Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-04-15

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All times shown according to UTC.

Time Nick Message
04:56 masak joined #bioclipse
05:10 egonw joined #bioclipse
05:24 masak egonw: moin
06:16 egonw moin
06:16 zarah oh hai egonw
06:16 egonw hi masak
06:28 CIA-73 bioclipse: carl_masak * r9801 /bioclipse2/trunk/plugins/ (4 files in 3 dirs):
06:28 CIA-73 bioclipse: Revert "[net.bioclipse.jseditor] prevented Eclipse console from opening"
06:28 CIA-73 bioclipse: This reverts commit 25d71ac1f1a8675be47fd628b66485fd3b994720.
06:29 CIA-73 bioclipse: carl_masak * r9802 /bioclipse2/trunk/plugins/net.bioclipse​.jseditor/src/net/bioclipse/jseditor/ac​tions/RunRhinoScriptAsJobAction.java:
06:29 CIA-73 bioclipse: [RunRhinoScriptAsJobAction] whitespace therapy
06:29 CIA-73 bioclipse: - tabs, spaces, indentation
06:29 CIA-73 bioclipse: - wrapped long lines
06:29 CIA-73 bioclipse: carl_masak * r9803 /bioclipse2/trunk/plugins/net.bioclipse.js​execution/src/net/bioclipse/jsexecution/ex​ecution/helper/ThreadSafeConsoleWrap.java:
06:29 CIA-73 bioclipse: [ThreadSafeConsoleWrap] whitespace therapy
06:29 CIA-73 bioclipse: - tabs, spaces, indentation
06:29 CIA-73 bioclipse: - wrapped long lines
06:30 CIA-73 bioclipse: carl_masak * r9804 /bioclipse2/trunk/plugins/net.bioclipse.js​execution/src/net/bioclipse/jsexecution/ex​ecution/helper/ThreadSafeConsoleWrap.java:
06:30 CIA-73 bioclipse: [ThreadSafeConsoleWrap] word choice
06:30 CIA-73 bioclipse: s/cut/truncated/, because that's what it's called. Also, used the constant
06:30 CIA-73 bioclipse: defined instead of the magic number it abstracts away.
06:30 CIA-73 bioclipse: carl_masak * r9805 /bioclipse2/trunk/plugins/net.bioclipse.js​execution/src/net/bioclipse/jsexecution/ex​ecution/helper/ThreadSafeConsoleWrap.java:
06:30 CIA-73 bioclipse: [ThreadSafeConsoleWrap] whitespace therapy
06:30 CIA-73 bioclipse: - introduced blank lines between methods
06:30 CIA-73 bioclipse: - coalesced three identical comments into one
06:31 Gpox joined #bioclipse
06:31 CIA-73 bioclipse: carl_masak * r9806 /bioclipse2/trunk/plugins/ (3 files in 3 dirs):
06:31 CIA-73 bioclipse: [n.b.jseditor] only write to console if console is shown
06:31 CIA-73 bioclipse: The code (in getRhinoConsole()) that detects whether the Console has been
06:31 CIA-73 bioclipse: opened could use a cleanup. It currently uses the deprecated
06:31 CIA-73 bioclipse: IWorkbenchPage.getViews(). Using IWorkbenchPage.findView() would be nicer,
06:31 CIA-73 bioclipse: but I couldn't get that to work.
06:31 masak oh, and it fixes bug #729. I forgot to write that.
06:31 Gpoks joined #bioclipse
06:31 egonw masak: make sure to talk to jonalv today...
06:32 egonw we found some console things regarding blocking threads and something else
06:32 masak egonw: I'm leaving a bit after 10 o'clock.
06:32 egonw moin Gpox
06:32 egonw masak: sure, I'm not your agenda :)
06:32 masak nope.
06:32 egonw just informing you we found some unexpected problems yesterday
06:32 egonw but have to say...
06:32 masak sounds intriguing.
06:32 egonw forgot what it was exactyl
06:32 masak oki.
06:43 CIA-73 bioclipse: carl_masak * r9807 /bioclipse2/trunk/plugins/net.bioclipse​.scripting.ui/src/net/bioclipse/scripti​ng/ui/business/JsConsoleManager.java:
06:43 CIA-73 bioclipse: [JsConsoleManager] fixed no-msgbox-on-undef-result
06:43 CIA-73 bioclipse: The original mechanism had bitrotted when the js execution mechanism was
06:43 CIA-73 bioclipse: upgrading from passing strings to passing objects. Solution: funky
06:43 CIA-73 bioclipse: string-based instanceof (to avoid unwanted dependencies).
06:43 CIA-73 bioclipse: Fixes bug #891.
06:43 zarah bug #891 | http://tinyurl.com/dmd2s7
06:50 masak git++
06:50 egonw masak: theoretically, post summer question...
06:51 * masak listens
06:51 egonw consider I want to have a Groovy console
06:51 masak aye.
06:51 egonw what would I be thinking about needing to do?
06:51 egonw not planning...
06:51 masak there is one, in the attic of SVN history.
06:51 egonw just brainstorming
06:51 masak just go to the proper XML file and revive it.
06:51 masak the one in n.b.scripting.ui, I'd imagine.
06:51 masak it has a comment with the revision number.
06:52 egonw you think it would still work?
06:52 masak quite possibly.
06:52 egonw :)
06:52 masak or it would break, but the fixes would be simple.
06:53 masak wow, the RConsoleView is a thing of beauty.
06:53 * masak changes that
07:09 olass joined #bioclipse
07:09 olass hi
07:10 zarah oh hai olass
07:10 olass masak: sory if I was unclear about the console for JSeditor output
07:10 olass I just meant I did not like it to pop up
07:10 masak olass: you were unclear, but it's OK.
07:10 olass do you think output going there is fine?
07:10 masak it was quite fun to try to find a fix to the actual problem too.
07:10 olass :)
07:11 masak olass: I have no opinion in the matter.
07:11 olass ok
07:11 masak olass: I do think that the code I traversed when fixing this needs serious attention, though.
07:11 olass in what way?
07:11 masak refactoring.
07:12 masak it's annoying to find the exact same code in several places, and have to fix every copy of it.
07:12 masak it's annoying to find the same non-informative comment having been copied several times in the same file.
07:13 masak etc. you know.
07:13 egonw joined #bioclipse
07:13 olass masak: I agree with you
07:14 olass far from all code in Bioclipse is clean
07:14 olass masak++ for trying to improve this in many occasions
07:14 olass egonw: around?
07:15 masak I'm being motivated not so much by a sense of duty, as by a sense of disgust.
07:15 olass lol
07:15 olass egonw: would it seem appropriate for the CDKManager to have a method to do atom typing on a molecule?
07:16 * olass is trying to design scripts
07:16 egonw yes, around
07:16 egonw not quite awake yet though
07:17 egonw and just relocated to sauna house
07:18 olass aah, there's nothing that wakes you up like a really hot sauna in the morning!
07:18 egonw really?
07:18 egonw mmm... should try that once
07:18 olass :)
07:18 olass egonw: would it seem appropriate for the CDKManager to have a method to do atom typing on a molecule?
07:19 * olass is trying to design informative scripts
07:19 egonw doesn't it already?
07:19 egonw or is that in CDK extra
07:19 olass think so
07:19 olass but anyway
07:19 olass is that implicitly done when needed?
07:19 egonw it's pretty low level
07:19 olass ok
07:19 egonw yes
07:19 olass then I'm fine as it is
07:19 egonw at least, it must on the Bioclispe Script level
07:20 olass egonw: is it XMPP today?
07:20 olass let me know if you need my input
07:20 olass a Gist to call the existing descriptor service would be very nice
07:21 egonw yes, yes
07:21 olass :)
07:21 egonw yes, maybe XMPP today
07:21 * olass is just trying to wake egonw up
07:21 egonw you're just giving me headache
07:21 olass oops
07:21 egonw or, maybe that's because of something else...
07:21 egonw not sure
07:21 olass beer yesterday?
07:22 egonw no, last episode of Merlin
07:22 egonw boy, is that a crappy series
07:22 olass I once in my youth made wine in the bathroom... a sauna would be an even better place...
07:22 egonw swedish tv sucks
07:22 olass egonw: I agree
07:23 egonw tv sucks in general
07:23 olass but would extend it to: almost TV sucks
07:23 olass all
07:23 egonw right
07:23 olass I like discovery ch
07:23 olass and some sports channels
07:23 olass from time to time a good move
07:23 olass and news
07:23 masak TV is so last century.
07:24 olass My TV is almost never used
07:24 olass I'd say every third day for an hour or so
07:24 * olass is back to work
07:24 * olass will close some bugs
07:28 olass egonw: still around?
07:28 egonw yes
07:29 masak olass: the interaction between the R-JS bridge and the new JS async model is... interesting...
07:29 masak :/
07:30 olass egonw: I thought about in sample data not having JS scripts as files, but list GISTS in an EP and they would be downloaded when sample data was installed
07:30 olass however
07:30 olass that limits offline installation of bioclipse
07:30 olass so
07:30 olass I thought of the following:
07:31 olass When building Bioclipse we have a script that downloads the gists and writes them in teh sampledata/data/javascript/ folder
07:31 olass egonw: what do you think about this?
