Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-11-14

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All times shown according to UTC.

Time Nick Message
05:58 masak joined #bioclipse
08:10 egonw joined #bioclipse
08:30 Gpox joined #bioclipse
08:38 egonw Gpox: had trouble getting some simple JCP scripts going
08:38 egonw Gpox: filed a bug report for you
08:39 egonw masak: one for you too...
08:39 masak saw that one, yes. thanks.
08:39 egonw assigned according to you because I think you might have ideas about it...
08:39 masak aye.
08:39 egonw need those issues fixed asap, so will look at them myself too...
08:39 egonw so, any clue you have is valuable
08:39 masak gotcha.
08:39 egonw or suggestion on how to fix
08:40 egonw or whatever
08:40 masak haven't looked at it yet, but sounds like it could be trouble in the ScriptingConsole
08:40 masak ...as far-fetched as that sounds :)
08:41 egonw :)
08:41 Gpox Display.getDefault().asyncExec( new Runnable(){...
08:43 egonw the updateView() should use that?
08:56 egonw Gpox: testing that patch
08:57 egonw shows be in setInput()
08:57 egonw should be in setInput()
09:01 egonw Gpox: thanx!
09:01 egonw that works :)
09:01 masak egonw: what do I need to open an MDL molfile in the CDK 1.2.x-based JChemPaint editor?
09:01 egonw right click on it
09:01 masak net.bioclipse.cdk.jchempaint?
09:01 egonw Open With
09:01 egonw yes
09:01 egonw cheminfo feature
09:02 masak ah.
09:02 masak I usually add plugins one by one, not by feature. will try that, though.
09:02 egonw yeah, open bioclipse.product
09:02 egonw select bioclipse_feature and chemoinformatics_feature
09:03 egonw and hit run
09:03 masak egonw: I have errors in n.b.cdk.jcp
09:03 egonw ok, what are they?
09:03 masak egonw: I vaguely remember having to make CDK manually. is that correct?
09:03 egonw did you update all plugins?
09:03 masak yup.
09:03 egonw did you import nb.cdk.jchempaint.view?
09:04 egonw into your Eclipse workspace?
09:04 masak seems not.
09:04 * masak does so
09:04 egonw CDK is now as plugins in bioclipse trunk
09:04 masak good.
09:04 egonw Gpox: wishlist for the JCP editor
09:04 egonw margins
09:04 egonw and a white background
09:05 egonw it should have a margin left, right, top, bottom, of half a bond length or so
09:07 masak egonw: imported n.b.cdk.jcp.view. the error persists.
09:07 egonw what error?
09:07 masak the first one's on line 123 in JChemPainEditor.java
09:08 masak widget.redraw();
09:08 masak The method redraw() is undefined for the type JChemPaintEditorWidget
09:09 Gpox update n.b.cdk.jcp
09:09 masak Gpox: oki
09:10 masak Gpox: I'm all updated already. nothing happened.
09:12 Gpox odd
09:12 masak aye.
09:13 masak I don't know how to proceed from here.
09:14 jonalv joined #bioclipse
09:15 jonalv oh hai
09:15 CIA-53 bioclipse: goglepox * r7675 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint.view/src/net/bioclipse/cd​k/jchempaint/view/JChemPaintWidget.java: Made background white.
09:15 masak jonalv: OH HAI
09:16 Gpox JChemPaintEditorWidget should extends JChemPaintWidget from n.b.cdk.jcp.view might need to do a clean or something
09:17 * masak does a clean or something
09:17 CIA-53 bioclipse: carl_masak * r7676 /bot/trunk/zarah.pl: [zarah] now recognizes "OH HAI" as a greeting
09:27 CIA-53 bioclipse: egonw * r7677 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java: Make editor dirty when setting new input
09:27 CIA-53 bioclipse: egonw * r7678 /bioclipse2/trunk/plugins/net.bioclipse.cdk​.jchempaint.business/src/net/bioclipse/cdk/​jchempaint/business/JChemPaintManager.java: Wrap as Runnable: fixes thread exception (closes #121)
09:27 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=121
09:29 masak maybe a tinyurl would be better there, too?
09:33 egonw dunno
09:33 egonw the tinyurl does not have the bug number
09:33 egonw maybe if you add some text in front:
09:33 egonw bug #121: http://tinyurl.foo/bar
09:34 thomasku joined #bioclipse
09:34 masak egonw: 'xactly.
09:35 masak egonw: busy now with jonalv tasks, but will fix later.
09:36 egonw no worries
09:37 egonw zarah: is not really like a priority
09:37 zarah egonw: excuse me?
09:37 egonw and I guess we could much use your help elsewhere
09:37 egonw like with the script console!
09:39 masak egonw: I'll help you if you tell me how to run your plugin.
09:39 masak right now, I'm stuck on that.
09:39 egonw did you get the compile problems fixed?
09:39 masak no, that's what I'm stuck on.
09:40 egonw ok, so, what's the current error?
09:40 masak the one I gave above
09:40 masak should I paste it again?
09:40 egonw agin?
09:40 egonw last one I saw was the redraw thingy
09:40 masak aye.
09:40 masak that one.
09:41 egonw did you do what Gpox suggested?
09:41 egonw did you update org.openscience.cdk.render?
09:41 masak yes, even though I already had a fresh wc.
09:41 masak I always update _everything_, just as jonalv++ does
09:42 masak egonw: almost none of the org.openscience.cdk plugins compile
09:43 egonw ok, but that's a different error then you listed above
09:43 jonalv egonw: have we officially moved over to 3.4.1 now?
09:43 egonw give me one of those
09:43 masak org.openscience.cdk.render has an error in MANIFEST.MF
09:43 masak javax.vecmath
09:43 jonalv I have many cdk plugins not compiling since they need 3.4.1...
09:43 egonw jonalv: no, don't think so
09:43 masak cannot be resolved.
09:44 egonw jonalv: where do you see that?
