Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-08-25

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All times shown according to UTC.

Time Nick Message
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07:51 jonalv oh hai
07:51 zarah saluton jonalv
08:09 shk3 joined #bioclipse
08:11 jonalv hi shk3
08:11 shk3 hi jonalv
08:19 edrin joined #bioclipse
08:19 edrin hi
08:19 zarah hello edrin, you fantastic person you
08:21 jonalv people, vote for: https://bugs.eclipse.org/b​ugs/show_bug.cgi?id=262795
08:21 jonalv it's so sad this has not been fixed yet...
08:23 olass jonalv: I voted
08:23 jonalv olass++
08:24 jonalv olass: we should have had bioclipse.net mail adresses for Eclipse bugzilla. That woould have ben nice :)
08:24 egonw jonalv++
08:24 jonalv egonw: vote! :)
08:25 jonalv Gpox: vote! :)
08:25 egonw jonalv: sure... what bug did you file for those bioclipse.net email addresses?
08:25 jonalv egonw: I didn't
08:25 jonalv egonw: I want you to vote on https://bugs.eclipse.org/b​ugs/show_bug.cgi?id=262795
08:31 jonalv egonw: what cdk manager methods makes use of the getConformers method in CDKMolecule?
08:31 egonw dunno
08:31 jonalv egonw: more generally, are we using it very much at all?
08:33 jonalv egonw: I thought you would be the one to ask...
08:33 egonw make a call graph
08:34 jonalv yea... ...or not...
08:35 jonalv egonw: gorget that I asked...
08:48 egonw jonalv: I think Ola worked with that... sounds Balloon material to me
08:48 jonalv egonw: yea...
08:49 egonw myexperiment.downloadWorkflow(889)
09:03 CIA-63 bioclipse.rdf: Egon Willighagen master * r0d324b0 / (25 files in 10 dirs): Added the MyExperiment: first function: downloadWorkflow(Integer) - http://bit.ly/mYCH8
09:04 egonw olass: this download method is much like the gist one...
09:04 egonw *except*
09:04 egonw it knows the proper file name
09:04 olass soudns good
09:15 egonw let's see if I can now fix that Xerces not found classpath problem for the JOELib plugin
09:54 egonw I fucking hate Xerces!
10:05 egonw please don't let it make me patch JOELib :(
10:23 egonw olass: ping
10:23 egonw I get this exception:
10:23 egonw Caused by: java.lang.IllegalArgumentException: wrong number of arguments
10:23 egonw at sun.reflect.NativeMethodAc​cessorImpl.invoke0(Native Method)
10:23 egonw so, somewhere the wrong method is called...
10:24 egonw and I don't know which method my manager is not implementing...
10:27 egonw grpmh
10:51 egonw fortunately JOELib2 is still using my CML code :)
10:58 CIA-63 bioclipse.qsar: Ola Spjuth master * r20e8d29 / plugins/net.bioclipse.qsar/src/net/bio​clipse/qsar/business/IQsarManager.java : Removed annotations for doCalculation() - http://bit.ly/DOgCL
10:58 CIA-63 bioclipse.qsar: Ola Spjuth master * rd6e6893 / plugins/net.bioclipse.qsar/src/net/bio​clipse/qsar/business/QsarManager.java : Improved progressMonitor and do not catch OperationCanceledException. - http://bit.ly/bcVn3
10:58 CIA-63 bioclipse.qsar: Ola Spjuth master * rb25074e / plugins/net.bioclipse.qsar.ui/src/net/bi​oclipse/qsar/ui/builder/QSARBuilder.java : Better monitor workload division between tasks. - http://bit.ly/kGq0g
10:58 CIA-63 bioclipse.qsar: Ola Spjuth master * ra9b95c8 / plugins/net.bioclipse.cdk.qsar/src/net/bioclip​se/cdk/qsar/impl/CDKDescriptorCalculator.java : Correctly handle CDK workload in progress monitor. - http://bit.ly/w8Fmc
11:07 egonw ok, lunch now
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11:43 CIA-63 bioclipse.core: jonalv master * r15f0c01 / plugins/net.bioclipse.core/src/net/bioclipse/manag​ers/business/AbstractManagerMethodDispatcher.java : Fixed handling of OperationCanceledException and subprogressmonitors - http://bit.ly/1blulC
11:43 CIA-63 bioclipse.core: Ola Spjuth master * r80525ef / (40 files in 20 dirs): Merge branch 'master' of git@github.com:olas/bioclipse.core - http://bit.ly/4dmHa7
11:44 jonalv joined #bioclipse
11:46 CIA-63 bioclipse.qsar: Ola Spjuth master * r6a86c38 / (25 files in 12 dirs): Migrated QSAR project to NWO together with jonalv++. - http://bit.ly/MoIo0
11:50 CIA-63 bioclipse.qsar: Egon Willighagen master * r6629c67 / plugins/net.bioclipse.qsar/onto​logy/descriptor-algorithms.owl : Added missing <definition> provided by Rajarshi. - http://bit.ly/1roHJr
11:52 olass egonw: why have a separate bioclipse.joelib git repo?
