Camelia, the Perl 6 bug

IRC log for #cdk, 2007-09-25

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All times shown according to UTC.

Time Nick Message
05:42 thomas_ku joined #cdk
05:42 thomas_ku moin
06:56 carsten joined #cdk
07:21 jpansanel moin
07:22 carsten Hello!
07:35 jonalv joined #cdk
07:45 jpansanel joined #cdk
07:45 CIA-31 joined #cdk
07:45 jpansanel joined #cdk
07:52 CIA-13 joined #cdk
07:56 CIA-13 bioclipse: jonalv * r3816 /trunk/playground/plugins/net.biocl​ipse.structuredb/src/net/bioclipse/​structuredb/domain/BaseObject.java: Added timestamps for created and edited
07:58 CIA-13 bioclipse: jonalv * r3817 /trunk/playground/plugins/net.bioclipse.structure​db/src/net/bioclipse/structuredb/persistency/dao/ (6 files): Added structureDao and UserDao
07:58 CIA-13 bioclipse: jonalv * r3818 /trunk/playground/plugins/net.biocl​ipse.structuredb/src/net/bioclipse/​structuredb/persistency/mapping/: removed one file per table mapping
08:00 CIA-13 bioclipse: jonalv * r3819 /trunk/playground/plugins/net.bioc​lipse.structuredb/src/net/bioclips​e/structuredb/persistency/tables/ (BaseObject.sql User.sql): fixed some minor errors in tables
08:00 CIA-13 bioclipse: jonalv * r3820 /trunk/playground/plugins/net.bioclip​se.structuredb/src/log4j.properties: Added log4j.properties file
08:01 CIA-13 bioclipse: jonalv * r3821 /trunk/playground/plugins/net.bioclipse.​structuredb/src/applicationContext.xml: added the new dao beans
08:02 CIA-13 bioclipse: jonalv * r3822 /trunk/playground/plugins/ne​t.bioclipse.structuredb/src/ (sqlMap.xml sqlMapConfig.xml): Changed to on big mapping file
08:02 CIA-13 bioclipse: jonalv * r3823 /trunk/playground/plugins/net.bioclipse​.structuredb/tests/net/bioclipse/struct​uredb/persistency/dao/IGenericDao.java: removed IGenericDao from the tests. It should be in src
08:05 olas joined #cdk
08:26 egonw joined #cdk
08:28 egonw moin
08:28 egonw hi olas
08:28 egonw olas: eclipse 3.2 or 3.3 based export?
08:42 olas 3.3
08:42 egonw cool
08:42 olas Did not have time yesterday
08:42 olas And today will be many meetings
08:42 egonw got that running for about a week now
08:42 egonw olas: ack
08:42 egonw olas: let's come up with a planning then...
08:42 olas ok
08:42 egonw I don't have much time today either...
08:42 olas Unfortunately not many peoiple at complife
08:43 egonw but we need to get going, because not much time left before CompLife...
08:43 egonw indeed :(
08:43 olas You got the mail from Thorsten?
08:43 egonw no
08:43 olas he sent to your old adress
08:43 olas address
08:43 egonw not after his 11 Sept that is...
08:43 egonw OK
08:43 egonw mom
08:43 egonw will check
08:43 * olas is forwarding
08:44 egonw I had a forward on that address to my gmail account
08:44 egonw for about a day...
08:44 egonw but way too much spam on that address...
08:44 olas I see
08:44 egonw even with thoughest spam filter :(
08:44 olas fwd to your gmail done
08:44 egonw OK, I see it
08:44 olas Seems it will be rather informal
08:45 egonw indeed...
08:45 egonw which would not be bad...
08:45 egonw would give us time to do some hacking... :)
08:45 olas right!
08:45 olas so maybe we shouldn't put too much effort in the tutorial
08:45 olas but just demo some simple stuff
08:45 olas and show them the tutorials
08:46 olas But we should probably make a new release, and make sure it works with the tutorials, right?
08:46 olas or should we stick with 1.1.3?
08:47 egonw yes, just do that tutorials we did in Uppsula...
08:47 egonw or subset more likely
08:47 olas so stick with 1.1.3?
08:47 egonw no, 1.1.3 was too much of a disaster...
08:47 olas or new release?
08:47 egonw new release
08:47 olas ok
08:47 egonw bug fix or 1.1.3 I would say
08:47 egonw BTW, saw the SWT JChemPaint widget ?
