Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-05-05

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All times shown according to UTC.

Time Nick Message
02:16 stain joined #bioclipse
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11:16 olas joined #bioclipse
11:16 olas hi all
12:08 egonw hi olas
12:12 CIA-44 joined #bioclipse
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13:38 rojasm joined #bioclipse
13:44 CIA-45 bioclipse: ospjuth * r5544 /bioclipse2/trunk/plugins/net.bioclipse​.biomoby.tests/src/net/bioclipse/biomob​y/tests/services/TestDropActions.java: Adapted drop test to use new ServiceManagerHelper.
13:46 steinbeck joined #bioclipse
13:46 olas hi steinbeck
13:47 steinbeck Hi olas
14:27 CIA-45 bioclipse: jonalv * r5545 /bioclipse2/trunk/plugins/ (5 files in 4 dirs): Refactoring of HSQLDB-connecting. Now uses jdbc:hsqldb:file protocol instead of instantiating a server on my own.
14:28 olas how does that work out?
14:28 olas solves any problems?
14:29 jonalv it seems so yea
14:32 olas great :-)
14:41 CIA-45 bioclipse: jonalv * r5546 /bioclipse2/trunk/plugins/net.bioclipse.hsql​db/src/net/bioclipse/hsqldb/HsqldbUtil.java: removed "file:" from path to database file
15:25 jonalv olas or egonw: My structuredb test: "testCreatingAndRetrievingStructures" dies because readerFactory.createReader(instream) returns null. Could one of you maybe help me with why?
15:27 olas I can look at it but expect that egonw is needed
15:28 egonw jonalv:  please email the cdk-user ML
15:29 egonw I can have a look at it tomorrow
15:29 olas I'll look in 2 mins
15:30 jonalv I have probably done something stupid but I can't figure out why...
15:30 jonalv or what
15:30 CIA-45 bioclipse: ospjuth * r5547 /bioclipse2/trunk/plugins/net​.bioclipse.cdk10.jchempaint/ (.classpath .settings/ META-INF/MANIFEST.MF): Removed J2SE-1.5 requirement as that messes up things on Mac.
15:31 egonw hahahaha
15:32 egonw ah, those poor people with those machines which just look good
15:32 olas grr
15:32 jonalv :)
15:32 olas took me 3 hours to figure out :-(
15:32 masak olas: he's right, you know
15:32 olas not you too!?!
15:32 olas masak likes his Mac
15:32 * jonalv didn't expect this from masak
15:33 masak well, yes, I like it
15:33 olas (or at least I thought so?)
15:33 masak sure, sure
15:33 masak but the magic is mostly on the surface
15:33 masak ask viklund any day
15:33 masak he's been down to some scary places
15:33 olas What makes viklund an authority in this field?
15:33 masak and they're just as dangerous and uncharted as on any Unix system
15:33 olas right
15:34 olas like Ubuntu
15:34 masak 'xactly
15:34 masak (except that Ubuntu is not even Unix, like Mac OS X is)
15:34 masak but some crappy clone of it called Linux or something
15:34 masak gotta go! ciao! :)
15:35 * egonw has to leave too
15:35 egonw jonalv: email me your stacktrace, if you like...
15:35 jonalv that's the problem I don't have any stack trace... :)
15:35 jonalv it just gives null
15:36 jonalv but please run the tests in net.structuredb.
15:36 jonalv tests
15:36 egonw jonalv: ok, ping me tomorrow...
15:37 jonalv oi
15:37 jonalv oki
15:37 * olas is updating before he can continue to check out anything at all
15:37 olas will probably take me an hour or two :-(
15:37 jonalv is it that slow now?
15:38 olas yup
15:38 jonalv aouch
15:41 olas nu speedade det på
15:42 olas lite
15:49 olas ok, nere
15:49 * olas skall köra test
15:51 olas vilken klass/test?
15:51 jonalv business.structuredbManagertest
15:51 olas oki
15:53 olas jag har en idé
15:53 olas du har inte reggat några format
15:53 olas hmm
15:53 jonalv huh?
15:53 olas det har du kanske ändå...
16:04 * olas will continue in english
16:10 CIA-45 bioclipse: jonalv * r5548 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Switched to using ICDKMolecule instead IMolecule. It better represents the abstraction level we are at.
16:49 CIA-45 bioclipse: ospjuth * r5549 /bioclipse2/trunk/plugins/net.bi​oclipse.structuredb.tests/tests/ (4 files in 2 dirs): Added 2 CML files to replace Mol files as parsing of MOLfiles seems broken in CDKManager. Updated Test for these files.
17:24 CIA-45 bioclipse: jonalv * r5550 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Work on importing sdf files into the structuredb. It doesn't quite work yet
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17:38 CIA-45 bioclipse: jonalv * r5551 /bioclipse2/trunk/plugins/net.bioclipse.str​ucturedb.tests/tests/net/bioclipse/structur​edb/business/StructuredbManagerTest.java: fixed a few setup things
18:13 CIA-45 bioclipse: ospjuth * r5552 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business.test/src/net/bioclipse/​cdk/business/test/CDKManagerTest.java: Added test for bug 1958097 (MOL-files not detected by CDKManager)
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18:19 egonw olas: MDLV2000Format is what you are looking for
18:19 olas oh
18:20 olas thx
18:20 egonw MDL published (at least) 3 MDL molfile formats
18:20 olas are all supported in CDK?
18:20 egonw yes, but not 100%
18:21 olas should I have MDLFormat, MDLV"000Format, Mol2Format?
18:21 olas or should I remove any?
18:21 egonw Mol2Format not
18:21 olas ok
18:21 egonw MDLFormat not either
18:21 olas so only 2000?
18:21 egonw maybe V3000 too
18:23 olas ok
18:24 olas ok, works now.
18:24 olas great
18:24 CIA-45 bioclipse: ospjuth * r5553 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Added correct MDLFormatV2000 and V3000 to support mol-files (aka MDL-files). Test now passes.
18:24 olas egonw: Now added: MDLV3000Format, MDLV2000Format, CMLFormat, SDFFormat and PDBFormat. OK? any more? less?
18:25 egonw what are you adding it too, anyway?
18:25 olas parsemolecules med CDKManager
18:25 olas för loading
18:26 olas not for save
18:29 egonw in what context? not an editor, right?
18:29 olas in the manager
18:29 olas no, not editor
18:30 olas for scripting, expansion of entities in Navigator
18:30 olas nvm, we can update them later
18:36 olas ok, bye for tonight
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