Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-01-16

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All times shown according to UTC.

Time Nick Message
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07:24 masak @tell egonw yes, command echoing is the #1 request right now. will add it today.
07:24 zarah Consider it noted.
07:24 masak @stop
07:24 zarah masak: Stopping task 'bc2/console-egonw-single-line-refactor' after 17 h 51 m at 21 h 53 m out of 2 h (1094%).
07:26 edrin joined #bioclipse
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08:06 egonw joined #bioclipse
08:06 olass joined #bioclipse
08:07 olass moin
08:07 zarah oh hai olass
08:07 zarah olass: You have new messages. Write '/msg zarah @messages' to read them.
08:07 egonw hi olass
08:07 olass @msg
08:07 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
08:07 zarah olass: 12 h 50 m 35 s ago, egonw said that my services are up and running now
08:07 egonw @msg
08:07 zarah egonw: 42 m 59 s ago, masak said yes, command echoing is the #1 request right now. will add it today.
08:07 olass egonw: good
08:07 olass egonw: does it accept cml?
08:07 egonw yes
08:07 egonw :)
08:07 olass good
08:08 egonw and it outputs CML too
08:08 egonw had to fix the CDKMolecule.getCML()
08:08 egonw which outputed a document
08:08 egonw so with <?xml>
08:08 egonw it now uses the CMLXOM Convertor directly
08:08 olass ok
08:09 egonw I'm guessing, but not 100% sure, that no one relies on that <?xml> PI
08:09 olass probably so
08:09 olass since save is not really working yet
08:10 olass might you look at formats and save soon?
08:10 egonw yes, will continue with formats...
08:10 olass I'll help you with testing if you like
08:10 egonw saveCML is seriously broken
08:10 egonw it saves MDL molfiles :)
08:10 olass lol
08:10 egonw umm...
08:10 masak oh! XML documents don't need the <?xml> PI to be well formed.
08:10 egonw there are a few things I need you to look at
08:10 egonw 1. CML format detection (see bug report)
08:11 olass hmm
08:11 egonw 2. how can we have the file format show up in the Properties View
08:11 olass gilleain wrote that latest...
08:11 egonw masak: right
08:11 egonw olass: check the bug report...
08:11 olass what is PI?
08:11 egonw I added a patch
08:11 olass egonw: will do
08:11 egonw Processing Instruction
08:11 olass ah
08:11 egonw olass: just tell me to apply the patch, if you agree
08:12 masak olass: http://www.w3.org/TR/REC-xml/#sec-pi
08:12 * olass is looking at the bugs now
08:25 olass_ joined #bioclipse
08:25 egonw @tell jonalv reading material: http://pubs.acs.org/doi/full/10.1021/ci800305f
08:25 zarah egonw's link is also http://tinyurl.com/a6djvp
08:25 zarah Consider it noted.
08:27 edrin masak: bc console is now working for me
08:27 zarah edrin: You have new messages. Write '/msg zarah @messages' to read them.
08:27 edrin and rhino plugin too
08:27 olass_ [09:24] *** Irssi: Join to <#bioclipse> was synced in 5 secs
08:27 olass_ [09:26] <@olass> egonw: is it important to use a describer for CML?
08:27 olass_ [09:26] <@olass> Eclipse strongly favors as fast algos as possible for this
08:27 olass_ [09:26] <@olass> testing the first element is REALLY fast
08:27 olass_ [09:26] <@olass>              <parameter
08:27 edrin obviously it was the settings!
08:27 olass_ [09:26] <@olass>                    name="element"
08:27 olass_ [09:26] <@olass>                    value="{http://www.xml-cml.org/schema}*">
08:27 edrin @msg
08:27 zarah edrin: 13 h 10 m 58 s ago, egonw said that my CML services work now, and that a 500 on invalid CML is a good thing...
08:27 olass_ [09:27] <@olass> what else could it be than this?
08:27 olass_ [09:30] <@olass> egonw?
08:27 olass_ hi edrin
08:27 edrin hi olass
08:28 olass_ you had the same experiene as I did with my scirp, I take it?
08:28 edrin @tell jonalv everything is working for me now with optimized bio settings :)
08:28 zarah Consider it noted.
08:28 edrin olass: it was slightly different: the add thing worked
08:28 egonw olass: yes, didn't the patch suggest to test the first element?
08:28 edrin olass: i wrote you two emails
08:29 egonw olass: XML-Lite Editor?
08:29 olass_ egonw: soundsgood
08:29 edrin egonw: could you maybe try to run ola's script at your instance
08:29 edrin olass: cant explain this right now...
08:29 olass_ ok
08:30 olass_ sad that it is problematics
08:30 olass_ I have no idea where to dig into this
08:30 edrin maybe javascript has some problem to reflect xmlbeans properly?
08:30 edrin olass: the junit stuff now 100% works for you?
08:30 edrin olass: could you ask egon to run the script?
08:31 olass_ egonw: could you run my script?
08:31 olass_ :-)
08:31 olass_ http://gist.github.com/47421
08:31 egonw what's the Gist?
08:31 egonw ah... Ö)
08:31 egonw :)
08:33 olass edrin: still there?
08:33 olass I got your bug report on starting Bioclipse
08:34 olass it doesn't work still, I take it?
08:37 CIA-28 bioclipse: egonw * r8335 /bioclipse2/trunk/features/net.​bioclipse_feature/feature.xml: Added nb.ioformats (implements #246)
08:39 egonw zarah: that's a bug number too, you know...
08:39 zarah egonw: I'm just a bot, you expect me to understand that?
08:39 egonw yes, I did
08:41 olass @tell edrin: ping me when back
08:41 zarah Consider it noted.
08:44 sneumann joined #bioclipse
08:45 egonw hej sneumann!
08:49 sneumann morning
08:49 CIA-28 bioclipse: egonw * r8336 /bioclipse2/trunk/plugins/n​et.bioclipse.ui/plugin.xml: Use a Describer to recognize the root element (implements #245)
08:49 olass morning sneumann
08:49 olass egonw: did my script work at your place?
08:50 olass I suspect this is an OS X xml issue...
08:50 egonw thanx for the reminder ... :)
08:55 jonalv joined #bioclipse
08:55 jonalv hi
08:55 zarah ni hao jonalv
08:55 zarah jonalv: You have new messages. Write '/msg zarah @messages' to read them.
08:57 egonw olass: yes, the script works for me
08:57 olass egonw: ok
08:57 egonw I get to see 7 values
08:57 olass ok, good
08:58 olass masak: might you try my script too?
08:58 olass see above gist link...
08:58 olass hmm
08:58 jonalv edrin: so you got everyhting working?
08:58 masak olass: I'm in the middle of a few somethings, but yes, I'll try it before lunch.
08:59 olass jonalv: maybe  it's better if you test it?
08:59 olass oh, if you have time
08:59 egonw yes, command feedback first, please :)
08:59 egonw rather difficult to see what happens without it :)
08:59 jonalv olass: uhm what, where, how?
08:59 olass mom
08:59 jonalv dad!
08:59 olass script http://gist.github.com/47421
08:59 olass test run it
08:59 olass it doesn't work on my mac
08:59 masak egonw: I'm not really on duty at present. but yes, command feedback first.
09:00 olass but works with edrin (windows) and egonw (linux)
09:00 olass if no luck with you, then I say this is an OS X issue
09:00 olass if works with you, I have a strange config problem somewhere
09:00 egonw masak: ah, right...
09:00 egonw masak: sorry bout that
09:01 masak egonw: np. I usually don't show up here when I'm not working.
09:01 masak egonw: but I'm interesting in people's reactions to the new console...
09:01 masak s/ing/ed/
09:01 olass @tell shk3: Please use Java5 in Bioclipse!
09:01 zarah Consider it noted.
09:02 jonalv olass: what plguins do I need?
09:02 olass don't you have all checked out :-)
09:02 CIA-28 bioclipse: ospjuth * r8337 /bioclipse2/trunk/plugins/net.bioclipse.c​dk.ui/src/net/bioclipse/cdk/ui/handlers/ (Create2dHandler.java Create3dHandler.java): Removed @override interfaces since that is a Java6 parameter. shk3: please only use Java5 in Bioclipse!
