Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-04-03

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All times shown according to UTC.

Time Nick Message
06:29 egonw joined #bioclipse
06:31 olass joined #bioclipse
06:31 olass moin
06:31 zarah ni hao olass
06:31 olass mornin egonw
06:32 egonw hi olass
06:32 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
06:32 egonw @msg
06:32 zarah egonw: 9 h 45 m 9 s ago, edrin said http://www.youtube.com/watch?v=ZUBQknWU​EYU&eurl=http%3A%2F%2Fwww.spiegel.d​e%2Fnetzwelt%2Fweb%2F0%2C1518%2C616948-​7%2C00.html&feature=player_embedded
06:33 egonw nice
06:35 olass very funny
06:37 rojasm joined #bioclipse
06:41 egonw rojasm: ping
06:59 Gpox joined #bioclipse
07:08 CIA-58 bioclipse: goglepox * r9577 /bioclipse2/trunk/plugins/net​.bioclipse.cdk.ui/plugin.xml: Comment out SDFile molecules children se bug #766
07:08 zarah bug #766 | http://tinyurl.com/c7cskz
07:41 edrin joined #bioclipse
07:41 edrin hi
07:41 zarah privet edrin
07:52 jonalv joined #bioclipse
07:53 masak joined #bioclipse
07:54 CIA-58 bioclipse: goglepox * r9578 /bioclipse2/trunk/cdk-externals/tr​unk/org.openscience.cdk.control/sr​c/org/openscience/cdk/controller/ (ControllerHub.java IChemModelRelay.java MoveModule.java): Added fireStructureChanged to be able to notify moves fixes bug #734
07:54 zarah bug #734 | http://tinyurl.com/d7eztg
07:55 CIA-58 bioclipse: egonw * r9579 /bioclipse2/trunk/plugins/ne​t.bioclipse.jmol/plugin.xml: Disabled the JmolScriptEditor for now (fixes #788)
07:55 zarah bug #788 | http://tinyurl.com/d4mcth
07:57 masak ah, commits.
07:57 egonw Gpox: what happened to IChemModelEventRelayHandler?
07:57 egonw why do we have change events in both that interface and ControllerHub?
07:58 egonw I don't like that code duplication
07:58 egonw moreover, and more importantly
07:58 egonw we need distinction between coordinated changes
07:58 egonw and graph changes
07:59 edrin hi egonw
07:59 egonw hi edrin
07:59 edrin did you have time to read and comment the text?
08:00 egonw no, but I should have today
08:00 edrin ok
08:00 Gpox egonw: short answer the IChemModelEventRealyHandler is hidden in the ControllerHub
08:01 Gpox you only have the IChemModelRelay in the MoveModule
08:02 egonw so, the correct way of fixing things, would be to make it visible, right?
08:02 Gpox IChemModelRealay needs a big cleanup anyways
08:02 egonw right now, we have two APIS
08:02 egonw which are not even compatbile
08:02 egonw Gpox: yes, it does
08:02 egonw it's shocking how much bit rot has gotten into it in just 2 months
08:03 egonw it much looks like JCP 2.1 code :(
08:03 egonw quite disappointing...
08:03 egonw I had hoped the design was better
08:03 Gpox you should have a moveAtoms(Set, Vector) in the hub indicate a move
08:03 egonw and would not encourage work arounds
08:03 egonw it failed there
08:04 shk3 joined #bioclipse
08:16 olass egonw, jonalv: default workspace location user.home/bioclipse ok with you?
08:16 egonw yes
08:16 egonw it's just the default
08:16 egonw I can immediately change it :)
08:17 egonw only thing I worry about
08:17 jonalv yes sounds good. I was wondering about if we could make things the same on linux and ?Mac though...
08:17 egonw is that people might actually have downloaded BC2
08:17 egonw and unpacked it in $HOME/bioclipse
08:17 jonalv Bioclipse-workspace perhaps then?
08:18 jonalv I think I would like that better actually
08:18 jonalv it tells what it is...
