Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-12-08

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All times shown according to UTC.

Time Nick Message
05:45 egonw joined #bioclipse
08:43 jonalv joined #bioclipse
08:49 edrin joined #bioclipse
08:49 jonalv hi
08:49 zarah hi jonalv
08:55 egonw hi jonalv, edrin
08:55 egonw bbl
08:55 edrin hi
08:55 zarah hi edrin
08:55 * egonw is working on a InChI plugin
08:57 jonalv hm I recognize that. What was it it was again? :)
09:29 charlgren joined #bioclipse
09:32 gilleain joined #bioclipse
09:46 edrin left #bioclipse
09:49 jonalv egonw: ping
09:49 egonw pong
09:49 jonalv egonw: Is it ok with you if I increase memory for Bioclipse 2?
09:50 egonw that's something you should ask Ola
09:50 egonw to me it's fine
09:50 jonalv I wanna use: -Xmx512M -XX:MaxPermSize=128m
09:50 egonw make it so
09:50 jonalv oki I will
09:50 egonw and file a bug report for Ola to approve
09:50 jonalv hehe
09:51 jonalv Birt needs -XX:MaxPermSize=128m
09:51 egonw make sure to mention that in bug report that Birt needs it
09:54 CIA-32 bioclipse: jonalv * r7985 /bioclipse2/trunk/plugins/net.b​ioclipse.ui/bioclipse.product: increased memory usage of Bioclipse 2. (Birt needs -XX:MaxPermSize=128m and -Xmx512M seems like a good idea when running many plugins and working with many big files)
09:59 egonw jonalv: ping
09:59 jonalv egonw: pong
09:59 egonw when managers throw exceptions
09:59 egonw they have to be BioclipseException, right?
09:59 jonalv no
09:59 jonalv managers may throw whatever exception they want tp throw
10:00 jonalv BioclipseException is pure evilness and probably something that we should work towards getting rid of...
10:00 egonw ah, ok
10:00 egonw good
10:00 jonalv :)
10:08 gilleain ack! I don't think that my java recognises -XX options...
10:10 gilleain .java -XX:MaxPermSize
10:10 gilleain Unrecognized VM option 'MaxPermSize'
10:10 gilleain Could not create the Java virtual machine.
10:11 gilleain oh, wait. it's an eclipse thing? n/m
10:11 jonalv gilleain: I don't think it's an eclipse thing...
10:11 gilleain oh.
10:12 jonalv but write some number there too...
10:13 gilleain doesn't matter : it's a java 6 thing
10:14 egonw ah, so we can't use it
10:14 gilleain (so it won't work on macs, which still have java5)
10:14 jonalv gilleain: whata re your sources saying it's a java 6 thing?
10:15 jonalv gilleain: I am on a mac running java 5...
10:15 gilleain @google java hotspot vm options
10:15 zarah gilleain: http://java.sun.com/javase/tech​nologies/hotspot/vmoptions.jsp
10:15 jonalv or rather 1.5
10:15 gilleain weird. so am i.
10:17 jonalv it's listed there
10:17 jonalv it doesn't say anything about java 6...
10:17 jonalv gilleain: are you having trouble starting Bioclipse after I made the change?
10:18 gilleain no, so I guess it's okay.
10:19 gilleain sorry, I thought that it was java6 specific.
10:19 gilleain my mistake
10:19 jonalv gilleain: oki
10:36 egonw lovely :)
10:39 egonw http://gist.github.com/33421
10:39 egonw time for some coffee
10:57 CIA-32 bioclipse: egonw * r7986 /bioclipse2/trunk/plugins/net.bioclipse​.core.tests/src/net/bioclipse/core/test​s/coverage/AbstractCoverageTest.java: Added an extra assertion, fixing a NPE when the manager does not have any test class annotation
11:31 egonw zarah: are you keeping track of RSS feed? or is that a different bot?
11:31 zarah egonw: eh... wha'?
11:31 egonw zarah: you're not tracking this feed then: http://wiki.bioclipse.net/index.php?tit​le=Special:Recentchanges&feed=atom ?
11:31 zarah egonw's link is also http://tinyurl.com/5akwkx
11:31 zarah egonw: that was not so easy for a little bot to understand
11:31 egonw @tell masak where's that RSS tracking bot?
