Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-06-25

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Time Nick Message
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07:38 jonalv join cdk
07:38 jonalv names
07:38 jonalv names
07:38 jonalv ah /names
07:39 * jonalv is trying to learn to live with emacs for irc...
07:46 olas joined #bioclipse
08:15 CIA-34 bioclipse: jonalv * r5919 /bioclipse2/trunk/plugins/ (5 files in 3 dirs):
08:15 CIA-34 bioclipse: [IServiceContainer, AbstractServiceContainer, ServiceContentProvider]
08:15 CIA-34 bioclipse: Moved listener methods up to the interface
08:15 CIA-34 bioclipse: [AbstractServiceObject]
08:15 CIA-34 bioclipse: White space
08:15 CIA-34 bioclipse: [Structuredb]
08:15 CIA-34 bioclipse: cleaned imports
08:29 Gpox joined #bioclipse
08:45 CIA-34 bioclipse: jonalv * r5920 /bioclipse2/trunk/plugins/net.bioclipse​.structuredb/src/net/bioclipse/structur​edb/business/StructuredbManager.java:
08:45 CIA-34 bioclipse: [StructuredbManager]
08:45 CIA-34 bioclipse: Squeezed all rows in on 80 cols
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09:37 CIA-34 bioclipse: ospjuth * r5921 /bioclipse2/trunk/plugins/net.bioc​lipse.core/src/net/bioclipse/core/ (4 files in 2 dirs): Renamed Molecule to SmilesMolecule, and added method List<IMolecule> getConformers to IMolecule.
09:38 CIA-34 bioclipse: ospjuth * r5922 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Implemented getConformers by throwing NotImplementedException.
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09:40 olas jonalv: should you or I update structuredb?
09:40 olas hmm, I'll leave that to you
09:40 olas (maybe time to implement IMolecule?)
09:46 jonalv olas: Structure implemetns IMolecule
09:48 CIA-34 bioclipse: carl_masak * r5923 /bot/trunk/zarah.pl: [zarah] regularized actions into a table
10:14 edrin joined #bioclipse
10:14 edrin hi
10:15 edrin http://xkcd.com/441/
10:16 masak edrin++ # absolute url
10:17 shk3 hi
10:17 shk3 still fighting with bc2
10:17 shk3 seems spring is the problem now
10:17 shk3 "(IValidateCMLManager) finderTracker.waitForService(1000*30);"
10:17 shk3 return null
10:17 shk3 how to debug this?
10:17 shk3 I have no clue what is the problem,
10:17 shk3 not even roughly.
10:35 shk3 nobody can help me?
10:35 shk3 :-(
10:51 egonw joined #bioclipse
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11:05 edrin hi egonw
11:10 jonalv shk3: are you still having problems?
11:10 masak shk3: nobody can help you during lunch
11:11 masak but now people are back
11:30 shk3 great
11:30 shk3 well, still problems with spring
11:30 shk3 when doing "(IValidateCMLManager) finderTracker.waitForService(1000*30);"
11:30 masak I'm sure jonalv will be delighted to help you
11:30 shk3 it returns null
11:30 shk3 and I have no idea what to do
11:30 shk3 or how to debug
11:30 jonalv is it commited?
11:30 shk3 no
11:31 shk3 shall I commit?
11:31 jonalv I just thought maybe I could look at it...
11:31 shk3 yes, I will try to clean up a bit and then to commit
11:31 jonalv I must admit that I am not great at finding those errors though I have stent some time on it myself :)
11:36 * shk3 is to lunch now
11:37 edrin question: I have a xml schema, what is the easiest way to validate an xml doc with this schema?
11:37 edrin (in Java)
11:42 malick joined #bioclipse
11:46 egonw_ edrin: have Java call the CL util xmllint
11:48 masak egonw_: is that very platform-agnostic?
11:48 masak there seems to be a library called javax.xml.validation
11:48 masak http://java.sun.com/j2se/1.5.0/docs/api/j​avax/xml/validation/package-summary.html
11:49 masak nevery used it myself, though
11:49 masak s/y//
11:54 edrin masak: sounds great to me. .xsd files are just .xml files with schema content?
11:55 masak edrin: something like that
11:55 edrin cool
11:55 masak there's a schema standard somewhere
11:55 masak ah, here: http://www.w3.org/XML/Schema
11:56 edrin yes
11:58 * olas will hold a presentation entitled: "Pharmacophores in Bioclipse" at BMC in Uppsala, Sweden, at 15.00 CET.
