #bioclipse
14:40 jonalv egonw: okey now I am back in a situation where I can work again. What was your best suggestion?
14:41 egonw best?
14:41 egonw you mean, the option I think would be best?
14:41 jonalv egonw: yea what should I try?
14:41 egonw or the one that will work best?
14:41 egonw no clue about the last...
14:41 egonw but I'd go for
14:41 egonw :
14:42 egonw make a new branch, from the version of master from which you branched earlier
14:42 egonw then apply the changes you made to your current branch to this newly created branch
14:42 egonw then rebase with master
14:43 egonw btw... also don't cherry pick in your patch branch from other branches
14:43 egonw as you seem to have have done...
14:43 egonw that is, you merged from gpox' branch, right?
14:43 egonw don't do that in your patch branch
14:44 egonw but in an independent third branch, into you pull from your patch branch, and gpox's patch branch
14:44 egonw that might also be a reason why merging your patch into trunk fails
14:45 jonalv egonw: I can't find the commit that created the branch... :(
14:46 egonw http://bioclipse.svn.sourceforge.net/vie​wvc/bioclipse?view=rev&revision=7972
14:46 zarah egonw's link is also http://tinyurl.com/6t5loj
14:47 egonw svn log is your friend
14:50 jonalv egonw: how do I do this? :(
14:51 egonw what?
14:51 jonalv apply the commits except a certain few commits
14:52 CIA-28 bioclipse: ospjuth * r8251 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Updated test plugin.
14:52 egonw cherry-pick is an option
14:55 jonalv masak: just said that I didn\t want to do cherry
14:55 masak but cherry-pick seems to be the one you want.
14:57 egonw well, if your previous branch only contained your patches...
14:57 egonw then you could just merge or pull
14:57 egonw but since you added patches from other branches already, you lost that option
14:58 egonw well...
14:58 egonw you could do that...
14:58 egonw and then remove the unwanted patches...
14:58 egonw but I'd likely go for cherry-picking now...
15:19 CIA-28 bioclipse: ospjuth * r8252 /bioclipse2/trunk/plugins/se.uu.farmb​io.hivpred.model/src/org/hivdrc/hivpr​ed/conversion/EMFDOMConversion.java: catch an Exception.
15:41 egonw [15:46:42] <egonw> http://bioclipse.svn.sourceforge.net/vie​wvc/bioclipse?view=rev&amp;revision=7972
15:41 zarah egonw's link is also http://tinyurl.com/6t5loj
15:41 egonw jonalv: that one
16:05 gilleain joined #bioclipse
16:14 CIA-28 bioclipse: ospjuth * r8253 /bioclipse2/trunk/plugins/se.uu.farmbio.hivp​red.client.tests/src/se/uu/farmbio/hivpred/c​lient/tests/PluginTestHivpredManager.java: Update params to fix unit test running. Still no luck.
16:56 de__maas left #bioclipse
17:49 olass joined #bioclipse
17:49 olass hmm
17:49 olass irc seems unstable today
17:49 olass @msg
17:49 zarah olass: You have no new messages.
17:51 egonw olass: ping
17:51 olass pong
17:52 egonw you planned a meeting for tomorrow?
17:52 olass yes
17:55 egonw at what time?
17:56 olass dunno
17:56 olass 10?
17:56 olass when all are there
17:56 egonw ok
17:56 egonw bbl
18:03 edrin going home now
18:03 edrin olass: will you be around? I will try to fix the thing...
18:03 olass 'edrin: sorry, must go now...
18:04 olass please email me outcome
18:07 edrin left #bioclipse
18:46 olass joined #bioclipse
18:53 egonw masak: any clue how we can get a file format contenttype String show up in the Properties View ?
18:53 masak not even the beginning of one, sorry.
18:54 masak but I imagine there'd be some tutorial on the Eclipse RCP homepage that does.
18:54 egonw I think it used to show up there automatically...
18:54 masak oh.
18:54 egonw I'll ask ola tomorrow
18:54 egonw at least in BC1...
18:54 egonw but maybe that was done differently...
19:42 CIA-28 bioclipse: edrin_t * r8254 /xws/trunk/xws4j/src/net/bioclipse/xws/clie​nt/xmpp/modules/MessageAdHocCommands.java: debug info now correct
19:46 edrin1 joined #bioclipse
20:02 olass joined #bioclipse
20:02 olass edrin1: any progress?
20:15 CIA-28 bioclipse: egonw * r8255 /bioclipse2/trunk/plugins/net.bioclipse.rdf/ (14 files in 7 dirs): Added RDF plugin, which will show knowledge about a molecule
20:16 CIA-28 bioclipse: egonw * r8256 /bioclipse2/trunk/features/​net.bioclipse.rdf_feature/ (. .project build.properties feature.xml): Added Bioclipse RDF feature
20:16 CIA-28 bioclipse: egonw * r8257 /bioclipse2/trunk/plugins/ne​t.bioclipse.rdf/plugin.xml: Better category name
20:16 CIA-28 bioclipse: egonw * r8258 /bioclipse2/trunk/plugins/net.biocli​pse.rdf/src/net/bioclipse/rdf/views/ (RDFContentProvider.java RDFLabelProvider.java RDFView.java): Now uses data providers, so that the data shown updates on IStructuredSelection events
20:19 CIA-28 bioclipse: egonw * r8259 /bioclipse2/trunk/cdk-externals/trunk/ (124 files in 18 dirs): Added CDK code for format detection
20:20 CIA-28 bioclipse: egonw * r8260 /bioclipse2/trunk/plugins/net.bioclipse.ioformats/ (13 files in 6 dirs): Set up Describer using the CDK matchers
20:49 CIA-28 bioclipse: edrin_t * r8261 /xws/trunk/xws4j-hivpred-client/: deleted.
20:50 CIA-28 bioclipse: edrin_t * r8262 /xws/trunk/ (4 files in 4 dirs): deleted.
20:52 CIA-28 bioclipse: edrin_t * r8263 /xws/trunk/xws4j-hivpred-client/: Initial import.
21:01 CIA-28 bioclipse: edrin_t * r8264 /xws/trunk/xws4j-hivpred-client/ (159 files in 52 dirs): Initial import

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