07:31 olass now we need to manually copy the gist into this folder
07:32 olass sine many gists are ood examples of scripting bioclipse, many should be in the sampledata/data/javascript folder
07:32 olass egonw: let me know what you think
07:33 egonw yes, sounds interesting...
07:33 egonw but first we need an environment, which downloads those, and tests if those still run
07:33 egonw but that can be combined I guess
07:33 egonw so:
07:33 egonw net.bioclipse.data.gist
07:33 egonw and
07:33 egonw net.bioclipse.data.gist.tests
07:33 egonw ?
07:34 egonw the first doing the downloading adn the EP
07:34 egonw the latter testing if those scripts still work...
07:34 egonw masak: ping
07:34 masak egonw: pong
07:34 egonw masak: I need some info
07:34 masak who doesn't? :)
07:34 egonw masak: can you explain how I can run a Gist in JS with the ability to detect if it throwed exceptions?
07:35 egonw and fail in that case or so...
07:35 egonw that is
07:35 egonw how can I see if a JS works?
07:35 egonw from either Java code or a Java script
07:35 masak the js env returns an exception if one was thrown during execution.
07:35 egonw so
07:35 egonw I can best make a unit test setting up a new JS env
07:35 egonw from Java
07:35 egonw with JUnit
07:36 egonw and just detect exceptions throws?
07:36 egonw and just detect exceptions thrown?
07:36 masak I suppose.
07:36 masak try it.
07:36 egonw ok, thanx
07:37 egonw got some demo code for setting up a dedicated JS env?
07:37 masak egonw: no, since before bc 2.1 there is only One True JS env.
07:37 masak (except for the heretic ones that edrin has created)
07:38 egonw fine
07:38 masak (you might want to look at his code)
07:38 egonw how do I get one?
07:38 egonw how do I get the one?
07:38 masak ah.
07:38 masak have a look at JsThread.
07:38 masak you run commands with .enqueue
07:38 masak this can also be done through the js manager.
07:39 egonw and the js manager method will pass the exception?
07:44 masak yes. as a return value.
07:50 egonw olass: why did you reopen 890?
07:50 egonw @pz 890
07:50 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=890
07:51 olass did not work for me
07:51 olass did you commit?
07:52 CIA-73 bioclipse: carl_masak * r9808 /bioclipse2/trunk/plugins/net.bioclipse.scripting​/src/net/bioclipse/scripting/JsEnvironment.java: [JsEnvironment] updated stale JavaDoc comment
07:52 olass egonw: teh method is void here...
07:52 egonw void?
07:53 olass public void download(int gist, IFile target, IProgressMonitor monitor)
07:53 olass should it not be
07:53 CIA-73 bioclipse: carl_masak * r9809 /bioclipse2/trunk/plugins/ (4 files in 3 dirs):
07:53 CIA-73 bioclipse: [net.bioclipse.r] reinstated js injection in R
07:53 CIA-73 bioclipse: You can now write
07:53 CIA-73 bioclipse: > `answer` * 100
07:53 CIA-73 bioclipse: [1] 4200
07:53 olass public String download(int gist, IFile target, IProgressMonitor monitor)
07:53 CIA-73 bioclipse: and have the js variable 'answer' be interpolated into the R expression.
07:53 egonw ummm...
07:53 CIA-73 bioclipse: Fixes bug #856.
07:53 egonw 890 was just about the rename
07:53 masak olass: OK, status report. I got through the tickets marked P1 and P2. there are two tickets marked P3 that I will not do today.
07:53 zarah bug #856 | http://tinyurl.com/cqnx7h
07:53 olass masak++
07:53 masak olass: might have time for them later in the week, but no hard promises.
07:53 egonw olass: ah, no
07:53 olass thanks a lot masak
07:54 olass masak: good luck with your presentation
07:54 egonw olass: ok, question
07:54 olass sure
07:54 egonw why do you want it to return a patch
07:54 egonw why do you want it to return a path
07:54 masak olass: the two P3 tickets are "Inline help incorrectly presented" and "Tab complete on cdk.*". neither of these is critical, methinks, just annoying.
07:54 egonw if you actually give it the patch yourself?
07:54 olass so I can execute it directly
07:54 masak olass: thanks. I'll need it. ;)
07:54 egonw olass: so, you want:
07:54 olass egonw: right
07:54 olass egonw: I am right now submitting a bug
07:55 olass wait 30 secs
07:55 egonw js.execute(gist.download(84188, "/Virtual/glu.jsW)) ?
07:55 masak olass: also, for some reason, I really liked working like this. we should try it again, even when there's no real time shortage.
07:55 olass masak: very fine with me
07:55 egonw olass: ic the problem
07:55 egonw I closed the wrong bug report
07:56 egonw damn, I really need to get more sleep
07:56 olass egonw: ok, see bug #903
07:58 olass egonw: also commented on bug 890 with this
07:58 olass I feel quite strongly about this
07:59 olass if a method ends with creating a file, it should return a workspace-relative path to it
07:59 olass this greatly simplifies in scripting
07:59 olass egonw: I hope you agree
08:00 egonw I'm too tired to disagree
08:00 egonw well...
08:00 egonw I think it is pretty lame to have a method copy a parameter is was passsed
08:00 egonw welcome echo()
08:01 egonw echo("hello world")
08:08 olass egonw: for consistency
08:09 olass egonw: fire up teh sauna!
08:09 olass teh=the
08:10 masak please son't use the equals sign like that.
08:10 masak s/son't/don't/
08:11 maclean joined #bioclipse
08:11 * olass doesn't know perl
08:11 olass is R syntax ok?
08:11 masak olass: but you do know algebra, I'm sure.
08:12 masak olass: anything that doesn't violate common conventions.
08:12 olass masak: some :)
08:12 olass masak: ok, ok
08:13 masak http://en.wikipedia.org/wiki/Equals_sign
08:13 zarah masak's link is also http://tinyurl.com/dlxev6
08:16 maclean R is more like python than perl
08:16 maclean or, rather, python is like R.
08:19 egonw how do I get from an IFile to something like
08:19 egonw /Virtual/foo.bar?
08:21 maclean .getFullPath()?
08:21 egonw at least not getname()
08:21 egonw trying
08:21 maclean (the IFile method, that is)
08:22 egonw no, that returns an IFile
08:22 maclean it returns an IPath
08:22 egonw yes, that's what I mean
08:22 egonw but I need a string
08:23 maclean IPath.toString()
08:23 maclean ?
08:23 egonw yes
08:23 egonw that does the job
08:23 egonw thanx
08:23 maclean np
08:24 egonw olass: ping
08:24 olass pong
08:24 egonw olass: I want to remove bioclipse.product from SVN
08:24 egonw it's severely slowing me down
08:24 egonw and make a template instead
08:24 olass ?
08:24 olass please explain
08:24 jonalv joined #bioclipse
08:25 olass good morning jonalv
08:25 egonw what do you not understand?
08:25 olass [10:27] < egonw> olass: I want to remove bioclipse.product from SVN
08:25 egonw svn remove bioclipse.product
08:25 olass ???
08:25 maclean !!!
08:25 egonw svn commit -m "Nuked the bloody bastard"
08:25 maclean how is it slowing you down?
08:26 egonw because it changes all the time, and one must not commit those changes
08:26 maclean ohhh.
08:26 olass egonw: get in the sauna immediately and stay there for 30 minutes!
08:26 egonw so I get to back them out, bla, bla
08:26 olass yes yes
08:26 olass but that is not teh fault of bioclipse.product
08:26 olass it's the fault of developers
08:26 egonw no, of eclipse, I know
08:26 egonw no developers problem
08:26 egonw eclipse
08:27 masak time to go.
08:27 * masak waves
08:28 * egonw waves back
08:28 jonalv ohh ai
08:29 maclean jonalv : a question?
08:29 jonalv maclean: shoot!
08:29 maclean er... about scroll-wheel zooming in jmol : does it work for you now?
08:29 maclean @pele 581
08:29 jonalv maclean: no
08:29 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=581
08:29 maclean D:
08:30 maclean what machine/jvm are you using?
08:30 jonalv maclean: a macbook
08:30 maclean weird. I am on a macbook (pro)... hmmm
08:30 jonalv java.version=1.5.0_16
08:31 jonalv maclean: but it works for me in windows...
08:31 maclean so it's specific to certain macs only. grrr.
08:31 maclean (osx-specific bugs)--
08:32 maclean so, resolution : WONTFIX, or WORKSFORME?
08:33 maclean or, I guess I could put it on that wiki page I made for unresolvable bugs...
08:33 jonalv maclean: perhaps throw the bug at me and I can have it in my growing collection of things I need to have a look at some time...
08:33 maclean ok.
08:34 maclean although, if its a jvm bug, there's likely no way you can fix it - only work around it.
08:34 maclean OH! It may be to do with your particular mouse, of course.
08:35 jonalv maclean: yes, I must have a look at that some time
08:36 maclean I am not, of course, blaming your mouse. I am sure it is a fine mouse.
