Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-02-06

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

All times shown according to UTC.

Time Nick Message
00:30 ilogger2 joined #bioclipse
00:50 stain joined #bioclipse
02:54 stain joined #bioclipse
08:04 Gpox joined #bioclipse
08:06 edrin joined #bioclipse
08:26 egonw joined #bioclipse
08:56 olass joined #bioclipse
08:56 olass hi
08:57 zarah privet olass
08:57 zarah olass: You have new messages. Write '/msg zarah @messages' to read them.
08:57 olass @msg
08:57 zarah olass: 13 h 59 m 12 s ago, edrin said pls try webservices plugin/manager again, this works for me
09:27 CIA-55 bioclipse: ospjuth * r8627 /bioclipse2/trunk/plugins/net.bioclipse.data/ (data/SMILES/ data/SMILES/sample30.smi plugin.xml): Added a sample SMILES file to sample data.
09:28 jonalv joined #bioclipse
09:28 jonalv oh hai
09:28 zarah hello jonalv, you fantastic person you
09:31 edrin joined #bioclipse
09:31 shk3 joined #bioclipse
09:31 edrin hi
09:31 zarah hi edrin
09:31 olass hi edrin
09:31 olass edrin: testing ws plugin now
09:31 edrin ok
09:31 * jonalv afk
09:32 edrin ve really no clue why it is/was not working
09:32 olass me neither
09:33 edrin try webservices.downloadPdb("1JR8")
09:34 shk3 welcome to another day of extreme weather
09:34 egonw ah, another 2 cm of snow?
09:35 egonw edrin, olass: #xmpp
09:35 egonw please
09:36 shk3 "we are experiencing heavy snow fall"
09:36 egonw so, another afternoon off then?
09:37 masak joined #bioclipse
09:38 shk3 we will see
09:39 * egonw is working on CDK 1.1.5 (RC for 1.2.0), and will update Bioclipse then...
09:39 egonw 1.1.5 just needs one bug fix
09:39 egonw Gpox: ping
09:39 Gpox egonw: pong
09:40 egonw Gpox: gilleain had another batch of patches to jcp-prim
09:40 egonw shall I make another export?
09:40 egonw that is...
09:40 egonw can you cover possible compile problems on the BC2 side?
09:41 Gpox sure
09:44 egonw good
09:51 olass edrin: ok, tested webservices plugin
09:52 olass works
09:52 olass but fails if virtual project is closed
09:52 olass just needed to open that
09:52 olass should be done automatically IMO
09:52 olass will file a bug
10:03 olass edrin: around?
10:03 olass Is there no testing plugin net.bc.webservices.tests?
10:03 olass @tell edrin: Is there no testing plugin net.bc.webservices.tests?
10:04 zarah Consider it noted.
10:06 Gpox joined #bioclipse
10:07 olass @tell edrin Does the source of src-axis1 need be included in the build.props? Is not the compiled enough?
10:07 zarah Consider it noted.
10:08 olass @tell edrin: Could we also bundle Axis2 deps with webservices plugin?
10:08 zarah Consider it noted.
10:08 olass Gpox: If one accidentally(?) has closed the /Virtual project, it makes some things fail
10:09 olass do you think this is good or should it automatically open Virtual folder?
10:09 edrin olass: no, there is no testing plugin
10:09 zarah edrin: You have new messages. Write '/msg zarah @messages' to read them.
10:09 olass edrin: ok
10:09 olass will add one then
10:09 edrin @msg
10:09 zarah edrin: 5 m 36 s ago, olass said Is there no testing plugin net.bc.webservices.tests?
10:09 zarah edrin: 2 m 29 s ago, olass said Does the source of src-axis1 need be included in the build.props? Is not the compiled enough?
10:09 zarah edrin: 1 m 36 s ago, olass said Could we also bundle Axis2 deps with webservices plugin?
10:09 egonw I would say /Virtual must not be closable...
10:09 olass Gpox: is that possible?
10:10 olass ok, I will file a bug
10:10 edrin olass: i think compiled is enough... i even think the src-axis1 stuff isn't currently used
10:10 edrin olass: i think axis2 is not compatible with axis1
10:10 olass ok, then we should have two plugins
10:10 olass let's worry about that later hen
10:11 edrin ok
10:11 olass will you test remove src-axis1?
10:12 edrin maybe, have to check if it is really not required first
10:15 olass edrin: I will edit webservices now and add a test plugin
10:16 egonw olass: do we have two free ports for components for ws1?
10:16 edrin olass: ok
10:16 egonw for, say, qsar.ws1.bmc.uu.se and rdf.ws1.bmc.uu.se ?
10:16 edrin :)
10:17 * egonw is building up a nasty headache :(
10:17 egonw too much coffee I guess
10:51 egonw is it possible to move commits from a local branch to another branch, and delete them from the first?
10:51 egonw in git?
10:53 olass egonw: git can do anything, right?
10:53 olass :-)
10:53 egonw yeah, it's really just a matter of *how* to do it ... :)
10:53 egonw I actually think 'git switch'...
10:53 egonw but not sure
10:53 masak olass: I know you're joking, but git actually can do anything. I read a web page about it yesterday.
10:54 olass can git write my dissertation? Now that's a syntax I'd like to learn...
10:54 masak git dissert ...
10:55 olass not to be consfused with git dessert...
10:55 masak it's a little bit different from other SCMs, but once you learn the underlying model, it's really handy.
10:55 olass I guess so...
10:56 * olass needs food, water, and coffee
10:56 egonw coffee-fee?
11:12 egonw olass: ping
11:12 egonw olass: going to update CDK twice...
11:12 olass egonw: pong
11:12 olass sure
11:12 egonw once now, and once later today or tomorrow
11:12 olass ok, good to know
11:12 egonw will send email when second updated happened
11:13 olass yes
11:13 egonw ok
11:14 edrin Hi Johannes,
11:14 edrin Sure, you may use the icons :)
11:14 edrin Enviado desde mi iPhone
11:15 edrin hola!
11:17 egonw excellent :)
11:17 egonw edrin++
11:20 edrin Enviado desde mi iPhone <- does this mean he mailed with his iphone?
11:20 masak edrin: 'from', I think.
11:21 masak it's an automatic footer that iPhones add to emails.
11:27 egonw OK, will have to go offline for a while to get focused on some BC2 work...
11:27 egonw ping me if urgent
11:35 maclean joined #bioclipse
11:35 maclean
11:37 masak møøse
11:42 maclean :)
11:43 masak sauna &
11:46 Gpox joined #bioclipse
11:50 egonw http://github.com/KentBeck/junit/tree/master
11:50 zarah egonw's link is also http://tinyurl.com/cbq6vu
11:52 masak Kent Beck meets github. cool!
11:52 egonw who is Kent Beck?
11:53 masak he's the guy who more or less invented the term 'Refactoring'.
11:53 egonw ic
11:53 maclean huh
11:53 masak http://en.wikipedia.org/wiki/Kent_Beck
11:53 zarah masak's link is also http://tinyurl.com/bolgcx
11:54 maclean I like refactoring :)
11:54 masak sorry, was thinking about Martin Fowler.
11:54 masak Kent Beck is this Smalltalk/XP guy.
11:55 maclean oh, noes. I /don't/ like X-treme programming
11:55 masak maclean: I don't like any kind of dogma.
11:55 maclean indeed
12:04 shk3 olass: I had a look at this update problem
12:04 olass yes?
12:04 olass any clues?
12:04 shk3 for me, it looks like no auto update is run
12:04 shk3 no
12:04 olass ok
12:05 olass it is for me too
12:05 shk3 but i find no trace of -noupdate or so
12:05 olass but both egonw and jonalv did experience -noUpdate
12:05 olass strange
12:05 egonw shk3: can you do me a favor and do a review of a patch?
12:05 shk3 sure
12:05 egonw https://sourceforge.net/tracker2/?func=detail&am​p;aid=2405759&amp;group_id=20024&amp;atid=320024
12:06 egonw http://github.com/egonw/cdk/commits/newJNIInChI
12:06 zarah egonw's link is also http://tinyurl.com/bjnvr5
12:07 shk3 patch is for 1.2 branch?
