Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-08-22

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All times shown according to UTC.

Time Nick Message
05:23 egonw joined #bioclipse
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06:44 Gpox joined #bioclipse
07:13 malick joined #bioclipse
07:17 CIA-51 bioclipse: goglepox * r6696 /bioclipse2/trunk/plugins/net.bioclipse.cdk.ui/sr​c/net/bioclipse/cdk/ui/model/BuilderThread.java: Fixed Jobs not ending when canceled
07:39 jonalv joined #bioclipse
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08:06 maclean joined #bioclipse
08:12 CIA-51 bioclipse: ospjuth * r6697 /bioclipse2/trunk/plugins/net.bioclipse.qsar/ (3 files in 2 dirs): Exported activator and made descriptormodel accessible from the qsarmanager.
08:32 shk3 joined #bioclipse
08:34 CIA-51 bioclipse: shk3 * r6698 /bioclipse2/trunk/plugins/net.bioclipse.cd​k10.jchempaint/src/net/bioclipse/cdk10/jch​empaint/ui/editor/AbstractJCPEditor.java: avoids npe
08:38 CIA-51 bioclipse: ospjuth * r6699 /bioclipse2/trunk/plugins/net.bioclipse​.qsar/src/net/bioclipse/qsar/business/ (IQsarManager.java QsarManager.java): Implemented getDescriptorByCategory.
08:39 CIA-51 bioclipse: ospjuth * r6700 /bioclipse2/trunk/plugins/net.biocli​pse.qsar.test/src/net/bioclipse/qsar​/test/business/TestQsarManager.java: Tests for getDescriptorsByCategory.
08:41 maclean which plugins are required for the qsar stuff? net.bioclipse.qsar, and qsar.edit, but also...
08:42 olas maclean: doesnät work yet
08:42 olas but look in the qsar feature
08:42 maclean ohhh, right. thanks.
08:46 olas interested? :-)
08:46 olas I'll let you know when I have something working
08:46 olas right now it's only tests
08:46 maclean well, I was just curious as to what it does. I guess it's seeing the large number of commits. :)
08:47 olas haha
08:47 olas yes
08:47 olas Hope to have something tangible soon
08:47 maclean cool.
08:48 olas I need t owork on this, I am to present it in a month on a conference
08:48 olas so MUST have something at least :-)
08:49 maclean It can be good to have a get-it-working target.
08:54 jonalv yea, I am working on the datamodel ver 2 (with annotations)  for the structuredb project for the same reason... :)
08:54 jonalv (paper + pen)++
08:55 olas coffee++
09:02 thomas_ku joined #bioclipse
09:06 CIA-51 bioclipse: ospjuth * r6701 /bioclipse2/trunk/features/net.bi​oclipse.qsar_feature/feature.xml: Updated QSAR feature to include cdk.qsar.
09:06 CIA-51 bioclipse: ospjuth * r6702 /bioclipse2/trunk/plugins/net.biocl​ipse.qsar/src/net/bioclipse/qsar/de​scriptor/model/BaseEPObject.java: Handle case when no icon available.
09:07 CIA-51 bioclipse: ospjuth * r6703 /bioclipse2/trunk/plugins/net.bioclipse.q​sar.ui/src/net/bioclipse/qsar/ui/editors/ (5 files): DescriptorViewer is now populated from DescriptorModel and add/remove buttons correctly centered vertically.
09:20 olas @help
09:20 zarah olas: avaliable commands are boo clear-messages google help hi karma messages restart seen slap tell thanks
09:20 olas masak: @ask does not exist?
09:21 masak @ask olas I don't know, does it?
09:21 zarah Consider it noted.
09:21 masak olas: it does, but right now it's an exact synonym for tell
09:21 masak this will probably change
09:21 olas ok
09:21 zarah olas: You have new messages. Write '@messages' to read them.
09:21 olas ok
09:21 olas @clear
09:21 zarah olas: Messages cleared.
09:35 malick left #bioclipse
09:36 * jonalv <- lunch
09:45 CIA-51 bioclipse: ospjuth * r6704 /bioclipse2/trunk/plugins/net.bioclipse.ui/icons/ (alt_window_16.gif alt_window_32.gif source.gif): Removed unused logos.
10:12 CIA-51 bioclipse: ospjuth * r6705 /bioclipse2/trunk/plugins/net.bioclipse.qsar/ (4 files in 3 dirs): Added a basic propertySource for qsar items.
10:13 CIA-51 bioclipse: ospjuth * r6706 /bioclipse2/trunk/plugins/net.bioclipse.qsar.ui/ (8 files in 2 dirs): Added icons to descriptor view.
10:50 maclean Ack! Bioclipse is throwing off lots of errors about log4j - I moved my workspace, so it could be a library problem?
