Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-03-09

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Time Nick Message
06:25 CIA-55 bioclipse: egonw * r9243 /bioclipse2/trunk/cdk-externals/trunk/or​g.openscience.cdk.control/src/org/opensc​ience/cdk/controller/ControllerHub.java: Fixed drawing of naphtalenes by fixed chosing where to put the double bonds (fixes #640)
06:25 zarah bug #640 | http://tinyurl.com/ap9asw
07:42 masak joined #bioclipse
08:18 olass joined #bioclipse
08:19 olass moin
08:19 zarah saluton olass
08:19 olass hi masak
08:21 masak good morning olass
08:24 masak olass: no Uppsala today?
08:24 olass no
08:24 olass tomorrow
08:24 masak pity, then it'll be harder for me to sell in my lunch box to jonalv.
08:25 masak he'll surely arrive today without one, and then extol on the impossibility of making one while being away during the weekend.
08:27 olass very likely
08:27 olass he'll probably be raging with fury
08:28 masak saying "inconcievable!" or some such.
08:34 rojasm joined #bioclipse
08:34 masak rojasm: mornin'
09:01 CIA-55 bioclipse: ospjuth * r9244 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (CDKManager.java ICDKManager.java): Added methods for checking validity of a SMARTS and one to return IAtomContainer with substructures from a SMARTS query.
09:01 CIA-55 bioclipse: ospjuth * r9245 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.business.test/src/net/bioclipse/cdk/​business/test/CDKManagerPluginTest.java: Added more extensible tests for SMARTS querying.
09:07 CIA-55 bioclipse: ospjuth * r9246 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.business.test/src/net/bioclipse/cdk/​business/test/CDKManagerPluginTest.java: Added test for invalid SMARTS.
09:10 CIA-55 bioclipse: ospjuth * r9247 /bioclipse2/trunk/plugins/net.​bioclipse.cdk.smartsmatching/ (4 files in 3 dirs): Use new CDKManager SMARTS methods.
09:15 shk3 joined #bioclipse
09:20 rojasm moin all
09:20 zarah oh hai rojasm
09:32 Gpox joined #bioclipse
09:35 jonalv joined #bioclipse
09:39 jonalv oh hai
09:39 zarah oh hai jonalv
09:39 jonalv zarah: ping
09:39 zarah jonalv: pong
09:48 CIA-55 bioclipse: jonalv * r9248 /bioclipse2/trunk/plugins/net.biocli​pse.cdk.business/src/net/bioclipse/c​dk/business/CDKManagerFactory.java: throw exception when we can't get the manager.
10:12 shk3 hi olass
10:12 olass hi shk3
10:13 shk3 one question
10:13 shk3 the manager method
10:13 CIA-55 bioclipse: ospjuth * r9249 /bioclipse2/trunk/plugins/net.bioclipse.jmol/ (14 files in 5 dirs): Added the JmolScriptEditor from BC1. Solves #311. Since JmolView is removed and multiple editors are not supported, the content cannot be run on Jmol. Filed as other bugs.
10:13 shk3 Activator.getDefault().getCDKManager().​loadMolecule(cdkres).getAtomContainer()
10:13 shk3 does not detect aromaticity, it seems.
10:13 shk3 is this intended?
10:14 shk3 cdres is an IFile
10:16 olass ask egonw
10:17 olass I don't know
10:18 shk3 ok
10:19 edrin joined #bioclipse
10:19 egonw hi shk3
10:20 shk3 hi egonw
10:20 egonw the method is not called loadMoleculeAndPerceiveAromaticity
10:20 egonw so, yes, that was intentionally
10:21 shk3 are you alright?
10:21 shk3 or suffering from multiple personalities syndrom?
10:22 jonalv we are only suffering from multiple behind onw keyboard syndrome
10:22 shk3 ah
10:22 shk3 good to hear that
10:23 shk3 shouldn't the manager offer a perceiveAromaticity method?
10:24 jonalv shk3: yes it probably hsould. Would you file a bug repport for that?
10:24 shk3 sure
10:27 shk3 I will do it right now
10:27 shk3 if that's ok
10:27 olass shk3: please ask in the bug report to annotate the manager inline help that it does not do this. To me it is unintuitive but maybe there is a good reason for it, and in any case it needs to be well documented.
10:27 shk3 implement it, I mean
10:27 olass sure
10:27 shk3 thought so
10:27 olass just write a junit test
10:27 shk3 documentation is not clear on that
10:27 olass that must be updated
10:28 olass please file a bug report to egonw about that as well
10:28 olass the scripting language is far from consistent...
10:28 olass but is getting very poweerful
10:29 olass masak: are you in charge of the ui.business?
10:29 CIA-55 bioclipse: goglepox * r9250 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint.view/src/net/bioclipse/​cdk/jchempaint/view/SWTRenderer.java: Saves both fb and bg colors
10:29 masak olass: not that I know of.
10:29 olass ok
10:29 * olass looks at SVN who wrote it
10:29 olass masak + Gpox it seems
10:30 masak ah, yes.
10:30 masak indeed.
10:30 olass I will start working on bug #654
10:30 CIA-55 bioclipse: goglepox * r9251 /bioclipse2/trunk/cdk-externals/trunk/org.ope​nscience.cdk.render/src/org/openscience/cdk/r​enderer/generators/SelectionGenerator.java: Draw selection for bonds
10:30 masak @pz 654
10:30 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=654
10:36 shk3 odd code in CDKManager line 721:
10:36 shk3 if (cdkmol instanceof IMolecule) {
10:36 shk3 imol = (org.openscience.cdk.interfaces.IMolecule)
10:36 shk3 cdkmol.getAtomContainer();
10:36 shk3 }
10:37 jonalv pastebin!
10:37 shk3 IMolecule in the if is net.bc.core.domain.IMolecule
10:37 shk3 is this ok?
10:37 olass no idea
10:37 olass ask egonw
10:37 olass he's our cdk guru
10:38 shk3 well, testing for instanceof X and then cast to Y
10:38 shk3 sounds odd
10:39 shk3 no matter if cdk or not
10:39 shk3 but I am waiting for egonw/jonalv to comment
10:39 jonalv shk3: I agree with you. it seems strange. Who wrote the code? You should ask the author I think...
10:40 jonalv shk3: but when I look at the code it doesn't seem that bad. it's the atomContainer that gets casted, right?
10:41 shk3 ah right
10:42 jonalv olass: was there a cheminforamtics feature releease last friday?
10:42 shk3 it's created with ICDKMolecule cdkmol = create(mol);
10:42 olass no
10:42 olass no time :(
10:42 shk3 so the instance of is not needed, it looks like
10:43 shk3 and the else will never be called
10:43 jonalv k
10:45 shk3 ospjuth in rev 7145
10:45 shk3 olass: could you have a look if you have a second?
10:46 shk3 cdkmanager line 718
10:46 olass sure
10:46 olass mom
10:46 shk3 and the if in 721 will always be true, I think
10:46 shk3 but I may be wrong
10:47 CIA-55 bioclipse: ospjuth * r9252 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.smartsmatching/src/net/bioclipse/cdk/sma​rtsmatching/views/SmartsMatchingView.java: Removed debugging
10:47 olass yes, something seems incorrect here
10:48 olass shk3: feel free to fix things
10:48 olass just run all junit tests before and after
10:48 olass you have my blessing :-)
10:48 * olass is happy if you fix things
10:49 olass I am not so fluent in cdk...
10:49 shk3 I try my best
10:49 olass don't we all ;)
10:54 jonalv zarah: seen edrin
10:54 zarah edrin was last seen 22 h 37 m 34 s ago in #bioclipse saying 'do they create a binding now?'
10:54 jonalv edrin: ping
10:54 jonalv zarah: ping me when edrin returns
10:54 zarah jonalv: ping, dear
10:54 masak jonalv: not implemented yet.
10:54 masak I'm surprized it doesn't warn.
10:54 masak zarah: tell me when edrin returns
10:54 zarah masak: Unknown syntax, I... I just don't get it.
10:55 masak ah.
10:55 masak only warns for 'tell'.
11:00 CIA-55 bioclipse: carl_masak * r9253 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): moved JmolConsoleView.java from n.b.scripting.ui to n.b.jmol
11:00 CIA-55 bioclipse: carl_masak * r9254 /bioclipse2/trunk/plugins/net.bioclipse.jmol/ (3 files in 3 dirs): [net.bioclipse.jmol] added Jmol console
11:01 jonalv zarah: tell edrin Please don't use tabs in the Bioclipse repo. Things get very complicated for poor me when you do... :(
11:01 zarah Consider it noted.
11:01 masak the bc2 part, that is.
11:01 masak we don't care about tabs in the bc1 part, or in the cdk part.
11:03 olass masak: about bug 690...
11:03 olass I sort of thought that was sorted out
11:03 masak @pz 690
11:03 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=690
11:03 olass I get a stacktrace in Eclipse but no error on console
11:04 masak olass: that is a subcase of the general problem we have with exceptions and the console.
11:04 masak I'll mark this ticket as a duplicate of that other bug.
11:04 olass please please make it prio
11:04 masak olass: aye.
11:04 olass it must at least say "error"
11:05 olass now it indirectly says it works..
11:05 masak olass: I don't like the current situation more than you do.
11:05 olass just wanted to make sure you were aware of it
11:05 masak olass: however, there's a little thing called "threads" that we decided to use in the console.
11:05 olass yes...
11:05 masak after that nothing is easy.
11:05 * olass is not good with threads
11:05 * masak neither
11:06 olass jonalv is good with threads
11:06 olass maybe he can help you?
11:06 masak I was hoping that, too.
11:06 olass jonalv++ //for reading the threads book
11:06 masak this will require at least two minds.
11:06 olass yes
11:06 olass and is very important for bc2
11:06 olass very VERY important
11:06 jonalv olass: I have only started reading that book...
11:06 jonalv olass: I gave up
11:07 olass jonalv: could you help masak discussing/thinking about this?
11:07 olass we can't ignore it
11:07 jonalv olass: perhaps we should find a "Head on treading in java" book? :)
11:08 masak :)
11:08 olass buy whatever book you like
11:08 jonalv olass: I am a bit busy but if masak discusses I will answer...
11:08 masak I'll see what I can do.
11:08 olass 2 minds > 1 mind
11:08 olass great
11:08 masak unless 'mind' is negative. :P
11:08 olass yes
11:09 olass let's hope jonalv's mind is not....
11:09 olass (and not yours either)
11:09 olass then we're back on 0
11:09 olass unless booth are negative
11:09 olass then we're on plus again
11:10 masak no, that's multiplication.
11:10 masak this would be addition.
11:12 masak food &
11:15 jonalv I just did cool stuff
11:24 jonalv lunch
11:27 egonw joined #bioclipse
11:28 egonw moin
11:28 zarah hi egonw
11:28 egonw ok, that was 3 hours waisted
11:28 egonw well, 2...
11:28 egonw read 3.5 papers
11:45 egonw mmm...
11:45 egonw the good thing of the forced upgrade is that my machine is more responsive...
11:47 masak sounds a bit like Windows, actually.
11:47 egonw hahaha
11:47 egonw except that yesterday it was not sluggish at all
11:47 egonw it's just even faster
11:47 masak true.
11:56 CIA-55 bioclipse: shk3 * r9255 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.business/src/net/bioclipse/cdk/business/ (CDKManager.java ICDKManager.java): added a perceiveAromaticity method to the manager
11:56 CIA-55 bioclipse: shk3 * r9256 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business.test/src/net/bioclipse/​cdk/business/test/CDKManagerTest.java: added tests for the perceiveAromaticity method
11:57 CIA-55 bioclipse: shk3 * r9257 /bioclipse2/trunk/plugins/net.biocli​pse.nmrshiftdb/src/net/bioclipse/nmr​shiftdb/wizards/PredictWizard.java: using the perceiveAromaticity
12:58 jonalv olass: I like the SMARTS matcher
12:59 jonalv olass++
12:59 olass danke :)
12:59 jonalv olass: How do I see my query after I have written it once?
12:59 olass click it
12:59 olass properties view
12:59 olass you can edit it there too
13:00 jonalv olass: ah, nice
13:00 jonalv olass: perhaps an action "properties" on the context menu that brings the properties view to the front?
13:00 jonalv or activates it...
13:00 olass please file a bug
13:00 olass a good idea
13:00 jonalv oki
13:01 egonw olass: gist?
13:01 egonw oh, you promised a blog
13:01 olass yes
13:02 olass but requires the SMARTS bug fixed first
13:02 olass else the plugin is broken
13:02 jonalv olass: what feature is that plugin in?
13:02 olass cheminfo
13:03 egonw olass: need to make a print first...
13:03 egonw will then look at the SMARTS bug
13:03 olass ok
13:03 olass egonw one question
13:03 olass how determine contentype for a file?
13:03 olass programmatically?
13:03 * egonw is looking at the code of shk3
13:03 egonw ContentTypesPluginTest
13:04 egonw currently broken
13:05 egonw needs to following fix
13:05 shk3 but works in bioclipse
13:05 egonw and the test files...
13:05 egonw works in bioclipse?
13:05 shk3 mom, there is an example somewhere
13:05 egonw how do you run the test from within bioclipse?