09:03 olass actually, just xws4j
09:03 jonalv olass: what features do I need to run?
09:03 olass xws4j-feature
09:03 olass and biolipse core
09:03 jonalv k
09:04 * egonw commences in net.bioclipse.git
09:04 egonw ETA: 1 hour
09:04 CIA-28 bioclipse: ospjuth * r8338 /bioclipse2/trunk/plugins/net.bioc​lipse.cml/src/net/bioclipse/cml/ha​ndlers/CMLValidationHandler.java: Removed @override for overriding interfaces since that is a Java6 parameter. shk3: please only use Java5 in Bioclipse!
09:05 egonw olass: but only for methods, right?
09:05 egonw ummm... nevermind... that sounds stupid...
09:05 * olass neverminds
09:05 egonw kobain neverminds
09:06 jonalv olass: the script gives me this output: http://pastebin.com/f7cc16d3c
09:06 egonw same here
09:06 egonw looks good
09:06 olass oh, so it works!
09:06 olass good and bad
09:06 egonw os/x--
09:06 olass good: it works
09:06 egonw apple just sucks wrt java
09:06 olass jonalv: that was OS X right?
09:07 jonalv olass: yup
09:07 egonw oh...
09:07 egonw os/x++
09:07 jonalv and very cool that it works
09:07 olass yes
09:07 jonalv edrin++ olas++
09:07 masak @karma x
09:07 zarah x has a karma of 0
09:07 * olass will clean and update all paths
09:07 egonw @karma os/x
09:07 zarah os/x has a karma of 0
09:08 masak (os/x)++
09:08 masak @karma os/x
09:08 * egonw hopes os and x are not integers
09:08 zarah os/x has a karma of 1
09:08 jonalv zarah: ping
09:08 zarah jonalv: pong
09:08 egonw == (os+x)/x
09:08 egonw @karma os+x
09:08 zarah os+x has a karma of 0
09:08 * egonw wonders if it is already weekend....
09:23 CIA-28 bioclipse: ospjuth * r8339 /bioclipse2/trunk/plugins/net.bioclips​e.ui/src/net/bioclipse/ui/contenttypes​/MdlMolFileCoordinatesDescriber.java: Added copyright header. Solves #242.
09:24 edrin olass: the startup problem is solved since i started with bioclipse.product!
09:24 zarah edrin: You have new messages. Write '/msg zarah @messages' to read them.
09:24 edrin @msg
09:24 zarah edrin: 43 m 4 s ago, olass said ping me when back
09:24 olass edrin: great!
09:24 olass so masaks console now works for you?
09:24 edrin yes
09:24 edrin my plugin, too
09:25 edrin it was only the .product
09:25 olass good that this is resolved
09:25 olass edrin: everyone seems to be able to run my hivpred script except me...
09:25 grandm44 joined #bioclipse
09:25 grandm44 hi all
09:25 zarah oh hai grandm44
09:25 olass hi
09:25 zarah olass: where have you been? I've been worried.
09:25 grandm44 i've been playing with bc 2;)
09:26 olass zarah: you are a bot, I don't expect you to uderstand that.
09:26 zarah olass: you've just exceeded my capabilities :/
09:26 edrin olass: i still wonder why the iof.getHIVPredOutputDocument(result); does not work...
09:26 olass edrin: yes...
09:26 olass that might be due to schema differences
09:26 olass btw, gave you some new bugs
09:26 olass se pelezilla @pz
09:26 olass @pz
09:26 zarah olass: Pelezilla is at http://pele.farmbio.uu.se/​cgi-bin/bugzilla/index.cgi
09:26 edrin could be because the schema did not validated on this http tool...
09:27 egonw hi grandm44
09:27 edrin olass: onthe other hand the code works in the xws4j-hivpred-client project
09:27 grandm44 hi egonw
09:28 olass edrin: Let me know if you solve it, I don't know how to attack it
09:28 olass pretty happy it works as well as it does now
09:28 olass though not 100%..
09:28 egonw do we have a wizard which takes one parameter as input?
09:28 olass for what?
09:29 edrin jonalv: could you also try this slightly modified script here: http://pastebin.com/m68a02acc
09:29 egonw jonalv?
09:29 egonw olass: say, an URL?
09:29 olass a wizard for doing what?
09:29 olass xmpp services?
09:29 edrin masak: question... i have an idea about the js console
09:29 egonw say, download from URL
09:30 olass egonw: no, not yet
09:30 olass (I think)
09:30 masak edrin: let's hear it.
09:30 egonw OK, I'm on it then...
09:30 edrin masak: i want a startRecord() and stopRecord() function in rhino.
09:31 masak hm.
09:31 jonalv egonw: XmlObject is not an instance of HIVPredOutputDocument
09:31 edrin jonalv: same here
09:31 masak edrin: what's the advantage of not recording all the time?
09:31 edrin egonw: true for you, too? http://pastebin.com/m68a02acc
09:32 edrin masak: the thing is... imagine i want to write a new script...
09:32 egonw edrin: will test later
09:32 edrin against a xws for example
09:32 edrin then i could play around in the console with it
09:32 jonalv I am wondering if we really should record scripts at all. I mean what's the point? Perhaps we onlyu should record gui actions?
09:32 edrin and finally dump all in a .js script
09:32 edrin finally i can clean the code in the script
09:33 edrin jonalv: that would be cool because of the dynamic interfaces of xws
09:33 edrin dynamic input/output binding
09:34 jonalv edrin: please explain
09:34 edrin jonalv: 1. discover service in xmpp
09:34 masak edrin: recording could definitely use some revolutionary ideas.
09:34 edrin masak: you mean "solve"
09:34 edrin ?
09:34 edrin 2. create binding
09:35 edrin 3. discover the api of binding with tab completion
09:35 edrin 4. do the stuff
09:35 edrin 5. save script in .js and clean code
09:35 jonalv edrin: okey but why do you want to record this?
09:35 jonalv hm...
09:35 edrin jonalv: so i can adapt stuff afterwards
09:36 jonalv you already have all the command on the js-console...
09:36 jonalv perhaps they are bettter than the record can create...
09:36 jonalv they are at least not worse...
09:37 jonalv on the other hand if you both use the gui and the console than you might want a complete recording of all of it when you try to make a script out of it...
09:38 jonalv yea scripting is an intresting idea and what is there right now is just a very simple proof of concept thing which does not quite perform in all situations...
09:44 grandm44 I played a little with bc2.
09:44 grandm44 First, with the "official 2.0.0.alpha02.linux.gtk.x86_64" release: when I add the chemoinformatics feature via the "search for new features" menu entry, I get this error: "An exception occured while downloading feature from "http://update2.bioclipse.net/features/net.biocli​pse.chemoinformatics_feature_2.0.0.A20081028.jar""
09:44 zarah grandm44's link is also http://tinyurl.com/9z9wzz
09:44 grandm44 Second, about yesterday's svn release: after "Set target platform" I tried both with bioclipse.product:
09:44 grandm44 1) to enable all plugins from workspace (then add the required ones), and
09:44 grandm44 2) to enable the minimum plugins (net.bioclipse.core, net.bioclipse.logger, net.bioclipse.scripting, net.bioclipse.scripting.ui, net.bioclipse.ui, net.bioclipse.ui.buiness, net.bioclipse.usermanager, net.bioclipse.chemoinformatics-feature, net.bioclipse.chemoinformatics, net.bioclipse.cdk.business, net.bioclipse.cdk.ui, net.bioclipse.cdk.ui.sdfeditor, net.bioclipse.cdk.jchempaint, net.bioclipse.cml, all cdk plugins), then add the requi
09:44 grandm44 red ones.
09:45 grandm44 I can create CML or MOL files, but unfortunately I don't have the chemoinformatics perspective, so I can't play with jchempaint.
09:45 egonw or you running BC2 via features?
09:46 egonw or via a list of plugins?
09:46 grandm44 tried via features with "official alpha release"
09:46 grandm44 tried with list of plugins with svn release
09:47 egonw ok, please try this for the SVN version:
09:47 egonw (btw, not sure why that jar did not download...)
