Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-03-04

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All times shown according to UTC.

Time Nick Message
05:44 annzi joined #bioclipse
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06:49 egonw moin
06:49 zarah hello egonw, you fantastic person you
06:49 egonw moving to the BMC now
07:29 sneumann joined #bioclipse
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08:20 annzi joined #bioclipse
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12:12 annzi joined #bioclipse
12:22 Gpox Eclipse 3.6 "the fourth milestone features Virtual Folders that exist only in the workspace and not backed by a directory in a users file system"
12:23 annzi left #bioclipse
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13:42 jonalv egonw: pull request for extension point sent :)
13:42 egonw http://timvdm.blogspot.com/2010/​03/avogadros-packmol-plugin.html
13:42 zarah egonw's link is also http://tinyurl.com/ya2wxgx
13:42 egonw must read
13:42 egonw jonalv++
13:42 jonalv egonw: oh test run it first :)
13:46 egonw ah indeed
13:46 egonw jonalv-- (for putting the cheminformatics.rdf plugin in the rdf.ui feature :)
13:47 egonw jonalv: please do add copyright/license headers
13:47 * jonalv trusts egonw to put it at some good place
13:48 egonw to b/plugins/net.bioclipse.chemoinformatics.rdf/src/​net/bioclipse/chemoinformatics/rdf/Activator.java
13:48 egonw jonalv++ (for the new copyright/license header design)
13:48 jonalv egonw: ah seems the automagics missed that file...
13:48 egonw *-*-*-* is more creative than just **** :)
13:48 jonalv egonw: will you merge that commit and then I patch it?
13:49 egonw jonalv++ (for putting the copyright line in the right format!!!)
13:49 egonw yes, will merge this one as is
13:49 jonalv egonw: yea the old one is interpreted as Javadoc and is actually not correct hence
13:50 egonw jonalv-- (for incorrectly doing the copyright header of RDFEditor.java
13:50 egonw )
13:51 egonw but
13:51 egonw jonalv++ (for an overall very much appreciated job!)
13:51 egonw will now try to run it :)
13:51 jonalv egonw: please be more constructive with the critique, in what way was it incorrect?
13:52 egonw mom
13:52 egonw will show you in a sec...
13:56 samuell joined #bioclipse
13:56 jonalv samuell: I am looking at your screen cast. Cool stuff samuell++
13:57 egonw samuell++
13:57 CIA-57 bioclipse.rdf: jonalv master * r5c1d25f / (14 files in 11 dirs): Use factories from EP when opening resource - http://bit.ly/aPPdW9
13:57 CIA-57 bioclipse.rdf: Egon Willighagen master * r8f289dd / plugins/net.bioclipse.rdf.ui/src/net/b​ioclipse/rdf/ui/editors/RDFEditor.java : Merged copyright statements: one is clearer; improved header format to use less characters and still not be JavaDoc - http://bit.ly/aAIWUq
13:57 jonalv samuell: one question though: Why do I not get entire blog post through planet bioclipse? It jsut had a link named "read more" or soemthing like that...
13:58 egonw common feature
13:58 egonw so that you are forced to actually visit the blog
13:59 * jonalv does not like it
13:59 jonalv actually I dislike it strongly
14:01 jonalv egonw: you removed my fancy stars and stripes :/
14:01 jonalv hehe
14:01 egonw yeah, it solves:
14:02 egonw 1. misuse of electrons
14:02 egonw 2. does not get messed up by your long email address :)
14:02 jonalv egonw: misuse of electrons?
14:11 egonw quite so
14:15 jonalv hmpf
14:18 jonalv egonw: it would be nice to do something special to the nodes which can be doubleclicked
14:18 egonw like an icon?
14:18 egonw yes, I have been thinking of that...
14:18 jonalv egonw: yea or another color or something
14:18 egonw we have the icons for the IBioResource file formats anyway...
14:19 jonalv yea Icon is a good way I think
14:19 egonw and zest can put them in the node thingy
14:19 jonalv egonw: sounds perfect
14:19 egonw mom, let me check...
