Camelia, the Perl 6 bug

IRC log for #bioclipse, 2008-01-15

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All times shown according to UTC.

Time Nick Message
07:09 egonw joined #bioclipse
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08:09 masak joined #bioclipse
08:22 viklund joined #bioclipse
08:27 olas joined #bioclipse
08:27 egonw hi olas
08:27 olas hi egonw
08:35 thomas_ku joined #bioclipse
09:02 Annzi joined #bioclipse
09:04 jonalv joined #bioclipse
09:13 steinbeck joined #bioclipse
09:14 steinbeck moin
09:20 egonw_ joined #bioclipse
09:26 jonalv hi
09:56 thomas_ku_ joined #bioclipse
10:28 EskilA joined #bioclipse
10:48 jonalv joined #bioclipse
10:48 * jonalv @lunch
11:56 thomas_ku joined #bioclipse
12:19 olas egonw: how do you cite joelib?
12:20 olas search on pubmed yields 1 hit:"Feature selection for descriptor based classification models. 2. Human intestinal absorption (HIA)."
12:20 olas PMID: 15154759
12:30 egonw_ olas: Joerg thesis
12:31 egonw_ mom, let me check if I have those details
12:32 egonw_ will email the detailf
12:32 egonw_ s/f/s/
12:33 egonw_ sent
12:41 edrin joined #bioclipse
12:41 edrin hi
13:03 * egonw_ will have his PhD defense on April 2 2008
13:03 edrin congrats ;)
13:03 egonw_ I'll be happy to except those on the 2nd or after that :)
13:04 edrin egonw: i added disco support to the xmpp ws lib now.
13:05 edrin it's quite cool. you can now "browse/discover" xmpp items like xmpp ad hoc services+functions
13:05 edrin right now you can do this:
13:06 edrin c = ClientFactory.createClient(...);
13:11 edrin c.connect();
13:11 edrin xitem = c.getXmppItem("xyservice.server.com", "");
13:11 edrin xyservice = xitem.discoverAsync(); // or discoverSync(listener);
13:11 edrin if (xyservice instanceof Service) { // Service is derived from XmppItem... // list available functions, invoke a function}
13:11 edrin else if (xyservice instanceof XmppItem) { // list "child" XmppItems that can be a service or yet another XmppItem, server whatever...}
13:16 edrin discoverAsync() and discoverSync() disocvers information about an XmppItem, in general a Description, other XmppItems with Description that are associated with it, and in case it it a xmpp ws all Functions with description of the service.
13:16 egonw_ edrin: will chat later
13:16 egonw_ in a meeting now
13:16 edrin k, no problem
13:26 edrin /msg
13:39 edrin hm...
14:04 jonalv lucky you... :)
14:13 olas egonw: thanks for the reference by email!
14:28 EskilA_ joined #bioclipse
14:39 edrin olas: did you read my email? the one that is already one week old or so...?
14:56 olas oh, will check edrin...
15:02 thomas_ku joined #bioclipse
15:17 egonw_ thomas_ku:
15:17 egonw_ ERROR 2008-01-15 15:17:21,723 Could not clone
15:17 egonw_ java.lang.ClassNotFoundException: org.openscience.cdk.applic​ations.taverna.CMLChemFile
15:17 egonw_ at net.sf.taverna.raven.repository.impl​.LocalArtifactClassLoader.findClass(​LocalArtifactClassLoader.java:195)
15:17 egonw_ at net.sf.taverna.raven.repository.impl​.LocalArtifactClassLoader.findClass(​LocalArtifactClassLoader.java:154)
15:17 egonw_ deleted the JCP jar now...
15:17 egonw_ with no effect...
15:20 thomas_ku egonw: so you are not able to use any cdk worker?
15:21 egonw_ trying the SMILES one now
15:24 egonw_ ah, interesting...
15:24 egonw_ the CMLChemFile actually is *not* part of the ./repository/org/openscience/cdk/1.​1.0.20080114/cdk-1.1.0.20080114.jar
15:24 egonw_ oh wait...
15:24 egonw_ it should not too
15:24 egonw_ wrong jar
15:25 egonw_ it is part of the 0.4.2.0/cdk-taverna-0.4.2.0.jar
15:25 thomas_ku thats correct
15:26 thomas_ku cmlChemfile is within the cdk-taverna jar
15:26 egonw_ so, no idea what is going on
15:26 egonw_ it knows about the jar
15:26 egonw_ otherwise the local node would not show up
15:27 egonw_ but cannot load that class from the same jar :(
15:27 thomas_ku egon so you are not able to use any cdk worker like smiles correct?
15:28 thomas_ku or does the smiles one work
15:28 egonw_ correct
15:28 egonw_ no, nothing works
15:28 thomas_ku ok thats not good
15:29 egonw_ indeed, bloody anoying
15:29 thomas_ku I fear it will be a really stupid error
15:29 egonw_ probably...
15:29 egonw_ my quest continues...
15:29 egonw_ but not now
15:29 egonw_ I'll keep you informed...
15:29 egonw_ cu later
15:30 thomas_ku can you sent me your config file and pom file for the libs and the plugin installation
15:30 thomas_ku via mail
15:30 thomas_ku so that I can have look into them?
15:30 egonw_ will do that tomorrow
15:30 thomas_ku ok
15:30 egonw_ btw, which config file?
15:30 thomas_ku cu
15:30 thomas_ku the plugin config files for the installion
15:31 thomas_ku which you use on your local webserver
15:31 thomas_ku so that taverna find the right plugin
15:31 egonw_ ack
15:31 egonw_ bye
15:31 thomas_ku cu
15:39 olas edrin: around?
15:39 olas I did read your email but have not had time to test anything
15:39 olas been extremely busy with a grant proposal
15:40 olas I can see that things are progressing very nicely for you
15:40 olas What is the status of acceptance of the XEP?
16:05 Annzi left #bioclipse
16:24 * jonalv would like to apologize for messing up the check out process of Bioclipse 2 without updating the wiki page. He is currently busy with updating said wiki page.
16:25 CIA-20 bioclipse: jonalv * r4676 /branches/bioclipse2/core/plugins/net.bi​oclipse.recording/META-INF/MANIFEST.MF: Removed unwanted dependency
16:46 edrin olas: i think i will submit it again with a working example
16:56 olas I see
17:09 * jonalv has updated the compilation instructions for Bioclipse 2. Things are depedning on each other in some very unpleasant ways for the moment.
17:13 olas cu 2morrow
17:13 olas bye
17:13 olas left #bioclipse
17:14 jonalv I must admit that I didn't get the javascript terminal to work though...
17:14 jonalv Anyone else get java.lang.NoClassDefFoundError: net/bioclipse/scripting/OutputProvider in bc2?
17:15 edrin jonalv: who is deveoping besiden masak and you (and maybe Ola)?
17:15 jonalv kaskelot,
17:15 jonalv :)
17:16 jonalv perhaps egonw have it checked out and could have tried  but I just realised he is not here
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