Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-02-10

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All times shown according to UTC.

Time Nick Message
01:06 CIA-55 bioclipse: edrin_t * r8700 /bioclipse2/trunk/plugins/ (5 files in 3 dirs): fixed all manager functions. stuff now put in "Webservices" folder
05:34 CIA-55 bioclipse: egonw * r8701 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Wrap getContents() in a BufferedInputStream so that mark/reset works (addresses #439)
05:34 zarah bug #439 | http://tinyurl.com/c2tmvk
05:57 CIA-55 bioclipse: egonw * r8702 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Code cleanup: reuse of code; now returns 'Unknown' if format is not recognized
05:57 CIA-55 bioclipse: egonw * r8703 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Moved NULL check to correct location (fixes #435)
05:57 zarah bug #435 | http://tinyurl.com/b73ufz
06:59 masak joined #bioclipse
07:14 rojasm joined #bioclipse
07:29 Gpox joined #bioclipse
07:35 Gpoks joined #bioclipse
07:38 sneumann joined #bioclipse
07:41 CIA-55 bioclipse: goglepox * r8704 /bioclipse2/trunk/plugins/net.bioclipse.i​nchi.business.test/META-INF/MANIFEST.MF: Changed for net.bc.inchi.business to net.bc.inchi in net.bc.inichi.business.test
07:52 CIA-55 bioclipse: goglepox * r8705 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MoleculesEditorLabelProvider.java: Made 'Generated' text half the size in MoleculesTable
08:05 rojasm joined #bioclipse
08:09 CIA-55 bioclipse: goglepox * r8706 /bioclipse2/trunk/plugins/net.biocli​pse.cdk.ui/src/net/bioclipse/cdk/ui/​views/MoleculeContentProvider.java: Limit use of SDFElement in CN for large files
08:10 CIA-55 bioclipse: goglepox * r8707 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui/src​/net/bioclipse/cdk/ui/model/MoleculesFromSDF.java: Removed use of BioclipseStore for MoleculesFromSDF
08:11 CIA-55 bioclipse: goglepox * r8708 /bioclipse2/trunk/plugins/n​et.bioclipse.cdk.business/ (2 files in 2 dirs): Removed use of BioclipseStore and Node in CDKAdapterFactory
08:15 egonw joined #bioclipse
08:18 egonw moin
08:18 zarah privet egonw
08:41 masak egonw: ping
08:42 egonw pong
08:42 masak egonw: time for a short meeting over here :)
08:42 egonw ok
09:28 sneumann_ joined #bioclipse
09:32 edrin joined #bioclipse
09:34 jonalv joined #bioclipse
09:34 jonalv oh hai
09:34 zarah hi jonalv
09:34 edrin hi
09:34 zarah edrin: where have you been? I've been worried.
09:34 masak moin
09:34 zarah privet masak
09:40 edrin huh?
09:44 masak edrin: she's just being silly.
09:48 egonw masak: please remove that one... too personal
09:49 masak egonw: agree. removing.
09:58 CIA-55 bioclipse: carl_masak * r8709 /bot/trunk/zarah.pl: [zarah] removed 'where have you been' greeting
09:58 CIA-55 bioclipse: carl_masak * r8710 /bot/trunk/zarah.pl: [zarah] now doesn't greet people back if they spoke recently
09:58 masak zarah: restart, dear.
09:59 zarah joined #bioclipse
09:59 masak @plan bc2/console-egonw..
09:59 zarah masak: Syntax: @plan <task name> <number>h
10:00 masak @plan old bc2
10:00 zarah masak: bc2/console-egonw-single-line-refactor: 2 h planned, 2 h 25 m elapsed
10:00 zarah masak: bc2/managerdocs-finder: 1 h 30 m planned, 1 h 52 m elapsed
10:00 zarah masak: bc2/managerdocs-finder-html-skin: 1 h 15 m planned, 1 h 30 m elapsed
10:00 zarah masak: bc2/scriptconsole-backspace-bug: 30 m planned, 2 m elapsed
10:00 zarah masak: bc2/scriptconsole-literal-tab-bug: 30 m planned, 15 m elapsed
10:00 CIA-55 bioclipse: egonw * r8711 /bioclipse2/trunk/plugins/net.biocl​ipse.core.tests/src/net/bioclipse/c​ore/tests/AbstractManagerTest.java: Commented out methods that still expect the @Job annotation: not removed, because they have to be rewritten
10:14 edrin joined #bioclipse
10:14 edrin no ola today?
10:26 egonw he's here...
10:26 egonw working hard on bug fixes for BC2 RC1
10:48 olass joined #bioclipse
10:52 egonw olass: I commited a fix for the AbstractManagerTest
10:52 olass saw that
10:52 olass good
10:52 olass (for now)
10:52 egonw please verify that it compiles for you too
10:52 olass ok
10:53 egonw yes, bug report stands
10:53 olass lunch?
10:53 olass (I have a box)
10:53 egonw same here
10:53 olass now?
10:53 egonw and it is almost empty
10:53 egonw ok
10:53 olass lol
10:53 egonw can use a chocolate
10:53 egonw and a break
11:01 edrin hi olass
11:01 edrin olass: i updated webservice plugin
11:01 edrin olass: i tried to run the test
11:02 edrin something run, and failed, but not sure if i did it correct
11:02 edrin it took me 2 h just to check out the billions of cdk plugins required to run the plugin
11:34 olass edrin: blame egonw
11:34 olass :-)
11:34 masak joined #bioclipse
11:34 olass edrin: I agree it is not perfect for webservice plugin to depend on cdk
11:35 olass on the other hand, post 2.0 we will redesign the entire service infrastructure
11:35 olass so things will change then anyways
11:38 egonw anyone here with experience with the eclipse PyDev plugin?
11:40 maclean joined #bioclipse
11:41 CIA-55 bioclipse: goglepox * r8712 /bioclipse2/trunk/plugins/net.bi​oclipse.logger/log4j.properties: Changed logging to rolling 5 files 3MB each
11:42 CIA-55 bioclipse: goglepox * r8713 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui/src​/net/bioclipse/cdk/ui/model/MoleculesFromSMI.java: Use CdkManager.loadSMILESfile() to load .smi files
11:47 masak egonw: you gave me #443 not long ago. I can look at it, but I didn't write the biomoby plugin.
11:49 edrin olass: does the webservice test works for you?
11:50 olass have not tried them again
11:50 olass will do later today
11:50 edrin ok
11:50 egonw masak: that's because you are the bioinformatics dude
11:50 olass edrin: please reassign the bug to me when you want my input on something
11:50 edrin at least, i think the plugin should be ok now
11:50 egonw masak: I did not give it to you... Pele actually did...
11:50 olass edrin: my bug list is my todo list for bioclipse
11:50 olass so no bug -> I might miss it
11:51 egonw all bioinformatics bugs automatically go to you for deciding who is to blame for that bug
11:51 egonw masak: likewise, cheminfo bugs automatically go to me
11:51 egonw and bioclipse core bugs to ola
11:51 olass and core to me
11:51 olass :-)
11:51 egonw :)
11:51 olass @botsnack
11:51 zarah ;)
11:52 masak egonw: I thought something like that might be the case. reassigning.
12:07 egonw olass: did not see Sam was not in the list...
12:07 egonw forwarded the message myself
12:07 olass ack
12:10 CIA-55 bioclipse: ospjuth * r8714 /bioclipse2/trunk/plugins/net.bioclipse​.scripting.ui/src/net/bioclipse/scripti​ng/ui/views/ScriptingConsoleView.java: Added SWT.BORDER to the Text widgets in ScriptingConsoleView. Now it is clearer to me where input and output goes.
12:14 masak egonw: sorry, I actually understood your comment above ('I did not give it to you... Pele actually did...') as meaning that you actually wanted the bug. my mistake.
12:15 masak olass: did you write the biomoby plugin?
12:15 egonw masak: ah, ic...
12:15 olass yes
12:15 masak olass: reassigning to you then.
12:15 olass ok
12:15 * olass have no idea what this is about
12:19 egonw talk plural again?
12:20 masak royal "we"
12:20 egonw olass: which house near Stkhm did you buy again?
12:20 egonw the one on the island just south of the railway station?
12:21 masak "an apartment with a moat?! WTF?"
12:21 egonw next to that large parking place and the water?
12:21 olass it's nothing, really. Just a small penthouse where we like to live
12:21 egonw with a nice spacious patio in the middle?
12:22 olass We very much enjoy the proximity to the water and the city
12:22 olass yes, and to ensure noone bothers us we have plenty of guards...
12:25 CIA-55 bioclipse: ospjuth * r8715 /bioclipse2/trunk/plugins/net.bioclipse​.scripting.ui/src/net/bioclipse/scripti​ng/ui/views/ScriptingConsoleView.java: Added code to propagate focus from output to input on click. Not sure if this is desired behaviour, so placed TODO for masak and commented on bug #262.
12:25 zarah bug #262 | http://tinyurl.com/b2vxgo
12:25 masak I'm not sure either.
12:26 masak but I will update and test it.
12:28 olass egonw: should cdk.debug really go in bioclipse release?
12:29 egonw maybe as CDK Feature
12:29 olass yes
12:29 olass now it is in chemoinfo feature
12:29 egonw ok, file an enhancement report
12:29 olass ok'
12:31 masak olass: no, that is not what we want. now you cannot copy from the output text field with keyboard shortcuts.
12:31 masak olass: really like the borders, though.
12:31 olass masak: right, suspected that
12:31 masak I have to figure out why the input box and the output text are not of the same width.
12:31 olass ok, bug is back to you
12:31 masak goodie.
12:32 masak I will start by doing a partial revert.
12:32 CIA-55 bioclipse: ospjuth * r8716 /bioclipse2/trunk/plugins/net.bioc​lipse.tests/META-INF/MANIFEST.MF: Now only contains references to tests in release 2.0.
12:33 masak egonw: now that the release is Thursday, will you still have your RDF talk on Thursday?
12:33 egonw no
12:33 masak what's the new date and time?
12:34 olass ?
12:34 * masak looks forward to that talk
12:34 olass wednesday was it, right?
12:34 egonw masak: I will still have the talk on Wednesday
12:34 olass wed at 13?
12:34 masak oh.
12:34 egonw 13:15, I think
12:34 * masak thought that was a meeting with Jarl
12:34 olass egonw: 13 is better for me
12:34 masak but maybe that was 14.15
12:34 olass (and you)
12:35 olass but ok, 13.15 is fine
12:37 masak olass: before I revert, do you have a story behind the commented-out code you committed? I'd like to know because it seems like a better solution than the one you actually decided on.
12:37 egonw olass: talk is scheduled 13:15-14:15
12:37 olass masak: no, it was my first try
12:37 olass wipe it
12:37 egonw 30 minute talk, 30 minute discussion
12:37 olass :-(
12:37 olass ok
12:37 masak olass: sure, but -- why didn't it work?
12:38 olass masak: no idea
12:38 masak olass: it does look better.
12:38 olass thought so too
12:38 olass try it if you like
12:38 * masak tries it if he likes
12:52 CIA-55 bioclipse: jonalv * r8717 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): fixes bug #321 (I hope)
12:52 zarah bug #321 | http://tinyurl.com/dgme6t
12:53 CIA-55 bioclipse: jonalv * r8718 /bioclipse2/trunk/plugins/net.bioclip​se.scripting/src/net/bioclipse/script​ing/business/JSJobCreatorAdvice.java: fixes bug #422 (I hope)
12:53 zarah bug #422 | http://tinyurl.com/bh2sj7
12:53 egonw "I hope"?
12:53 egonw isn't that easy to check?
12:54 jonalv the reported problem seems to work
12:57 masak is that good or bad? :)
13:04 * egonw hates to see problems still work fine
13:06 CIA-55 bioclipse: goglepox * r8719 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MoleculeTableContentProvider.java: Fixes NPE when opening .smi
13:06 olass masak: for inspiration: http://commons.wikimedia.org​/wiki/Category:Science_icons
13:06 zarah olass's link is also http://tinyurl.com/abajld
13:07 * masak feels inspired
13:10 CIA-55 bioclipse: goglepox * r8720 /bioclipse2/trunk/plugins/net.bioclipse.cdk.u​i.sdfeditor/src/net/bioclipse/cdk/ui/sdfedito​r/editor/MultiPageMoleculesEditorPart.java: Removed single-2D page (fixes bug #446)
13:10 zarah bug #446 | http://tinyurl.com/cm2kl7
13:12 olass @pz transparen
13:12 zarah [444] Make image bioclipse.png in net... http://tinyurl.com/be57c3
13:12 zarah [45] Bioclipse system icons              http://tinyurl.com/bxxc9k
13:12 zarah Entire list at http://tinyurl.com/afaqnx
13:13 CIA-55 bioclipse: ospjuth * r8721 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (7 files in 5 dirs):
13:13 CIA-55 bioclipse: Intro updates:
13:13 CIA-55 bioclipse: * Go to update site action implemented with nice icons (solves bug #344)
13:13 CIA-55 bioclipse: * Branding image added (filed bug #444 for setting bg transparent)
13:13 zarah bug #344 | http://tinyurl.com/ajdpxh
13:13 zarah bug #444 | http://tinyurl.com/be57c3
13:46 CIA-55 bioclipse: ospjuth * r8722 /bioclipse2/trunk/plugins/net​.bioclipse.ui/bioclipse.png: Added bioclipse.png for intro page.
13:46 olass jonalv: done
13:46 olass jonalv: di
13:47 olass jonalv: did
13:47 olass jonalv: did that
13:47 jonalv oki
13:47 * olass likes the sound of jonalvs icr client through the wall
13:47 olass icr=irc
13:48 egonw olass: who made that PNG?
13:49 egonw is it EPL?
13:49 egonw if CC or GNU FDL, it could show up on wikipedia/bioclipse
13:49 olass it's MINE
13:49 olass my own
13:49 olass ... my precious ...
13:49 egonw good...
13:50 egonw can you upload the image to WP?
13:50 egonw than we can add it to the Bioclipse page
13:50 olass sure thing
13:50 olass file me a bug :-)
13:53 CIA-55 bioclipse: ospjuth * r8723 /bioclipse2/trunk/plugins/net.bioclipse​.webservices/src/net/bioclipse/webservi​ces/business/IWebservicesManager.java: Made downloadPDB unpublished since CDK cannot parse PDBs in Bioclipse (yet).
14:06 olass maclean: are you looking at the flickering on windows?
14:06 maclean no
14:06 olass I guess we sort of need to identify the problem
14:06 maclean yes
14:07 olass I will file a bug
14:07 maclean I don't have much experience with SWT graphics
14:07 olass same here
14:08 maclean although, in general, some kind of offscreen buffer might be in order
14:15 olass maclean, Gpox: bug #451 filed as blocker
14:16 maclean @bug 451
14:16 maclean hmmm
14:16 zarah http://tinyurl.com/b4c8sl
14:16 CIA-55 bioclipse: goglepox * r8724 /bioclipse2/trunk/plugins/net.bioc​lipse.core/src/net/bioclipse/core/ (10 files in 2 dirs): Removed ui.filesystem and internal.zip from net.bioclipse.core bug #398
14:16 maclean ah
14:16 zarah bug #398 | http://tinyurl.com/bfdwsh
14:31 CIA-55 bioclipse: ospjuth * r8725 /bioclipse2/trunk/plugins/net.bioclipse.ui/src/ne​t/bioclipse/ui/ApplicationActionBarAdvisor.java: Lowered menu placing CheatSheets in help menu a few steps.
14:33 shk3 joined #bioclipse
14:40 steinbeck joined #bioclipse
14:40 egonw hi steinbeck
14:40 steinbeck Cheers
14:48 olass hi steinbeck
14:49 steinbeck Hi olass
15:00 masak anyone have any experience with downloading JDK for Windows?
15:00 masak I'm hopelessly lost on Sun's site right now.
15:00 masak it appears that I need Java to be able to download Java...
15:01 maclean doesn't windows come with a jvm?
15:02 masak maclean: I have no idea. but Firefox doesn't seem to think that I have Java installed.
15:02 maclean oh
15:02 maclean weird
15:02 masak I have "Enable Java" checked.
15:03 masak oh, and I underestimated how much I would hate being back in Windows. :)
15:03 maclean :}
15:03 masak it has actually gotten _worse_ since I stopped using it seven years ago.
15:05 masak I've turned off the sounds, the "cute" candy color scheme, the helpful dialog boxes and the automatic updates. which means I have a chance to use it for actual work.
15:05 maclean heh
15:05 masak but so far I haven't been able to download Java.
15:05 maclean the sun site is detecting my osx, so I can't see what steps you would use. I could boot up this xp machine, of course..
15:06 * masak reads troubleshooting FAQ
15:08 masak I see a file called jdk-6u12-windows-x64-p.exe -- that's the Java SE Development Kit 6u12. That's "Release 6, Update 12"
15:09 masak it's 64.39 MB, which seems too small to me, but what do I know?
15:09 masak I can save this file, but Windows doesn't want to acknowledge it as an executable.
15:10 egonw note that it is likely a 64bit version...
15:10 masak aye.
15:10 masak I thought this was a 64-bit computer.
15:11 masak egonw: but it's a good implicit suggestion, I'll try the 32-bit version and see if I fare any better.
15:12 masak ah, and the error message actually says "not a Win32 app", so that should be it.
15:14 masak that worked. egonw++
15:21 CIA-55 bioclipse: jonalv * r8726 /bioclipse2/trunk/plugins/net​.bioclipse.ui/bioclipse.png: Made the Bioclipse B transparent. fixes bug #444
15:21 zarah bug #444 | http://tinyurl.com/be57c3
15:22 egonw what is 'B transparent' ?
15:22 masak egonw: no, it's a "Bioclipse B"
15:22 egonw ah, ic :)
15:23 jonalv hehe
15:23 egonw olass: ping
15:23 olass pong
15:23 egonw already got 3 replies from the Jmol community on GROMACS use
15:23 egonw there seems reasonable support for GROMACS in Jmol...
15:23 olass ok
15:24 egonw forwarded the two most interesting ones
15:27 maclean "In a bold move today, the Gromacs developers finally decided not to wait for Duke Nukem Forever before releasing Gromacs 4.0, and just put out release candidate 1.."
15:27 maclean :)
15:28 masak maclean: in the Perl 6 community, there are lots of opportunities to get to know variants of that joke.
15:28 maclean heh
15:29 maclean Also: release by Christmas.
15:29 masak aye, but that one's ours.
15:29 masak makes a difference.
15:39 olass egonw: I'm on the jmol list
15:40 egonw ack
15:43 CIA-55 bioclipse: ospjuth * r8727 /bioclipse2/trunk/plugins/net.​bioclipse.ui/introContent.xml: Removed deprecated intro content file.
15:44 * egonw is leaving to go home
15:44 CIA-55 bioclipse: ospjuth * r8728 /bioclipse2/trunk/plugins/net.bioclipse.ui/intro/ (19 files in 3 dirs): Pimped the welcome page with icons.
15:46 egonw Pimp my Bioclipse
15:46 egonw nice title for an award scheme for bioclipse
15:54 CIA-55 bioclipse: ospjuth * r8729 /bioclipse2/trunk/plugins/​net.bioclipse.data/intro/ (5 files in 3 dirs): Pimped intro page for data plugin.
15:56 CIA-55 bioclipse: jonalv * r8730 /bioclipse2/trunk/plugins/net​.bioclipse.ui/bioclipse.png: downsized the "Bioclipse B" logo
15:56 masak getting the following exception when trying to start Bioclipse in Eclipse in Windows: http://gist.github.com/61435
15:56 masak anyone had that?
16:00 masak problem solved. solution: save the product file.
16:28 CIA-55 bioclipse: ospjuth * r8731 /bioclipse2/trunk/plugins/net.bioc​lipse.data/src/net/bioclipse/data/​wizards/NewDataProjectWizard.java: Set Sample Data as default name for data projects. Solves bug #401.
16:28 zarah bug #401 | http://tinyurl.com/cujalo
16:28 edrin masak: could you solve the bug with the line break in the console?
16:28 masak edrin: I was just looking at it.
16:29 masak edrin: for the first time ever, I can confirm it on my box.
16:29 edrin and did you think about the "dynamic ClassLoader issue"
16:29 masak edrin: sure did, and we discussed it at the office.
16:29 edrin masak: shk3 did not reproduce it on his OS
16:29 masak which OS is that?
16:30 edrin dunno, linux?
16:30 masak no, it only appears on Windows, I think.
16:30 maclean linux
16:30 maclean er, I mean, that is shk3's os
16:30 masak right.
16:31 edrin masak: i still did not figure out why the DynamicImport-Packages: * does not work... it should, Spring even supports/discusses this. and it partially seems to work, as i have seen the plugin to use various rhino runtimes, confusion, thus it should work...
16:32 masak edrin: generally, I think what you want to do should be done inside managers.
16:32 edrin it could be that the classloader used by the plugin at runtime is slightly different from the ClassLoader used when running the script context
16:33 masak possibly.
16:33 edrin masak: i think it's not what I want to do, it is what I must to do
16:33 masak someone's forcing you to include other namespaces into js?
16:33 edrin and unfortunately it is not possible with the javascript syntax
16:34 masak edrin: maybe another scripting language on the JVM, then?
16:35 edrin well, we would not even need rhino javascript engine, if we do not have the possibility to use it's power, when being limited to the "manager only" concept
16:35 masak edrin: I disagree.
16:35 edrin why another scripting language?
16:35 masak js still buys us a lot, even if we only use it through managers.
16:36 masak edrin: you said the js syntax was not enough. other scripting languages have more permissive syntax.
16:36 edrin the js syntax is enough, if you can use Packages
16:36 edrin you can use Packages
16:37 maclean there are languages with more permissive syntax than js?
16:37 masak maclean: oh yes.
16:37 masak maclean: js is actually quite conceptually clean, after all.
16:37 masak but the semicolon thing was a mistake, IMHO.
16:37 edrin but we must have a way to provide Packages to the js Packages(ClassLoader) from the plugins
16:38 masak edrin: I'm not sure I've fully understood your need to have Packages available in the js env yet.
16:38 masak given that, it's difficult for me to emphasize with your proposed solutions, which seem very cumbersome and tricky.
16:39 edrin that's because you never tried to write a script that uses objects from Java interfaces
16:39 masak edrin: possibly.
16:39 masak could you show me such a script?
16:39 masak I want to understand what it is you can't do.
16:40 edrin masak: another example is cdk, you could use cdk in js fully, but only if you do what I say
16:40 edrin masak: sure
16:40 masak edrin: we're not aiming for full access, we're aiming for a useable product to as many users as possible.
16:41 jonalv edrin: who is the target user for this?
16:42 jonalv It sounds very complicated... Like something that you might as well do in Java using Eclipse and some Bioclipse plugins
16:42 * masak agrees
16:43 edrin js> obj = { run: function () { print("\nrunning"); } }
16:44 edrin js> r = new java.lang.Runnable(obj);
16:44 edrin from http://www.mozilla.org/rhino/ScriptingJava.html
16:44 zarah edrin's link is also http://tinyurl.com/5tb29w
16:44 edrin section:"Implementing Java interfaces"
16:44 masak ok, that seems like a reasonable example.
16:44 masak I can imagine wanting to do that.
16:44 * olass will run to the train now
16:44 edrin jonalv: writing javascripts is not restricted to javascript console
16:44 olass bye
16:44 masak olass: hasta la vista!
16:45 jonalv edrin: I have never claimed that you must stay in the console
16:45 jonalv but this is not working?
16:45 masak edrin: I'm all for importing the interfaces from java.lang
16:45 masak that seems like a reasonable thing to do
16:45 masak but maybe we should hide them in the tab completion.
16:46 Gpox joined #bioclipse
16:46 jonalv edrin: Do you have any contact with the rhino people? Maybe they can help?
16:46 edrin jonalv: ok, in a script you will most likely stumble on this interface issue
16:46 jonalv not if you "only use managers"
16:46 edrin jonalv, masak: the example i showed you is working of course, because java.lang is in the classloader of course
16:47 CIA-55 bioclipse: goglepox * r8732 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/outline/CDKChemObject.java: Added equals and hashCode to CDKChemObject both uses IChemObject for comparing.
16:47 masak edrin: good.
16:47 edrin but as soon as you want to use an interface of one of the cool libs some of us are developing you cannot do this because they are not in rhino's classloader
16:48 masak edrin: but then your example was insufficient to make me understand why you need this.
16:48 CIA-55 bioclipse: goglepox * r8733 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/outline/JCPOutlinePage.java:
16:48 CIA-55 bioclipse: JCPOutline now reacts on selections from active editor
16:48 CIA-55 bioclipse: and updates internal tree viewer accordingly
16:48 edrin target users are me, egon, dunno who else right now
16:48 CIA-55 bioclipse: goglepox * r8734 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java: Selections form outline is now turned into real selections in JCP editor
16:48 edrin i need it to show the listener/async concept of rhino
16:48 masak edrin: if your example works, it's not and example of something you'd like to see working.
16:49 CIA-55 bioclipse: goglepox * r8735 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.jchempaint/plugin.xml:
16:49 CIA-55 bioclipse: Added 'Add Hexagon' to popupmenu for JChemPaint
16:49 CIA-55 bioclipse: and added property definition to debug
16:49 CIA-55 bioclipse: goglepox * r8736 /bioclipse2/trunk/cdk-externals/trunk/org.ope​nscience.cdk.render/src/org/openscience/cdk/r​enderer/generators/HighlightGenerator.java: Draws bond highlight as a oval
16:49 edrin masak: what does this mean?
16:50 masak edrin: it means that your example was not a very good one.
16:50 masak edrin: you need to show me something that you _want to work_.
16:50 masak not something that already works.
16:50 CIA-55 bioclipse: goglepox * r8737 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.jchempaint/plugin.xml:
16:50 CIA-55 bioclipse: Added core.experessions.definitions for selected atoms and bonds.
16:50 CIA-55 bioclipse: Updated existing menu items to use definition.
16:50 CIA-55 bioclipse: fixes bug #327
16:50 zarah bug #327 | http://tinyurl.com/bc5m2x
16:50 masak remember, the end goal here was to make me understand why you want to fiddle with class loaders and stuff.
16:50 edrin masak: i am talking about interfaces in general
16:51 masak edrin: I'd like to see a specific example of when you'd need this.
16:51 masak edrin: olass++ has suggested that you make your case via an email to the Bioclipse list instead of trying by IRC, which might be less effective.
16:51 edrin to write some sample scripts
16:52 masak edrin: I don't understand that.
16:52 masak edrin: I can write some simple scripts, and I don't need a special class loader.
16:53 masak I'm sorry to be sinking into such sophistry, I'm just trying to protect the very product you want to complicate without providing adequate rationale.
16:54 edrin masak: look, if you want to write a cool script that uses the features of the scientifc lib you wrote, for example cdk, and then you share the script via gist, others can use it. but this makes sense of course only if you can use your lib from javascript. and to use your lib from javascript you must be able to access it from javascript
16:54 masak we use managers for that.
16:54 jonalv edrin: that's what we have managers for
16:55 jonalv edrin: but I must add. I am not against you making the other thing working as well
16:55 masak I am, so far.
16:55 jonalv I just don't see it important enough to spend my own time on it
16:55 edrin jonalv: but you cannot create/overload an object from an interface via a manager, at least i could not figure out how this should work
16:56 edrin jonalv: i did not say that you must spend your time to get this working
16:56 jonalv edrin: can't you use java lang runnable and callbacks?
16:56 jonalv her comes the dots: ...
16:56 jonalv :)
16:57 edrin jonalv: unfortunately not because my lib was not designed like this
16:57 edrin no lib is designed for rhino
16:57 edrin rhino must be designed to for the libs
16:57 jonalv it seems to me like your problem is with rhino...
16:57 jonalv have you considered asking the rhino people about this?
16:58 masak Bioclipse was designed to use rhino with managers.
17:01 shk3 shouldn't it be the day for a bioclipse release today?
17:02 jonalv shk3: I think it was postponed to thursday. some blokcker bugs...
17:03 shk3 ok
17:03 shk3 I will not be here thursday to monday
17:03 shk3 that means the speclipse update will need to wait till then
17:04 shk3 anything I can help with today and tomorrow?
17:05 jonalv honestly I don't know. I think we are on track. (I hope)
17:05 masak it's the most on track we've ever been, IMO.
17:10 shk3 great
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18:56 CIA-55 bioclipse: ospjuth * r8738 /bioclipse2/trunk/plugins/net.biocl​ipse.inchi.business/src/net/bioclip​se/inchi/business/Activator.java: Updated PluginID in Activator.
18:57 CIA-55 bioclipse: ospjuth * r8739 /bioclipse2/trunk/plugins/net.bioclipse.da​ta/src/net/bioclipse/data/Activator.java: Updated PluginID in Activator.
18:59 CIA-55 bioclipse: ospjuth * r8740 /bioclipse2/trunk/plugins/net.bioclips​e.data/src/net/bioclipse/data/samples/ (ExtendedSampleDataAction.java SampleDataAction.java): Made cancelled SampleDataInstallation operations behave nicely and extended them to work from introduction. Solves 452.
19:01 CIA-55 bioclipse: ospjuth * r8741 /bioclipse2/trunk/plugins/net.bioclipse.data/ (3 files in 2 dirs): WizardTitleImages in common wizards: Added sample wizardtitle in InstallDataWizard. Image needs updating. Bug #414 still open.
19:01 zarah bug #414 | http://tinyurl.com/d5ef6v
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22:49 Topic for #bioclipseis now An open source workbench for chem- and bioinformatics - http://www.bioclipse.net/ | BioclipseWiki => http://wiki.bioclipse.net/ !! | logs => http://colabti.org/irclogge​r/irclogger_logs/bioclipse & http://moritz.faui2k3.org/irc​log/out.pl?channel=bioclipse || Bioclipse2 beta released! See http://bioclipse.blogspot.com/

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