Camelia, the Perl 6 bug

IRC log for #cdk, 2009-03-02

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All times shown according to UTC.

Time Nick Message
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08:34 jpansanel poin
08:34 jpansanel moin
08:34 zarah saluton jpansanel
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09:01 jonalv o/
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10:07 thomasku moin
10:07 zarah saluton thomasku
10:08 thomasku egonw around`?
10:08 egonw hi thomasku
10:08 thomasku hi egonw
10:08 thomasku a cdk question
10:08 egonw sure
10:09 thomasku I updated my local cdk repositry for the cdk-1.2.x branch
10:09 thomasku and tried to build it with ant in eclipse
10:09 egonw thomasku: I got a question too... can the cdk-taverna plugin be split up in a 1.5 parts, and 1.6 parts?
10:09 egonw thomasku: theoretically, that should work
10:09 thomasku but it recommanded that I would need ant version 1.7.1
10:10 egonw correct
10:10 thomasku but I have no idea how I could update this within eclipse...
10:10 egonw ah... good point
10:10 egonw neither do I, actually...
10:10 egonw @google eclipse ant 1.7.1
10:10 zarah egonw: http://runnerwhocodes.blogspot.com/2008/​07/moving-to-ant-171-for-eclipse-34.html
10:10 thomasku so you build it on the console right?
10:10 egonw yes, that should still work
10:11 egonw thomasku: that google hit is informative
10:11 thomasku that is no problem for me too because there I have installed it
10:11 egonw it explains how to set a new Ant HOME
10:11 thomasku yeah just read it
10:13 thomasku regarding the splitting: it should theoretically work but I fear you will get many problems...
10:14 egonw which part actually depends on J6, and why?
10:15 thomasku the clustering part of the ART2A algorithm depends on J6
10:15 thomasku because it uses some xml function of J6
10:15 thomasku for the storing of the results
10:15 egonw OK, but the CDK parts do not depend on it?
10:16 egonw so, we can make a CDK specific plugin, and a datamining plugin?
10:16 egonw that is... a data generation plugin and a data analysis plugin
10:16 egonw both part of the CDK-Taverna super plugin...
10:16 egonw which has nothing in itself
10:17 egonw just thinking aloud...
10:17 egonw no idea if it makes sense to refactor that...
10:17 egonw or to just port the calculation stuff to T2 first...
10:19 thomasku I would think that I makes no sense to refactor it for the current Taverna release
10:19 thomasku for the T2 it would be a good choice...
10:19 egonw ack
10:20 thomasku but not sure if t2 depends on J5 or J6
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16:07 CIA-62 cdk: gilleain * r14276 /cdk/branches/jchempaint-primary/src/main/o​rg/openscience/cdk/renderer/Renderer.java: Ported across bugfix/improvement from Arvid's r9134 - "Replaced over complicated code to figure out zoom".
16:34 CIA-62 cdk: shk3 * r14277 /cdk/branches/jchempaint-primary/src/main/​org/openscience/cdk/io/ReaderFactory.java: molecules and reactions get rendered (but reactions need boxes, arrows etc.)
16:46 carsten joined #cdk
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17:45 CIA-62 cdk: shk3 * r14278 /cdk/branches/jchempaint-primary/src/main/o​rg/openscience/cdk/renderer/Renderer.java: molecules and reactions get rendered (but reactions need boxes, arrows etc.)
17:50 CIA-62 cdk: shk3 * r14279 /cdk/branches/jchempaint-primary/src/main/​org/openscience/cdk/io/ReaderFactory.java: this should net get committed
17:56 timvdm joined #cdk
17:58 CIA-62 cdk: shk3 * r14280 /jchempaint/trunk/src/main/org/openscience/jc​hempaint/dialog/EnterElementSwingModule.java: bond length no longer hard coded
18:21 CIA-62 cdk: gilleain * r14281 /cdk/branches/jchempaint-primary/src/main/o​rg/openscience/cdk/renderer/Renderer.java: Return an empty rectangle, rather than null if the chem model is empty.