10:50 * jonalv <- back
10:51 shk3 hi jonalv
10:51 jonalv hi
10:51 zarah hi jonalv
10:52 shk3 I want to start having managers in the spectrum plugin
10:52 jonalv I think you should
10:52 shk3 shall I do an ISpectrum and work with that?
10:52 jonalv sounds like a plan
10:52 shk3 similiar to IMolecule and the cdkmolecule etc.?
10:52 jonalv yea
10:53 shk3 ok, I will try
10:53 jonalv if you think it fits
10:55 shk3 i think spectrum should be another basic object type
10:55 shk3 I will see how it works
10:56 jonalv sounds good
11:26 CIA-51 bioclipse: carl_masak * r6707 /bioclipse2/trunk/plugins/net​.bioclipse.biojava.ui/icons/ (6 files): [net.bioclipse.biojava.ui] added icons for different kinds of molecules
12:13 egonw joined #bioclipse
12:19 malick joined #bioclipse
12:23 olas hi egonw
12:23 olas egonw: need your help
12:24 olas you got my mail?
12:24 olas BO ontologies
12:24 olas I need it, and I need it NOW
12:24 olas can I download it and read it offline?
12:25 egonw yes, replied
12:25 olas just right now?
12:25 * olas has not received any mail
12:25 * egonw is outside with his laptop using a free FON.com network
12:25 egonw yes, a few minutes ago
12:26 egonw 14:14
12:26 egonw and 14:15
12:26 olas ok
12:26 egonw so, 10 mins ago
12:26 olas got your cdk reply
12:26 egonw the otherone is a minute behind
12:26 egonw ok, got to leafve
12:26 egonw it's starting to rain
12:26 egonw bye
12:26 olas bye
12:35 CIA-51 bioclipse: jonalv * r6708 /bioclipse2/trunk/plugins/ (31 files in 12 dirs): [Structuredb] Wrote domain tests for annotations
12:37 CIA-51 bioclipse: ospjuth * r6709 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk.qsar.test/: Initial import.
12:39 CIA-51 bioclipse: ospjuth * r6710 /bioclipse2/trunk/plugins/n​et.bioclipse.cdk.qsar.test/ (15 files in 9 dirs): Initial structure and tests for CDKs descriptor calculations.
12:48 maclean joined #bioclipse
12:59 CIA-51 bioclipse: jonalv * r6711 /bioclipse2/trunk/plugins/ (7 files in 2 dirs): [Structuredb] Wrote domain tests for properties
13:09 CIA-51 bioclipse: ospjuth * r6712 /bioclipse2/trunk/plugins/net.bioclipse.qsa​r/src/net/bioclipse/qsar/descriptor/model/ (7 files): Extended propertysources for descriptor model object.
13:29 CIA-51 bioclipse: ospjuth * r6713 /bioclipse2/trunk/plugins/ (5 files in 5 dirs): Added "definition" field in descriptor, to match Blue Obelisk descriptor ontology.
13:38 malick joined #bioclipse
13:41 CIA-51 bioclipse: ospjuth * r6714 /bioclipse2/trunk/plugins/ (5 files in 5 dirs): Added descriptor attribute 'description' with tests.
13:48 malick left #bioclipse
13:50 CIA-51 bioclipse: carl_masak * r6715 /bot/trunk/zarah.pl: [zarah] repaired regular expression which checks for jonalv's keyboard layout
13:50 zarah joined #bioclipse
13:54 CIA-51 bioclipse: carl_masak * r6716 /bot/trunk/zarah.pl:
13:54 CIA-51 bioclipse: [zarah] actually fixed regular expression which checks for jonalv's
13:54 CIA-51 bioclipse: keyboard layout
13:54 zarah joined #bioclipse
13:55 jonalv You can read books but you can not read meat.
13:55 jonalv right...
13:55 jonalv very much friday...
13:59 masak jonalv: maybe you should start talking about Raelians instead.
13:59 jonalv Raelians? what's a raelian?
13:59 zarah jonalv: C-u C-\ swedish-postfix RET
13:59 masak haha
14:02 masak jonalv: not sure you really want to know, but http://en.wikipedia.org/wiki/Ra%C3%ABlism
14:02 zarah masak's link is also http://tinyurl.com/6374yv
14:03 masak their symbol is a David's star with a swastika in it
14:04 maclean Or perhaps timecube?
14:04 CIA-51 bioclipse: ospjuth * r6717 /bioclipse2/trunk/plugins/ (6 files in 5 dirs): Refactored out Parameters as a class, and gace it an attribute "description" to describe the parameter.
14:13 CIA-51 bioclipse: jonalv * r6718 /bioclipse2/trunk/plugins/net.bioclipse.struc​turedb/src/net/bioclipse/structuredb/domain/ (11 files): [structuredb] made domain tests pass
14:32 CIA-51 bioclipse: gilleain * r6719 /bioclipse2/trunk/plugins/net.bioc​lipse.data.sampledata/plugin.xml: The sequence and spectra directories were not referenced
14:34 maclean stephan : you also have to remove/re-add the sample project from within bioclipse to see those directories.