08:36 maclean :)
08:51 rednael [master] Multiple inheritence for content types?  http://chemicalrcp.blogspot.com/2009/04/mu​ltiple-inheritence-for-content-types.html
08:51 zarah rednael's link is also http://tinyurl.com/dn7b8n
08:51 egonw mmmm... rednael--
08:52 maclean I like how it starts its statements with "master". Respectful!
08:52 egonw :)
08:53 jonalv rednael: do you think you are the master?
08:53 egonw jonalv: 'masters' do not talk to mere mortals
08:53 jonalv egonw: yes master
08:54 jonalv uhm
08:54 jonalv hang on
08:54 jonalv :)
08:56 CIA-73 bioclipse: egonw * r9810 /bioclipse2/trunk/plugins/n​et.bioclipse.ui/.gitignore: Ignore the bastard
08:57 CIA-73 bioclipse: egonw * r9811 /bioclipse2/trunk/plugins/net.bioclipse.gist.test/ (15 files in 7 dirs): Added missing test plugin
08:57 CIA-73 bioclipse: egonw * r9812 /bioclipse2/trunk/plugins/net.bioclipse.gist/ (3 files in 2 dirs): Now returns the file name (fixes #890)
08:58 zarah bug #890 | http://tinyurl.com/d9ddar
09:02 egonw olass: ping
09:02 olass pong
09:03 egonw the ws manager is *not* saving it in some designated folder
09:03 egonw that is done by the wizard
09:03 egonw the wizard uses: WEBSERVICES_PROJECT
09:03 egonw which == "Web service Results/"
09:03 egonw (thank $HOLYNESS masak is gone)
09:04 egonw do you still want this hardcoded in the gist manager?
09:04 egonw even though your ref manager does not do that?
09:10 olass egonw: does it not?
09:11 olass hmm
09:11 olass it should IMO
09:11 egonw no, does not seem so
09:11 olass ok, I will file a bug for edrin
09:11 olass (after I confirm)
09:11 olass yes, I think it should be done this way
09:13 olass egonw: I cannot confirm
09:13 olass > webservices.downloadPDBAsFile("1kra")
09:13 olass /Users/ola/bioclipse-workspace/Web service Results/WSDbfetch Entries/1kra.pdb
09:13 olass it does this here
09:13 olass egonw: please try again
09:14 egonw I don't understand the code then
09:15 egonw it magically converts "" into /Web service Results/WSDbfetch Entries/
09:15 egonw oohhh...
09:16 egonw ok, figured it out...
09:25 maclean joined #bioclipse
09:49 CIA-73 bioclipse: ospjuth * r9813 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.ui.sdfeditor/src/net/bioclipse/cdk​/ui/wizards/SelectFilesWizardPage.java: Set label provider in SDF wizard to WorkbenchLabelProvider.
09:52 CIA-73 bioclipse: egonw * r9814 /bioclipse2/trunk/plugins/net.bioclipse​.gist/src/net/bioclipse/gist/business/ (GistManager.java IGistManager.java): Added download(int) that puts things in a Gists/ project (implements #903)
09:53 egonw lunch
10:03 egonw olass, Gpox, maclean: ping
10:03 maclean pong
10:03 jonalv :(
10:03 egonw olass, Gpox, maclean: should the jCP editor open files with partial 2D coordinates
10:03 maclean jonalv : ping
10:03 jonalv maclean: pong :)
10:03 egonw jonalv: ping, I have more Jmol work for you
10:04 maclean :)
10:04 olass egonw: I don't know
10:04 maclean egonw : hmmm
10:04 jonalv egonw: pong :)
10:04 maclean egonw : what is the situation
10:04 egonw it crashed with NPEs
10:04 Gpox pong
10:04 maclean no, I mean : what is the use case
10:04 maclean ?
10:05 egonw a CML file of which only some atoms have 2D coords
10:05 maclean well, sure - but why would this happen? If it's sort of rare, and accidental, then it might be nice to just lay-out those atoms that have no coords.
10:06 maclean If it happens for a particular reason, then maybe..well, I don't know actually.
10:06 egonw maclean: there are at least two bug reports about this use case
10:07 egonw of independent people
10:07 maclean link me up.
10:08 maclean That is to say: " could you please provide me with the links to said bug reports, if you would be so kind".
10:08 egonw yes, understood
10:09 egonw just finished cc-ing you on those reports :)
10:10 egonw so, no resolution on this?
10:10 egonw it's either a bug in the CML coord detection code or in JCP...
10:10 egonw but a serious bug it is
10:11 shk3 joined #bioclipse
10:11 maclean Well, it's not really a bug.
10:11 egonw but it is
10:11 maclean But its not.
10:11 egonw the two locations disagree on expected behvaiour
10:11 egonw one must be faulty
10:11 maclean I will explain?
10:12 egonw this is going to be interesting...
10:12 egonw yes, please do
10:12 maclean It is a situation that is not handled. So the code works properly, but not all situations are catered for.
10:13 maclean Partial 2D coordinates is not planned for.
10:14 maclean Anyway, probably the best solution is just to re-layout.
10:14 * maclean is now reading the bug reports
10:16 maclean ahhhh. Generated hydrogens that don't have coordintes. I see.
10:16 egonw Metallica rulez
10:16 maclean (you could have just said that... :)
10:17 rednael joined #bioclipse
10:18 rednael [Planet Bioclipse] I just came up with yet-another-way-of-making-a-Bioclipse-Manager  http://jonalv.blogspot.com/2009/04/i-ju​st-came-up-with-yet-another-way-of.html
10:18 zarah rednael's link is also http://tinyurl.com/cl3fhh
10:18 egonw rednael++
10:18 egonw jonalv: no master anymore :)
10:18 jonalv rednael++
10:18 maclean Impertinent bot!
10:18 shk3 olass: you have a second?
10:19 egonw @karma rednael
10:19 zarah rednael has a karma of 3
10:20 maclean egonw : so one of these two situations is genuine (the generated hydrogens), the other is better exception handling for the user doing something foolish (opening a file with 3D coords only in a 2D editor).
10:20 egonw maclean: well
10:20 egonw I think the foolish guy was actually just using ui.open()
10:20 egonw any such call will result in that situation
10:20 maclean And, actually, I think that the hydrogens could be given coords appropriate to the rest of the atoms.
10:20 egonw and that's no longer foolish, I'd say
10:21 maclean oh. so ui.open is broken?
10:21 egonw no, content type detection
10:21 egonw if you say single molcule 2D
10:21 shk3 olass isn't around?
10:21 egonw but cannot open it in JCP tied to that content type
10:21 egonw one must be wrong
10:21 egonw shk3: lunch, perhaps?
10:23 egonw what would the world be without hard rock and grunge...
10:23 egonw must have been a sad place
10:24 maclean shk3 says that the old jcp used to remove the atoms that had no 2D coords.
10:24 egonw shk3: sure? didn't it just not draw those?
10:26 shk3 sure
10:26 shk3 just looked at the code
10:27 maclean So the problem is that the content describer does a quick scan - therefore only detecting ANY 2D/3D coords - and then JCP doesn't properly check all the atoms.
10:27 egonw maclean: exactly
10:27 egonw so, both code bases disagree on what the content type should be
10:27 maclean In which case, JCP should do a better check, and do something about it - layout, not draw, mark as problematic, throw an error, raise a dialog.
10:27 egonw maclean: well, that is the question
10:28 egonw do we want to have files with partial 2D coordinates open in JCP at all
10:28 maclean Yes.
10:28 egonw you say yes... OK
10:28 egonw Gpox: what about you?
10:28 * jonalv <- lunch
10:28 egonw shk3, olass: and you?
10:28 egonw jonalv: you?
10:29 shk3 not sure
10:29 egonw the distadvantage of 80-ties music and being in an empty house is the tempation of singalongs...
10:29 shk3 I think offering coordinate generation would be the best
10:29 egonw scary
10:31 maclean 'Offering' == 'dialog'.
10:32 maclean sing away egon : we can't hear you :)
10:36 egonw .... Pruple Rain ...
10:36 egonw ... only want to see ...
10:36 egonw screaming... I know, I know...
10:38 egonw maclean: please blog your reply to rajarshi too
10:38 egonw and use the tag cdkws2009
10:38 egonw and at it to the workshop wiki page
10:38 maclean Blog : "Yes" ?
10:39 egonw https://apps.sourceforge.net/mediawiki/cdk/​index.php?title=CDK_Workshop_2009#Coverage
10:39 egonw https://apps.sourceforge.net/mediawiki​/cdk/index.php?title=CDK_Workshop_2009
10:39 maclean I could twitter that (if I used that abomination)
10:39 egonw #cdkws2009
10:40 maclean egonw : did you sees Rajarshi's blog entry on changes to the CDK (and my brief, short comment :) ?
10:40 egonw have not read it yet
10:40 egonw but asked him to blog about it
10:41 maclean We seemed to have many of the same concerns.
10:41 egonw yes, not surprisingly...
10:41 egonw the current API is about 10 years old
10:41 maclean Oh, right, wait - was my reply to his blog what you were talking about? Or about the coordinate stuff?
10:41 egonw well, 9 years
10:42 egonw maclean: ah, please blog the reply :)
10:42 maclean (sorry, I have a cold, and my mind is not running 100%)
10:42 maclean Ohhhh.
