Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-02-02

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All times shown according to UTC.

Time Nick Message
06:31 egonw joined #bioclipse
07:38 masak joined #bioclipse
07:58 sneumann_ joined #bioclipse
08:10 Gpox joined #bioclipse
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08:37 jonalv joined #bioclipse
08:43 egonw joined #bioclipse
08:44 sneumann_ morning
08:44 sneumann_ I tried the http://gist.github.com/170410
08:44 sneumann_ is there an easy way to put the result
08:44 sneumann_ res=metaprint2d.calculate(mollist);
08:44 sneumann_ into my workspace instead of the console ?
08:45 masak good question.
08:45 masak what will res contain after that calculation?
08:45 sneumann I had hoped for molecules
08:46 masak in that case, one should be able to open them in an editor with ui.open(res)
08:46 sneumann I'll try
08:46 masak but I know there's a bug ticket for exactly that.
08:46 sneumann ump. I wont try
08:51 sneumann hm. doesn't work, fails silently. no response, no error.
08:51 masak sneumann: are you running it from within Eclipse?
08:51 sneumann yup
08:51 masak sneumann: does the console in Eclipse show a backtrace?
08:52 sneumann no
08:52 masak huh. strange.
08:52 masak that's a different issue than the one I thought you'd run into.
08:53 sneumann > ui.open(res)
08:53 sneumann > print("hi")
08:53 sneumann hi
08:53 zarah ni hao sneumann
08:53 sneumann wel,, thank you zarah.
08:55 masak :)
09:00 sneumann just for completeness:
09:00 sneumann DEBUG - ui.open has @GuiAction - running in gui thread
09:00 sneumann on the shell console
09:08 masak as it should.
09:25 annzi joined #bioclipse
09:41 * jonalv tries to reproduce what sneumann did
09:44 jonalv sneumann: res seems to be a hashmap
09:47 jonalv sneumann: When I write 'help metaprint2d.calculate' it seems like it is possible to store the metaprint2d props in the atomcontainer by adding a boolean param set to true to the method call
09:47 egonw sneumann: olas is in a meeting... ask him when he is back
09:47 egonw jonalv: sounds good
09:48 jonalv if AC=Atom Container that is... (jonalv is not to happy about abbreviations in help texts...)
10:04 egonw jonalv: agreed, file a bug report
10:10 egonw joined #bioclipse
10:33 egonw joined #bioclipse
10:49 annzi joined #bioclipse
11:26 egonw joined #bioclipse
12:06 sneumann hi, just creating my bc2.2 workspace
12:06 sneumann following samuells http://wiki.bioclipse.net/index.php?title=​Checking_out_Bioclipse_2.2&oldid=3992
12:06 zarah sneumann's link is also http://tinyurl.com/yhhafg5
12:07 sneumann First impression is that git://github.com/olas/bioclipse.core.git
12:07 sneumann is not enough to get goin,
12:07 sneumann it complains about missing cdk stuff.
12:35 annzi joined #bioclipse
13:01 sneumann So I just installed the BIRT feature from eclipse.org, and that solved net.bc.birt
13:01 sneumann Would be great to have that on the wiki.
13:01 sneumann Erm, I guess I should add it then ...
13:02 sneumann Question: what is the minimal git I need to fix net.bc.cdk.business ?
13:02 sneumann it needs cdk.core/cdk.data/cdk.interfaces ?
13:24 sneumann egonw: fresh checkout of your git master,
13:24 sneumann DescriptionResourcePathLocationType
13:24 sneumann Project 'org.openscience.cdk.swt.control.basic' is missing required source folder: 'src'org.openscience.cdk.swt.control.basicBuild pathBuild Path Problem
13:24 annzi joined #bioclipse
13:25 sneumann but closing them worked fine
13:40 olass joined #bioclipse
13:41 jonalv http://www.h-online.com/open/news/ite​m/Bioclipse-2-2-released-919837.html
13:41 zarah jonalv's link is also http://tinyurl.com/ykuofz5
13:41 jonalv sad that the image screen shoot if from Bioclispe 1 though. (At least I think it is)
14:03 sneumann net.bioclipse.product
14:03 sneumann Network connection problems encountered during search.
14:03 sneumann Unable to access "http://update2_2.bioclipse.net".
14:03 sneumann Unable to access site: "http://update2_2.bioclipse.net" [Server returned HTTP response code: "503 Service Unavailable" for URL: http://update2_2.bioclipse.net.]
14:03 sneumann Server returned HTTP response code: "503 Service Unavailable" for URL: http://update2_2.bioclipse.net.
14:03 sneumann Unable to access site: "http://update2_2.bioclipse.net" [Server returned HTTP response code: "503 Service Unavailable" for URL: http://update2_2.bioclipse.net.]
14:03 sneumann Server returned HTTP response code: "503 Service Unavailable" for URL: http://update2_2.bioclipse.net.
14:06 sneumann olass, jonalv: can you do sth about the 503 ?
14:58 jonalv sneumann: I am back, is our update site down?
15:00 sneumann I am working on it, I get
15:00 sneumann DNS Domain 'update2_2.bioclipse.net' is invalid: Non recoverable errors.
15:00 sneumann if I use some other proxy it seems to work
15:02 jonalv okey I am trying to see if I can raeach it. It's not much I can do though. olass is the one who has set that up...
15:04 sneumann seems to be a proxy problem on our side
15:04 jonalv sneumann: yea I can reach it wirhout problem
15:24 CIA-71 bioclipse.core: Carl Masak master * r160b886 / plugins/net.bioclipse.doc/​parse-file-for-annotations :
15:24 CIA-71 bioclipse.core: [net.bioclipse.doc] fixed doc generation bug
15:24 CIA-71 bioclipse.core: jonalv++ for noticing. - http://bit.ly/9LHbbf
15:42 annzi joined #bioclipse
16:08 CIA-71 bioclipse.core: Carl Masak master * raa9a0d1 / plugins/net.bioclipse.doc/​parse-file-for-annotations :
16:08 CIA-71 bioclipse.core: [net.bioclipse.doc] now parses all method variants
16:08 CIA-71 bioclipse.core: Previously, only the last variant was included. This is to be considered
16:08 CIA-71 bioclipse.core: a bug. - http://bit.ly/achfOx
16:17 CIA-71 bioclipse.core: jonalv master * rcb755ee / plugins/net.bioclipse.gist/src/net/bio​clipse/gist/business/IGistManager.java : fixed spelling error in @PublishedMethod note - http://bit.ly/9uRAZf
16:31 egonw joined #bioclipse
16:32 egonw jonalv: ping
16:32 jonalv egonw: pong
16:32 egonw got some minutes to talk me through your reports?
16:32 egonw first of all... thanx for reviewing the manager
16:33 egonw !
16:33 egonw much appreciated
16:33 jonalv egonw: I printed the Manager documentation and read it thought while guarding the sutdnets... :)
16:33 jonalv more things commming from that... :)
16:33 egonw what manager documentation?
16:33 jonalv |read it thorugh while guarding the students
16:34 jonalv egonw: the autogenerated from the @PublisehdManager docs...
16:34 egonw where did you get that?
16:34 egonw we should advertise that more
16:34 egonw I did not know we did that for 2.2
16:35 jonalv I am unsure if it actually is updated for 2.2
16:36 jonalv egonw: you can find it on the web if you follow these instrucitons
16:36 jonalv bioclipse.org/help
16:37 jonalv klick Bioclipse scripting, and then Scripting Language Documentation
16:37 jonalv masak said something about a small horse when I asked him how to link to that page...
16:38 jonalv egonw: anyway, what was your question?
16:38 egonw can you talk me through your bug reports...
16:38 egonw I need more info here and there
16:38 egonw small horse?
16:38 egonw zarah: where can I find the Bioclipse documentation?
16:38 zarah egonw: are you making fun of me?
16:38 jonalv egonw: well I am not going though all of them but if you have specific questins then fire away
16:39 egonw @pz 1840
16:39 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1840
16:39 jonalv egonw: ah
16:39 jonalv egonw: what aboutthat one?
16:39 egonw question pending... hang on
16:40 egonw you refer there to the manager method as lin 1036, correct?
16:40 egonw and, more importantly... how do you expect it to be fixed?
16:41 egonw should the method be removed altogether, or the @PublishedMethod annotation?
16:41 egonw short, what is the expected behavior
16:41 egonw @pz 1847
16:41 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1847
16:41 egonw where is it exactly that you expect the List of Molecules to be specified
16:41 egonw ?
16:42 egonw I have not seen any anotation approach for that?
16:42 jonalv egonw: yes, the expected behavior is that that method should not be publisehd. It is taking an on the fly implementation of the BioclipseUIJob. This is not somethign that we do from JavaScript
16:42 egonw jonalv: I do not understand your expected behavior
16:42 egonw what is 'not be published'
16:42 egonw does that refer the the IFooManager API
16:42 egonw or to the @PublishedMethod annotation?
16:43 jonalv egonw: about 1847 I expected a line like "This method returns a List of molecules from..." in the text on behvaior
16:44 jonalv egonw: 'not be publised' == does not have the @PublisehdMethod annotation
16:44 egonw like that?
16:44 egonw List of molecules
16:44 egonw not List<IMolecule> ?
16:44 egonw jonalv: but the BioUIJob stuff must be in the IFooManager API?
16:44 jonalv egonw: I am beginning to think that maybe we should have a Returns parameter in that annotation too...
16:45 egonw @pz 1842
16:45 zarah http://pele.farmbio.uu.se/cgi-bi​n/bugzilla/show_bug.cgi?id=1842
16:45 jonalv egonw: yea the method should still be there it should just not be Publisehd since it is not meant to be called from JavaScript
16:45 egonw how long can @PublishedMethod text be anyway
16:45 egonw ?
16:45 egonw I thought those had to be short?
16:45 jonalv egonw: hm why? I don't see any reason to keep em short
16:46 egonw it's just that I 'learned' that at some point
16:46 * jonalv can't think of a reason to keep them short
16:46 egonw btw, I am very much in favor of a returns="" field for @PublishedMethod
16:47 jonalv egonw: file a bug :)
16:47 egonw btw, speaking of typos... quite a few in your bug reports :)
16:48 jonalv egonw: yea I know, I hvae balck blet in tpyos :/
16:48 egonw ok, I think I have enough clues... tack
16:48 jonalv oki
16:57 CIA-71 bioclipse.core: Carl Masak master * rddc0590 / plugins/net.bioclipse.doc/​parse-file-for-annotations : [net.bioclipse.doc] now DTRT with backslashes in strings - http://bit.ly/ckzZX3
17:10 jonalv egonw: why the jcp manager have a method called getIsCompact?
17:10 jonalv egonw: that just seems wrong
17:10 egonw jonalv: http://baoilleach.blogspot.com/2010/02/s​imilarity-searching-using-openbabel.html
17:10 zarah egonw's link is also http://tinyurl.com/yz2qnsf
17:10 egonw jonalv: why is that wrong??
17:11 jonalv masak: help
17:11 masak hahah. :)
17:11 masak it's not objectively wrong.
17:11 masak but it's not stellar API design either. :P
17:12 annzi joined #bioclipse
17:12 jonalv oh hai annzi
17:13 egonw looking forward to a jonalv/masak joint proposal on getActiveEditors() in managers
17:13 annzi hi jonalv
17:13 jonalv egonw: what was wrong with this nameing pattern: http://java.sun.com/j2se/1.4.2/docs/api/​java/util/Collection.html#isEmpty%28%29
17:13 zarah jonalv's link is also http://tinyurl.com/ckmh4
17:13 jonalv egonw: what bug ticket was that?
17:14 egonw sorry, you lost me
17:14 egonw called for dinner now
17:14 egonw bbl
17:14 jonalv (gah!!)
18:42 egonw s_wolf: ping
18:42 egonw bist du online?
19:30 sneumann joined #bioclipse
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21:11 levu joined #bioclipse
21:14 levu hi, i'm not so familiar with eclipse related software, do i need eclipse for starting bioclipse (Ubuntu 9.10, Java version 6-15-1)?
21:15 levu or maybe should i ask if i _can_ use it with eclipse so that i don't need to download thew huge 85 MB
21:45 levu left #bioclipse
21:48 sneumann__ @tell egonw where to get the dependencies for BC SDK, especially GMF runtime, I only find GMF experimental SDK
21:48 zarah Consider it noted.

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