08:47 olas well, do we really need a new release or just update the plugins on the update site?
08:47 olas no
08:48 olas where?
08:48 olas Your blög?
08:48 egonw bioclipse-commit :)
08:48 olas saw the commit
08:48 egonw it's quite cool actually...
08:48 egonw the JCP renderer has a collapsed mode...
08:49 egonw where atom symbols are not drawn, but small colored boxes instead
08:49 egonw when the widget gets smaller than a certain size, it automatically goes into collapsed mode :)
08:49 olas cool!
08:49 egonw very nice to play with...
08:49 olas can it be put in a table?
08:49 egonw it's a default SWT widget architecture...
08:49 egonw so, yes
08:50 olas Then we can finally create that QSAR table with structure in it!
08:50 olas BTW, how much is missing with QSAR in Bioclipse?
08:50 egonw right, should be trivial now
08:50 olas I mean, descriptor generation/dataset setup?
08:50 egonw stabality
08:50 egonw stability
08:50 olas what is unstable?
08:50 jbrefort joined #cdk
08:51 olas What is missing?
08:51 egonw does not spit warnings for missing 3D coordinates
08:51 egonw that sort of things...
08:51 olas oh, I see
08:51 egonw though it should put NaN in the table...
08:52 olas Would also be great to have a reference plugin that calculates descriptors via a Web service
08:52 egonw yes, it would
08:53 egonw which would just take InChI input
08:53 olas But with some descriptors, it works?
08:53 egonw yes
08:53 egonw there is one more issue
08:53 egonw it does not work nicely with SDFResource yet...
08:54 egonw or with multiple CDKResource
08:56 olas I see
08:57 olas do we calculate descriptors for one molecule at a time?
08:57 egonw so much to do, so little time :(
08:57 olas I know, frustrating
08:57 egonw no, the code supports doing more than one molecule in one go
08:57 olas cool that we have gotten some more people involved here in Uppsala
08:57 olas That helps me a lot!
08:57 egonw OK, let me write up a tutorial now...
08:57 egonw that allows to explore what it does easily...
08:57 olas if code supports multiple molecules, what is the problem?
08:58 olas ok
08:58 egonw stability, I think...
08:58 egonw and IIRC SDF support is missing...
08:58 olas ok
08:58 egonw not difficult to add, of course...
08:58 thomas_ku Has anybody experience with java profiler? Which is the best?
08:58 olas I have no experience
09:00 egonw thomas_ku: I have had good experience with the combination of Eclipse and Netbeans
09:00 olas egonw: I think we should let jonalv try to set up the table with the the structure widget, he is experienced with these things
09:00 egonw thomas_ku: I have written that up somewhere... mom
09:00 egonw olas: masak was going to look at the widget too...
09:01 egonw let them figure it out together :)
09:01 masak joined #cdk
09:19 alexandros_p hello
09:19 egonw hi alexandros_p
09:19 alexandros_p how are you egonw?
09:19 egonw don't ask
09:19 egonw you'll always get the same answer: busy
09:20 alexandros_p :-)
09:20 egonw olas: still here?
09:30 CIA-13 bioclipse: egonw * r3824 /trunk/plugins/net.bioclipse.tutorial.qsar/ (32 files in 18 dirs): Added infrastructure for a QSAR tutorial
09:31 CIA-13 bioclipse: egonw * r3825 /trunk/plugins/net.bioclipse.tutorial.qsar/bin/: Forgot to remove the bin dir upon copy.
09:39 CIA-13 bioclipse: egonw * r3826 /trunk/plugins/net.bioclipse.tutoria​l.qsar/src/net/bioclipse/tutorials/ (2 files in 2 dirs): Removed obsolete classes.
09:39 CIA-13 bioclipse: egonw * r3827 /trunk/plugins/net.bioclipse.tutorial.qsar/src/n​et/bioclipse/tutorials/workshop/QSARPlugin.java: Fixed a trivial compile error: wrong constructor name.
09:54 egonw jpansanel: got a few minutes?
10:12 egonw damn... that's one big commit
10:13 egonw takes ages to commit
10:13 CIA-13 bioclipse: egonw * r3828 /trunk/plugins/net.bioclipse.data.bl​ueobelisk/data/chemical-structures/ (544 files in 31 dirs): Updated to Chemical Structures 2.0.1: fixes CML syntax problems, and I hope they now properly work with the QSAR engine
10:14 egonw *that* will boost my OHLOH statistics :)
10:14 egonw jpansanel: cheers! :)
10:35 jpansanel egonw :
10:35 jpansanel yes ?