09:44 egonw don't see that in SVN
09:44 jonalv egonw: manifest for: net.bioclipse.cdk.jchempaint.view
09:45 egonw Gpox: that was not intentional I assume>
09:45 egonw ?
09:45 egonw or does jcp.view depend on 3.4.1?
09:45 Gpox no
09:46 egonw org.eclipse.swt;bundle-version="3.4.1",
09:46 egonw org.eclipse.jface;bundle-version="3.4.1",
09:46 egonw org.eclipse.ui;bundle-version="3.4.1",
09:46 egonw bloody annoying that Eclipse 3.4 auto adds these bundle-version stuff... :(
09:46 masak egonw: jonalv and I are leaving this issue until you've resolved it for us :)
09:51 CIA-53 bioclipse: egonw * r7679 /bioclipse2/trunk/plugins/net.bioclipse.c​dk.jchempaint.view/META-INF/MANIFEST.MF: Removed deps on 3.4.1
09:52 CIA-53 bioclipse: egonw * r7680 /bioclipse2/trunk/plugins/net.bioclipse.cdk​.jchempaint.business/src/net/bioclipse/cdk/​jchempaint/business/JChemPaintManager.java: Updated header
09:52 egonw masak, jonalv: try now
09:53 * masak tries
09:53 egonw btw, removing that bundle-version was trivial, you could have done that too...
09:53 masak I'm sure I could have.
09:53 jonalv egonw: absolutley but I didn't want to do that in case something actually depended on that version...
09:53 masak question is, why wasn't it done already? :P
09:53 egonw ask the author then
09:54 jonalv yea well I asked the guy responsilible for chemoinformatics in Bioclipse ;)
09:55 masak egonw: all errors remain.
09:55 jonalv egonw: everything compiles for me :)
09:55 masak the .redraw() one, as well as the org.openscience.cdk.render one
09:56 egonw masak: I don't have an error in the .render MANIFEST here...
09:56 * masak thinks about doing a clean rebuild
09:56 egonw what is the error you have?
09:57 masak egonw: 'cannot resolve javax.vecmath'
09:57 egonw do you actually have that plugin in your workspace?
09:58 masak no, I don't.
09:58 egonw well, that could explain it, I guess :)
09:58 masak fixing.
10:00 masak sorry, I should have thought of that. I don't pull in everything into my workspace, just the things I know I need.
10:00 egonw :)
10:00 masak now it looks much better.
10:00 * jonalv imports _everything_ :)
10:00 masak jonalv++
10:00 masak no red spots on any project :D
10:03 masak egonw: jonalv says he thinks this bug will keep me busy for a while...
10:03 masak (#122)
10:04 egonw zarah: bug #122
10:04 zarah egonw: excuse me?
10:04 egonw zarah: bug 122?
10:04 zarah egonw: are you making fun of me?
10:04 * jonalv helps masak out with that bug. (Hopes it will speed things up) :)
10:04 egonw @pelezilla bug 122?
10:04 zarah http://tinyurl.com/5pb3dq
10:05 jonalv egonw: the new jchempaint is not in the chemoinformatics feature yet is it?
10:05 egonw it is
10:06 jonalv ah found it..
10:07 jonalv egonw: I can not reproduce #122
10:08 egonw ah, neither can I
10:09 egonw i actually gives the
10:09 egonw index out of bounds at posittion -77 now
10:09 egonw hahaha
10:10 masak egonw: that number probably depends on what you've written in the console.
10:10 jonalv oh I get -76
10:10 masak egonw: ok, this is bad. looking.
10:10 jonalv I fumbled...
10:10 egonw jonalv: ah, so you can reproduce it :)
10:10 egonw good...
10:10 jonalv yea
10:10 egonw masak: now it's your turn
10:10 masak egonw: you have my full attention now.
10:11 masak ok, I can fairly confidently say that the NEWLINE patch introduced this.
10:12 egonw sounds like masak will start to write unit tests for the JSConsoleManager
10:12 masak egonw: harder than it sounds.
10:12 egonw http://wiki.bioclipse.net/index.php?title​=List_of_stable_managers_in_bioclipse_2.0
10:12 zarah egonw's link is also http://tinyurl.com/68dyxn
10:12 egonw http://wiki.bioclipse.net/index.php?title=List_of_​stable_managers_in_bioclipse_2.0#JsConsoleManager
10:12 zarah egonw's link is also http://tinyurl.com/68dyxn
10:12 masak all this talk of stable managers, and not one horse...
10:13 jonalv egonw: what is the critera for a manager to be stable?
10:13 gilleain joined #bioclipse
10:14 * jonalv reads the actual site.
10:14 jonalv it has changed since last time... :)_
10:14 jonalv sry :)
10:15 CIA-53 bioclipse: carl_masak * r7681 /bioclipse2/trunk/plugins/​net.bioclipse.encryption/: Initial import.
10:16 CIA-53 bioclipse: carl_masak * r7682 /bioclipse2/trunk/plugins/​net.bioclipse.encryption/ (12 files in 7 dirs):
10:16 CIA-53 bioclipse: Initial import. String encryption library, to be used
10:16 CIA-53 bioclipse: for password-based encryption.
10:26 egonw jonalv: not sure, aks ola
10:26 egonw but at least:
10:26 egonw full unit testing
10:26 egonw of all published methods
10:26 jonalv k
10:26 egonw at least as plugin tests
10:26 egonw and the requirements for API patterns which we discussed Tue
10:26 egonw otherwise, no clue
10:28 egonw OK, next problem
10:28 egonw I need access to javax.vecmath classes in the JSConsole
10:28 egonw how do I do that?
10:28 egonw new Point2d() does not work
10:31 egonw how do I add support to this library to the JSConsole?