13:06 CIA-55 bioclipse: egonw * r9258 /bioclipse2/trunk/plugins/net.biocl​ipse.ui.tests/META-INF/MANIFEST.MF: Fixed Activator class
13:06 egonw rojasm: ping
13:06 egonw rojasm: when will you fly back from the CDK workshop?
13:06 shk3 MoleculeFileContentProvider line 567
13:06 shk3 line 56
13:07 shk3 I meant:
13:07 shk3 the test does not work
13:07 shk3 but it works in moleculefilecontentprovider
13:11 olass shk3: my question was, if I have an IFile, how do I determine the ContentType for this?
13:12 shk3 moleculefilecontentprovider does this
13:12 olass oh, nvm
13:12 olass found it
13:13 olass contentTypeManager.findContentTypeFor(stream, "file.xml");
13:13 shk3 IContentTypeManager contentTypeManager = Platform.getContentTypeManager();
13:13 shk3 InputStream stream = ((IFile)resource).getContents();
13:13 shk3 IContentType contentType = contentTypeManager.findContentTypeFor(stream, ((IFile)resource).getName());
13:15 egonw shk3: why are those tests not working?
13:15 egonw how do you see they should be fixed?
13:15 shk3 I I only would know,,,
13:15 shk3 for me, the test class does not run
13:15 shk3 mom
13:15 egonw so, it's pretty dead code?
13:15 egonw see the fix earlier
13:16 egonw with that one, the unit tests run
13:16 shk3 ah
13:16 shk3 mom
13:19 shk3 anyway
13:19 shk3 my eclipse is mad
13:19 shk3 great if you fixed it
13:19 jonalv who knows jmol?
13:19 shk3 I couldn't see what the problem was
13:19 jonalv does jmol have an IRC room?
13:20 egonw #jmol
13:20 egonw but hardly ever populated
13:20 egonw I can go there, if you like :)
13:22 olass jonalv: post on jmol list
13:22 olass it's very acyive
13:22 olass and people are friendly
13:22 jonalv oki
13:22 masak acylive?
13:22 masak like sour milk?
13:23 olass masak: no, thats lactobacillus acylive
13:23 masak oh right.
13:23 olass this is jonalvathanucillus acyive
13:23 olass much more dangerous
13:23 masak but very tasty!
13:24 jonalv \me puts finger in ears
13:24 jonalv *lalalalala*
13:24 olass like a semla
13:24 CIA-55 bioclipse: jonalv * r9259 /bioclipse2/trunk/plugins/ (5 files in 4 dirs): Work on adapting jmol to new world order
13:24 olass a megalomaniac commit msg IMO
13:25 * olass wishes he too could propose a new world order
13:25 CIA-55 bioclipse: jonalv * r9260 /bioclipse2/trunk/plugins/net.bioclips​e.jsexecution/src/net/bioclipse/jsexec​ution/execution/ScriptExecution.java: log stacktraces when running JavaScript scripts from editor (at DEBUG level)
13:25 jonalv olass: you are too old. You created the world
13:25 jonalv I only change it
13:25 CIA-55 bioclipse: jonalv * r9261 /bioclipse2/trunk/plugins/net.bioclipse.jmol/src​/net/bioclipse/jmol/business/IJmolManager.java: added publishedmanager annotation to jmol manager
13:25 olass like God and Linneaus?
13:26 olass (according to Linenaus=
13:26 * olass is too old :(
13:26 jonalv haha
13:26 jonalv I didn't mean it like that
13:27 jonalv klapa snel olas
13:27 olass *murmel*
13:27 olass *BITE*
13:27 jonalv aouch
13:28 * masak makes a funny dance to distract olass and jonalv from each other
13:28 olass uhm
13:28 olass better make coffee
13:28 olass this is getting weird
13:28 jonalv olass: what is masak doing? That looks silly!
13:28 * olass hunts off for caffeine
13:33 shk3 egonw: I am now getting lots of FileNotFounds in the test
13:33 shk3 did it work for you?
13:33 egonw no, that's what I got too...
13:33 egonw so, that's why I asked...
13:33 egonw how are those tests supposed to work :)
13:35 shk3 I will look at it
13:35 shk3 couldn't really test till now
13:35 shk3 because of the activator problem
13:52 CIA-55 bioclipse: carl_masak * r9262 /bioclipse2/trunk/plugins/net.bioclipse.cd​k.smartsmatching/src/net/bioclipse/cdk/sma​rtsmatching/views/SmartsMatchingView.java: [SmartsMatchingView.java] cleaned up commented-out code
13:53 olass masak: ?
