Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-08-12

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

All times shown according to UTC.

Time Nick Message
04:43 thomas_ku joined #bioclipse
06:11 Gpox_ joined #bioclipse
06:17 Gpox joined #bioclipse
06:20 olas joined #bioclipse
06:20 olas hi
06:20 zarah hi olas
07:45 jonalv joined #bioclipse
07:45 jonalv moin
07:45 zarah hi jonalv
07:45 olas hi jonalv
08:03 gilleain joined #bioclipse
08:04 jonalv joined #bioclipse
08:30 shk3 joined #bioclipse
08:35 ilogger2_ joined #bioclipse
08:39 shk3 hi all
08:39 zarah hi shk3
08:40 shk3 i still can't write a test for saveMolecule since I can't create an IFile in a test.
08:40 shk3 anybody an idea?
08:41 olas jonalv wrote a MockedFile
08:41 olas jonalv: ping
08:41 jonalv olas: pong
08:42 olas can you help shk3?
08:42 olas mockFile?
08:42 jonalv oh yea sry
08:42 jonalv backtracking
08:42 * jonalv is starting up eclipse, hang on
08:43 jonalv I only mocked the read functionality though...
08:44 jonalv but it's probably totally possible to mock the write functionality
08:44 shk3 hm
08:44 shk3 which plugin/package?
08:46 jonalv net.bioclipse.cdk.business.test
08:46 jonalv in net.biclipse.cdk.MockIFile
08:48 shk3 ah, for me to have setcontents would be enough
08:48 shk3 shouldn't be a problem to do that, should it?
08:49 jonalv nope
08:49 jonalv try it at least :(
08:49 jonalv gah
08:49 jonalv I have been on swedish keyboard all weekend :)
08:49 gilleain sounds uncomfortable.
09:01 maclean joined #bioclipse
09:01 maclean weird
09:02 olas what's weird?
09:03 maclean I don't understand irc, that's what's weird. oh well.
09:03 olas who does :-)
09:10 gilleain joined #bioclipse
09:27 EskilA joined #bioclipse
09:55 CIA-49 bioclipse: shk3 * r6559 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.business.test/src/net/bioclipse/cdk/ (MockIFile.java business/test/CDKManagerTest.java): added a test for saveMolecule
10:01 shk3 shall I implement the save as for jcp?
10:01 shk3 or wait till the new jcp is ready?
10:04 * jonalv -> lunch
10:05 gilleain riiiiight. pdb files need an "END" record. aha...
10:12 malick joined #bioclipse
10:14 olas shk3: please do it now
10:14 olas we need it for new JCP as well
10:14 shk3 ok
10:14 olas will just transfer that code to new JCP
10:14 shk3 how is jcp doing?
10:14 shk3 when do you think is it ready?
10:37 maclean joined #bioclipse
10:39 gilleain joined #bioclipse
10:42 CIA-49 bioclipse: shk3 * r6560 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: there were things in which were not needed
10:42 shk3 hm, I need to use net.bc.cdk.business in net.bc.cdk10.jcp
10:43 shk3 i added the dependeny
10:43 shk3 is this ok?
10:43 shk3 I get
10:43 shk3 java.lang.LinkageError: loader constraint violation: when resolving interface method "net.bioclipse.cdk.business.ICDKManager.save(Lor​g/openscience/cdk/interfaces/IChemModel;Lorg/ecl​ipse/core/resources/IFile;Ljava/lang/String;)V" the class loader (instance of org/eclipse/osgi/internal/bas​eadaptor/DefaultClassLoader) of the current class, net/bioclipse/cdk10/jchempaint​/ui/editor/AbstractJCPEditor, and the class loader (instance of
10:43 shk3 org/eclipse/osgi/internal/bas​eadaptor/DefaultClassLoader) for resolved class, net/bioclipse/cdk/business/ICDKManager, have different Class objects for the type org/openscience/cdk/interfaces/IChemModel used in the signature
10:47 shk3 this is cdk vs. cdk10, I think
10:47 shk3 what do you think?
10:49 shk3 jonalv?
11:04 shk3 joined #bioclipse
11:07 olas shk3: adding that dep is NOT ok
11:08 olas we have things split between plugins for a reason
11:08 olas please duplicate code instead
11:12 shk3 hm, code duplication is also not good.
11:12 shk3 and there is no business in cdk10