10:42 egonw feel free to blog about the other stuff too :)
10:42 maclean Now it makes sense.
10:42 egonw btw, if you have a bioclipse category or so...
10:42 maclean Nein, tack.
10:42 egonw please let me know the RSS for that...
10:42 egonw if you want me to add that to Planet Bioclipse
10:42 egonw @planet
10:42 zarah egonw: http://planet.bioclipse.net
10:43 egonw ... there was a time ...
10:43 maclean A bioclipse category. Hmmm. I don't...think..that I do.
10:43 egonw ... there are people dying ...
10:43 egonw ... we are the world ...
10:43 egonw all together now
10:43 egonw ... great big family ...
10:43 egonw ... love is all we need ...
10:44 egonw (Idiots... those dying people do not need love, they need AIDS medicin !)
10:44 egonw I think they had plenty of 'love' already
10:44 maclean :)
10:44 * olass is back from lunch
10:44 * olass will now backlog
10:45 egonw ... wow wow wow...
10:45 egonw (that was Cindy)
10:45 maclean olass : warning egon has been singing.
10:45 egonw and a bit of me
10:46 maclean oh, and egonw : I had a question about atom typing of protein ligands from PDB files. Do you have a minute?
10:46 egonw sure
10:46 egonw #cdk ?
10:46 maclean indeed
10:47 olass shk3: what do yopu mean with this?[12:21] < shk3> olass: you have a second?
10:48 shk3 hi olass
10:48 shk3 I had a question
10:48 shk3 sent you an email
10:49 olass ok
10:53 olass shk3: responded
10:53 olass egonw: read your song
10:53 shk3 thanks
10:54 olass egonw: you seem to be in a strange mood today
10:54 olass egonw, Gpox: I had a call from Lars at AZ during lunch
10:54 egonw olass: post grant writing syndrome
10:54 olass he found quite a few major bugs in JCP
10:54 egonw olass: he filed at least two
10:55 olass yes, he mentioned at least 5
10:55 egonw one is a regression due to the scrollbars
10:55 olass many are hopefully easy fixes
10:55 olass but
10:55 egonw ... quite living on dreams ...
10:55 egonw .. in a cold, cold ...
10:55 olass we shouldall take a few minutes drawing in JCP
10:56 olass especially you with chemistry knowledge
10:56 olass I will try to as well
10:56 egonw olass: I think Gpox is aware of at least of some of the problems...
10:56 olass sounds good
10:56 olass but it also means there will bea beta5
10:56 olass before RC1
10:56 egonw ... Ich has es gesehen ...
10:56 egonw hab
10:57 olass @tell egonw STOP SINGING
10:57 zarah Consider it noted.
10:57 egonw ... du bist by mir ...
10:57 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
10:57 egonw bei
10:57 egonw crarppy German with English accent
10:58 egonw brilliant piano, btw
10:58 olass @slap egonw
10:58 * zarah would never hurt egonw!
10:58 egonw zarah++
10:58 olass zarah: traitor!
10:58 zarah olass: I did not understand that
10:58 olass zarah: you are the idiot
10:58 egonw ... das es um ein Verbrechen handelt ...
10:58 zarah olass: are you making fun of me?
10:58 olass zarah: you are the stupid one
10:58 zarah olass: no, YOU are the stupid one! :)
10:59 egonw zarah: :)
10:59 zarah egonw: eh... wha'?
10:59 * olass is back to work
11:05 CIA-73 bioclipse: ospjuth * r9815 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Changed ArrayList to BioList in generate2D and generate3d. We should always use BioList as implementation when returning a List<IMolecule> since that allows for recording and opening with ui.open(myBioList)
11:05 olass Gpox, maclean or egonw: is it possible to zoom JCP without the mouse wheel, like in jmol?
11:05 egonw olass: please read the backlog and reply to my question
11:05 egonw Gpox: you to, when you are back, please
11:05 olass egonw: what question?
11:05 egonw see backlog
11:05 * olass is already backlogged
11:05 olass you have been singing to much
11:06 olass that has covered all tracks of any question
11:06 olass was it partial 2D?
11:06 egonw right
11:06 olass egonw: I don't know
11:06 olass what do you propose?
11:06 olass a warning seems appropriate
11:06 egonw fix the CML describer to check all atoms
11:07 olass egonw: sounds ok if not too heavyweight
11:07 egonw but I could live with the JCP editor showing a message "Generated Coordiantes"
11:07 olass yes, me too
11:07 egonw yes, that would be heavy weight
11:07 olass we cannot have heavyweight contenttypes
11:07 egonw ok, will file a bug report for Arvid then...
11:07 olass that is incorrect
11:08 olass good
11:08 egonw olass: well, it could be simpler, when we properly did CML conventions
11:08 olass contenttypes MUST be very quick
11:08 egonw olass: how do I get students?
11:08 olass egonw: yes
11:08 egonw I need students
11:08 egonw preferable summer students
11:08 egonw whatever
11:08 olass egonw: put up a page with projects
11:08 egonw drones
11:08 egonw OK, then what?
11:08 olass well, advertise for it
11:09 egonw OK, how can I create a page for farmbio.uu.se ?
11:09 olass you need to ask Magnus
11:09 olass and
11:09 olass you need to sort out if they should be payed
11:09 egonw can they?
11:09 egonw how does that work?
11:09 egonw who would pay?
11:09 olass if Jarl wants to
11:10 olass but I suspect not
11:10 egonw same
11:10 egonw here
11:10 olass so
11:10 egonw as he needs to spend that money on travel stuff for me
11:10 olass you need to clearly state that in the page that they will not get payed but academic credit, a research project
11:10 olass Jarl can give academic points for that
11:11 olass that is how we did it with annzi in Moss
11:13 maclean olass : zooming in jcp - if you say "jcp.setZoom(0.5 * jcp.getZoom())"
11:14 maclean and then "jcp.updateView()"
11:14 maclean ...does that work?
11:15 olass mom
11:15 olass testing
11:16 olass maclean: yes, that works
11:16 maclean cool
11:16 olass hmm, I think the last updateView should not be needed...
11:17 maclean should not be, or is not?
11:17 * jonalv is back and baclogged (much singing going on here)
11:17 olass well, it is not
11:17 olass oh
11:17 olass it is needed
11:17 maclean ah.
11:17 olass but should not be needed
11:17 olass IMHO
11:18 * maclean is not so sure
11:18 olass well, if I interact with JCP from scripting, the results should be shown
11:18 maclean updateView is scriptable
11:18 olass else the help should clearly say that you need to call updateView() to actually see the results
11:19 maclean that is certainly true
11:19 maclean explicit view updates has the advantage that you can go:
11:19 olass but I really don't see the use case when user dos not want to see JCP updated after setting the Zoom
11:19 maclean setA(); setB(); setC(); updateView()
11:20 maclean and not have it update each time.
11:20 olass it is not expensive
11:20 olass what do you gain?
11:20 maclean but I realise as I type this, that its not a great advantage
11:20 olass :)
11:20 olass ok, I will file a bug report
11:20 olass or
11:21 olass yes, will do
11:22 maclean I guess the really fancy way to do things would be to maintain the updateView method in the public api, as well as having a 'setAutoUpdate(true|false)' method
11:22 maclean Then the user could choose to not update with each change if they wanted...
11:22 olass maclean: yes
11:23 olass with default to true IMO
11:23 olass will  include this in the bug
11:23 maclean default to true, very yes.
11:28 olass maclean: do you want the bug?
11:28 olass are you allowed to work on bioclipse? ;)
11:28 olass better not I guess
11:29 maclean better not
11:29 olass is it possble to zoom JCP without mouse wheel, like jmol?
11:29 olass hold shift and drag?
11:30 olass else I'll file a bug for that
11:30 maclean ok
11:31 maclean sorry,  I mean : no.
11:31 maclean so, 'ok' = 'go ahead and file a bug'.
11:32 olass done
11:33 maclean for some reason, ever since jonalv complained about zooming being the 'wrong' way on the mouse wheel, and since it was changed, I have been getting it wrong.
11:33 jonalv lol
11:33 maclean it's like I'm stuck on the way I implemented it first.
11:34 jonalv I just wanted it to work in the same way as, Inkscapde and Gimp
11:34 maclean true
11:35 maclean I guess it's the difference between 'pulling' the molecule towards you and 'flying' the camera away from it.
11:35 maclean A fixed or mobile camera model, in other words :)
11:37 olass @tell masak: I'd like to write bug 887, 901, 858 as P2 on your TODO-postit
11:37 zarah Consider it noted.
11:37 egonw olass: arvid's bug list is growing big time again...
11:38 olass yes
11:38 olass I know
11:38 egonw olass: I think we need a meeting tomorrow morning and redistribute tasks a bit
11:38 olass sounds good
11:38 olass many meetings tomorrow
11:38 maclean who is this Lars guy?
11:38 olass he works at AZ and collaborates with our group
11:39 maclean I see.
11:39 olass and is a beta tester :)
11:39 maclean Clearly :)
11:39 olass (one of the few :( )
11:40 maclean Well, there may be others, who just don't stubmit bug reports
11:40 egonw or are not allowed
11:40 maclean Oh. Right, you have to have an account.
