Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-10-28

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All times shown according to UTC.

Time Nick Message
06:13 egonw joined #bioclipse
06:34 Gpox joined #bioclipse
07:36 CIA-52 bioclipse: goglepox * r7467 /bioclipse2/trunk/plugins/ (2 files in 2 dirs):
07:36 CIA-52 bioclipse: JmolEditor no longer depends on MoleculesIndexEditorInput
07:36 CIA-52 bioclipse:  - bug 55: Jmol plugin should not depend on a CDK plugin
07:36 CIA-52 bioclipse: http://pele.farmbio.uu.se/bugs/show_bug.cgi?id=55
07:36 zarah CIA-52's link is also http://tinyurl.com/5wezny
07:49 CIA-52 bioclipse: goglepox * r7468 /bioclipse2/trunk/plugins/net.biocl​ipse.cdk.business/src/net/bioclipse​/cdk/domain/CDKAdapterFactory.java: Added log message when an exception is caught
07:54 olass joined #bioclipse
07:54 olass hi
07:54 zarah hi olass
08:32 CIA-52 bioclipse: egonw * r7469 /bioclipse2/trunk/plugins/ (27 files in 17 dirs): Factored out jmol.cdk, to loose the dependency of net.bioclipse.jmol on CDK plugins, paving the way for the Jmol Feature (closes #55)
08:32 CIA-52 bioclipse: egonw * r7470 /bioclipse2/trunk/plugins/ne​t.bioclipse.jmol.cdk/icons/ (. molecule3D.png): Added missing icon
08:32 CIA-52 bioclipse: egonw * r7471 /bioclipse2/trunk/features/net.bioclips​e.chemoinformatics_feature/feature.xml: Added jmol.cdk
08:32 CIA-52 bioclipse: egonw * r7472 /bioclipse2/trunk/plugins/ne​t.bioclipse.jmol/plugin.xml: Removed the view, as it was moved to jmol.cdk
08:33 CIA-52 bioclipse: egonw * r7473 /bioclipse2/trunk/plugins/net.​bioclipse.jmol.cdk/plugin.xml: Removed perspective; fixed class and ID of the View
09:01 CIA-52 bioclipse: egonw * r7474 /bioclipse2/trunk/features/ (5 files in 2 dirs): Added Jmol feature and have the chemoinformatics feature depend on the new Jmol feature and no longer on the Jmol plugin
09:01 CIA-52 bioclipse: egonw * r7475 /bioclipse2/trunk/plugins/net.bioclipse.jmol/sr​c/net/bioclipse/jmol/views/StatusListener.java: Attempt to output Jmol messages to the JS console (failed)
09:01 CIA-52 bioclipse: egonw * r7476 /bioclipse2/trunk/features/net.bi​oclipse.jmol_feature/feature.xml: Added cheminformatics plugin, for category definitions
09:03 CIA-52 bioclipse: egonw * r7477 /bioclipse2/branches/jmolPerspective/: Removed merged branch
09:20 thomasku joined #bioclipse
09:45 edrin joined #bioclipse
09:45 edrin hi
09:45 zarah hi edrin
09:45 edrin hi egonw
09:45 edrin egonw: I solved the class loading problem...
09:47 egonw yes, saw the commit :)
09:47 egonw did not understand the remaining issue though
09:50 edrin well
09:51 olass joined #bioclipse
09:51 egonw ha, you made it to UU?
09:51 olass egonw: working from home?
09:51 olass yes
09:51 olass 2 hours late
09:51 egonw yes, see my email last weekend
09:51 olass I HATE SJ
09:52 egonw add net.bioclipse.jmol.cdk
09:52 egonw and merged the Jmol Feature into trunk
09:52 egonw now working on the loadMolecule() problems
09:55 edrin if you do
09:55 edrin output_object = iofactory.getOutputObject(r); // this function will return an object that implements the XMLBeans interface XmlObject; beside this it is an instanceof (for example) ProteinSequenceOutput. has the method ProteinSequenceOutput.getProteinsequence(). Problem: the javascript console does not reflect functions of ProteinSequenceOutput but does only reflect functions of XmlObject. beside this it cannot execute these functions when just typing t
09:57 olass egonw: I desperately need the loadMolecule()
09:58 egonw sure, I understand
09:58 edrin egonw: btw. the problem with multiple allowed root elements defined in XML Schemata is solved, too i think. iofactory eats now all of them and also autogenerates create-function for all of the beside createInputObject() that always just creates the first one described in schema...