11:12 shk3 but anyway
11:12 shk3 will do it
11:13 olas if you have alternative way then please enlighten us
11:13 olas cdk10 should ge anyway
11:13 olas go
11:14 shk3 no alternative
11:14 shk3 what do you think is the timescale for jcp in trunk?
11:14 ilogger2 joined #bioclipse
11:15 olas what do you mean?
11:15 olas cdk trunk?
11:15 CIA-49 bioclipse: ospjuth * r6561 /bioclipse2/trunk/plugins/ (net.bioclipse.qsar/ net.bioclipse.qsar.ui/):
11:16 shk3 the new jcp
11:16 shk3 what's your guess for when it will be ready?
11:16 shk3 and cdk10 removed
11:16 olas no idea
11:16 shk3 fair enough
11:16 olas this fall is my guess/hope
11:16 shk3 me neither
11:16 shk3 would be great
11:16 olas Gpox: do you have a better guess?
11:17 olas when Egon starts here and can work with Gpox, I think it will boost the development
11:18 shk3 definitly
11:23 CIA-49 bioclipse: ospjuth * r6562 /bioclipse2/trunk/plugins/net.bioclipse.qsar.ui/ (37 files in 12 dirs): Updated package names + ID to qsar.ui.
11:24 CIA-49 bioclipse: ospjuth * r6563 /bioclipse2/trunk/plugins/net.bioclipse.qsar/: Initial import.
11:26 CIA-49 bioclipse: ospjuth * r6564 /bioclipse2/trunk/plugins/net.bioclipse.qsar/ (61 files in 13 dirs): Added XML Schema, EMF model and generated code for QSAR in Bioclipse.
11:27 CIA-49 bioclipse: ospjuth * r6565 /bioclipse2/trunk/plugins/​net.bioclipse.qsar.edit/: Initial import.
11:30 CIA-49 bioclipse: ospjuth * r6566 /bioclipse2/trunk/plugins/net.bioclipse.qsar.edit/ (44 files in 12 dirs): Added plugin to hold generated edit code for the QSAR EMF model. Also has some test classes.
11:51 edrin joined #bioclipse
11:51 olas hi edrin
11:51 edrin hi olas
11:52 edrin olas: did you maintain to run a jabber server?
11:53 olas mom
11:53 olas telephone
11:55 edrin ok
12:07 olas edrin: sorry, have not tried it yet
12:07 olas will go to uppsala tomorrow
12:07 edrin ok
12:07 olas I need accounts for the BMC comp dept
12:08 olas and besides, I'm sort of waiting for the next part in the tutorial opn the wiki ;-)
12:08 * olas will be away for 30 mins
12:08 olas ttl
12:22 maclean joined #bioclipse
14:05 maclean joined #bioclipse
14:27 CIA-49 bioclipse: ospjuth * r6567 /bioclipse2/trunk/features/net​.bioclipse.molfilter_feature/: Initial import.
14:27 olas SF is not fast today...
14:27 CIA-49 bioclipse: ospjuth * r6568 /bioclipse2/trunk/features/net​.bioclipse.molfilter_feature/ (.project build.properties feature.xml): Added molfilter feature standard setup.
14:28 CIA-49 bioclipse: ospjuth * r6570 /bioclipse2/trunk/features/​net.bioclipse.qsar_feature/ (.project build.properties feature.xml): Added qsar feature standard setup.
14:29 CIA-49 bioclipse: ospjuth * r6569 /bioclipse2/trunk/features/n​et.bioclipse.qsar_feature/: Initial import.
14:39 CIA-49 bioclipse: ospjuth * r6571 /bioclipse2/trunk/features/net.bi​oclipse.qsar_feature/feature.xml: Updated deps in feature.
14:40 CIA-49 bioclipse: ospjuth * r6572 /bioclipse2/trunk/plugins/net.bioclipse.qsar.ui/ (5 files in 4 dirs): Replaced hardcoded qsar.xml with a generated based on EMF model.
16:27 CIA-49 bioclipse: ospjuth * r6573 /bioclipse2/trunk/plugins/net.bioclipse.qsar.ui/ (29 files in 3 dirs): The first steps to making QSAREditor use EMF model. Molecules can now be added and writes XML on doSave().
17:06 olas bye for today
17:06 olas left #bioclipse
17:51 egonw joined #bioclipse
17:52 egonw @tell olas a paper on BioJava has appeared: http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed​&Cmd=ShowDetailView&TermToSearch=18689808
17:52 zarah egonw's link is also http://tinyurl.com/6bfw9t
17:52 zarah Consider it noted.
18:55 edrin joined #bioclipse
18:58 edrin hi egonw
20:35 edrin joined #bioclipse

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