12:07 egonw yes
12:07 egonw rajarshi already reviewed it
12:08 egonw but for 1.2 I need another reviewer
12:11 shk3 the code looks good
12:11 egonw OK, please add comment on SF
12:11 shk3 can't say if the 64 bit stuff works
12:12 egonw someone tested 64bit
12:12 egonw one is working, other not... IIRC
12:12 egonw I think I relayed the message to Sam
12:12 maclean me, iirc
12:12 egonw maclean: :)
12:13 maclean although it's a little confusing as to what 64 bit actually means on these macbooks
12:18 shk3 I would do a new jcp development release later today
12:18 shk3 any objections?
12:19 maclean shk3 : do those files with v-large coordinates work? Sepcifically, the wedge bonds?
12:19 maclean ^specifically
12:19 shk3 did you work on that?
12:20 maclean well, the changes that I made last night should fix scaling for arbitrary coordinate spaces
12:21 maclean for double bonds, and highlights, I just haven't tested for wedges...
12:21 shk3 wedges still look the same
12:21 egonw shk3: no, sounds excellent...
12:21 maclean oh :(
12:21 egonw please make a tag
12:21 shk3 i did an update
12:21 shk3 right now
12:21 shk3 so I should have the latest code
12:22 maclean but double bonds work now, right? with bigmol?
12:22 shk3 yes
12:22 shk3 mom
12:22 shk3 did not use bigmol
12:23 shk3 yes
12:23 shk3 work there as well
12:24 maclean ok. what was the test file you used for large coordinates? you showed me yesterday, but I don't remember its name
12:25 shk3 it's attached to the bug re: zoom
12:25 maclean ahhh. ta.
12:26 shk3 what do you think about my suggestion re: undo/redo
12:26 shk3 I would like to implement that
12:27 maclean what do I think? mom
12:28 maclean remind me :  did you write this down somewhere?
12:28 maclean https://sourceforge.net/tracker2/in​dex.php?func=detail&amp;aid=2412232​&amp;group_id=20024&amp;atid=120024
12:28 shk3 see my email from 2009-01-14 14:52
12:29 shk3 it's not in the bug report, should go there
12:29 shk3 but I would like to hear opinions on my suggestion
12:30 * shk3 is for lunch
12:32 egonw shk3: here at uppsala we're kind of busy banging out bugs in the BC2 beta code...
12:32 egonw shk3: undo/redo will come after BC 2.0... so, we will get back on this...
12:32 egonw just not right now, sorry about that
12:39 Gpox joined #bioclipse
13:04 masak it's very peaceful here at the office today.
13:06 maclean I'm sure it is at my office too. It's very peaceful here at hom
13:07 maclean ..e
13:08 shk3 just that fiona girl is running around all the time
13:08 shk3 Is it ok if I the "do missing unit test for getNoMolecules(String path)" bug?
13:09 maclean she does dash in and out.
13:10 maclean I guess that people that go to meetings do that
13:10 maclean :)
13:10 maclean shk3 : highlighting should now work properly in that chebitest molecule (and all molecules, for that matter)
13:11 shk3 going to test it
13:12 shk3 yes, it does
13:12 shk3 great
13:12 shk3 getting there
13:14 shk3 with jcp
13:14 shk3 I would like to get feedback from the selections about the selection made
13:14 shk3 for updating statusbar
13:14 shk3 I would think a listener would be the right thing
13:14 shk3 what do you think?
13:15 egonw hook in with the controller hub feedback loop
13:15 shk3 controller hub feedback loop?
13:15 shk3 what's that?
13:16 maclean hmmm
13:16 egonw those three methods to get informed how things changed
13:16 maclean number of atoms in the selection?
13:17 egonw it does not have a selectionChanged method yet....
13:17 egonw arg....
13:17 egonw thread overload...
13:17 * egonw 's brain is core dumping
13:17 egonw no free threads left
13:18 maclean egonw.reboot()
13:18 shk3 ah, ok
13:18 shk3 there is structureChanged
13:18 shk3 structurePropertiesChanged
13:18 shk3 and coordinatesChanged
13:19 shk3 so you think there should be selectionChanged as well
13:19 shk3 ?
13:19 maclean could be
13:19 egonw yes, think so
13:19 maclean er...I see a selectionChanged method
13:20 maclean in IChemModelEventRelay
13:20 egonw ah, so we already do have that...
13:20 egonw good
13:20 shk3 ah
13:20 maclean nice time travel patching, there :)
13:20 egonw huh?
13:21 maclean never mind
13:21 shk3 but it's not used in the controllerhub
13:21 shk3 it seems
13:22 maclean well, no, the hub doesn't handle selections
13:22 shk3 no, but
13:22 shk3 it holds an instance of IChemModelEventRelay
13:22 shk3 Handler
13:23 maclean ohh an ICHERH...
13:23 shk3 shall I register the Ichemmodeleventreleayhandler directly on the selection object=
13:23 shk3 ?
13:23 maclean how would that work?
13:24 maclean hmmm
13:24 shk3 well, ISelection gets a setICHERH method
13:24 shk3 and the respective implementation calls selectionchanged
13:24 shk3 if necessary
13:25 shk3 and the jcppanel
13:25 shk3 or whichever component
13:25 shk3 would register an ICHERH
13:25 shk3 and propagate to status bar
13:25 shk3 isn't that the way to do it?
13:26 maclean okay I suppose
13:26 olass shk3: please do the getNoMols bug!
13:26 egonw sorry... I can't think about it now...
13:26 shk3 I will do it
13:26 shk3 never mind
13:26 maclean yeah, this selection stuff can be done later, I think it needs more extensive planning
13:26 shk3 and do a release later
13:27 shk3 today anyway
13:27 shk3 olass: ok, assigned to me
13:27 olass grea
13:27 olass t
14:19 shk3 peacefull office is gone. drilling started again.
14:19 egonw they are drilling away the snow?
14:25 olass it is a central thing at EBI, drilling down into data
14:28 maclean olass++
14:28 olass :-)
14:31 CIA-55 bioclipse: egonw * r8628 /bioclipse2/trunk/cdk-externals​/trunk/org.openscience.cdk.io/ (3 files in 3 dirs): Updated to SVN version 14071
14:33 CIA-55 bioclipse: egonw * r8629 /bioclipse2/trunk/cdk-externals/t​runk/org.openscience.cdk.io/src/ (102 files in 3 dirs): Removed classes now on ioformats
14:33 CIA-55 bioclipse: egonw * r8630 /bioclipse2/trunk/plugins/ (3 files in 3 dirs): Added missing dependencies
14:35 CIA-55 bioclipse: egonw * r8631 /bioclipse2/trunk/cdk-externals/trunk/ (11 files in 5 dirs): Updated from jchempaint-primary (commit 14076)
14:39 maclean yay!
14:39 egonw more commits pending...
14:41 maclean oh
14:41 maclean probably shouldn't have started a whole-workspace update then...
14:45 CIA-55 bioclipse: egonw * r8632 /bioclipse2/trunk/cdk-externals/trunk/ (79 files in 68 dirs): Updated to CDK 1.1.4.20090206, commit 14071
14:50 egonw still not done
14:51 CIA-55 bioclipse: egonw * r8633 /bioclipse2/trunk/cdk-externals/trunk/ (35 files in 26 dirs): Updated to CDK 1.1.4.20090206, commit 14091
14:51 CIA-55 bioclipse: egonw * r8634 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Added missing dependency on cdk.ioformats
14:52 egonw one left
14:52 CIA-55 bioclipse: egonw * r8635 /bioclipse2/trunk/plugins/net.bioclipse​.structuredb/src/net/bioclipse/structur​edb/business/IStructuredbManager.java: Removed unused import
14:52 shk3 found a problem in the code while writing test
14:52 egonw ah, good
14:53 egonw that's why we write tests :)
14:53 shk3 egonw, do you have a second to discuss it
14:53 egonw yes
14:53 shk3 or shall we wait?
