Camelia, the Perl 6 bug

IRC log for #cdk, 2008-04-04

| Channels | #cdk index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
05:29 rojasm joined #cdk
05:46 jbrefort joined #cdk
06:33 rojasm joined #cdk
06:35 rojasm moin
06:37 wiswedel joined #cdk
07:06 carsten joined #cdk
07:47 egonw joined #cdk
07:48 egonw hi wiswedel
07:55 wiswedel Hi Egon :-)
07:56 jpansanel moin
07:56 jpansanel hi egonw
07:56 jpansanel congratulation for your PhD !
07:56 egonw hi jpansanel
07:56 egonw jpansanel: thanx!
08:01 jonalv joined #cdk
08:14 egonw jonalv: the database stuff looks good
08:15 egonw it's not really detailed, but the overall picture looks good
08:15 egonw the authentication stuff is always tricky...
08:15 egonw you seem to aim at some sort of versioning?
08:15 egonw with created and edited?
08:16 jonalv yea that was more like for having a light weight auditing
08:16 jonalv what do you mean with: "authentication stuff"?
08:17 egonw who was access to what...
08:33 CIA-19 bioclipse: jonalv * r5343 /bioclipse2/trunk/plugins/net.bioclipse.st​ructuredb.tests/tests/net/bioclipse/struct​uredb/persistency/dao/GenericDaoTest.java:
08:33 CIA-19 bioclipse: Moved applicationContext.xml back into root of the source folder. Structuredb
08:33 CIA-19 bioclipse: will have double layers of Spring managed classes. A standard Bioclipse manager
08:33 CIA-19 bioclipse: will wrap around many strucutredbInstancemanagers that will be created from
08:33 CIA-19 bioclipse: applicationContext.xml one for each created database instance.
08:34 CIA-19 bioclipse: jonalv * r5344 /bioclipse2/trunk/plugins/​net.bioclipse.structuredb/ (2 files in 2 dirs):
08:34 CIA-19 bioclipse: Moved applicationContext.xml back into root of the source folder. Structuredb
08:34 CIA-19 bioclipse: will have double layers of Spring managed classes. A standard Bioclipse manager
08:34 CIA-19 bioclipse: will wrap around many strucutredbInstancemanagers that will be created from
08:34 CIA-19 bioclipse: applicationContext.xml one for each created database instance.
08:43 CIA-19 bioclipse: jonalv * r5345 /bioclipse2/trunk/plugins/net.bioclipse.s​tructuredb/src/net/bioclipse/structuredb/ (5 files in 2 dirs): business -> privatebusiness
08:45 CIA-19 bioclipse: jonalv * r5346 /bioclipse2/trunk/plugins/net.bioclipse.structure​db/src/net/bioclipse/structuredb/privatebusiness/ (6 files): structuredbManager -> structuredbInstanceManager
08:48 rojasm joined #cdk
09:00 egonw hi rojasm
09:03 CIA-19 bioclipse: jonalv * r5347 /bioclipse2/trunk/plugins/net.bioclipse.structure​db/src/net/bioclipse/structuredb/privatebusiness/ (3 files): Started work on structuredbInstancemanagers
09:03 CIA-19 bioclipse: jonalv * r5348 /bioclipse2/trunk/plugins/net.bioclipse.stru​cturedb/src/net/bioclipse/structuredb/privat​ebusiness/StructuredbInstanceManager.java: Started work on structuredbInstancemanagers
09:07 de_maas joined #CDK
09:27 thomas_ku joined #cdk
09:27 thomas_ku moin
09:40 jonalv egonw, I am not sure the who has access to what is totally solved. If you have access to the database instance you have access to everything
09:40 jonalv things that not everyone should have access to will simply have to be in another database instance...
09:53 egonw ah... right... no, that won't work in all situations... :)
09:53 jonalv okey?
09:53 egonw it's a discussion we had regarding metware.sf.net last week
09:53 egonw yeah, it's ok
09:53 egonw metware will actually need record level access control :)
09:54 egonw but that a whole other story
