Camelia, the Perl 6 bug

IRC log for #bioclipse, 2012-05-04

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All times shown according to UTC.

Time Nick Message
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09:58 egonw jonalv: does the manager proxy method matching between IManager and Manager involve exceptions being thrown?
10:01 egonw hi olass, somebody
10:01 egonw I guess UU is having lunch...
10:48 * jonalv is back
10:48 jonalv egonw: the matching should not involve exceptions no
10:48 jonalv egonw: however the proper exception handling is depending on checked exceptions being declared
10:49 egonw ok, good
11:06 andra Hello, egonw introduced me to bioclipse plugin development. As a hello world, I wrote a first call where a pubmed entry could be extracted
11:07 andra Does anyone know if there is already a pubmed plugin, or could I volunteer to write that as a first plugin project?
11:12 egonw andra++
11:12 egonw @karma andra
11:12 zarah andra has a karma of 1
11:26 egonw so, no one aware of current pubmed functionality in bioclipse?
11:26 egonw andra: there is a pubchem manager, but I do not recall using eutils for that
11:27 egonw you could check
12:04 olass andra: I think an EUtil manager would be a great addition
12:04 olass it has long been on the todo-list
12:04 olass and I don't think we have gotten around to implementing it
12:12 CIA-46 chembl.rdf: Egon Willighagen 3-openphacts * r319147d / (namespaces.php targets.php): Added links to Uniprot (+12 more commits...) - http://git.io/ey8D6g
12:44 CIA-46 chembl.rdf: Egon Willighagen 3-openphacts * r51fe7b0 / chembl.owl : Removed outdated .owl ontology - http://git.io/o-wqlg
12:44 CIA-46 chembl.rdf: Egon Willighagen 3-openphacts * r526e1cd / assays.php : Output of assay organism info (implements #20) - http://git.io/0-p_VQ
12:58 CIA-46 chembl.rdf: Egon Willighagen 3-openphacts * r703735f / assays.php : Also output the taxonomy data - http://git.io/2p2Gtg
13:05 andra great then I will start working on extending the one call (getpubmedentry) I already have
13:11 egonw olass: ping
13:11 egonw or jonalv
13:11 egonw can either of you add andra to some bioclipse team?
13:12 egonw or work from his repos first?
13:12 jonalv hi andra :)
13:12 egonw either case, I'll setup things on hudson in due time
13:12 olass andra: please clone and submit patches for now
13:12 jonalv well egonw, what repo will he be working on?
13:13 jonalv or is that she?
13:13 * jonalv has no idea
13:13 egonw he
13:13 olass we need some sort of process before we give people commit bit to a repo
13:14 olass a few good-looking patches that are verified would make me a bit happier
13:14 egonw olass: that's why a prefer to put things into new repositories :)
13:14 egonw but what repos should it have to go in anyway?
13:14 olass pubchem?
13:14 olass or a new plugin net.bioclipse.eutil?
13:15 olass it depends on scope IMHO
13:15 olass perhaps a new plugin is best, and we make decisions about where to include it later?
13:15 olass else I need to know more what it will contain
13:24 andra I prefer to play a bit first
13:25 andra I really need to be more confident before commiting to a specific role within a dev team
13:25 andra I am a "he"
13:26 andra The reason why I got interested in Bioclipse I that I need a framework to do my text mining work
13:26 andra I am currently using Whatizit from the ebi to do most of the tasks
13:26 jonalv andra: then fork on github, play around and send a pullrequest when you have something that you want to share
13:27 andra My end objective would be to make the whatizit plugin. So I make both and send the pull requests once ready
13:28 jonalv You can off course use the dev list to ask for feedback on what you hve done if you want
13:28 olass andra: sounds great!
13:28 olass good luck and ping here if you need any pointers
13:29 andra great thanks
13:33 CIA-46 chembl.rdf: Egon Willighagen 3-openphacts * radcd2b0 / targetTypes.nt : Added skos:Concept's for the other target types - http://git.io/pLr_HA
13:48 andra Is there a webcontainer in Bioclipse?
13:48 CIA-46 chembl.rdf: Egon Willighagen 3-openphacts * r162d353 / targets.php : Also use subClassOf for other targets; see also targetTypes.nt - http://git.io/5ZFpHA
13:54 CIA-46 bioclipse.qsar: Ola Spjuth 2.5.x * rb2621b6 / (74 files in 9 dirs):
13:54 CIA-46 bioclipse.qsar: Implemented response label and placement.
13:54 CIA-46 bioclipse.qsar: Also changed to tab-separation in CSV (duh!). - http://git.io/0Fnl8Q
13:55 olass zaetnick: please try now
13:57 egonw andra: what do you mean with webcontainer?
14:01 zaetnick olass: ok … it seems the build isn't triggered again
14:02 olass hmm...
14:02 * olass triggers it
14:03 olass andra: like a servlet container like Tomcat or Virgo?
14:04 olass andra: there are Eclipse bundles for that but we have not played around with them so much
14:04 olass I think it will be easy to get one going though
14:04 olass e.g. Eclipse starts one container for serving the Help system
14:05 egonw what is a webcontainer?
14:05 egonw andra: there is a HTML 'editor' that can be used to open HTML pages...
14:06 andra A webcontainer is used to open html content
14:06 egonw there is a browser manager
14:06 andra I now have implemented both the getPubmedentries and SearchPubmed
14:07 andra Both return xml, but I want to be able to view single page, sort of openURL()
14:07 andra but that does not seem to work
14:08 andra @olass no simpler. It should work like open("http://www.pubmed.org/1234567") and would open a small window with that specific page
14:09 andra I will google for the eclipse packages though
14:14 olass andra: just opening a URL should work in Bioclipse
14:14 olass hold on and I'll look it up
14:14 olass you want Java code, right?
14:16 egonw andra: btw -> http://pele.farmbio.uu.se/jenkins/
14:16 olass andra: http://pastebin.com/KPLpyg58
14:16 olass not so nice code but gets the job done for now
14:17 olass built-in browser needs to be improved...
14:37 CIA-46 bioclipse.statistics: Valentin Georgiev 2.5.x * r24e022b / (2 files): Fix SaveRSessionHandler file name - http://git.io/2gkdww
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