14:20 egonw check out: http://wiki.eclipse.org/index.php​/GEF_Zest_Visualization#Tutorials
14:20 zarah egonw's link is also http://tinyurl.com/y9mes2h
14:20 egonw 'Zest Viewers' part
14:20 egonw in short
14:21 egonw I think you only need to overwrite LabelProvider.getIcon() in RDFLabelProvider...
14:21 jonalv egonw: seems so
14:21 egonw and have the extension point export an icon, just like the 'editor' EP
14:21 jonalv egonw: sounds like a plan
14:22 jonalv egonw: I am on it
14:22 jonalv egonw: I am just gonna report the results of the lab reports...
14:25 * egonw is writing up replies to a grant application...
14:31 samuell Sry ... was in meeting
14:31 samuell (reading up irc log now)
14:31 egonw is the bioclipse.net transition completed now?
14:31 egonw it looks nice!
14:31 egonw samuell++
14:31 egonw olass++
14:32 samuell thx ... well, the skin is not there yet ...
14:32 samuell Per is working on it
14:32 samuell I guess
14:33 samuell I mean, the final skin
14:33 CIA-57 bioclipse.rdf: jonalv master * rdc98819 / plugins/net.bioclipse.chemoinformatics.rdf/src/n​et/bioclipse/chemoinformatics/rdf/Activator.java : added copyright statement - http://bit.ly/9rN2dk
14:34 samuell jonalv: Sry ... I've been afraid of using too much space on planet bioclipse, in case somebody rather want to skip to later posts ...
14:35 samuell Hope you'll all register at bioclipse.net so you can help keep the content up to date :)
14:42 samuell egonw: The annotations were done online at YouTube ... worked very well
14:42 egonw really? got a URL for a tutorial on that?
14:43 samuell It's very easy to use in fact ... just activate the "annotations editor" at the right top corner when you're in "edit" mode on a video
14:44 egonw that's pretty cool!
14:44 samuell (I was suprised by the ease of use and quality of the feature)
14:44 egonw I have to check up on that
14:44 samuell Indeed
14:44 samuell Yep, can indeed recommend that for further Bioclipse screencasts! :)
14:47 jonalv egonw: did you see your todo in the RDFEditor?
14:47 egonw not yet :)
14:48 egonw yes, got it
14:48 jonalv egonw: it was regarding how to get the http://www.bioclipse.net/structuredb/#Molecule
14:48 zarah jonalv's link is also http://tinyurl.com/yas9535
14:48 jonalv which is still hard coded
14:48 egonw yes, understood
14:48 jonalv egonw: I realise I am gonna need taht again..
14:48 edrin left #bioclipse
14:56 jonalv lol
14:56 jonalv I think I have messed up
14:58 egonw :)
14:58 jonalv I don't understand how it coudl have worked before
14:58 jonalv egonw: it worked for you right?
14:58 egonw I could double click, yes
14:59 jonalv egonw: strange...
14:59 egonw maybe my WS was still using the old code?
14:59 jonalv egonw: no idea, strange thing is that it worked for me too
14:59 jonalv I just don't see how it can work
15:04 jonalv hm it was not so easy... :(
15:11 CIA-57 bioclipse.rdf: Egon Willighagen master * re06fba8 / plugins/net.bioclipse.rdf.ui/src/net/b​ioclipse/rdf/ui/editors/RDFEditor.java : Replaces hard-coded URI by a matching between any Resource rdf:type with the service supported URI - http://bit.ly/aV6Lcu
15:12 jonalv egonw++
15:32 masak joined #bioclipse
15:58 edrin joined #bioclipse
15:59 edrin hi
15:59 zarah hello edrin, you fantastic person you
15:59 edrin (again) :)
15:59 egonw hi edrin
16:08 masak joined #bioclipse
16:15 CIA-57 bioclipse.rdf: Egon Willighagen master * r8e22fbc / (29 files in 11 dirs): Removed StructureDB-RDF, unmaintained - http://bit.ly/9Yb5vB
16:15 CIA-57 bioclipse.rdf: Egon Willighagen master * r263d902 / (4 files): Added a feature for the RDF-Cheminformatics integration - http://bit.ly/9YFmaL
16:15 CIA-57 bioclipse.rdf: Egon Willighagen master * r31c9f6d / features/net.bioclipse.rdf​.ui_feature/rdfui.product : Removed dependencies on the Pellet and the Cheminformatics features - http://bit.ly/cqcWS9
16:15 CIA-57 bioclipse.rdf: Egon Willighagen master * r2efe126 / features/net.bioclipse.rdf.ui_feature/feature.xml : Depend on the RDF feature instead of including it - http://bit.ly/8YrXdq
16:15 CIA-57 bioclipse.rdf: Egon Willighagen master * re54077e / features/net.bioclipse.rdf.ui_feature/feature.xml : Removed the cheminformatics.rdf plugin, now in the RDF-Cheminformatics Integration Feature (net.bioclipse.cheminformatics.rdf_feature) - http://bit.ly/ajkrVM
16:30 egonw jonalv: ping
16:30 jonalv egonw: pong
16:30 egonw is the EP definition now in chemoinfromatics.rdf?