09:54 jonalv please tell me why and make it convincing because I might not want to make things more complicated than needed... :)
09:54 egonw I'll report when we worked thing out...
09:54 egonw this is complex enough for BC purposes, I think
09:54 jonalv good :)
09:54 egonw well, so far, it was complex enough for us too...
09:54 egonw but we actually have to go further...
09:54 jonalv okey
09:54 egonw and are exploring options now...
09:55 jonalv I am trying to get some grips with IAtomContainer and the bioclipse intrafaves IMolevule and ICDKMolecule. There are many decission to make here...
09:56 egonw looking forward to your analysis...
09:56 jonalv I want to keep the Bioclipse interfaces small and just encapsulate CDK resources to be able to use them
09:56 egonw have to pick up my son from school now
09:57 jonalv hm I won't write a document...
09:57 jonalv cya
09:57 egonw what about using the IMolecule interface for the IBioResource CDKMolecule?
09:57 jonalv oh it extends it
09:57 egonw oh, perfect
09:57 jonalv or are you reffering to a cdk interfae?
09:57 egonw yes
09:57 egonw cdk.interfaces.IMoleule
09:57 jonalv in that case it doesn't
09:58 egonw ah :)
09:58 egonw ok, cu later
09:58 jonalv yea
10:02 CIA-19 bioclipse: jonalv * r5349 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/domain/ICDKMolecule.java: added getAtomcontainer to ICDKMolecule and a small TODO comment (question style)
10:02 CIA-19 bioclipse: jonalv * r5350 /bioclipse2/trunk/plugins/ (8 files in 5 dirs): Work with internal managers
11:22 rojasm joined #cdk
11:23 CIA-19 bioclipse: jonalv * r5351 /bioclipse2/trunk/plugins/net.bioclipse.s​tructuredb/src/net/bioclipse/structuredb/ (8 files in 2 dirs): changed privatebusiness -> internalbusiness since it doesn't imply as much which masak suggested the first one did...
11:25 rojasm left #cdk
11:47 jbrefort joined #cdk
11:49 egonw joined #cdk
12:10 CIA-19 bioclipse: ospjuth * r5352 /bioclipse2/trunk/plugins/net.bioclipse.bio​moby.tests/src/net/bioclipse/biomoby/tests/ (old/testBiomoby.java services/TestDBServices.java): Added tests for multiple Biomoby downloads.
12:12 CIA-19 bioclipse: ospjuth * r5353 /bioclipse2/trunk/plugins/net.biocli​pse.biomoby/src/net/bioclipse/biomob​y/services/DownloadGenbankMoby.java: Removed unused class
12:12 CIA-19 bioclipse: ospjuth * r5354 /bioclipse2/trunk/plugins/net.bioclipse.biomoby/ (10 files in 3 dirs): Implemented multiple MobyService calls wrapped in a job. DownloadFromGenbank fully operational.
12:13 CIA-19 bioclipse: ospjuth * r5355 /bioclipse2/trunk/plugins/net.​bioclipse.services/plugin.xml: Added serviceType for downloadGenbank.
12:41 CIA-19 bioclipse: jonalv * r5356 /bioclipse2/trunk/plugins/ (10 files in 6 dirs):
12:41 CIA-19 bioclipse: Fixed cascades on delete. Currently I am leaning towards the behavior that a
12:41 CIA-19 bioclipse: structure can be in a library or not in a library and if a library is removed
12:41 CIA-19 bioclipse: the structures in it aren't deleted but merely not in a library any longer. But
12:41 CIA-19 bioclipse: maybe this behavior is more what's expected if a structure could be in many
12:41 CIA-19 bioclipse: libraries? I am a bit uncertain...
15:48 wiswedel left #cdk
17:02 carsten joined #cdk
17:46 CIA-18 joined #cdk
18:59 rojasm joined #cdk
20:57 CIA-18 cdk: miguelrojasch * r10584 /cdk/branches/miguelrojasch-CMLReact​/src/main/org/openscience/cdk/formul​a/MolecularFormulaManipulator.java: added JavaDoc

| Channels | #cdk index | Today | | Search | Google Search | Plain-Text | summary