08:18 olass I agree and thought exactly the same thing
08:18 olass shk3: can you make it so?
08:19 olass user.home/bioclipse-workspace instead of user.home/bioclipse
08:20 shk3 yes
08:20 shk3 for all platforms?
08:20 olass yes
08:21 olass on windows:  "My Documents\bioclipse-workspace"
08:21 olass shk3: ok?
08:21 olass shk3: why is it impossible to set workspace as an onput arg?
08:21 shk3 my documents should be user.home?
08:21 olass no idea but sounds likely
08:21 shk3 because if you set them there, you cannot change later
08:22 shk3 and for the switch workspace, we need to change it
08:22 olass hmm, right
08:22 olass it complicates for testing
08:22 shk3 the input args go into the bioclipse.ini file
08:22 olass I see your point
08:22 shk3 and this is used before everything else
08:27 CIA-58 bioclipse: shk3 * r9580 /bioclipse2/trunk/plugins/net.bioclipse.core/sr​c/net/bioclipse/core/PickWorkspaceDialog.java: changed default workspace to bioclipse-workspace
09:00 Gpox joined #bioclipse
09:31 CIA-58 bioclipse: ospjuth * r9581 /bioclipse2/trunk/plugins/ (31 files in 10 dirs): Updated QSAR-ML schema, model, code, edit, and tests to handle descriptor results.
10:01 CIA-58 bioclipse: carl_masak * r9582 /bioclipse2/trunk/plugins/net.bioclipse.ui/ (4 files in 2 dirs):
10:01 CIA-58 bioclipse: [net.bioclipse.ui] changed to transparent icons
10:01 CIA-58 bioclipse: They are still really ugly, but it's a first step.
10:02 masak I actually did that one yesterday, but thanks to the wonderfulness that is 'git svn', you get it today. :)
10:06 rojasm joined #bioclipse
10:14 shk3_ joined #bioclipse
11:18 egonw lunch time
11:24 CIA-58 bioclipse: ospjuth * r9583 /bioclipse2/trunk/plugins/ (16 files in 8 dirs):
11:24 CIA-58 bioclipse: Schema and code updates:
11:24 CIA-58 bioclipse: * Removed transient 'changed' attribute to track changes in model, this will be implemented as preference instead.
11:24 CIA-58 bioclipse: * Decided that id for defining descriptors must be unique and moved BO reference from id to 'ontologyid' attribute. Also removed namespace since only one BO ontology is supported anyway.
11:25 CIA-58 bioclipse: ospjuth * r9584 /bioclipse2/trunk/plugins/net.bioclip​se.qsar.ui/src/net/bioclipse/qsar/ui/ (3 files in 2 dirs): Refactored out addDesciptorToModel to QSARManager and commented out uses of changed attribute + removed all occasions of namspace for descriptors after schema change.
11:28 egonw olass: there is no JNATI tutorial, is there?
11:29 olass no
11:29 olass what do you need it for?
11:29 olass ballon?
11:29 egonw no, that gromacs lib
11:29 olass egonw: did balloon run for you?
11:29 egonw did not try after my reported first attemp
11:29 egonw t
11:47 olass egonw: could you please now?
11:47 olass it works on win and mac
11:47 olass so I see no reason for it to fail on linux
11:48 egonw olass: http://jni-inchi.svn.sourceforge.net/viewvc/jni​-inchi/trunk/src/main/java/net/sf/jniinchi/JniI​nchiWrapper.java?revision=157&view=markup
11:48 zarah egonw's link is also http://tinyurl.com/cfzstr
11:48 egonw uh... wrong paster
11:48 egonw crap
11:48 egonw mom
11:48 olass ok
11:48 egonw Balloon failed: Balloon execution failed. Reason: java.io.IOException: java.io.IOException: /home/egonw/var/Projects/SourceForg​e/git-svn/bioclipse2/plugins/net.bi​oclipse.balloon.linux/exec/balloon: cannot execute
11:49 olass you have probably not set priviliges to RUN on balloon at that location
11:49 egonw indeed
11:49 olass hmm
11:49 egonw quite common
11:49 olass how can we make sure this is in SVN?