09:58 egonw olass: working on it
09:58 olass thx
09:58 edrin olass: i updated xws4j-binding and the bc2-plugin of xws4j
09:59 olass ok
09:59 olass have not used them yet
09:59 olass will try to get my service up today (hopefully)
09:59 edrin olass: you can now create a bindnig for your function from bioclipse console ;)
10:00 olass great
10:00 edrin it will generate code, you can use this code from the console directly at runtime or just copy it from the target_directory to your java project "to quickly write a (autogenerated) client against your service" ...
10:01 edrin olass: good to hear this
10:01 edrin egonw: did i describe the problem in console properly ?
10:03 egonw I did not understand it...
10:03 egonw but then again...
10:03 egonw I have no knowledge on how this JavaScript thingy is working
10:03 olass masak can help with that
10:03 olass it's his boat
10:03 edrin ok :)
10:03 edrin is he available?
10:04 olass he is learning chineese
10:04 olass but he is here 25%
10:04 olass donät know his schedule though
10:04 olass he's not here right now
10:05 edrin ok
10:09 edrin olass, egonw, this Fabio seems to like our proposal somehow...
10:11 egonw indeed, nice :)
10:11 olass yup
10:16 edrin ismb seems to be a research institute
10:40 edrin in hi presentation bioclipse is mentioned as a xmpp adopting application, however wrong spelling ...
10:41 egonw as long as he gave the URL
10:41 edrin he did not ...
10:42 edrin just named the application
10:42 edrin page 8
10:42 egonw ok, so we just make sure that any gg with "bio eclipse clipse io data xmpp xws io-data" or subsets hits Bioclipse.net
10:50 olass egonw: what's your IP at bmc?
10:50 olass last digits?
10:51 olass 45.xx?
10:51 olass I need to borrow it for the day
10:51 olass Jonas is here
10:51 olass BIRT-guy
10:52 egonw olass: got it?
10:52 olass egonw?
10:53 olass yup
11:01 egonw olass: what should be the proper value be of:
11:01 egonw Bundle-RequiredExecutionEnvironment
11:01 olass nothing
11:01 egonw not J2SE-1.5, but instead?
11:01 olass empty
11:01 olass now: lunch
11:01 egonw oh... interesting...
11:01 egonw actually picked that up from BC2 :)
11:01 egonw ok, but good
11:01 egonw removing it is easy
11:07 CIA-52 bioclipse: egonw * r7478 /bioclipse2/trunk/cdk-externals/trunk/ (97 files in 48 dirs): Synchronized with CDK 1.2.x r12849
11:38 egonw olass: ping
11:40 olass pong
11:41 egonw ok, it was not me who broke loadMolecule()
11:41 egonw the mehods are untouched
11:41 egonw so, something else must have been broken
11:42 egonw but no clue what
11:42 egonw ResourcePathTransformer
11:42 egonw is a possible source of trouble
11:42 egonw but not sure yet
11:43 egonw knowing which commit broke it would help...
11:43 olass oh no
11:48 olass Gpox will assit
11:48 olass assist
11:49 olass I need to help charlgren with managers (he's here now)
11:49 egonw ok
11:49 edrin olass: did you get it connecting=
11:49 edrin ?
11:57 olass I'll be in a meeting with Jarl now
11:59 edrin ok
11:59 edrin :)
12:03 CIA-52 bioclipse: egonw * r7479 /bioclipse2/trunk/plugins/net.biocli​pse.core.tests/src/net/bioclipse/cor​e/ResourcePathTransformerTest.java: Added test which could have caused the loadMolecule() trouble
12:41 CIA-52 bioclipse: egonw * r7480 /bioclipse2/trunk/plugins/net.biocli​pse.core.tests/src/net/bioclipse/cor​e/ResourcePathTransformerTest.java: Test for another assumption about repeated getContents()
12:41 CIA-52 bioclipse: egonw * r7481 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Fixed loadMolecule
12:48 egonw olass: loadMolecule is working again
12:48 egonw going offline
12:49 egonw might drop by at UU
14:04 charlgren joined #bioclipse
14:36 CIA-52 bioclipse: ospjuth * r7482 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Quick fix to loadMolecules() by Egon at olas office. Egon: Please verify this.
