Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-01-28

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All times shown according to UTC.

Time Nick Message
00:01 CIA-55 bioclipse: edrin_t * r8513 /bioclipse2/trunk/plugins/net.bioclips​e.webservices/src/net/bioclipse/webser​vices/scripts/WebservicesManager.java: download of pdb file works now
06:37 masak joined #bioclipse
07:57 Gpox joined #bioclipse
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08:30 jonalv joined #bioclipse
08:48 jonalv joined #bioclipse
08:48 jonalv OH HAI
08:48 zarah hello jonalv, you fantastic person you
08:48 zarah jonalv: You have new messages. Write '/msg zarah @messages' to read them.
08:49 jonalv '/msg zarah @messages
08:49 masak jonalv: I should perhaps add "...but without the quotes" :P
08:52 egonw joined #bioclipse
08:59 olass joined #bioclipse
08:59 olass hi
08:59 zarah saluton olass
08:59 olass zarah: right...
08:59 zarah olass: are you talking to *me*?
08:59 olass zarah: no
08:59 zarah olass: I see.
09:00 masak olass: saluton!
09:00 olass masak: right...
09:00 masak olass: are you talking to *me*?
09:00 olass masak: actually, NO
09:00 masak olass: I see.
09:00 olass @slap masak
09:00 * zarah hits masak with a hammer, so he breaks into a thousand pieces
09:01 olass oh..
09:01 masak ouch.
09:01 olass zarah: that was a bit too much IMHO
09:01 zarah olass: you've just exceeded my capabilities :/
09:01 olass zarah: I see
09:01 zarah olass: please rephrase or stop trying to be witty :)
09:01 masak @slap olas
09:01 * zarah slaps olas
09:01 masak better :)
09:01 olass poor olas
09:01 * olass likes olas
09:01 masak dang. :)
09:01 jonalv :)
09:02 * olass is answering mails on devel ML
09:02 masak olass++
09:03 olass egonw: is voting for bugs possible in pelezilla?
09:03 olass and how does that appear in mylyn?
09:03 olass I mean, I can see the option "vote for this bug"
09:04 olass just wondered if/how we honor that option in our priorities
09:04 olass egonw: let me know when you have time
09:04 egonw moin
09:04 zarah privet egonw
09:05 egonw olass: yes, voting is possible
09:05 olass egonw: does it increase prio on bug?
09:05 olass I see no attribute "no votes" in mylyn
09:05 olass no=number of
09:05 egonw no sure voting can be done via mylyn
09:05 egonw don't think it changes the priority
09:06 olass me meither
09:06 egonw prio is developer oriented
09:06 egonw votes is user oriented
09:06 olass but if someone votes for a bug and we work in mylyn, how can we take advantage of this?
09:06 egonw not sure
09:11 olass egonw: I'd be extremely happy if you (when you have time) could take a look at bug 301
09:11 egonw not before friday
09:11 olass Gpox can surely help with implementation
09:11 olass but he (and we others) need guidance
09:11 egonw oh... 301 is about CML content types?
09:12 shk3 joined #bioclipse
09:12 olass no, how to treat e.g. SDFiles without coordinates in SDFEditor
09:12 jonalv @pz 301
09:12 olass or if SDFile has 3D coordinates
09:12 zarah http://tinyurl.com/d2y6mo
09:12 olass there is a wiki page
09:12 egonw yes, will work on this...
09:12 egonw but not now...
09:12 olass great
09:12 egonw in the middle of a talk by Chris :)
09:12 olass egonw++ //when you have time
09:13 egonw olass: I am going to make a Metabolomics Feature soon
09:13 olass cool
09:13 egonw as really nice show case of chemoinformatics
09:13 olass there are so many things we will do after 2.0
09:13 olass (that's why we need to get 2.0 out)
09:13 egonw yes
09:14 olass egonw: bug 301 needs advice and new bugs
09:14 egonw olass: I might have time this afternoon to reply on bug reports
09:14 egonw but not this morning
09:14 olass ok
09:14 egonw so, hang on...
09:14 egonw BTW, the workshop is *really* nice
09:15 egonw I had a 10 minute time slot yesterday to present metware.org
09:15 egonw and prominently mentioned Uppsala and Bioclipse...
09:23 maclean joined #bioclipse
09:24 maclean ni hao
09:25 shk3 btw, what is the jchempaint-feature about? looks like jcp is in chemoinformatics feature as well.