10:31 CIA-53 bioclipse: carl_masak * r7683 /bioclipse2/trunk/plugins/net.bioclipse​.scripting.ui/src/net/bioclipse/scripti​ng/ui/views/ScriptingConsoleView.java:
10:31 CIA-53 bioclipse: [ScriptingConsoleView]
10:31 CIA-53 bioclipse: * fixed .substring glitch introduced in the NEWLINE refactoring
10:31 CIA-53 bioclipse: * this fix closes #122
10:31 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=122
10:31 egonw masak: will verify
10:32 egonw do I need to make a manager to make javax.vecmath.Point2d visible?
10:32 egonw how does that work?
10:32 egonw is there a wiki page on that?
10:35 CIA-53 bioclipse: carl_masak * r7684 /bot/trunk/zarah.pl: [zarah] now reports a tinyurl upon matching bug refs from CIA-NN
10:38 zarah joined #bioclipse
10:40 masak zarah++
10:49 CIA-53 bioclipse: jonalv * r7685 /bioclipse2/trunk/plugins/net​.bioclipse.encryption.tests/: Initial import.
10:51 CIA-53 bioclipse: jonalv * r7686 /bioclipse2/trunk/plugins/net​.bioclipse.encryption.tests/ (13 files in 7 dirs): test for net.bioclipse.encryption
10:53 egonw masak, Gpox, jonalv: I really need some pointers on how to make javax.vecmath.Point2d visable in the JSConsole
10:54 masak egonw: we tend not to encourage that. (i.e. exposing things that are not managers.)
10:54 egonw masak: yeah, that's fine...
10:54 egonw masak: so I create a manager?
10:54 masak (that's another way of saying that we don't really have a structure for handling that.)
10:54 masak egonw: yes.
10:54 CIA-53 bioclipse: jonalv * r7687 /bioclipse2/trunk/plugins/​net.bioclipse.encryption/ (4 files in 3 dirs): added some factory methods
10:55 egonw javax.vecmath.business?
10:55 egonw with vecmath.newPoint2d
10:55 masak egonw: probably not
10:55 * jonalv has no time now. egonw could you explain the use case later?
10:55 masak since you don't own the javax namespace, Sun does
10:55 * jonalv gtg
10:55 masak lunch &
10:55 egonw no one owns namespaces
10:55 masak egonw: I know.
10:56 egonw but if you insist
10:56 masak it was a short way of describing the actual situation.
10:56 egonw net.bioclipse.vecmath.business
10:56 egonw nevermind
10:56 egonw I'll just introduce jcp.newPoint2d
10:56 egonw I though I should do it in a clean way... :(
10:57 gilleain why do you need to make points from the console anyway?
10:57 egonw he gilleain!
10:57 gilleain (also : "oh hai")
10:57 egonw did not notice you being around :)
10:57 egonw for scripting JChemPaint
10:57 gilleain Yeeesss.
10:58 gilleain But...
10:58 egonw will blog about that this afternoon
10:58 gilleain o-k.
10:58 egonw and I want the JChemPaint manager to copy one-to-one the scripting commands
10:58 egonw so no: addAtom(x,y)
10:58 egonw because the scripting layer of JCP has addAtom(Point2d)
10:58 egonw actually...
10:59 egonw you'd rather have addAtom(x,y) instead
10:59 egonw for the console?
10:59 egonw I can do that...
10:59 egonw s/Point2d/x,y/
10:59 gilleain Er. I didn't say that.
10:59 gilleain I don't want either, particularly.
11:00 egonw neither?
11:00 egonw how so?
11:00 gilleain But ask yourself : is the user going to be typing "jcp.addAtom(10, 20)"
11:00 gilleain In what situation is this going to occur?
11:00 egonw not Joe the Plumber, no
11:00 gilleain :)
11:00 egonw for example, for unit tests?
11:00 gilleain Ahh.
11:00 egonw or scripts?
11:00 egonw just imagine a local script:
11:01 egonw replaceCarbonMyFavoriteFunctionalGroup()
11:01 egonw unfoldTBOC()
11:01 egonw I can imagine so many scripts I may want to run
11:01 gilleain Hmmm.
11:02 gilleain I'm just comparing in my mind with 3D molecular viewers.
11:02 egonw decomposeIntoUgiReactants()
11:02 egonw anyway...
11:02 egonw for me, it's primarily now to test the interface
11:02 gilleain And very rarely do I say "addAtom(10, 20, 30)"
11:02 egonw which we use to translate mouse events in JCP edit events
11:03 egonw gilleain: oh, then you have not subscribed to the Jmol ML yet
11:03 egonw people *are* doing this in 3D
11:03 egonw really
11:03 egonw this is not, wouldn't it be cool, but actual use cases
11:03 gilleain Yeah, I've seen the ridiculously overblown scripting language of Jmol over the past 2 years of commits.
11:04 egonw it's just a collection of functionality that people use and requested
11:04 egonw overblown?
11:04 gilleain Hmmm.
11:04 gilleain Yup.
11:04 egonw yeah, people like to do funcky stuff
11:04 egonw scientists are weird
11:04 gilleain I admit that the line/plane stuf is nice.
11:05 gilleain But I would always caution against adding stuff that won't be used. Even if it is requested. Speculative programming.
11:06 egonw even if it is requested?
11:07 egonw so, what do you do when Chris comes up to your desk then?
11:07 CIA-53 bioclipse: egonw * r7688 /bioclipse2/trunk/plugins/net.biocli​pse.cdk.jchempaint.business/src/net/​bioclipse/cdk/jchempaint/business/ (IJChemPaintManager.java JChemPaintManager.java): Added method to create a Point2d
11:07 egonw who says seneca will be used by anyone?
11:07 gilleain Good question.
11:07 egonw there are plenty of products which already exist and do the same
11:08 egonw and that have commercial support
11:08 egonw sounds like speculative programming to me :)
11:08 gilleain I'm talking about features, rather than products.
11:08 egonw ah, the whole is more than the parts?
11:09 gilleain sometimes less is more.