11:31 zarah Consider it noted.
11:32 * egonw is issuing 'git merge addInChIManager'
11:32 egonw done
11:32 gilleain \o/
11:32 egonw mmm... that was not much fun :(
11:32 gilleain why?
11:33 egonw too quick
11:33 egonw no time to enjoy the merge :(
11:33 gilleain lolwhat
11:33 egonw wel...
11:33 egonw fortunately, there is still the 'git svn dcommit'
11:33 egonw which takes ages
11:33 gilleain oh good.
11:33 egonw here comes...
11:33 * egonw is off for lunch
11:33 egonw bbl
11:33 gilleain cya
11:34 CIA-32 bioclipse: egonw * r7987 /bioclipse2/trunk/plugins/ne​t.bioclipse.inchi.business/ (18 files in 8 dirs): Copied in template code for inchi.business
11:34 CIA-32 bioclipse: egonw * r7988 /bioclipse2/trunk/plugins/net.bi​oclipse.inchi.business/.project: Tuned for import into my eclipse workspace
11:35 CIA-32 bioclipse: egonw * r7989 /bioclipse2/trunk/plugins/net.bioclip​se.inchi.business/src/net/bioclipse/ (10 files in 4 dirs): Redid code for inchi manager
11:35 CIA-32 bioclipse: egonw * r7990 /bioclipse2/trunk/plugins/ne​t.bioclipse.inchi.business/ (META-INF/MANIFEST.MF META-INF/spring/context.xml plugin.xml): Updated config stuff
11:36 CIA-32 bioclipse: egonw * r7991 /bioclipse2/trunk/plugins/ne​t.bioclipse.inchi.business/ (3 files in 2 dirs): Added generate() method for generating InChIs and a stub for InChIKeys, but need to patch our version of the CDK first
11:38 CIA-32 bioclipse: egonw * r7992 /bioclipse2/trunk/cdk-externals/net.sf.jniinchi/ (5 files in 3 dirs): Upgraded JNI-InChI to 0.5
11:40 CIA-32 bioclipse: egonw * r7993 /bioclipse2/trunk/cdk-externals/trunk/​org.openscience.cdk.inchi/src/org/open​science/cdk/inchi/InChIGenerator.java: Manually applied CDK patch #2405759
11:41 CIA-32 bioclipse: egonw * r7994 /bioclipse2/trunk/plugins/net.bioclipse.inch​i.business/src/net/bioclipse/inchi/business/ (IInChIManager.java InChIManager.java): Enabled InChIKey generation
11:41 CIA-32 bioclipse: egonw * r7995 /bioclipse2/trunk/cdk-externals/net​.sf.jniinchi/META-INF/MANIFEST.MF: Fixed version number for current jar
11:42 CIA-32 bioclipse: egonw * r7996 /bioclipse2/trunk/features/net.bioclips​e.chemoinformatics_feature/feature.xml: Added inchi to cheminformatics perspective
11:44 CIA-32 bioclipse: egonw * r7997 /bioclipse2/trunk/plugins/net.​bioclipse.inchi.business.test/ (15 files in 8 dirs): Copied cdk.debug.test as template for inchi.business.test
11:45 CIA-32 bioclipse: egonw * r7998 /bioclipse2/trunk/plugins/ (11 files in 6 dirs): Refitted to test InChIManager
11:46 CIA-32 bioclipse: egonw * r7999 /bioclipse2/trunk/plugins/ (3 files in 3 dirs): Added the required unit tests
11:47 CIA-32 bioclipse: egonw * r8000 /bioclipse2/trunk/plugins/net.bioclipse.tests/ (3 files in 2 dirs): Added InChIManager testing to overall suites
11:47 CIA-32 bioclipse: egonw * r8001 /bioclipse2/trunk/plugins/net.​bioclipse.inchi.business.test/ (2 files in 2 dirs): Added the required plugin unit tests
12:11 egonw ha, 8000th commit :)
12:13 jonalv w00t :)
12:23 edrin joined #bioclipse
12:40 jonalv egonw: ping
12:40 egonw pong
12:40 jonalv There is a meeting at the hspoital on thursday at 10:00.... :(
12:40 jonalv I should probably be there...
12:41 egonw :( indeed
12:41 zarah egonw: You have new messages. Write '@messages' to read them.