11:50 olass problematic
11:50 olass was no prob on windows apparently :)
11:50 olass win runs everything, everywhere, from everyone
11:51 egonw indeed :)
11:51 CIA-58 bioclipse: carl_masak * r9585 /bot/trunk/zarah.pl:
11:51 CIA-58 bioclipse: [zarah] now does nothing on private ++/--
11:51 CIA-58 bioclipse: Guess I could add an error message too, but I'll punt on that.
11:53 egonw olass: going to fix it in SVN
11:53 olass egonw: great
11:53 egonw olass: but you still need to mend to code to check if it can execute the code
11:53 olass please do it for the mac version too
11:54 egonw and give a user friendly error message if not
11:54 olass yes
11:54 olass how do I do that in java?
11:54 egonw because /home should really be mounted noexec
11:54 egonw File.isExecutable or so
11:54 egonw IFile likely has something similar
11:55 olass ah
11:55 olass yes
11:55 olass will you file me a bug?
11:55 olass or shall I do it myself?
11:56 egonw files
11:56 egonw filed
11:56 olass danke
11:56 olass egonw: works after chmod?
11:56 egonw no idea
11:57 egonw first fixing SVN
11:57 olass let me know
11:57 olass :)
12:00 masak zarah: reboot, dear.
12:00 CIA-58 bioclipse: egonw * r9586 /bioclipse2/trunk/plugins/net.bioc​lipse.balloon.linux/exec/balloon: Balloon chmod +x
12:01 zarah joined #bioclipse
12:04 egonw 5 bug reports left for the big 800
12:04 egonw olass: chmod +x works
12:04 olass right
12:04 egonw but please see the two additional bug reports
12:05 olass sure
12:05 olass but it runs now?
12:05 olass did you chmod the mac version too?
12:05 egonw yes
12:05 olass great
12:05 egonw yes, but that did have no effect
12:05 egonw so I think that one already was +x
12:05 olass ok
12:05 olass (could be my doing)
12:11 CIA-58 bioclipse: ospjuth * r9587 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Adapted tests to use ontologyID instead of previous ID.
12:20 CIA-58 bioclipse: ospjuth * r9588 /bioclipse2/trunk/plugins/net.bioclipse.qsar.ui/sr​c/net/bioclipse/qsar/ui/builder/QSARBuilder.java: Always treat all structures and descriptors as dirty until preference for this is implemented.
12:21 CIA-58 bioclipse: carl_masak * r9589 /bioclipse2/trunk/plugins/n​et.bioclipse.ui/plugin.xml: [n.b.ui] actually switched to the tspnt icons
12:22 CIA-58 bioclipse: carl_masak * r9590 /bioclipse2/trunk/plugins/net.bioclipse.u​i.business/src/net/bioclipse/ui/business/ (IUIManager.java UIManager.java): [n.b.ui.business] added newFile("foo") to UI manager
12:22 masak olass: there you go.
12:23 egonw masak:++
12:23 olass oki
12:23 olass danke
12:23 masak olass: ne dankinde. :)
12:23 olass na ja
12:25 maclean joined #bioclipse
12:28 rojasm joined #bioclipse
12:45 olass egonw: are you OK with the chemoinfo feature including the balloon feature?
12:46 olass or should I keep them separate?
12:46 egonw keep them separate
12:46 olass well, for the release I mean
12:46 egonw we have to think about this anyway...
12:46 olass in SVN they will always be separate
12:46 egonw one feature, one license?
12:46 olass no
12:46 egonw that's needed fro some things anyway
12:46 olass right
12:47 olass ok, will be a separate feature alltogether
12:47 olass so no probs
12:47 olass yes, this is as it must be
12:47 egonw anyway...
12:47 egonw I marked it as such in pz
12:47 egonw as there was no balloon feature there
12:47 olass there is
12:47 egonw moreover...
12:47 olass hmm
12:47 egonw there is also maintainability
12:47 egonw one feature == one maintainer
12:48 olass oh, it's in the wrong location
12:48 egonw one contact
12:48 olass balloon_feature is in plugins, not features
12:48 olass will move it
12:48 egonw huh?
12:48 egonw I'm talking about Pelezilla
12:48 olass ok
12:49 egonw but, yes, please fix that the balloon_feature location :)
12:51 CIA-58 bioclipse: ospjuth * r9591 /bioclipse2/trunk/ (2 files in 2 dirs):
12:52 olass moved balloon_feature to the features folder
12:52 olass egonw: did you add a balloon category for pelezilla?
12:52 egonw no
12:52 olass ok, then I'll do it
12:52 egonw should I have done that?
12:52 olass @pz
12:52 zarah olass: Pelezilla is at http://bugs.bioclipse.net
12:53 maclean how will features and plugins be organised in the (super) long-term? Like when there are bio- as well as chem- informatic plugins?
12:53 egonw example?
12:53 maclean viz : double the number of plugins, say.
12:53 egonw what problem do you forsee?
12:54 maclean a HUGE list of plugins?
12:54 maclean :)
12:54 olass yes
12:54 egonw what's the problem with that?
12:54 egonw olass knows I like to finally get that 2000 plugins
12:54 olass I guess we shoudl structure us into projects, like eclipse does
12:54 egonw no fuzz about 5 plugins should be enough for everyone
12:55 olass logical collections of features + plugins for a specific project
12:55 olass maclean: for now I'm happy with how things are
12:55 olass but I see your point
12:55 egonw where each project has a single guy contact and responsible for maintaining it
12:55 maclean oh, of course
12:55 egonw or girl
12:55 olass someting like that
12:55 egonw and black people of course
12:55 olass or other
12:56 maclean egon!
12:56 maclean o_O
12:56 maclean :)
12:56 egonw sorry... saw this stupid blog item yesterady
12:57 egonw from some american complaining about the few minorities in cheered US assisting profs
12:57 maclean ugh positive discrimination is never a good idea
12:57 egonw nothing wrong with discrimination...
12:57 egonw the fact that no one can distinguish good and bad discrimination is the problem
12:58 egonw I guess most people are too stupid to see the difference
12:58 maclean true
12:58 egonw between equal rights/obligations, and being equal
13:00 rojasm1 joined #bioclipse
13:00 maclean anyway, this is a long way from my original question ;)
13:00 egonw ah, yes... fridays
13:00 egonw maclean: but you are correct... we discussed this internally half a year ago too...
13:00 egonw and postponed it until after 2.0.0
13:01 maclean egonw : did you see that question on the Jmol list about an interface for searching protein structures ?
13:01 maclean I sent a long reply to him, but didn't post it to the list, as it was quite detailed.
13:01 egonw no
13:02 egonw blog your reply?
13:02 egonw in your spare time, of course
13:02 maclean Hmmm. could do
13:02 maclean Ha!
13:02 egonw just an idea, no expectation
13:03 maclean I should put up some of the images I've been making for the continually-postponed group talk...
13:04 egonw looking forward to it
13:04 maclean I was partly replying off-list as it was discussion of grant application ideas, and the guy even said in his mail something like "I'd like to keep this open, but pleas - no poaching of ideas :)"
13:05 maclean It's where 'open science' meets the reality of applying for funding...
13:09 egonw yes
13:11 maclean In protein crystallography, I understand that people are even secretive about what they are doing _right now_ as it might tip other groups off as to what structures are easy to crystallise. Oh well.
13:20 jonalv http://wiki.bioclipse.net/index.​php?title=How_to_make_a_manager
13:20 zarah jonalv's link is also http://tinyurl.com/dypvah
13:20 jonalv (in case anyone missed that...) :)
13:22 maclean nice and colorful :)
13:24 jonalv :)
13:28 shk3 joined #bioclipse
13:32 maclean but more importantly jonalv++ (documentation)
13:32 jonalv maclean: have you read it? :)
13:32 maclean I'm ... skimming ... it at the moment
13:33 jonalv oki
13:33 maclean One fine day, I might actually make a proper plugin or feature (or project, whatever)
13:33 jonalv yea
13:35 egonw jonalv: you're at BMC?
13:35 jonalv egonw: yup
13:35 jonalv only me here...:)
13:35 egonw ok, please check email
13:36 jonalv oki, let's hope it scans out in the margins :)
13:40 maclean urgh! curse you, blogspot! I put that code in -pre- tags, why did you mess up the indenting?
13:46 jonalv olass: Bioclipse 2.0 RC1 will be net.bioclipse.core_feature and net.bioclipse.chemoinformatics_feature right?
13:47 olass and balloon
13:47 olass all else will be on update site
13:47 olass at least I think so
13:47 jonalv okey so that is not in the chemoinformatics feature?
13:47 olass no, different license
13:48 jonalv ah so it must be on the update site too then?
13:48 olass as egonw++ pointed out
13:48 olass no
13:48 olass but a separate feature
13:48 jonalv so we can have multiple licenses on the "core" zip file?
13:48 olass sure
13:48 olass we already have
13:49 olass if they are compatible
13:49 olass and teh balloon license is compatible
13:49 olass I asked the author
13:50 jonalv what's the name of the core feature now?
13:50 jonalv I an't find it...
13:50 jonalv isn't it net.bioclipse.core_feautre?
13:52 jonalv ah there it was
13:52 jonalv strange...
13:53 jonalv olass: are you running Eclipse 3.4.2 now?
13:54 jonalv has it been realeased yet?
13:54 olass yes
13:54 olass many weeks agop
13:54 jonalv hm is it much better?
13:55 jonalv I guess I need to get it...
13:55 maclean can you update to Eclipse 3.4.2 from within 3.4.1 ?
13:56 edrin olass, egonw, i added two sequence diagrams to the g-doc, how do you like them?
13:57 egonw I think adding Process there is too much detail
13:58 jonalv my computer needs a reboot :(
13:58 jonalv brb
14:01 olass edrin: they are nice
14:01 olass but please focus on references
14:01 olass else we never get to the goal
14:01 edrin egonw: ok, the result would then look then just them same with removed process "thread"
14:02 edrin i will add all the references as soon as you have done/read the comments
14:02 edrin olass: remove the process thing in the sequence diagram
14:02 edrin seminar, back in 1.5h
14:03 olass k
14:04 olass will unfortunately not have time for release today :(
14:04 olass monday it is
14:04 olass fridays are always bad
14:04 * olass just have too many things on the table now
14:05 maclean get a bigger table.
14:14 jonalv joined #bioclipse
14:19 jonalv zarah: hi
14:19 zarah hello jonalv :)
14:19 jonalv all: ji :)
14:19 jonalv |hi
14:37 * jonalv is running Eclipse 3.4.2 now and the irritating graphics bug is fixed
14:37 jonalv jippie :)
14:38 jonalv now to see if Bioclispe starts as welll :)
14:39 maclean jonalv : what graphics bug?
14:39 jonalv the mouse over thing on mac
14:39 maclean also, what platform..oh right mac
14:40 maclean how did you upgrade (I know this is a stupid question, I'm sorry)
14:40 maclean (It won't let me do it from within eclipse)
14:41 jonalv maclean: no I did a clean installl
14:41 jonalv I am setting up all the configs now...
14:41 jonalv it sucks actually...
14:41 maclean ah, ok, but doesn't that mane a lot of re-installing of plugins
14:41 maclean s/mane/mean/
14:41 maclean +?
14:42 jonalv but it was time to do it and if I ahve to throw away time on this better to throw away friday afternoon on it...
14:42 jonalv maclean: it sure does...
14:42 maclean :( * 100
14:42 * maclean rolls up sleeves
14:42 jonalv maclean: if you have a btetter option I will do it your way next time...