11:10 egonw yes, I don't forget about Yin/Yang
11:10 egonw ummm
11:10 egonw yes, and don't forget about Yin/Yang
11:10 gilleain A short list of well-implemented essential features is better than a long list of half-implemented ones.
11:10 egonw ah yes
11:10 egonw hence the JCP scripting langauge :)
11:11 egonw better to have a well-tested essential feature, than ...
11:11 egonw well, happy that you like the scripting language
11:11 gilleain I'm sure I will.
11:13 egonw did you like Goslar?
11:14 egonw shk3 already gave some news
11:14 gilleain Kind of.
11:14 gilleain There was a huge range of topics.
11:14 egonw which bit did you not like?
11:14 gilleain Well having a rubbish poster was my fault, but still not fun.
11:15 gilleain I saw Andrew Dalke's poster.
11:15 egonw how so?
11:15 egonw you had bad reviews?
11:15 egonw or did the printing go wrong?
11:15 gilleain And broke into a conversation between him and the Cactvs guy.
11:15 egonw Ihlenfeldt?
11:15 gilleain Could be.
11:16 egonw :)
11:16 egonw yeah, though public
11:16 gilleain He claims that OpenBabel is unusable.
11:16 egonw oh, does he
11:16 egonw well... I worked with cactvs...
11:16 gilleain A strong opinion, I thought.
11:16 egonw well, wolfgang has been in the business for a long time
11:16 egonw he does know what he is talking about...
11:17 gilleain Quite possibly.
11:17 egonw I don't know enough about OB internals to say he is wrong
11:18 gilleain I read that thread about open vs closed source, was interesting.
11:18 egonw in andrews blog?
11:18 gilleain Similar to the talk at GCC about Open Publishing.
11:18 gilleain Yup.
11:18 egonw people often mix up pratical problems with problems about the ideas
11:18 gilleain It all boils down to : "where's the money?".
11:18 egonw I like open source because of the ideas
11:19 egonw I don't care so much about practical issues
11:19 egonw but people complain about practical issues
11:19 gilleain Like too many features? :)
11:19 egonw a lot of open source chemistry tools is actually funded
11:20 egonw there are few people who do this work unpaid...
11:20 egonw so there is the money
11:20 egonw however, it does require an academic position
11:20 egonw and some do not want or cannot fight for such a position...
11:20 egonw open source commercial companies is difficult too...
11:20 egonw which make some conclude that the latter is impossible
11:21 gilleain You mentioned PyMol in that thread. I have been one of the eyeballs ; there are quite a few of us "power"-users.
11:21 egonw yes, think so too
11:21 egonw CDK has that too
11:21 egonw I have no clue about Andrews BSD projects, but they might simply lack a community
11:21 egonw and without a community, no bazaar model
11:21 egonw that does not make opensource fail
11:21 egonw that would make his projects fail
11:22 egonw businesses fail too
11:22 egonw and I need not mention commercial bio/cheminformatics companies failing...
11:22 gilleain Well, he was saying that it wasn't essential to let other people re-use your source for good science, only that they should be able to SEE it.
11:22 egonw though they are typically bought for an apple and a egg by another company
11:23 egonw gilleain: yes
11:23 egonw that made the discussion more tricky too...
11:23 egonw because he was only interested in peer review, as in two-author peer review
11:23 egonw as in publishing...
11:23 egonw well, that's not the kind of peer review opensource people are interested in
11:25 egonw anyway, it indeed was a nice discussion
11:25 egonw makes you strengthen your own arguments a bit more :)
11:25 gilleain True.
11:26 egonw gilleain: ok... let's talk some JCP business
11:26 CIA-53 bioclipse: goglepox * r7689 /bioclipse2/trunk/cdk-externals/trunk/org.o​penscience.cdk.render/src/org/openscience/c​dk/renderer/elements/RenderingModel.java: Changed center to only take dimensions and added field extent
11:26 gilleain Uh-oh.
11:26 egonw did you and stefan book flight and sorts?
11:26 gilleain Oh, right that. Yes, we did.
11:26 egonw can you please send me flight info, where you're staying and sorts?
11:26 gilleain Will do.
11:27 egonw we have a sort of primitive SWT-based JCP editor now...
11:27 egonw doesn't do overly much now...
11:27 egonw but it's running and functional...
11:27 gilleain I tried it.
11:27 egonw which I'm working hard now on getting the chemical editing layer online
11:27 CIA-53 bioclipse: goglepox * r7690 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint.view/src/net/bioclipse/cd​k/jchempaint/view/JChemPaintWidget.java: Added margins to the widget
11:30 egonw and I love to see something similar as Java2D applet or application...
11:31 egonw which means that both our team as the EBI team have a good insight in how all components fit together
11:31 egonw Gpox: does that cdk commit mean I have to make a new export?
11:32 gilleain I have a very simple test app in my branch. It just draws.
11:33 egonw it's a start :)
11:33 Gpox egonw: ah yes i edited the wron file
11:33 CIA-53 bioclipse: goglepox * r7691 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.jchempaint.view/src/net/bioclipse/cd​k/jchempaint/view/JChemPaintWidget.java: Forgot to do the actual margin stuff
11:33 egonw please to to bring the relaying of ouse events online, using the proper CDK classes for that
11:33 egonw Gpox: meaning?
11:34 egonw Gpox: do or don't I need to make a new export?
11:34 Gpox you don't need to as i commitd to the bioclipse render plugin
11:35 egonw ok
11:36 CIA-53 bioclipse: egonw * r7692 /bioclipse2/trunk/plugins/net.bioclipse.cdk.​jchempaint.business/src/net/bioclipse/cdk/jc​hempaint/business/IJChemPaintManager.java: Added missing annotation
11:41 egonw Gpox: thanx, margins look good
11:41 gilleain Gpox: what is the superFlip method doing, and why is there a drawTextUpsideDown method?
11:42 egonw yes, getClosestAtom() now works :)
11:45 shk3 joined #bioclipse
11:45 egonw ok, lunch time
11:45 egonw hi shk3!
11:45 CIA-53 bioclipse: egonw * r7693 /bioclipse2/trunk/plugins/net.bioclipse.cdk.​jchempaint/src/net/bioclipse/cdk/jchempaint/ (2 files in 2 dirs): Fixed getHub by relaying to the JCPEditorWidget, fixing getCloestAtom
11:45 shk3 hi egonw
11:45 Gpox gilleain: it was originaly for fliping the text upside down, it dose some tranparenty things to which is why it is still in there it don't filip any more though
11:45 egonw shk3: bioclipse2 requires Java5
11:45 egonw sorry about that
11:45 egonw that's a OS/X thing
11:45 gilleain Ohh.
11:47 shk3 egonw: I have 1.6 - should be allright, shouldn
11:47 shk3 't it?
11:47 egonw no, it isn't
11:47 shk3 ah
11:47 shk3 why not?
11:47 egonw because now you have code that only runs on J6
11:47 gilleain O. S. X.
11:47 shk3 but I have code level set to 1.5
11:49 egonw try running it with java 1.5
11:49 jonalv joined #bioclipse
11:49 egonw ok, really going for lunch now
11:51 gilleain hmmm. scale(x) = s * x + 0.5
11:51 gilleain I guess that this is because of double->int conversion?
11:57 CIA-53 bioclipse: jonalv * r7694 /bioclipse2/trunk/plugins/ (3 files in 3 dirs): added net.bioclipse.encryption.tests tests to allBioclipseTestsSuites
12:08 egonw back
12:09 egonw ok, removeAtom works too :)
12:22 CIA-53 bioclipse: egonw * r7695 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Implemented the full current IChemRelay API, and added @published annotation
12:29 egonw Gpox: around?
12:29 egonw shk3: around?
12:30 egonw Gpox: can you port the atom moving code to make use of the editing interface?
12:30 egonw Gpox: you'd need to add a method moveAtomTo(IAtom, Point2d) for that, or something similar
12:31 egonw Gpox: also... right now when you click, it does not keep the atom in mind, and just moves the closest atom
12:31 egonw Gpox: the old JCP would remember the closest atom upon clickDown and only move that one...
12:32 egonw Gpox: oh, and ... maybe you can do the moveBondTo(IBond, Point2d) too then...
12:32 egonw shk3: CDK1.2.x is now using CMLXOM... as you know, and like to move BC2 too, but since the spectrum plugin is using it too, I won't do that until you are ready for it...
12:33 egonw shk3: please let me know when you are ready for that move
12:33 Gpox egonw: ok, I will look at it
12:33 egonw Gpox: just change the code in cdk.controller
12:33 egonw I'll port those patches upstream
12:34 egonw will now focus on CDK 1.2.x, and will try to release 1.1.2 this afternoon
12:56 gilleain ack. bioclipse scripting is horribly broken on windows.
12:58 egonw masak will love to hear that :)
12:58 masak gilleain: any new brokenness, or just the old usual?
12:59 masak gilleain: FWIW, I've been looking at the newlines thing lately
12:59 gilleain It hangs, then crashes java.
12:59 egonw gilleain: stacktrace?
12:59 masak gilleain: that's not good.
12:59 gilleain Even just typing "help<return>"
12:59 masak gilleain: I saw it working on Windows a couple of days ago.
12:59 gilleain No stacktrace. Just crashes. Wil check.
13:00 gilleain I may not have updated something vital?
13:00 gilleain I updated scripting, and scripting.ui
13:01 masak gilleain: you could try backing the n.b.scripting.ui plugin to r7505 (the rev before the refactor) and see if the problem goes away. that'd help me.
13:01 gilleain ok.
13:01 masak thanks.
13:03 edrin joined #bioclipse
13:03 edrin hi
13:03 zarah hi edrin
13:03 edrin hi egonw
13:03 gilleain Aha.
13:03 egonw hi edrin
13:03 egonw edrin: read it
13:04 edrin :)
13:04 gilleain It does go away.
13:04 egonw but have not written up my comments
13:04 masak gilleain: that's a shame.
13:04 gilleain but the terrible squares are back.
13:04 masak gilleain: well, it's your choice. terrible squares or hanging.
13:04 gilleain Squares.
13:05 gilleain The hanging was one thing, the endless scroll bar was another.
13:05 masak gilleain: the patch which fixes the squares apparently also hangs bc on windows.
13:05 masak gilleain: you're very welcome to put together a ticket about all the symptoms
13:05 masak @pz
13:05 zarah [Bug 77] paths in windows slash problems http://tinyurl.com/578aen
13:05 zarah [Bug 78] CR/LF problems on windows       http://tinyurl.com/6eznsa
13:05 zarah [Bug 70] Faulty instanceof as IMolecu... http://tinyurl.com/5u7vag
13:05 zarah [Bug 73] Bioclipse 2.0.0 final is not... http://tinyurl.com/6phlff
13:05 zarah [Bug 113] The js console says "unexpe... http://tinyurl.com/5hey86
13:05 zarah Entire list at http://tinyurl.com/59wwod
13:05 gilleain Does it get stuck in an endless loop of printing out newlines, then reading them in, then printing them out.
13:06 masak gilleain: dunno.
13:06 masak gilleain: it works here on Mac.
13:06 egonw works here too
13:06 gilleain Because, the scrollbar seems to be endlessly updating.
13:06 gilleain (in HEAD)
13:06 egonw ah, so a loop, causing outofmemory
13:06 masak gilleain: good to know. all clues are appreciated.
13:07 gilleain I will ticket it up.
13:07 edrin ok
13:08 masak gilleain++
13:21 egonw masak: ummm :
13:21 egonw [14:13] <CIA-37> cdk: egonw * r13114 /cdk/branches/cdk-1.2.x/src/test/ (2 files in 2 dirs): Added unit test for bug #2234820
13:21 egonw [14:13] <zarah> bug #2234820 | http://tinyurl.com/6zdd2v
13:21 egonw :)
13:22 egonw pele: "Bug #2234820 does not exist. "
13:22 masak egonw: yes. something wrong with that?