13:53 masak olass: ¿
14:00 egonw joined #bioclipse
14:02 CIA-55 bioclipse: shk3 * r9263 /bioclipse2/trunk/plugins/n​et.bioclipse.ui.tests/src/ (2 files in 2 dirs): tests work
14:08 CIA-55 bioclipse: ospjuth * r9264 /bioclipse2/trunk/plugins/net.bioclipse.jmol/s​rc/net/bioclipse/jmol/editors/JmolEditor.java: Added plugin ID and updated Javadoc.
14:25 CIA-55 bioclipse: egonw * r9265 /bioclipse2/trunk/plugins/net.​bioclipse.jmol/jars/Jmol.jar: Uploaded Jmol bug fix release 11.6.18
14:33 CIA-55 bioclipse: ospjuth * r9266 /bioclipse2/trunk/plugins/​net.bioclipse.ui.business/ (9 files in 5 dirs): Added EP for matching IBioObjects to editors. Solves #654.
14:39 olass shk3: my JCP does not compile now
14:39 shk3 which jcp?
14:39 shk3 bc?
14:39 olass bc2
14:40 shk3 I am updating
14:40 shk3 mom
14:40 olass ok, updating cdk plugins
14:40 olass sry
14:40 olass hopefully this solves the prob
14:40 * olass is lookign fwd to testing undo/redo
14:40 olass yup
14:40 olass solved
14:40 shk3 ah
14:41 shk3 what's not too nice about undo/redo is that buttons are not deactivated
14:41 shk3 when nothing is to redo/undo
14:41 shk3 you could thinkg eclipse does that automagically
14:41 shk3 but unfortnately not
14:43 CIA-55 bioclipse: ospjuth * r9267 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk.jchempaint/ (4 files in 3 dirs): Added functionality for determining JCP editor from an ICDKMolecule according to bug #654.
14:43 zarah bug #654 | http://tinyurl.com/bpvswj
14:54 CIA-55 bioclipse: ospjuth * r9268 /bioclipse2/trunk/plugins/net.bioclipse.jmol.cdk/ (6 files in 4 dirs): Added functionality for determining Jmol editor from an ICDKMolecule according to bug #654. Fails due to bug #694.
14:54 zarah bug #654 | http://tinyurl.com/bpvswj
14:54 egonw joined #bioclipse
15:18 CIA-55 bioclipse: carl_masak * r9269 /bioclipse2/trunk/plugins/net.bioclipse.scripting​/src/net/bioclipse/scripting/JsEnvironment.java: [JsEnvironment] cleaned up and moved stuff
15:19 CIA-55 bioclipse: carl_masak * r9270 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java: [JsConsoleView] exceptions are now printed on the console
15:19 * masak marks #236 as fixed
15:28 olass aah!!
15:28 olass masak++ //236 has been a nasty one
15:28 masak aye.
15:29 masak hopefully it's over now.
15:29 masak please confirm and close.
15:29 olass will do
15:29 * jonalv is n rev670 of jmol
15:29 * jonalv wonders how many revs there are...
15:29 jonalv more than 10000 !!!!
15:29 jonalv (aouch...)
15:30 masak :)
15:30 masak maybe they also use git-svn.
16:20 CIA-55 bioclipse: jonalv * r9271 /bioclipse2/trunk/plugins/net.bioclipse.jmol/sr​c/net/bioclipse/jmol/business/JmolManager.java: throw exception when the AOP has not worked instead of do some of what it should have done
16:21 CIA-55 bioclipse: jonalv * r9272 /bioclipse2/trunk/plugins/net.bioclipse.jmol/s​rc/net/bioclipse/jmol/editors/JmolEditor.java: squuesed in the code within 80 cols and changed some indentation during a read through in order to see what it does :)
16:42 edrin left #bioclipse
17:32 olass @ping
17:32 zarah olass: pong, honey
17:59 shk3 olass: tested undo/redo?
18:06 olass shk3: nope
18:07 olass guess you didn't hear that
18:08 olass @tell shk3: if undo/redo is finished, please mark bug as fixed
18:08 zarah Consider it noted.
18:20 CIA-55 bioclipse: ospjuth * r9273 /bioclipse2/trunk/plugins/net.​bioclipse.cdk.smartsmatching/ (2 files in 2 dirs): Added "Show Properties" in context menu. Solves #692.
19:43 |newbie| joined #bioclipse
20:19 olass bye
20:40 egonw joined #bioclipse

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