14:38 CIA-52 bioclipse: ospjuth * r7483 /bioclipse2/trunk/plugins/net.bio​clipse.jmol/META-INF/MANIFEST.MF: Added missing dep. Dunno why this has gotten lost?
15:14 CIA-52 bioclipse: ospjuth * r7484 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.business.test/src/net/bioclipse/cdk/​business/test/CDKManagerPluginTest.java: Updated some tests to actually test something.
15:26 egonw joined #bioclipse
15:33 egonw olass: did you commit that fix for loadMolecule*s*() ?
15:33 olass yes
15:33 olass r7482
15:33 egonw ok, excellent
15:33 egonw 32 minutes today :)
15:38 shk3 joined #bioclipse
15:39 egonw hi shk3
15:39 shk3 hi egonw
15:39 shk3 btw, why did olas become olass?
15:40 shk3 we have got webspace for the speclipse feature
15:40 shk3 but I can't put things there directly.
15:40 shk3 need to send a zip to the external services group, who will put it on webspace.
15:40 shk3 do you think this is ok?
15:40 edrin shk3: i thnk because he forgot his olas pwd
15:41 shk3 or do I need frequent and fast access?
15:41 shk3 ah, better write down your passwords...
15:41 olass na ja
15:41 olass zip file is OK
15:41 egonw zip should be fine I think
15:41 olass but you probably want to update it frequently
15:42 egonw once a week?
15:42 egonw that should be OK for the ESG
15:42 olass whenever you like
15:42 shk3 yes, think so.
15:42 shk3 just can't guarantee it's done on the spot
15:43 shk3 ok, what do I need to setup the page?
15:44 shk3 is there an explanation in the wiki?
15:44 olass for what?
15:44 olass update site?
15:44 olass just unpack it in a folder
15:44 olass and point to it
15:45 shk3 how to make the update site, I mean
15:51 egonw Project -> New -> Update Site
15:51 egonw add the Speclipse feature
15:51 egonw then Build All
15:51 egonw IIRC
15:51 egonw never actually done if fully to the end
15:53 CIA-52 bioclipse: shk3 * r7485 /bioclipse2/trunk/plugins/net.biocli​pse.nmrshiftdb/src/net/bioclipse/nmr​shiftdb/wizards/SubmitWizard.java: exception handling
15:55 shk3 ok, trying to do it...
15:56 egonw install it on localhost:80 first, to test it
15:56 shk3 btw, what about version numbers?
15:56 egonw ask olass
15:56 shk3 also in plugins, is there a policy?
15:56 shk3 olass?
15:57 olass yes
15:57 shk3 what about versin numbers?
15:57 olass we now at: 2.0.0.A20081028
15:57 olass current date
15:58 shk3 ah, looks like the plugins get that automatically?
15:59 edrin olass: working now!
16:00 olass what?
16:06 egonw olass: ping
16:07 olass pong
16:07 egonw I have two failing tests left:
16:07 olass egonw++ //Good job
16:07 egonw testLoadMoleculeFromSMILESFile
16:07 egonw and testloadMoleculesFromSMIELSCheck
16:08 egonw but when running as plugin
16:08 egonw I get all sorts of test file not found
16:08 egonw does that sort of work for you?
16:08 olass yes
16:10 egonw ok, then I commit and ask you to verify mol2 stuff
16:11 egonw hang on...
16:15 CIA-52 bioclipse: egonw * r7486 /bioclipse2/trunk/cdk-externals/trunk/org.openscie​nce.cdk.atomtype/src/org/openscience/cdk/atomtype/ (SybylAtomTypeMatcher.java mapper/AtomTypeMapper.java): Synchronized with CDK 1.2.x r12852
16:17 egonw olass: please try
16:17 egonw I'll move to the SMILES tests
16:17 egonw btw, how come the plugin tests work for you, but not for me?
16:17 olass let's see tomorrow
16:18 olass only update cdk.atomtype?
16:19 shk3 looks like in bioclipse, I can't add a new update site
16:19 olass you can
16:19 olass preferences
16:19 shk3 ah
16:19 olass update siupdate site
16:20 shk3 ok
16:20 shk3 Bioclipse_feature_patch Feature (1.3.2) requires feature "net.bioclipse_feature (1.3.1)".