12:41 egonw @msg
12:41 zarah egonw: 32 s ago, masak said I have it locally on my computer. I could upload it to svn if you want. it's not really ready for use, though.
12:41 jonalv so would it be okey if I came to you after that?
12:41 egonw sure!
12:42 jonalv I guess I better eat before going to you then since I might not make it till your lunch time...
12:42 jonalv sorry I sort of messed up...
12:44 egonw happens
12:44 egonw no worries :)
12:46 jonalv egonw: do you know when olas wil be back?
12:46 egonw I understood from Martin that he should fly in tomorrow
12:46 egonw no, actually... today, I think
12:47 jonalv okey
12:56 edrin interesting
12:56 edrin :)
13:57 shk3 joined #bioclipse
13:57 egonw hi shk3
13:58 shk3 hi egonw
13:58 shk3 can run bioclipse again
13:58 shk3 but loading of managers fails
13:58 egonw ha, really happy to hear that...
13:58 shk3 looks like for all managers
13:59 egonw did you find out what the problem was?
13:59 egonw or did it magically restore itself?
13:59 egonw (which too often happens)
13:59 shk3 it looks like I need to choose plugins manually in the run configuration
14:00 egonw mmmm... I'll ask Ola how asap how to debug this kind of problems...
14:00 egonw because he is keen on running based on features...
14:00 egonw ok... but loading managers fails?
14:00 egonw that's spring internals...
14:00 egonw don't know much about that...
14:05 shk3 anybody here has some idea about the spring stuff?
14:05 shk3 jonalv?
14:05 jonalv shk3: yes
14:06 shk3 you know what to do? great!
14:06 jonalv uhm
14:06 jonalv shk3: do you have a question?
14:06 egonw jonalv: see above
14:06 egonw his BC runs again
14:06 shk3 for me, loading of mangers fails
14:06 shk3 looks like all of them
14:06 shk3 what to do?
14:07 egonw shk3: you got a stacktrace?
14:07 shk3 I have no idea
14:07 egonw console output?
14:07 jonalv I need a little more info than "it's not working"
14:08 shk3 I am trying to find something
14:09 shk3 http://pastebin.com/md44c272
14:10 shk3 before that, there is a java.lang.ClassNotFoundException: org.apache.log4j.Category
14:10 jonalv shk3: could you paste everything?
14:10 shk3 could that be the reason?
14:10 jonalv yes that\s the reason
14:11 shk3 http://pastebin.com/m164312ce
14:11 shk3 hope that is everyting
14:11 shk3 ah, so it log4j
14:11 jonalv that doesn't look like a Bioclipse stack trace...
14:11 shk3 it is...
14:11 egonw Import-Package: org.apache.log4j
14:12 egonw add that to your MANIFEST.MF
14:12 jonalv They usually start with: log4j.configuration = file:/Users/jonathan/Work/Bioclipse2Repo/trunk​/plugins/net.bioclipse.logger/log4j.properties
14:12 jonalv bioclipse.defaultLogDir = /Users/jonathan/Library/Logs/Bioclipse
14:12 jonalv but I guess if log4j is not working... :)
14:12 egonw shk3: see for example cdk.business
14:13 jonalv yea that should help. shk3 what are you trying to run?
14:13 shk3 the import package thing is there
14:13 shk3 just bioclipse
14:13 shk3 but no manager works
14:13 shk3 also not cdk
14:13 jonalv and you have clicked arr required plugins until no more plugins are added?
14:13 shk3 yes
14:13 jonalv |add required plugins
14:14 jonalv how many times did you hit that button?
14:14 shk3 valide plugins says
14:14 shk3 no problems were detected
14:14 jonalv you have clicked more than once?
14:14 jonalv and you are only running standard bioclipse parts?
14:15 jonalv Perhaps you are running a log4j plugin...
14:15 jonalv You may not do that...
14:15 jonalv then it breaks
14:15 shk3 running a log4j plugin?
14:16 egonw jonalv: meaning that the log4j plugin should not be in the list of plugins in the Run Configuration?
14:16 shk3 i will deselect all and try again
14:16 jonalv egonw: sort of yea
14:16 shk3 there is no log4j plugin in that list for me anyway
14:16 jonalv it should be log4jover something
14:17 jonalv I don't remember what it is called
14:17 shk3 jcl104.over.slf4j
14:18 shk3 that's what I have in the list and it is selected
14:18 jonalv and slf4j.log4j12
14:19 shk3 are you sure the manger is dependent on that?