09:25 shk3 do we need the jcp feature?
09:25 shk3 if not, it is confusing?
09:26 egonw jchempaint is JChemPaint-RCP
09:26 egonw it's a jchempaint.product
09:26 egonw where we can easily add other feature, like Jmol, to offer functionality that JChemPaint-Swing cannot
09:27 maclean hi egonw : you're still in a talk aren't you? :)
09:27 egonw well, discussion now
09:27 shk3 ah
09:27 shk3 do we need a feature to make a product?
09:27 egonw shk3++
09:28 egonw for the visible fix for the CML validation action
09:28 maclean oh, and I've finally made the renderer independent of awt/swing, so that it can be used in bioclipse
09:28 egonw yes, think so (olass, correct me if wrong)
09:28 egonw maclean: please discuss that with Gpox how that affects his swt integration
09:29 maclean but the changes are quite substantial, so I don't want to just commit it  - I'm thinking of making it one large patch
09:29 olass shk3, egonw: We use features for building products, yes
09:29 olass there is no struct requirement for this but simplifies a lot
09:29 shk3 ah
09:29 olass just plugin features in and out of the product
09:30 olass if it is plugin-based, we ned to worry more about deps
09:30 olass just more coplicated
09:30 maclean Gpox can review it (indeed, is uniquely qualified to do so)
09:30 olass maclean: file a bug to him
09:30 maclean olass: oki
09:31 * shk3 will join the metabolomics discussion
09:32 egonw shk3, maclean: there is no MB afternoon program... can I join you at the EBI?
09:32 maclean egonw : sure
09:34 maclean I think shk3 is on his way to the discussion.
09:35 egonw yes, he just arrived
09:41 olass Gpox: I'd like to vote for bug 174 (properties in MoleculesTable) ;-)
09:43 edrin joined #bioclipse
09:43 edrin hi
09:43 zarah privet edrin
09:47 olass FYI, if people vote for a bug, it does appear in mylyn, just below the Priority in the Attributes section.
09:47 olass so go ahead and vote!
09:48 olass (BTW voting must be done from web interface and you need to be registered to vote)
10:07 jonalv uhm, net.bioclipse.specmol. What is that? :) (it's not compiling on my machine...)
10:10 egonw speclipse
10:15 maclean joined #bioclipse
10:18 egonw olass++ for bugs.bioclipse.net
10:19 olass :-)
10:19 egonw and planet.bioclipse.net
10:20 olass jonalv: speclipse is managed at EBI
10:20 jonalv oki
10:20 * jonalv is going through the cdk manager looking for threading problems and doing indentation
10:21 jonalv (a script and some autoindentation usign tabs has toally screwed up the indentation of that file...)
10:31 CIA-55 bioclipse: carl_masak * r8514 /bioclipse2/trunk/manager-apidocs/render-as-html: [managerdocs] replaced HTML::EscapeEvil with homegrown escaping
10:36 shk3 specmol not compiling?
10:36 shk3 compiles for me
10:38 maclean_ joined #bioclipse
10:57 de__maas joined #bioclipse
10:57 de__maas Ggrandm44: still looking for a tutorial on CDK?
10:58 de__maas grandm44: still looking for a tutorial on CDK?
11:09 shk3 jonalv: can you tell me about your problems with specmol?
11:09 Gpox joined #bioclipse
11:09 CIA-55 bioclipse: shk3 * r8515 /bioclipse2/trunk/plugins/net.biocli​pse.specmol/src/net/bioclipse/specmo​l/wizards/SelectFileWizardPage.java: small bugfix
11:15 CIA-55 bioclipse: shk3 * r8516 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business.test/src/net/bioclipse/​cdk/domain/tests/TestCDKMolecule.java: the test for this
11:16 CIA-55 bioclipse: shk3 * r8517 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (CDKManager.java ICDKManager.java): added a manager method to extract entries from sdf
11:18 CIA-55 bioclipse: shk3 * r8518 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui.sdfeditor/ (6 files in 3 dirs): using this method
11:22 egonw does anyone know how to continue a 'git svn dcommit' which was cut off to lost internet connection?
11:23 maclean_ erk, no - sorry.