13:22 egonw nah... I just need to teach zarah that cdk bugs are not bioclipse bugs
13:23 masak ah.
13:23 masak I could intro a cutoff somewhere.
13:23 masak or link correctly to CDK bugs as well :)
13:23 egonw yeah, never mind for now
13:23 egonw please fix the console
13:23 egonw :)
13:24 gilleain I've found that pressing <return> twice can trigger the endless loop (of doom).
13:26 masak egonw: I did fix the console! but it broke even more on Windows as a result.
13:26 egonw :)
13:26 egonw yeah, sorry that you are responsible for it
13:26 egonw I'm happy that it's not me...
13:26 masak Windows is an ungrateful master.
13:26 gilleain For me it's :(, not :).
13:27 egonw masak: master of disaster?
13:27 gilleain Windows is like the endless ocean : really, really annoying and difficult to debug.
13:27 masak gilleain: I'll do what I can. unfortunately I must leave for a few hours soon, and I've promised the rest of the workday to jonalv. but leave a beautifully crafted ticket for me, and I promise to do what I can.
13:28 * masak has never debugged an ocean
13:28 gilleain I'm almost done with it.
13:28 masak gilleain: good for you!
13:28 masak gilleain: oh. thought you meant Windows.
13:28 masak :)
13:28 gilleain Oh, right, no not that.
13:29 masak to bad.
13:29 masak gilleain: looking forward to the ticket.
13:30 masak must go now.
13:30 masak have a nice weekend, everyone!
13:30 gilleain Do I assign it to masak, or leave it as the default of ola?
13:32 egonw no, assign to masak
13:33 gilleain And "URL", and "Depends On"?
13:33 egonw URL: www.microsoft.com ?
13:33 gilleain Heh.
13:33 egonw "depends on" is for other bug reports
13:34 egonw one bug fix, may depend on something else to be fixed first
13:34 egonw e.g.
13:34 egonw world donimation
13:34 egonw would depend on
13:34 egonw bioclipse 2.0.0 to be released
13:34 egonw (and a few other things)
13:35 gilleain A world prepared to be dominated? :)
13:35 egonw that's a non-issue
13:35 egonw otherwise they would have never reelected G.W.Bush
13:36 egonw oh wait... they didn't .... hahahaha
13:36 egonw not the majority at least
13:37 egonw do you think the CIA is monitoring IRC too?
13:37 egonw or just phone, etc
13:37 gilleain The UK government wants to.
13:38 gilleain Or, wants to record that you talked to me, today, in this chat room, but not what we said.
13:38 gilleain Which is insane.
13:38 egonw well, at least better than recording exactly what we chatted about...
13:39 egonw (but yes, a real attack on privacy)
13:39 egonw and stupid too...
13:39 egonw because the can just google for what we chat about here :)
13:39 gilleain Trying to record even that much info, for every irc channel, every phone call, and every email would be zettabytes of info.
13:39 gilleain Well, lots, anyway.
13:39 egonw in NL XS4ALL once counted that...
13:39 egonw was about 7CDs of information per second
13:39 egonw for just that dutch provider :)
13:40 gilleain knowing the uk government, it would cost billions to set up, then they would leave one of the hard disks on a train, or in a pub.
13:40 gilleain anyway, back to bug report #2.
13:41 egonw hehehehe :)
13:41 edrin egonw: how did you the small part i wrote?
13:42 egonw needs tuning
13:42 egonw some reorganization
13:42 egonw some stuff is too detailed for the public
13:42 edrin ok
13:42 egonw lacks some needed introduction into stuff
13:42 edrin ok
13:42 egonw but
13:43 egonw it's a good start
13:43 edrin lets see :)
13:43 egonw it needs to focus on how it addresses current tihngs in bioinformatics...
13:43 egonw how does it help current practices
13:43 edrin want to finish it soon..##
13:43 egonw ETA?
13:43 edrin eta?
13:43 egonw estimated time (of) arrival
13:44 edrin no clue
13:44 edrin not after December. do you think thats realistic ?
13:48 egonw can't say... really busy myself...
13:48 egonw but a lot of practical work is done...
13:48 egonw will really try to do the Taverna2 node asap
13:48 egonw but really tied up in getting JChemPaint for Bioclipse 2.0 done
13:48 egonw until the end of next week...
13:49 shk3 egonw: replacing the jumbo.jar with the xmlxom jar in the cml plugin should do it
13:49 shk3 I think
13:50 egonw yes, indeed
13:50 edrin ok
13:50 shk3 I don't use any "real jumbo" stuff
13:50 egonw shk3: but it might require some changes to your code
13:50 shk3 and the plugin is named cml, not jumbo anyway
13:50 shk3 I will do these
13:50 egonw because the CMLXOM has a few changes
13:50 egonw ok
13:50 shk3 can you update the plugin
13:50 shk3 and I will see?
13:50 egonw after releasing CDK 1.1.2
13:50 egonw actually...
13:51 egonw no, I'll try it now...
13:53 shk3 let's try+#
13:53 shk3 i am getting a coke
13:58 shk3 egonw: there is also a jumbo.jar still, right?
13:59 shk3 might be good to put this into the plugin as well, just to have it ready.
13:59 egonw yes, indeed
13:59 egonw will do that too
14:17 egonw arghh...
14:17 egonw nb.cml contains functionality too
14:17 egonw not just libs
14:21 shk3 hm, yes
14:21 shk3 but I think they are not used
14:22 egonw ValidateCMLManager is not used?
14:22 egonw well, it's useful I guess
14:22 shk3 no, this is
14:22 shk3 sorry
14:22 shk3 mom
14:23 egonw but it is using Jumbo functionality, I think...