14:19 shk3 because
14:19 jonalv but it seems that I have org.apache.log4j (1.2.13.v200806030600) too and it works for me..
14:19 shk3 the manager code looks like this
14:19 jonalv I am pretty sure that Spring uses log4j yea...
14:19 shk3 ISpecmolManager manager = null;
14:19 shk3 try {
14:19 shk3 manager = (ISpecmolManager) finderTracker.waitForService(1000*10);
14:19 shk3 } catch (InterruptedException e) {
14:19 shk3 LogUtils.debugTrace(logger, e);
14:20 shk3 }
14:20 shk3 if(manager == null) {
14:20 shk3 throw new IllegalStateException("Could not get the SpecMol manager");
14:20 shk3 }
14:20 shk3 return manager;
14:20 shk3 and this is from where I get the exception
14:20 shk3 from the if(manager==null)
14:20 jonalv shk3: try with increasing the tiomeout
14:20 shk3 I will try to print the stack trace in the catch, if that is called
14:21 jonalv go for 60 secs instead of 10 secs
14:21 jonalv just to see that it doesn't time out trying to get the manager
14:22 shk3 om
14:22 shk3 om
14:22 shk3 ok
14:22 jonalv sry?
14:23 shk3 should be: ok
14:23 egonw the speclipse feature boots fine here
14:24 egonw shk3: just for sanity checking...
14:24 jonalv is there some heavy operations performed when instatiating the manager?
14:24 egonw when booting bare Bioclipse... what does the fifth line say?
14:24 jonalv For example I had similar prpoblems with strucutredb
14:24 egonw java.version=??
14:24 jonalv starting hsqldb can take a while
14:24 jonalv but they went away when I increased the timeout
14:24 egonw shk3: that is...
14:25 shk3 the timeout doesn't help
14:25 egonw can u please c/p the first 10 lines of the console output when booting a bare bioclipse, without any functionality...
14:25 shk3 no heavy opertions
14:25 egonw run plugin, net.bioclipes.ui, I think, + requirements
14:25 shk3 as far as i can see
14:26 shk3 since it's done via fucking spring, i have no idea what really happens
14:26 shk3 log4j.configuration = file:/home/shk3/workspace_bioclipse4/​net.bioclipse.logger/log4j.properties
14:26 shk3 bioclipse.defaultLogDir = /home/shk3
14:26 jonalv nut it works for egon?
14:26 shk3 INFO - Probable log file location: /home/shk3/bioclipse.log
14:26 shk3 !SESSION 2008-12-08 14:25:27.801 -----------------------------------------------
14:26 shk3 eclipse.buildId=unknown
14:26 shk3 java.version=1.5.0_15
14:27 shk3 java.vendor=Sun Microsystems Inc.
14:27 shk3 BootLoader constants: OS=linux, ARCH=x86, WS=gtk, NL=en_GB
14:27 shk3 Framework arguments:  -product net.bioclipse.ui.product
14:27 shk3 Command-line arguments:  -product net.bioclipse.ui.product -data /home/shk3/workspace_bioclipse​4/../runtime-bioclipse.product -dev file:/home/shk3/workspace_bioclipse4/​.metadata/.plugins/org.eclipse.pde.co​re/bioclipse.product/dev.properties -os linux -ws gtk -arch x86 -consolelog
14:27 shk3 !ENTRY org.eclipse.core.resources 2 10035 2008-12-08 14:25:33.015
14:27 shk3 !MESSAGE The workspace exited with unsaved changes in the previous session; refreshing workspace to recover changes.
14:27 shk3 WARN - The workspace exited with unsaved changes in the previous session; refreshing workspace to recover changes.
14:27 shk3 DEBUG - Detected argument 0: -product
14:27 shk3 DEBUG - Detected argument 1: net.bioclipse.ui.product
14:27 shk3 DEBUG - Attempting to start Spring Bundle Extender...
14:27 shk3 i am sure it does
14:28 shk3 as I said, all managers fail for me
14:28 jonalv so the spring bundle extender, does it in fact start?
14:28 egonw what comes after that last DEBUG line?
14:28 shk3 so it must be something with my configuration, I think
14:28 egonw the first look quite alike mine
14:28 shk3 08-Dec-2008 14:25:33 org.springframework.osgi.extende​r.internal.ContextLoaderListener start
14:28 shk3 INFO: Starting org.springframework.osgi.extender bundle v.[1.0.2]
14:28 shk3 08-Dec-2008 14:25:34 org.springframework.osgi.extende​r.internal.ContextLoaderListener addAnnotationBPP
14:28 shk3 INFO: Disabled automatic Spring-DM annotation processing; [ org.springframework.osgi.extender​.annotation.auto.processing=null]
14:28 shk3 08-Dec-2008 14:25:34 org.springframework.context.sup​port.AbstractApplicationContext prepareRefresh
14:28 shk3 INFO: Refreshing org.springframework.osgi.context.sup​port.OsgiBundleXmlApplicationContext@8a52b6: display name [OsgiBundleXmlApplicationConte​xt(bundle=net.bioclipse.core, config=osgibundle:/META-INF/spring/*.xml)]; startup date [Mon Dec 08 14:25:34 GMT 2008]; root of context hierarchy
14:28 shk3 DEBUG - Spring Bundle Extender started.
14:28 egonw please go on (or use the pastebin for just everything)
14:28 shk3 INFO - Bioclipse cache dir: /home/shk3/runtime-bioclipse.product/tmp
14:29 egonw that looks ok
14:29 egonw ok := what I have too
14:31 egonw jonalv: can I unit test what a manager sends to the console?
14:32 shk3 http://pastebin.com/m98c91b9
14:32 jonalv egonw: I am not sure I understand the question
14:32 Gpox joined #bioclipse
14:32 egonw shk3: from the start please
14:32 jonalv Gpox: hi
14:32 egonw shk3: that is... the complete output... including the first lines you already posted here, please
14:32 shk3 hm, the console isn't long enough
14:32 egonw hi Gpox!
14:32 egonw shk3: then check this file:
14:32 Gpox hi
14:32 zarah hi Gpox
14:33 egonw /home/shk3/bioclipse.log
14:33 shk3 http://pastebin.com/d23e377d6
14:34 egonw thanx,
14:36 jonalv I would say that you are missing the plugin containing the log4j stuff
14:37 jonalv could you check in run cinfigurations which plguins you arerunning that contains the word "log4j"
14:38 shk3 it's there via the import
14:39 jonalv apharently it isn't
14:39 jonalv that's what it is complaining about...
14:39 shk3 so what to do?
14:40 jonalv I am still waiting for that list of plugins containing the word log4j
14:40 egonw shk3: how many plugins do you have selected...
14:40 egonw ?
14:41 egonw I'm running Ubuntu too...
14:41 egonw so should match...
14:41 egonw I have 73
14:41 shk3 how to find this number?
14:41 egonw is listed in the RUn Configuretion window, Plug-ins tab
14:42 shk3 so i need to count manually?
14:43 egonw no
14:43 egonw should be below the buttons Select All... Add Requires Plug-ins...
14:44 egonw it should say something like
14:44 egonw 73 out of 1221 selected
14:44 egonw just below the 'Only show selected plug-ins' checkbox
14:45 shk3 201 out of 463 selected
14:45 zx joined #bioclipse
14:45 egonw shk3: ok, that's too much...
14:45 egonw shk3: just the bioclipse core:
14:46 egonw see: http://wiki.bioclipse.net/index.p​hp?title=Checking_out_Bioclipse_2
14:46 egonw 6 plugins + the deps -> ~73 plugins
14:46 egonw make sure to do step 10 on that page
14:46 shk3 79 out of 463
14:46 egonw sounds better
14:46 egonw still a discrepency of 6... but close enough
14:47 egonw please hit the VErify button
14:47 egonw ummm
14:47 egonw Validate Plug-ins
14:47 egonw that's the one I mean
14:47 egonw what does that give?
14:47 zx ping *
14:47 egonw zx: pong
14:48 egonw zx: what's up?
14:48 zx egonw: who owns the BioClipse blog?
14:48 zx egonw: I want it syndicated on planet.eclipse.org ;)
14:48 shk3 it tells me that 3 plugins need java 1.6
14:48 egonw zx: you own planet.eclipse.org?
