Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-03-02

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All times shown according to UTC.

Time Nick Message
06:38 annzi joined #bioclipse
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07:48 annzi joined #bioclipse
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11:49 sneumann wow: http://cactus.nci.nih.gov/chemical/structure/CN​%28Cc1cnc2nc%28N%29nc%28N%29c2n1%29c3ccc%28cc3%​29C%28=O%29NC%28CCC%28O%29=O%29C%28O%29=O/twirl
11:49 zarah sneumann's link is also http://tinyurl.com/yjo3kxq
11:49 sneumann tinyurl rulez :-)
11:54 samuell_ :)
12:50 olass joined #bioclipse
12:50 olass hi all
12:50 zarah hi olass
12:50 olass zarah: you are the fat one
12:50 zarah olass: no, YOU'RE the fat one! :)
12:52 olass @gg bioclipse
12:52 zarah olass: http://www.bioclipse.net/
13:22 samuell_ huu!
13:22 samuell_ :(
13:25 olass joined #bioclipse
13:28 egonw joined #bioclipse
13:33 CIA-57 bioclipse.core: Arvid Berg master * re32e543 / externals/nu.psnet.quickimage/META-INF/MANIFEST.MF :
13:33 CIA-57 bioclipse.core: Chnaged quickimage back to original version
13:33 CIA-57 bioclipse.core: Quickimage is an external plugin and it's version
13:33 CIA-57 bioclipse.core: should reflect upstream versioning - http://bit.ly/9naUwd
13:48 egonw jonalv: sure, let's talk
13:49 jonalv egonw: I think |I amanaged to start it
13:49 jonalv is it possible to download example data from inside it?
13:51 egonw yeah, you can download any RDF data from the web
13:51 egonw save it as N3
13:51 egonw and open it in the editor
13:52 jonalv egonw: okey, well can you point me to some? I guess we want it to contain molecules?
13:54 jonalv egonw: ?
13:55 egonw_ joined #bioclipse
13:56 egonw jonalv: sorry, lost connection for a sec
13:56 jonalv ah okey
13:56 egonw http://pele.farmbio.uu.se/rdf/
13:56 zarah egonw's link is also http://tinyurl.com/yldmewm
13:58 jonalv egonw: oki thanks, now how to get that thing opened in the editor?
13:58 egonw double click?
13:58 jonalv it doesn't seem I ahve the editor
13:58 egonw or, right click, Open With
13:58 jonalv IT should be included in the rdf feature right?
13:59 egonw no
13:59 egonw it's in the RDF UI feature
13:59 jonalv oh
13:59 jonalv and that is not in the rdf product
13:59 jonalv hang on
14:00 jonalv ah right there we go
14:00 jonalv fancy stuff :)
14:09 jonalv egonw: okey I am test running. What is it you want that selection event to contain?
14:10 jonalv you said something about showing properties?
14:11 jonalv So what are the properties to show when for example clicking that Integer 1?
14:11 jonalv egonw: I mean does it have any more properties than being the integer 1?
14:12 egonw nothing
14:12 egonw ok, let me hack that up...
14:12 jonalv egonw: so what is it you want me to do? :)
14:14 egonw write the listening bits
14:15 jonalv egonw: I don't think I understand
14:15 jonalv egonw: what is wrong with what is there already?
14:16 egonw what is there then?
14:21 jonalv it listens to selections
14:22 jonalv egonw: it shows properties for molecules...
14:25 egonw yes, because then an IMolecule gets sent around
14:25 egonw and I want this for a general RDFResource too...
14:25 egonw there are a couple of common properties to expect for those
14:25 egonw rdfs:label
14:25 egonw rdf:type
14:26 jonalv egonw: okey are there classes for these properties which I can jsut simply use?
14:27 egonw no, that's what I am hacking up right now
14:29 jonalv egonw: oh I thought Jena had this sort of things
14:29 egonw ah, yes, it does
14:29 egonw jonalv: you would suggest to just send around a Resource object as found in the Jena lib...
