Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-09-21

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All times shown according to UTC.

Time Nick Message
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07:00 egonw Gpox: 1. what's the state of the controllerhub patches?
07:00 egonw Gpox: 2. please comment on my rendering parameter patch... I guess we can use some typing magic there?
07:01 egonw to have something along the lines of IGeneratorParameter<Integer> ? not sure how that exactly works, but you know, I think...
07:03 Gpox 1. Need to rebase onto the latest jchempaint-primary and try to remove the methods from the interface at least, maybe the ControllerHub aswell
07:11 samuell joined #bioclipse
07:12 samuell Good morning vrybody
07:12 * samuell is working from G�vle. Coming to Uppsala later today.
07:13 olass joined #bioclipse
07:14 jonalv hi samuell
07:14 jonalv hi olass
07:15 olass o/
07:18 mgerlich joined #bioclipse
07:18 samuell hi
07:18 zarah privet samuell
07:29 jonalv egonw: ping
07:29 egonw on phone
07:29 jonalv :(
07:29 jonalv Gpox: ping
07:29 Gpox jonalv: pong
07:30 jonalv Gpox: The molecules editor shows properties from SDF files right?
07:30 Gpox yes
07:30 jonalv Gpox: can you point me to the code that does that? I need to know how to get that sort of props out of cdk...
07:31 Gpox IAtomcontainer.getProperties()
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07:33 jonalv Gpox: oki thanks
07:34 jonalv Gpox: are they Strings?
07:34 jonalv Gpox: it's Map<Object, Object> though...
07:34 Gpox I think they are but ask egonw to be sure
07:35 jonalv egonw: if they are that Map should be Map<String, String>...
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07:46 egonw samuell: ack, I am working at home, very busy on another grant application... big one, this one is, and good chances
07:46 egonw Gpox: ack
07:47 egonw IAtomContainer.getProperties() might possible be updated for some typing magic too...
07:47 egonw anyway... it's Object to allow more than just String
07:48 jonalv egonw: are you sure you want to allow more than "just String"?
07:48 samuell egonw: Ok!
07:48 jonalv :)
07:48 egonw jonalv: unless you give me good arguments otherwise, I think I'd say yes
07:49 * samuell don's know what "ack" means...
07:49 jonalv egonw: intresting, may I turn it around and ask: What more than just String would one want to have there?
07:49 * samuell just learned what it means, on wikipedia
07:49 egonw what about Car ?
07:50 jonalv samuell: acknowledgeded (but it's too hard to spell)
07:50 egonw moreover because the English speaking world does not even agree on the spelling :)
07:50 samuell Ah, ok
07:51 * jonalv sometimes wonder what they do agree upon...
07:54 egonw war on irak
07:54 jonalv I guess...
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08:24 CIA-52 bioclipse.structuredb: jonalv master * r474905a / plugins/net.bioclipse.structuredb/src/​net/bioclipse/structuredb/internalbusi​ness/IStructuredbInstanceManager.java : fixed typo in javadoc - http://bit.ly/xw9ny
08:24 CIA-52 bioclipse.structuredb: jonalv master * rf1f0a76 / plugins/net.bioclipse.structuredb/src/net/biocli​pse/structuredb/business/StructuredbManager.java : import from SDF creates annotations for properties - http://bit.ly/2EfcSA
08:37 jonalv Gpox: How do I get the molecules editor to show my properties now?
08:40 jonalv Gpox: ping? :)
08:40 Gpox looking at it now
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08:47 jonalv Gpox: any progress?
08:48 Gpox jonalv: there is no interface yet, for a quick solution edit MoleculeTableContentProvide​r.getAvailableProperties() to include your model
08:50 jonalv Gpox: uhm but that won't work. Then I would add a dep from sdf editor to StructureDB right?
08:52 Gpox yes, logically getAvailableProperties() should be in IMoleculesEditorModel
08:52 jonalv Gpox: so why not add it?
08:53 Gpox no reason
08:53 jonalv Gpox: could you?
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09:42 Gpox jonalv: done
09:42 masak Gpox: jonalv went for an early lunch.
09:49 * jonalv is back for a couple of minutes
09:55 jonalv Gpox: commited?
09:55 Gpox yes, in my fork on github
09:55 jonalv Gpox: what project?
09:56 Gpox chemoinformatics
09:58 Gpox I sent you a pull request
09:58 jonalv yes
10:06 CIA-52 bioclipse.structuredb: jonalv master * r249c5c7 / plugins/net.bioclipse.structuredb/src/net/bioc​lipse/structuredb/DBMoleculesEditorModel.java : added stub implementation to keep things compiling - http://bit.ly/V0vZH
10:06 samuell joined #bioclipse
10:07 * jonalv afk
10:07 Gpox jonalv: tip Collections.emptyList()
10:07 masak \o/