09:47 egonw open the bioclipse.product
09:47 grandm44 done
09:47 egonw go to the Configuration Tab
09:47 egonw Remove All
09:47 egonw then save (important=
09:47 egonw then save (important)
09:48 egonw then add net.bioclipse_feature
09:48 egonw as well as:
09:48 egonw jchempaint_feature, chemoinformatics_feature
09:48 egonw and
09:48 egonw sampledata_feature
09:48 egonw and run
09:49 egonw then in BC2:
09:49 egonw File -> New
09:50 egonw Data -> New Sample Data project
09:50 egonw that will create a new project in your Bioclipse Explorer
09:50 egonw in '2D structures', double click on 0037.mdl and 0037.xml
09:51 shk3 joined #bioclipse
09:52 grandm44 ok, done
09:52 egonw does that open a 2D editor for you too?
09:52 grandm44 no :(
09:52 egonw ok, please update from SVN, and try again...
09:53 egonw there was a bug yesterday, which should be fixed now
09:53 grandm44 ok, doing the whole stuff
09:53 olass grandm44: if you right-click  0037.mdl, what options do you get under "Open with..." ?
09:53 grandm44 anyway thank you for your time, i keep you posted
09:53 egonw grandm44: ok
09:53 de__maas joined #bioclipse
09:53 olass Bioclipse remembers last editor
09:54 olass if you used text editor last time, it will use text again
09:54 olass even if new editors are installed with higher priority
09:54 olass to overcome this, clear your runtime workspace
09:54 olass (in the run config dialog)
09:54 grandm44 olaas: MDL mol file editor, text editor, system editor, default editor
09:55 olass select MDL mol editor
09:55 olass now works?
09:55 egonw grandm44: it just shows a white editor screen, right?
09:55 grandm44 it was already selected
09:55 olass ok
09:55 olass then it is indeed not working
09:55 grandm44 egow :yes
09:55 egonw olass: I had that too, yesterday... but that should be fixed now
09:56 egonw grandm44: you see, SVN is under heavy development :)
09:56 grandm44 ok, time to wipe everything :)
09:56 egonw wipe? not just update?
09:57 grandm44 or this :)
10:06 edrin grandm44: do you and your research have a webpage?
10:08 grandm44 edrin: http://www.ensic.inpl-nancy.fr/DCPR/
10:08 zarah grandm44's link is also http://tinyurl.com/86vdc2
10:12 olass egonw: I need a saveMolecule(..) that alows me to save it to another path that does not exist, and I want to be able to do this in a junit test.
10:12 olass I don't think this works currently
10:12 olass what do you think?
10:12 egonw last time I checked it worked...
10:12 egonw have been using that...
10:12 egonw mom
10:13 jonalv dad!
10:13 masak grandpa!
10:13 egonw http://gist.github.com/18315
10:13 olass String newFilename="/testFiles/atpWithM2Dprops.mol";
10:13 olass uri = getClass().getResource(newFilename).toURI();
10:13 olass url=FileLocator.toFileURL(uri.toURL());
10:13 egonw later today you can do:
10:13 olass this does not work
10:13 egonw gist.load(18315)
10:14 egonw olass: that's a syntax I have never used before
10:14 olass opens an editor with the gist?
10:14 egonw no idea if that works...
10:14 olass egonw: what works?
10:14 egonw olass: yes, that's the idea
10:15 egonw http://gist.github.com/18315
10:15 egonw that workED
10:15 egonw will test it now
10:15 olass thx
10:16 egonw yes, that saveCML() worked
10:16 egonw except that it saved MDL molfile, not CML
10:16 egonw can you live with that...
10:16 olass Gpox: how do I save a molecule to Virtual orTemp folder?
10:16 egonw or shall I fix that to save CML?
10:17 egonw no, save to Virtual seems broken
10:17 olass yes
10:17 egonw no, save to "/Virtual" seems broken
10:17 olass I think it is scheduled for termination
10:17 egonw right :)
10:17 egonw virtual??
10:17 olass by Gpox
10:17 egonw I  hope not...
10:17 olass in favor of a file-based temp dir
10:17 egonw I was just going to use it...
10:17 olass why?
10:17 egonw oh...
10:18 egonw so that SDF works in Virtual too...
10:18 olass /Virtual means you have the file in memory, AND the parsed file in memory
10:18 olass very memory consuming
10:18 olass Gpox: correct me if I'm wrong
10:19 Gpox Virtual is a memory resource and it seams stupid to store files in it, better to only have parsed resources for easy access
10:19 olass I agree
10:19 olass but we need a temp folder
10:20 egonw OK, i'll see where things go...
10:20 egonw anyway, I think I like a $TMP folder backed Virtual...
10:21 olass yes, why not?
10:22 de__maas left #bioclipse
10:24 olass edrin: is bug 239 still valid?
10:26 CIA-28 bioclipse: goglepox * r8340 /bioclipse2/trunk/plugins/net.bioclipse.core/src/​net/bioclipse/core/ResourcePathTransformer.java:
10:26 CIA-28 bioclipse: Quick fix to allow ResourcePathTransformer to work with saving.
10:26 CIA-28 bioclipse: '/Virtual/foo.bar' is decided to be a workspace file if
10:26 CIA-28 bioclipse: project 'Virtual' exists otherwisse it will default
10:26 CIA-28 bioclipse: to a absolute path on systems with '/' as root
10:28 Gpox fixes bug #197
10:29 masak @pz 197
10:29 jonalv zarah: ping
10:29 zarah jonalv: pong, sweetie
10:29 edrin olass: do you have an url?
10:30 masak @pz #197
10:30 zarah http://tinyurl.com/8yeuwr
10:31 olass edrin: to what?
10:31 edrin @pz 239
10:31 zarah http://tinyurl.com/9o4nsg
10:31 edrin olass: no
10:31 edrin it is working now
10:31 olass ok, please close it
10:32 olass egonw: is it OK if I add the method
10:32 olass /**
10:32 olass * Save a list of molecules to file
10:32 olass * @param molecules The molecules to save
10:32 olass * @param path Path to file to save to
10:32 olass * @param filetype either CML or SDF
10:32 olass * @throws BioclipseException
10:32 olass * @throws CDKException
10:32 olass * @throws CoreException
10:32 olass */
10:32 olass @Recorded
10:33 olass public void saveMolecules(List<? extends IMolecule> molecules, String path, String filetype)
10:33 olass throws BioclipseException, CDKException, CoreException;
10:33 olass ?
10:33 olass just delegates to IFile via resourcePathTransformer...
10:33 jonalv olass: aaah pastebin
10:33 masak olass: please don't do that.
10:33 olass egonw?
10:33 olass masak why not?
10:33 masak olass: it hurts.
10:33 olass it should be working now
10:33 olass even with virtual
10:33 jonalv olass: use some pastebin solution instead
10:33 masak olass: that's what nopaste is for.
10:33 egonw olass: if you add the proper unit test for it...
10:34 olass egonw: are you rewriting teh saveMolecule and saveMolecules ?
10:34 egonw no, not yet
10:35 olass why do we have saveCML(path) and also saveMolecule(path, filetype=cml)?
10:35 egonw did not see your reply on whether MDL molfile is not enough for now...
10:35 olass is this deliberate?
10:35 egonw olass: no idea
10:35 egonw I did not engeneer that code
10:35 olass I need MDL and CML
10:35 olass and SDF
10:35 olass so single mols in MDL and CML, multiple mols in SDF and CML
10:36 olass this is very important to me
10:36 egonw olass: I think we have a serious problem with identifying who wrote a piece of code...
10:36 egonw I can hapilly hack away in it... (this afternoon=
10:36 egonw I can hapilly hack away in it... (this afternoon)
10:36 olass egonw: sounds good
10:36 shk3 the saveCML was already there when I added saveMolecule
10:36 zarah shk3: You have new messages. Write '/msg zarah @messages' to read them.
10:36 egonw but changing an API would really require chatting with the original author
10:36 olass not at this point
10:36 shk3 so I left it and made it to use saveMolecule
10:36 egonw and I have no clue who wrote these save things...