10:36 egonw jpansanel: wanted to ask you something, but forgot what...
10:36 egonw jpansanel: anyway... I updated the Bioclipse plugin to 2.0.1 of chemical structures
10:36 jpansanel cool
10:37 jpansanel I'm modeling some new structures
10:37 jpansanel (sugar)
10:39 jpansanel When finished, I'll release
10:51 CIA-13 bioclipse: egonw * r3829 /trunk/plugins/net.bioclipse.statistics/sr​c/net/bioclipse/model/MatrixResource.java: Fixed an ArrayIndexOutOfBoundsException: files may be empty (stupid, but happens). It should create an empty matrix then.
10:55 CIA-13 bioclipse: egonw * r3830 /trunk/plugins/net.bioclipse.descriptor/src/net​/bioclipse/jobs/DescriptorCalculationJob.java: A bit more verbose: output how many resources will be processed.
11:27 CIA-13 bioclipse: egonw * r3831 /trunk/plugins/net.bioclipse.data.bl​ueobelisk/data/chemical-structures/ (17 files in 17 dirs): Removed index files
11:28 egonw cool!
11:28 * egonw just created a 44x26 QSAR descriptor matrix :)
11:30 egonw works like a charm :)
11:31 CIA-13 bioclipse: egonw * r3832 /trunk/plugins/net.bioclipse.​descriptor/src/net/bioclipse/ (2 files in 2 dirs): Fixed taking multiple resources into account
11:31 egonw OK, enough bioclipse for today
11:31 * egonw is back to writing
11:34 olas no noo
11:34 olas egonw: more bioclipse!
11:34 olas :-)
11:34 egonw yeah, yeah...
11:34 egonw hang on,...
11:34 egonw one more commit to come
11:34 egonw and one more bug report :)
11:35 * olas has to go to a meeting as well so will continue updating the "update function" later and/or tomorrow
11:35 egonw olas: before we actually do that...
11:35 egonw we should go through the bug list, and prioritize
11:36 egonw and maybe priority what features should make the main release
11:36 olas yes, but not now
11:36 * olas is off for a meeting
11:36 olas ttl
11:42 CIA-13 bioclipse: egonw * r3833 /trunk/plugins/net.bioclipse.tutorial.qsar/ (4 files in 2 dirs): Completed calculation cheat sheet tutorial
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14:49 CIA-13 bioclipse: jonalv * r3834 /trunk/playground/plugins/​net.bioclipse.structuredb/ (9 files in 4 dirs): Two tests fails. I can't seem to get anything except but null from the database for the moment. The rest of the tests die horrible in errors...
15:33 CIA-13 cdk: egonw * r8959 /trunk/cdk/src/org/openscience/cdk/test/ (3 files in 2 dirs): Moved Test class to test-experimental package: the tested class is experimental, not standard.
15:38 CIA-13 jmol: hansonr * r8316 /trunk/Jmol/src/org/jmol/viewer/ (Compiler.java Jmol.properties): version=11.3.26 bug fix for() as first command in script or line
15:38 CIA-13 cdk: egonw * r8960 /trunk/cdk/src/org/opensci​ence/cdk/math/Primes.java: Updated the JavaDoc for the recently added primes.
15:39 CIA-13 cdk: egonw * r8961 /trunk/cdk/src/org/openscience/​cdk/test/math/PrimesTest.java: Fixed the test for the recently added primes, and split up two situations into separate tests.
16:16 CIA-13 cdk: egonw * r8962 /trunk/cdk/src/org/openscience​/cdk/test/MstandardTests.java: Fixed Nightly compile problem: removed obsolete import.
16:20 CIA-13 bioclipse: jonalv * r3835 /trunk/playground/plugins/​net.bioclipse.structuredb/ (8 files in 3 dirs):
16:20 CIA-13 bioclipse: One dao test passes. It tests that a set of libraries can be persisted. And that
16:20 CIA-13 bioclipse: they all come back from persisting. They don't come back completly for the
16:20 CIA-13 bioclipse: moment. (The creator field among others is null after they have been loaded) but
16:20 CIA-13 bioclipse: the tests only checks that all of them comes back not that the whole of them
16:20 CIA-13 bioclipse: do... :)
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