19:56 CIA-62 cdk: thomaskuhn * r14282 /cdk-taverna/trunk/src/main/java/org/​openscience/cdk/applications/art2aCla​ssification/Art2aClassificator.java: Remove some bug's regarding the serialization of a ART2A classification result
19:58 CIA-62 cdk: thomaskuhn * r14283 /cdk-taverna/trunk/src/main/java/org/openscience​/cdk/applications/taverna/CDKTavernaConfig.java: Add two static class variables which are needed for the database handling
19:58 CIA-62 cdk: thomaskuhn * r14284 /cdk-taverna/trunk/src/main/java/org/openscienc​e/cdk/applications/taverna/LocalWorkerCDK.java: Remove the interface and add its functionality to the existing CDKLocalWorker interface
19:59 CIA-62 cdk: thomaskuhn * r14285 /cdk-taverna/trunk/src/main/java/org/o​penscience/cdk/applications/taverna/ac​tions/AbstractCDKProcessorAction.java: Add an serial id
20:00 CIA-62 cdk: thomaskuhn * r14286 /cdk-taverna/trunk/src/main/java/org/op​enscience/cdk/applications/taverna/arom​aticity/DetectHueckelAromaticity.java: Interface change see commit no r14282
20:01 CIA-62 cdk: thomaskuhn * r14287 /cdk-taverna/trunk/src/main/java/org/opens​cience/cdk/applications/taverna/atomtype/ (PerceiveMM2AtomTypes.java PerceiveMMFF94AtomTypes.java): Interface change see commit no r14282
20:02 CIA-62 cdk: thomaskuhn * r14288 /cdk-taverna/trunk/src/main/java/or​g/openscience/cdk/applications/tave​rna/atomtype/PerceiveAtomType.java: Interface change see commit no r14282 and extending the handling of unknown atom types
20:02 CIA-62 cdk: thomaskuhn * r14289 /cdk-taverna/trunk/src/main/java/org/​openscience/cdk/applications/taverna/​bioclipse/BioclipseResultViewer.java: Interface change see commit no r14282
20:03 CIA-62 cdk: thomaskuhn * r14290 /cdk-taverna/trunk/src/main/java/org​/openscience/cdk/applications/tavern​a/database/pgchem/DBConnector.java: Change the result set type
20:10 CIA-62 cdk: thomaskuhn * r14291 /cdk-taverna/trunk/src/main/java/org/open​science/cdk/applications/taverna/database​/pgchem/GetFingerprintVectorFromDB.java: Add a new Worker: This loads a fingerprint vector from the database
20:11 CIA-62 cdk: thomaskuhn * r14292 /cdk-taverna/trunk/src/main/java/org/ope​nscience/cdk/applications/taverna/databa​se/pgchem/GetMolecularWeightFromDB.java: Get the molecular weight for a set of molecules from the database. The molecules are stored within the database
20:12 CIA-62 cdk: thomaskuhn * r14293 /cdk-taverna/trunk/src/main/java/org/openscience/c​dk/applications/taverna/database/pgchem/GetMolecul​eDataForMoleculeSubstructureFromMoleculeID.java: Worker which performs a substructure search of molecules on the database using the database functionality
20:12 CIA-62 cdk: thomaskuhn * r14294 /cdk-taverna/trunk/src/main/java/org/opens​cience/cdk/applications/taverna/database/p​gchem/GetMoleculeIDsAndOriginFromDB.java: Add a new worker for loadint the molecular id's and the origin of the molecules
20:12 CIA-62 cdk: thomaskuhn * r14295 /cdk-taverna/trunk/src/main/java/org/o​penscience/cdk/applications/taverna/da​tabase/pgchem/GetMoleculesFromDB.java: Interface change see commit no r14282
20:13 CIA-62 cdk: thomaskuhn * r14296 /cdk-taverna/trunk/src/main/java/org/opensc​ience/cdk/applications/taverna/database/pgc​hem/GetMoleculesFromDBForSubstructure.java: Loads molecules from a database table after performing a substructure search
20:13 CIA-62 cdk: thomaskuhn * r14297 /cdk-taverna/trunk/src/main/java/org/op​enscience/cdk/applications/taverna/data​base/pgchem/GetQSARVectorFromDB.java: Update the worker for better performing. Reduces the database calls and the memory usage
20:14 CIA-62 cdk: thomaskuhn * r14298 /cdk-taverna/trunk/src/main/java/org/open​science/cdk/applications/taverna/database​/pgchem/GetSelectedMoleculesFromDB.java: Interface change see commit no r14282