10:37 shk3 if I remember correctly
10:37 egonw and I have no clue who originally wrote these save things...
10:37 olass since we are so unstable it is OK for you
10:37 shk3 @messages
10:37 zarah shk3: 1 h 35 m 39 s ago, olass said Please use Java5 in Bioclipse!
10:37 shk3 grrr
10:37 shk3 I switches to java five 10 times
10:37 shk3 where is java 6 left
10:37 shk3 ?
10:37 egonw olass fixed it already
10:38 olass egonw: you are the responsible person for chemoinfo, that gives you the authority for that (IMO at least, you might disagree)
10:38 egonw some @override uses
10:38 olass shk3: fixed already
10:38 olass just very anoying
10:38 olass annoying
10:38 olass (like a paste here, I'll try to stay away from it)
10:38 egonw shk3: I use a BC2 dedicated workspace
10:39 olass that is probably a good idea
10:39 egonw shk3: each workspace can have it's own set of installed JDKs
10:39 egonw shk3: some of my other WSs have Java6, but my BC2 is hard set to only know about Java5
10:40 jonalv olass, egonw: YEa I think we have problems identifying who has written what. Question is just what we can do about it?
10:40 egonw svn/git annotate does not get you far enough :(
10:40 olass this is early in devel
10:40 olass we have to live with it for now
10:40 egonw also noticing that someone has been hacking in code I am responsible for is impossble...
10:41 olass after a release things must be more formalized
10:41 olass with patches maybe?
10:41 olass egonw: I like patches more and more
10:41 egonw olass: good :)
10:41 olass just need to learn git
10:41 egonw olass is seeing the light at the end of the tunnel
10:41 olass well, it's not bright light
10:42 olass seems to be hard to learn...
10:42 egonw it will become brigher
10:42 olass sure
10:42 egonw you just have to be careful to run to fast...
10:42 egonw and fall in the abysses just outside the tunnel
10:42 egonw (like me and jonalv have done)
10:42 egonw you'll live...
10:42 egonw just a big climb back up the mountain :)
10:42 egonw and then things just fly
10:43 * egonw has been reading to much literature, he thinks
10:43 jonalv :)
10:44 egonw (btw, I *can* recommend the Otherland quattrology)
10:44 egonw (??? what is the next after trilogy??)
10:45 jonalv egonw: Tad Williams?
10:46 jonalv egonw: I can also recommend Robin Hobb :)
10:52 masak tetrology?
10:52 egonw jonalv: yes, Tad
10:53 masak lunch &
10:53 * jonalv @lunch
10:55 olass @tell jonalv I'd really appreciate that wiki page for long running jobs in JS
10:55 zarah Consider it noted.
11:02 olass egonw: can an MDL molfile not contain properties?
11:02 olass like a single entry in an SDFile?
11:02 egonw no, you need a MDL SD file for that
11:02 olass why?
11:02 egonw yes, a single entry SD file is fine
11:02 olass that is SO bad
11:02 egonw because the MDL molfile format does not support properties
11:03 egonw which is why I prefer CML
11:03 * olass thought SDFile is many MDL molfiles
11:03 egonw almost, yes
11:03 egonw + properties :)
11:03 olass grr
11:03 * olass HATES legacy formats
11:03 egonw join the club
11:03 egonw we're called Blue Obelisk
11:10 CIA-28 bioclipse: ospjuth * r8341 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.business.test/src/net/bioclipse/cdk/​business/test/CDKManagerPluginTest.java: Adapted saveSDFwithProps to use /Virtual file, and wrote new test for saving CMLmolecules with properties to /Virtual file.
11:32 edrin egonw: you said it eats now cml? what was the problem=
11:32 edrin ?
11:32 egonw the schema
11:32 edrin ok
11:32 egonw originally, I hoped to force a single CML element
11:32 egonw but I did not manage to compose a basic XML Schema to refer to the CML element
11:33 egonw so, I now just pass the full CML XML Schema as port description
11:33 egonw and have the service do the rest
11:33 edrin so is it possible to generate bindings for all your services now in bioclipse :-?
11:33 egonw have not, and will not try that :)
11:33 egonw actually...
11:33 egonw I did start it...
11:33 egonw but BC2 just froze :)
11:33 edrin and?
11:33 edrin why?
11:33 edrin is it that big?
11:34 egonw dunno
11:34 egonw proc load was not 100%
11:34 egonw well, try it...
11:34 egonw the service is up and running :)
11:34 edrin you should see the compile of the schema in the eclipse debug console...
11:34 edrin xmlbeans prints to it
11:34 edrin i cant i am in the lab
11:37 egonw ack
11:50 CIA-28 bioclipse: goglepox * r8342 /bioclipse2/trunk/plugins/ (6 files in 3 dirs):
11:50 CIA-28 bioclipse: Cleand up 2D structure views.
11:50 CIA-28 bioclipse: Added part listener to react editor closing.
11:50 CIA-28 bioclipse: resolves bug #184
11:50 zarah bug #184 | http://tinyurl.com/77sfzt
12:08 jonalv olass: oki perhaps that's what I should do now then... :)
12:08 zarah jonalv: You have new messages. Write '/msg zarah @messages' to read them.
12:08 jonalv zarah: just tell me...
12:08 zarah jonalv: 1 h 12 m 50 s ago, olass said I'd really appreciate that wiki page for long running jobs in JS
12:12 gilleain joined #bioclipse
12:18 CIA-28 bioclipse: goglepox * r8343 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.jchempaint/plugin.xml:
12:18 CIA-28 bioclipse: Changed editor id to match popupmenu registration.
12:18 CIA-28 bioclipse: Now works for both MDL and CML
12:19 CIA-28 bioclipse: goglepox * r8344 /bioclipse2/trunk/plugins/ (9 files in 6 dirs): Removed unused imports and some other cleanup.
12:36 jonalv olass: describing this is gonna take a while...
12:45 egonw why am I always struggling with regexp in Java???
12:46 egonw in Perl it is so easy...
12:46 egonw :(
12:46 gilleain regular expressions are never easy
12:46 egonw I think Sun is really doing something wrong with java.regexp
12:46 egonw never had trouble with it in Perl...
12:46 masak gilleain: I'm not sure I agree...
12:46 gilleain well, it's built into the language in perl.
12:46 gilleain masak: well, you wouldn't :p
12:47 egonw yes, I think that in Java you have to escape things, really makes it bad
12:47 egonw let alone the incomprehensible Pattern, Match classes
12:47 gilleain masak : did you see the s/\//\//g in one of my bug reports yesterday. I liked that regex.
12:48 egonw ummm... you sure about that one?
12:48 gilleain You don't have to make a Pattern class every time, just if you want to re-use it.
12:48 egonw replace each '/' with '/' ?
12:48 masak gilleain: I missed it. :) I'd have written that as s[/][/]
12:48 masak s[/][/]g
12:49 gilleain Well, it was meant to substitute / for \
12:49 masak ok, s[/][\\]g, then.
12:50 gilleain Also, I knew the alternate slash stuff, I like # for that: s#/#\\#g
12:50 gilleain Although knowing my regex-luck, that probably doesn't work. Accursed Perl.
12:53 egonw I hate it when I forget to add in the while (line != null): line = reader.readLine();
12:53 egonw a foreach support for that would be nice too
12:53 gilleain heh. I was doing that yesterday:
12:53 gilleain for (String line : new IterableFile("path/to/file")) {
12:54 gilleain where IterableFile is a (pretty dumb) utility class.
12:55 egonw nice
12:56 jonalv zarah: seen olass
12:56 zarah olass was last seen 1 h 52 m 37 s ago in #bioclipse saying 'grr'
12:56 jonalv he just disaapareared?
12:56 gilleain problem is, you can't yield in java, so it has to read the whole file into a string array before you can read it. but that's okay sometimes.