16:31 jonalv egonw: it's a mess
16:31 jonalv egonw: everythign is a mess
16:31 egonw :)
16:31 * egonw is moving the EP to the rdf.ui plugin
16:32 * egonw sees now why jonalv is not understanding why it works at all :)
16:32 jonalv egonw: yea...
16:43 CIA-57 bioclipse.rdf: Egon Willighagen master * r8a61159 / (3 files in 3 dirs): Moved the EP scheme to the right plugin: net.bioclipse.rdf.ui - http://bit.ly/c8LOq7
16:43 CIA-57 bioclipse.rdf: Egon Willighagen master * r9108322 / plugins/net.bioclipse.rdf.ui/plugin.xml : Removed a unused and obsolete EP definition - http://bit.ly/dzC60N
16:44 jonalv guys how do I find the path to my icon image file?
16:49 egonw dunno
16:56 egonw @ask annzi to update her presentation with a slide on how SPARQL/RDF and MoSS link together, and send that presentation to Anna Gaulton and John Overington (and cc me)
16:56 zarah Consider it noted.
17:07 jonalv egonw: what have you done?
17:07 egonw huh?
17:07 jonalv egonw: it was working then I updated and then it stopped working...
17:08 jonalv egonw: did you chagne soemthing?
17:08 jonalv |change something
17:08 egonw yes, see the commits
17:10 * egonw is away for dinner, bbl
17:10 jonalv egonw: oh yea I managed to figure it out
17:10 * jonalv has an icon now :)
17:13 jonalv egonw: pull request for icon patch sent
17:21 jonalv egonw: Whenever you find some bonus time could you pu together a filde for the rdf editor which contains a sequence so we can start worling on opening the sequence editor and such?
18:55 sneumann joined #bioclipse
20:20 egonw_ joined #bioclipse
20:26 egonw_ @ask Gpox if he has seen http://intellectualcramps.blogspot.com/2​010/03/buckminster-plugin-on-hudson.html
20:26 zarah egonw_'s link is also http://tinyurl.com/y9csu49
20:26 zarah Consider it noted.
21:47 edrin_ joined #bioclipse
21:53 CIA-57 bioclipse.rdf: Egon Willighagen master * r0e21bcf / (14 files in 7 dirs): Added the ChEMBL manager to return the QSAR data for a particular target from ChEMBL - http://bit.ly/9uygHW
21:54 CIA-57 bioclipse.rdf: jonalv master * rcf35f65 / (6 files in 6 dirs): Added icon to things that can be opened - http://bit.ly/buAOOA
21:54 CIA-57 bioclipse.rdf: Egon Willighagen master * r76ddb5c / features/net.bioclipse.cheminfo​rmatics.rdf_feature/feature.xml : Added missing dependency - http://bit.ly/d4ki4w
21:54 CIA-57 bioclipse.rdf: Egon Willighagen master * r08afe9b / (13 files in 7 dirs): Added an extension to allow recognition of protein sequences. Double click is limited by ui.open(IProtein) not working - http://bit.ly/avzVHL

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