Camelia, the Perl 6 bug

IRC log for #cdk, 2007-09-21

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All times shown according to UTC.

Time Nick Message
04:34 jpansanel joined #cdk
04:34 CIA-31 joined #cdk
05:02 CIA-31 jmol: hansonr * r8301 /trunk/Jmol/src/org/opensc​ience/jmol/app/webexport/ (3 files): 11.3.26 bug fix for webPageMaker setDocument(0), writing to div that does not exist
05:47 CIA-31 jmol: hansonr * r8302 /trunk/Jmol/src/org/opensc​ience/jmol/app/webexport/ (5 files): screwy still
05:49 jbrefort joined #cdk
05:55 thomas_ku joined #cdk
05:55 thomas_ku moin
06:38 CIA-31 jmol: hansonr * r8303 /trunk/Jmol/src/org/opensc​ience/jmol/app/webexport/ (JmolPopIn.html JmolPopIn.js WebPanel.java): still trying
06:57 CIA-31 jmol: hansonr * r8304 /trunk/Jmol/src/org/openscience/j​mol/app/webexport/WebPanel.java: trying...
07:03 CIA-31 jmol: hansonr * r8305 /trunk/Jmol/src/org/ (2 files in 2 dirs): 11.3.26 bug fix for WebPageMaker not writing files -- problem with sun.net.www.protocol.jar.JarUR​LConnection$JarURLInputStream
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08:06 jonalv joined #cdk
08:25 jpansanel moin
08:26 jbrefort hi jpansanel
08:33 egonw joined #cdk
08:34 egonw moin
08:35 jpansanel moin egonw
09:25 steinbeck joined #cdk
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10:10 CIA-31 bioclipse: jonalv * r3798 /trunk/playground/plugins/​net.bioclipse.structuredb/ (5 files in 5 dirs): Now the setupTestEnvironment (create the tables for dao testing) is beginning to work.
10:18 * egonw is away for lunch
10:19 * olas is dining in front of his laptop
10:38 * jonalv should eat real soon now...
10:38 CIA-31 bioclipse: jonalv * r3799 /trunk/playground/plugins/​net.bioclipse.structuredb/ (6 files in 3 dirs): Moved table creation code from testservermanager to a Tablecreator which can be used booth when testing and when deploying
11:01 carsten joined #cdk
12:28 CIA-31 cdk: egonw * r8958 /trunk/cdk/src/org/openscience/cdk/te​st/tools/CDKValencyCheckerTest.java: Fixed the suite() method.
12:35 CIA-31 bioclipse: jonalv * r3800 /trunk/playground/plugins/net.bioc​lipse.structuredb/src/net/bioclips​e/structuredb/persistency/tables/ (BaseObject.sql TableCreator.java): TableCreator code with a (strangely) broken regexp
12:46 CIA-31 bioclipse: jonalv * r3801 /trunk/playground/plugins/net.bioclipse.​structuredb/src/net/bioclipse/structured​b/persistency/tables/TableCreator.java: Changed from string.match to creating a Matcher from Pattern but I still can't match a ';' at the end of a line...
12:49 olas left #cdk
13:30 CIA-31 bioclipse: jonalv * r3802 /trunk/playground/plugins/net.bioclipse.​structuredb/src/net/bioclipse/structured​b/persistency/tables/TableCreator.java: The TableCreator seems to be working according to my evil plans... :)
13:43 carsten joined #cdk
13:46 CIA-31 bioclipse: jonalv * r3803 /trunk/playground/plugins/net.bioc​lipse.structuredb/src/net/bioclips​e/structuredb/persistency/tables/ (5 files): Wrote the sql for all the tables. Next step will be to create dao tests and start performing the iBatis mapping
13:58 CIA-31 bioclipse: jonalv * r3804 /trunk/playground/plugins/net.bioclipse.structured​b/tests/net/bioclipse/structuredb/persistency/dao/ (LibraryDaoTest.java StructureDaoTest.java UserDaoTest.java): Created dao tests. They fail nicely.
14:13 egonw BTW, the transition of IBond.setOrder(IBond.ORDER) is not trivial
14:13 egonw of=to
14:18 egonw OK, will have to go somewhere now... bbl
14:31 CIA-31 bioclipse: biocoder * r3805 /trunk/plugins/net.bioclipse.statistics/src/​net/bioclipse/editors/MatrixGridEditor.java: Working on MatrixGridEditor context menu
14:43 CIA-31 bioclipse: jonalv * r3806 /trunk/playground/plugins/​net.bioclipse.structuredb/ (10 files in 5 dirs):
14:43 CIA-31 bioclipse: added a few jars needed by the framework.
14:43 CIA-31 bioclipse: Began writing on Spring config file applicationcontext.xml.
14:43 CIA-31 bioclipse: And created sqlMapConfig file and the actual mappings. Run into trouble with resource loader which doesn't find the mapping files. Something is wrong with the path to them.
15:01 CIA-31 blueobelisk: rajarshi * r114 /userscripts/trunk/ (3DStructureView.user.js ChemGM.user.js): Added the userscripts from IU
15:01 CIA-31 bioclipse: jonalv * r3807 /trunk/playground/plugins/net.bioclip​se.structuredb/src/sqlMapConfig.xml: Now the resource references to the mapping files are correct.
15:09 rguha joined #cdk
15:09 rguha jbrefort: thanks for looking into the CDX stuff
15:10 jbrefort np
15:10 jbrefort you should use the can format, it seems to work ;)
15:10 rguha right
15:11 rguha are there plans to update the ordinary SMILES parser? I thought the canonicalization was part of that
15:11 jbrefort I have no idea, just working on cdx and cdxml
15:11 rguha aah, ok
15:11 jbrefort SMILES are quite mysterious for me
15:12 rguha :)
15:12 jbrefort I don't even understand what @ and @@ really mean
15:13 jbrefort on of the samples has two C*, one is @ and the other @@ in the export, but both are S
15:13 jbrefort unless I have forgotten the CIP thing
15:14 rguha my understanding is that you can use either @ or @@ as long as the subsequent ordering of the neighbors matches the CIP rules
15:14 rguha so if the ordering CIP-correct in the clockwise direction use @@ and if the ordering is correct in the @ direction use @
15:15 jbrefort probably
15:15 rguha but I have to admit (to my embarassment) I have forgotton a lot of chirality :(
15:25 egonw hi rguha
15:25 rguha egonw: hi
15:25 rguha I put the GM stuff into the BO SVN
15:27 egonw yes, saw that
15:27 egonw thanx!
15:27 rguha np
15:27 egonw I hope the editor will be satisfied now
15:27 rguha hopefully
15:27 rguha btw, did you make any progress on the markush framework?
15:28 egonw no
15:28 rguha ok
15:28 rguha interesting functionality - I'd like to see what Ola would do with it
15:29 CIA-31 bioclipse: jonalv * r3808 /trunk/playground/plugins/net.bioc​lipse.structuredb/src/net/bioclips​e/structuredb/persistency/mapping/ (Library.xml Structure.xml): Wrote some mappings. It seems as if the mappings don't know about stuff written in other files. Maybe all of it will have to move into one file instead.
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