11:58 olas if you are around, feel free to drop by
12:00 edrin let's see if I can make it...
12:01 * edrin hehe
12:03 * egonw_ is looking forward to the sheets on slideshare
12:04 jonalv slideshare?
12:04 jonalv what's that?
12:08 jonalv test
12:08 jonalv test
12:09 jonalv testing
12:10 egonw_ jonalv: http://chem-bla-ics.blogsp​ot.com/search?q=slideshare
12:10 egonw_ bye
12:10 CIA-34 bioclipse: biocoder * r5924 /bioclipse2/trunk/plugins/net.bi​oclipse.chart/src/net/bioclipse/ (3 files in 3 dirs):
12:10 CIA-34 bioclipse: * moved display(...) from ChartUtils to ChartView.
12:10 CIA-34 bioclipse: * Added tab support to ChartView so that it can contain several charts.
12:14 * olas likes commits!
12:16 CIA-34 bioclipse: ospjuth * r5925 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business/src/net/bioclipse/cdk/ (4 files in 2 dirs): Added CDKConformer that extends CDKMolecule and implements getConformers(). Also added loadConformers() methods in managers.
12:17 CIA-34 bioclipse: ospjuth * r5926 /bioclipse2/trunk/plugins/net.b​ioclipse.cdk.business.test/src/ (2 files in 2 dirs): Wrote test for loadConformers()
12:17 CIA-34 bioclipse: biocoder * r5927 /bioclipse2/trunk/plugins/net.biocli​pse.statistics/src/net/bioclipse/sta​tistics/editors/MatrixEditor.java: Minor: Removed unused variable
12:34 edrin I will do soon megacommit
12:34 olas nice!
12:34 * olas likes megacommits too
12:36 CIA-34 bioclipse: jonalv * r5928 /bioclipse2/trunk/plugins/ (9 files in 4 dirs): The service view now updates when structuredb instances are created and removed
12:39 jonalv it's raining commits today! :)
12:48 CIA-34 bioclipse: shk3 * r5929 /bioclipse2/trunk/plugins/net.bioclipse.cml/: Initial import.
12:49 CIA-34 bioclipse: shk3 * r5930 /bioclipse2/trunk/plugins/net.bioclipse.cml/ (74 files in 17 dirs): Initial import.
12:50 shk3 ok, so please try
12:50 shk3 on any file, there should be an additinal menu item
12:50 shk3 "validate cml"
12:50 shk3 this gives the error
12:52 CIA-34 bioclipse: carl_masak * r5931 /bot/trunk/zarah.pl: [zarah] implemented greeting, fixed regexpes, added "ey" as greeting
12:52 edrin shk3: well, how do you validate the cml file?
12:52 jonalv shk3: I will have a look at it after olas presentation
12:53 shk3 via jumbo
12:53 shk3 but that's not yet implemented
12:53 shk3 (well, it is for bc1)
12:53 edrin ok
12:53 shk3 I just need to get the "framework" running first
12:53 edrin what is jumbo?
12:54 shk3 the pmr cml software
13:36 jonalv shk3: back
13:36 jonalv shk3: What should I test now? :)
13:42 CIA-34 bioclipse: jonalv * r5932 /bioclipse2/trunk/plugins/net.bioclipse.cml/src/ne​t/bioclipse/cml/managers/ValidateCMLManager.java: removed @Override from method overriding from an interface. Java 1.5 doesn't support this and Bioclipse is still java 1.5
13:43 jonalv shk3: ping
13:45 jonalv shk3: I got a Runtimeexception explaining what went wrong and all when starting. Didn't you thet? Exception in thread "Thread-5" java.lang.RuntimeException: service object: net.bioclipse.cml.managers.ValidateCMLManager@b67fb8does not implement IBioclipseManager
13:48 CIA-34 bioclipse: carl_masak * r5933 /bot/trunk/zarah.pl: [zarah] implemented url shortening
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14:00 shk3 jonalv: sorry
14:00 shk3 for being late
14:00 shk3 I did not get anything.
14:00 shk3 no idea why.
14:00 shk3 but this sounds like it helps
14:00 shk3 thanks
14:00 jonalv hm you don't get any log at all?
14:01 shk3 where is the log supposed to be?