16:20 shk3 ???
16:20 egonw olass: yes
16:21 shk3 did i create a patch?
16:22 shk3 where does 1.3.1/1.3.2 come from?
16:24 olass old stuff
16:24 olass should be 2.0.0.A2008xxxx
16:24 shk3 hm, the version of the speclipse_feature is 1.0.0 right now
16:25 shk3 do plugins get automatic version numbers?
16:25 shk3 all my plugins are 2.0.0.Ablah without me doing anything
16:25 egonw from the MANIFEST.MF
16:26 shk3 how does it get in there?
16:26 shk3 sorry, don't understand this right now
16:27 egonw net.bioclipse.nmrshiftdb/META-INF/MANIFEST.MG
16:27 shk3 yes
16:28 olass shk3: I updated them
16:28 olass for a while I thought I'd export them
16:28 egonw olass: one down, one to go
16:28 olass egonw++ //Keep going
16:28 shk3 ah ok, so that needs to be done manually
16:28 olass indeed
16:28 olass a lot of manual stuff for a release
16:28 shk3 so I am setting the one in the feature as well
16:28 olass yes
16:30 shk3 but still i can't see where this 1.3.1/2 comes from
16:30 shk3 sounds like eclipse version numbers
16:30 olass explain in detail
16:30 olass so I can assist
16:30 shk3 thanks
16:31 shk3 i installed my update site locally
16:31 olass ok
16:31 shk3 (containing the feature in versin 1.0.0)
16:31 olass file:///path/to/updatesite/
16:31 shk3 no, I used apache
16:31 shk3 so I installed http://localhost/...
16:32 shk3 as update site
16:32 olass local site is just a folder on your computer
16:32 olass that's the easiest
16:32 olass but do as you like
16:32 shk3 ok, but apache should work as well
16:32 olass yes
16:32 CIA-52 bioclipse: egonw * r7487 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Added support to force loading from a particular IChemFormat
16:32 shk3 I do help->search for new features
16:32 shk3 speclipse update site is in
16:32 shk3 great
16:32 shk3 I am selecting this
16:33 shk3 and get error message Bioclipse_feature_patch Feature (1.3.2) requires feature "net.bioclipse_feature (1.3.1)".
16:34 olass what?
16:34 shk3 no idea
16:34 olass check what your feature depends on
16:34 olass did you just check speclipse feature?
16:34 olass or add required?
16:35 olass and only your update site, no bioclipse update site also?
16:36 shk3 the feature doesn't contain any other features, just plugins
16:36 shk3 I only check speclipse
16:37 shk3 but somehow it gets a dependency or so
16:37 olass no deps in speclipse feature?
16:38 olass are you 100% sure?
16:38 shk3 getting the same error when i try to select chemoinformatics feature
16:38 shk3 well, 100% sure is hard to be, isn't it?
16:38 shk3 but i can't find anything
16:39 shk3 when I am in the speclips feature and I go to required features/plugins
16:39 shk3 and do compute, it includes everything
16:39 shk3 cdk etc.
16:39 shk3 but I don't need these, do I?
16:40 shk3 or should it depend on chemoinformatics feature?
16:41 shk3 I will download bc from sf and try with this, I think
16:42 egonw cheminfo feature sounds about right
16:42 egonw since you need JCP
16:43 egonw olass: that last one is more definately not a ReaderFactory problem
16:43 olass what is the last one?
16:44 egonw testlaodMoleculesFromSMILESCheck
16:44 egonw code just looks broken
16:44 olass that has always failed
16:44 olass leave it then
16:45 egonw check CDKManager lines 1000-1016
16:45 olass thought you could shed a light on why it fails ;-)
16:45 egonw yes, sure... the code sucks
16:45 egonw who wrote that shit?
16:45 olass I donät know
16:45 olass could be me
16:45 egonw if it;s in the first column, then it's not
16:45 olass or Gpox
16:45 egonw otherwise check it's in the first column
16:45 egonw ???
16:45 olass mohahaha
16:46 olass probably me
16:46 * egonw runs 'git annotate'
16:47 egonw indeed :)
16:47 egonw how do the tests perform when run as plugin tests?