14:52 olas maclean: that was on purpose!
14:52 maclean Oh.
14:52 maclean Sorry.
14:53 olas They will be re-added when we actually have functionality for it in the releases
14:53 maclean Ohhhh. right.
14:53 maclean Ooops.
14:53 olas no worries
14:53 olas but please revert
14:56 CIA-51 bioclipse: gilleain * r6720 /bioclipse2/trunk/plugins/net.bioc​lipse.data.sampledata/plugin.xml: Reverted forbidden change.
14:56 maclean By the way, I like the scripting very much (especially tab-completion!)
14:57 maclean However, I get these non-printable characters on windows (boxes).
14:57 maclean I can't work out why yet.
14:57 masak maclean: when you do, please submit a bug report
14:57 masak and I'll try to fix it, despite not being on Windows
14:58 maclean Okay. I could just randomly change things and then check them in, if you prefer (joking, joking :).
14:59 masak olas: we should have a WrathBot that puts severe curses on people who break style guidelines in source :)
15:00 maclean Like aligned semicolons? Or k&r style brackets? I have seen some ... interesting ... code recently.
15:02 maclean And by 'recently' I mean recent to me - much of it is very old code.
15:02 masak maclean: actually, I can endure most styles, as long as they're internally consistent
15:04 maclean Hmmm. I am very intolerant when it comes to code. But I'm trying not to be.
15:05 masak of course, the world would be a brighter place if everyone just adhered to my coding style :)
15:05 shk3 I did a manager in the spectrum plugin
15:06 shk3 what do I need to do to make it work on the console?
15:06 masak shk3: register it in the plugin.xml file
15:06 shk3 tab completion does not give my new name
15:06 masak see some plugin that's already registered
15:06 shk3 ah, sorry, looked in the wrong plugin.xml
15:07 shk3 had the suspicion, but couldn't find anything
15:07 shk3 no wonder if it's the wrong one
15:18 CIA-51 bioclipse: carl_masak * r6721 /bioclipse2/trunk/plugins/net.bioclipse.​biojava.ui/src/net/bioclipse/biojava/ui/ (4 files in 2 dirs):
15:18 CIA-51 bioclipse: [net.bioclipse.biojava.ui] zooming now works
15:18 CIA-51 bioclipse: two known issues:
15:18 CIA-51 bioclipse: * selections are b0rked after zooming.
15:18 CIA-51 bioclipse: * vertical scrolling only affects the sequences,
15:18 CIA-51 bioclipse:  not the sequence names
15:26 CIA-51 bioclipse: shk3 * r6722 /bioclipse2/trunk/plugins/net.bioclipse.spectrum/ (13 files in 8 dirs): added a manager
15:26 CIA-51 bioclipse: shk3 * r6723 /bioclipse2/trunk/plugins/net.bioclipse.core/​src/net/bioclipse/core/domain/ISpectrum.java: added an ISpectrum
15:41 maclean Okay, I added a bug report for the problem with the jsConsole on windows. I should have added that I will be happy to test this on windows.
15:42 jonalv oh since I  have been responsible for testing on windwos up till now I am very happu to get some help :)
15:42 * jonalv is gonna read that bug rapport now :)
15:43 maclean Well, there's got to be some kind of upside to working on this horrendous OS :)
15:43 jonalv hehe
15:43 jonalv I have it with parallels on my mac :)
15:44 maclean Ahhh. I dream of such a situation.
15:44 jonalv hm maclean could you point me to that bug? I am a bit curious...
15:45 maclean Id 2067712
15:45 maclean I could cut&paste the url also
15:45 jonalv maclean: how confusing you are gilleain on sf and maclean here...
15:45 maclean http://sourceforge.net/tracker/inde​x.php?func=detail&amp;aid=2067712&a​mp;group_id=150681&amp;atid=778609
15:45 zarah maclean's link is also http://tinyurl.com/6ekvta
15:46 maclean It was a mistake on my part to sign in with an alias when irc was giving me trouble...
15:47 jonalv mhm, intresting bug. I am sure masak++ will fix it :)
15:47 masak we'll see. what is it that Windows can't do this time?
15:47 maclean The scripting stuff is very impressive code, I must say.
15:48 jonalv cool
15:48 maclean It stubbornly refuses to use the correct line-endings.
15:48 masak maclean: what line endings?
15:48 maclean It seems that if you output '\n' it gets it wrong.
15:49 masak what's strange is that it's Windows that has '\r\n', and Unix has '\n'
15:49 masak so the trouble should not occur on Windows...
15:49 maclean Yes. That's true.