11:40 egonw ha
11:40 egonw @pz 911
11:40 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=911
11:40 egonw how appropriate :)
11:41 jonalv egonw: regarding 911...
11:42 egonw yes...
11:42 jonalv egonw: will you get very angry if I mark it as works for me?
11:42 jonalv :)
11:42 egonw no, if you point me to the final API
11:43 egonw I'm reading your blog now...
11:43 egonw but that changes the API, right?
11:43 egonw but if that is the *final* one...
11:43 egonw I'm fine with it
11:43 egonw please add the *
11:43 jonalv egonw: the final api for the new world order is on the wiki. If youare refering to the final api for my latest thoughts on managers than that is something toally different... :)
11:43 egonw please add the *final* version to the bug report
11:43 egonw but the wiki API does not work
11:44 egonw as you did not know how to get something returned
11:44 jonalv egonw: I don't think there will ever be a *final* perfect way to create managers...
11:44 egonw and if I do not know how to make it according to the final API I cannot fix the bug reports
11:44 egonw I only care about the final 2.0.0 one
11:44 jonalv egonw: well put it this way. That api does not support that.
11:44 egonw I only care about the final 2.0 one
11:45 olass http://wiki.bioclipse.net/index.php?title=H​ow_to_make_a_manager#Manager_best_practices
11:45 zarah olass's link is also http://tinyurl.com/dypvah
11:45 jonalv hm
11:45 olass jonalv: hm to manager best practices?
11:45 jonalv olass: yes an no
11:45 jonalv uhm not only
11:46 olass jonalv: uhm to manager best practices?
11:46 jonalv I am looking forward to your oppinions on the blog post
11:46 jonalv I thought I should run things through you people this time
11:46 olass jonalv: who's opinions?
11:46 jonalv Since I clearly didn't hae the entire picture clear to me last time...
11:46 jonalv the Bioclipse developers
11:47 jonalv olass, egonw, maclean: You will comment won't you? :)
11:47 olass jonalv: why not have a meeting instead?
11:47 olass much more direct
11:47 olass faster
11:47 olass reduces lag
11:47 olass fun
11:47 maclean "run past". "Run through" is something you do with a sword.
11:47 olass social
11:47 jonalv olass: whatever, I just don't think we can bring maclean and shk3 and besides only me and Gpox is in UA today...
11:48 maclean I may have difficult making it to Upsala today.
11:48 jonalv maclean: aha *lol*
11:48 olass maclean: well, we're talking about tomorrow
11:48 maclean Oh, right. Okay then.
11:49 olass :)
11:49 egonw and next weeks programme is full too
11:49 jonalv olass: but I did actually have any form of comments in my mind when I wrote that...
11:50 olass ok
11:50 olass jonalv: you'll get my comments tomrrow in the meeting, is that ok with you?
11:50 jonalv it's just that I don't wanna go ahead and write yet another system that only does what I thought ws needed and not what all of you need...
11:50 olass if you need them now then I propose a skype call
11:50 olass faster
11:50 olass better
11:50 jonalv olass: I should be able to hold out until tomorrow.
11:50 olass :)
11:51 jonalv but if you want to skype of course we can do that :)
11:52 egonw jonalv: replied
11:52 maclean the problem may be trying to find an api that is consistent across all programs that could possibly be made in the fields of chem- and bio- informatics.
11:52 maclean which is not easy.
11:52 egonw ... she calls friends ...
11:53 egonw ... sweet summer sweat ...
11:53 egonw ... wine ...
11:53 maclean quick! find another blog post for egon! he's singing again!
11:53 jonalv maclean: I think it's more of a meta api
11:53 maclean jonalv : true.
11:56 egonw ... lalalala ... (guitar kicked in)
11:57 egonw jonalv: getting back to the NWO...
11:57 jonalv egonw: yes...
11:57 egonw so, how you do define being compatible with the final NWO?
11:58 egonw how I know when I can close a "fix to NWO" bug?
11:58 jonalv egonw: time to invalidate a bunch of bugs?
11:58 egonw dunno
11:58 egonw you tell me
11:58 egonw I rather see zero failing unit test on the CDKManagerPluginTest
11:59 jonalv egonw: yes that is what I want to as well
11:59 jonalv |to see
12:01 jonalv egonw: I don't really know what we should do. I am starting to think it should be up to the guy responsible for each manager how he want to implement it. And in that case feel free to invalidate those bugs if you want to.
12:01 jonalv egonw: I mean some of the managers clearly works and how they are implemented is sort of beside the point...
12:02 egonw then I will file a bug report against core to stop complaining about methods not allowed to be called
12:02 jonalv egonw: sry?
12:03 egonw if managers can do what they like...
12:03 egonw then Bioclipse should not complain about it
12:03 jonalv egonw: it is actually the managers themself that are complaining...
12:03 egonw true
12:03 egonw ok, let me rephrase that
12:04 egonw then I will revert all patches that made CDKManager methods complain about the methods being called
12:04 egonw no, better
12:04 jonalv is it just me that feels like the managers suddenly got a life of their own? :)
12:04 egonw will file a bug report against the commiter who made those commits
12:04 egonw jonalv: sorry, there is no easy way out of this)
12:05 jonalv egonw: since they clearly are bugs that makes sense. But I already have a bug ticket for that so I don't know what point is.
12:05 egonw ah, ok
12:05 jonalv All I am saying is that we probably should take the cdk manager first and wait a little with all the rest...
12:05 egonw good, sounds like my job is done :)
12:05 jonalv egonw: nope you job is about to begin :)
12:06 jonalv egonw: we should have one of your famous "hack sessions" you and me and get some order to the cdkmanager and more importantly it's tests
12:07 egonw OK, tell me...
12:07 egonw let's start that hack session
12:07 egonw I will write the
12:07 egonw AbstractNewWorldOrderManagerTest
12:07 egonw rigth now
12:07 jonalv egonw: I think we will have to have that meeting with olass first...
12:08 egonw ah, ok
12:08 egonw I'll go ahead with that new class anyway...
12:08 egonw ping me when you get back
12:08 jonalv egonw_: get back from what?
12:08 olass jonalv: meeting with me?
12:08 egonw that meeting
12:08 jonalv that was tomorrow....
12:08 olass ah, tomorrow?
12:08 olass ok
12:08 jonalv or?
12:09 olass just don't let it slow you down :)
12:09 * jonalv hates irc it';s som complicated to communicate this way...
12:09 olass we could have a skype call...
12:09 jonalv olass: oki
12:09 jonalv mom
12:12 jonalv olass: okey let\s skype then...
12:12 olass call me when you like
12:33 jonalv olass. egonw: Would a CML molecule make any sense? I mean adding an IMolecule fromCML to the moleculeManager...
12:33 jonalv and and IMolecule fromCMLFile
12:33 egonw more detail please
12:33 jonalv in that case I could try these new things on that manager and those two methods...
12:33 egonw what is 'molecularManager' ?
12:33 egonw what is fromCMLFile?
12:34 jonalv egonw: net.bioclipse.core.business.MoleculeManager
12:34 egonw what is that??
12:35 jonalv phone
12:35 egonw a phone?
12:35 egonw why do we have phones in Bioclipse2??
12:35 * jonalv is skyping with olass
12:35 maclean now THAT would be fancy.
12:35 egonw skypinh with olass...
12:35 egonw do you want his number?
12:36 maclean phone.call("egon")
12:36 egonw if you just give me your credit card info...
12:36 egonw ah, crap... wrong channel again
12:36 maclean :)
12:36 egonw maclean: easy
12:36 egonw with XMPP stuff we already haev
12:36 maclean that's true
12:36 egonw or do you want sound too?
12:37 maclean oh definitely.
12:37 maclean and video
12:37 egonw I hope BC2.1 will have a net.bioclipse.irc plugin that will have people join #bioclispe
12:37 egonw or #bioclipse-user
12:38 maclean heh. the danger of accidentally outputting a log file to the irc channel seems high.
12:43 CIA-73 bioclipse: egonw * r9816 /bioclipse2/trunk/plugins/net.bioclipse.​core.tests/src/net/bioclipse/core/tests/​AbstractNewWorldOrderManagerTest.java: Added class to test for NWO compatibility
12:44 jonalv egonw: I think I should start doing this in a small example manager...
12:44 egonw better
12:45 egonw use an existing small manager
12:45 egonw GistManager
12:45 egonw or InChIManager
12:45 egonw and then we will create unit tests on the fly
12:45 jonalv yes that was why I was looking at the MoleculeManager...
12:45 egonw ic
12:45 jonalv but yes the gist manager is another valid option
12:45 jonalv perhaps a better one
12:46 * jonalv reads it now
12:46 jonalv however it has 0 methods working with IBIoObjects
12:46 egonw http://www.surveymonkey.com/s.aspx​?sm=kBmeSUXENlGK6B_2f6CcTAyQ_3d_3d
12:46 zarah egonw's link is also http://tinyurl.com/cpmfdu
12:47 egonw survey on how people use Eclipse
12:47 egonw jonalv: so?
12:47 egonw then do the InChI one
12:47 jonalv so I don't get that situation tested...
