Camelia, the Perl 6 bug

IRC log for #bioclipse, 2007-10-12

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
06:59 viklund joined #bioclipse
07:27 viklund joined #bioclipse
08:12 jonalv joined #bioclipse
08:32 olas joined #bioclipse
08:33 olas hi
08:33 EskilA joined #bioclipse
08:33 CIA-31 bioclipse: ospjuth * r3977 /trunk/playground/plugins/net.bioclip​se.biomoby/src/net/bioclipse/actions/ (TestBiomoby3.java TestBiomoby4.java): The BioMoby tests now run (fixed secondary data)
08:34 olas viklund: how are things progressing with the service?
08:34 olas I am expecting a mail with input/output once you have decided on that
08:54 egonw joined #bioclipse
08:55 viklund olas: jodå, det går frammåt, sakta men säkert.
08:55 viklund Jag tänker slänga upp en mockup idag
08:57 viklund oops, wrong language...
08:57 viklund whatever...
09:01 egonw new PFAAT release: http://www.biomedcentral.com/1471-2105/8/381
09:13 olas Can we include that in Bioclipse?
09:13 olas egonw: that and JalView are strong candidates
09:13 olas viklund: could you at EBC not compare the two tools?
09:14 olas PFAAT2 and JalView
09:14 viklund I guess we can, yes,
09:14 viklund I'm not probably the right person to do it though.
09:15 egonw olas: did you not have contact in the past with someone behind PFAAT?
09:15 olas no, but JalView
09:31 egonw olas: your biomoby commit is just about using one, right? not setting one up, right?
09:31 olas yes
09:32 olas Bioclispe is a client
09:32 olas (right now at least)
09:32 egonw ok, just making sure :)
09:32 egonw what was this with biomart?
09:32 olas well, just wanted to know what it is and what we can use it for
09:32 egonw you had that page online...
09:33 egonw it seems that our group is going to use it
09:33 olas not experienced with it but heard a lot about it :-)
09:33 olas we should maybe have a biomart plugin
09:34 egonw yes, very possibly indeed...
09:34 egonw would fit well with the current db things in progress
09:35 jonalv oh, what is it?
09:35 egonw a database architecture for life science data...
09:35 olas jonalv: please read on www.biomart.org
09:35 olas http://www.biomart.org/install.html
09:36 egonw it has a SOAP interface to access data...
09:36 egonw would be great to have a node in the Bioclipse2 navigator to open biomart databases
09:36 olas yes
09:36 olas Extremely good
09:37 olas http://www.genome.org/cgi/content/full/14/1/160 is a publication
09:37 jonalv It seems interesting although I am not quite sure I understand exactly what it is
09:38 egonw btw, did you see: http://www.bioclips.com/
09:38 olas no
09:38 jonalv Eclipse crached again... :(
09:38 olas :-)
09:38 olas haha
09:38 olas BioClips
09:39 egonw they are around longer than bioclipse.net :(
09:39 jonalv wow
09:39 egonw maybe time for a BioClipse plugin for Bioclipse ? :)
09:39 egonw maybe time for a BioClips plugin for Bioclipse ? :)
09:39 jonalv hehe
09:51 viklund olas: Can you pleas just check this wsdl:
09:52 viklund http://artedi.ebc.uu.se/course/temperatures.wsdl
09:53 olas ok
09:53 viklund I get an infinite loop in my perl-test-script when I try to load it
09:53 egonw lunch time
09:53 viklund so it's not actually using it that needs testing, it dosn't work
09:53 olas it's valid
09:54 olas do you want me to build a java client?
09:54 viklund hmm, strange... I get an infinite loop in my SOAP::Lite...
09:54 viklund nope
09:54 viklund the service dosnt exist ;p
09:54 olas Just because it's valid doesn't mean it works...
09:55 olas targetNamespace="http://localhost/Temperatures"
09:55 olas I see
09:55 viklund yep
09:55 viklund you can try a new one very soon though
09:55 olas ok
09:55 viklund now
09:55 olas now?
09:56 viklund redownload the wsdl, and test it, targetNamespace is accesible now
09:56 olas ok
09:58 olas no
09:58 olas Denied access to method (as_celsius) in class (Temperatures) at /usr/lib/perl5/vendor_perl/5.8.8/SOAP/Lite.pm line 2509.
09:59 viklund hmm
09:59 viklund I thought some things would be easier with objects, but maybe not...
10:02 olas It is
10:02 olas we really should have a model object
10:02 olas holding all information
10:02 olas for more complex cases, that is a must
10:02 viklund yes...
10:02 viklund maybe test another thing then..
10:02 olas I would strongly suggest you looking into BioMoby
10:03 olas They are standardizing these things and have generators to generate perl
10:03 viklund I'll try to access the stuff without wsdl and see if that works
10:03 viklund I will
10:03 olas good
10:03 olas We (in Bioclipse) think BioMoby is the future for services
10:15 viklund ;)
10:27 olas left #bioclipse
11:10 viklund the service should work not though...
11:10 viklund does someone else now how to test it?
11:10 viklund not a yn00 service but the previous service...
14:27 viklund joined #bioclipse
20:57 egonw joined #bioclipse
22:19 bjarni joined #bioclipse
22:19 ilogger2 joined #bioclipse
22:19 ChanServ joined #bioclipse
22:20 CIA-31 joined #bioclipse

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary