Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-01-13

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
00:26 CIA-54 bioclipse: edrin_t * r8214 /xws/trunk/net.bioclipse.rhi​no/src/net/bioclipse/rhino/ (4 files in 2 dirs): bug fixes...
07:34 Gpox joined #bioclipse
07:39 Gpox joined #bioclipse
08:35 olass joined #bioclipse
09:05 edrin joined #bioclipse
09:05 edrin hi
09:05 zarah hi edrin
09:08 edrin olass: you xws function output did/does not validate to your schema output
09:08 edrin your
09:21 shk3 joined #bioclipse
09:23 charlgren joined #bioclipse
09:29 olass edrin: thanks for that
09:29 olass will check it out
09:29 shk3 joined #bioclipse
09:31 edrin olass: regarding the no creation of binding event you reported:
09:32 olass yes?
09:32 edrin xmpp.getIoFactory(function) does not return null if binding is not found, it throws an exception
09:32 olass ok
09:33 edrin so you should do try {} catch {} in javascript :)
09:33 edrin i think this is possible
09:33 edrin too
09:33 olass well, I think the console should echo exceptions
09:33 jonalv joined #bioclipse
09:34 olass jonalv: does not the console echo exceptions?
09:34 olass IMO it should
09:34 olass well, just the message I guess
09:34 edrin olass: it does not
09:35 edrin hi jonalv, i found the bug/problem
09:35 edrin got my mail?
09:35 jonalv edrin: yea
09:36 edrin can you reproduce the problem for you now, too
09:36 jonalv uhm I haven\t tried. It sounded to me like you had things working and masak looking at it so I thought I could go back to working on structuredb...
09:37 edrin of course
09:37 CIA-54 bioclipse: goglepox * r8215 /bioclipse2/branches/gpox-newMoleculeTable​/plugins/net.bioclipse.cdk.ui/src/net/bioc​lipse/cdk/ui/model/MoleculesFromSDF.java: Limits CN to expand SDFiles larger than 1MB. related to bug #111
09:37 zarah bug #111 | http://tinyurl.com/74ofyl
09:37 edrin but this is not a scripting problem, it is a core problem
09:38 CIA-54 bioclipse: goglepox * r8216 /bioclipse2/branches/gpox-newMoleculeTable​/plugins/net.bioclipse.cdk.ui/src/net/bioc​lipse/cdk/ui/model/MoleculesFromSMI.java: Removed usage of BioclipsStore
09:38 jonalv edrin: I thought you said you had it working now...
09:39 CIA-54 bioclipse: goglepox * r8217 /bioclipse2/branches/gpox-​newMoleculeTable/plugins/ (2 files in 2 dirs): Removed usage of BioclispeStore
09:56 CIA-54 bioclipse: goglepox * r8218 /bioclipse2/trunk/plugins/ (6 files in 2 dirs): Merge branch 'moleculeTable' into merge
10:17 edrin jonalv: yes it is working if the *old* javascript console was opened in the workbench. this is not good because the usage of the platform managers should not depend on the javascriptconsole to be active before using the managers...
10:19 jonalv edrin: What is it that is not working if not the old javascript console is open?
10:32 CIA-54 bioclipse: jonalv * r8219 /bioclipse2/branches/jonalv-RunJSComman​dsAsJobs/plugins/net.bioclipse.scriptin​g/src/net/bioclipse/scripting/business/ (BioclipseUIJob.java JSJobCreatorAdvice.java): fixed (I hope) JSJobCreatorAdvice resolves bug #235
10:32 zarah bug #235 | http://tinyurl.com/8n86z9
10:32 gilleain joined #bioclipse
10:35 edrin jonalv: that inititalisation of the managers
10:36 edrin jonalv: for example on my eclipse the new js console does not work if the old js console was not actviated once before
10:37 jonalv aha, well masak is working on the new console in a branch and I am sure it will work when he is done and have merged that branch
10:37 jonalv edrin: Can't you live with opening both for now?
10:37 edrin yes i can
10:38 jonalv good
10:39 edrin jonalv: just that i think that there is something really not good in the workbench initialization if the instantiation of the managers depend on the scripting plugin and therefore the bioclipse platform depends on the scripting environment
10:40 jonalv edrin: oh if that is so then that is bad. I just thought that the new js/console depended on the old...
10:41 edrin no, the initialization of managers depends
10:41 edrin at least i think so ;)
10:41 jonalv I don't think so
10:42 jonalv I can use the structuredb manager from the gui without openining the javascript editor
10:42 jonalv or console
10:43 edrin jonalv: could be, but i guess that the gui is using it's own classes...
10:43 jonalv edrin: wht do you mean?
10:43 edrin i mean, the GUI belongs to the plugin itself
10:43 edrin or am i wrong?
10:43 jonalv well yes but the structuredb manager uses the cdk manager as well
10:44 edrin i think the GUI code access the manager not through the eclipse API by asking there for it, it would rather use it directly because it is in the plugin
10:44 jonalv I am afraid I don't understand the general problem since it is clearly working
10:44 edrin how do you get the cdk manager?
10:44 jonalv edrin: yes
10:44 jonalv through the activator I think
10:45 jonalv that is the way we are doing things
10:46 edrin jonalv: was the javascript consoles never opened since restart of bioclipse?
10:46 jonalv but edrin you can't ask Eclipse for extension points from plugins that have not been started. There is nothing strange with that...
10:47 jonalv edrin: I closed the javascript console and restarted Bioclipse and the structuredb gui still works
10:47 edrin jonalv: you are right, but the bioclipse core should start them all on startup. at least their managers
10:47 jonalv edrin: no
10:47 edrin otherwise the manager concept will not work
10:47 jonalv then startup would take ages
10:47 jonalv we want lazy starting of plugins
10:47 jonalv that is at least what I thought
10:48 edrin do you?
10:48 edrin hm
10:48 jonalv if you don\t have the jsvascript console visible then there is no reason to start up all plugins
10:48 jonalv only when the javascript console is visible do we have to fire up all plugins. That is a bit sad but it must be like that
10:49 jonalv off course we could start _all_ plugins at startup but I am not sure that is a good idea...
10:50 edrin jonalv: well, what is the concept of the managers then if not *all* plugins are supposed to use them?
10:50 edrin you cant bundle all tasks to the js environment plugin
10:50 jonalv edrin: you lost me...
10:50 edrin imagine someone wants to use managers in another project. he cant because the are not initialized
10:51 gilleain can't they be initialized on demand?
10:51 jonalv if you need a manager you make sure that the plugin containing that manager is started...
10:51 edrin jonalv: ok
10:51 jonalv that happens when you ask for that manager
10:51 edrin then i just have to add initialiizitiohn code
10:51 jonalv for the moment you get a manager thougth the activator of that plguin
10:52 jonalv when that code in that Activator is run that plugin is started
10:52 edrin jonalv: maybe i did it the wrong way in my plugin then
10:52 jonalv it\s not very beutiful but it seem to be working...
10:52 edrin but obviously the new js console is doing it the wrong way then, too?
10:53 jonalv edrin: so it sems yea, but I think the new js-console is sort of still dependent on it\s parent - the old one...
10:53 edrin jonalv: i thougght i am using the eclipse API the correct way (and that the eclipse API is supposed to get the managers, if not iniialized it should initialize them...
10:54 edrin but this seems to not work
10:54 jonalv intresting
10:54 edrin gilleain: that's what i thought should automatically happen
10:55 jonalv what part of the Eclipse API are you refering too?
10:56 jonalv edrin: I think that the Eclipse API you are reffering to only contains extension points from already started plugins but I am not familiar with that part of the Eclipse API...
10:57 jonalv but perhaps we have missed something when implementing that...
10:57 edrin jonalv: this part in Activator.java of RHINO
10:57 edrin try {
10:57 edrin 120 service = element.createExecutableExtension("service");
10:57 edrin 121 }
10:57 edrin http://bioclipse.svn.sourceforge.net/v​iewvc/bioclipse/xws/trunk/net.bioclips​e.rhino/src/net/bioclipse/rhino/Activa​tor.java?revision=8214&view=markup
10:57 zarah edrin's link is also http://tinyurl.com/9qedy9
10:57 jonalv since we honestly haven\t tried what it is you are doing...
10:57 edrin jonalv: yes, you doo
10:58 edrin jonalv: the js console is doing it the same way, i looked it up
10:58 jonalv only in the same plugin I think
10:58 jonalv oh okey
10:58 edrin in anycase
10:58 jonalv then I don\t know
10:58 edrin this is standard eclipse API, i would expect it to work, but maybe i am wrong
10:58 edrin :)
10:59 edrin in any case even if i am doing it the wrong eclipse-way right now
10:59 edrin it should work in bioclipse at least in the correct eclipse-way
10:59 jonalv hm I want to reproduce your problem. How do I do that again? :)
11:00 edrin jonalv: opne bioclipse, close the old js console.
11:00 jonalv check
11:00 edrin and the new one
11:01 edrin then close bioclipse again, keep workspace settings, thus the old js console is not started up
11:01 edrin start bioclipse, DO NOT start the old bc console
11:01 jonalv and then start the new?
11:02 edrin yes, this fails for me.
11:02 edrin on the other hand you can also try to run a scipt from the rhino editor (newly checked out, i fixed som things yesterday
11:03 jonalv I get the cdk manager in the new js-console even though the old one isn\t started...
11:03 jonalv which I think I should...
11:03 edrin for me the new console does not even start, i never saw the new console
11:03 jonalv intresting
11:03 jonalv I am on mac now...
11:04 edrin can you try on windows?
11:04 edrin also try the newly checked out net.bioclipse.rhino plugin ?
11:04 jonalv I will update and try on windows after lunch
11:04 edrin ok
11:05 edrin jonalv: btw. it a bioclipse.core exception i get, see my old mails
11:05 jonalv edrin: you get the exception that is thrown when it can\t get he manager from the container, right?
11:08 olass joined #bioclipse
11:14 * jonalv heads for lunch
11:27 edrin jonalv: yes
11:27 edrin hi olass
11:27 olass hi edrin
11:28 olass I hear you have doubts about the Bioclipse2 core design
11:29 olass we should schedule a skype conference and try to sort things out with the scripting engine/JS editor etc
11:37 olass Gpox, jonalv: Have you tried soylatte with OS X? http://landonf.bikemonkey.org/static/soylatte/
11:37 zarah olass's link is also http://tinyurl.com/299vnb
11:37 egonw joined #bioclipse
11:40 gilleain olass: it uses the X-server, so no, not really :)
11:41 gilleain (I can never be bothered with xwindows based stuff on macs)
12:07 edrin olass: it's not really a design issue
12:07 edrin i think the problem i currently have is a bug
12:10 edrin olass: may I ask, did you test the js currently developed editor editor?
12:11 edrin olass?
12:22 olass edrin: hi
12:22 edrin hi
12:22 * olass is back from lunch now
12:22 zarah hi edrin
12:22 olass edrin: please explain
12:22 olass test our js editor?
12:23 olass I see you imported a new. Why?
12:23 * jonalv is back
12:23 edrin the (old js console has some issues and was not working
12:23 olass yes, I kno
12:23 olass masak is working on it
12:23 olass (and jonalv I guess)
12:23 edrin olass: the current js editor in svn is a buggy and discontinued sourceforge editor
12:24 olass I know
12:24 olass it's the best we have
12:24 edrin did you try mine?
12:24 olass The big JS editor of WTP comes with too many deps
12:24 olass no
12:24 olass We'll gladly switch editor if yours is better
12:24 edrin dunno if it is so much better
12:25 olass did you take the editor from bc1?
12:25 edrin it's quite new, not tested much
12:25 edrin no
12:25 edrin it's new
12:25 olass ok
12:25 olass sounds good
12:25 edrin wrote it currently
12:25 edrin it's currently in svn:/xws/net.bioclipse.rhino
12:25 jonalv edrin: what are the main differences compared to that sourceforge projects one?
12:26 edrin that it's not buggy :)
12:26 edrin i hope at least
12:26 edrin and it is not disconinued
12:26 jonalv that sounds like good points
12:26 jonalv :)
12:27 jonalv How are you doing the syntax highlightning?
12:27 edrin olass: the main reason for the new rhino editor in xws is that the scripting core environment in bc2 was not working for me...
12:28 olass edrin: the editor we can switch but the scripting env we must fix
12:28 edrin it was buggy, crashing my apli all the time
12:28 olass edrin: we cannot replace it at this time
12:28 olass we need to fix it
12:28 jonalv there seem to be some Windows issues here...
12:28 olass can you assist with this maybe?
12:28 jonalv I am also feeling crashes right now in windows...
12:29 olass jonalv: good that you can reproduce
12:29 edrin back
12:30 edrin olass: sure, i dont want to overtake the scripting environment
12:30 olass ;-)
12:30 edrin i just needed something to work with
12:31 olass no problem, I understand your decision
12:31 olass and even better if you improve the JS editor
12:31 olass a very welcome contribution!
12:31 edrin beside the getting js to work on windows, too, there are some other things:
12:32 edrin olas, the js console does not show exceptions
12:32 edrin errors are not shown with line numbers :(
12:32 olass please file a bug for masak
12:32 olass he has a new console in a branch
12:33 jonalv edrin: line numbers in the js/script?
12:33 olass it's well on the way
12:33 edrin the new console does not show up for me but crashs, too
12:33 edrin jonalv: yes
12:33 edrin jonalv: it does not say error in line x
12:33 edrin just error
12:33 jonalv edrin: yea true...
12:34 jonalv edrin: good point :)
12:35 edrin i will switch the pipe i pass the script to in the js editor plugin from the current standalon to the new js ui thing as soon as it is stable
12:35 jonalv edrin: it is strange that you can't get the new javascript console to work. I just got it to work in Windows
12:35 edrin yes
12:35 jonalv I had to restart and reset target platform because something was crazy (that\s why it kept crashing for me before...)
12:35 edrin jonalv: can you reproduce the manager init problem i have?
12:36 jonalv edrin: not with cdk manager at least. Perhaps I need to test with another manager?
12:36 edrin jonalv: so you can access the cdk manager from my rhino plugin?
12:37 jonalv from the new javascript console
12:37 edrin olass: did you try the editor?
12:37 olass no
12:37 edrin jonalv: sure you can access it from the new console...
12:38 edrin jonalv: you must not have ever opened the js consoles (new and old) before you use the rhino editor plugin...
12:41 jonalv edrin: ah I thought you said that the new javascript consoel couldn't handle managers until the old console haad started. Then I missunderstood you...
12:42 edrin jonalv: the new one never started up for me :/
12:43 jonalv edrin: which makes me think that you and I have some differences in our set-ups...
12:43 edrin could be
12:44 jonalv edrin: I got this script working:
12:44 jonalv rhino.showMessage(cdk.fromS​MILES("CCCC").getSMILES());
12:44 jonalv using your editor
12:44 edrin this works?
12:44 jonalv and not starting any of the consoles before
12:44 jonalv edrin: for me it does
12:45 jonalv in windows
12:45 jonalv edrin: now if we only could get it to work for you...
12:46 edrin jonalv: was the js consoles closed when you started up the bioclipse and were they never opened!?
12:46 jonalv edrin: yes that is correct
12:46 edrin jonalv: try this script: http://paste2.org/p/129201
12:47 jonalv edrin: what plugins do I need for that one_
12:47 edrin for me the problem is still there
12:47 edrin the following:
12:47 edrin net.bioclipse.core
12:48 edrin net.bioclipse.logger
12:48 edrin net.bioclipse.rhino
12:48 jonalv se.uu.farmbio.hivpred.client is not compiling for me. I am running Eclipse 3.4
12:48 edrin net.bioclipse.scripting
12:48 edrin net.bioclipse.scripting.ui
12:48 edrin net.bioclipse.ui
12:48 edrin net.bioclipse.xws4j
12:49 edrin jonalv: all you need is xws4j, you d not need the other client
12:49 jonalv k
12:49 edrin (for this script)
12:49 edrin jonalv: remove all plugins that are not essential for this test
12:49 edrin (like cdk
12:49 edrin )
12:50 jonalv gruff, (okey, doing that)
12:50 olass jonalv: hivpred not compiling is your fault (you haven't taught me git yet (so I can't work in a branch))
12:51 jonalv olass: lol
12:54 jonalv edrin: org.mozilla.javascript.EcmaError: ReferenceError: "xmpp" is not defined. (line: #40)
12:54 edrin jonalv: oh, the first time, the new js console showed up
12:54 jonalv edrin: is that what I should get_
12:54 edrin jonalv: ok: in the debug window
12:54 edrin yes
12:55 edrin in eclipse do you see the errors?
12:55 jonalv edrin: no stack trace in eclispe no
12:55 edrin bioclipse.core could not setInitializationData() ...
12:56 jonalv edrin: nope I don't get that
12:57 edrin the new js console does not catch excpetions, too
12:57 edrin it seems it also has the Systems.endline not being used problem
12:58 edrin formating problesm
12:58 jonalv edrin: masak is still building on a mac so I guess it does yea...
12:58 edrin :/
12:58 jonalv edrin: He is gonna be using Windows through parallells on his next computer though... :)
12:59 edrin jonalv: this will make it impossible to fix this bugs afterwards, shk3 and me failed to fix the bug in the olf console...
13:00 jonalv edrin: that is why I am insisting he tries the new console in windows while he developes it
13:00 edrin yes, :)
13:00 jonalv edrin: however I think it should work. It\s a second attempt and now he has learnt about the pitfalls...
13:01 jonalv however I don't understand what's going on with your script...
13:01 jonalv why don't I get an error in Eclipse?
13:02 edrin Failed to get a service: Plug-in "net.bioclipse.core" was unable to execute setInititializationData on an instance of of "net.bioclipse.core.busines​s.MoleculeManagerFactory".
13:04 jonalv hm might it be that I am not runnign that plugin?
13:04 jonalv I thought I where...
13:04 jonalv mom
13:04 zarah dad!
13:05 edrin jonalv: Failed to get a service: Plug-in "net.bioclipse.core" was unable to execute setInititializationData on an instance of of "net.bioclipse.scripting.ui.​business.UIManagerFactory". when trying to start the new bc console
13:05 jonalv edrin: org.mozilla.javascript.WrappedException: Wrapped net.bioclipse.xws4j.exceptions.Xws4jException: Could not create default client: the plug-in has set invalide account data in preferences. (line: #21) when running your script now
13:06 edrin jonalv: this means it is working
13:06 jonalv (I had missed the xws4j plugin) (don't ask me why)
13:06 jonalv yey :)
13:07 edrin i still get Failed to get a service: Plug-in "net.bioclipse.core" was unable to execute setInititializationData on an instance of of *something* and this ERROR does not depend on rhino plugin or anything from me
13:07 edrin it occurs when i open the new bc console
13:07 edrin btw. the new bc console is missing a scroll bar for horizontal corlling
13:07 edrin the old one did as well
13:08 jonalv edrin: could I ask you to reset target platform and rebuild?
13:08 edrin however now the new bc console does not show up anymore
13:08 edrin jonalv: doing this all the time
13:08 jonalv I don't understand this
13:08 jonalv why does it work for me and not for you?
13:08 jonalv so frustrating
13:08 edrin jonalv: maybe it is the eclipse version?
13:09 edrin do you have newest?
13:09 jonalv but I am running 3.4.1 on OSX and 3.4 in Windows
13:09 jonalv and it works for me on both systems...
13:09 edrin upgrade windows?
13:10 edrin did you really completely close js console? or is there still the tiny hidden js console button on bottom left of your bc ?
13:10 jonalv I guess I should do that to make sure that is not what is going on but it is messy...
13:11 jonalv edrin: yea I clicked the x and closed it
13:11 jonalv edrin: are you using subclipse?
13:11 edrin yes
13:11 jonalv I am thinking that perhaps you should try a new check out...
13:12 edrin yes maybe
13:12 edrin i can try this tonight
13:12 jonalv I would like that
13:12 edrin jonalv: so olas hivpred script is working in the *new* rhino_plugin
13:13 edrin ?
13:13 olass edrin: no
13:13 olass it is not currently working :-(
13:13 jonalv uhm what\s the "new rhino_plugin"? :)
13:13 olass but might be my fault
13:13 edrin olass: ?
13:13 edrin why not?
13:13 edrin yesterday night it was working for me
13:14 jonalv if org.mozilla.javascript.WrappedException: Wrapped net.bioclipse.xws4j.exceptions.Xws4jException: Could not create default client: the plug-in has set invalide account data in preferences. (line: #21) means it is working then it is working for me...
13:14 edrin i could run it from my editor
13:14 olass you said hivpred does not validate ouput?
13:14 edrin olass: yes, but of course the generalized getOutpuObject always would work
13:14 edrin jonalv: yes, but that's not a bug, it's a feature
13:15 edrin olass: the iofactory.getHIVPredOutputDocument fails because validation fails
13:15 jonalv edrin: I just have one question for you: "Can we remove the 'Run script in Main thread' alternative?"
13:15 jonalv I don't like that one. I want JS-scripts to run in seperate threads...
13:16 edrin jonalv: the plug-in has set invalide account data in preferences. <- go to bioclipse preferences/ XMPP / enter your xmpp account data there ( you must have an account at ws1.bmc.uu.se
13:17 jonalv aha, makes sence actually. I won't do that now though if that is okey with you?
13:17 jonalv |sense
13:18 edrin jonalv: in the past i had some scripts that were editing the eclipse ide, thus they needed access to the GUI thread, was easier this way... but sure one could run script in a different thread by default. BUT: jonalv: are you 100% sure that all manager calls are thread safe ???
13:19 edrin jonalv: sure :) but!-> you cant try the XMPP Service Discovery then
13:19 edrin and you cant predict hiv susceptibilities
13:19 jonalv edrin: I am 100% sure that if they are not than that is not my problem but that manager's implementors problem.
