Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-08-17

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All times shown according to UTC.

Time Nick Message
05:32 egonw joined #bioclipse
07:07 Gpox joined #bioclipse
07:08 egonw hi Gpox
07:08 Gpox hi
07:08 zarah hi Gpox
07:13 CIA-63 bioclipse.sdk: Egon Willighagen master * r55b3f90 / (14 files in 3 dirs): Fixed a number of template problem that I did not notice before; test plugin template should work well now - http://bit.ly/2qhfS8
07:13 CIA-63 bioclipse.sdk: Egon Willighagen master * rd256aba / (3 files in 3 dirs): Release 1.0.3 - http://bit.ly/qHcMB
07:16 egonw grmp...
07:16 egonw more template errors :(
07:17 egonw I think I'll just have to install bioclipse.core in my Bioclipse SDK test run environment...
07:20 * egonw booting his first autogenerated plugin...
07:21 CIA-63 bioclipse.sdk: Egon Willighagen master * r1f37cf7 / (3 files in 2 dirs): Fixed three last template errors. Autogenerated stubs for the business and the test project now compile. - http://bit.ly/K1Rdy
07:23 egonw ha... close to booting successfully
07:23 egonw one more template error
07:27 CIA-63 bioclipse.sdk: Egon Willighagen master * r3d5867a / (2 files in 2 dirs): Fixed the hooks to have Bioclipse pick up the manager: the interfaces and factory are in the .business sub package - http://bit.ly/vlSyg
07:33 mgerlich joined #bioclipse
07:39 olass joined #bioclipse
07:40 olass moin
07:40 zarah oh hai olass
07:40 egonw hi olass
07:40 olass hej hej
07:40 egonw had a good holiday?
07:40 olass yes, very
07:40 olass stayed in country estates in Vä'rmland and played golf
07:47 egonw argh...
07:47 egonw another template problem
07:47 egonw my fault ...
07:47 egonw need coffee
07:48 egonw olass: sounds very nice
07:48 olass indeed
07:49 egonw olass: can I remove the doc.developers from bioclipse.core and add it to bioclipse.sdk ?
07:49 olass sure
07:49 olass sounds good
07:49 egonw ack
08:33 sneumann joined #bioclipse
08:40 CIA-63 bioclipse.sdk: Egon Willighagen master * r846597d / plugins/net.bioclipse.sdk/templates/net.b​ioclipse.foo.business/src/Activator.java : Removed duplicate Manager in imported type - http://bit.ly/18tLjf
08:41 CIA-63 bioclipse.sdk: Egon Willighagen master * r7b86b20 / (3 files in 3 dirs): Release 1.0.4
08:44 masak joined #bioclipse
08:46 jonalv joined #bioclipse
08:47 jonalv o/
08:48 egonw ok, finally
08:48 egonw all: Bioclipse SDK 1.0.4 uploaded
08:48 egonw which finally works properly
08:48 masak \o/
08:48 egonw including unit test suite project
08:53 jonalv \o/
08:56 jonalv egonw: someone has removed throws CDKException from cdk methods but the calls to these methdos are still catching the esceptions. Do you know anything about this?
08:56 CIA-63 bioclipse.core: Egon Willighagen master * r3176d18 / (3 files): Removed obsolete feature - http://bit.ly/sr9tW
08:56 egonw yeah
08:56 egonw jonalv: please let me know where, and I'll fix it
08:56 egonw sorry about that
08:57 jonalv jchempaint and sdfeditor
08:57 * jonalv is at the hospital now. Gonna try and get some order to Brunn...
08:57 egonw jonalv++
08:58 jonalv zarah: seen olass
08:58 zarah olass was last seen 1 h 8 m 59 s ago in #bioclipse saying 'sounds good'
08:58 jonalv where is he now?
08:58 egonw at BMC
08:59 egonw thesis work
09:00 jonalv is he strict do not disturb mode or do you think he can give me some pointers to how he handled Birt?
09:01 masak jonalv: I think he's in some kind of meeting with TheJarl.
09:02 jonalv masak: okey
09:02 jonalv masak: thanks
09:02 masak np.
09:05 shk3 joined #bioclipse
09:07 CIA-63 bioclipse.cheminformatics: Egon Willighagen master * rdc42439 / (3 files in 3 dirs): Removed obseleted catches of CDKException, fixing compile errors introduced in 807524777b83c5e318491cec5bc2e2157787a7bc - http://bit.ly/bJmk5
09:16 CIA-63 bioclipse.sdk: Egon Willighagen master * re054983 / plugins/net.bioclipse.doc.dev​elopers/META-INF/MANIFEST.MF : Removed unneeded requirement - http://bit.ly/C0AfC
09:27 CIA-63 bioclipse.sdk: Egon Willighagen master * ra607f6b / (3 files in 3 dirs): Release 1.0.5: added net.bioclipse.doc.developers - http://bit.ly/G65Tn
09:33 egonw ok, enough SDK work for now
09:33 egonw all: please test it as much as possibly
09:41 CIA-63 bioclipse.core: Egon Willighagen master * rb0ad2ad / features/net.bioclipse.sdk_feature/feature.xml : Removed SDK feature from bioclipse.core; it's now in the bioclipse.sdk repository - http://bit.ly/sKrU1
09:58 olass joined #bioclipse
10:32 sneumann joined #bioclipse
11:00 jonalv olass: Do you have some time the comming days?
11:02 egonw jonalv: did you speak to jpansanel today yet?
11:02 egonw jonalv: he was asking after you
11:02 jonalv egonw: nope I ahve not
11:03 egonw masak: I'm quiting twitter
11:03 egonw masak: as brand
11:03 egonw masak: I'm switching to the Open identi.ca
11:03 egonw right forwarding identi.ca to twitter, but will phase that out...
11:31 jonalv olass: ping
11:34 masak egonw: understood. I'm staying with Twitter -- what matters to me is that they're not a closed garden like Facebook.
11:35 egonw I have not tried, but I should be able to listen with laconi.ca to your twitter tweets too
11:36 egonw laconi.ca being the open source software behind identi.ca
11:45 jonalv egonw: I want to add Brunn to pelezilla. Can you give me ermissions?
11:46 jonalv afk
11:47 egonw done (I hope, please test)
11:52 jonalv egonw: is it wrong to add Brunn to the Bioclispe 2 components?
11:52 egonw dunno
11:52 jonalv egonw: maybe I should add it as a seperate product instead...
11:52 egonw is it Bioclipse2 based?
11:52 egonw it is, irght?
11:52 egonw then I see no problem
11:52 jonalv egonw: yes
11:53 jonalv it's a seperate sourceforge project but
11:53 jonalv it's on github these days so... :)
11:53 jonalv I\ll add it as a Bioclipse 2 component
11:53 egonw yahoo!
11:54 egonw my first Bioclipse SDK created plugins!
11:54 jonalv w00t
12:07 * egonw is happy with the new SDK :)
12:07 egonw (team Uppsala)++
12:09 masak 'o-
12:09 masak um, \o/ # Swedish keyboard layout fail
12:13 egonw we can now expect a tsunami of NWO Bioclipse managers
12:14 jonalv woho :)
12:14 CIA-63 bioclipse.social: Egon Willighagen master * r0819aa8 / (24 files in 9 dirs): Added Bioclipse SDK generated template for a twitter manager (me hides so that olas does not see it) - http://bit.ly/mRJSD
12:16 olass egonw: are tsunamis positive?
12:17 egonw if you need irrigation ?
12:24 CIA-63 bioclipse.social: Egon Willighagen master * rb9c55a4 / (4 files in 2 dirs): Added a prefs page for Twitter account settings - http://bit.ly/129wrG
12:24 CIA-63 bioclipse.social: Egon Willighagen master * r4894149 / .gitignore : Ignore those annoying bin folders... should add that to the SDK templates - http://bit.ly/3gxLOs
12:25 egonw oh wow...
12:25 egonw who has been adding bug reports today ? :)
12:25 egonw we've silently passed the 1500 bug reports
12:25 jonalv that might be me...
12:25 egonw @pz 1500
12:25 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1500
12:26 jonalv I moved brunn ffrom the sourceforee bug system to our bugzilla...
12:26 egonw yes, I figured that
12:26 egonw masak: I guess you will be happy to be able to twitter while testing Bioclipse BioJava scripts ?
12:27 egonw masak: just put at the end of your test script: twitter.setStatus("Yeah, the scripts now works to the last line!")
12:27 jonalv lol
12:27 jonalv egonw++
12:28 masak :)
12:29 egonw olass: though it sort of makes XMPP services report when they are done a bit obsolete
12:29 egonw olass: though it sort of makes XMPP services report via SMS when they are done a bit obsolete
12:30 jonalv egonw: there is more than one way to do it :)
12:33 olass egonw: I don't use twitter, so SMS is still important to me (and 99.9% of the sane world)
12:34 jonalv gah I must set a target milestone for my bugs :(
12:37 egonw so cute how olass always thinks his world is the only world :)
12:38 olass egonw: right..
12:38 jonalv yea but with twitter we have something that masak ueses (who does not use sms)
12:38 masak I still don't see twitter as a "ding! your script is finished" reminder service.
12:38 masak there are better tools for that. email, for example.
12:39 egonw well, it's just testing the SDK
12:53 * egonw thinks he found a bug in the SDK...
12:53 egonw exploring...
13:03 egonw found the culprit
13:05 CIA-63 bioclipse.sdk: Egon Willighagen master * r90feacf / plugins/net.bioclipse.sdk/templates/net.biocl​ipse.foo.business/META-INF/spring/context.xml : Fixed entries for the Java and JavaScript manager interfaces - http://bit.ly/11S5Ls
13:13 CIA-63 bioclipse.ds: Ola Spjuth master * rbce2bd3 / (2 files in 2 dirs): Updated deps and renderers after CDK API renderer changes. - http://bit.ly/hxaxj
13:22 CIA-63 bioclipse.sdk: Egon Willighagen master * rf765255 / (4 files in 3 dirs): Added .gitignore files to automatically ignore the Eclipse autogenerated bin/ folder - http://bit.ly/SXW0O
13:22 CIA-63 bioclipse.sdk: Egon Willighagen master * rc1fc4b5 / features/net.bioclipse.sdk_feature/feature.xml : Fixed update site URL - http://bit.ly/vVfaY
13:22 CIA-63 bioclipse.sdk: Egon Willighagen master * r58cc4b5 / (3 files in 3 dirs):
13:22 CIA-63 bioclipse.sdk: Release 1.0.6.
13:22 CIA-63 bioclipse.sdk: * fixes the Spring context.xml to correctly point to the Java and
13:22 CIA-63 bioclipse.sdk:  JavaScript manager interfaces
13:22 CIA-63 bioclipse.sdk: * adds .gitignore files to ignore autogenerated bin/ folders
13:22 CIA-63 bioclipse.sdk: * Fixed update site URL in feature.xml - http://bit.ly/DrckM
13:49 egonw I'm getting all sorts of weird spring/script errors...
13:50 * jonalv is getting weird Hibernate errors. egonw wanna swap with me? :/
13:50 egonw yeah, I'd just drop hibernate is fast as I could :)
13:51 egonw I know how to solve the hibernate problem all right :)
13:51 masak Hibernate doesn't get any more agreeable by dropping it. :/
13:51 egonw true, but the hibernate problem is fixed nevertheless
13:52 jonalv egonw: you sort of have a bigger problem after that...
13:52 masak "now you have three problems." :)
13:53 egonw IJSJobCreatorAdvice found found...
13:53 egonw not good...
13:55 jonalv egonw: you shouldn't use IJSJobCreatoradvice unless you are dong old world order and I don't think you should do that
13:55 egonw dunno where the exception is coming from...
13:56 masak "Hey mister, we don't think you're supposed to be here..."
13:56 egonw unless you put it it in the SDK templates, it's something else going on...
13:56 * masak 's associating funny today
13:57 jonalv masak: do you rememebr where you heard that: "Hey mister..."
13:57 jonalv ?
13:58 masak jonalv: that last quote is something you sometimes say.
13:58 masak I don't remember if that's the origin of the quote.
13:58 jonalv masak: it's something moose said...
13:58 masak yes.
13:59 jonalv masak: you should ask Gpox about it but I am not sure he has heard that story...
13:59 masak jonalv: I think 'hey mister' is from the SpeedMouse show by the Umbilical Brothers.
14:00 masak 'ballOOOOn, mister!'
14:00 jonalv masak: yea that hey mister part is
14:00 jonalv nooo a red ballon
14:01 CIA-63 bioclipse.core: Egon Willighagen master * r3363a83 / (11 files in 3 dirs): Removed plugin that is now available from bioclipse.sdk - http://bit.ly/PxSBq
14:03 egonw can someone please try updating bioclipse.core and try to run bioclipse.product?
14:05 jonalv egonw: oki
14:07 jonalv egonw: seems to work
14:07 jonalv egonw: anything in particualr I should look for?
14:07 egonw nope
14:08 egonw now I know at least that it is a config problem here..
14:08 egonw thanx
14:10 egonw ok, update classpath + pde fix deps worked
14:39 egonw masak: http://friendfeed.com/egonw/ae7b54b4/t​weet-send-using-jtwitter-library-with
14:39 zarah egonw's link is also http://tinyurl.com/p3hllc
14:40 masak egonw: nice!
14:41 CIA-63 bioclipse.social: Egon Willighagen master * rda2d99d / plugins/net.bioclipse.twitter​/META-INF/spring/context.xml : Fixed context.xml to make Spring pick up the correct interfaces - http://bit.ly/11eY3C
14:41 CIA-63 bioclipse.social: Egon Willighagen master * rc72ee1a / plugins/net.bioclipse.twitter.tests/sr​c/net/bioclipse/twitter/tests/business​/AbstractTwitterManagerPluginTest.java : Removed unused imports - http://bit.ly/Pj9Ro
14:41 CIA-63 bioclipse.social: Egon Willighagen master * r6fb7cfb / (5 files): Added a Bioclipse Social features - http://bit.ly/UDZxF
14:41 CIA-63 bioclipse.social: Egon Willighagen master * r1bcf1fb / (3 files in 2 dirs): Implemented twitter.setStatus() - http://bit.ly/4eUNzS
14:49 mgerlich huh
15:08 jonalv mgerlich: "huh" what? :)
15:08 egonw yeah, was wondering if I was gonna ask that too...
15:09 egonw mgerlich: there was some question on that on the Taverna mailing list...
15:09 egonw about an twitter activity...
15:09 egonw and I though... well, that can't be difficult to do in Bioclipse
15:09 egonw and I had to get the new Bioclipse SDK a test run anyway...
15:10 egonw jonalv: btw, I am thinking about a new annotation @SocialPing
15:11 egonw (or some better name)
15:11 jonalv egonw: okey what does it do?
15:11 egonw which will see what social providers are around (using an extension point)
15:11 egonw and when a method is annotated like that...
15:11 egonw your proxy will automatically send a message
15:12 egonw e.g. gist.download() could be annotated such
15:12 mgerlich sorry mistyped into the wrong channel :)
15:12 egonw so that when someone has some social plugin installed...
15:12 egonw such as the new twitter one...
15:12 jonalv egonw: what are your use case?
15:12 egonw it would send the call (in JavaScript terms) to twitter
15:12 egonw Fun (tm)
15:12 egonw more seriously...
15:13 egonw I am thinking about this use case
15:13 egonw the Open Notebook Science guys are really into the Social Web
15:13 egonw and I am about the write a script that verifies the data from the Solubility project...
15:13 egonw what better way of reporting the outcome via the social web?
15:13 egonw that I can already do with the current frame work, though
15:14 egonw (and will do)
15:14 jonalv yes
15:14 jonalv I am afraid you lost me
15:14 jonalv you can already do it but you want to do it anyway?
15:15 egonw no, not gonna do that annotation in the foreseeable future...
15:15 egonw just a though...
15:15 egonw +t
15:15 egonw as said... "I am thinking about..."
15:16 jonalv egonw: oh okey...
15:36 egonw masak: if you wonder why a twitter plugin and not laconi.ca... I could not find a convenient lib for the latter
15:37 masak ok.
15:38 egonw actually, it is your fault!
15:38 egonw I was just about the apologize
15:39 egonw but then I realized, that I could not have done that, because I would have lost a prospective user!
15:39 egonw you :)
15:39 egonw anyway...
15:39 egonw special thing for olass: net.bioclipse.sms
15:40 olass egonw: sounds interesting. When can I try it?
15:40 masak I still don't feel an overwhelming need to tweet from Bioclipse...
15:40 masak ...but I might have a look at the code. :)
15:43 * masak just got the Groovy console working
15:43 egonw ah cool
15:43 masak it was a two-line fix from what I already had.
15:43 egonw masak++
15:44 egonw ah, you big mess up
15:44 jonalv masak: so next step is to get the managers into groovythen
15:44 masak jonalv: aye.
15:44 egonw no no
15:44 egonw jonalv: I rather see managers in clojure
15:44 egonw automultithreading manager jobs
15:44 masak ooh, me too! :)
15:45 masak clojure++
15:45 egonw jonalv: I'm working on your CDKMoleculePropertySource bug
15:45 egonw jonalv: please notice that I'll add extra methods to ICDKMolecule
15:46 egonw which will likely break DBMolecule
15:47 jonalv egonw: what methods?
15:47 egonw void setProperty(String propertyKey, Object value)
15:47 egonw the equiv of getProperty()
15:48 egonw equiv -> counterpart
15:48 jonalv egonw: I guess we have to implment those for DBMoleucle then...
15:49 egonw yeah, only way to fix your bug report
18:14 CIA-63 bioclipse.cheminformatics: Egon Willighagen master * r714fbbb / (2 files): Added setProperty(String propertyKey, Object value) to the ICDKMolecule interface - http://bit.ly/RFJVz
18:14 CIA-63 bioclipse.cheminformatics: Egon Willighagen master * r8fde195 / plugins/net.bioclipse.cdk.business/src/net/bioc​lipse/cdk/domain/CDKMoleculePropertySource.java : Updated to acccept an ICDKMolecule instead of the implementation CDKMolecule (fixes #1489) - http://bit.ly/U7uhU
18:14 zarah bug #1489 | http://tinyurl.com/n8mj3o

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