14:02 shk3 only have got a log in .metadata
14:02 shk3 and this only says
14:02 jonalv on the terminal in Eclipse
14:02 shk3 java.lang.IllegalStateException: Could not get validate CML manager
14:02 shk3 at net.bioclipse.cml.managers.Activator.ge​tValidateCMLManager(Activator.java:58)
14:02 jonalv sry the console
14:02 shk3 which doesnt help much
14:02 shk3 same on the console
14:03 jonalv interesting, so we don't get the same behavior
14:04 shk3 looks like
14:04 shk3 anyway, I will try to fix this
14:04 jonalv yup
14:04 shk3 thanks for looking at it
14:05 jonalv np
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14:06 olas wb egonw
14:08 CIA-34 bioclipse: jonalv * r5934 /bioclipse2/trunk/plugins/net.biocl​ipse.structuredb/src/net/bioclipse/​structuredb/domain/Structure.java: quick and dirty fix to conform to new conformer standard. getConformers just returns a list with self in structure for the moment...
14:17 CIA-34 bioclipse: ospjuth * r5935 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.business/src/net/bioclip​se/cdk/business/ICDKManager.java: Publish conformer methods to console.
14:23 olas egonw: do you want H explicit when generating SMILES?
14:23 olas or should we remove H from the SMILES string?
14:24 egonw remove
14:24 olas how?
14:25 olas how remove hydriogens from IAtomcontainer?
14:25 olas is there a convenienceMethod?
14:25 masak heh, iac.convenienceMethod() // DWIM
14:26 olas ok
14:27 olas DWIM?
14:27 olas Dont Wait In March?
14:27 masak "Do What I Mean"
14:27 olas aah
14:27 olas almost the same
14:27 * olas will not wait in march
14:27 masak in some cases, yes
14:30 egonw olas: the regular suspect would be cdk.tools.manipulators.AtomContainerManipulator
14:31 shk3 indeed
14:31 shk3 method removeHydrogens(IAtomContainer atomContainer)
14:31 olas yup
14:31 olas found it
14:31 olas but it does not work :-(
14:31 olas still get SMILES with explicit H
14:32 shk3 it returns a copy
14:32 shk3 the original ac is unchanged
14:32 shk3 did you see that?
14:33 olas hmm
14:33 olas oh
14:33 olas thx
14:33 masak that's the problem with methods returning a copy :)
14:34 masak they are often called 'add', 'remove' etc
14:34 masak making it seem like they change the original object
14:34 masak even BigInteger gets this wrong
14:34 shk3 hm, ja, ok
14:34 shk3 but still
14:35 shk3 on the other hand
14:35 olas nice
14:35 olas now it's better
14:36 CIA-34 bioclipse: ospjuth * r5936 /bioclipse2/trunk/plugins/net.bioclipse.c​dk.business/src/net/bioclipse/cdk/domain/ (CDKConformer.java CDKMolecule.java): Generate SMILES without hydrogens, and make CDKConformers able to generate SMILES.
14:37 CIA-34 bioclipse: ospjuth * r5937 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business.test/src/net/bioclipse/​cdk/business/test/CDKManagerTest.java: Test passes for Conformer loading.
14:38 shk3 jonalv: would it be ok if you try once more?
14:38 shk3 I did the change, but still an error
14:38 shk3 but no real message.
14:39 jonalv k
14:41 shk3 k?
14:41 shk3 well, I commit
14:42 jonalv k is short ok which I think is short ffor okey which probably is short for somwthing too :)
14:42 CIA-34 bioclipse: shk3 * r5938 /bioclipse2/trunk/plugins/net.bioclips​e.cml/src/net/bioclipse/cml/managers/ (IValidateCMLManager.java ValidateCMLManager.java): next try
14:42 shk3 the nature of ok is heavily debated, but that OT here :-)
14:43 jonalv yea
14:45 jonalv shk3: okey so please explain the problem... :)
14:45 jonalv the cml manager is added to the javascript enviornemnt
14:47 shk3 but when I run it,
14:47 shk3 the line
14:47 shk3 (IValidateCMLManager) finderTracker.waitForService(1000*30)
14:47 shk3 which should give me the manager
14:47 shk3 returns null.
14:47 shk3 But I need the manager, to do the actual work, don't I.
14:47 jonalv true
14:48 jonalv whee is this code called?