13:20 edrin jonalv: was there somewhere a rule that managers must be thread save!?
13:20 edrin maybe i missed this
13:20 jonalv edrin: I will try it some other day. I have a branch to attend to :)
13:20 olass edrin: I think this is what jonalv's branch is about, right?
13:20 jonalv edrin: if there where no such rule let's make one now!
13:20 olass what are the implications?
13:21 edrin jonalv: are you sure you want this?
13:21 olass what are the downsides?
13:21 edrin olass, jonalv this is a very important question i fear
13:21 jonalv edrin: how else would we do this?
13:21 olass edrin: please explain
13:21 edrin jonalv: do manager stuff in the gui thread
13:21 jonalv the gui shouldn\t be totally locked down when you are running a javascript...
13:22 olass well, long running calls should run as Eclipse Jobs
13:22 edrin olass: yes
13:22 olass jonalv: please explain the idea about your branch and Jobs
13:22 olass to edrin
13:22 olass maybe that clears things out?
13:22 edrin the problem is, if you want to have rhino instances running in a different thread all managers have to be thread save
13:22 jonalv the js-editor creates an Eclipse job when it runs the javascript
13:22 edrin i thought so
13:23 olass edrin: what does it mean to be thread safe?
13:23 edrin net.bc.rhino did/does this, too
13:23 jonalv edrin: all js-scripts are run by the javascript worker thread
13:24 edrin olass: for example if your manager alters the GUI, for example adds a button somewhere or something like this, you cant simply do this from another thread
13:24 jonalv the job actually just waits for that that thread to finnish running the js-script
13:24 jonalv edrin: that is what that swt asynchexec thing is for
13:24 olass edrin: when we need GUI thread, we just do getDIsplay().getDefault().syncExec(...)
13:25 edrin olass: this is really risky, because if plugin developers do not know about this threading risks we will have a lot buggy software
13:25 olass in what respect?
13:25 edrin i know
13:25 edrin olass: because the managers would be accessed from different threads
13:26 olass that is possible
13:26 jonalv edrin: we can't avoid that...
13:26 edrin thus all managers must be thread safe. but programming a thread safe manager is not as easy as someone might thinl
13:27 edrin and programmers must be really skilled to do this
13:27 edrin all used object must be synchronized
13:27 olass edrin: we could lock managers for long running jobs, Eclipse Jobs has locking mechanisms
13:27 edrin for example all List and Map implementations
13:28 olass I'll let jonalv and masak discuss this with you. I am no threading expert, and jonalv is in charge of manager design
13:29 edrin ok
13:29 olass edrin: do you have a suggestion?
13:29 olass all in GUI thread does not sound good to me...
13:29 edrin just realized :(
13:29 edrin olass: I fully agree
13:30 edrin but in conclusion this means all managers must be 100% thread safe !
13:30 gilleain uh-oh
13:32 edrin hm?
13:32 CIA-54 bioclipse: ospjuth * r8220 /bioclipse2/trunk/plugins/se.uu.farmbio.hiv​pred.client/src/net/bioclipse/xmpp/hivpred/ (3 files in 3 dirs): Fixed resultview appearing on finished calculation.
13:33 gilleain just "uh-oh". thread safety is a pain.
13:33 jonalv I thought I already had told you people that the managers need to be thread safe...
13:34 jonalv the thinbg is that they shouldbn't contain too much status anywya so there shouldn't really be too hard or am I thinking wrong now?
13:34 jonalv |state
13:36 edrin jonalv: well as soon as a manager function does several things: eclipse API might be involved...
13:37 edrin and this is not always thread safe, is it?
13:37 edrin i am not even sure if net.bioclipse.xws4j is fully thread save
13:40 jonalv edrin: I guess everyone could just synchonize on the manager call but there might be better slutions out there...
13:40 jonalv it should be up the the implementor of the manager...
13:40 jonalv brb
13:41 edrin synchronizing manager calls does not help much
13:41 edrin synchronized does not mean it is subsequently doing all call behind it synchronized
13:41 edrin on this call...
13:43 CIA-54 bioclipse: ospjuth * r8221 /bioclipse2/trunk/plugins/se.uu.farmbi​o.hivpred.client/META-INF/MANIFEST.MF: Now only requires Eclipse 3.4.0.