20:15 CIA-62 cdk: thomaskuhn * r14299 /cdk-taverna/trunk/src/main/java/org/op​enscience/cdk/applications/taverna/data​base/pgchem/InsertMoleculeIntoDB.java: Interface change see commit no r14282
20:15 CIA-62 cdk: thomaskuhn * r14300 /cdk-taverna/trunk/src/main/java/org/ope​nscience/cdk/applications/taverna/databa​se/pgchem/InsertQSARResultsIntoDB.java: Interface change see commit no r14282
20:15 CIA-62 cdk: thomaskuhn * r14301 /cdk-taverna/trunk/src/main/java/org/open​science/cdk/applications/taverna/database​/pgchem/IterativeGetMoleculeFromDB.java: Interface change see commit no r14282
20:16 CIA-62 cdk: thomaskuhn * r14302 /cdk-taverna/trunk/src/main/java/org/opens​cience/cdk/applications/taverna/database/p​gchem/IterativeHasNextMoleculeFromDB.java: Interface change see commit no r14282
20:16 CIA-62 cdk: thomaskuhn * r14303 /cdk-taverna/trunk/src/main/java/org/openscie​nce/cdk/applications/taverna/database/pgchem/ (2 files): Interface change see commit no r14282
20:18 CIA-62 cdk: thomaskuhn * r14304 /cdk-taverna/trunk/src/main/java/org/openscience/​cdk/applications/taverna/database/pgchem/action/ (2 files): Rename the action for the configuration of database connections
20:19 CIA-62 cdk: thomaskuhn * r14305 /cdk-taverna/trunk/src/main/java/org/​openscience/cdk/applications/taverna/​isomorphism/IsomorphismTester.java: Add a worker which checks if two molecules are isomorph
20:19 CIA-62 cdk: thomaskuhn * r14306 /cdk-taverna/trunk/src/main/java/org/​openscience/cdk/applications/taverna/ (21 files in 4 dirs): Interface change see commit no r14282
20:22 CIA-62 cdk: thomaskuhn * r14307 /cdk-taverna/trunk/src/main/java/org/​openscience/cdk/applications/taverna/ (16 files in 5 dirs): Interface change see commit no r14282
20:22 CIA-62 cdk: thomaskuhn * r14308 /cdk-taverna/trunk/src/main/java/org/​openscience/cdk/applications/taverna/​qsar/model/ART2AClassificator/tools/ (9 files): Interface change see commit no r14282
20:23 CIA-62 cdk: thomaskuhn * r14309 /cdk-taverna/trunk/src/main/java/org/openscie​nce/cdk/applications/taverna/qsar/model/weka/ (15 files): Removed old Weka workers classes which uses old data handling schema
20:23 CIA-62 cdk: thomaskuhn * r14310 /cdk-taverna/trunk/src/main/java/org/openscience/​cdk/applications/taverna/qsar/model/weka/action/ (10 files): Removed old Weka workers classes which uses old data handling schema
20:25 CIA-62 cdk: thomaskuhn * r14311 /cdk-taverna/trunk/src/main/java/org/​openscience/cdk/applications/taverna/ (11 files in 4 dirs): Interface change see commit no r14282
20:25 CIA-62 cdk: thomaskuhn * r14312 /cdk-taverna/trunk/src/main/java/org/​openscience/cdk/applications/taverna/ (5 files in 3 dirs): Interface change see commit no r14282
20:26 CIA-62 cdk: thomaskuhn * r14313 /cdk-taverna/trunk/src/main/java/org/ope​nscience/cdk/applications/taverna/tools/ (4 files): Interface change see commit no r14282
20:27 CIA-62 cdk: thomaskuhn * r14314 /cdk-taverna/trunk/src/main/java/org/ope​nscience/cdk/applications/taverna/tools/ (5 files in 2 dirs): Interface change see commit no r14282
20:27 CIA-62 cdk: thomaskuhn * r14315 /cdk-taverna/trunk/src/test/java/org/ope​nscience/cdk/applications/taverna/databa​se/pgchem/GetMoleculesFromDBTest.java: Change test methode name
20:29 CIA-62 cdk: thomaskuhn * r14316 /cdk-taverna/trunk/src/test/java/o​rg/openscience/cdk/applications/ta​verna/io/ReadMDLRXNFileTest.java: Remove empty lines
20:30 CIA-62 cdk: thomaskuhn * r14317 /cdk-taverna/trunk/src/test/java/org/o​penscience/cdk/applications/taverna/is​omorphism/IsomorphismTesterTest.java: Add a junit test for a new worker
20:30 CIA-62 cdk: thomaskuhn * r14318 /cdk-taverna/trunk/src/test/java/org/ope​nscience/cdk/applications/taverna/qsar/D​escriptorCalculatorLocalWorkerTest.java: Remove test for an old class
20:31 CIA-62 cdk: thomaskuhn * r14319 /cdk-taverna/trunk/src/test/java/org/opensci​ence/cdk/applications/taverna/qsar/model/ART​2AClassificator/ART2AClassificatorTest.java: Add suppress warnings and a small change in creating the fingerprint for the test
20:32 CIA-62 cdk: thomaskuhn * r14320 /cdk-taverna/trunk/src/test/java/org/​openscience/cdk/applications/taverna/​qsar/model/ART2AClassificator/tools/ (2 files): Change the creating of the fingerprint item for this test
20:32 CIA-62 cdk: thomaskuhn * r14321 /cdk-taverna/trunk/src/test/java/org/openscience/c​dk/applications/taverna/qsar/model/ART2AClassifica​tor/tools/GetMoleculeIDsForGivenClassesTest.java: Adjust the result of one unit test
20:33 CIA-62 cdk: thomaskuhn * r14322 /cdk-taverna/trunk/src/test/java/org/openscie​nce/cdk/applications/taverna/qsar/model/weka/ (13 files): Remove unit test for deleted classes
20:35 CIA-62 cdk: thomaskuhn * r14323 /cdk-taverna/trunk/src/test/java/or​g/openscience/cdk/applications/tave​rna/renderers/PNGCreationTest.java: Remove commented out line
20:36 CIA-62 cdk: thomaskuhn * r14324 /cdk-taverna/trunk/src/test/java/org/ope​nscience/cdk/applications/taverna/tools/ (2 files): Change the creating of the fingerprint item for this test
20:37 CIA-62 cdk: thomaskuhn * r14325 /cdk-taverna/trunk/src/test/java/org/​openscience/cdk/applications/taverna/​tools/ExtractIDFromMolFileTest.java: Add a further unit test
20:38 CIA-62 cdk: thomaskuhn * r14326 /cdk-taverna/trunk/src/test/java/org/opensc​ience/cdk/applications/taverna/tools/Remove​MOLFilesWithoutStructureFromListTest.java: Add a further unit test
20:41 CIA-62 cdk: thomaskuhn * r14327 /cdk-taverna/trunk/src/test/java/org/opensc​ience/cdk/applications/taverna/tools/chebi/​ExtractDataFromChebiStructureTSVTest.java: Adjust the result of one unit test
20:42 CIA-62 cdk: thomaskuhn * r14328 /cdk-taverna/trunk/src/test/reso​urces/data/sdf/starliteMols.sdf: Add a new test file
20:43 CIA-62 cdk: thomaskuhn * r14329 /cdk-taverna/trunk/src/test/resources/data/txt/ (. atomtypingresult.txt atomtypingresult2.txt): Add new test files for the atom typing result analysis
20:47 CIA-62 cdk: thomaskuhn * r14330 /cdk-taverna/trunk/src/main/java/org/​openscience/cdk/applications/taverna/​qsar/model/ART2AClassificator/tools/ (4 files in 2 dirs): Add worker for analysis the ART2A classification result
20:47 CIA-62 cdk: thomaskuhn * r14331 /cdk-taverna/trunk/src/main/java/org/​openscience/cdk/applications/taverna/​tools/AnalyseAtomTypingResult.java: Add a worker which analysis the Atom typing result
20:48 CIA-62 cdk: thomaskuhn * r14332 /cdk-taverna/trunk/src/main/java/org/openscience​/cdk/applications/taverna/tools/ChartTool.java: Changes to the Charttool to support different new options
20:48 CIA-62 cdk: thomaskuhn * r14333 /cdk-taverna/trunk/src/main/java/org/o​penscience/cdk/applications/taverna/to​ols/ExtractIntermedIDFromMolFile.java: Extracts the intermed id's from a mol file
20:49 CIA-62 cdk: thomaskuhn * r14334 /cdk-taverna/trunk/src/main/java/org/ope​nscience/cdk/applications/taverna/tools/ (2 files):
20:50 CIA-62 cdk: thomaskuhn * r14335 /cdk-taverna/trunk/src/main/java/org/opensc​ience/cdk/applications/taverna/tools/ScaleF​ingerprintItemArrayBetweenZeroAndOne.java: Worker for scaling the fingerprint item between zero and one
20:51 CIA-62 cdk: thomaskuhn * r14336 /cdk-taverna/trunk/src/main/resources/ (3 files in 2 dirs): Add the new worker to the configuration file and remove some old ones...