14:42 maclean jonalv : I was hoping that YOU had the solution! :)
14:43 jonalv it's sort of good to work trought the procedure on how to set up the devlopment environemtnt for BIoclispe though and spot the pitfalls...
14:43 jonalv only good thing about it...
14:43 maclean I suppose...
14:43 maclean *grmph*
14:45 Gpox I updated with 'Software Updates' from within eclipse
14:46 jonalv !!!
14:46 jonalv :)
14:46 jonalv Gpox: and that worked?
14:47 Gpox yes
14:47 jonalv cool
14:47 jonalv I guess I must try that for the next update then...
14:47 jonalv but I am almost there now
14:48 maclean !!!
14:48 maclean It didn't let me do that.
14:48 maclean Double-grr.
14:48 egonw jonalv: ping
14:48 egonw INFO - Bioclipse manager: structuredb added to Javascript environment.
14:48 egonw INFO - Bioclipse manager: rdf added to Javascript environment.
14:48 egonw INFO - Bioclipse manager: structuredb added to Javascript environment.
14:48 jonalv egonw: plong
14:48 egonw jonalv: clearly something goes wrong
14:48 jonalv egonw: twice?
14:48 egonw where does it get the 'structuredb' from...
14:48 egonw ?
14:48 olass_ joined #bioclipse
14:49 egonw the NS for my version is 'structrdf'
14:49 olass_ edrin: around?
14:49 egonw but seems not used...
14:49 jonalv egonw: uhm "NS"?
14:49 egonw namespace
14:49 jonalv and with nameswpace you eman what exactly?
14:50 egonw ok, very practical...
14:50 egonw where is that message printed?
14:50 * jonalv whisehd all Bioclipse plugins would compile...
14:50 jonalv in the code that reads managers from the extension point net.bioclispe.core.scriptingContrinution
14:51 jonalv I think that should be in net.bioclipse.core but it wouldn't suprise me if it's in net.bioclispe.scripting...
14:53 egonw ok, JsEnvironment
14:53 jonalv egonw: yup
14:54 jonalv gah the Eclipse default text size is tiny
14:57 maclean hmmm. the only errors I get are in the encryption/usermanager, and cml plugins.
14:58 jonalv maclean: biojava, biomoby, cdk10, and rdf.ui
14:58 jonalv what's problems have you t with encryption usermanager?
14:58 egonw jonalv: cdk10 is outdated
14:58 maclean well, I don't have cdk10 anymore
14:58 jonalv they compile for me
14:58 egonw rdf.ui -> sorry, please file a bug report and I'll fix it
14:59 egonw oh... rdf.ui needs Zest
14:59 jonalv egonw: cdk10 is still in trunk and I would like everything in trunk to compile...
14:59 egonw I guess you forgot to install that?
14:59 egonw :)
14:59 maclean encryption/usermanager needs org.apache.commons
14:59 jonalv egonw: huh? How do I do that? :)
14:59 egonw jonalv: please check where cdk10 is located
14:59 egonw not in plugins/
14:59 egonw via Ganymedes update site
14:59 jonalv egonw: but in trunk
14:59 maclean 'forgot to install' == 'not in the eclipse download'
15:00 egonw it would have if you would not have been so Dutch to only download the bare Ganymedes minimum :)
15:00 egonw maclean: anyway... agreed
15:00 * maclean is extremely Dutch
15:00 egonw it would be nice if we had a way to have those things easily added...
15:01 egonw other bits need GEF, EMF
15:01 maclean Buckminster!!!
15:01 egonw which also do not come by default
15:01 maclean (probably)
15:01 egonw Mylyn
15:01 egonw that reporting stuff
15:01 jonalv I actually got mylyn...
15:01 egonw too
15:01 egonw :)
15:01 egonw oh... and egit
15:01 egonw still have not tried to install egit in Bioclipse'
15:01 jonalv egonw: do you use that?