13:45 olass edrin: I can't run my hivpred script anymore
13:45 olass Caused by: java.lang.ClassCastException: org.apache.xmlbeans.impl.va​lues.XmlComplexContentImpl
13:46 olass java.lang.NoSuchMethodException: org.hivdrc.hivpred.impl.HIVPredInputTypeIm​pl.<init>(org.apache.xmlbeans.SchemaType, boolean)
13:46 olass edrin: what could be wrong?
13:47 olass script: http://paste2.org/p/129210
13:50 olass hmm
13:50 edrin olass: in what line is the error?
13:50 olass yes, service is down
13:50 olass :-(
13:51 olass sysadmin is working on the s2s thingy
13:51 olass (I hope)
13:52 edrin ok :)
13:52 CIA-54 bioclipse: shk3 * r8222 /bioclipse2/trunk/plugins/net.bioclipse.bibtex/ (3 files in 2 dirs): removed code duplication
13:52 edrin yes, i cant see them in psi
13:52 edrin olass: how do you like the editor!?
13:52 edrin looking
13:53 olass will go to see the sysadmin (again) :-(
13:53 olass edrin: you have a screenshot?
13:53 olass brb
13:53 edrin no
13:54 edrin but it's in xws/net.bioclipse.rhino
13:54 edrin but maybe i should rename it to net.bioclipse.jseditor
13:54 edrin ?
13:59 CIA-54 bioclipse: shk3 * r8223 /bioclipse2/trunk/plugins/net.bioclipse.specmol/ (2 files in 2 dirs): removed code duplication
14:00 CIA-54 bioclipse: goglepox * r8224 /bioclipse2/branches/jonalv-​RunJSCommandsAsJobs/plugins/ (6 files in 2 dirs): Merge branch 'moleculeTable' into merge
14:04 CIA-54 bioclipse: shk3 * r8225 /bioclipse2/trunk/plugins/​net.bioclipse.nmrshiftdb/ (2 files in 2 dirs): problem with prediction resolved
14:05 CIA-54 bioclipse: goglepox * r8226 /bioclipse2/branches/jonalv-RunJSCommandsAsJobs/ (156 files in 59 dirs):
14:05 CIA-54 bioclipse: Merge branch 'moleculeTable' into merge
14:05 CIA-54 bioclipse: Atempted cherry picking of jonal-RunManagersWithJobs
14:21 CIA-54 bioclipse: shk3 * r8227 /bioclipse2/trunk/plugins/net.bioclip​se.nmrshiftdb/src/net/bioclipse/nmrsh​iftdb/wizards/ServerWizardPage.java: ok, it makes a difference if you used keyPressed or keyReleased...
14:27 CIA-54 bioclipse: jonalv * r8228 /bioclipse2/branches/jonalv-RunJSCommandsAsJobs​/plugins/net.bioclipse.scripting/src/net/biocli​pse/scripting/business/JSJobCreatorAdvice.java: Added code to run BioclipseUIJob from JSJobCreatorAdvice
14:29 CIA-54 bioclipse: goglepox * r8229 /bioclipse2/branches/jonalv-RunJSComma​ndsAsJobs/plugins/net.bioclipse.cdk.bu​siness/src/net/bioclipse/cdk/business/ (CDKManager.java ICDKManager.java): Added createSDFFileIndex(IFile, BioclipseUIJob)
14:29 CIA-54 bioclipse: goglepox * r8230 /bioclipse2/branches/jonalv-RunJSCommandsAsJ​obs/plugins/net.bioclipse.cdk.ui.sdfeditor/ (2 files in 2 dirs): Uses new UIjob runner for managers
14:46 olass @tell edrin: please mark fixed bugs as "FIXED" in pelezilla so that I can close them.
14:46 zarah Consider it noted.
14:47 olass edrin: will test your JSEditor now
14:50 olass edrin: looks ok
14:50 olass what are the benefits to the existing?
14:51 olass I see no outline, no content assist either
14:51 olass looks like the one in bc1 :-)
15:03 edrin olass: yes, it has no special features yet. but it has no bugs
15:03 zarah edrin: You have new messages. Write '/msg zarah @messages' to read them.
15:03 edrin meaning the syntax highlighting works
15:03 olass ok
15:03 edrin and this was not always the case in the sf one
15:03 olass that is an improvement
15:04 edrin olass: do the scripts you wrote run in it? i mean does it access the managers?
15:04 edrin @msg
15:04 zarah edrin: 21 h 21 m 57 s ago, olass said I still see xws4j-09.01.02.jar in plugin net.bioclipse.xws4j. Did you not update that?
15:04 zarah edrin: 17 m 40 s ago, olass said please mark fixed bugs as "FIXED" in pelezilla so that I can close them.