16:50 olass testSaveMol2 fails
16:50 olass org.openscience.cdk.excepti​on.NoSuchAtomTypeException: The AtomType C.3 could not be found
16:51 olass I updated only atomtype cdk plugin
16:51 olass any more cdk plugins I should update?
16:51 egonw no, don't think so
16:51 olass org.openscience.cdk.excepti​on.NoSuchAtomTypeException: The AtomType C.3 could not be found
16:51 olass at org.openscience.cdk.config.AtomTypeFacto​ry.getAtomType(AtomTypeFactory.java:292)
16:51 olass at org.openscience.cdk.atomtype.Sybyl​AtomTypeMatcher.findMatchingAtomTy​pe(SybylAtomTypeMatcher.java:110)
16:52 olass at org.openscience.cdk.io.Mol2Writer.​writeMolecule(Mol2Writer.java:220)
16:52 olass at org.openscience.cdk.io.Mol2Wri​ter.write(Mol2Writer.java:123)
16:52 olass at net.bioclipse.cdk.business.CDKMa​nager.save(CDKManager.java:392)
16:52 egonw that's outdate
16:52 egonw or wrong otherwise
16:53 egonw SybylAtomTypeMatcher.findMatchingAto​mType(SybylAtomTypeMatcher.java:110)
16:53 egonw that findMatching is really at line 106
16:53 olass hmm
16:53 olass will update again
16:54 egonw private SybylAtomTypeMatcher(IChemObjectBuilder builder) {
16:54 egonw InputStream stream = this.getClass().getResourceAs​Stream(SYBYL_ATOM_TYPE_LIST);
16:54 egonw factory = AtomTypeFactory.getInstance(stream, SYBYL_ATOM_TYPE_LIST, builder);
16:54 egonw cdkMatcher = CDKAtomTypeMatcher.getInstance(builder);
16:54 egonw InputStream mapStream = this.getClass().getResource​AsStream(CDK_TO_SYBYL_MAP);
16:54 egonw mapper = AtomTypeMapper.getInstance(CDK_TO_SYBYL_MAP, mapStream);
16:54 egonw }
16:54 egonw make sure the header looks like that
16:54 egonw that's the fix
16:54 olass cdk.atomtype?
16:54 olass oh, that's cdk.business
16:54 egonw [17:15] <CIA-52> bioclipse: egonw * r7486 /bioclipse2/trunk/cdk-externals/trunk/org.openscie​nce.cdk.atomtype/src/org/openscience/cdk/atomtype/ (SybylAtomTypeMatcher.java mapper/AtomTypeMapper.java): Synchronized with CDK 1.2.x r12852
16:55 egonw ok, called away for dinner
16:55 egonw bbl
16:55 olass thx
17:09 olass egonw: for backlog
17:09 olass I stepped through the process save mol2
17:09 olass it boils doewn to: AtomTypeConfigurator was null!
17:10 olass in     private void readConfiguration(InputStream ins, String format, IChemObjectBuilder builder) {
17:16 olass hmm maybe not
17:16 olass factory does not contain any atomtypes
17:16 olass so reading from file fails in that case
17:22 egonw in between dinner sessions
17:22 egonw please write a unit test that fails when run as plain unit test...
17:22 egonw oh... wait
17:23 egonw I got an idea
17:24 egonw in SybylAtomTypeMatcher
17:24 egonw the two final static Strings
17:24 egonw line 51,52
17:24 egonw make those strings start with a '/'
17:24 egonw like:
17:24 egonw private final static String SYBYL_ATOM_TYPE_LIST = "/org/openscience/cdk/dict/​data/sybyl-atom-types.owl";
17:24 egonw private final static String CDK_TO_SYBYL_MAP = "/org/openscience/cdk/dict/d​ata/cdk-sybyl-mappings.owl";
17:24 egonw ok, back to dinner
17:24 egonw bbl
17:28 shk3 seems to work by and large
17:28 shk3 the nmrshiftdb plugin is included in feature, but does not show up in bioclipse
17:28 shk3 I think this is a dependency problem
17:28 shk3 trying to solve this...
17:31 olass shk3: what version of bioclispe do you depend on?
17:33 shk3 2.0.0.A20081022
17:37 shk3 looks like the new cdk plugins are not included in the chemoinformatics feature.
17:37 shk3 is this correct?