14:30 egonw well, why not...
14:30 jonalv egonw: no I think we have to create anothe object based on the one
14:30 jonalv that is probably cleaner
14:30 egonw yes, probably...
14:30 egonw I like that more too
14:30 jonalv egonw: But first step is to read the Jena objects...
14:30 egonw read?
14:31 jonalv hence I wonder which ones are possible and whether your example contains all that we need to support
14:31 egonw not just an API with the relevant 'properties' with get methods?
14:31 jonalv egonw: yea well in some sense
14:31 egonw what about this API:
14:31 egonw public interface IRDFResource {
14:31 jonalv egonw: yea an API. That's what I am trying to say...
14:32 egonw public String getRDFSLabel();
14:32 egonw public String getRDFType():
14:32 egonw }
14:32 egonw ?
14:32 egonw or would you prefer a more general thing with:
14:32 egonw public interface IRDFResource {
14:32 egonw public List<Foo> getPropertyTypes();
14:32 egonw public String getProperty(Foo type);
14:33 egonw }
14:33 egonw ?
14:33 jonalv egonw: I am not familiar with all the properties these objects have. I don't even have a complete list of these objects. Hence I would like to start from that...
14:33 egonw the we do the first
14:33 egonw and when we get sick of the 200 properties, we swtich :)
14:34 jonalv yea I guess but let's put together a list of objects we must support shall we?
14:34 egonw list of objects?
14:35 egonw you lost me there
14:35 jonalv yea which classes implemenitng com.hp.hpl.jena.rdf.model.Resource do we have to support?
14:35 jonalv egonw: or have I missunderstood soemthing?
14:36 egonw only that one...
14:36 egonw but you only need to care about the above interface
14:36 egonw which I'll commit in a sec
14:37 jonalv oh so there is only one implementation of that interface and the intresting stuff is stored as a string called the model?
14:38 CIA-57 bioclipse.rdf: Egon Willighagen master * rf19d9b8 / plugins/net.bioclipse.rdf/src/net/bi​oclipse/rdf/model/IRDFResource.java : Added IRDFResource interface, for which we want to show the fields in the properties view - http://bit.ly/cXQa57
14:38 samuell_ olass: I guess the "Latest News" should be copied over, and created as "news article"s on new website. Maybe you can do it?
14:38 egonw jonalv: you are not mixing the properties stuff with the extension point, are you?
14:38 olass samuell_: yes, will do
14:39 jonalv egonw: 'mixing' like 'mixing up'?
14:40 samuell_ egonw, masak, jonalv et al: Due to troubles with bioclipse.net, we are thinking to switch to a barebone Drupal setup, throwing over the current content there ... and implement the new design later, as soon as Per is done with it
14:40 samuell_ (that is, maybe even tonight, if possible)
14:40 masak what kind of trouble with bioclipse.net?
14:40 egonw jonalv: yeah, something like that
14:41 egonw frontpage is broken
14:41 * jonalv curls up in a corner calling for his mummy
14:41 egonw as well as news page
14:41 samuell_ So, I will configure up the basics of the plugin/module catalog
14:41 masak jonalv: http://en.wikipedia.org/wiki/Mummy
14:41 zarah masak's link is also http://tinyurl.com/5nlda5
14:41 samuell_ Please register at http://bioclipsedraft.rilspace.com/ , and I'll give you the permissions so you can enter info about your plugins
14:41 zarah samuell_'s link is also http://tinyurl.com/yhkjxu6
14:42 samuell_ (We will work on that URL until we have moved the database to the bioclipse.net server)
14:44 jonalv egonw: I am busy writing adresses on letter now
15:16 egonw jonalv: here you go
15:16 CIA-57 bioclipse.rdf: Egon Willighagen master * r5409897 / (2 files in 2 dirs): Now sends around a selection event for any resource, which is not recognized as a supported IBioObject -
15:22 samuell_ olass: Screenshots are now added by simply clicking "Create new content > Screenshot". (No category needed).
15:22 samuell_ Slideshow plugin (Lightbox) added, preview at http://bioclipsedraft.rilspace.com/screenshots
15:22 zarah samuell_'s link is also http://tinyurl.com/ygnfg3j
15:23 samuell_ Is the preview size of images big enough? (Have restricted to max 800x800 now)
15:23 samuell_ (For ppl with small screens)
15:23 samuell_ Sry, forgot to give public permission to the screenshots ... 1 sec
15:24 * egonw wonders if embedding screencasts is possible too
15:26 samuell_ Now
15:27 samuell_ egonw: Should be no prob!
15:27 samuell_ At least if having them as flash files ...
15:27 samuell_ But there are a number of solutions
15:28 egonw I get my screencasts as Ogg/Vorbis...
15:28 egonw but I could convert, I guess...
15:35 samuell_ Yeah, I think ffmpeg can do flv ...
15:36 samuell_ Will look into it after the module catalog is up
15:42 * jonalv is back
15:43 olass samuell_++
15:43 olass samuell_: What category should I use for screenshots?
15:43 olass make something up?
15:44 samuell_ olass: You don't need to add anything
15:44 samuell_ I removed that restriction
15:44 olass and how should the Body look like?
15:45 CIA-57 bioclipse.core: Carl Masak master * rf8e9066 / plugins/net.bioclipse.scripting.ui/src/net/biocli​pse/scripting/ui/views/ScriptingConsoleView.java :
15:45 CIA-57 bioclipse.core: [ScriptingConsoleView] now recognizes keypad Enter
15:45 CIA-57 bioclipse.core: Not only the big Enter button on the alphabetic keypad, but also the
15:45 CIA-57 bioclipse.core: small one on the numeric keypad, will execute the command. - http://bit.ly/9fx4la
16:06 jonalv egonw: ping
16:07 jonalv egonw: Do you know about some NullSelection?
16:07 jonalv For when nothing is selectedin the editor
16:07 jonalv also it could be used when selecting things which we don't have anything else to send for
16:08 jonalv egonw: Right now no selection event is sent when clicking on something which is not a resource...
16:12 egonw no, I am not aware of NullSelection...
16:12 egonw is that an existing class?
16:12 egonw sounds pretty useful to me :)
16:13 jonalv egonw: yea but I can't find any such class...
16:18 jonalv egonw: will you be in UA anything this week?
16:18 egonw UA?
16:19 jonalv egonw: Uppsala, I thought you used that abbreviation...
16:20 jonalv maybe that's olass
16:20 olass yup
16:20 egonw UU, BMC ... I use/know those :)
16:20 egonw but Uppsala Area makes sense
16:20 olass UppsalA
16:20 egonw that too :)
16:20 jonalv egonw: so, will you?
16:21 egonw yeah, talk from Annzi on Thu
16:24 jonalv egonw: can we talk then?
16:24 jonalv maybe we need to talk before that though...
16:24 jonalv egonw: do you think we could skype?
16:25 egonw yes
16:25 egonw hang on
18:32 samuell_ Website down for maintenance!
18:32 samuell_ (FYI)
18:33 samuell_ When it is up running again (within half an hour or so), please help to check that things work
18:34 samuell_ (We had to do this quick, as the front page + some more pages were broken, as you might have seen)
18:54 CIA-57 bioclipse.rdf: Egon Willighagen master * r839e8f1 / (2 files): Added IAdaptable as superinterface - http://bit.ly/aqbsZl
18:54 CIA-57 bioclipse.rdf: Egon Willighagen master * r5049b3b / (6 files in 2 dirs): Added resource for rdf Literal - http://bit.ly/94lSex
18:54 CIA-57 bioclipse.rdf: Egon Willighagen master * r57a81ce / plugins/net.bioclipse.rdf.ui/src/net/b​ioclipse/rdf/ui/editors/RDFEditor.java : Sent around an selection event for properties (Zest edges) too, and an EMPTY selection for everything else - http://bit.ly/ciDIoG
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