Camelia, the Perl 6 bug

IRC log for #bioclipse, 2007-11-19

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All times shown according to UTC.

Time Nick Message
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09:50 CIA-18 bioclipse: ospjuth * r4259 /branches/bioclipse2/core/​plugins/net.bioclipse.ui/ (META-INF/MANIFEST.MF plugin.xml): Use TabbedProperies. Standard layout so far.
10:11 olas egonw: around?
10:11 olas I want to include CDK in Bioclispe2 hierarchy
10:11 olas and thought we'd use the latest version for that
10:11 olas so
10:12 olas what is your opinion?
10:12 olas Or should we link to the plugin in trunk?
10:16 egonw what's the ETA for the first BC2 development/test release?
10:17 egonw CDK trunk/ is getting reasonable mature now...
10:17 egonw still in quite some flux
10:17 egonw but of enough quality to go into the BC2 alpha branch
10:24 olas BC2 has no ETA yet
10:24 olas very early so far
10:24 egonw than I see no problem
10:24 egonw I would be very happy actually...
10:24 olas what would be best would be a symlink inside the SVN repo
10:25 olas ok
10:25 egonw yes...
10:25 olas then let's have the latest CDK in BC2?
10:25 egonw yes
10:25 olas Can you build that?
10:25 egonw is BC2 good enough for me to give it a test drive?
10:25 olas no
10:25 olas but maybe after today
10:25 olas we hope to have a console today and a first editor
10:25 olas that's why I need CDK
10:26 olas so far it's just some junit tests and an empty workbench
10:26 olas but logging/exception handling and scripting functionality is underway
10:26 olas Me, I work with the visual stuff
10:26 olas and will try to get the first editor up to investigate the parsing process
10:28 olas egonw: If I set up a ne plugin in BC2 hierarchy7, can you put the latest jars there?
10:28 olas ne=new
10:31 egonw so, no symlink?
10:33 olas in that case no
10:33 olas then we use the latest CDK in BC2
10:33 olas and stick with the current in head
10:33 olas ok?
10:33 egonw yes
10:34 egonw CDK has moved to a more patchy kind of development
10:34 egonw where patches only go into trunk when well tested...
10:34 olas sounds good
10:34 * olas will set up the new plugin and post info here
10:35 * egonw will now check out the BC2 source
10:36 egonw what about 1.1.x ?
10:36 egonw we should plan a 1.2 release
10:36 egonw with a hack session to get rid of as much bugs as possible
10:37 CIA-18 bioclipse: ospjuth * r4260 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.cdk/: Initial import of new CDK plugin for Bioclipse2 hierarchy.
10:37 olas yes
10:38 olas and after that only focus on BC2
10:38 olas That would be good.
10:38 CIA-18 bioclipse: ospjuth * r4261 /branches/bioclipse2/chemoin​formatics/net.bioclipse.cdk/ (15 files in 9 dirs): Initial import of new CDK plugin for Bioclipse2 hierarchy.
10:38 olas but there are so many bugs that I will not fix for 1.1.x
10:38 olas that's why we want a cor erewrite
10:39 olas but we should release a 1.1.5 at least
10:39 olas where QSAR and Moby is working at least partly
10:39 olas and scripting
10:39 olas egonw: done
10:40 olas plugin can be found at: /branches/bioclipse2/chemoin​formatics/net.bioclipse.cdk/
10:40 olas please install the jars there
10:40 olas and use eclipse versioning of the plugin:
10:40 olas x.x.x.v20071119
10:40 olas in our case we decided that we use the branch 1.3.1 for Bioclipse2
10:41 olas so 1.3.1.v20071119 would be a good ID
10:41 olas does that sound OK with you?
10:46 egonw olas: please mark the bugs that won't/can't be fixed in 1.1.x as such... maybe we should prefix those with "BC2:" or so?
10:46 egonw or use a category for that...
10:47 olas yes
10:47 egonw yes 1.3.1 sounds good, as beta series for 2.0... maybe better even 1.9.x ?
10:47 egonw that would allow possibilities for 1.4 based on 1.0/1.2
11:09 egonw olas: ping
11:26 olas joined #bioclipse
11:26 olas egonw: pong
11:26 * olas is back from lunch
11:29 egonw good :)
11:30 egonw does BC2 hase a new navigator yet?
