Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-01-03

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Time Nick Message
06:14 thomas_ku joined #bioclipse
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13:37 CIA-20 bioclipse: jonalv * r4613 /branches/bioclipse2/bioinformatics/​plugins/net.bioclipse.biojava.busine​ss/META-INF/spring/context-osgi.xml: commented out nonworking code for now...
13:40 masak actually, I think bioclipse2 sits well in branches/ right now
13:41 masak until it replaces bc1, that is
13:43 egonw so, the question is... will BC1 see further development...
13:43 egonw other than bug fixing...
13:44 masak egonw: after bc2 replaces it? depends on the user base, I guess
13:45 egonw well... that suggests there are resources available for support...
13:45 olas IMO: BC2 will completely replace BC1
13:45 olas the question is really about timing
13:46 masak and convincing all users to switch :)
13:46 olas there are so many stability issues with BC1 that I'd like BC2 to replace it as fast as possible
13:46 egonw yeah, sounds like a plan
13:46 olas but we need some work in order to get there
13:46 olas then we can migrate plugin by plugin
13:46 olas egonw: the most pressing is JCP
13:47 olas a ne JCPEditor in BC2
13:47 olas I need your help with that
13:49 egonw ok, a quick chat...
13:49 egonw haven't started with the new JCP yet
13:49 egonw not really...
13:49 egonw so, let's talk porting the old JCP for now...
13:49 egonw we should not wait for the new code... ETA, this summer
13:51 egonw now, in BC2, I think it is a good idea so link editor with file format...
13:51 egonw so, not have a general 2D editor...
13:51 egonw but a CMLEditor
13:51 egonw and a MDLMolfileEditor
13:51 egonw etc...
13:52 egonw olas, what do you think?
13:54 egonw given the diversity CML files can hold...
13:54 egonw each type of content could trigger a certain tab
13:54 egonw e.g. a JCP tab
13:54 egonw or a SpecMol tab
13:54 egonw but having this strong format/editor link is a good thing...
13:55 egonw (alternatively, have many CMLEditors... which would be good too... cleaner probably...)
13:55 egonw Uppsala, still here?
13:57 jonalv Uppsala here, olas is in Stockholm... :)
13:57 masak but the rest of us are here
13:59 * olas is back
13:59 olas sorry
13:59 olas egonw: Yes, porting old JCP to BC2 is fine
13:59 olas the problem is: old JCP is really dirty code
13:59 olas and CDK knowledge is required
14:00 olas the only change is (and that is actually not a big change but a simplification)
14:00 olas that we donät use BioResource anymore
14:00 CIA-20 bioclipse: carl_masak * r4614 /branches/bioclipse2/ (4 files in 3 dirs): * removed superfluous overrides
14:01 olas Please take a look at the JmolEditor in bc2 where I have demonstrated the use of an MPE without BioResource
14:01 olas simply let the text editor do the save
14:02 olas and if you are in JCP, serialize to text first and then call textPage.save()
14:02 olas but this is a good time to clean up some
14:02 olas it is really dirty code
14:02 olas egonw: you with me?
14:03 egonw yeah...
14:04 egonw well, would have to dig into the JCPEditor code...
14:04 egonw did look at it, but did not write it, and it is indeed complex
14:04 olas could we get Stefan to do it?
14:04 egonw maybe...
14:04 olas we could ask him...
14:04 egonw sure
14:04 egonw he still commits every now and then...
14:05 egonw I will not have time before next thursday...
14:05 olas ack
14:05 egonw what about dedictated editors...
14:05 egonw such as a MDLMolfileEditor
14:05 egonw I really think BC2 should do that
14:05 olas why so?