12:48 jonalv I think the gist one is fine actually. It works with files :)
12:48 egonw right
12:49 jonalv egonw: requesting your permission to screw up your code in the gist manager :)
12:50 jonalv oh did I say screw up?
12:50 jonalv I mean refactor
12:50 egonw permission granted to send me a patch for review
12:50 egonw or put up a git repos
12:51 jonalv oki
12:51 jonalv worksforme
12:51 jonalv egonw: how do I put up a git repo for that?
12:53 egonw https://apps.sourceforge.net/mediawiki/cd​k/index.php?title=Development_with_Git#Ho​w_can_I_publish_a_branch_on_my_web_server.3F
12:54 jonalv egonw: oh thankyou
12:55 jonalv egonw: uhm and where on pele would this be? :)
12:55 egonw /var/www
12:55 egonw /var/www/git
12:55 jonalv egonw: directly there?
12:55 egonw i think
12:56 egonw yes
12:56 egonw next to:
12:56 egonw bugzilla.git
12:56 egonw cdk.git
12:56 egonw and rajarshi.git
12:56 jonalv then it is /var/www/git
12:56 egonw yes, see above
12:57 jonalv aha
12:57 jonalv missed that row :)
12:57 egonw :)
12:57 jonalv I will place it there and then ask you to pull from it when I am done then? :)
12:57 CIA-73 bioclipse: goglepox * r9817 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.ui.sdfeditor/src/net/bioclipse/cdk/u​i/sdfeditor/editor/JCPCellPainter.java:
12:57 CIA-73 bioclipse: Takes paint rectangle x,y into account when drawing 'Generated'
12:57 CIA-73 bioclipse: Partial fixes missing text
12:58 CIA-73 bioclipse: goglepox * r9818 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.ui.sdfeditor/src/net/bioclipse/cdk/u​i/sdfeditor/editor/JCPCellPainter.java: Draws 'Generated' after the structure fixes bug #774
12:58 zarah bug #774 | http://tinyurl.com/cd2sak
12:59 CIA-73 bioclipse: ospjuth * r9819 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: generate3dcoordinates now returns BioList and not ArrayList, as specified in http://wiki.bioclipse.net/index.php?title=H​ow_to_make_a_manager#Manager_best_practices
12:59 zarah CIA-73's link is also http://tinyurl.com/dypvah
13:01 CIA-73 bioclipse: ospjuth * r9820 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Changed several ArrayList to BioList according to http://wiki.bioclipse.net/index.php?title=H​ow_to_make_a_manager#Manager_best_practices
13:01 zarah CIA-73's link is also http://tinyurl.com/dypvah
13:02 egonw wow, that "How to make a manager" method did not tell me anything on when is what needed
13:02 egonw do I need all?
13:02 egonw which are the actual methods I need to implement, and which not?
13:02 egonw which annotation is the bare minimum
13:03 egonw what annotation require what follow up methods
13:03 egonw jonalv: do you want bug reports on that page?
13:03 * jonalv backlogs
13:03 jonalv egonw: yes that soundsl ike a good idea
13:13 olass shk3: I'm sorry to say this but I reopened bug 838
13:13 olass it is a long task and requires a progressmonitor
13:13 olass now bioclipse just freezes on 3D generation
13:13 shk3 I am waiting for jonalvs input on this
13:13 shk3 sorry
13:14 olass jonalv: could you give shk3 input for this?
13:14 jonalv olass: no
13:14 shk3 but I won't do anything on this new world order thing till it is reasonably stable
13:14 shk3 I don't mind that it changes
13:14 shk3 I understand that
13:14 jonalv olass: or rather I guess I could but it
13:14 shk3 but I really don't see why I should keip up with changes every other day
13:15 olass jonalv: can you maybe do it?
13:15 jonalv shk3: I think that if what you have done is working and there is nothing more to gain by changing then you shouldn't
13:15 olass jonalv: but I need that progress bar
13:15 shk3 btw, the progresss bar thing is in 830
13:15 jonalv olass: okey
13:15 olass ah
13:15 olass sry
13:15 shk3 I will close 838 again, because it has nothing to do with progress bars
13:16 jonalv olass: If you need it I will lay everything else to the side and go fix it for you
13:16 olass jonalv: it's not that urgent
13:16 jonalv olass: okey how urgent is it?
13:16 olass but before friday would be good
13:16 jonalv olass: then it is urgent
13:16 jonalv I am not working friday...
13:16 olass (it's important for the workshop)
13:16 jonalv I will travel friday...
13:17 olass jonalv: let's talk tomorrow
13:17 olass don't bother until then
13:17 jonalv olass: I don't think we have much time to fix things tomorrow either.
13:17 jonalv olass: if you want it for the workshop then I want to start with it today
13:17 olass *sigh* these meetings
13:18 shk3 sorry that I can't be of much help
13:18 olass jonalv: is a progressbar an advanced request in NWO?
13:18 jonalv olass: can I have a bug ticket?
13:18 olass 830?
13:18 olass or 838?
13:18 jonalv shk3: it's my mess...
13:18 shk3 but it is really hard for me to implement things while you work out how they should be done
13:18 olass shk3: I understand you
13:18 shk3 830
13:18 jonalv shk3: my point exactly
13:18 olass I have the same issue in QSARManager
13:18 jonalv @pz 830
13:18 olass which I have not even tried to get in NWO
13:18 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=830
13:19 olass and will do once things stabilize
13:19 * olass is very happy about this decision
13:19 jonalv shk3: I will steal 830 from you now and do it instead of everything else
13:19 jonalv shk3: okey?
13:20 olass shk3: please mark this in 838 and mark as fixed
13:20 olass ah nice
13:20 jonalv shk3: and I will probably need hel from you... :)
13:20 olass saw it now
13:23 jonalv bah my third world order is gonna need a name...
13:25 olass jonalv: Multi-threaded managers?
13:25 egonw "all we need is some food" ?
13:25 olass egonw: STOP SINGING!
13:26 egonw no, no
13:26 jonalv LOL
13:26 egonw this was a name for the *third world* order
13:26 egonw ... girl, you were made for me ...
13:26 egonw (that's singing)
13:27 jonalv zarah: I think egonw is talking to you. ARen't you the only girl here?
13:27 zarah jonalv: excuse me?
13:27 olass egonw: why the naming of dl:ed gists?
13:27 olass /Gists/Gists95194.0.js
13:27 olass what is the .0 ?
13:27 jonalv version number?
13:27 olass and why the plural s in Gists
13:27 egonw because otherwise someone will complain when he downloads the gist a second time
13:27 olass Gist95194 sounds more logical
13:28 jonalv Gist95194.0 I think
13:28 olass reopening bug
13:28 egonw olass: sure, use download(84188, "/Whatever/you/like/best")
13:28 olass :)
13:28 olass egonw: seriously, why should a user complain?
13:28 olass ah
13:28 olass ok
13:29 egonw cause he would get a 'I already have that file, idiot'
13:29 egonw users don't like that
13:29 olass well, a gist is always up to date
13:29 olass afile is not
13:29 olass hence overwrite woudl always be a good idea
13:29 olass but I see that this is the case now
13:29 olass doing it a second time overwrites the file
13:31 egonw what?
13:31 egonw does it?
13:31 egonw that would be a bug
13:31 olass so the 0 is not the gist version read from the gisthub?
13:33 egonw no
13:33 egonw just to not have to overwrite files
13:34 * olass likes gists overwriting since a gist is always right
13:35 egonw that 903 reopening was nonsense
13:35 egonw at least the comment
13:36 olass ok?
13:36 olass sorry
13:36 olass I just think creating an Empty project is not desirable
13:36 olass sorry if you think it useless
13:37 egonw yes, but if they accidentally downloaded the wrong gist
13:37 egonw I very much expect them to try again
13:37 egonw until they have the right one
13:37 egonw don't you?
13:37 olass I just thought you wanted to be aware of the bug
13:37 egonw or have you been so seen so many disappointed Bioclipse users that you think they will give up after one try?
13:37 egonw what bug?
13:37 olass lol
13:37 olass empty project created
13:38 olass but sure, it is very minor...
13:38 egonw it's a feature
13:38 olass but very easy to fix too
13:38 egonw it's AI
13:38 egonw it's thinking ahead of schedule
13:38 olass :)
13:38 egonw .. yesterday, ...
13:38 egonw ... oh, I believe ...
13:47 CIA-73 bioclipse: ospjuth * r9821 /bioclipse2/trunk/plugins/net.bioclips​e.data/data/Javascripts/gencoords.js: Added a JS to generate all types of coordinates (2D, 3D, 5D) on a list of SMILES. Also available as gist 95755.
13:48 egonw JCP sucks
13:48 egonw seriously
13:48 egonw lars is right
13:48 egonw the current version has very many regressions
13:48 egonw things that used to work are now broken
13:49 egonw what happened here?
13:49 egonw olass: this is really bad news
13:49 egonw the next one will certainly not be the RC1
13:49 olass yes
13:49 maclean Gremlins
13:49 olass *sigh*
13:49 olass egonw: I'm happy you also test it
13:50 olass let's talk to Gpox tomorrow
13:50 olass and arrange priorities
13:50 olass jonalv: can you be at bmc 9.30 tomorrow?