10:33 olass Gpox: what is your github username?
10:34 Gpox goglepox
11:43 jonalv Gpox: But how is the values retrieved from the molecules?
11:46 Gpox MoleculeTableContentProvider.getValue(...)
11:47 Gpox It tries with ICDKMolecule.getProperty() and then fallbacks on IAtomContaainer.getProperty()
11:47 jonalv Gpox: what is the fallback condition?
11:47 jonalv Gpox: nulll?
11:47 Gpox yes
11:48 * jonalv mumbles something about null values all over the places...
11:48 jonalv Gpox: oki
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12:56 olass stain: around?
12:56 olass stain: How would you describe Raven in one sentence? A build tool?
12:57 olass does it require compilation at runtime or can you use it to just bundle together jars?
12:57 masak "Raven is a build tool for Java programs based on Rake and Ruby Gems."
12:58 olass yes, but what does that mean in practice at runtime?
12:59 masak olass: I've only just heard about it, but I think it uses Ruby Gems instead of Java jars.
13:00 olass stain: I'd value your input
13:00 * masak reads more about Raven
13:01 masak feels like some Ruby developer got tired of Maven and took matters into her own hands.
13:04 masak yep -- 'Matthiew Riou created Raven because he felt that XML was "painfully awkward when it comes to building things."'
13:06 olass masak: the Raven I am asking about is Maven at runtime
13:06 olass maybe there are several initiatives with teh same name
13:06 olass stain: do you know?
13:06 masak maybe.
13:11 masak or perhaps you're simply referring to Maven Runtime as Raven for some reason. http://maven.apache.org/shared/maven-runtime/
13:11 zarah masak's link is also http://tinyurl.com/lwosac
13:13 olass "perhaps you're simply referring to Maven Runtime as Raven for some reason" < sounds a bit like you think I'm making up my own words
13:14 olass please don't
13:14 olass Taverna has used Raven for years in their architecture
13:14 olass to extend the Taverna platform
13:14 sneumann there was an interesting thread recently on their mailing list
13:15 sneumann [Taverna-hackers] activity plug-in does not work since this week
13:15 olass yes, I know they have struggled with Raven for a long time
13:15 olass and AFAIK I think they wanted to move towards OSGI because of that
13:15 sneumann the thread start to get interesting at Wed, 16 Sep 2009 10:16:16 +0100 (11:16 CEST)
13:15 olass will look at it
13:16 sneumann Yes, their move to OSGi beyond Taverna 2.1
13:17 olass sneumann: thx, yes this explains things a bit more
13:17 olass "Then we have Raven which is the current classloader system used in Taverna instead of the default bootstrap classloader in Java.  It uses the Maven pom files to find the jars that plugins need and keeps them all separated so that different plugins can use different versions of the same jars.  This is the part that we are planning to replace with OSGI bundles."
13:18 olass strange that Raven has so few references online
13:18 olass bad naming I guess
13:18 olass overlapping with Ruby's build system
14:02 masak aye. all I found was references to the Ruby build tool.
14:03 masak olass: apologies if I made it sound like you were making up words.
14:03 olass masak: no worries ;)
14:03 olass jonalv is the master of that
14:03 olass borken for example
14:04 masak wait, isn't that a real word?
14:04 olass nope
14:04 masak wow.
14:04 olass it is not defined in a proper english dictionary
14:04 masak then that dictionary is clearly borken :)
14:04 olass which sort of is the purpose of a dictionary, to define words and their usage
14:05 olass masak: how is work coming along btw?
14:05 masak olass: I'm mid-refactor. it looks partly good already.
14:05 masak need to fix a lot of small things.
14:05 * olass too
14:10 masak but it's always fun to work with visuals. they provide immediate feedback.
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14:26 olass Gpox: do you have a github username?
14:28 masak goglepox
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16:33 Gpox git++
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22:05 stain oh no, are you making fun of our Raven? Only us on the inside are allowed to ridicule it!
22:05 stain There's two different Ravens.. One of them is the Ruby one, the other one is the Java one which we invented
22:05 stain the art of Googling was perhaps not as strong in those days
22:08 stain I think this is our only 'reference'.. http://www.mygrid.org.uk/dev/blog/?p=16
22:08 zarah stain's link is also http://tinyurl.com/nwtvln
22:08 stain my advice - don't try :) Classloaders are hard!
22:08 stain too bad olass went offline..

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