14:05 egonw instead of having a CDKEditor or JCPEditor
14:05 olas please elaborate
14:05 egonw because is more close to the RCP-way
14:06 egonw e.g. separation of format detection from the editor-saving
14:06 egonw e.g. highlighting in the editor
14:06 olas I disagree
14:06 olas Having a single editor is simpler for users
14:06 egonw e.g. having explicit what formats are supported
14:07 egonw I don't get that logic
14:07 egonw the editors would have the same functionality
14:07 egonw JCP + source editor
14:07 olas Could you formalize this in a mail to bioclipse-devel?
14:07 egonw well... if 2D coords...
14:07 egonw yes, I think so
14:07 olas then I will comment on it
14:07 jonalv you might be talking around eachother rihgt now but I don't understand you completely
14:08 olas read the mail
14:08 olas when it arrives
14:08 egonw jonalv: you might be right, if I only knew what you think we are talking about
14:08 olas write the mail and explain :-)
14:09 egonw bbl
14:37 egonw olas: something like this: http://wiki.bioclipse.net/​index.php?title=CDK_plugin ?
14:38 egonw btw, search seems broken in the wiki
14:43 CIA-20 bioclipse: carl_masak * r4615 /branches/bioclipse2/core/plugins/ (10 files in 3 dirs):
14:43 CIA-20 bioclipse: [net.bioclipse.core]
14:43 CIA-20 bioclipse: [net.bioclipse.ui]
14:43 CIA-20 bioclipse: * moved these from core to ui
14:43 CIA-20 bioclipse: ** ConsoleEchoer
14:43 CIA-20 bioclipse: ** EchoListener
14:43 CIA-20 bioclipse: ** EchoEvent
14:44 masak yes. the sad part is that now, net.bioclipse.core is pretty empty
14:44 masak all the partying has moved elsewhere
14:44 olas haha
14:44 masak except for a proof-of-concept Sequence
14:44 olas maybe move them all back?
14:44 masak olas: no can do
14:44 olas :-)
14:44 masak each single move had a good reason
14:45 masak it was a sort of chain reaction thing
14:45 olas maybe core is not needed?
14:45 egonw for the .product file?
14:46 jonalv egonw, what do you mean?
14:46 egonw never mind
14:46 masak olas: well, if we still believe in Sequence, we believe in core
14:46 masak ...I think
14:48 olas .product is in core.ui
14:49 olas as core.ui depends on core and not the reverse
14:50 jonalv which is the source of our problems
14:50 masak jonalv: I'm in
14:51 masak awaiting further instructions
14:52 masak Swing is like a big corporate building that needs to be infiltrated from below
14:52 masak or something
14:52 jonalv ui starts first and can't use stuff in core when starting since core has not started yet... :(
14:53 masak egonw: search on bc wiki worksforme
14:53 egonw here, it finds nothing
14:53 jonalv which is why we had to move the stuff
14:54 masak egonw: try searching for "base2"
14:54 masak that brings up a few results for me
14:55 jonalv egonw, In what way is the search broken in the wiki?
14:55 egonw try: CDK
14:55 egonw and manually ensure 'CDK' *is* present... http://wiki.bioclipse.net/​index.php?title=CDK_plugin
14:56 masak confirmed
14:56 masak that is indeed strange
14:56 jonalv confirmed
14:56 jonalv yes indeed
14:56 masak bug in mediawiki?
14:56 masak that's what they get for trying to reinvent googling :)
14:56 jonalv 'cdk' gives one hit
14:58 masak jonalv: not here it doesn't
14:58 jonalv lol
14:58 masak it says "Showing below 0 results starting with #1."
14:58 masak which in itself is pretty daft
14:58 jonalv lol
14:58 jonalv Itä's not funnt
14:58 jonalv funny
14:58 masak no :)
15:07 jonalv I hate dependencies
15:09 masak then be glad we're not in Soviet Russia, at least
15:10 masak ...though right now it seems that they do
15:51 jonalv olas, ping?
15:52 jonalv egonw, you don't happend to have some time over?
15:52 egonw did you see Bioclipse on the front page of: http://postgenomic.com/ ?
15:52 egonw a tiny bit I have
15:52 jonalv hm that might not enough...