14:48 jonalv *where
14:50 shk3 CMLValidationHandler
14:50 shk3 line 12
14:50 shk3 there needs to be the .validate() at the end, but right now I do not even get the manager
14:51 jonalv okey and how do I get that method called? :)
14:52 shk3 via the menu item "validate cml"
14:52 jonalv ah
14:52 jonalv oki
14:52 shk3 that was my understanding at least
14:52 jonalv yea seams reasonable :)
14:53 shk3 have a business method, call that from the handler, the handler is registered to the menu item
14:54 jonalv yup, I wonder why it doesn't work :)
14:54 * jonalv is locking at it. Hopes to find something :)
14:55 olas unlock it, jonalv
14:56 egonw olas: deliberately left #cdk ?
14:56 jonalv okey I can't spell some words... sorry
14:56 olas egonw: I am trying to help cdk as much as I can
14:56 egonw much appreciated...
14:56 olas just feel my help isn't appreciated
14:57 egonw sorry about that
14:57 egonw it really is...
14:57 egonw I did not intend to disapprove of what you did
14:57 olas I know, since there is nothing to disaprove on
14:58 jonalv shk3: The strange thing is that it works for me... I don't get null....
14:58 egonw to some extend...
14:58 egonw I have not checked how you fixed the NPE, but it might not be the way it should be done...
14:58 egonw a NPE can be 'fixed' in many ways...
14:58 olas perhaps
14:58 olas but rajarshi should review commits, if he is in charge of that code
14:58 olas IMO
14:58 egonw ah, well yes, but...
14:58 shk3 jonalv :-?
14:58 egonw nice that you mention this...
14:59 egonw this used to be the case...
14:59 shk3 (if you understand that smilie)
14:59 egonw Chris, Rajarshi and I do monitor the commit list...
14:59 egonw but there are too many lists...
14:59 egonw so that system does not scale to the size of current CDK development...
14:59 jonalv shk3: sort of. I am at a loss as to what to do now though...
14:59 egonw which is why we are formalizing policy a bit...
14:59 egonw a bit more like the Linux kernel is developed...
14:59 egonw patches are approved...
14:59 egonw we are experimenting...
15:00 egonw and maybe we can have a looser 'sign off' for fixes like this...
15:00 shk3 ok, the activator.java
15:00 shk3 for me,
15:00 egonw it's good that you bring this up, and has to be decided on...
15:00 shk3 goes to line 58
15:00 shk3 meaning exampleManager is null
15:00 egonw too many stuff in CDK is broken, because people (including me) thought he/she knew the best way to fix a NPE
15:00 egonw really...
15:01 shk3 oh yes, the ModelBuilder3D is a good example...
15:01 egonw well, I guess the BC1 even shows this...
15:01 egonw shk3: that's a more complicated example...
15:02 egonw shk3: that got broken because the ModelBuilder3D made assumptions which were not verified and not cross-checked with other code...
15:02 shk3 no, that got broken because somebody did something he thought to be good
15:02 shk3 but did not run the tests
15:02 egonw don't think that is correct
15:03 egonw it did not get broken because changes the the 3D builder were made...
15:03 egonw instead, some other code was 'fixed'...
15:03 egonw which broke the builder
15:03 shk3 don't think so, but let's forget it
15:04 jonalv shk3: so it waits 30 secs and then returns null for you? (That is very strange...)
15:04 egonw if you like
15:04 jonalv shk3: what system you on?
15:04 shk3 jonalv: yes, exactly
15:04 olas egonw: if I click on a molecule with 3 conformers, what should display in jmol and 2DViewer respectively?
15:04 shk3 kubuntu latest
15:04 shk3 so you get the exampleManager?
15:04 egonw olas: in Jmol, three models
15:04 olas and 2D?
15:04 egonw which you can flip trough with 'model X'
15:05 olas yup
15:05 jonalv shk3: I get you manager yea... :)
15:05 egonw 3 conformers got 1 2D structure
15:05 olas that might need updates to the CDKJmolAdapter...
15:05 egonw so, the first?
15:05 egonw they should all be identical
15:05 olas sounds reasonable
15:05 olas hmm
15:05 olas I guess I can create a workaround for the jmol stuff
15:06 jonalv shk3: could you see if your javascript envirnment has the cml manager? (just write cml in the javascript console and hit enter)
15:06 olas by converting a ConformerContainer to a ChemModel with 3 models
15:06 shk3 starting bc
15:06 olas that should do the trick
15:06 shk3 takes a second
15:06 olas ok, will do that
15:07 shk3 cml gives me
15:07 shk3 ReferenceError: "cml" is not defined
15:07 jonalv shk3: hm this is strange...