14:53 shk3 ok
14:53 shk3 the problem is this:
14:53 egonw no, two threads sort of finished now
14:53 egonw so, two new threads can be started :)
14:53 egonw pick one
14:53 shk3 the readerfactory throws in exception if it's called on a smi file
14:53 shk3 the CDKManager has code for checking if it's smiles
14:53 egonw yes, SMILES files are not recognized in the RF
14:53 shk3 which is after reader creation
14:54 shk3 and well never be used therefore
14:54 shk3 so what to do?
14:54 shk3 change reader factory
14:54 shk3 or cdk manager?
14:54 egonw smiles files are to difficult to detect
14:54 shk3 cdkmanager expect readerfactory to return null
14:54 egonw easily mistaken for other formats
14:54 shk3 not throw an exception for smiles
14:54 shk3 yes
14:54 egonw what is the stacktrace?
14:55 shk3 there is none
14:55 shk3 readerfactory 263 throws the exception
14:55 shk3 because in readerfactory 259 npe
14:55 egonw ok, can you write a unit test for that for the 1.2.x branch?
14:55 egonw to reproduce that exception
14:55 egonw will fix it then
14:56 shk3 ok, so the readerfactory needs changing?
14:56 egonw BC2 should probably use .smi extension
14:56 egonw well..
14:56 egonw it should not throw an exception
14:56 shk3 ok
14:56 egonw just return null if it cannot find a matching format
14:56 * maclean just clicked on a link to a java file from svn console in eclipse, and it helpfully opened in XCode. duhhh.
14:56 shk3 then i will commit my failing test for cdkmanager
14:56 shk3 and make a test for cdk
14:56 egonw ok, thanx
14:59 CIA-55 bioclipse: shk3 * r8636 /bioclipse2/trunk/plugins/net.bioc​lipse.cdk.business/src/net/bioclip​se/cdk/business/ICDKManager.java: added test for nomolecules (bug #88)
14:59 zarah bug #088 | http://tinyurl.com/6rapvc
14:59 CIA-55 bioclipse: shk3 * r8637 /bioclipse2/trunk/plugins/net.bioclipse.​cdk.business.test/src/net/bioclipse/cdk/​business/test/CDKManagerPluginTest.java: added test for nomolecules (bug #88) - fails due to cdk having problems with smiles
14:59 zarah bug #088 | http://tinyurl.com/6rapvc
15:09 maclean "Unable to create editor ID net.bioclipse.cdk.ui.editors.jchempaint: The editor class could not be instantiated. This usually indicates a missing no-arg constructor or that the editor's class name was mistyped in plugin.xml."
15:10 maclean !!!
15:12 maclean "The activator net.bioclipse.cdk.business.Activator for bundle net.bioclipse.cdk.business is invalid"
15:16 Gpox I get this error too. I believe it is caused by a NPE at net.bioclipse.cdk.business.CDKManagerHelper.​registerAllFormats(CDKManagerHelper.java:65)
15:16 maclean hmm, okay, takk
15:16 egonw mmm... did not have compile errors here...
15:16 egonw what's the error for that line?
15:17 Gpox io-formats.set have moved from org.os.cdk.io to ioformats
15:17 maclean It's not a compile error, for me - but the jcp editor doesn't work.
15:17 egonw ah, ic
15:17 egonw mom
15:18 Gpox tyring to use org.openscience.cdk.io.Activator.class.​getResourceAsStream("/io-formats.set");
15:18 egonw right
15:18 egonw mom
15:18 egonw fixing that
15:23 egonw OK, needs to make a bugfix in cdk-eclipse for this
15:23 egonw -s
15:27 CIA-55 bioclipse: ospjuth * r8638 /bioclipse2/trunk/features/ (2 files in 2 dirs): Moved webservices plugin from core to chemoinfo feature since now depends on cdk.
15:27 CIA-55 bioclipse: ospjuth * r8639 /bioclipse2/trunk/features/net.b​ioclipse.sampledata/feature.xml: Feature updated for new refactored sample data structure.