14:23 egonw I'll comment out the tricky bits and file a bug report
14:23 egonw will fix that when I added jumbo
14:24 shk3 confused that with net.bc.xom
14:24 shk3 there is unused stuff in there
14:24 egonw file a bug report please
14:28 gilleain Uh-oh. Javascript console (latest) doesn't seem to work properly on my mac, either. (and yes, will file a bug report...)
14:29 edrin gilleain: that's because masak tries to fix the systems.newline variable
14:29 egonw heheh :)
14:29 edrin i tried to fix it once...
14:29 gilleain Ah, ok.
14:30 edrin but completely gave up
14:30 gilleain It's a tricky pancake, I can see that.
14:30 edrin i think he has to fix several functions
14:32 masak joined #bioclipse
14:32 * masak is back, surprisingly
14:32 * gilleain is suitably surprised
14:32 * jonalv is suprised
14:33 charlgren joined #bioclipse
14:33 jonalv masak: what happend? :)
14:33 * masak is surprised, too
14:33 masak jonalv: someone wasn't home.
14:33 jonalv masak: oh :(
14:34 jonalv masak: I will head over to BMC as soon as I have finnished adding all these bug to the brunn bug list...
14:34 masak jonalv: great.
14:34 jonalv &me will have work for a qouple of weeks with Brunn bugs and features... :)
14:35 masak heh.
14:40 masak egonw: why does the new JChemPaint editor always ask if I want to save on closing Bioclipse? I haven't changed the molecule at all.
14:42 egonw masak: file a bug report
14:42 egonw need to look at that
14:42 egonw better: need to fix the CDK event model
14:43 * masak files ticket
14:49 * jonalv heads to bmc
15:03 CIA-53 bioclipse: carl_masak * r7696 /bot/trunk/zarah.pl: [zarah] now returns the Home Page of Bugzilla on empty @pelezilla request
15:07 masak @reboot
15:07 zarah joined #bioclipse
15:07 masak @pelle
15:07 zarah masak: Pelezilla is at http://pele.farmbio.uu.se/​cgi-bin/bugzilla/index.cgi
15:08 masak zarah: thank you.
15:08 zarah masak: no, YOU'RE the cute one! :)
15:11 edrin masak: j.s.-console is not working
15:12 masak edrin: oh hai.
15:12 masak edrin: I know.
15:12 masak edrin: but please describe your symptoms.
15:12 edrin i just heared it mentioned here
15:12 masak aha.
15:12 masak @pz scripting hangs
15:12 edrin i still have no new checkout
15:12 zarah [Bug 77] paths in windows slash problems http://tinyurl.com/578aen
15:12 zarah [Bug 123] scripting hangs the UI         http://tinyurl.com/67c3my
15:12 zarah [Bug 124] string index out of bounds ... http://tinyurl.com/6lgvoh
15:12 zarah [Bug 118] Stacktrace when booting Bio... http://tinyurl.com/6hw87d
15:12 zarah [Bug 7] Open With -> Other -> JChemPa... http://tinyurl.com/5fk4y6
15:12 zarah Entire list at http://tinyurl.com/56pb7t
15:12 masak bug #123
15:14 jonalv joined #bioclipse
15:21 CIA-53 bioclipse: carl_masak * r7697 /bot/trunk/zarah.pl: [zarah] tweaked @pelezilla search a bit. now works as on the web site
15:35 gilleain egonw: around? anoval?
15:36 egonw anoval?
15:37 egonw I had a big fight with eclispe classpaths once more...
15:37 egonw I hate it that you have to configure things 5 times, in 10 localtions :(
15:37 gilleain It's like "around", or "asquare". Anyway. I'm trying to test jcp scripting.
15:38 gilleain I do "p = jcp.newPoint2d(50,50)"
15:38 gilleain then, "a = jcp.getClosestAtom(p)"
15:38 gilleain and get "null".
15:39 gilleain Obviously, I have a JchempaintEditor open.
15:41 gilleain Helloooooooo.
15:42 gilleain Hmm. Busy, I guess. Never mind, will try again later.
15:43 jonalv egonw: did you win the fight?
15:43 CIA-53 bioclipse: carl_masak * r7698 /bioclipse2/trunk/plugins/ (2 files in 2 dirs):
15:43 CIA-53 bioclipse: [net.bioclipse.encryption[.tests]]
15:43 CIA-53 bioclipse: * refactor s/PlainText/Plaintext/
15:45 egonw jonalv: yes, think so :)
15:46 jonalv egonw: congratulations to the victory then :)
15:48 CIA-53 bioclipse: egonw * r7699 /bioclipse2/trunk/cdk-externals/tr​unk/org.openscience.cdk.libiocml/ (2 files in 2 dirs): Updated CDK libiocml for CMLXOM (closes #)
15:50 CIA-53 bioclipse: egonw * r7700 /bioclipse2/trunk/plugins/net.bioclipse.cml/ (4 files in 3 dirs): Using CMLXOM now, instead of the older Jumbo jar
15:51 CIA-53 bioclipse: egonw * r7701 /bioclipse2/trunk/plugins/net.bioclipse.cml/src/ne​t/bioclipse/cml/managers/ValidateCMLManager.java: Commented out code that depends on Jumbo functionality; will be brought back online once jumbo has it's plugin too
15:51 CIA-53 bioclipse: egonw * r7702 /bioclipse2/trunk/plugins/net.bioclipse.cml/ (.classpath META-INF/MANIFEST.MF build.properties): Updated to CMLXOM
15:53 zarah joined #bioclipse
15:56 egonw shk3: ok, back to you
15:56 egonw at least .nmrshiftdb needs updating
16:05 shk3 ok, will try to update cml plugin
16:09 jonalv egonw: I saw a commit about jumbo. Should I be worried for structuredb?
16:09 egonw yes
16:09 egonw if that uses CMLXOM
16:10 egonw I have it checked out and don't see compile issues
16:11 CIA-53 bioclipse: jonalv * r7703 /bioclipse2/trunk/plugins/ (4 files in 2 dirs): [Encryption] Created Encrypter stubb and wrote tests for it + added some assertions to test for EncryptedPassword
16:17 shk3 egonw: any idea what happened to the getMetadataListElements() method in CMLMolecule?