11:52 egonw was easier
11:53 egonw because I do not have write access to bioclipse.qsar
11:53 olass has that ever stopped you before :)
11:53 egonw (or at least not that I am aware of)
11:53 olass send me patches
11:53 egonw no, it's pragmatic
11:53 olass ack
11:53 egonw I am sending you patches
11:53 egonw just differently :)
11:57 CIA-63 bioclipse.qsar: Ola Spjuth master * r1db0436 / (3 files):
11:57 CIA-63 bioclipse.qsar: Added feature for qsar.xmpp.
11:57 CIA-63 bioclipse.qsar: This implies a dependency to xws4j. - http://bit.ly/RPADk
12:10 egonw olass:
12:10 egonw ah, wait
12:10 egonw nvm
12:20 egonw olass: cannot continue with QSAR
12:34 olass egonw: fixed now
12:34 CIA-63 bioclipse.qsar: Ola Spjuth master * r72fd12c / (6 files in 2 dirs): Fixed NWO deps and constructors. - http://bit.ly/3aFN4C
12:38 masak joined #bioclipse
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12:56 CIA-63 bioclipse.qsar: Ola Spjuth master * reb5f8b7 / (4 files in 4 dirs):
12:56 CIA-63 bioclipse.qsar: Improved progress monitors for XMPP, REST, and CDK
12:56 CIA-63 bioclipse.qsar: Now supports cancelation and better messages. - http://bit.ly/3IriIG
13:01 egonw olass: I have the very cryptic error:
13:01 egonw http://bioclipse.pastebin.com/m3a684235
13:01 zarah egonw's link is also http://tinyurl.com/mxy9rg
13:01 egonw "java.lang.IllegalArgumentException: wrong number of arguments"
13:01 egonw oh... jonalv++
13:02 egonw for making the things somewhat more informative!
13:02 egonw olass: -> qsar.addResourcesAndResponsesToQsarModel
13:02 jonalv egonw: huh_ Ö=
13:02 jonalv gah
13:02 jonalv egonw: huh? :)
13:02 egonw the exception now reports what method was wrongly called..
13:06 olass egonw: hmm
13:07 olass seems you return null as result
13:07 olass L/QSARTest1/molecules/CAS.5.sdf=null
13:07 olass or could be
13:07 olass did you pull?
13:07 olass how can I reproduce?
13:08 olass oh
13:08 olass I can by myself :(
13:08 egonw I'm getting it all the time :(
13:08 olass yes
13:08 olass it's another NWO bug
13:08 egonw no
13:08 olass will get jonalv to assit me with this
13:08 egonw I had it before the NWO move too
13:09 olass strange
13:10 olass this must be jonalv's code
13:10 olass he will help me in a sec
13:20 shk3 is there a bioclipse patch tracker?
13:33 olass egonw: please pull bioclipse.qsar
13:33 olass oh
13:33 olass please pull bioclipse.core
13:33 olass jonalv++ fixed the problem
13:33 egonw shk3: the same as the bug tracker
13:34 CIA-63 bioclipse.core: Ola Spjuth master * rc477fa8 / plugins/net.bioclipse.core/src/net/bioclipse/manag​ers/business/AbstractManagerMethodDispatcher.java : Fix from jonalv++ to not run methods as BioclipseJob when interface declares IProgressMonitor. - http://bit.ly/11UpCT
13:52 olass egonw: does that solve your problems with QSAR?
13:57 egonw yes, it does
13:57 egonw it does not make JOELib run yet...
13:57 egonw but that's another thing... :(
13:57 egonw "No information object available for descriptor with name joelib2.feature.types.atomlabel.AtomBondOrderSum" :(
13:59 jonalv egonw, olassÖ Any suggestions for how to handle the fact that CDK does not seem to be able to handle molecule 1282 in the Chebi dataset_
14:00 egonw still need to look at that
14:00 egonw in between urgent grant writing
14:00 egonw fuck me for not having grant application texts ready, just for fun
14:00 * jonalv was planning on doing some performance measuring but he is sort of stuck. Any suggestions for how to get rid of that one?
14:01 egonw jonalv: just remove that one from your test set...
14:01 jonalv egonw: sry, what?
14:01 egonw and put it in a bug report
14:01 egonw molecule 1282
14:01 egonw just remove that one from the SD file...
14:01 egonw plain text editor...
14:01 egonw count...
14:01 egonw Cut
14:01 jonalv egonw: and just how would you remove it. That't what I want a good tip for...
14:01 egonw and then Paste in Firefox or Mylyn
14:01 jonalv plain text editor and count to 1282?
14:02 jonalv ...well that's one way...
14:04 egonw please file the bug for me...
14:04 * egonw is, for the first time, making a list of conference talks he has given all time...
14:04 egonw why don't I just have that ready ?!?!?
14:05 CIA-63 bioclipse.structuredb: jonalv FileStore * r0294aaa / (8 files in 7 dirs):
14:05 CIA-63 bioclipse.structuredb: Fixed insert & read from FileStore, no updates yet
14:05 CIA-63 bioclipse.structuredb: Can now import and retrieve molecules. Missing things so far include updae and delete but there is enough to perform some performace measurements at least. - http://bit.ly/f4CEB
14:08 jonalv vim++
14:09 jonalv egonw: it't the hydrogen nucleus...
14:14 egonw what's up with it?
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14:17 olass egonw: ping
14:18 olass can I replace, in the SPARQL query, 'qsar:' with 'http://www.blueobelisk.org/ontolo​gies/chemoinformatics-algorithms/#'
14:18 zarah olass's link is also http://tinyurl.com/6n5gee
14:18 egonw yes
14:18 egonw but then you need to wrap it in <>
14:19 egonw qsar:foo
14:19 egonw becomes
14:19 egonw <http://www.blueobelisk.org/ontolo​gies/chemoinformatics-algorithms/#>
14:19 egonw <http://www.blueobelisk.org/ontologi​es/chemoinformatics-algorithms/#foo>
14:19 zarah egonw's link is also http://tinyurl.com/6n5gee
14:19 zarah egonw's link is also http://tinyurl.com/6n5gee
14:19 olass ah
14:19 olass thx
14:19 egonw the brackets indicate it is a resource
14:21 olass egonw++ //it works now
14:31 jonalv gah CDK seeems to have problems with just about all molecules in that Chebi file... :(
14:38 egonw wha' r u doin' ?
14:40 shk3 egonw: your remaining nmrshiftdb submits have a single O as structure. Is that correct?
14:40 egonw yes
14:40 egonw they sometimes call that water
14:40 egonw often used a solvent
14:41 egonw also major component of about any living organism
14:41 olass I drink it a lot
14:41 egonw olass: ah, you drink a lot of oxygen, good!
14:41 olass yes
14:41 egonw shk3: seriously...
14:41 egonw shk3: I should not have added explicit hydrogen?
