Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-10-23

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All times shown according to UTC.

Time Nick Message
01:52 m4r1in_ joined #bioclipse
05:44 Gpox joined #bioclipse
06:46 thomasku joined #bioclipse
07:11 egonw joined #bioclipse
07:23 CIA-52 bioclipse: shk3 * r7353 /bioclipse2/trunk/plugins/net.bioc​lipse.data.sampledata/plugin.xml: added spectra samples to plugin.xml
07:29 CIA-52 bioclipse: ospjuth * r7354 /bioclipse2/trunk/plugins/ (5 files in 5 dirs): Updated versions to 2.0.0.A20081022
07:30 CIA-52 bioclipse: goglepox * r7355 /bioclipse2/trunk/plugins/net.bioclipse.c​dk.jchempaint/src/net/bioclipse/cdk/jchem​paint/widgets/JChemPaintSWTWidget.java: Check for resize with 0 with or height, fixes scale issue
07:30 CIA-52 bioclipse: ospjuth * r7356 /bioclipse2/trunk/features/net.bioclips​e.chemoinformatics_feature/feature.xml: Removed org.openscience.cdk.jchempaint from cehmoinfo feature.
07:32 CIA-52 bioclipse: jonalv * r7357 /bioclipse2/trunk/plugins/ (9 files in 7 dirs): [structuredb] Started adopting the structuredbManager and it's tests to the new world order although there are still a couple of failing DAO tests (and corresponding internal business tests)
07:34 CIA-52 bioclipse: egonw * r7358 /bioclipse2/trunk/plugins/net.bioclipse.cdk10/ (. src/): Removed the externals
07:40 CIA-52 bioclipse: jonalv * r7368 /bioclipse2/trunk/plugins/ (5 files in 3 dirs): [structuredb] Work on creating annotations
07:48 CIA-52 bioclipse: carl_masak * r7369 /bot/trunk/zarah.pl: [zarah] added sub for testing inter-person messaging
07:48 CIA-52 bioclipse: carl_masak * r7370 /bot/trunk/zarah.pl: [zarah] reverted last commit -- experiment successful
07:49 CIA-52 bioclipse: carl_masak * r7371 /bot/trunk/zarah.pl:
07:49 CIA-52 bioclipse: [zarah]
07:49 CIA-52 bioclipse: * moved join-specific code to irc_join
07:49 CIA-52 bioclipse: * added new logic to op me when I enter channels
07:49 CIA-52 bioclipse: * (unauthorized op requests are simply ignored by ChanServ)
07:49 CIA-52 bioclipse: carl_masak * r7372 /bot/trunk/zarah.pl: [zarah] slight fix
07:49 CIA-52 bioclipse: carl_masak * r7373 /bot/trunk/zarah.pl:
07:49 CIA-52 bioclipse: [zarah] restricted opping to only some channels, since it turned out that
07:49 CIA-52 bioclipse: ChanServ does not ignore op attempts
07:50 CIA-52 bioclipse: carl_masak * r7374 /bot/trunk/zarah.pl: [zarah] now ops people based on "trusts" file
07:50 CIA-52 bioclipse: carl_masak * r7375 /bot/trunk/zarah.pl:
07:50 CIA-52 bioclipse: [zarah] now whispers back to people who wisper to her, a "not yet supported"
07:50 CIA-52 bioclipse: message
07:53 egonw Gpox: CDK is using this to load those owl files (olas incarnation of the problem):
07:53 egonw ins = this.getClass().getClassLoader()​.getResourceAsStream(fileName);
07:53 egonw which should be the right approach, AFAIK
07:55 Gpox yeah it looks right
08:04 Gpox http://www.eclipsezone.com/e​clipse/forums/t101557.rhtml
08:04 zarah Gpox's link is also http://tinyurl.com/6dkpfu
08:07 egonw tack
08:08 egonw not that we could use getEntry() for Jmol or CDK...