13:50 maclean It's probably my fault - the scrollbar/zooming may have screwed things up :(
13:50 olass we need the time...
13:50 egonw why the fuck did I not make more noise when people suggested to put in all old functionality first
13:50 egonw and go from there
13:50 jonalv olass: yes I guess I can do that
13:51 egonw let's cram in as much as possible
13:51 egonw that's what we want
13:51 egonw no stable minimal funcitonality, but workable things
13:51 olass we need a stable JCP
13:51 egonw no, just every bit of crappy of old JCP functionality
13:51 olass :(
13:51 jonalv @google capten obvious
13:51 zarah jonalv: http://www.nyaatorrents.org/%3Fp​age%3Dtorrentinfo%26tid%3D54261
13:51 jonalv lol
13:52 egonw maclean: no, it's just that our development model has not worked
13:52 maclean egonw : is this the 'clean new code : yes. old dusty code : no" argument?
13:52 egonw I was too naive that the design was clear enough
13:52 egonw other thought that adding a method here and there cannot hurt
13:52 maclean And how did you reply to that question before I asked it?
13:52 egonw :)
13:52 egonw ... easy lover ...
13:52 jonalv why does the doCreation method take a boolean make3D? It makes my head hurt... :(
13:53 egonw jonalv++
13:53 egonw mine too
13:53 egonw it's bad design pattern
13:54 egonw I hate the pattern "Let's cram in another boolean to have it do different things"
13:54 * jonalv goes and buys Coca Cola. *We needs it....* :)
13:55 jonalv it might look like a good idea but it's not so fun when another guy needs to grokk the code...
13:55 jonalv it's not so easy for a bear of a very small brain...
13:55 jonalv afk
13:57 maclean Arvid's code!
13:58 maclean I can tell from the:
13:58 maclean if(make3D)
13:58 maclean atom.setPoint2d( null );
13:58 CIA-73 bioclipse: ospjuth * r9822 /bioclipse2/trunk/plugins/net.b​ioclipse.data/data/Javascripts/ (dnaiso.js downloadPDB.js): Rename downloadPDB.js to dnaiso.js since we have multile JS downloading PDBs.
13:58 maclean no space between 'if' and bracket. and spaces in the method call. :)
13:59 egonw maclean: run '[git|svn] annotate' to make sure
13:59 maclean I don't really mind that much.
14:00 maclean methodName( arg ) can look clearer sometimes. especially for numbers : "translate( 10 );"
14:03 CIA-73 bioclipse: ospjuth * r9823 /bioclipse2/trunk/plugins/net.bioclipse​.data/data/Javascripts/dlPDBrotate.js: Added another script to download and rotate 1D66 in jmol. Also available as Gist 79822.
14:03 maclean I'm just such a whitespace fanatic.
14:11 CIA-73 bioclipse: ospjuth * r9824 /bioclipse2/trunk/plugins/net.bioclip​se.data/data/Javascripts/multimol.js: Added a JS to show basic manipulation of multiple molecules in Bioclipse. Also available as gist 95790.
14:11 jonalv maclean++ //whitespace fanatic
14:11 maclean :)
14:12 jonalv maclean: do you have my coding style pinpoijnted as well? :)
14:12 maclean Er. No actually. I don't think so.
14:12 egonw ... jump ...
14:12 jonalv :(
14:12 maclean Maybe I haven't seen enough of your code. Or you use java conventions, so I don't notice.
14:13 jonalv maybe
14:13 maclean Egon doesn't seem to have a characteristic style, either.
14:13 stain_ Eclipse -> Reformat is my favourite
14:13 stain_ except on those long lines..
14:13 maclean shift-apple-f
14:14 egonw stain_: reformat is evil, if part of a patch making code changes
14:14 stain_ no, you do a separate reformat-patch first
14:14 egonw file = "/Sample Data/SDF/Fragments2.sdf";
14:14 egonw iterator = cdk.createMoleculeIterator( file );
14:14 egonw searchMol = cdk.fromSMILES("C");
14:14 egonw results = cdk.createMoleculeList();
14:14 egonw i = 0;
14:14 egonw wrong console
14:14 stain_ (   spaces   );
14:18 egonw olass: happy with another API change?
14:18 egonw in CDK manager
14:18 egonw oh boy...
14:18 egonw we are going to have so much fun with testing Gists
14:18 egonw I'm sure zero will work in beta5
14:19 maclean zero?
14:19 maclean Oh, right.
14:19 maclean Sorry.
14:19 egonw well, maybe 3%
14:19 egonw let's be optimistic :)
14:19 egonw .. isn't that ironic ...
14:20 egonw olass: that's an OK?
14:20 egonw good
14:23 egonw jonalv: ummm...
14:23 egonw check @824
14:23 jonalv @pz 824
14:23 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=824
14:24 jonalv egonw: lol
14:24 egonw that was 15 minutes waisted
14:25 * jonalv is trying to figure out why it matters...
14:25 jonalv oh
14:25 jonalv never mind
14:25 jonalv *lol*
14:29 egonw jonalv: well, you have enough chatting with Ola now...
14:30 egonw so, what's the story of the NWO?
14:30 jonalv egonw: I got a bug which needed to be fixed for the workshop so I am on it now
14:30 jonalv sry
14:30 egonw OK
14:30 jonalv progressmonitor for the 3d/2d generation actions
14:31 jonalv I needed to rewrite quite some things... :/
14:31 * jonalv is eating his own dog food, and shk3s
14:34 jonalv okey I am lost now
14:34 jonalv fuck
14:35 jonalv *jonalv dissapears into a crying little wet spot*
14:40 jonalv where is shk3?
14:40 jonalv BLAME BLAME BLAME!
14:40 CIA-73 bioclipse: egonw * r9825 /bioclipse2/trunk/plugins/net.​bioclipse.cdk.jchempaint/doc/ (convert.html moleculefromsmiles.html molecules.html): Added missing stylesheets
14:40 jonalv olass: I can't fix this without rewriting all of it...
14:41 jonalv it's one big mess...
14:41 CIA-73 bioclipse: egonw * r9826 /bioclipse2/trunk/plugins/net.​bioclipse.cdk.jchempaint/doc/ (4 files): Remove TODOs
14:41 jonalv Why the fuck is he using a static method implemented in one random class and then calling that one from a bunch of other random classes?
14:42 jonalv one huge method that does _EVERYTHING_ and is static
14:42 egonw isn't that good?
14:42 * egonw ducks
14:42 jonalv zarah: slap egonw
14:42 * zarah places her fist firmly on egonw's jaw
14:42 egonw happy I ducked
14:42 egonw zarah: missed me!
14:42 zarah egonw: eh... wha'?
14:43 jonalv but honestly, this is so not jsut a little bad. It's _VERY_ bad
14:43 jonalv I ahve jsut spend about 2 hours trying to refacutore it just to give up.
14:43 jonalv I am going to have to start over
14:43 jonalv Now that I realise what actually the code was doing...
14:46 maclean jonalv : stefan has left for the day.
14:46 jonalv maclean: lucky bastard
14:46 jonalv :(
14:46 maclean I can cover his chair in thumb-tacks if you'd like...
14:47 * jonalv smiles and nods (Always a good thing to do when you are not exaclty sure what the other person is talking about)
14:47 maclean ha :) Never mind.
14:48 maclean Stefan also has a characteristic code style. But he doesn't like me mentioning it anymore...
14:48 jonalv would they actually have any effect if you try to sit on them?
14:48 jonalv it is very heacy towards the right side of the screen...
14:49 olass sorry guys, need to run off and buy a car
14:49 maclean it is what I call 'german' code : agglutinative.
14:49 olass will be back later in the evening
14:49 maclean If that's how you spell that word.
14:49 olass and continue work
14:50 jonalv olass: oki :)
15:19 * jonalv heads to swim and think about this. Probably some for of special solution is needed... :/
15:22 CIA-73 bioclipse: egonw * r9827 /bioclipse2/trunk/plugins/net.bioclips​e.rdf/src/net/bioclipse/rdf/business/ (IRDFManager.java RDFManager.java): Renamed method to make place for a non-reasoning sparql query engine
15:23 CIA-73 bioclipse: egonw * r9828 /bioclipse2/trunk/plugins/net.bioclips​e.rdf/src/net/bioclipse/rdf/business/ (IRDFManager.java RDFManager.java): Added sparql(), now without reasoning
15:25 egonw ... can you hear me, major Tom ...
15:28 maclean You're very lucky that I am not singing what I was listening to - either Wu-Tang, or Carter USM...
17:22 CIA-73 bioclipse: egonw * r9829 /bioclipse2/trunk/plugins/net.bioclipse.rdf/ (META-INF/MANIFEST.MF build.properties): Some metastuff cleanup: removed non-existing dirs, added '.' to classpath
17:22 CIA-73 bioclipse: egonw * r9830 /bioclipse2/trunk/plugins/ne​t.bioclipse.rdf/plugin.xml: Added RDF related content types (but why are they not picked up??
17:22 egonw @tell olass can you please look at the commit to net.bioclipse.rdf/plugin.xml that added two content type (commit 9830)... when I run the RDF feature, they are not picked up at lall
17:22 zarah Consider it noted.