16:18 egonw no
16:18 egonw yes
16:18 egonw I think I do
16:18 egonw addMetadataListElements has been removed
16:18 egonw so likely the get too
16:18 egonw you'll need to use a general getChild method now, I think
16:18 egonw that is...
16:19 egonw appendChild was the replacement for addBondType(CMLBondType)
16:19 shk3 ok
16:21 CIA-53 bioclipse: carl_masak * r7704 /bioclipse2/trunk/plugins/ (2 files in 2 dirs):
16:21 CIA-53 bioclipse: [encryption]
16:21 CIA-53 bioclipse: * fleshed out stubs
16:21 CIA-53 bioclipse: * minor touch-ups
16:28 shk3 egonw: I am getting
16:28 shk3 java.lang.NoClassDefFoundError: Could not initialize class org.xmlcml.cml.element.CMLSpectrum
16:28 shk3 when trying to open a spectrum.
16:28 shk3 But the class is in nb.cml and is exported.
16:29 shk3 any idea?
16:44 egonw no
16:44 egonw you have rev 7702?
16:47 shk3 of nb.cml?
16:47 shk3 yes
16:51 shk3 would it be ok if i commit nb.spectrum and you try?
16:51 egonw yes
16:58 shk3 ok, commited spectrum and nmrshiftdb
16:58 shk3 at least it compiles
16:58 shk3 please try to open any spectrum file from the sample data
16:58 CIA-53 bioclipse: shk3 * r7705 /bioclipse2/trunk/plugins/ (5 files in 3 dirs): adopted to new cml
17:02 CIA-53 bioclipse: carl_masak * r7706 /bioclipse2/trunk/plugins/​net.bioclipse.encryption/ (2 files in 2 dirs):
17:02 CIA-53 bioclipse: [encryption]
17:02 CIA-53 bioclipse: * shifted in a real algorithm
17:05 egonw shk3, jonalv: the next few patches split out the library from the manager
17:05 egonw shk3, jonalv: so you'll have to import this new plugin:
17:05 egonw externals/org.xmlcml.cmlxom
17:06 egonw closing #125
17:06 jonalv uhm okey is this where jumbo is gonna be now?
17:06 CIA-53 bioclipse: egonw * r7707 /bioclipse2/trunk/externals/org.xmlcml.cmlxom/ (19 files in 9 dirs): Put CMLXOM in a separate plugin, away from the manager code
17:06 egonw net.bioclipse.jumbo
17:06 egonw but I guess you mean CMLXOM?
17:06 * jonalv has no idea
17:06 egonw :)
17:06 egonw you mean things like CMLMolecule?
17:07 egonw that's about XMLCOM
17:07 egonw that's about CMLXOM
17:07 egonw ok, dinner about ready.
17:07 jonalv I don't know actually...
17:07 egonw may have to leave any sec now
17:07 jonalv k
17:07 egonw I have structuredb in my workspace
17:07 egonw and see no red marks
17:07 CIA-53 bioclipse: egonw * r7708 /bioclipse2/trunk/ (12 files in 11 dirs): Use the new org.xmlcml.cmlxom plugin
17:07 jonalv okey then I guess it's ok
17:08 CIA-53 bioclipse: egonw * r7709 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): These plugins actually depend on the ValidateCMLManager
17:08 egonw bbl
17:15 charlgren joined #bioclipse
17:15 CIA-53 bioclipse: egonw * r7710 /bioclipse2/trunk/features/net.bioclips​e.chemoinformatics_feature/feature.xml: Added CMLXOM plugin
17:16 CIA-53 bioclipse: egonw * r7711 /bioclipse2/trunk/plugins/net.bioclipse.cdk​.jchempaint.business/src/net/bioclipse/cdk/​jchempaint/business/JChemPaintManager.java: Fixed an NPE source (closes #128)
17:16 zarah bug #128 | http://tinyurl.com/5c4rel
18:16 charlgren joined #bioclipse
18:46 CIA-53 bioclipse: shk3 * r7712 /bioclipse2/trunk/plugins/net.biocl​ipse.spectrum/lib/JCampParser.jar: the jcamp library was java 1.6
19:16 edrin left #bioclipse
20:41 CIA-53 bioclipse: egonw * r7713 /bioclipse2/trunk/features/net.biocl​ipse.speclipse_feature/feature.xml: Removed plugins available from the dependency on the chemoinformatics feature
20:41 CIA-53 bioclipse: egonw * r7714 /bioclipse2/trunk/externals/o​rg.xmlcml.cmlxom/plugin.xml: Removed obsolete extensions
20:42 CIA-53 bioclipse: egonw * r7715 /bioclipse2/trunk/externals/org.xm​lcml.cmlxom/META-INF/MANIFEST.MF: Added missing log4j needed at runtime
20:42 CIA-53 bioclipse: egonw * r7716 /bioclipse2/trunk/externals/org.​xmlcml.cmlxom/build.properties: Cleaned up, with net.bioclipse.xom as example
20:42 CIA-53 bioclipse: egonw * r7717 /bioclipse2/trunk/plugins/net.bioclip​se.spectrum/src/net/bioclipse/spectru​m/wizards/FolderContentProvider.java: Don't care about closed folders (closes #119)
20:42 zarah bug #119 | http://tinyurl.com/5g2sez
20:43 CIA-53 bioclipse: egonw * r7718 /bioclipse2/trunk/plugins/net.biocli​pse.nmrshiftdb/src/net/bioclipse/nmr​shiftdb/wizards/PredictWizard.java: Fixes a NPE: when nothing is selected yet, which happens in my case; timing issue? Stefan, please review. (addresses bug #129)
20:43 zarah bug #129 | http://tinyurl.com/685q5y

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