12:57 gilleain [12:43] * olass (n=olas@83.251.99.201) Quit ("Computer has gone to sleep")
12:57 jonalv masak: http://wiki.bioclipse.net/index.php?ti​tle=How_to_run_manager_methods_in_jobs
12:57 zarah jonalv's link is also http://tinyurl.com/3sc3vo
13:23 CIA-28 bioclipse: egonw * r8345 /bioclipse2/trunk/plugins/net.bioclipse.gist/ (15 files in 7 dirs): Added a 'download from gist' wizard
13:26 jonalv http://wiki.bioclipse.net/index.php?ti​tle=How_to_run_manager_methods_in_jobs
13:26 zarah jonalv's link is also http://tinyurl.com/3sc3vo
13:26 jonalv zarah: tell olass http://wiki.bioclipse.net/index.php?ti​tle=How_to_run_manager_methods_in_jobs
13:26 zarah jonalv's link is also http://tinyurl.com/3sc3vo
13:26 zarah Consider it noted.
13:41 olass joined #bioclipse
13:42 olass hi
13:42 zarah hello olass, you fantastic person you
13:42 zarah olass: You have new messages. Write '/msg zarah @messages' to read them.
13:42 olass @msg
13:42 zarah olass: 15 m 28 s ago, jonalv said http://wiki.bioclipse.net/index.php?ti​tle=How_to_run_manager_methods_in_jobs
13:42 olass jonalv++
13:42 jonalv olass: oh don't prasie me until you have read it...
13:43 olass :-)
13:45 egonw how do I pop up a message to the user again, without running in thread access trouble?
13:46 * egonw is searching hos BC2 workspace
13:47 egonw ok, MOSS plugins has somethine
13:48 egonw ok, no
13:56 egonw bla
13:56 egonw it worked...
13:56 egonw but not so happy about the current code... Ö(
13:56 egonw :(
13:56 CIA-28 bioclipse: egonw * r8346 /bioclipse2/trunk/plugins/net.bioc​lipse.gist/src/net/bioclipse/gist/​wizard/GistNumberWizardPage.java: Check for positive integers
13:57 jonalv egonw: what are you talking about? :)
13:57 egonw the "Download from Gist" wizard
13:57 CIA-28 bioclipse: egonw * r8347 /bioclipse2/trunk/plugins/net.bioclipse.gist/src/​net/bioclipse/gist/wizard/NewFromGistWizard.java: Report when a Gist does not exist
13:57 jonalv oh, cool
13:57 egonw GUI equivalent of gist.load(18315)
13:57 jonalv will it have search as well?
13:57 egonw the wizard is OK, the code is not so clean, IMO
13:58 egonw no search
13:58 egonw just by number
13:58 jonalv :(
13:58 gilleain one step at a time!
13:58 jonalv good point
13:58 egonw ok, will now write a manager...
13:58 egonw jonalv: got 5 minutes?
13:58 egonw to explain me the new annotation and interfaces?
13:58 jonalv egonw: you could probably have 10 :)
13:58 egonw (or a wiki URL?)
13:59 jonalv egonw: there is no annotation
13:59 jonalv it's all done by method signatures now
13:59 egonw oh...
13:59 egonw ok... can handle that
13:59 jonalv egonw: http://wiki.bioclipse.net/index.php?ti​tle=How_to_run_manager_methods_in_jobs
13:59 zarah jonalv's link is also http://tinyurl.com/3sc3vo
13:59 egonw even on fridays
14:00 jonalv it's very much friday today...
14:00 gilleain heh. gist plugin seems to work.
14:00 egonw so no @Job anymore?
14:00 jonalv egonw: nope
14:00 egonw gilleain: good :)
14:00 olass egonw: I really need the saveCML to work...
14:00 olass is it hard to fix?
14:00 olass (or did I just not update)
14:00 jonalv egonw: just provide a method with a monitor...
14:00 egonw what's your problem with it?
14:00 olass it saves me mdl
14:00 egonw OK.
14:00 egonw that should be easy to fix
14:01 jonalv egonw: actually there are a little more to it... :)
14:01 egonw jonalv: so all annotation is obsolete now?
14:01 olass egonw: please ping me when saveCML works
14:01 de__maas joined #bioclipse
14:01 jonalv yea, I should remove them
14:01 olass need to write a presentation for teaching on tuesday :-(
14:01 olass might take me an hour
14:01 * gilleain chuckles at downloading gist 18315->run->open with jmol
14:02 jonalv olass: and I won't be there to see it... :(
14:02 olass jovalv: would be waste of time for you
14:02 olass it's _REALLY_ basic
14:02 gilleain egonw++
14:03 jonalv egonw: how can I avoid writing: git stash;git svn rebase;git stash apply
14:03 jonalv each time because I want to keep changes to my product...
14:03 egonw you should commit things you want to save
14:04 jonalv but I don't wanna change the bioclipse.product in svn each time I acommiot...
14:04 egonw ah, right
14:04 egonw yes, that's a nasty one...
14:04 egonw maybe we should add it to .gitignore
14:04 egonw annoys me big time too
14:04 CIA-28 bioclipse: egonw * r8348 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Don't overwrite the passes filetype
14:04 egonw olass: please update to that rev
14:04 olass ok
14:05 egonw BTW, why the hell does it force CML files to end with ".cml"??
14:05 jonalv egonw: if we ignore it we won't get it at all, right?
14:05 jonalv that wouldn't work either...
14:05 egonw and MDL molfiles as .mol
14:05 jonalv sounds like a good standard to me...
14:05 egonw I hate it...
14:05 egonw fortunately olass thinks I am the cheminfo god, so I get to decide :)
14:05 jonalv calling CML files for .cml is rather good practice, not?
14:06 egonw bwahahahah
14:06 gilleain the createSDFile function was shk3's by the way
14:06 gilleain I know because he always uses StringBufferInputStream :)
14:06 CIA-28 bioclipse: ospjuth * r8349 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (CDKManager.java ICDKManager.java): added saveMolecules(..) to path, delegates to IFile via ResourcePathTransformer.
14:06 jonalv egonw: is there a gist feature?
14:07 egonw feature?
14:07 egonw no, was hoping to make it part of Bioclipse default
14:07 jonalv oki
14:07 egonw I think it is an excellent way to get novice started...
14:07 jonalv yea
14:07 jonalv well
14:07 egonw olass: why the hell does it force CML files to end with ".cml"??
14:07 olass egonw: you are the closest thing to a cheminf god we have at least
14:07 olass you decide
14:07 olass I donät like that either
14:08 egonw I like to give people the freedom the misname their files anyway they like
14:08 egonw ah... but you added that code
14:08 egonw (git blame)++
14:08 egonw OK, will remove it then... now...
14:09 jonalv egonw: how do I find a gist to download?
14:09 egonw http://delicious.com/tag/bioclipse+gist
14:09 zarah egonw's link is also http://tinyurl.com/5gqjet
14:09 CIA-28 bioclipse: ospjuth * r8350 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.business.test/src/net/bioclipse/cdk/​business/test/CDKManagerPluginTest.java: Test new method to save SDFiles using a Virtual path.
14:09 egonw jonalv: if you are interested in the cdk manager, try:
14:10 egonw http://delicious.com/tag/b​ioclipse+gist+manager:cdk
14:10 zarah egonw's link is also http://tinyurl.com/6xhm3r
14:10 jonalv egonw: we should link that page from within Bioclipse
14:10 jonalv or even show that list somehow... :)
14:11 olass egonw++ //saveCML works now
14:11 egonw yes, would be nice to be able to show that list in Bioclipse too...
14:11 CIA-28 bioclipse: egonw * r8351 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Removed annoying feature (IMHO) to not ignore the file name the user wants to give a file
14:11 gilleain Btw : I get problems with the net.bioclipse.encryption plugin.
14:11 jonalv egonw: nice to get to download but it saves it as .txt
14:11 gilleain It says that it is missing org.apache.commons.codec?
14:12 egonw jonalv: yes, because the Gist may be a JavaScript
14:12 egonw but generally anything...
14:12 jonalv egonw: hm that is a problem...
14:12 egonw have you tried naming it .js
14:12 egonw ?
14:12 gilleain that works
14:12 egonw I have not tried that yet :)
14:13 gilleain heh : commiting without testing? That's code-confidence :)
14:13 jonalv yea that works but I would prefere to not have to do that. It's sort of counterintuitive
14:13 egonw yes, works
14:13 sneumann bye, nice weekend
14:13 jonalv especially since you just argued that .cml shouldn't be enforced...