14:48 shk3 i tried with 1.6 as well
14:48 egonw shk3: ok, it lists problems?
14:48 shk3 then no problems detected, but still managers dont work
14:49 zx egonw: noone really owns it, but I maintain it
14:49 egonw ok, ic...
14:49 zx egonw: https://bugs.eclipse.org/bugs/enter_bug.cgi?pro​duct=Community&component=PlanetEclipse.org
14:49 zx egonw: file a bug and I can add the blog quickly :)
14:49 egonw olas is the main blogger of bioclipse.blogger.com
14:49 zx I'm interested to see people build on Eclipse in other domains
14:50 egonw ola should return from holiday this week...
14:50 egonw I'll ask him
14:50 zx I co-lead PDE at Eclipse so it's interesting to see that little snippet above about verifying plug-ins ;)
14:50 egonw zx: :)
14:50 egonw bioclipse has a really funky set up...
14:50 egonw as it adds Spring to do some extra discovery of things...
14:50 egonw goed beyond my understanding though... (not added by me)
14:51 egonw it mostly works...
14:51 egonw but when it doesn't, it's rather hard to debug :(
14:51 * jonalv is the guilty for the Spring OSGI stuff... :)
14:51 egonw shk3: please run with 1.5
14:51 zx that's fine, there's valid reasons for choosing things like Spring OSGi
14:51 egonw and tell me about those validate problems...
14:51 zx If you need something more lightweight, Equinox OSGi has Declarative Services (DS)
14:52 egonw shk3: please run the set target platform again... and then redo adding the 6 plugins + requirements, and then validate once more...
14:52 jonalv zx: what we are using Spring for is primarily AOP
14:52 egonw shk3: the validate is not supposed to list any problems
14:53 shk3 somehow i now have 138 selected and no validate problems
14:53 zx well, the validation problem in his case seems that some plug-ins require Java 6 and he has Java 5
14:53 zx which is fine unless you really need those few plug-ins ;)
14:53 egonw zx: whcih is interesting as bioclipse plugins are supposed to work with 1.5 not 6
14:53 jonalv what plugin requiers java 6?
14:53 shk3 but now I can't start and get
14:53 shk3 java.lang.IllegalArgumentException: The System Bundle's start level can not be modified.
14:54 egonw because of the OS/X developers
14:54 egonw shk3: I get that fixed, by rerunning the set target platform...
14:54 jonalv shk3: reset target platform one more time for me would you_ :)
14:54 egonw but you just did that, right?
14:54 gilleain hmmm. I haven't tried bioclipse on my mac recently...
14:54 shk3 did it frequently, but not right now
14:54 egonw zx: in particular, what shk3 is trying to run now, is strictly 1.5
14:55 egonw zx: while you are around...
14:55 egonw zx: might you happen to know how to tweak progress monitors to have it show graphical output?
14:55 egonw like a 2D image of something it is working on?
14:56 egonw or, say the best calculated result so far as image?
14:56 shk3 well, no validate problems
14:56 shk3 but still log4j not found
14:56 jonalv hm so there still is some big problems with that log4j setup...
14:58 egonw zx: http://pele.farmbio.uu.se/bugs/show_bug.cgi?id=154
14:58 zarah egonw's link is also http://tinyurl.com/6mpsnf
14:58 egonw zx: filed a bug report with your planet eclipse request for Ola
14:58 shk3 ok, somehow got rid of it
14:58 shk3 managers work
14:58 shk3 have a meeting now
14:58 zx egonw: you're not going to be able to use the existing progress dialog infrastructure as far as I know
14:58 shk3 hope my bioclipse still works when I am back
14:58 egonw zx: ok, we were afraid of that
14:58 jonalv shk3: me too :)
14:58 * shk3 is at a meeting
14:59 zx egonw: you can do something like Job.getJobManager() and use a job manager to hook into the progress event of your specific type of jobs and than display a custom dialog indicating progress
14:59 egonw ack
14:59 egonw gilleain: that's about the approach you took now?
14:59 zx egonw: which isn't that bad as you were going to have to provide that custom figure drawing stuff anyway
14:59 gilleain whatwhatwhat
15:00 zx egonw: you can probably get away from overriding ProgressMonitorDialog to death
15:00 zx egonw: that's my quickly thought up solution without looking at it in depth of course ;)
15:00 gilleain as far as I could tell, ProgressMonitors were created (instansiated) deep inside eclipse.