11:23 de__maas left #bioclipse
11:23 CIA-55 bioclipse: shk3 * r8519 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui.sdfeditor/ (html/extract.html toc.xml): added help for this
11:38 olass shk3: please write standalone commit messages. "added help for this" and "the test for this" is not enough.
11:38 olass also "small bugfix" is not enough
11:39 olass "fixed bug XX" is much better
11:39 shk3 sorry
11:39 olass shk3: I am not perfect either
11:39 shk3 no?
11:39 olass i think we all can get better on this
11:39 shk3 that's a shame
11:39 egonw but please even describe 'how you fixed the problem' or 'what caused the bug'
11:39 olass actually, I really get frustrated when I read my old commit messages from time to time...
11:40 olass I sort of envision that an SVN log could at some point be transformed to a changelog...
11:41 olass right now we have none :-(
11:41 olass egonw: so you see priv msg?
11:41 olass yup :-)
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12:31 grandm44 @ping
12:31 zarah grandm44: pong
12:33 grandm44 @tell de__maas: Yes I'm still looking for a good CDK tutorial. Do you have something interesting ?
12:33 zarah Consider it noted.
12:36 masak grandm44: you might want to try that without the colon...
12:36 masak :/
12:42 maclean joined #bioclipse
12:42 grandm44 masak: won't he get the message? Previously, I saw it worked with the colon.
12:42 * masak checks
12:43 masak oh, it works. nvm.
12:43 masak zarah++
12:43 masak just don't do several colons :P
12:43 grandm44 :)
12:48 masak @tell olass::: you'll never get this message! :D
12:48 zarah Consider it noted.
12:48 olass @ping
12:48 zarah olass: pong
12:48 olass @msg
12:48 zarah olass: You have no new messages.
12:48 masak :)
12:52 grandm44 quod erat demonstrandum
12:53 maclean masak : SVG emitter? For rakudo?
12:53 masak maclean: what have you been reading? :)
12:53 masak that's hobby stuff!
12:53 maclean oh, your use.perl blog
12:54 * masak is flattered
12:54 masak yes, the SVG emitter is coming along fine, except for all the problems I'm having with Rakudo right now.
12:55 maclean I should start following parrot development again...
12:55 masak maclean: you really should.
12:55 masak especially Rakudo.
12:56 maclean I've been making overloaded methods today, in java, and wishing for a more dynamic language. sigh.
12:57 maclean specifically, wishing for ducktyping.
12:58 masak ducktyping is nice, to a point.
12:59 masak but even a well-played use of inheritance-based method dispatch can be wonderful.
13:00 maclean I just have a feeling that I can do better than "calculateBounds(IMoleculeSet)", "calculateBounds(IReactionSet)"...
13:01 masak maclean: make them methods instead?
13:01 masak also, why do you implement one set for each type?
13:01 maclean haha. nooo.
13:01 maclean noooo-ooo.
13:01 maclean I'm not so bold as to make changes to the core types in the cdk! :)
13:01 masak ah, but that's another thing, then.
13:02 masak that's a decision built into the current API.
13:02 maclean And, yes I don't understand the I<Type>Set classes.
13:02 masak (not saying it's bad, by the way. I don't know CDK well enough)
13:02 maclean And I would prefer if they implemented Iterable<ContainedType>...
13:02 maclean but never mind. (also wrong channel :)
13:03 masak sort of, yes.
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13:13 jonalv olass: keeping busy?
13:13 * jonalv just got about 10 new mails...
13:13 * olass has done administrative tasks all day
13:13 olass boring but necessary
13:14 * olass is taking his responsibilities as coordinator seriously
13:14 jonalv good
13:29 egonw joined #bioclipse
13:39 olass gotta run to the train now
13:40 olass tomorrow I'll not be online
13:40 olass be back on friday
13:40 olass might buy internet on train later today
13:40 jonalv zarah: tell masak Now the HTML looks like this in instead: "Returns true if the paramater named molecule1 and the paramater named molecule2 are isomorph. \n(Performs an isomophism test without checking fingerprints" I am not sure that is perfect...
13:40 zarah Consider it noted.
13:40 olass else will work offline
13:40 olass bye for now
13:40 jonalv olass: bye
13:40 jonalv :/
13:46 de__maas joined #bioclipse
13:53 grandm44 zarah: why don't you tell de__maas he's got a message?