14:41 shk3 in theory not
14:41 egonw heheheh
14:42 jonalv egonw: I thinksomething is very broken in the combination ChEBI and CDK in Bioclipse.... :(
14:42 shk3 but it seems the single-atom-case is somehow confusing
14:42 egonw jonalv: next week I'll fix it
14:42 shk3 but I will have a look at it
14:42 * shk3 is drinking Pepsi right now
14:42 * shk3 is not expected to recognize water
14:47 egonw shk3: btw, nmrshiftdb does seem to have remembered my personal info...
14:48 shk3 i don't know what's wrong there
14:48 * olass is happy that all QSAR tests now passes again, apart from a small one filed as bug 1566
14:48 shk3 it works for me
14:48 shk3 I tried it several times
14:48 * olass will now relocate to Stockholm
14:48 olass see you later
14:49 egonw I'll ping you when it is reset again... maybe a batch import or some back u+
14:49 * egonw 's computer is cloning a large repository, and will take a 15 minute drink breaks
14:49 egonw and submit some solvent NMR spectra meanwhile
15:07 CIA-63 bioclipse.qsar: Ola Spjuth master * r4b7e32b / plugins/net.bioclipse.qsar/src/net/bioc​lipse/qsar/business/OntologyHelper.java :
15:07 CIA-63 bioclipse.qsar: Corrected Category IDs to have complete BO NS
15:07 CIA-63 bioclipse.qsar: ANd placed FIXMEs for bug 1566. - http://bit.ly/16s2Z8
15:07 CIA-63 bioclipse.qsar: Ola Spjuth master * rc6c0fc1 / plugins/net.bioclipse.qsar/src/net/biocli​pse/qsar/descriptor/model/Descriptor.java : Convenience method to add Categories to Descriptors. - http://bit.ly/eilqm
15:07 zarah bug #1566 | http://tinyurl.com/l23eob
15:07 CIA-63 bioclipse.qsar: Ola Spjuth master * r6224671 / plugins/net.bioclipse.qsar/src/net/bio​clipse/qsar/business/QsarManager.java : Fixed NPE when no responses should be removed. - http://bit.ly/3dY9kF
15:07 CIA-63 bioclipse.qsar: Ola Spjuth master * rbb4f132 / (2 files in 2 dirs):
15:07 CIA-63 bioclipse.qsar: Removed obsolete test and adapted for changed
15:07 CIA-63 bioclipse.qsar: BODO hierarchy categories. - http://bit.ly/18pf47
15:08 masak did the hivpred plugin survive the move to some git repo?
15:17 CIA-63 bioclipse.qsar: Ola Spjuth master * r2ba6a1e / (2 files in 2 dirs):
15:17 CIA-63 bioclipse.qsar: Removed dep to REST in qsar tests and updated
15:17 CIA-63 bioclipse.qsar: tests for patched hierarchy in OWL. - http://bit.ly/14VQkr
15:50 Gpox joined #bioclipse
16:35 CIA-63 bioclipse.structuredb: jonalv master * re6eb368 / plugins/net.bioclipse.structuredb/src/net/biocli​pse/structuredb/business/StructuredbManager.java : added debug time for smart query - http://bit.ly/25lQwg
16:35 CIA-63 bioclipse.structuredb: jonalv FileStore * rb360742 / plugins/net.bioclipse.structuredb/src/net/biocli​pse/structuredb/business/StructuredbManager.java : added debug time for smart query - http://bit.ly/L9x7j
16:44 edrin egonw: available?
16:44 egonw yo, what's up?
16:46 edrin They say: Please use sentence case in the title, ... "Web" should be written "web".
16:46 egonw ok, fair
16:46 egonw easy
16:46 egonw that's journal preferences
16:47 edrin egonw: got my private message?
17:10 edrin left #bioclipse
19:35 olass joined #bioclipse
19:35 olass hi
19:35 zarah hello olass, you fantastic person you
19:35 olass moin
19:35 zarah hello olass, you fantastic person you
20:13 sneumann joined #bioclipse
20:35 sneumann_ joined #bioclipse

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