15:00 gilleain i can't spell that word
15:01 egonw gilleain: but your seneca code is hooking into it, not?
15:01 gilleain no
15:01 egonw ah, ok
15:01 gilleain It's not possible, as far as I can tell.
15:01 egonw zx: which means that zx's tips are really useful
15:02 egonw zx: thanx!
15:05 zx egonw: np, feel free to ask questions in #eclipse as that's where most of us hang out
15:08 egonw zx: ok, posted question...
15:30 gilleain thanks, egonw, it will be good to get a custom progress working.
15:30 egonw yes, that would be cool indeed
15:31 egonw with the best found chemical graph so far for seneca
15:31 egonw drewling already...
15:31 egonw I hope the spelling is right :)
15:31 gilleain drewling?
15:31 gilleain drawn?
15:31 egonw ok, apparently not... :)
15:32 egonw what happens we you see really nice food
15:32 egonw your mouth starts watering...
15:32 egonw 'kwijlen' in dutch
15:33 gilleain http://book.javanb.com/eclipse-rich-client-​platform-designing-coding-and-packaging-jav​a-applications-oct-2005/ch17lev1sec8.html
15:33 zarah gilleain's link is also http://tinyurl.com/5johpt
15:34 gilleain Ahhh, "drooling"!
15:34 egonw ah :)
15:37 gilleain hmmm.
15:37 gilleain Warning
15:37 gilleain The progress view relies on the Workbench's progress provider. If you add your own provider, the progress view stops working as there can only be one progress provider registered at a time.
15:38 egonw :(
15:40 gilleain Not sure what that means, but I will try it out, and not commit it if it screws up the other plugins...
15:41 egonw cough *branch* cough
15:41 egonw cough *github* cough
15:42 gilleain nasty cough you have there. :)
15:42 egonw yeah, really nasty one...
15:43 egonw everyone seems to have it hear...
15:53 shk3 after updating, I have erros in org.os.cdk.inchi
15:53 shk3 INCHI_KEY
15:53 shk3 and
15:53 shk3 JniInchiOutputKey
15:54 shk3 cannot be resolved
15:55 gilleain update the cdk plugins?
15:56 egonw net.sf.jniinchi in particular
15:59 CIA-32 bioclipse: egonw * r8002 /bioclipse2/trunk/plugins/net.bioclipse​.core.tests/src/net/bioclipse/core/test​s/coverage/AbstractCoverageTest.java: Fixed test: it was not yet implemented (fixes #153)
15:59 zarah bug #153 | http://tinyurl.com/5cu8ma
16:00 CIA-32 bioclipse: egonw * r8003 /bioclipse2/trunk/plugins/ (5 files in 4 dirs): Added three missing test methods
16:05 shk3 is the JChemPaintSWTWidget used somewhere or by somebody?
16:08 egonw JChemPaintEditor
16:08 gilleain Actually, we just found that there are two.
16:09 gilleain What with the original jcp, the summer-of-code one, arvids, and mine, we have quite a few..
16:09 jonalv hehe
16:09 egonw take arvids
16:10 egonw don't use any cdk10.* classes
16:10 gilleain indeed
16:11 shk3 it looks like the net.sf.jniinchi plugin has
16:11 shk3 Export-Package: net.sf.jniinch
16:11 shk3 in manifest,
16:12 shk3 but no such classes?
16:12 CIA-32 bioclipse: egonw * r8004 /bioclipse2/trunk/plugins/net.bioclipse​.core.tests/src/net/bioclipse/core/test​s/coverage/AbstractCoverageTest.java: Mmm... now really, really fixed...
16:12 egonw shk3: confirmed
16:13 egonw no idea why that did not show up when I ran the plugin tests for the manager...
16:13 egonw ah. because there is no problem
16:13 egonw try a project Refresh
16:13 egonw make sure that your workspace picked up the new 0.5 jar
16:16 shk3 it's picked up
16:16 shk3 but still problems
16:16 egonw verify that your 0.5 jar has net.sf.jniinchi too
16:17 shk3 ah, it wasn't in the build path
16:17 shk3 seems there were conflict in .classpath
16:18 CIA-32 bioclipse: gilleain * r8005 /bioclipse2/trunk/plugins/net.bioclipse.cdk.​jchempaint/src/net/bioclipse/cdk/jchempaint/ (4 files in 2 dirs): Fixed weird spelling of class name (MosueEventRelay?).