13:53 zarah grandm44: that was not so easy for a little bot to understand
13:54 grandm44 :/
13:56 jonalv grandm44: she will tell him that when he says something. logging in is not enough
13:56 jonalv |joining
13:57 grandm44 ah! ok
14:12 de__maas Oeps am I missing something?
14:12 zarah de__maas: You have new messages. Write '/msg zarah @messages' to read them.
14:14 de__maas Aha, well I'm not  sure if there are actual tutorials but I had a great help going through the examples of Rajarshi
14:14 de__maas http://cheminfo.informatics.i​ndiana.edu/~rguha/code/java/
14:14 zarah de__maas's link is also http://tinyurl.com/cqtnrf
14:16 shk3 jonalv: having problems with specmol?
14:17 jonalv shk3: uhm I had compile problems
14:17 shk3 but you no longer have?
14:18 jonalv shk3: I don't know
14:18 jonalv hang on
14:18 jonalv shk3: Access restriction: The type Point2d is not accessible due to restriction on required library /System/Library/Java/Extensions/vecmath.jar
14:19 jonalv in SelectByClickModule
14:20 shk3 hang on
14:21 shk3 vecmath should come from javax.vecmath plugin
14:21 shk3 where is /System/Library...?
14:22 jonalv shk3: no idea. sounds like some inner parts in java
14:23 shk3 yes
14:23 shk3 cdk uses vecmath as well
14:25 jonalv okey
14:29 shk3 removed dependency on javax.vecmath and it still works
14:29 shk3 ah no
14:29 shk3 just the error doesn't show up
14:30 shk3 but can't see why your setup isn't using the plugin
14:30 maclean hmmm
14:30 maclean ahh!
14:30 maclean the /System/Library/Java is where java lives on osx
14:31 maclean (note to self : don't try to start sentences with paths)
14:31 jonalv okey
14:31 jonalv so you can fix it?
14:32 maclean it's not being exported?
14:33 maclean no, wait that doesn't make sense
14:33 shk3 sorry, don't understand this
14:33 shk3 it looks like you have vecmath in your system installation
14:34 shk3 and this is not exported
14:34 shk3 but I don't know how and why and where to export
14:34 Gpox I have a fix for it
14:34 shk3 normally, the plugin should be used
14:36 CIA-55 bioclipse: goglepox * r8520 /bioclipse2/trunk/plugins/net.​bioclipse.specmol/.classpath: Fixes access restriction for vecmath on mac
14:36 Gpox try it now
14:37 Gpox the problem is this line in the .classpath <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CON​TAINER/org.eclipse.jdt.internal.debug.u​i.launcher.StandardVMType/J2SE-1.5"/>
14:37 shk3 which should be?
14:38 Gpox the last part should be removed <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
14:38 * jonalv 's entire workspace actually compiles now. yey :)
14:39 shk3 thank Gpox
14:39 shk3 Gpox ++
14:39 jonalv Gpox++
14:42 de__maas grandm44: I had a great help going through the examples of Rajarshi:  http://cheminfo.informatics.i​ndiana.edu/~rguha/code/java/
14:42 zarah de__maas's link is also http://tinyurl.com/cqtnrf
14:45 jonalv @pz
14:45 zarah jonalv: Pelezilla is at http://pele.farmbio.uu.se/​cgi-bin/bugzilla/index.cgi
15:01 grandm44 de__maas: thanks for the link, I'll have a look
15:02 de__maas OK , have fun :)
15:03 de__maas BTW, there is also a seperate cdk channel #cdk
15:44 Gpox jonalv: What happens when you have two methods like this loadMolecules( IFile, IProgressMonitor) and loadMolecules(IFile, xxx, IProgresMonitor) in a manager?
16:07 Gpox jonalv: never mind if doesn't work in trunk either filing bug
16:07 Gpox @pz 321
16:07 zarah http://tinyurl.com/dgme6t
16:23 de__maas left #bioclipse
16:59 CIA-55 bioclipse: goglepox * r8521 /bioclipse2/trunk/plugins/net.bioclipse.core/src/​net/bioclipse/core/ResourcePathTransformer.java: Added more comments to ResourcePathTransformer
18:19 edrin left #bioclipse
21:29 edrin joined #bioclipse
23:13 olass_ joined #bioclipse
23:14 olass_ moin
23:14 zarah ni hao olass_
23:17 olass_ edrin: awake?
23:17 olass_ @msg

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