15:02 maclean egit did nothing for me
15:02 * jonalv takes that as a no
15:02 egonw no, but I will now that they decided to make it a proper Eclipse project
15:02 egonw jonalv: forgive me for being a slow typer
15:02 maclean Oh except, when I saved, it showed a mini-progress and said "updating git decoration triggers'
15:02 egonw (and slow thinker... hey. it's Friday!)
15:02 jonalv yes it sure is
15:03 jonalv I still can't get rdf.ui to compile though...
15:03 egonw jonalv: can I ask you to pull from a git with a branch for structuredb.rdf?
15:03 jonalv what is it I ned? I thought I installed Zest...
15:03 egonw and see if you see something obviously wrong in my osgi*.xml ?
15:04 jonalv egonw: I will not lift a finger on that project until after tuesday, too risky
15:04 egonw ok, fair
15:04 jonalv egonw: Feel free to ask general questions about Spring OSGI config xml files though...
15:05 egonw indeed :)
15:05 egonw was just about to do that
15:05 egonw can you explain me how it works?
15:05 egonw I have a bean defined
15:05 egonw with the IStructuredbManager interface
15:05 jonalv okey
15:05 egonw and it has prop target="XXX"
15:06 egonw now, in context.xml I have that bean XXX defined with the class pointing to my class
15:06 egonw but for some reason it loads something else...
15:06 egonw being the StructuredbManager...
15:06 jonalv it loads something else?
15:06 egonw and not my class that implements that interface too
15:06 egonw yes, causing the above INFO lines
15:07 jonalv oh, hang on
15:07 egonw now, I guess there would be something wrong with the osgi:service element?
15:07 egonw or so?
15:07 egonw I have no clue
15:07 jonalv when doing things the way I do we can only have one manager implementing one interface
15:08 egonw oh goodies
15:08 egonw so much for an interface
15:08 jonalv you are exporting a second object and tieing it to the IStructuredbInteface right?
15:08 egonw yes
15:08 egonw I should extend that interface?
15:08 jonalv but when it fetches it just takes the first object it fins for that interfaces I think
15:09 egonw so I should just extend that interface?
15:09 egonw so that both have a unique interface?
15:09 egonw though the second would actually be the first too...
15:09 jonalv that is probabl ythe easiest way. I am sure there are ways to do more complicated things and not just take the first in line but actually look through them all and take a certain one but I am not familiar with those methods...
15:10 egonw but I want to make sure that the GUI stuff for structuredb would work on my code too
15:10 maclean yes, wait a minute - what is the point of these interfaces that are implementable by only one class?
15:10 edrin egonw, please keep on adding text :)
15:10 egonw maclean: that would sound like a waiste of interfaces, not?
15:11 maclean well, there's only so many to go around :)
15:11 jonalv actually the "other" implementation of the interface is the proxy object
15:11 * maclean goes to get a cup of tea instead of playing the fun 'guess which plugins to re-install' game
15:12 maclean oh, right yes the proxy
15:12 maclean forgot about that
15:12 maclean gilleain.gets('tea')
15:13 egonw me.writes('IInterface')
15:13 jonalv huh?
15:13 jonalv IInterface?
15:13 jonalv where is masak when I need him?
15:24 egonw INFO - Bioclipse manager: structuredb added to Javascript environment.
15:24 egonw INFO - Bioclipse manager: rdf added to Javascript environment.
15:24 egonw INFO - Bioclipse manager: structrdf added to Javascript environment.
15:24 egonw that's better
15:25 egonw jonalv: what CMLManager?
15:25 egonw the one with validate?
15:26 egonw as in 2.6?
15:32 jonalv egonw: the one that is prublsiehd under tha variable name cml and reachable from the JavaScript console by that name...
15:32 egonw yes, that's 2.6
15:33 jonalv egonw: sry
15:33 jonalv what is 2.6?
15:33 egonw 2.6 in the URL you gave
15:34 jonalv egonw: I am sure you have a good point if only I could understand it...
15:34 egonw no worries.. it's friday
15:34 jonalv egonw: ah you are saying that the manager is already there?