17:51 olass joined #bioclipse
17:51 egonw hi olass
17:51 olass hi
17:51 zarah hi olass
17:51 zarah olass: You have new messages. Write '/msg zarah @messages' to read them.
17:52 olass @msg
17:52 zarah olass: 29 m 5 s ago, egonw said can you please look at the commit to net.bioclipse.rdf/plugin.xml that added two content type (commit 9830)... when I run the RDF feature, they are not picked up at lall
17:52 olass egonw: how do I test them?
17:52 egonw boot bioclipse with the RDF feature
17:53 egonw will attach two test files
17:53 egonw to the report
17:53 egonw forgot that
17:53 olass I don't see a bug
17:53 egonw ah, right
17:53 olass is there one?
17:53 egonw very soon
17:53 olass :)
17:53 * olass is updating rdf in the meantime
17:55 olass egonw: any progress with the XMPP service?
17:55 egonw no
17:56 olass you will not do it?
17:56 egonw was working on the descriptor ontology
17:56 egonw trying
17:56 olass ok
17:56 egonw but so much came in between today
17:56 egonw with other P1 bug reports
17:56 olass ok
17:57 olass but a gist for the existing descriptor would be quite easy to create, right?
17:57 olass I mean, it is up and running
17:57 egonw yes
17:57 shk3 joined #bioclipse
17:58 egonw olass: test files attached
17:58 olass to what?
17:58 olass did you assign a bug to me?
17:59 * olass is syncing his bug list
17:59 egonw yes, 917
18:00 olass @bug 917
18:00 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=917
18:03 shk3_ joined #bioclipse
18:04 olass egonw: ok, found the content types
18:04 olass egonw: do like this
18:04 olass Open bioclipse preferences
18:04 olass type content in the search box
18:04 olass in the Content Types page, you see the contenttypes you have registered
18:04 egonw done
18:04 egonw yes
18:04 olass I see your there
18:04 egonw .n3 is given
18:05 olass hence they are picked up
18:05 olass so
18:05 egonw indeed...
18:05 egonw weird
18:05 olass set a breakpoint in the describer
18:06 olass and see if it matches your provided parameter
18:06 egonw well, neither is working
18:06 olass will
18:06 olass n3 seems top work
18:06 egonw mmm...
18:07 olass if I right-click teh n3, it says type= n3
18:07 egonw not here...
18:07 olass it does here
18:07 egonw ok, good
18:07 egonw that's good news
18:07 egonw ha...
18:07 egonw I moved it to another folder
18:07 egonw does the thing cache types or so???
18:08 egonw that's something to remember...
18:08 olass don't think so
18:08 egonw well, I moved the .xml one too now
18:08 egonw and then it is properly picked up...
18:09 olass egonw: is this very important?
18:09 olass for the workshop?
18:09 egonw for the QSAR stuff, yes
18:10 olass hmm
18:10 olass I will only do some minor scrpts
18:10 olass and I'm already done with them
18:11 olass but really looking fwd to doing the QSAR after the workshop
18:11 egonw btw, the workshop for me is more than just my presentation
18:11 olass :)
18:11 egonw but lots of talking to people too
18:11 olass yes
18:11 egonw among which OWL, RDF stuff
18:11 olass same here
18:11 olass but even more for you I guess
18:11 olass I'm looking fwd to meeting van Drie most
18:11 egonw yes, that will be nice indeed
18:11 olass I have chatted so much and skyped several times
18:12 olass will be nice to talk to him IRL
18:35 egonw olass: http://gist.github.com/95946
18:37 olass egonw: what do I need this for?
18:37 olass sorry, don't understand
18:37 egonw gist.download(95946)
18:37 olass yes, but for what?
18:37 olass I already have the ontology
18:37 olass and parsed it
18:37 egonw never mind
18:37 olass and queried it
18:37 olass with jena
18:37 olass is this a better way?
18:38 egonw yes, it actually would
18:38 egonw but that was not the point
18:38 egonw point was: pinpointing errors in the ontology
18:38 olass aha
18:38 egonw like descriptors not classified
18:38 olass what is this?
18:39 olass http://cdk.git.sourceforge.net/git/gitweb.cgi?p=cd​k;a=blob_plain;f=src/main/org/openscience/cdk/dict​/data/descriptor-algorithms.owl;h=032d3ba4b446cdb3​c5e82723f34f74e4297f0ff3;hb=refs/heads/cdk-1.2.x
18:39 zarah olass's link is also http://tinyurl.com/cf6gzz
18:39 olass where does this come from?
18:39 egonw that's the URL to the ontology
18:39 egonw a remote copy in the CDK Git repository
18:39 olass not the best URL...
18:39 egonw [20:39:02] <zarah> olass's link is also http://tinyurl.com/cf6gzz
18:39 egonw ?
18:39 olass can you set fixed URLS to this?
18:40 olass its a long and ugly URL
18:40 egonw no, unfortunately not
18:40 egonw yes, it is
18:40 egonw oh, but a local copy is much better anyway
18:40 olass indeed
18:40 egonw this just makes it work everywhere...
18:40 olass and faster
18:40 egonw yes
18:42 olass egonw the gist gives error
18:42 olass org.mozilla.javascript.EcmaError: ReferenceError: "ons" is not defined. (line: #5)
18:43 egonw replace with owl
18:43 egonw or check the new gist version
18:43 egonw sorry about that
18:44 shk3__ joined #bioclipse
18:44 egonw shk3_: not so good connection?
18:48 egonw oops...
18:48 egonw wrong button
18:48 egonw wrong script
18:52 egonw olass: ping
19:18 egonw I wonder what that trick was to create java classes from Bioclipse' javascript...
19:36 egonw @tell olass I am stuck... need to get the String of the XMPP return value ... but no clue how
19:36 zarah Consider it noted.
19:39 olass mom, in tel
19:39 zarah olass: You have new messages. Write '/msg zarah @messages' to read them.
19:42 egonw ok, forget it...
19:42 egonw I'll just add a hack to the xmpp manager
19:42 egonw this is stupid
19:48 CIA-73 bioclipse: egonw * r9831 /bioclipse2/trunk/plugins/net.bioclipse.​xws4j/src/net/bioclipse/xws4j/business/ (IXwsManager.java XwsManager.java): Added a convenience method to convert a DOM Element to String
20:11 egonw olass: https://gist.github.com/95987/0489e​6b2abc532193151acd83f64f804cd08be4b
20:17 CIA-73 bioclipse: egonw * r9832 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Added a convenience method to convert a String into a typed CMLElement
20:21 egonw olass: it's a nice example of reusing existing DOM models
20:21 egonw instead of making a CML binding on the fly
20:21 olass you can explain tomorrow
20:22 olass I need to sleep now :(
20:22 olass ..tired...
20:22 olass you seem to have worked yourway up during the day
20:22 olass rnow you seem full of energy!
20:22 olass egonw: now you seem full of energy!
20:22 egonw no, not really
20:23 egonw it's just that hacking works under any condition
20:23 egonw which is why I am good at this job
20:23 egonw programming is my primary language
20:23 egonw Dutch comes second
20:23 egonw and no matter how tired I am...
20:23 egonw programming works...
20:23 egonw and typically makes me more lazy -> better code
20:24 olass your gist fails
20:24 olass org.mozilla.javascript.EvaluatorException: Can't find method $Proxy37.toString(com.sun.org.apache​.xerces.internal.dom.ElementNSImpl). (line: #8)
20:24 egonw did you update?
20:24 olass hmm, no
20:24 olass just thought abt that
20:25 egonw thought so
20:28 olass try disconnect
20:28 olass then run gist
20:28 olass fails
20:28 olass some problem with xmpp.connect from JSEditor
20:28 olass I suspect a thread access
20:28 egonw run it as a single line
20:28 egonw I have that too
20:28 olass indeed
20:28 olass Caused by: org.eclipse.swt.SWTException: Invalid thread access
20:29 egonw yes, another bug
20:29 egonw sorry, should have warned about that
20:29 olass did you file or shall I?
20:30 olass I can
20:30 olass ?
20:30 egonw please do
20:30 egonw did not file that one yet
20:33 olass bug #918
20:34 egonw olass++
20:39 olass nice, got your xmpp descriptor gist to work
20:40 olass it's a start
20:40 olass e.g. cannot set parameters
20:40 olass and only one mol and one descr
20:40 egonw no, true
20:40 egonw that will require more work
20:40 olass yes
20:40 olass dunno if I have tome for this in the workshop
20:41 olass but it can go in the cheat sheet
20:41 egonw no worries
20:41 olass and people can do it if they have time
20:41 olass maybe
20:41 egonw it's a bit of progress on the QSAR site
20:41 olass :)
20:41 egonw that papers needs to be finished too
20:41 olass I need to push that after teh cdk ws
20:41 olass QSAR paper and release Bioclipse2
20:41 egonw ha, lars is doing more debugging
20:42 olass QSAR actually is some work for both of us
20:42 olass the writing is actually quite good already
20:46 egonw OK, also going offline now
20:46 olass me too
20:46 olass bye
20:46 egonw cu tomorrow
20:46 olass yes
20:52 charlgren joined #bioclipse

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