15:04 edrin olass: xws.jar is updated now
15:05 edrin olass: how can i find "my bugs" in pelezilla
15:09 edrin olass: is doing egonw better now?
15:12 olass @pz
15:12 zarah olass: Pelezilla is at http://pele.farmbio.uu.se/​cgi-bin/bugzilla/index.cgi
15:19 stain joined #bioclipse
15:24 CIA-54 bioclipse: goglepox * r8231 /bioclipse2/branches/jonalv-RunJSCommandsAsJ​obs/plugins/net.bioclipse.cdk.business/src/n​et/bioclipse/cdk/business/CDKManager.java: Added monitor canceled check in createSDFFileIndex
15:24 CIA-54 bioclipse: goglepox * r8232 /bioclipse2/branches/jonalv-RunJSComma​ndsAsJobs/plugins/net.bioclipse.cdk.bu​siness/src/net/bioclipse/cdk/business/ (CDKManager.java ICDKManager.java): Added uiJob to numbersOfEntriesInSDF
16:23 shk3 hi olass
16:24 Gpox joined #bioclipse
16:29 maclean joined #bioclipse
16:42 shk3 olass?
16:42 olass shk3: hi
16:44 shk3 what are release plans for bioclipse?
16:44 olass @gg bioclipse2 roadmap
16:44 zarah olass: http://irclog.perlgeek.de/text.pl%3Fch​annel%3Dbioclipse%3Bdate%3D2007-11-19
16:44 olass hmm
16:44 olass no
16:45 olass http://wiki.bioclipse.net/index.p​hp?title=Bioclipse2_release_plan
16:45 zarah olass's link is also http://tinyurl.com/5guree
16:45 shk3 jan 23rd
16:45 shk3 ok
16:46 shk3 we need to work on documentation
16:47 olass yes, that is important
16:47 shk3 you once said plugins can customize the wellcome screen?
16:47 shk3 I think that would be great
16:48 shk3 every plugins should give short descriptions of tasks which can be done with the plugin
16:48 olass yes
16:48 shk3 these should be shown on welcome screen
16:48 shk3 and link to cheatsheets
16:48 shk3 or so
16:48 olass shk3: could you please investigate this?
16:48 olass I have no time
16:48 shk3 plus we need help texts, of course
16:49 olass I think the texts are the most important
16:49 shk3 they need to be there
16:49 shk3 but we also need to answer the "what can I do after I downloaded this product"-question
16:50 shk3 will the download have any features/plugins included?
16:50 olass not decided yet
16:50 olass maybe
16:51 shk3 if not, the wellcome screen needs to say "install features first" prominently
16:51 olass agreed
16:52 shk3 is there a reason why help->wellcome is not in bioclipse
16:52 shk3 it is in eclipse?
16:52 olass please add it
16:53 shk3 no idea about it
16:53 shk3 you?
16:53 olass no
16:54 shk3 so I will research it
16:54 olass you can always read eclipse source
17:14 CIA-54 bioclipse: ospjuth * r8233 /bioclipse2/trunk/plugins/net.bioclipse.services/ (6 files in 2 dirs): Added a CNF for databases. Solves #217.
18:00 CIA-54 bioclipse: jonalv * r8234 /bioclipse2/branches/jonalv-​RunJSCommandsAsJobs/plugins/ (9 files in 5 dirs): getting BioclipseUIJob to work. Moleculestable example is now working. (Hope I haven't broken the other cases too much...)
18:01 CIA-54 bioclipse: jonalv * r8235 /bioclipse2/branches/jonalv-RunJSCommandsA​sJobs/plugins/net.bioclipse.structuredb/sr​c/net/bioclipse/structuredb/Database.java: removed job creation from gui code. (didn't know it was there...)
18:02 CIA-54 bioclipse: jonalv * r8236 /bioclipse2/branches/jonalv-RunJSCommands​AsJobs/plugins/net.bioclipse.structuredb/​src/net/bioclipse/structuredb/business/ (IStructuredbManager.java StructuredbManager.java): removed unneeded method
18:03 CIA-54 bioclipse: jonalv * r8237 /bioclipse2/branches/jonalv-RunJSComman​dsAsJobs/plugins/net.bioclipse.ui/src/n​et/bioclipse/ui/jobs/BioclipseJob.java: indentation
18:56 edrin left #bioclipse
21:01 edrin1 joined #bioclipse
22:58 CIA-61 joined #bioclipse

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary