Camelia, the Perl 6 bug

IRC log for #bioclipse, 2012-01-13

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All times shown according to UTC.

Time Nick Message
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10:05 egonw_ moin moin
10:05 jonalv hi egonw
10:15 egonw Q: does "man manager.foo" not autodetect the returned object class/type ?
10:18 sneumann Hi
10:18 zarah privet sneumann
10:18 sneumann Is there a command line client for IRC to send messages ?
10:18 sneumann i.e.
10:19 sneumann ircsend -s server.freenode.net -c bioclipse -m "message" ?
10:20 jonalv egonw: no, how could it?
10:24 egonw jonalv: introspection / reflection ?
10:27 jonalv hm, I think the manager implementer is free to sepcify exactly what Class the method returns. The API probably just specifies the interface though. Right?
10:27 egonw sneumann: not yet... we're still waiting for the command line version of bioclipse... then, just use the bioclipse twitter manager :)
10:28 jonalv lol egonw++
10:37 egonw sorry... did I say yet I was in a meeting...
10:37 egonw egonw-- (twitter != IRC)
10:37 egonw sorry for the noice
10:37 * egonw notes we need an IRC manager in Bioclipse
10:51 egonw mmm... anyone interested in a Bioclipse manager for OntoCat?
10:51 egonw http://www.ontocat.org/browser/trunk/ontoCAT/​src/uk/ac/ebi/ontocat/examples/Example4.java
10:51 zarah egonw's link is also http://tinyurl.com/7n5wdxk
12:30 Bagarn When someone download and install Bioclipse, are the any .cml-files included?
12:32 jonalv Bagarn: well depends on what you mean
12:32 jonalv there is the sample data
12:32 jonalv which is included in the download but not in the workspace unless the user installs sample data
12:34 Bagarn it's just so you have some file to open in one of the steps of one of the cheat sheet... =)
12:35 jonalv Bagarn: ah, then maybe the cheat sheets lacks a comment about the sample data unless the user has some other data available
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15:27 Bagarn Gpox: I found some errors in the cheat sheet, but I'm not sure if they appears 'cos I'm running Biopclipse in Eclipse...
15:31 Bagarn 1) when I try to open the help page (i.e. the webpage) nothing happends, it's as I didn't clicked at all...
15:33 Bagarn 2) When I use the print command in the JavaScript console the printed message is written in Eclipses console, and not in Bioclipses.
15:39 egonw what do you mean with 'Bioclipse in Eclipse' ?
15:39 egonw booted it with bioclipse.product ?
15:40 Bagarn I start Bioclipse by pressing the "run" button in Eclipse.
15:45 egonw can you try the run button in the editor for the bioclipse.product file, please?
15:46 Bagarn ok.
15:50 Bagarn egonw: "Launch an Eclipse application"?
15:50 egonw checking...
15:50 Bagarn in that case i get thesame results....
15:50 egonw yes, that title is right
15:51 egonw what does js.say("give you")?
15:51 egonw that is, where does that go?
15:52 Bagarn it seems to work:
15:52 Bagarn > js.say("give you")
15:52 Bagarn give you
15:53 egonw in the bioclipse javascript console?
15:53 egonw if so, that looks good
15:53 egonw what command that you use to get something in the Eclipse console?
15:53 Bagarn japp, and nothing in Eclipse console
15:54 egonw sounds good
15:55 Bagarn so instead of using print you are suposed to use js.say?
15:56 egonw yes, think so
15:56 egonw I think that's the main reason for js.say to exist :)
15:57 Bagarn ok, then it's just to change in the cheat sheet.=)
16:32 jonalv ah, Bagarn++
16:32 jonalv oh egonw++ too :)
16:45 Bagarn Gopx: After thinking a little more I have three problems that I thing you should look at:
16:45 Bagarn 1) I can't open the help web-page, no matter where I click
16:45 Bagarn 2) When I try to open a molecule using the "Click to perform" in the cheat sheet, I just get an error:
16:45 Bagarn > ui.open(cdk.fromSMILES("C1CCCCC1CC(CN(CC))CO"))
16:45 Bagarn The object could not be opened. No suitable editor could be found for object: CDKMolecule:C12H25NO
16:45 Bagarn 3) Bioclipse can't find Gist.
16:46 Bagarn Do you want them all as bug-reports in Bugzilla?
16:49 egonw 2 is a known bug, and filed in bugzilla
16:49 egonw regression in the currnet branch indeed
16:49 Gpox @pz 3003
16:49 zarah http://pele.farmbio.uu.se/bug​zilla36/show_bug.cgi?id=3003
16:51 Bagarn I thoght some of them might been known before, thats why I asked before sending them in. What about the other tow? or shall we tak it on monday?
16:51 Bagarn *two
16:52 Gpox you should alway search in bugzilla before filing to see if they are already there
16:52 Gpox but there is also a way to mark them as duplicates if they are filed twice
16:58 Bagarn ok, I do that on monday (I haven't sent in any of them get). =)
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