17:43 olass yes
17:43 olass I have not done a new release yet
17:44 shk3 ok
17:44 shk3 the nmrshiftdb plugin uses these
17:44 shk3 should I include them in the speclipse feature for the time being?
17:51 olass no
17:51 olass wait for my release
17:51 CIA-52 bioclipse: shk3 * r7488 /bioclipse2/trunk/plugins/net.biocl​ipse.spectrum/META-INF/MANIFEST.MF: cleaned up dependencies
17:51 olass hopefully today
17:51 * olass is making progress
17:53 egonw olass: did the slash solve the problem
17:53 egonw ?
17:53 olass alsah?
17:53 olass slash?
17:53 olass what slash?
17:53 egonw [18:24] <egonw> in SybylAtomTypeMatcher
17:53 egonw [18:24] <egonw> the two final static Strings
17:53 egonw [18:24] <egonw> line 51,52
17:53 egonw [18:24] <egonw> make those strings start with a '/'
17:53 egonw [18:24] <egonw> like:
17:53 egonw [18:24] <egonw>     private final static String SYBYL_ATOM_TYPE_LIST = "/org/openscience/cdk/dict/​data/sybyl-atom-types.owl";
17:53 egonw [18:24] <egonw>     private final static String CDK_TO_SYBYL_MAP = "/org/openscience/cdk/dict/d​ata/cdk-sybyl-mappings.owl";
17:53 egonw [
17:53 shk3 olass: ok
17:54 olass egonw: have not tried that
17:54 olass got it working anyway
17:54 egonw please do
17:54 egonw oh...
17:54 egonw how?
17:54 olass anyway?
17:54 olass why?
17:54 olass what?
17:54 egonw when?
17:54 * olass is confused now
17:54 olass what are we talking about?
17:54 egonw mol2 atom types
17:55 olass hmm
17:56 olass I am not sure what I am running against
17:56 * olass will clean and rerun
17:56 CIA-52 bioclipse: shk3 * r7489 /bioclipse2/trunk/plugins/net.bioclipse.specmol/ (4 files in 3 dirs): removed xpp lib, depends on plugin
17:57 olass making progress
17:57 olass metaprint2d tests start to pass now
17:57 olass from SMILES at least
17:57 olass testing from file now
17:59 olass clean all is slow
18:08 olass egonw: around?
18:08 olass AT null for atom: Atom(1250112, S:O, H:0, 2D:[(-0.8452, -0.4953)], AtomType(1250112, FC:0, NC:0, EV:0, Isotope(1250112, MN:16, Element(1250112, S:O, ID:a12))))
18:08 olass how can that be?
18:09 edrin olass: when will you go on holidays?
18:09 olass friday afternoon
18:10 edrin ok
18:10 edrin and be back when?
18:10 olass dec 8th
18:10 edrin wow
18:10 olass I know
18:11 olass never had this long holliday ever
18:11 olass blame it on my girl
18:12 olass :-)
18:13 olass egonw: ping
18:15 edrin egonw: do you have a jabber account already?
18:24 edrin cu later :) mb :)
18:24 edrin left #bioclipse
18:27 egonw olass: I'm back
18:27 olass ran into a strange problem
18:27 olass trying to pinpoint it down
18:28 olass will let you know :-)
18:28 egonw ok
18:28 egonw I wish I could run the plugin variants too
18:32 olass what happens if you right-click -> run as junit plugin?
18:32 egonw I get files not found
18:32 egonw /test bla
18:34 olass go run config
18:34 olass you have run set target platform?
18:35 olass make sure it runs the bioclipse product
18:35 olass and only required plugins
18:35 egonw huh?
18:35 egonw which config?
18:35 egonw bioclipse.product?
18:36 egonw as in run configuration?
18:39 egonw checking that
18:39 olass make sure run config points to run the product
18:39 egonw net.bioclipse.ui.product, correct?
18:39 olass and not eclipse
18:39 olass yes
18:39 egonw it was set to eclipse...