15:43 egonw Gpox, maclean: patch on its way now
15:43 egonw sorry for the incovenience
15:44 maclean n/p
15:44 egonw +n
15:44 egonw underlying cause was that upon an patch some weeks ago, the io-formats stuff was moved into a new plugin, but not deleted from the old plugin
15:45 egonw had other stuff related to that to fix earlier today too...
15:45 egonw oversaw this one
15:46 CIA-55 bioclipse: egonw * r8640 /bioclipse2/trunk/cdk-externals/trunk/ (27 files in 27 dirs): Export the pkgs where the Activators are
15:46 CIA-55 bioclipse: egonw * r8641 /bioclipse2/trunk/plugins/n​et.bioclipse.cdk.business/ (2 files in 2 dirs): Uses the correct plugin to get the format specs from
15:50 egonw OK, let's see of all the effort on updating to the latest CDK from SVN actually fixed that BC2 bug
15:52 egonw well... it removed the stack trace...
15:52 egonw but the problem is actually worse...
15:52 egonw Gpox: ping
15:52 Gpox egonw: pong
15:53 egonw can you test the drugbank sd file?
15:53 egonw only the first structure shows up now
15:53 egonw :(
15:53 egonw can you please try too?
15:54 egonw I don't get stack traces
15:55 egonw it seems to count the correct number of entries...
15:55 egonw I suspect another CDK problem...
15:56 egonw Gpox: which manager methods is the SDF editor using?
15:58 egonw OK, who wrote: numberOfEntriesInSDF() ?
15:58 Gpox only createSDFIndex
15:58 egonw shk3: was that the method you just wrote a test for?
15:59 Gpox Loading is done in MoleculeTableVontentProvider​.SDFileMoleculesEditorModel
15:59 shk3 getNoMolecules
15:59 egonw ok
16:00 shk3 numberOfEntriesinSDF is used in there
16:00 maclean where is the bioclipse working directory on osx?
16:00 maclean (if that question makes sense, of course)
16:02 maclean oh, never mind, found something
16:03 egonw maclean: right click on any project -> Properties
16:03 maclean ok
16:04 maclean huh ~/Library/Application Support, eh?
16:06 * egonw sees bad weather for the Tue release...
16:08 maclean yay! now it works again...mysteriously
16:10 egonw @tell masak you already have a bug report about exceptions not mentioned in the JS console, right?
16:10 zarah Consider it noted.
16:20 egonw OK, that drugbank file is not good
16:22 CIA-55 bioclipse: ospjuth * r8642 /bioclipse2/trunk/plugins/net.​bioclipse.webservices.tests/: Initial import.
16:23 CIA-55 bioclipse: goglepox * r8643 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.jchempaint/plugin.xml: Removed visibility for IAtomConteiner for atom menu
16:24 CIA-55 bioclipse: goglepox * r8644 /bioclipse2/trunk/plugins/net.bio​clipse.cdk.jchempaint/plugin.xml: Added 'Add hexagon' command to jcp-popupmenu
16:24 CIA-55 bioclipse: ospjuth * r8645 /bioclipse2/trunk/plugins/net​.bioclipse.webservices.tests/ (14 files in 8 dirs): Added a test plugin for bug #372: webservices plugin. Having problems with commons logging in junit test.