14:13 egonw jonalv: but saving Shakespeare as JavaScript is?
14:13 egonw sneumann: bye!
14:13 gilleain there could be a "save as" control in the dowload wizard?
14:14 jonalv egonw: I don't think I said that...
14:14 gilleain if you know that it is javascript, eg.
14:14 egonw gilleain: umm... the second wizard page?
14:14 jonalv yea what gilleain said!
14:14 gilleain egonw: suppose so.
14:15 gilleain well, you can rename it on that page anyway in fact.
14:15 jonalv I say add plugin to the core feature!
14:15 egonw gilleain: indeed
14:16 egonw there is one bug...
14:16 gilleain huh. 27116 didn't download.
14:16 egonw the resource does not automatically open for me...
14:16 egonw because it does not exist
14:16 egonw redirects me too:
14:16 egonw http://gist.github.com/gists/new
14:16 zarah egonw's link is also http://tinyurl.com/7tcnp8
14:16 gilleain http://gist.github.com/27116
14:17 egonw ok, typo :)
14:18 gilleain hmm. FileNotFoundException
14:18 egonw hahahaha
14:18 gilleain http://gist.github.com/raw/27116/df1cf1fbcde9f
14:18 zarah gilleain's link is also http://tinyurl.com/7ra3g9
14:18 egonw ummm... my regexp does not include the '0'
14:18 egonw hahahaha
14:18 gilleain oops.
14:18 * egonw mubles 'idiot'
14:18 * egonw mumbles 'idiot'
14:19 gilleain ahh : ""/([1-9[a-f]]+)";"
14:20 gilleain ahh. that fixed it.
14:21 CIA-28 bioclipse: egonw * r8352 /bioclipse2/trunk/plugins/net.bioclipse.gist/src/​net/bioclipse/gist/wizard/NewFromGistWizard.java: OK, the hexadecial system includes the '0'... mmm :)
14:21 jonalv egonw: 33421 came back emnpty for me...
14:22 egonw sure
14:22 egonw check commit 8352
14:22 jonalv I thought there would be an exception...
14:22 gilleain oh, btw '#' is not a legal javascript comment character, I think.
14:24 egonw @pz has bug component for Gist, IIRC
14:24 zarah egonw: I couldn't find anything on 'has bug component for Gist, IIRC' in the database.
14:24 gilleain That is because you are a script, zarah, and are not able to parse sentences in a context-sensitive fashion.
14:24 jonalv egonw: regarding 33421
14:24 jonalv egonw: what is going on?
14:25 jonalv is there some internal state in the manager between row 2 and row 3?
14:25 egonw jonalv: huh?
14:26 jonalv egonw: could you explain what row 3 does?
14:26 jonalv and row 2
14:26 jonalv especially row 2
14:26 egonw row 3 of what?
14:26 jonalv 33421
14:26 jonalv :)
14:27 egonw mom, let me download that Gist
14:27 egonw the difference between generate() and generateKey()?
14:27 jonalv egonw: yea
14:27 egonw well... one generates an InChI, the other the InChIKey
14:28 jonalv but you don't catch any ichi
14:28 jonalv from that call...
14:28 * jonalv is afraid this won't work if multipole threads ar using the inchi manager simultansously...
14:28 egonw go on...
14:28 jonalv edrin++ has a point in that we might be doing something we will regret in enforcing thread safety on all managers...
14:29 egonw no, there should not be states
14:30 jonalv okey so I don't need to run generate before running generateKey then?
14:30 egonw no
14:30 jonalv so the call to generate in that script does nothing?
14:30 jonalv or rather it does something buit the result is just ignored?
14:30 egonw it does
14:30 egonw it generates the InChI
14:31 egonw and returns it
14:31 egonw inchiStr = inchi.generate(mol)
14:31 egonw I'll update the Gist
14:31 jonalv ah since you dind't print it or save it I got worried... :)
14:31 jonalv it might actually be okey then :)
14:32 jonalv I like the gist plugin btw. egonw++
14:32 egonw http://gist.github.com/33421
14:32 egonw yes, makes live easier
14:32 egonw that's what we develop Bioclipse for
14:32 gilleain Really?
14:33 gilleain I thought you developed bioclipse so that I had something to update every day :)
14:33 * gilleain likes updating
14:33 jonalv egonw: I liked that article btw. They seems to have built everything in their projkect already :)
14:33 gilleain I always thought that it was very kind of you all - making code all the time...
14:34 jonalv :)
14:34 egonw jonalv: I've met Modest in the past... nice guy
14:34 jonalv okey
14:34 egonw really a shame they did not reuse anything from the open source world
14:34 egonw needless duplication, I guess...
14:35 jonalv so I thought I saw jmol there. It was not then?
14:35 * egonw thinks gilleain should checkout KDE and Linux
14:35 gilleain Let's not go crazy, egon.
14:35 gilleain :)
14:35 jonalv lots of updates there? :)
14:35 egonw :)
14:36 gilleain Anyway I have a new MacBookPro, so I have no need for this 'linux' thing.
14:36 egonw sorry to hear about that
14:36 * jonalv quite often whished he ran Ubuntu on his MacBook
14:37 gilleain Blasphemy!
14:37 jonalv lol
14:37 gilleain I have java6, so I am happy.
14:37 egonw gilleain: like using OS/X for Java development?
14:37 jonalv OSX is cute and so but there are some things that are not as nice...
14:37 egonw gilleain: you have?
14:37 egonw OSX finally has J6?
14:37 gilleain 64bit does
14:37 gilleain since june
14:37 egonw ic... nice
14:38 * jonalv wonders if 32 will ever get...
14:38 gilleain nope
14:38 gilleain doubt it
14:40 jonalv @pz 257
14:40 zarah http://tinyurl.com/9qmvsk
14:40 jonalv Could I get some attention on this bug: http://tinyurl.com/9qmvsk
14:40 jonalv I thin it is important
14:40 jonalv am I the only one?
14:41 CIA-28 bioclipse: egonw * r8353 /bioclipse2/trunk/plugins/n​et.bioclipse.ui/plugin.xml: Renamed editor to address name conflict with the WST XML editor (that will solve major future confusion when people report, he, autocomplete does not work in the 'XML Editor', implements #247)
14:42 egonw no clue about 257
14:42 jonalv egonw: no clue?
14:42 gilleain jonalv: what onion?
14:42 jonalv egonw: don't you have an oppinion?
14:42 egonw jonalv: wiki.bioclipse.net?
14:42 egonw oh, opinion
14:42 egonw yes, sure upgrade
14:42 jonalv gilleain: the background of the Bioclipse wiki
14:43 jonalv it's the vanilla flavor wiki background
14:43 jonalv it feels very b to have that one...
14:43 gilleain very /b/ ? :)
14:43 gilleain b=bad?
14:43 jonalv free for interpration...
14:44 jonalv b as in bad or be as in not a
14:44 gilleain boring? banal? batty?
14:44 jonalv not sure what battty is but yea I think you get the pint
14:44 jonalv |point
14:45 jonalv |got the point
14:45 gilleain 'batty' means mad in British English. It means something else in Jamaican English.
14:46 jonalv hm do I dare to ask?
14:46 gilleain Best not.
14:47 olass @gg batty jamaican
14:47 zarah olass: http://en.wikipedia.org/wiki/Batty_boy
14:47 olass right
14:47 gilleain indeed.
14:50 * jonalv just made it back from wikipedia. (dangerous place on days which are very much fridays...)
14:51 gilleain Wikipedia is a quicksand of pages. Especially on days beginning with "Frida".
14:53 CIA-28 bioclipse: egonw * r8354 /bioclipse2/trunk/features/net.​bioclipse_feature/feature.xml: Made the Gist plugin part of the BC2 Core. Rationale: it provides an easy way to have people download cool scripts, and learn about the scripting powers
14:53 olass +1
14:54 jonalv egonw: does delicious have some api which we can use to browse for annotated gists from tht wizard?