15:53 jonalv I had trouble getting some Spring stuff working on masak's system and was wondering if you would like to try...
15:53 jonalv I would instruct...
15:53 egonw OK
15:53 egonw sounds cool
15:53 jonalv :)
15:54 jonalv okey check out: net.bioclipse.biojava, net.bioclipse.biojava.business, net.bioclipse.recording, and net.bioclipse.target.plattform
15:55 jonalv *platform
15:55 egonw I got the full branches/bioclipse2
15:55 egonw that's fine, I assume...
15:55 jonalv aha
15:56 * jonalv has no idea of how that will work
15:56 egonw rebooting in my bc2workspace now
15:56 jonalv but I guess it should work
15:56 jonalv you probably should update it anyway
16:02 jonalv egonw, ping
16:02 egonw pong
16:02 egonw working on it...
16:02 jonalv oki
16:06 egonw got several compile errors
16:06 jonalv yep
16:06 jonalv you should
16:06 jonalv You are not using the target platform
16:06 egonw oh...
16:06 egonw huh?
16:06 jonalv :)
16:07 egonw ok, tell me what to do...
16:07 jonalv in net.bioclipse.targetPlatform
16:07 jonalv find target-platform.target
16:07 jonalv open it
16:07 jonalv up in the right corner choose "use target platform"
16:08 jonalv it adds all Spring stuff to the target plattform
16:09 egonw I got 'Set as Taget Platform'
16:10 jonalv ah that's it
16:10 jonalv :)
16:10 jonalv sry
16:11 egonw that helps a bit
16:11 jonalv only a bit?
16:12 egonw yeah... compile errors in cdk.ui
16:12 jonalv Shit nothing works for me right now. What worked earlier on for me now doesn't work at all
16:12 jonalv that can hardly be related or can it?
16:12 CIA-20 bioclipse: egonw * r4616 /branches/bioclipse2/chemoinformatics/net.biocli​pse.cdk.ui/src/org/openscience/cdk/applications/​jchempaint/action/AdjustBondOrdersAction.java: Fixed compile error
16:12 egonw no, don't think so
16:14 edrin joined #bioclipse
16:14 edrin hi all
16:14 edrin olas: thanks for your mail
16:14 edrin happy new year
16:14 jonalv right so what I want you to do is check which plugins it whiches to launch when you choose net.bioclipse.biojava.business and then click add required plugins because that seems to differ and create problems...
16:14 jonalv hi edrin
16:15 edrin hey jonalv
16:15 jonalv wish
16:15 jonalv that should be wishes right?? :)
16:19 egonw where do I do that?
16:19 jonalv in the run dialog
16:19 jonalv nothing special this time
16:20 jonalv just the normal run dialog where you say which plugins to run
16:20 egonw where's the .product for BC2 again?
16:21 jonalv it's in ui but why do you need it?
16:22 jonalv oh to create the run config
16:22 jonalv I se
16:22 egonw how do I get a run dialog otherwise?
16:22 egonw right :)
16:22 jonalv you can click the little arrow besides the play button and chose open run dialog
16:23 jonalv but if you don't have any it's probably eaier to create one from the product
16:24 egonw right...
16:24 egonw BC2 fired up
16:24 egonw now what?
16:25 jonalv oh the goal of this is to get an instance of the biojavamanager in the javascript console
16:25 jonalv what do you get if you write biojava in it?
16:25 jonalv Is it a plain java object or an instance of the biojavamanger or is it not declareed at all?
16:26 egonw I get an exception when opening the JS console
16:26 egonw jmol.Activator cannot be cast to net.bc.ui.Activator...
16:26 egonw will need to kill the Jmol plugin first...
16:26 jonalv 'key
16:27 jonalv I have a bad feeling about that bug though.
16:27 * jonalv think he casued it today...