15:49 maclean Hmmm.
15:50 masak but the System.getProperty("line.separator") is generally good advice
15:50 masak I'll run with it, and maybe things'll get better :)
15:51 maclean Hope so, it's very nice to have scripting!
15:51 masak ack.
15:53 maclean syn?
15:53 jonalv "syn"?
15:54 CIA-51 bioclipse: jonalv * r6724 /bioclipse2/trunk/plugins/ (32 files in 14 dirs):
15:54 CIA-51 bioclipse: Work on getting persistence tests to pass after name change from label to
15:54 CIA-51 bioclipse: annotation. A few more tests passes but there is much left to do at persistence
15:54 CIA-51 bioclipse: tests level. Hence internal business and business tests more or less fails
15:54 CIA-51 bioclipse: completely for the moment.
15:54 maclean Er. It was a bad joke : syn/ack...
15:54 jonalv uhm I guess there is always more english out there that I could learn... :)
15:56 masak jonalv: it's not English. it's serverish.
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15:59 CIA-51 bioclipse: jonalv * r6725 /bioclipse2/trunk/plugins/net.bioclipse.struc​turedb.tests/tests/net/bioclipse/structuredb/ (15 files in 5 dirs): [structuredb] changed from "persistency" to "persistence". Obviously there is no such thing as "persistency" in the english language...
15:59 * jonalv is learning more English...
16:00 masak jonalv: also, it's "apparently", not "obviously". :P
16:00 jonalv masak: that depends on what you are trying to say
16:00 jonalv I meant obviously
16:00 jonalv I didn't write for me I wrote for you
16:01 maclean 'Obviously' makes sense in that context.
16:01 masak ok, I give :)
16:02 jonalv now playing: Status Quo - In The Army Now
16:02 jonalv last.fm++
16:04 maclean What plugins does structuredb require? I have services, and services.embrace, but it still won't build.
16:04 olas hsqldb
16:05 maclean ahhh.
16:05 olas easiest is to open the manifest.mf, switch to dependency tab, and see red marks
16:05 maclean ahh. excellent. I see now.
16:06 jonalv maclean: It builds but if you wanna test run it you should take a trip back in time with svn because for the moment I am in the middle of big refactorings...
16:07 maclean oh.
16:07 maclean takk.
16:08 jonalv takk == tack?
16:09 maclean I thought it was Norwegian for thanks. I just like the word.
16:09 jonalv ah yea it probably is. In swedish it's "tack"
16:10 masak 'takk' is Norwegian for 'thanks', yes.
16:10 masak in Danish, it's 'tak'
16:11 maclean structureDB built, it needed usermanager, too. I should make a dependancy tree picture.
16:14 jonalv ah yea, it doesn't really use the usermanager I think. OR perhaps it takes some jar files from it...
16:14 maclean jasypt
16:14 jonalv exactly
16:14 jonalv thr
16:14 jonalv there is some license issues with that...
16:14 jonalv but we have talked to them
16:15 jonalv so it shouldn't be a problem. Still I wanna have the usermanager in a special feature with the license separate
16:15 maclean Ah well. It's clocking-off time. bye.
16:16 jonalv well here too
16:23 CIA-51 bioclipse: ospjuth * r6726 /bioclipse2/trunk/plugins/net.biocl​ipse.cdk.qsar.test/src/net/bioclips​e/cdk/qsar/test/TestCDKQsar.java: Updated CDK tests for new parameter class.
16:31 CIA-51 bioclipse: ospjuth * r6727 /bioclipse2/trunk/plugins/net.bioclipse.cdk.qsar/ (2 files in 2 dirs): Specified all CDK molecular descriptors with parameters, descriptions, definitions etc as extensions to descriptor extension point. A few hours of plumbing.
16:41 olas left #bioclipse
19:10 Usiu joined #bioclipse
19:10 Usiu Hi
19:10 Usiu Where I can find some examples how to developer  bioclipse plugin ?
19:10 Usiu develop
20:37 egonw joined #bioclipse
20:39 egonw moin
20:39 zarah hi egonw
21:09 Usiu how to make custom view in rcp ?
21:10 Usiu for example someking of canvas
21:10 Usiu like JSVGCanvas
21:10 egonw mom
21:11 egonw http://wiki.bioclipse.net/index.php?t​itle=Bioclipse2#Development_tutorials
21:11 zarah egonw's link is also http://tinyurl.com/6h4zlk
21:11 egonw Usiu: don't see a View tutorial...
21:11 egonw mom
21:12 egonw https://bioclipse.svn.sourceforge.net/svnroot​/bioclipse/bioclipse2/trunk/plugins/net.biocl​ipse.cdk.ui/src/net/bioclipse/cdk/ui/views/
21:12 egonw there's example code
21:12 egonw don't have time for more explanation right now...
21:14 Usiu thanks
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