11:30 egonw the core plugins do not seem to offer something like that
11:32 olas net.bioclipse.ui has that
11:32 olas core plugins have nothing to show
11:32 egonw OK, what's the view name?
11:32 olas no UI at all
11:32 olas should open by default
11:32 egonw B Explorer?
11:33 olas Bioclipse Explorer I think
11:33 egonw it did not
11:33 olas please clean runtime before start
11:33 egonw ack
11:33 * olas will add a noe on the wikiu
11:34 egonw OK, that helps
11:34 egonw I have to autoclean on each start now
11:34 olas no
11:34 olas just once
11:34 egonw I do get a error though:
11:34 egonw java.lang.NoClassDefFoundError: org/eclipse/core/internal/runt​ime/auth/AuthorizationHandler
11:34 egonw at org.eclipse.core.internal.runtime.In​ternalPlatform.initializeAuthorizati​onHandler(InternalPlatform.java:603)
11:34 egonw and many more lines...
11:34 olas hmm
11:34 olas what eclipse are you using?
11:34 egonw 3.3.1.1
11:35 olas hmm
11:35 olas wait a second
11:35 olas I am using 3.3 currently
11:35 olas could you post entire exception?
11:38 CIA-18 bioclipse: ospjuth * r4262 /branches/bioclipse2/core/plugins/ne​t.bioclipse.ui/src/net/bioclipse/ui/ (3 files in 2 dirs): Refactored workbenchadvisory hack to correct package
11:38 olas egonw: have you updated new cdk plugin with latest jars?
11:39 egonw no, not yet...
11:39 egonw doing all sorts of things at the moment...
11:39 olas please do
11:39 egonw multithreading turned on...
11:39 egonw olas: OK, hang on...
11:39 olas I need that for my editor :-)
11:39 egonw OK
11:40 olas oh: can I use the new JCP?
11:40 egonw you will
11:40 olas great
11:40 egonw well... the new renderer: yes
11:40 egonw the full new editor is not complete yet
11:40 olas oh
11:40 olas ane ETA for that?
11:40 olas any
11:41 egonw 12 months
11:41 olas !!!
11:41 olas oh no!
11:41 olas :-(
11:41 egonw no one is working on it right now...
11:41 egonw and I don't have had time myself yet
11:41 olas that's really really bad
11:41 egonw then we should make time for that
11:42 olas I have no time and no resources to put on that
11:42 egonw olas: I'll email
11:42 olas good
11:46 olas egonw, anyway, will there be problems getting JCPEditor to use new CDK?
11:47 olas I will simply copy in the net.bioclipse.cdk.jcp into Bioclipse2 directory, right?
11:47 egonw much of the editor functionality still needs to be ported
11:47 egonw sure
11:47 egonw of course you can use the 'old' JCP editor
11:47 olas good
11:47 olas Then I will adapt that for work with resources
11:48 olas as a first editor
11:48 olas (or maybe use Jmol, we'll see)
11:49 olas egonw: What if I say that the JCP packages should lie in net.bioclipse.cdk.ui?
11:49 olas any objections?
11:49 olas after all, it IS an editor that is based on CDK...
11:49 olas and why havea separate plugin?
11:50 olas we want to avoid plugin explosion
11:50 egonw can't remember why that was the case
11:50 olas must be from when JCP had it's own CDK version
11:50 olas ok, than you support my decision?