16:27 egonw java.lang.NoClassDefFoundError: org/eclipse/core/internal/runt​ime/auth/AuthorizationHandler
16:27 egonw at org.eclipse.core.internal.runtime.In​ternalPlatform.initializeAuthorizati​onHandler(InternalPlatform.java:603)
16:27 egonw that's on the console in eclipse
16:27 egonw ok, rebooted BC2
16:27 jonalv yes I have seen that before
16:27 egonw the JS console is open now
16:28 egonw js> biojava
16:28 egonw java.lang.Object@2b3574
16:28 jonalv it dissapeared when I choose Clear the configuration are before launching under the Configuration tab in the run dialog
16:29 jonalv yep you get a java.lang.Object
16:29 egonw right
16:29 egonw an instance
16:29 egonw that's OK?
16:29 jonalv That's what I am getting for the moment aswell so we are at the same step...
16:29 jonalv I had something different working earlier today but it's borken now somehow... :(
16:30 jonalv you got an instance of the manager earlier today...
16:30 jonalv That's pretty much what I am working on now...
16:30 jonalv Can you check one other thing for me?
16:30 * egonw just issued a R session
16:30 egonw which is taking up most of one of my cores :)
16:31 jonalv are you running the slf4j.log4j12 plugin now? (you shouldn't)
16:31 egonw oh, found this on the console in eclipse:
16:31 egonw COULD NOT GET BIOJAVA MANAGER SERVICE!
16:31 jonalv yep thought so... :(
16:31 jonalv but are you running that plugin?
16:31 egonw how do I check that slf4j thingy?
16:32 jonalv just check which plugins you are starting that's easiest
16:32 jonalv (once again in the run dialog)
16:32 jonalv under the plug-ins tab
16:32 edrin ok
16:32 jonalv it's in the target platform probably very near the bottom
16:32 edrin cu
16:32 egonw it's deselected now, but forgot to check what state it was
16:33 edrin left #bioclipse
16:33 egonw also cleared WS
16:33 egonw but still got that exception
16:33 jonalv strange
16:33 jonalv I thought it was something old left in the worksapce since I got rid of it by clearing my workspace
16:34 egonw DEBUG - Configured logging in plugin: net.bioclipse.ui
16:34 egonw Namespace for this attr is: rhino
16:34 egonw COULD NOT GET BIOJAVA MANAGER SERVICE!
16:34 egonw after typing 'biojava' in the JS console
16:34 egonw R> image(x)
16:34 egonw R died
16:34 egonw :)
16:34 jonalv well actually it comes when you open the JS console (or should)
16:35 jonalv it seems as the net.bioclipse.core Activator no longer get's runned
16:36 jonalv which means that my hack that starts the Spring bundle no longer get's runned and hence the spring bundle isn't started and that's why we can't get the biojava service
16:36 jonalv it all falls doen like a card house... :/
16:38 egonw right
16:38 egonw don't see it getting started here either
16:39 egonw I think this is caused by Eclipse-LazyStart: true
16:39 egonw and that there is no functionality left in .core
16:39 egonw as masak reported earlier
16:39 * jonalv is moving the code inte the activator in UI instead. That just has to be runned
16:39 egonw so, no need to start it
16:39 egonw yes, makes sense
16:39 egonw move more out of .core :)
16:39 jonalv hehe..
16:39 egonw that seems to do the job in Uppsala...
16:40 egonw carry water from the lake to the see
16:40 jonalv the probelm is that ui and not core is the first plugin to be started
16:40 jonalv that might be wrong...
16:40 egonw yeah, that sounds weird
16:41 jonalv but the product is in ui...
16:41 egonw that's why I said earlier regarding nothing left in .core:
16:41 jonalv maybe the product should be in core isntead
16:41 egonw [2008-01-03 15:47:38] <egonw> for the .product file?
16:41 jonalv I don't really know...
16:42 egonw right, it's called core for some reason one would think...
16:42 egonw olas: what were you thinking?!?!?