08:08 egonw but good reading material :)
08:09 CIA-52 bioclipse: ospjuth * r7376 /bioclipse2/trunk/plugins/net.bioclips​e.cdk.business.test/src/net/bioclipse/​cdk/business/test/CDKManagerTest.java: Added a SybylAtomTypePerceptionFromSMILES() that can be run inside a plugin test.
08:12 shk3 joined #bioclipse
08:13 egonw Gpox: Jmol uses:
08:13 egonw if ((url = this.getClass().getResource(fileName)) == null)
08:14 egonw OSgI problem?
08:15 olass joined #bioclipse
08:18 egonw I think I understand the CDK problem...
08:18 egonw which might actually be different from the Jmol problem...
08:28 jonalv joined #bioclipse
08:28 jonalv hi
08:28 zarah hi jonalv
08:33 edrin joined #bioclipse
08:34 jonalv hi edrin
08:34 edrin hi jonalv
08:37 egonw OK, email for pele should now be online
08:38 jonalv egonw++
08:38 egonw olass++ (for checking out the SMTP relay we could use)
08:38 egonw now, the only things remaining:
08:38 egonw putting the git backup online
08:39 egonw and 2: getting the stats graphics working...
08:39 egonw important when we set up good bug report dependency graphs
08:39 egonw olass: that's actually quite useful.
08:39 egonw olass: you could add a enhancement report: "release A3"
08:40 egonw and mark all bug blocking that release as blocking that "release A3" bug
08:40 egonw which should get you an excellent overview of how far the release is away from now...
08:40 egonw the graphics would be perfect to have then
08:42 * jonalv has a feeling that it was something we hwere to talk about today...
08:42 olass yes
08:43 jonalv olass: when? :)
08:43 olass is masak here?
08:44 olass we said to hold the meeting when masak is here
08:45 jonalv after 3 then...
08:46 jonalv He said that we could talk some without him if we where gonan talk for long... :)
08:47 olass we will talk short
08:47 olass so we wait
08:47 olass after lunch I guess
08:47 olass we really REALLY need to solve the classloading bug
08:47 olass egonw is working on it
08:48 olass bug 27 on pele
08:49 olass jonalv: maybe you can shed a light on the bug and help egonw? After all, you solved the classloading thingy for cml which was similar...
08:49 jonalv olass: is it related to cdk10?
08:49 olass no
08:49 olass cdk
08:49 olass see bug 27
08:50 egonw jonalv: I'd rather you look at the jmol.run("minimize") bug
08:50 egonw which is about class loading too, but seems to be a slightly different flavour
08:50 jonalv egonw: what number is that then?
08:50 egonw 2
08:51 jonalv lol I didn't save the adress to the bugzilla and google hasn't exactly picked it up... :(
08:52 jonalv uhm firefox++
08:52 shk3 hi egonw
08:52 shk3 in the spectrum plugin, instead of having xpp library in it,
08:53 shk3 I made it depend on org.xmlpull.xpp3 plugin
08:53 egonw excellent
08:53 shk3 which comes from cdk externals
08:53 shk3 is that ok?
08:53 egonw yes, perfect actually!
08:53 jonalv egonw: I get: The requested URL /cgi-bin/bugzilla/cgi-bin/bugzilla/show_bug.cgi was not found on this server. when i try to go to bug number 2... :(
08:53 egonw mmm :(
08:54 egonw ok, file a bug report adn state which php you were starting from...
08:54 egonw never mind...
08:54 egonw it's the footer, right?
08:54 jonalv it was the front page actually...
08:54 jonalv (I think)
08:55 jonalv (might have been footer of front page...)
08:56 malick joined #bioclipse
09:00 jonalv egonw: how do I getthe bug?
09:00 jonalv egonw: Do I have to write my complete long e-mail adress to get the bug?
09:03 olass ctrl + space
09:03 * jonalv isn't sure he likes bugzilla any longer...
09:03 olass mylyn has content assist
09:03 olass make a query "All open bugs"
09:03 olass I find that convenient
09:03 olass that'll get you the context too
09:03 jonalv olass: ah okey, won't that be _very many_?
09:04 olass the good thing is: you can have meny queries
09:04 olass and only use this long one when you need it
09:04 olass just don't expand it all other times
09:05 jonalv yea I guess...
09:05 olass hey, it's just a suggestion
09:05 jonalv but the queries can only be sorted alphabetically it seems... :(
09:06 egonw jonalv: should have assigned it to you...
09:06 egonw just like someone just did
09:08 jonalv yea I seized it. You told me to have a look at it... :)
09:13 egonw right
09:14 jonalv egonw: good work adding save to the cdk manager. I have two comments though. 1: On public demand we should try to stay within 80 cols. 2: please add params to publishMethod annotations of methods that takes more than 0 params.
09:15 egonw file bug reports
09:15 egonw really...
09:15 egonw I'll fix it...
09:15 jonalv egonw: Really I will fix it now. just think about it next time... :)
09:15 egonw fi you do not, I'll forget
09:15 egonw ok
09:15 egonw will try to remember
09:15 jonalv I am already fixing it :)
09:22 egonw OK, let's see if I can do without upgrading CDK 1.2.x
09:30 egonw grpmh...
09:39 egonw jonalv: http://gist.github.com/18315
09:41 gilleain joined #bioclipse
09:56 CIA-52 bioclipse: shk3 * r7377 /bioclipse2/trunk/plugins/net.bioclipse.spectrum/ (5 files in 4 dirs): removed xpp library
10:08 CIA-52 bioclipse: egonw * r7378 /bioclipse2/trunk/plugins/net.​bioclipse.jmol/jars/Jmol.jar: CUstom Jmol 11.6.1 jar with extra printStacktrace(System.err)
10:13 jonalv egonw: taht jmol version seems to contain other bugs... :(
10:13 jonalv egonw: jmol wont' start at all now...
10:13 * jonalv off to buy food
10:14 egonw oh...
10:14 egonw let me test
10:19 egonw yes, can verify the problem
10:20 egonw but the class is in the jar!?!?!?
10:42 egonw OK... I now officially RCP classpath issues
10:46 gilleain you now officially what?
10:46 egonw ah... ... hate ...
10:47 gilleain Ah, thought so. I have transferred from hating pack() to hating monitor.done().
10:47 egonw :)
10:52 gilleain ahhh. finally. (or "} finally {" :)
11:00 egonw jonalv: ok, figured out that Jmol problem
11:00 egonw was because I used git :)
11:00 egonw hahaha :(
11:05 jonalv egonw: so it works now?
11:05 egonw when I commited
11:06 egonw well, getting the stacktrace should work then
11:06 jonalv ah, okey well that's soemthing at leat :)
11:17 egonw jonalv: ok, watch the second commit:
11:18 jonalv is the CIA bot away again?
11:22 egonw :)
11:22 egonw it seems so
11:22 egonw ok, get rev7360
11:22 egonw I think that jar does much better
11:23 jonalv uhm what's the difference?
11:23 egonw $Date$ versus
11:23 egonw $Date something here$
11:23 jonalv egonw: that version can't have your fix...
11:23 egonw git did not 'set' $Date$
11:24 egonw why not?
11:24 jonalv egonw: it can?
11:24 egonw well... Jmol works again
11:24 egonw but I don't see the stack trace :(
11:24 jonalv it's from yesterday...
11:24 jonalv you did the fix today...
11:24 egonw sorry
11:24 egonw typo
11:24 egonw 7380
11:25 * jonalv updates again... :)
11:28 jonalv egonw: no, no stacktrace :(
11:35 egonw oh... there are *2* locations where such an exception is thrown :(
11:36 egonw and another one
11:37 egonw ok, one more jar comming...
11:37 egonw hang on
11:45 CIA-52 bioclipse: egonw * r7381 /bioclipse2/trunk/plugins/net.​bioclipse.jmol/jars/Jmol.jar: OK, another custom version: now with printStacktrace() in two more locations, hoping with the one jonalv is looking for
11:47 egonw ha, CIA-52, welcome back
11:54 jonalv yey jonalv is no debugging jmol in Bioclipse! :)
11:54 jonalv |now
11:54 jonalv :)
12:01 egonw jonalv: in getResource
12:02 malic1 joined #bioclipse
12:03 gilleain joined #bioclipse
12:14 egonw guys, when should a 'plugin' have an Activator, and when not?
12:16 egonw that is: should org.openscience.cdk.atomtype have an Activator or not?
12:16 egonw and why?
12:18 jonalv egonw: I have a patch ready for jmol that fixes the trouble now. Thanks Gpox++ who gave me some help... :)
12:18 egonw mom
12:18 jonalv or rather: how do I create a patch? :)
12:24 olass egonw: how's progress?
12:24 olass with the atom typing bug?
12:27 egonw not good
12:27 egonw the unjarring did not help
12:28 egonw I could use help :)
12:28 egonw jonalv: http://oscar-osgi.sourceforge.net/tutorial/
12:28 zarah egonw's link is also http://tinyurl.com/58loxj
12:28 egonw that's the tutorial you meant?
12:29 jonalv egonw: no but that looks intresting too :)
12:37 charlgren joined #bioclipse
12:42 gilleain gahhhhhhhh. why is the org.xmlcml.cml.base.CMLElement not found!?
12:43 olass is n.bc.cml in classpath?
12:44 gilleain just checking. It /used/ to work...
12:44 olass Gpox: you who solve everything, could you not help egonw with the classloading?
12:44 olass we are really stuck without that fix...
12:45 gilleain the plugin dependencies include n.bc.cml
12:47 olass egonw: http://forums.sun.com/thread.jspa?threadID=278932
12:47 zarah olass's link is also http://tinyurl.com/6h4tvm
12:48 olass egonw: http://rememberjava.com/java2ht​ml/2007/02/3/GetResource.shtml
12:48 zarah olass's link is also http://tinyurl.com/55kyth
12:48 olass just pointers...
12:48 gilleain Whenever I have tried to get resources from a jarfile, it's always been a headache.
12:48 olass you probaably already have tried them
12:48 egonw this is the default stuff
12:48 egonw which works outside eclipse
12:48 olass ok
12:49 egonw but not inside
12:49 gilleain (he pointed out helpfully :)
12:49 egonw or not for bioclipse anyway
12:54 Julio joined #bioclipse
12:54 Julio left #bioclipse
12:56 olass egonw: read this? http://www.eclipsezone.com/​eclipse/forums/t114975.html
12:56 zarah olass's link is also http://tinyurl.com/65adud
12:57 egonw olass: that's for loading stuff which is not even in a jar in a plugin
12:57 egonw but on your local HD
13:05 edrin egonw: I just read your last two lines, i have code to load external .jar at runtime... you need it?
13:05 egonw no
13:05 edrin i used it in rhino in bc1 to get external .jar at runtime...
13:27 olass I hear masak
13:28 olass Uppsala developers: let's have a meeting soon
13:28 olass anyone against?
13:29 masak joined #bioclipse
13:31 olass noone objects
13:33 jonalv since this is our last chance to meat all at once in about 1.5 months I really ythink we shouild have the meeting...
13:33 masak aye
14:04 sneumann joined #bioclipse
14:04 sneumann moin!
14:04 zarah hi sneumann
14:05 sneumann When Egon was here, he showed me the bioclipse reaction plugin
14:05 sneumann http://wiki.bioclipse.net/index​.php?title=Reaction_plugin#GOAL
14:05 zarah sneumann's link is also http://tinyurl.com/6r6hab
14:05 sneumann What is the rmr file format here ?
14:05 sneumann When Egonw was here, he showed me the bioclipse reaction plugin
14:06 gilleain I'll just check.
14:06 sneumann thanks.
14:09 gilleain hmmm. I can't find any examples in the source of the reaction plugin.
14:09 sneumann pity
14:09 gilleain I suspect that it is just a cml file
14:09 gilleain but with a different extension
14:10 sneumann rmr = reaction miguel rojas ?!
14:10 gilleain :)
14:11 gilleain Anyway, asking Miguel would seem to be best.
14:12 malic1 :)
14:33 m4r1in_ left #bioclipse
14:35 egonw reaction stuff was bioclipse1
14:35 egonw I don't think Miguel has had time yet to port this to BC2
14:36 egonw but in a meeting now...
14:36 egonw just having a short break
14:39 gilleain joined #bioclipse
14:49 shk3_ joined #bioclipse
14:53 masak egonw: ping
14:53 jonalv egonw: ping
17:06 gilleain left #bioclipse
17:39 egonw joined #bioclipse
17:42 charlgren joined #bioclipse
17:42 egonw moin
17:42 zarah hi egonw
17:46 egonw ok, who killed Pele?!?!
17:47 egonw :(
18:09 olass joined #bioclipse
18:09 olass moin
18:09 zarah hi olass
18:14 egonw ha olass
18:14 olass ha ha
18:14 egonw I'm in for an evening of org.openscience.cdk.* hacking
18:14 olass nice
18:14 egonw is pele working for you?
18:14 olass sorry I can't join you
18:14 egonw I can't access it
18:14 olass think so
18:14 olass hmm
18:14 egonw yeah, see all sorts of bug reports... :(
18:15 olass yup
18:15 olass seems to be working
18:15 egonw mmm...
18:15 egonw I get time outs on the the server
18:15 olass hmm
18:15 olass subimt failed, repository error....
18:16 egonw crap
18:16 olass ah, it's case sensitive in assignee
18:17 olass ok, now it worked
18:17 egonw just deleted my cdk-eclipse check out :(
18:17 olass Carl.Masak it was
18:17 olass not carl.masak@...
18:17 egonw shit
18:17 egonw not good
18:17 egonw lost my fixes for cdk-eclipse :(
18:17 olass NO
18:17 olass but you use git
18:17 olass so all is well
18:17 olass right?
18:19 olass must sign off now, need to prepare dinner. Nora is on her way home.
18:19 olass hope you are able to recover things
18:19 egonw ha, no deleted the whole cdk-eclipse folder
18:19 egonw ok, bye
18:19 olass bye, cu tomorrow
18:45 * edrin goes home
18:45 edrin left #bioclipse
21:39 CIA-52 bioclipse: egonw * r7382 /bioclipse2/trunk/cdk-externals/trunk/ (1620 files in 497 dirs): Using a .jar has classLoad trouble. Let's try src plugins
22:31 CIA-52 bioclipse: egonw * r7383 /bioclipse2/trunk/cdk-externals/trunk/ (107 files in 81 dirs): Added activators
22:31 CIA-52 bioclipse: egonw * r7384 /bioclipse2/trunk/plugins/net.bioclipse.cdk.busine​ss/src/net/bioclipse/cdk/business/CDKManager.java: Now properly loads atom types, I think...
22:36 CIA-52 bioclipse: egonw * r7385 /bioclipse2/trunk/cdk-externals/trunk​/org.openscience.cdk.smarts/src/org/o​penscience/cdk/smiles/smarts/parser/ (7 files): Added missing files
23:15 CIA-52 bioclipse: egonw * r7386 /bioclipse2/trunk/plugins/net.​bioclipse.jmol/jars/Jmol.jar: Jmol jar with UFF.txt fix (closes #33)

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