15:34 jonalv *lol*
15:35 jonalv then I am not too havppy about the name ValidateCMLMAnager
15:35 jonalv could we perhaps call it hust CmlManager?
15:35 jonalv |just
15:35 egonw ask the author
15:36 jonalv shk3: ?
15:36 maclean grr! "org.eclipse.wst.xml.core.catalogContributions" - is this in web standard tools?
15:36 egonw or just file a enhancement ticket
15:36 jonalv I really have to go
15:36 egonw maclean: yes, that's another one of those deps...
15:36 jonalv egonw: but you don't see any reason for not doing so?
15:36 maclean egonw: but I installed it! aarrghhhh.
15:36 egonw this is a minor thing, from my perspective
15:37 jonalv egonw: yes it sure is :)
15:37 egonw maclean: I managed to install the wrong WST too...
15:37 egonw maclean: it sucks, I know
15:37 egonw but I don't have a solution
15:37 maclean the WRONG one?
15:37 jonalv cya monday
15:37 maclean :((((
15:37 jonalv good weekend on you
15:37 egonw maclean: look for XML stuff in the update site
15:37 maclean oki
15:37 maclean bye jonalv
15:37 egonw no clue what feature it really is in...
15:38 egonw check our plugin deps to see which plugin you need
15:38 egonw but I 100% lost track of which feature the eclipse people to decide to put it in this time
15:38 maclean I wish there was a big "install whatever you need to make this work" button.
15:38 egonw same here
15:39 maclean it could be right next to the 'fix this code' button...
15:40 egonw with 'cure cancer' on the other side :)
15:40 maclean :)
15:40 egonw oh, and put create-all-constitutional-isomers just below it
15:41 maclean I'm working on that one
15:41 maclean I may have to have a dialog that says : "Warning - this may take 10,000 years. Ok/Cancel"
15:42 egonw :)
15:51 * egonw replied to maclean's blog
15:51 maclean more distractions!
16:10 edrin egonw: pls could you comment the text in g-d ?
16:10 edrin google docs
16:10 zarah edrin: http://docs.google.com/
16:10 egonw which section?
16:10 egonw I though I replied to all addressed at me
16:10 edrin no
16:11 egonw please tell me which one you like reply on...
16:11 edrin Integration with Desktop Tools
16:11 edrin there are many
16:12 edrin that are directly targeted to you
16:12 egonw I see taverna activity
16:12 egonw and one on CDK services
16:12 egonw yes, I will update that text
16:12 edrin in the discussion there are more general questions to you and ola, only ola responed so far
16:13 edrin egonw: in the Cloud Services for Bio- and Cheminformatics part you are talking about "descriptor" this is not explained, what is this, please add explaination
16:14 edrin the QSAR service is not mentioned at all
16:14 edrin where does it belong to?
16:15 edrin egonw: the SMS stuff ola suggested, should we add this?
16:16 edrin pls read through all the comments and fix/add info where you can
16:16 egonw yes, good discussion point, I think
16:22 egonw edrin: Taverna is still looking for summer students...
16:22 maclean this is insane. is there a way to find out where to get a plugin that contains an extension point?
16:22 egonw I always used trial-and-error
16:22 egonw very annoying indeed
16:22 egonw got to go for dinner now
16:22 egonw bbl
16:22 maclean bye
16:23 egonw edrin, first clarifications added
17:00 maclean zarah: tell egonw I had to comment out the section of the net.bioclipse.cml plugin's plugin.xml where it mentions "org.eclipse.wst.xml.core.catalogContributions" as I can find no way to fix it.
17:00 zarah Consider it noted.
17:00 maclean ta
17:10 edrin egonw: and the taverna stuff??
17:10 edrin ah it is
17:10 edrin ic
17:13 edrin egonw: "but is not yet checked if it matches the XML schemata published by the service" can we modify or remove this somehow?
17:15 maclean I think he's eating, edrin.
17:15 edrin ok
17:36 edrin left #bioclipse

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