Camelia, the Perl 6 bug

IRC log for #bioclipse, 2010-02-08

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All times shown according to UTC.

Time Nick Message
06:05 sneumann_ joined #bioclipse
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08:51 egonw moin
08:51 zarah saluton egonw
08:59 egonw annzi: http://chem2bio2rdf.wikisp​aces.com/SPARQL+Endpoints
08:59 zarah egonw's link is also http://tinyurl.com/ygwqh2b
09:00 olass joined #bioclipse
09:00 olass moin
09:01 zarah hello olass, you fantastic person you
09:01 zarah olass: You have new messages. Write '/msg zarah @messages' to read them.
09:01 egonw olass: at home?
09:01 olass @msg
09:01 zarah olass: 1 d 13 h 11 m 58 s ago, sneumann_ said thanks for the offer to help, saw that too late. This helped: rm -rf eclipse-bioclipse/.metadata/.plugins/​org.eclipse.pde.core/metfrag.product
09:01 olass yes
09:03 sneumann_ eclipse--
09:03 olass yes
09:28 egonw annzi: ping
09:29 annzi pong
09:29 egonw http://rdf.farmbio.uu.se/chembl/snorql
09:29 zarah egonw's link is also http://tinyurl.com/yd8w4pm
09:29 egonw and the matching /sparql/
09:29 egonw it's up and running
09:29 egonw olass: that's the SPARQL end point
09:29 egonw SNORQL is a Ajax interface to the SPARQL end point
09:30 egonw making it easier for humans to browse
09:30 olass I see
09:30 annzi this is great
09:31 olass I get error if I click on any of teh SPARQL results links
09:31 egonw where is that link?
09:31 * olass just pressed "Go" on the page
09:33 egonw ah, a SNORQL bug... lovely...
09:33 egonw or perhaps Virtuoso...
09:34 egonw olass: try hitting the Classes link on the right
09:35 egonw oh, bugger
09:35 egonw forgot to update the NS :(
09:37 egonw OK, the data it not good :(
09:37 egonw grmph :(
09:39 egonw it seems that the indexing went bad
09:59 egonw annzi: I'm going to reenter the data...
09:59 egonw which will fix the namespace, and hopefully too the index
10:02 annzi egonw: ok
10:39 egonw annzi: started reloading the data
10:57 egonw annzi: http://rdf.farmbio.uu.se/chembl/snorql/?query=SEL​ECT+DISTINCT+%3Fproperty+%3FhasValue%0D%0AWHERE+{%0D%0A++%3Chttp://rdf.farmbio.uu.se/chembl/target/t​102383%3E+%3Fproperty+%3FhasValue%0D%0A}%0D%0A
10:57 zarah egonw's link is also http://tinyurl.com/ycx4q7n
11:01 egonw olass: fixed that SPARQL problem
11:02 egonw http://rdf.farmbio.uu.se/chembl/snorql​/?query=SELECT+count(%3Fs)%0D%0AWHERE+{%0D%0A++%3Fs+a+%3Chttp://rdf.farmbio.uu.se/che​mbl/onto/%23Target%3E%0D%0A}%0D%0A
11:02 zarah egonw's link is also http://tinyurl.com/yjteqgw
11:02 egonw 7192 targets
11:14 annzi egonw: do you have a snapshot?
11:14 egonw snapshot?
11:17 egonw grmph...
11:17 egonw found another NS ugliness
11:21 annzi egonw: http://pele.farmbio.uu.se/chembl/snapshot.php
11:21 zarah annzi's link is also http://tinyurl.com/ya52gqq
11:22 egonw ah, that one is out of data
11:22 egonw please use the rdf server SPARQL end point
11:25 egonw annzi: targets and docs are reloaded...
11:25 egonw annzi: the compounds as up next
11:25 annzi yes I'm using that one. Is all data up such as activities etc?
11:25 egonw no
11:25 egonw will take an hour or two
11:26 annzi ok that explains alot :)
11:33 egonw annzi: http://rdf.farmbio.uu.se/chembl/snorql/?query=S​ELECT+DISTINCT+%3Fclass+count(%3Fclass)+WHERE+{%0D%0A++[]+a+%3Fclass%0D%0A}
11:33 zarah egonw's link is also http://tinyurl.com/ybfcck2
11:55 egonw annzi: please check your google wave and update the wave "UU Cheminformatics Journal Club"
12:00 * egonw is very pleased with the performance of the system :)
12:00 egonw olass++ (for pushing me to finally get an account :)
12:01 olass ;)
12:01 olass egonw: you are referring to ws1, right?
12:01 egonw yes
12:01 egonw aka rdf
12:01 olass ws1 is a pretty good machine
12:01 egonw compared to pele, it does not have so much momery
12:02 egonw only 1GB per core
12:02 olass no?
12:02 egonw pele has 2GB per core
12:02 olass ask the BMC data if you need more, not impossible to get them to upgrade this..
12:03 egonw so far, the system is doing fine
12:03 egonw it's an easy and cheap upgrade we can likely make anytime we like
12:04 olass ok
12:06 annzi egonw: did you invite me in?
12:06 egonw yes, think so
12:06 egonw ah, now I did
12:06 annzi got it now
12:06 egonw sorry about that
12:07 egonw I guess the image confused and scared me :)
12:07 annzi haha
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16:08 jonalv joined #bioclipse
16:09 jonalv oh hai
16:09 zarah privet jonalv
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18:35 egonw joined #bioclipse

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