Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-12-16

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All times shown according to UTC.

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10:04 CIA-13 bioclipse.hivdrc: Ola Spjuth master * r8eca141 / (8 files in 5 dirs): Updated model deps. - http://bit.ly/fXWHWv
10:56 CIA-13 bioclipse: ospjuth * r11759 /bioclipse2/trunk/ (23 files in 9 dirs): Removed duplicate methods and added dep to net.sf.xws4j instead.
11:01 CIA-13 bioclipse.hivdrc: Ola Spjuth master * r426dbc6 / (6 files in 5 dirs): Updated imports after refactoring. - http://bit.ly/eixONf
11:13 samuell How to periodically execute an action (with sleep in between), inside an Display.getDefault().asyncExec(new Runnable() ...
11:13 samuell ... without freezing Bioclipse
11:14 samuell I'm now having a while-loop, containing a sleep, inside the runnable object, but that freezes the whole thing ...
11:17 samuell :(
11:20 Gpox http://www.eclipse.org/articles/A​rticle-Concurrency/jobs-api.html
11:20 egonw http://download.oracle.com/javase/tuto​rial/essential/concurrency/sleep.html
11:20 zarah egonw's link is also http://tinyurl.com/37z3vtx
11:21 egonw samuell: it's not a Job you are after, right?
11:21 egonw I guess you want to keep an eye on something remote, like an Uppmax run?
11:21 samuell egonw: Yeah, exactly ... something like that
11:21 samuell (Checking the link)
11:21 Gpox you would put the asyncExec inside the loop and call it from another thread
11:22 Gpox the code in asyncExec is run on the UI thread and thus freeses the UI if you put it to sleep
11:23 samuell Yeah, but I tried already running from another thread, to no help
11:23 samuell ... I'm afraid i run into this bug: https://bugs.launchpad.net/sun-java/+bug/432677
11:24 samuell ... or sth related
11:35 samuell Gpox: ok ... so asyncExec does not start a new thread, you mean?
11:36 Gpox no it executes the code on the UI thread so you can update your ui
11:38 samuell Gpox: Yea, ok, IC
11:41 Gpox have a look at the second example from the jobs-api article it does waht you trying to do I think, you would call asyncExec from the done method on the JobChangeAdapter
11:42 Gpox it depends on what excatly you are trying to achiev
11:45 Gpox it would be eays to crate a remote progress tracker I think
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12:19 samuell Gpox: You were totally right ... it worked well when doing the loop in a separate thread ...
12:19 samuell (I thought I had tested this, but I had placed the loop in the wrong place)
12:20 samuell Gpox++
12:29 egonw Gpox++
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15:11 CIA-13 bioclipse.core: Arvid Berg master * ref99c42 / plugins/net.bioclipse.scripting.ui/src/net/bi​oclipse/scripting/ui/views/JsConsoleView.java : Solves bug 1956 with reflection. - http://bit.ly/e1hv1w
15:11 zarah bug #1956 | http://tinyurl.com/39sgxzh
15:20 CIA-13 bioclipse.balloon: Arvid Berg master * r76cd40c / plugins/net.bioclipse.balloo​n.tests/META-INF/MANIFEST.MF :
15:20 CIA-13 bioclipse.balloon: Changed junit from Require-Bundle to Import-Package
15:20 CIA-13 bioclipse.balloon: Using Import-Package allows for more flexibility
15:20 CIA-13 bioclipse.balloon: for what bundle provide the junit classes and
15:20 CIA-13 bioclipse.balloon: simplifies dependency management. - http://bit.ly/fVHtjL
15:48 egonw Gpox: you mean, it removes dependency management?
15:55 Gpox in a way. Before it required org.junit4 bundle to be able to compile and run the tests. Now it is satisfied with any bundle that provides the org.junit* pacakges
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16:04 egonw seems fair... only no safety against ABI changes I guess
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16:07 Gpox you are right. Could add a version but the it would have to be maintained
16:09 CIA-13 bioclipse.cheminformatics: Arvid Berg master * r0f3ad2b / features/net.bioclipse.chemo​informatics_site/feature.xml : Removed verson of chemoinformatics feature from site - http://bit.ly/hRnxVJ
16:09 CIA-13 bioclipse.cheminformatics: Arvid Berg master * r2319af0 / (2 files in 2 dirs): Removed version from plugin dependencies - http://bit.ly/ekQZYr
16:09 CIA-13 bioclipse.cheminformatics: Arvid Berg master * ra32ae0e / (2 files in 2 dirs): Removed import of jdt junit package - http://bit.ly/hK4FKy
16:09 CIA-13 bioclipse.cheminformatics: Arvid Berg master * rc12ab88 / (11 files in 11 dirs):
16:09 CIA-13 bioclipse.cheminformatics: Changed junit from Require-Bundle to Import-Package
16:09 CIA-13 bioclipse.cheminformatics: Using Import-Package allows for more flexibility
16:09 CIA-13 bioclipse.cheminformatics: for what bundle provide the junit classes and
16:09 CIA-13 bioclipse.cheminformatics: simplifies dependency management. - http://bit.ly/gXANrb
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21:25 samuell hi egonw
21:25 egonw hi samuell
21:25 * samuell is looking at the RDF export function
21:26 * samuell has read the answer on the comment on the blog post also, but will need to answer when getting more time ...
21:26 egonw no worries
21:26 samuell egonw: There is no way to output an RDF-store as as RDF/XML to a string, right?
21:27 egonw perhaps not implemented yet
21:27 egonw but should be possible
21:27 egonw file me a bug report
21:27 egonw I'll implement it
21:27 samuell Ok
21:27 samuell Yeah, there is saveRDFXML, so probably not too big difference
21:27 * samuell will file it ...
21:33 egonw tack
21:35 samuell ur welcome :)
21:35 samuell But ... now I realize that a multi-dimensional array would be much better even ... hmm...
21:36 samuell New bug, or should I add that to the opened bug?
21:36 egonw new bug will do fine
21:36 samuell oki
21:44 samuell Hmm, well, I realize though that I can do all this with sparql...
21:47 samuell js.print(rdf.sparql(rdfStore, "SELECT ?s ?p ?o WHERE { ?s ?p ?o } LIMIT X"))  ...
21:47 samuell ... so I should be able to get forward with my smw method, using that ...
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