16:42 egonw :)
16:42 jonalv oh well anyway that's why the core plugin is being drained on code...
16:43 jonalv or why we carry water from the sea if you want to put it so... :)
16:44 olas left #bioclipse
16:45 jonalv egonw, maybe we should talk about this with olas and then perhaps move stuff back again?
16:46 CIA-20 bioclipse: jonalv * r4617 /branches/bioclipse2/core/plugins/ (2 files in 2 dirs): moved the code starting the Spring-extender bundle into an Activaor that always get's runned
16:47 jonalv egonw, update and try again, now you should get a biojavamanager instead for an Object (I hope)
16:47 egonw hang on
16:47 egonw btw, please file a bug report for this...
16:47 egonw that the .product should move to .core
16:47 egonw and that the OSGi code should go into the .core Activator
16:47 egonw sign with both our names
16:48 egonw no running away from that for Ola
16:48 jonalv where do we have bug reports for bioclipse2?
16:48 egonw sf.net/projects/bioclipse
16:48 egonw there is a bioclipse2 group
16:48 egonw to indicate that it affects BC2 only
16:48 jonalv ah I haven't seen that...
16:49 jonalv will do real soon now only want to test one more thing...
16:49 egonw 62 [main] INFO org.springframework.osgi.extende​r.internal.ContextLoaderListener - Starting org.springframework.osgi.extender bundle v.[1.0.0.rc1]
16:49 egonw js> biojava
16:49 jonalv yep that's some logging
16:49 egonw net.bioclipse.biojava.business.BiojavaManager@14f7121
16:50 jonalv nice
16:50 jonalv try calling biojava.loadSequence("") and check the standard out
16:50 jonalv if it works something should get written to standard out
16:50 egonw null
16:50 jonalv yes it's not implemetned yet but the method get's called
16:51 egonw ah, ic
16:51 egonw any CDK functionality here?
16:51 jonalv you could write it if you want to...
16:51 jonalv There is a test for it... :)
16:51 jonalv not yet no...
16:51 egonw how do I add that?
16:51 jonalv I guess we will have cdk.doSomething() later on
16:51 egonw cdk.business?
16:51 jonalv yes
16:52 jonalv but since biojava.business isn't working yet you might want to wait with that...
16:52 egonw I set up a CDKManager?
16:52 egonw ok, will wait
16:52 egonw don't have time now anyway :)
16:52 jonalv :)
16:52 egonw so, and this works for both JS and Ruby and ... ?
16:52 jonalv but you can have a quick look at my code if you are curioues you might have time for that...
16:53 jonalv that's the idea
16:53 egonw R> library("xmcs")
16:53 egonw R died
16:53 egonw :)
16:53 jonalv soon R will not die when you enter something wrong only protest
16:54 egonw hehehe :)
16:54 egonw OK, enough BC2 for now
16:54 jonalv kaskelot, has a lot to say to the R people I think...
16:54 egonw that was much longer than I had really time for right now
16:54 jonalv ah okey
16:55 egonw time to go home...
16:55 * egonw will do some work from home
16:55 egonw need to get dinner first now :)
16:55 egonw bye
16:55 jonalv eating is good... :)
16:55 jonalv bye
16:57 * kaskelot has written a C language wrapper that provides a pseudo-tty for R so it doesn't die, will integrate properly and commit soon
16:57 jonalv woot
16:57 jonalv when is soon? :)
16:57 kaskelot I was going to do it today, but I obviously didn't get round to doing much of anything today
16:58 jonalv well the day isn't over yet... :)
16:58 kaskelot having a friend over for dinner about now, cooking is all I've done since I got out of bed
16:58 jonalv aouch
17:55 * jonalv going home
18:13 shk3 joined #bioclipse
20:58 CIA-20 bioclipse: shk3 * r4618 /trunk/plugins/net.bioclipse.specmol/ (2 files in 2 dirs): specmol creation more user friendly
21:22 DrGTO joined #bioclipse

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