16:24 zarah bug #372 | http://tinyurl.com/c98bn5
16:28 CIA-55 bioclipse: ospjuth * r8646 /bioclipse2/trunk/plugins/​net.bioclipse.webservices/ (10 files in 6 dirs):
16:28 CIA-55 bioclipse: Updated webservices plugin:
16:28 CIA-55 bioclipse: * Renamed package name 'scripts' to 'business'
16:28 CIA-55 bioclipse: * Updated API to not return IFile as we don't pass around those objects currently (we prefer paths as Strings)
16:28 CIA-55 bioclipse: * Added dep to CDK, now returns an ICDKMolecule from downloadPDB(id) and path to file from downloadPDBFile(id, string)
16:28 CIA-55 bioclipse: Needs work on resourcecreator, since should not save in /Virtual by default (scheduled for deprecation)
16:29 egonw olass: #423 was a dup of 410
16:29 olass ok
16:29 olass file that
16:30 egonw did so
16:32 olass :-)
16:33 egonw cheminformatics is so fucked up
16:33 egonw people can't even compose a proper SD file
16:33 egonw DrugBank file is broken
16:33 egonw looked at recent downloads
16:33 egonw same problem :(
16:33 olass legacy formats should be banned
16:34 egonw I suggest we remove DrugBank from the release
16:34 egonw it's rather interesting data, but not worth fixing the broken file
16:34 CIA-55 bioclipse: goglepox * r8647 /bioclipse2/trunk/plugins/net.bioclipse.co​re/src/net/bioclipse/core/Activator.java: Virtual is now open when getVirtualProject is called bug #418
16:34 zarah bug #418 | http://tinyurl.com/c38fkq
16:35 egonw olass: happy with that?
16:35 olass yes
16:35 egonw OK, will go ahead
16:36 egonw olass: what about Jerome's data?
16:37 olass egonw: could you very fast just hack up bug #421?
16:37 egonw is that a plugin?
16:37 olass dunno
16:37 olass 2.1
16:37 egonw yes, will do 421 now
16:37 olass or look in sample data
16:37 olass egonw++
16:37 * olass needs that to test webservices dl of PDBs
16:41 CIA-55 bioclipse: egonw * r8648 /bioclipse2/trunk/features/net.b​ioclipse.sampledata/feature.xml: Removed DrugBank data: SD file is broken, see bug #371
16:41 zarah bug #371 | http://tinyurl.com/anvpk7
16:46 CIA-55 bioclipse: ospjuth * r8649 /bioclipse2/trunk/plugins/net​.bioclipse.webservices.tests/ (3 files in 2 dirs): Converted test to JunitPluginTest since else logging did not work and everything failed.
16:46 CIA-55 bioclipse: ospjuth * r8650 /bioclipse2/trunk/plugins/net.bioclipse​.webservices/src/net/bioclipse/webservi​ces/business/WebservicesManager.java: Placed FIXMEs for bug #372.
16:46 zarah bug #372 | http://tinyurl.com/c98bn5
16:46 olass @tell edrin: bug #372 is now yours again.
16:46 zarah Consider it noted.
16:47 * shk3 is leaving
16:50 shk3 exit
16:57 edrin olass: ok, so nothing todo right now?
16:57 zarah edrin: You have new messages. Write '/msg zarah @messages' to read them.
16:57 edrin @msg
16:57 zarah edrin: 10 m 55 s ago, olass said bug #372 is now yours again.
16:58 edrin olass: for RC, no virtual anymore?
16:59 * egonw is away for dinner
16:59 CIA-55 bioclipse: egonw * r8651 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Added fromString() method (fixes #421)
16:59 zarah bug #421 | http://tinyurl.com/dhf8gf
16:59 egonw olass: back to you
16:59 egonw fromString() implemented
16:59 egonw olass: added unit test with CML
17:00 edrin ok
17:00 egonw not for other formats, but should generally work, as it used format detection
17:00 edrin eh?
17:00 edrin not for me
17:00 egonw that was for olass :)
17:00 edrin egonw: what does RDF mean btw?
17:00 egonw see wikipedia
17:00 egonw bbl
17:00 egonw dinner
17:10 CIA-55 bioclipse: ospjuth * r8652 /bioclipse2/trunk/plugins/net.bioclipse​.webservices/src/net/bioclipse/webservi​ces/business/WebservicesManager.java: Update for bug #372: Now uses new fromString()
17:10 zarah bug #372 | http://tinyurl.com/c98bn5
17:29 CIA-55 bioclipse: goglepox * r8653 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Rescaling fonts works better. (resolves bug #173)
17:29 zarah bug #173 | http://tinyurl.com/5pk76x
18:04 edrin olass: available?
19:17 edrin left #bioclipse
19:54 maclean joined #bioclipse
21:24 edrin joined #bioclipse
22:44 ilogger2 joined #bioclipse
22:44 zarah joined #bioclipse

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