16:18 egonw dinner
16:18 gilleain ahhh that's better.
16:18 egonw bbl
16:18 egonw gilleain: ha, you spotted it too :)
16:18 egonw cu later (or not)
16:18 gilleain it has been bugging me :)
16:19 gilleain cu l8er (|!)
16:43 Gpox joined #bioclipse
17:12 shk3 hi Gpox
17:13 Gpox hi shk3
17:14 shk3 I try to use the JChemPaintWidget
17:14 shk3 for drawing a molecule
17:14 shk3 but nothing shows up
17:14 shk3 I debugged it
17:15 shk3 and the paintControl method is never called
17:15 shk3 it seems like the paintlistener isn't working
17:15 shk3 is there anything special I need to do?
17:17 Gpox odd, do you use the setAtomContainer maby setModel, i think there is a if(ac != null) setVisible(ture) in there so it would not call paint if it dont have a AtomContainer
17:18 shk3 that's in paintControl
17:19 shk3 but I added a breakpoint before
17:19 shk3 and it's not stopping there
17:20 shk3 so the whole paintControl isn't called, it seems
17:21 Gpox it is done in updateView() witch is called form setAtomContainer()
17:22 Gpox so to draw you call setAtomContainer( with the container you want to draw)
17:22 shk3 ok, I have a llok at updateview
17:23 Gpox and dose it have 2d-coordinates?
17:24 shk3 yes
17:24 shk3 updateview is executed
17:25 shk3 also the redraw call there
17:25 shk3 but the paintlistener is never called
17:28 shk3 is there anything I need to do to get the paintlistener working?
17:29 Gpox it is in the constructor
17:29 shk3 yes
17:29 shk3 and that should be enough?
17:29 Gpox it is used in Java2DRenderView and JChemPaintEditor
17:31 Gpox just create it and call setAtomContainer(ac) should be enough, did updateView() call setVisible()?
17:31 Gpox with true
17:32 shk3 ye
17:32 shk3 double checking right now
17:33 shk3 yes, it does
17:34 Gpox then i am out of ideas
17:34 shk3 ah
17:35 shk3 style must be SWT.PUSH for it to work
17:36 Gpox you sure becaus JChemPaintEditor calls it with SWT.NONE
17:37 Gpox did you use any SWT constant before?
17:37 shk3 yes
17:37 shk3 the scroll constants
17:37 shk3 probably that was the problem
17:38 shk3 yes, none works as well
17:39 Gpox then use that, i might have to implement scroll in the future :)
17:40 shk3 thanks
17:43 shk3 is the jcpwidget prepared in any way for atom selections?
17:43 shk3 i need to know when the user clicks on an atom in it
17:45 Gpox checkout the JChemPaintEditorWidget it extends the JCPWidget with controller, it could probably be done better to allow others to reuse it
17:47 shk3 ok, so I need to put in controllerhub basically?
17:48 gilleain yes, and possibly make your own module for reacting to atom selections
17:48 gilleain since they will be sent to the nmr graph, yes?
17:48 shk3 which would be the active module
17:48 gilleain yes
17:48 shk3 yes
17:50 Gpox yeah, the jcpEditorWidget is a selection provider but that could be done better. Could you file a feature request on that?
17:51 shk3 the jcpeditorwidget is probably too much for my purpose?
17:51 shk3 I just need drawing and selection
17:52 Gpox yes
17:55 Gpox but is should be refactord to be of use in cases like this,  allowing you to get easy get acces to ControlerHub functionality
18:22 * egonw is back
18:41 edrin egonw: how did you implement inchi?
18:42 egonw not
18:42 egonw using third party code for that
19:07 CIA-32 bioclipse: egonw * r8006 /bioclipse2/trunk/plugins/net.bioclips​e.ui.business.tests/build.properties: Fixed to allow running of plugin tests
19:07 CIA-32 bioclipse: egonw * r8007 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Added a missing test
19:46 edrin left #bioclipse
21:19 edrin joined #bioclipse

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