14:54 egonw jonalv: yes, that should be possible
14:54 jonalv egonw: that would be _so_ cool :)
14:55 egonw jonalv: file a enhancement bug report
14:55 jonalv willl do :)
14:57 jonalv hm we will want a way to publish as gist too I think... :)
14:58 egonw yes, in the future we need to integrate egit
14:58 jonalv @gg egit
14:58 zarah jonalv: http://freshmeat.net/projects/jgit/
14:58 egonw it's the eclipse git plugin :)
14:59 jonalv ah well it's not very mature nor very good I think
14:59 egonw file bug reports :)
14:59 jonalv but perhaps it will get
14:59 egonw they do Mylyn, I think :)
15:00 jonalv egonw: are you using it?
15:00 egonw not at this moment
15:00 egonw but over they holidays, they did some good work again...
15:00 egonw so, might start using it...
15:00 jonalv I tried it a bit but when I uninstalled it it crached my Eclipse so I had to download a new one... :(
15:00 egonw it allows changing branches from within eclipse
15:01 egonw so, no Refresh horrors anymore
15:01 jonalv that's intresting :)
15:05 de__maas left #bioclipse
15:08 jonalv how should an object look on the console?
15:08 jonalv <User : name = jonalv>
15:08 jonalv could that be something?
15:09 egonw JSON?
15:09 jonalv @gg JSON
15:09 zarah jonalv: http://www.json.org/
15:09 jonalv intressant
15:10 gilleain "{ Username : jonalv }" then?
15:10 jonalv but I want to say the object type as well
15:10 jonalv that is important
15:10 jonalv the object type is User
15:10 jonalv the filed name is name
15:11 jonalv and the value is jonalv
15:11 jonalv that is what I want to present
15:11 gilleain { "User": { "name" : "jonalv" } }
15:11 gilleain http://www.json.org/example.html
15:11 zarah gilleain's link is also http://tinyurl.com/emxkb
15:12 * jonalv does not like it
15:12 gilleain haha. oh well.
15:12 jonalv why use { for both object spearation and list of params
15:12 egonw jonalv: on the other hand... there are is JSON Java libs around
15:12 jonalv that is two very different things in this case
15:13 gilleain I think lists are separated by commas
15:13 egonw and JavaScript is nice about it
15:13 egonw so, people can easily copy/paste that to the JS editor
15:13 jonalv egonw: I see these points
15:13 gilleain I may be getting it wrong ^
15:13 jonalv I am just not sure it's easily enough to erad
15:15 gilleain <user><name>jonalv</name><​pass>mypass</pass></user> ==
15:15 jonalv I mean is that the output you want when you run cdk.fromSMILES("CCC")
15:15 gilleain {"user" : { "name" : "jonalv", "pass" : "mypass" }}
15:16 jonalv oh that is important too. I definilty don\t want it to print the password...
15:17 gilleain true.
15:17 jonalv and for a molecule I don't think we want to output all fields
15:17 jonalv imagine printing an array of a couple of molecules...
15:17 jonalv no this is not what we want I think
15:17 egonw cdx has a method to dump all details
15:18 jonalv so we neeed something more light weight
15:18 jonalv I am about to implement toString methods on the structuredb domain objects but I am not quite sure what I want...
15:18 gilleain don't we currently just return the object_id from a function call?
15:19 jonalv gilleain: yea we call toString on the object...
15:20 jonalv but perhaps the { is not a bad idea
15:20 jonalv {User : name=jonalv, sudoer=true}
15:20 jonalv perhaops?
15:21 gilleain 'spose.
15:21 gilleain but then it's almost-but-not-quite-json
15:21 jonalv {DBMolecule : name="12345", smiles="CCCC"}
15:21 egonw and yet another format
15:22 jonalv it's just output from the console guys...
15:22 gilleain Well sure.
15:22 jonalv it should be humanly readable but not machine readable I think
15:22 egonw jonalv: ok, now really back to the IGistManager
15:22 egonw jonalv: so, no annotation at all?
15:22 egonw just extend IBioclipseManager?
15:23 jonalv egonw: no @Job annotation no. You still need the @publishclass an duch..
15:23 jonalv |such
15:23 egonw ok
15:24 jonalv egonw: have a look at structuredb or cdk for how to do it the new way
15:24 egonw yes, I have ICDKManager open
15:24 jonalv that is for what to write in the spring config xml and in the activator and the facory
15:24 jonalv managerfactory that is
15:25 jonalv we really should make that Eclipse plugin for Bioclispe development soonish... :)
15:25 egonw yes
15:25 egonw btw, what's the deal with IBioclipseJSManager again?
15:26 jonalv that is for future use actually
15:26 jonalv or hm
15:26 jonalv perhaps I used it somethere
15:27 jonalv no I think it could be removed but it makes it possible to distisguish a gui flavored manager from a js flavored one
15:27 jonalv that mgiht be useful sometime
15:27 egonw ok
15:28 jonalv in fact I used it in code that I refactored into not using any longer the other day...
15:28 jonalv ...I think at least... :)
15:28 jonalv it's not so easy for a bear with a very small brain...
15:42 gilleain EGONNN!
15:42 gilleain What is this yellow text on a white background on the wiki?
15:42 egonw hahaha
15:43 gilleain Answer : it is unreadable, that's what it is.
15:43 gilleain {:/
15:43 jonalv what page?
15:43 * jonalv wanan see :)
15:43 gilleain http://wiki.bioclipse.net/index.p​hp?title=Checking_out_Bioclipse_
15:43 zarah gilleain's link is also http://tinyurl.com/89pc4e
15:43 egonw gilleain: make it orange, or what ever
15:43 egonw but not red
15:44 gilleain sorry, that url is wrong
15:44 gilleain it should have a "2" at the end.
15:45 jonalv lol yellow text :)
15:45 gilleain now green
15:45 jonalv much better :)
15:46 gilleain in accordance with fashion, and logic.
15:57 olass joined #bioclipse
15:58 jonalv o/
15:58 olass oi?
15:58 jonalv it's a little man waving :)
15:58 olass allt väl?
15:58 olass all is well?
15:58 jonalv well enough
15:59 olass for a friday :-.)
15:59 jonalv yea
15:59 jonalv I have some strange structuredb behavior but I am ignoring it for the moment...
16:00 jonalv olass: and you?
16:01 olass not bad
16:01 olass ok I guess
16:01 olass a bit hungry
16:01 jonalv good good
16:01 jonalv :)
16:01 * jonalv is a bit tired :)
16:01 egonw gist.load(18315, "/Test/x.js")
16:03 jonalv what works?
16:03 jonalv cool :)
16:03 jonalv now you just need a progressmonitor for it too?
16:04 jonalv hm but can you really get progresscalls from that?
16:12 CIA-28 bioclipse: egonw * r8355 /bioclipse2/trunk/plugins/net.bioclipse.gist/ (9 files in 4 dirs): Added a manager to allow 'gist.load(18315, '/Test/x.js')
16:13 CIA-28 bioclipse: egonw * r8356 /bioclipse2/trunk/plugins/net.bioc​lipse.gist/src/net/bioclipse/gist/ (business/GistManager.java wizard/NewFromGistWizard.java): The wizard now uses the manager, so that the wizard issueing gets recorded :)
16:25 CIA-28 bioclipse: jonalv * r8357 /bioclipse2/trunk/plugins/net.bioclipse.struc​turedb/src/net/bioclipse/structuredb/domain/ (9 files): [StructureDB] added toString on all domain objects
16:29 CIA-28 bioclipse: goglepox * r8358 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint.view/src/net/bioclipse/cd​k/jchempaint/view/SWTFontManager.java: Added FontTest class to visualize fonts at different scale
16:30 CIA-28 bioclipse: goglepox * r8359 /bioclipse2/trunk/plugins/net.bioclipse.cdk.jchem​paint.view/src/net/bioclipse/cdk/jchempaint/view/ (JChemPaintWidget.java SWTFontManager.java): Added Font option to the constructor.
16:39 gilleain heh I just realised : be wary of making gist interaction _too_ easy, or it would be possible to have quined gists. :)
16:50 jonalv gilleain: "quined"?
16:51 gilleain well, it's not the right term, but scripts that downloaded themselves, or ran themselves, leading to endless recursion.