18:39 egonw ok, thanx
18:39 olass suspected that
18:39 egonw I'm sure this in the wiki
18:40 olass I got Metaprint2D to run now in Bioclipse
18:40 egonw since it more or less worked, I never thought I did this wrong
18:40 egonw ok, cool
18:40 olass egonw: yes
18:40 olass so release soon I hope
18:40 olass need some food now
18:40 olass brb
18:40 egonw ack
18:41 olass joined #bioclipse
18:41 * olass is going for food
18:41 olass brb
18:50 * shk3 is going home
18:50 * shk3 hopes he can do the update site tomorroq
19:10 CIA-52 bioclipse: ospjuth * r7490 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java:
19:10 CIA-52 bioclipse: Debug out for atom typing in sybylAtomType depiction
19:10 CIA-52 bioclipse: .
19:40 CIA-52 bioclipse: ospjuth * r7491 /bioclipse2/trunk/plugins/ (21 files in 21 dirs): Set version to 2.0.0.A20081028.
19:40 egonw olass: nothing I can do anymore?
19:41 olass not that I can think of
19:41 egonw btw, did not get the plugin tests working, even after set target platform and the correct product
19:41 egonw ok, good
19:41 olass cu tomorrow
19:41 egonw going to review some CDK patches then
19:41 egonw ok, cu
19:41 olass hmm
19:42 olass should the chemoinfo feature require the jmol feature?
19:42 olass is that so?
19:42 olass I guess so
19:42 egonw yes
19:42 egonw well, or just add the plugins .jmol and .jmol.cdk
19:43 olass nope
19:43 olass must test jmol feature too
19:43 olass since you REALLY wanted to have this in a feature :-)
19:43 egonw yes, but not necessarily today
19:43 olass no time to change now
19:44 olass hope it works
19:44 olass (for you)
19:44 olass if things donät export now I'll get really tired
19:45 olass WHAT?
19:45 olass jmol plugin is in chemoinfo feature?
19:45 olass right, there goes jmol feature
19:45 olass sry
19:45 egonw no worries
19:45 olass no time to change now
19:46 egonw right
19:47 CIA-52 bioclipse: ospjuth * r7492 /bioclipse2/trunk/features/ (3 files in 3 dirs): Set version to 2.0.0.A20081028 and fixed deps.
19:55 CIA-52 bioclipse: ospjuth * r7493 /bioclipse2/trunk/features/net.​bioclipse_feature/feature.xml: Updated license.
20:12 olass it did not work :-(
20:12 olass cdk does not work at runtime
20:12 olass grrrrrrrrrrrrrrrrrrrrr
20:12 egonw what?
20:13 egonw you're kidding
20:13 egonw right?
20:13 olass java.lang.NoClassDefFoundError: org/openscience/cdk/interfaces/IChemObjectBuilder
20:13 olass I have no idea why
20:14 olass will recompile one more time
20:14 olass after that I give up
20:14 olass :-(
20:14 olass :-( :-( :-( :-( :-(
20:14 olass a runtime error
20:14 egonw what is the rest of the stack trace?
20:14 egonw from which plugin?
20:15 egonw I think about all plugins depend on org.openscience.cdk.interfaces
20:15 olass http://paste2.org/p/93544
20:17 CIA-52 bioclipse: ospjuth * r7494 /bioclipse2/trunk/cdk-externals/trunk/org.​openscience.cdk.atomtype/src/org/openscien​ce/cdk/atomtype/SybylAtomTypeMatcher.java: Added / at beginning as suggested by egonw.
20:18 edrin joined #bioclipse
20:19 egonw olass: any context about what the hell it was doing?
20:19 egonw hi edrin
20:19 edrin hi
20:21 egonw it seems to be failing *really* early on... :(
20:25 edrin i get strange errors in svn...
20:25 edrin update C:/Dokumente und Einstellungen/edrin/eclipse-works​pace/net.bioclipse.xws4j-feature -r HEAD --force
20:25 edrin svn: Target path does not exist
20:25 edrin svn: REPORT of '/svnroot/bioclipse/!svn/vcc/default': 500 Internal Server Error (https://bioclipse.svn.sourceforge.net)
20:25 edrin svn: Target path does not exist
20:25 edrin svn: REPORT of '/svnroot/bioclipse/!svn/vcc/default': 500 Internal Server Error (https://bioclipse.svn.sourceforge.net)
20:25 edrin update C:/Dokumente und Einstellungen/edrin/eclipse-works​pace/net.bioclipse.xws4j-feature -r HEAD --force
20:25 edrin svn: Target path does not exist
20:25 edrin svn: REPORT of '/svnroot/bioclipse/!svn/vcc/default': 500 Internal Server Error (https://bioclipse.svn.sourceforge.net)
20:25 edrin svn: Target path does not exist
20:25 edrin svn: REPORT of '/svnroot/bioclipse/!svn/vcc/default': 500 Internal Server Error (https://bioclipse.svn.sourceforge.net)
20:25 edrin what is this=
20:26 edrin hm
20:26 edrin sorry
20:27 edrin will just checkout again
20:27 egonw sounds like a regular hickup
20:27 edrin what do you mean?