20:51 CIA-62 cdk: thomaskuhn * r14337 /cdk-taverna/trunk/src/test/java/org/o​penscience/cdk/applications/art2aClass​ification/TestArt2aClassificator.java: Change the way of creating the fingerprint items for the test classes
20:53 CIA-62 cdk: thomaskuhn * r14338 /cdk-taverna/trunk/src/test/java/org/​openscience/cdk/applications/art2aCla​ssification/TestArt2aCollection.java: Change the way of creating the fingerprint items for the test classes
20:54 CIA-62 cdk: thomaskuhn * r14339 /cdk-taverna/trunk/src/test/java/org/op​enscience/cdk/applications/taverna/qsar​/model/ART2AClassificator/GetSimpleKMea​nsClassificationResultAsCSVTest.java: New Junit test for a new worker
20:55 CIA-62 cdk: thomaskuhn * r14340 /cdk-taverna/trunk/src/test/java/org/​openscience/cdk/applications/taverna/​qsar/model/ART2AClassificator/tools/ (2 files): New Junit test for a new worker
20:56 CIA-62 cdk: thomaskuhn * r14341 /cdk-taverna/trunk/src/test/java/org/ope​nscience/cdk/applications/taverna/tools/ (3 files): New Junit test for a new worker
20:57 CIA-62 cdk: thomaskuhn * r14342 /cdk-taverna/trunk/src/test/java/org/opensci​ence/cdk/applications/taverna/tools/ScaleFin​gerprintItemArrayBetweenZeroAndOneTest.java: New Junit test for a new worker
20:58 CIA-62 cdk: thomaskuhn * r14343 /cdk-taverna/trunk/pom.xml: Add some new dependencies
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21:57 CIA-62 cdk: thomaskuhn * r14344 /cdk-taverna/trunk/src/main/java/org/o​penscience/cdk/applications/taverna/ba​sicutilities/MDLRXNV2000Reader.java: Remove unused class
22:03 CIA-62 cdk: thomaskuhn * r14345 /cdk-taverna/trunk/src/test/java/org/​openscience/cdk/applications/taverna/ (13 files in 2 dirs):
22:03 CIA-62 cdk: Change of the database test connection handling. Adding missing test classes for
22:03 CIA-62 cdk: some of the database worker! Important everyone how want to test the postgres
22:03 CIA-62 cdk: database features have to add the password for their database user within the
22:03 CIA-62 cdk: CDKTavernaTestData class
22:03 CIA-62 cdk: thomaskuhn * r14346 /cdk-taverna/trunk/src/test/java/org/openscie​nce/cdk/applications/taverna/qsar/model/weka/ (EMClusterWorkerTest.java SimpleKMeansWorkerTest.java): Change of the database test connection handling. Important everyone how want to test the postgres database features have to add the password for their database user within the CDKTavernaTestData class
22:04 CIA-62 cdk: thomaskuhn * r14347 /cdk-taverna/trunk/src/test/java/or​g/openscience/cdk/applications/tave​rna/renderers/PdfCreationTest.java: Change of the database test connection handling. Important everyone how want to test the postgres database features have to add the password for their database user within the CDKTavernaTestData class
22:06 CIA-62 cdk: thomaskuhn * r14348 /cdk-taverna/trunk/src/test/java/org/ope​nscience/cdk/applications/taverna/tools/​GetMolecularWeightDistributionTest.java:
22:06 CIA-62 cdk: Change of the database test connection handling. Adding missing test classes for
22:06 CIA-62 cdk: some of the database worker! Important everyone how want to test the postgres
22:06 CIA-62 cdk: database features have to add the password for their database user within the
22:06 CIA-62 cdk: CDKTavernaTestData class
22:20 CIA-62 cdk: thomaskuhn * r14349 /cdk-taverna/trunk/src/ (3 files in 2 dirs): Add an ART2A algorithm which uses Floats instead of Doubles to reduce the memory consumption
22:21 CIA-62 cdk: thomaskuhn * r14350 /cdk-taverna/trunk/src/main/java/org/​openscience/cdk/applications/art2aCla​ssification/FingerprintUtility.java: Add a utility class for the handling of fingerprint items
22:26 CIA-62 cdk: thomaskuhn * r14351 /cdk-taverna/trunk/src/test/java/or​g/openscience/cdk/applications/tave​rna/renderers/PdfCreationTest.java: Change the id of molecules to be loaded from the database
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