16:52 gilleain you would need to be able to run a script from the command line, though and maybe some other things.
16:54 gilleain Also, bioclipse viruses, I suppose.
16:54 egonw oh, cool
16:54 egonw then we can seel anti-virus software
16:54 egonw sell
16:54 gilleain haha.
16:58 CIA-28 bioclipse: egonw * r8360 /bioclipse2/trunk/cdk-externals/tru​nk/org.openscience.cdk.sdg/src/org/​openscience/cdk/layout/templates/ (. adamantane.cml cubane.cml diamantane.cml templates.list): Added missing templates (fixes #240 and #252)
16:58 zarah bug #240 | http://tinyurl.com/9hlrcz
16:58 egonw zarah: hej, you're missing one!
16:58 zarah egonw: are you making fun of me?
17:01 gilleain I can confirm that it works, with:
17:01 gilleain jcp.setModel(cdk.generate2dCoordinates(​cdk.fromSMILES("C12C3C4C1C5C4C3C25")))
17:01 gilleain interestingly:
17:01 egonw yeah
17:01 egonw the template files were missing
17:01 gilleain @gg cubane smiles
17:01 zarah gilleain: http://www.daylight.com/dayhtml​/doc/theory/theory.smiles.html
17:01 egonw no idea how that happened...
17:01 gilleain curses, that didn't work.
17:01 egonw is the template properly picked up?
17:02 gilleain yup. I get a cube in the jcp window
17:02 egonw good
17:02 gilleain try googling "cubane smiles" in a browser?
17:02 egonw gives me the same link
17:03 gilleain oh, I get the smiles as a top hit (thanks to wikipedia)
17:03 gilleain It looks like:
17:03 gilleain Cubane - Smiles: C12C3C4C1C5C4C3C25
17:03 egonw no, not here
17:04 egonw but I get redirected to google.se
17:04 gilleain huh. weird.
17:04 egonw I guess our local engine assumes Swedish are less dumb than America, and assume we can figure it out from the hits :)
17:05 gilleain hah, maybe. It seems that google takes stuff from the info box on wikipedia pages if they are in the query.
17:05 gilleain Also works with molar mass
17:07 gilleain egonw: do you want me to mark bug 252 as verified?
17:07 egonw no, closed
17:07 egonw after verification, that is
17:07 gilleain oh, right, okay.
17:09 egonw ok, really dinner time now...
17:09 egonw have a nice weekend!
17:10 gilleain U2
17:12 grandm44 have a nice week end all bc developpers
17:12 olass Gpox: there?
17:12 Gpox o/
17:12 olass how do I get the raw location of a data file in my plugin
17:12 olass outside of the src
17:13 olass like an icon
17:13 olass or a data file
17:13 olass (don't remember)
17:13 olass FileLocator.find something?
17:13 olass but how get the filesystem relative path?
17:15 olass any ideas Gpox?
17:15 Gpox no, what is it for?
17:16 olass for reading a data file in the plugin
17:16 olass so need to get the path to the data file
17:16 olass as a File
17:18 olass I think I solved it
17:19 olass yup
17:19 olass sorry
17:19 olass URL url = FileLocator.find( bundle, new Path(DATAFILE_ALL),null );
17:19 olass FileLocator.toFileURL(url).getFile();
17:19 olass that does the trick
17:20 CIA-28 bioclipse: goglepox * r8361 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java: Implemented doSave but diry management is still broken
17:20 CIA-28 bioclipse: goglepox * r8362 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java:
17:20 CIA-28 bioclipse: Removed instanceof check for Selection and adds empty selection if selection is not atoms and bonds
17:20 CIA-28 bioclipse: (fixes bug #177)
17:20 zarah bug #177 | http://tinyurl.com/7uhks2
17:28 olass Gpox: a question
17:28 olass in the new moleculesTable
17:28 olass how do I do refreshAllTables?
17:28 olass I used to do: molEditor.getCTable().refreshAllRows();
17:28 olass how can I do now?
17:28 olass things seem to have changed...
17:29 olass Gpox?
17:33 Gpox i belive that is not implemented
17:34 Gpox MoleculeTableviewer.refresh()
17:39 * jonalv calls this a week
17:39 jonalv cya for the next
17:39 gilleain cya
17:39 olass bye!
17:40 olass Gpox: consider this an RFE then :-)
17:41 Gpox RFE?
17:42 olass Request for Enhancement
17:42 olass will file you a bug too :-)
17:43 Gpox what is wrong with refresh on MoleculestableViewer?
17:45 olass < Gpox> i belive that is not implemented   <- was that not true?
17:46 olass is it implemented?
17:46 olass See bug 261
17:48 Gpox well you should use MoleculeTableViewer instead
17:50 CIA-28 bioclipse: goglepox * r8363 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.ui.sdfeditor/src/net/bioclipse/cdk/u​i/sdfeditor/editor/MoleculeTable.java: This class is deprecated use MoleculeTableViewer instead
17:51 olass hmm
17:52 gilleain shk3 and I were just noting that the Single Molecule View tab does not seem to work if you have only 3D coords.
17:53 shk3 and without any sort of warning
18:01 olass Gpox: I do like this:
18:01 olass MultiPageMoleculesEditorPart molPart=(MultiPageMoleculesEditorPart)part;
18:01 olass MoleculesEditor molEditor=molPart.getMoleculesPage();
18:02 olass Goix: how do I get the MoleculeTableViewer from that?
18:02 olass Gpox I mean
18:02 olass gilleain: it is not yet implemented what I know
18:04 gilleain oh right. oh well.
18:13 olass Gpox? still there?
18:13 olass haha, it was private!
18:13 * olass is making the MoleculeTableViewer public
18:14 olass hmm, at least a getter
18:33 * Gpox would prefere another way to propagate the update request
18:44 CIA-28 bioclipse: ospjuth * r8364 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.ui.sdfeditor/src/net/bioclipse/cdk/u​i/sdfeditor/editor/MoleculesEditor.java: Made the MolceulesTableViewer a field and accessible via API so I can do refresh() on the editor.
19:02 edrin left #bioclipse
20:36 edrin1 joined #bioclipse
20:42 egonw edrin1: all functions work now, both sync as well as async
20:42 egonw eating CML, spitting CML
20:42 * egonw is happy
20:42 egonw next on my list is that BeanShell thingy...
20:42 egonw or maybe the real plugin
20:42 egonw as CVS is said to be working again
20:46 edrin1 hi egonw
20:46 egonw hi
20:46 zarah hello egonw, you fantastic person you
20:46 egonw zarah: ??
20:46 zarah egonw: are you making fun of me?
20:46 edrin egonw: cool
20:48 egonw I think this is a nice show case, actually...
20:49 egonw as it really takes an existing schema in the wild
20:49 edrin i will try to create a binding against them now :)
20:49 egonw I'll get to writing the paper next week too, btw, and help you out with that
20:49 egonw edrin: ok... will go offline fairly soon, but please let me know your experiences with it... :)
20:50 edrin sure
20:50 edrin :)
20:50 edrin have a nice evening
20:51 edrin egonw: how big are these schematas!?
20:51 egonw umm...
20:52 egonw see net.bioclipse.cml/schema24
20:52 egonw see net.bioclipse.cml/schema24/schema.xsd
22:18 edrin egonw, still available?
23:01 CIA-28 bioclipse: edrin_t * r8365 /xws/trunk/xws4j-binding/src​/net/bioclipse/xws/binding/ (2 files in 2 dirs): adjusted binding ioFactory generator to do things Better!
23:39 CIA-28 bioclipse: edrin_t * r8366 /xws/trunk/xws4j/src/net/bioclipse/xws/ (client/adhoc/IoSchemata.java xmpp/iodata/IoDataElement.java): elab ioschemata desc
23:40 CIA-28 bioclipse: edrin_t * r8367 /xws/trunk/xws4j-binding/src​/net/bioclipse/xws/binding/ (3 files in 2 dirs): elab io schemata description
23:42 CIA-28 bioclipse: edrin_t * r8368 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/ (9 files in 4 dirs): updated to current binding subs

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