11:50 olas then
11:52 egonw sure
11:52 egonw :)
11:58 olas damn, have to solve logging plugin first
11:58 * egonw is struggling to get svn:externals working :(
12:04 CIA-18 bioclipse: egonw * r4263 /branches/bioclipse2/chemoinfor​matics/net.bioclipse.cdk/jars/: Removed jars to make place for svn:externals
12:07 CIA-18 bioclipse: egonw * r4264 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.cdk/: Get the 3rd party jars from the CDK repos
12:12 CIA-18 bioclipse: egonw * r4265 /branches/bioclipse2/chemoinfor​matics/net.bioclipse.cdk/src/: Get the CDK source directly from the CDK repos
12:22 CIA-18 bioclipse: jonalv * r4266 /branches/bioclipse2/core/plugins/ (net.bioclipse.spring/ spring/):
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12:51 CIA-18 bioclipse: carl_masak * r4267 /branches/bioclipse2/core/p​lugins/net.bioclipse.core/ (6 files in 4 dirs):
12:51 CIA-18 bioclipse: [net.bioclipse.core]
12:51 CIA-18 bioclipse: * Added rudimentary js console
12:51 CIA-18 bioclipse: * Window -> Show View -> Scripting -> Javascript Console
12:51 CIA-18 bioclipse: * At present, Java bindings don't work (as they do in bc1)
12:54 viklund joined #bioclipse
12:54 jonalv hi viklund
13:04 olas hi viklund
13:07 olas egonw: around?
13:07 egonw yes
13:08 viklund geh
13:08 viklund hej
13:08 olas I get a lot of red crosses in new net.bioclipse.cdk
13:08 egonw olas: yes, that's why I wrote:
13:08 egonw [13:30] <egonw> olas: I'm now tuning the build path
13:08 * jonalv is switching into work on bioclipse 2 today...
13:08 olas :-)
13:13 CIA-18 bioclipse: jonalv * r4268 /branches/bioclipse2/bioinformatics/plugins/ (15 files in 8 dirs): Some work on incorporating biojava.
13:24 edrin joined #bioclipse
13:24 edrin hi
13:25 jonalv hi edrin
13:25 edrin hello jonalv
13:27 olas hi edrin
13:27 edrin hi olas
13:27 masak hi edrin
13:27 olas egonw: how is the classpath coming along?
13:27 edrin hi masak
13:28 egonw olas: almost done...
13:28 egonw doing it jar by jar
13:28 egonw to get the smallest plugin size
13:28 egonw 10 errors left :)
13:29 egonw e.g. there are now 11 unused jars in jars/
13:29 egonw which should not get packaged now...
13:31 CIA-18 bioclipse: egonw * r4269 /branches/bioclipse2/chemoin​formatics/net.bioclipse.cdk/ (.classpath META-INF/MANIFEST.MF): Tuned classpath
13:32 egonw olas: done
13:32 olas thx
13:34 jonalv Is there a runnable bioclipse2 gui now? Would be great for me to see if a can crach it with my new extensionpoint for spring config files...
13:36 edrin you started the bioclipse2 ide already?
13:36 edrin isn't it thought to be the eclipse with a special perspective?
13:36 masak jonalv: yes.
13:37 masak edrin: yes. yes.
13:37 edrin is it already in svn?
13:38 jonalv edrin: yes there is a branch
13:39 edrin jonalv: how is it thought? is it a plugin for eclipse?
13:40 jonalv edrin: Hm yes that's the idea but we will make a rich client without any java tools
13:40 edrin and other (eclipse)-science-plugins could then depend on it
13:40 CIA-18 bioclipse: ospjuth * r4270 /branches/bioclipse2/core/pl​ugins/net.bioclipse.logging/ (6 files in 2 dirs): Included logging capabilities.
13:41 edrin is there a road-map for the bioclipse2?
13:41 CIA-18 bioclipse: ospjuth * r4271 /branches/bioclipse2/core/​plugins/net.bioclipse.ui/ (4 files in 3 dirs): Added logging and made a BioclipseActivator to use as base class Activator for all Bioclipse plugins.
13:41 jonalv there is the wiki
13:41 edrin ok
13:43 edrin i will have a look at this later today
13:50 jonalv I try to run the bc2 stuff but get a bunch of errors. Is it working for anyone?
13:50 jonalv java.lang.NoClassDefFoundError: org/eclipse/core/internal/runt​ime/auth/AuthorizationHandler
13:51 olas clean + uppdate classpath
13:51 olas and use eclipse 3.3 or newer
13:51 olas also check deps
13:51 olas and make sure run config has "add required plugins"
13:52 jonalv That did the trick. Thanks
13:55 jonalv Bioclispe 2 is working and it has a javascript console. Yey!
13:58 edrin it has already?
13:58 edrin nice
13:58 olas cool, have not tried that
13:58 olas does it work?
13:58 edrin only console or does it also provide running scripts already
13:58 jonalv yes for some definition of work
13:58 edrin what do you mean?
13:59 masak edrin: it's a console
13:59 masak it doesn't actually do anything yes
13:59 masak except evaluate js
13:59 edrin ok
13:59 masak I'm currently working on getting the extention-point framework working again
13:59 olas egonw: I get errors when checking out net.bioclipse.cdk
13:59 olas seems the manifest.mf is not updated
13:59 olas could that be so?
14:00 olas No jars listed on Classpath...
14:00 olas and none exported
14:00 egonw no uncommited things for the plugin
14:01 olas hmm
14:01 egonw did you update to ...
14:01 egonw to ,,,
14:01 olas latest version, yes
14:01 egonw to ,,,4271
14:01 egonw ?
14:01 olas no 4269
14:01 olas hmm
14:01 olas latest from repository
14:01 egonw should be good enough indeed
14:01 olas well, I can fix it
14:03 egonw oh... the jars are not exported...
14:03 egonw correct...
14:03 olas I fix
14:03 CIA-18 bioclipse: ospjuth * r4272 /branches/bioclipse2/chemoin​formatics/net.bioclipse.cdk/ (.classpath META-INF/MANIFEST.MF build.properties): Export jars
14:03 egonw they are in the .classpath though
14:04 egonw OK, please revert that patch
14:04 egonw 1. way too many jars in the classpath now
14:04 egonw 2. way too much exported
14:05 * egonw objects to no plugin explosion versus happy package export explosion
14:05 jonalv egonw: What seems to be the problem?
14:05 egonw [15:04] <egonw> 1. way too many jars in the classpath now
14:05 egonw [15:04] <egonw> 2. way too much exported
14:06 jonalv do you have an example I mean...
14:06 olas egonw: please resolve that
14:06 egonw 2: do not export non org.openscience.cdk packages
14:06 olas you know best
14:06 egonw 1: see my .classpath
14:07 jonalv so it's the cdk plugin you are talking about? I see....
14:07 CIA-18 bioclipse: egonw * r4273 /branches/bioclipse2/chemoin​formatics/net.bioclipse.cdk/ (.classpath META-INF/MANIFEST.MF build.properties): Reverted Ola's way too greedy patch
14:07 CIA-18 bioclipse: carl_masak * r4274 /branches/bioclipse2/core/p​lugins/net.bioclipse.core/ (6 files in 3 dirs):
14:07 CIA-18 bioclipse: [net.bioclipse.core]
14:07 CIA-18 bioclipse: * added extension capabilities to scripting system
14:08 masak now rhino.showMessage("this works again in bc2");
14:09 jonalv net.bioclipse.core.Activator.start is not runned when starting bc2. Shouldn't it be or am I thinking wrognly?
14:10 CIA-18 bioclipse: egonw * r4275 /branches/bioclipse2/chemoin​formatics/net.bioclipse.cdk/ (META-INF/MANIFEST.MF build.properties): Export what should be exported, and nothing more
14:10 masak jonalv: you're probably right, it should likely be run
14:11 jonalv why isn't it then?
14:11 masak it's probably my fault that it isn't
14:11 masak I probably just checked a box somewhere
14:11 masak thinking "yes, we'll like one of those"
14:11 masak and then not doing anything more about it
14:12 jonalv but what else should be done about it? I thought Eclipse magicly ran the Activator.run when starting anything in the plugin
14:13 jonalv Oh found it the Activator field in the plugin.xml is empty
14:13 jonalv that's likely it...
14:14 jonalv hm or not
14:14 jonalv ah
14:14 jonalv now it fails nicely
14:14 jonalv Activate this plugin when one if its classes is loaded should be checked aswell..
14:16 CIA-18 bioclipse: ospjuth * r4276 /branches/bioclipse2/chemoinfo​rmatics/net.bioclipse.cdk.ui/: Initial import.
14:18 masak jonalv: I see.
14:18 masak jonalv: care to commit the change?
14:18 jonalv no not now because as things are I totally crash all of it
14:18 jonalv ...or maybe I could do a partly commit
14:18 jonalv I'll do that...
14:37 jonalv olas: there is something wrong with null arguments to the navigator. Can you confirm?
14:37 CIA-18 bioclipse: ospjuth * r4280 /branches/bioclipse2/chemoinfo​rmatics/net.bioclipse.cdk.ui/ (172 files in 21 dirs): Initial import.
14:41 CIA-18 bioclipse: jonalv * r4281 /branches/bioclipse2/core/p​lugins/net.bioclipse.core/ (5 files in 5 dirs): Extensionpoint for aplicationcontext.xml files
14:54 CIA-18 bioclipse: ospjuth * r4282 /branches/bioclipse2/core/​plugins/net.bioclipse.ui/ (META-INF/MANIFEST.MF src/net/bioclipse/ui/Perspective.java): Added javascript console to default perspective
14:54 CIA-18 bioclipse: carl_masak * r4283 /trunk/plugins/net.bioclips​e.rhino/src/net/bioclipse/ (3 files in 2 dirs):
14:54 CIA-18 bioclipse: [net.bioclipse.plugins.bc_rh​ino.views.RhinoConsoleView]
14:54 CIA-18 bioclipse: [net.bioclipse.views.ScriptingConsoleView]
14:54 CIA-18 bioclipse: * separated scripting console from js
14:54 CIA-18 bioclipse: * this is Very Good(TM) for future console use
14:55 * egonw suggests the Uppsala team to give a virtual demo presentation later this week
14:55 masak good idea.
14:57 thomas_ku joined #bioclipse
14:59 * jonalv is reading about Spring and OSGI frameworks. (this might be advanced...)
15:00 egonw hi thomas_ku
15:00 CIA-18 bioclipse: egonw * r4284 /trunk/plugins/net.bioclipse.spectr​um.mzdata/src/net/bioclipse/plugins​/extensions/MZDataConvertor.java: Added missing license/copyright statement.
15:00 thomas_ku hi egonw
15:06 CIA-18 bioclipse: carl_masak * r4285 /branches/bioclipse2/core/plugins/net.bio​clipse.core/src/net/bioclipse/core/views/ (RhinoConsoleView.java ScriptingConsoleView.java):
15:06 CIA-18 bioclipse: [net.bioclipse.core.views]
15:06 CIA-18 bioclipse: * separated RhinoConsoleView from ScriptingConsoleView
15:06 CIA-18 bioclipse: * basically a model feature stolen from bc1
15:06 masak :)
15:06 * masak likes separation of concerns
15:07 masak I think the code actually became a bit smaller, too
15:08 CIA-18 bioclipse: egonw * r4286 /trunk/plugins/net.bioclipse.spectrum/src/​net/bioclipse/model/SpectrumResource.java: Added extra NPE test
15:08 CIA-18 bioclipse: egonw * r4287 /trunk/plugins/net.bioclipse.st​atistics/META-INF/MANIFEST.MF: There are no views
15:14 CIA-18 bioclipse: egonw * r4288 /trunk/plugins/de.ipbhalle.msbi.mzdata/.project: Can't find that jpox builder
15:23 egonw olas: around?
15:29 olas yes
15:29 CIA-18 bioclipse: ospjuth * r4289 /branches/bioclipse2/core/plugins/ne​t.bioclipse.ui/META-INF/MANIFEST.MF: Added deps
15:29 * egonw is trying to debug one or two nasty mzdata bugs
15:29 egonw I think I made a small step forward...
15:29 egonw one sec... testing
15:30 * olas has never gotten mzdata to work
15:30 egonw it sort of works...
15:30 * olas has not seen it
15:30 egonw but the real problem is that the resource is not editor based
15:30 olas ?
15:31 olas in Bioclipse2, it should just be to add it
15:31 egonw right
15:31 olas if it is resource-based
15:31 egonw lookign forward to that
15:31 egonw the problem I got now is...
15:31 olas so I wouldn't spend too much time on getting it into bioclipse1.1.x
15:31 egonw that when switching editor
15:31 egonw the close of the former editor unloads the resource
15:31 egonw while the new editor does not reload the resource
15:32 olas can't help you with that
15:32 egonw and, worse... the unload does not seem to trigger isParsed to be set to false...
15:32 olas strange
15:32 * olas does not want to dive into that again
15:32 egonw olas should not
15:32 olas editor sync is not easy
15:33 egonw this will fix itself with BC2
15:33 olas :-)
15:34 jonalv When BC2 comes we will all have free lunches all the time
15:34 jonalv or eh... maybee not?
15:34 olas yea, sure
15:34 egonw and lots of toffee's
15:34 masak wee!
15:35 olas how!
15:35 masak :)
15:35 masak jonalv: TANSTAAFL
15:35 masak look it up
15:37 jonalv olas, egonw you should read: <http://static.springframework.org/osg​i/docs/1.0-m3/reference/html_single/> and see if maybee I am biting more that I can chew...
15:37 egonw olas: what's the opposite of unLoad() ?
15:37 egonw for IBioResrouce?
15:38 jonalv egonw: me?
15:39 egonw jonalv: I have not idea about Spring
15:40 jonalv egonw: I see. It's very cool, powerful and (of course) also very complex...
15:40 olas jonalv: the book should be there tomorrow
15:41 jonalv great
15:41 olas can't/won't help with spring
15:41 olas no time :-(
15:41 jonalv I am not sure the books deals with this part though...
15:42 egonw olas: how can I undo a unLoad()?
15:42 jonalv All I am saying is that you might be forced to learn some Spring since if we do things this way it will be a central part of many plugins in bioclipse2
15:42 olas egonw: don't think that is possible
15:42 olas you can do loadParseParse() if you like...
15:42 egonw that will load it again?
15:42 olas jonalv: then please explain it to me tomorrow
15:42 egonw that would do
15:42 olas egonw: I hope so
15:43 egonw what class does that have?
15:43 egonw that is...
15:43 olas IBioresource newResource=oldResource.loadParseParse();
15:43 egonw which class provides that method
15:43 olas that should do it
15:43 olas the BioResource itself
15:43 jonalv olas: I will try but I am not sure I have fully grokked it yet
15:43 olas from memory
15:43 olas okidok
15:44 olas egonw: Should we use the latest Jmol in the new Bioclipse2?
15:44 egonw modelFile.getBioResource() does not have loadParseParse()
15:44 egonw olas: yes
15:44 egonw 11.3 branch
15:44 olas does the adaptor work with it?
15:44 egonw to be release next month
15:44 egonw no idea
15:44 egonw likely not
15:44 olas can you give me a jar?
15:44 olas oh, nevermind
15:44 olas will use old one now
15:44 egonw let's do the same svn:externals trick
15:44 olas to get things working
15:44 egonw OK
15:45 olas a copy will be just fine
15:45 egonw make sure to make it an Editor along you go
15:45 olas doing that
15:45 egonw great
15:46 egonw olas: do you mean loadParseParseTypes() ?
15:48 egonw OK, one bug down
15:48 olas Yes
15:48 olas that's the one
15:48 CIA-18 bioclipse: egonw * r4290 /trunk/plugins/net.bioclipse.spectrum/src/​net/bioclipse/model/SpectrumResource.java: NPE debugging is *impossible* if all exceptions are silently catched and disregarded... I hate any language that allows that
15:49 CIA-18 bioclipse: egonw * r4291 /trunk/plugins/de.ipbhalle.msbi.mzd​ata.editor/src/de/ipbhalle/msbi/Mzd​ata/presentation/MzdataEditor.java: Fixed switching from TextEditor to MzdataEditor
16:03 edrin left #bioclipse
16:04 egonw f**ck f**ck f**ck f**ckf**ck
16:04 egonw I hate Eclipse
16:05 egonw horrible platform
16:05 jonalv :) what is it now?
16:05 masak please sir, calm down
16:05 egonw the useless idiot who made th design decision that Eclipse RCP should disregard the stacktrace of null pointer exceptions ...
16:06 * masak does not like `null` much in general
16:06 jonalv eh? it disregards?
16:06 jonalv null is evil and should be avoided at all costs
16:06 masak seems to much to make nothingness a value in the first place
16:06 masak go null-less programming! :)
16:06 CIA-18 bioclipse: egonw * r4292 /trunk/plugins/ (5 files in 2 dirs): More NPE debugging, but no trace of the source :(
16:11 olas have you added -consoleLog to program arguments?
16:12 egonw no
16:12 egonw which idiot decided not to make that the default !?!?!?
16:12 egonw :)
16:13 masak egonw: probably someone who decided that log output is not a majority concern
16:14 egonw and which idiot decided that this should not be on the front page if the Bioclipse wiki ?!?!?!
16:14 egonw olas: was that you?
16:14 egonw damn useful cmd line option
16:14 masak egonw: is there a difference in tone between "!?!?!?" and "?!?!?!" ?
16:15 * egonw heads over to the wiki to create a NullPointerExceptionHorror wiki page
16:15 * jonalv ducks in case egonw comes back...
16:15 masak OutOfPatienceException
16:17 * olas is afraid
16:17 egonw http://wiki.bioclipse.net/index.php​?title=NullPointerException_Horror
16:17 masak :)
16:18 CIA-18 bioclipse: ospjuth * r4293 /branches/bioclipse2/core/plugins/net.bi​oclipse.ui/src/net/bioclipse/ui/editors/ (14 files in 3 dirs): Added old PDBEditor and KeywordEditor
16:18 CIA-18 bioclipse: ospjuth * r4294 /branches/bioclipse2/core/​plugins/net.bioclipse.ui/ (3 files in 2 dirs): Got logger working for other plugins as well
16:19 CIA-18 bioclipse: ospjuth * r4295 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.jmol/: Initial import.
16:20 CIA-18 bioclipse: ospjuth * r4296 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.jmol/ (19 files in 9 dirs): Initial import. Only dummy editor working so far.
16:47 olas egonw: around?
16:47 CIA-18 bioclipse: ospjuth * r4297 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.jmol/ (10 files in 4 dirs): Work on a MPE with Jmol on first tab and source on second. Does not work due to errors with CdkJmolAdapter. Egonw: Help!
16:47 olas I need help with the CdkJmolAdapter. Must be due to new CDK version in bioclipse2
16:47 egonw what's the error?
16:47 olas Could you check out /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.jmol/ and see if you can fix it?
16:47 egonw if it's a NPE. you'r on your own :)
16:48 egonw no, not now
16:48 olas no, a compile error
16:48 olas constructor not defined
16:48 egonw still stuggling with a stupid EMF upgrade bug
16:48 olas jmolViewer = createViewer(new SmarterJmolAdapter()); SmarterJmolAdapter not found
16:48 olas just some compile errors
16:48 olas When you have the time then
16:49 egonw those adapters were in the plugin itself
16:49 olas hmm
16:49 olas the smarter as well?
16:49 * olas is looking
16:49 olas no
16:49 olas not SmarterJmolAdapter
16:50 olas and constructor for JmolAdapter has changed
16:50 olas No hurry
16:50 olas when you have the time
17:03 CIA-18 bioclipse: egonw * r4298 /trunk/plugins/de.ipbhalle.msbi.mzd​ata.editor/src/de/ipbhalle/msbi/Mzd​ata/presentation/MzdataEditor.java: OK, getString() is broken, but don't complain about it. As I hate these NPEs, hiding a few more wont hurt :)
17:05 rojasm left #bioclipse
17:05 masak egonw++ # writing commit comments which are really excuses
17:11 egonw olas: I got 10 minutes
17:14 egonw olas: which jar you got downloaded?
17:15 egonw no, I think we need to talk with Bob about this
17:16 egonw OK, have to head home now
17:19 masak who's Bob?
17:26 jonalv Micrososft Bob?
17:26 * masak shudders involuntarily
17:26 masak ...and I've never even seen MS Bob
17:28 jonalv okey people wiht litle time and need to know something about Spring + ERCP check this presentation: <http://www.martinlippert.org/events/​SpringOne2007-Spring-EclipseRCP.pdf>
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18:22 CIA-18 bioclipse: jonalv * r4299 /branches/bioclipse2/core/plugi​ns/net.bioclipse.spring.osgi/: Initial import.
18:22 CIA-18 bioclipse: jonalv * r4300 /branches/bioclipse2/core/plug​ins/net.bioclipse.spring.osgi/ (18 files in 10 dirs): Initial import.
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