15:07 jonalv shk3: but that was at least along the same lines as your other problem
15:08 jonalv maybe we should see if someone else has the same behavior? (It's hard to help when it works for me...)
15:08 shk3 yes, sure
15:08 shk3 thanks anyway
15:09 shk3 btw: what I get on the console
15:09 shk3 when starting (this was there from first time I tried bc2) is
15:09 shk3 Caused by: java.lang.NoClassDefFoundError: Could not initialize class org.springframework.osgi.util.DebugUtils
15:09 jonalv shk3: never seen that either
15:11 shk3 are there any plugins I need to include when running?
15:11 shk3 I did not include everthing, perhaps I should try?
15:11 CIA-34 bioclipse: ospjuth * r5939 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/domain/CDKMolecule.java: CDKMolecule now uses getAtomContainer so that overriding classes can use standard methods.
15:15 shk3 hm, no difference
15:15 shk3 anybody else willing to test?
15:17 jonalv shk3: I will try it on my old computer running Ubuntu
15:19 shk3 great
15:29 jonalv it takes a while to get the old beast up and running though :)
15:32 jonalv brb
15:40 CIA-34 bioclipse: ospjuth * r5940 /bioclipse2/trunk/plugins/net.bioclips​e.core/src/net/bioclipse/core/domain/ (AtomIndexSelection.java FrameSelection.java): Added FrameSelection to allow for selecting frame in e.g. jmol.
15:42 jonalv shk3: It works for me on Ubuntu as well
15:43 CIA-34 bioclipse: ospjuth * r5941 /bioclipse2/trunk/plugins/net.bioclipse.core/src​/net/bioclipse/core/domain/ModelSelection.java: Renamed to ModelSelection.
15:44 jonalv shk3: Should I give it a test in Winodws under parallells? :)
15:45 shk3 hm, strange
15:45 shk3 if you can try, please do
15:45 jonalv oki
15:46 jonalv I have three screens in front of me now, one running windows, one running Mac OSX and one running Ubuntu. I kind of like this :)
15:47 shk3 the plugin is found in my bioclipse, because the menu item is there. but somehow the business stuff isn't, right?
15:48 jonalv yea
15:48 jonalv I wonder what happends if you try tab completion in the javascript console
15:48 jonalv what managaers do you get?
15:49 shk3 what letter should I start with?
15:50 jonalv none
15:50 shk3 that gives me clear as the only command, it seems
15:50 jonalv what plugins are you running?
15:51 shk3 all i checked out
15:51 shk3 it should be all in trunk
15:52 jonalv You are running ALL plugins and you have no managers in the javascript environment?
15:52 shk3 looks like :-(
15:52 jonalv sounds like you might have some problem with your setup...
15:52 shk3 which plugin is responsible for the managers stuff?
15:52 shk3 perhaps I miss the important one?
15:52 jonalv there is no Bioclipse plugin doingthat exactly
15:53 jonalv there is a osgi boundle in the target plattform which swt's up Spring containers
15:53 jonalv *sets
15:54 jonalv I'll stop the windows test then
15:54 jonalv there obviously something more strange going on here
15:55 jonalv what java version are you running?
15:55 shk3 1.6
15:55 shk3 I added all osgi stuff to my run configuration which I could find
15:55 shk3 perhaps that helps...
15:55 jonalv I was thinking you had to new versions but you are not exactly running cutting edge stuff are you?
15:56 jonalv The boundle is called something like Spring.extender I don't rememebr exactly
15:56 shk3 I checked out bc2 a few days ago for the first time
15:57 jonalv I have HArdy Heron Ubuntu at home. Maybe I should do a test and see if I can get Bioclipse 2 working on it...
15:58 shk3 where do I select the bundles?
15:58 shk3 in the run configuration, right?
15:58 jonalv yea
16:00 CIA-34 bioclipse: jonalv * r5942 /bioclipse2/trunk/plugins/net.bioclipse.s​tructuredb/src/net/bioclipse/structuredb/ (DataBase.java Label.java): [Structuredb] labels are now shown in the service view (and updated when created/removed)
16:08 shk3 I selected all plugins and it's still not yet working
16:16 shk3 I had hoped getting bioclipse running would be easier in bc2...
16:19 jonalv shk3: yea what eclipse version are you running?
16:19 jonalv and try with java 1.5
16:20 jonalv Bioclipse is not ifficially supported on java 1.6 :)
16:26 shk3 eclipse 3.3.2
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