20:27 egonw of the SVN server
20:33 olass egonw: solved the problem
20:33 olass it's your fault
20:33 olass you forgot to add the '.' to Bundle-ClassPath: .
20:33 egonw sure :)
20:33 CIA-52 bioclipse: edrin_t * r7495 /bioclipse2/trunk/plugins/net​.bioclipse.xws4j/.classpath: removed lib not needed...
20:33 egonw oh...
20:33 olass fixing
20:33 egonw I still have to get used that in Eclipse everything is different depending on how you run things...
20:33 egonw I hate this...
20:35 egonw fixed in cdk-eclipse
20:39 CIA-52 bioclipse: edrin_t * r7496 /xws/trunk/xws4j-binding/src/net/bioclips​e/xws/binding/tools/BindingCompiler.java: fixed path.separator
20:39 CIA-52 bioclipse: edrin_t * r7497 /bioclipse2/trunk/plugins/net.bioc​lipse.xws4j/src/net/bioclipse/xws4​j/DefaultBindingDefinitions.java: fixed path.separator
20:40 CIA-52 bioclipse: edrin_t * r7498 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/ (META-INF/MANIFEST.MF build.properties): removed lib not needed
20:45 egonw olass++
20:45 olass sadly it did not work now either...
20:45 olass but got a bnit further
20:45 olass will work more on the train home
20:45 olass gotta run now
20:45 olass cu tomorrow
20:45 olass bye
21:10 CIA-52 bioclipse: edrin_t * r7499 /xws/trunk/xws4j-binding/src/net/bioclips​e/xws/binding/tools/BindingCompiler.java:
21:22 CIA-52 bioclipse: edrin_t * r7500 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/ (10 files in 6 dirs):
21:25 edrin egonw: did they change something in bc again? my class loading trick does not work anymore...
21:26 egonw no, don't think so
21:26 edrin :(((
21:33 edrin gnah...
21:33 edrin in bc1 it always works
21:33 edrin in bc2 only problems...
21:34 egonw yeah... that's why Ola was working so late too...
21:34 egonw I have not figured out the fineprints either...
21:35 edrin the trick I was doing was to "manipulate the classloader of the running thread"...
21:37 egonw well... revert your checkout to the last commit that worked for you
21:37 edrin too late
21:37 egonw and then iterate through all commits and see what it makes it fail
21:37 egonw too late??
21:38 thomasku joined #bioclipse
21:38 edrin i think the code is ok... something in the bc2 changed...
21:40 edrin egonw: btw. could you urge masak to fix the javascript string formating bug i have on windows?
21:40 CIA-52 joined #bioclipse
21:40 ilogger2 joined #bioclipse
21:40 egonw did you file a bug report?
21:40 edrin i think this should exist already
21:41 edrin well, i told him, and he knows
21:41 egonw ok
21:41 edrin it's just he does not know HOW uggly this thing looks on windows
21:41 egonw as Ola said, he only works 25% on bioclipse
21:41 edrin ah
21:41 edrin ok,
21:41 egonw ah... screenshot
21:41 edrin what is he doing the rest 75%?
21:42 egonw not sure... but learning Japanes is one thing, IIRC
21:42 edrin ok
21:43 edrin is he a student?
21:43 egonw think so
21:43 egonw oh, and play with zarah
21:43 edrin hehe
21:44 edrin ah
21:54 edrin ah
21:54 edrin it's working again :)
21:55 edrin my mistake
21:56 CIA-52 bioclipse: edrin_t * r7501 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/ (5 files in 3 dirs):
21:58 edrin egonw: do you have a few minutes to play with plugin of xws4j?
22:04 edrin egonw: probably not :)
22:12 edrin nooooo

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