WPWG-20100525-transcript: Difference between revisions
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(Created page with ' - Tuesday May 25 2010, 08:31 - sjcarbon: morning' ben: howdy j-lo: hiya sjcarbon: hey! - 08:37 - ben: seth, probably you and I should chat for a few minutes after ben: …') |
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[[Category:Web Presence Working Group]] |
Latest revision as of 13:33, 25 May 2010
- Tuesday May 25 2010, 08:31 - sjcarbon: morning' ben: howdy j-lo: hiya sjcarbon: hey! - 08:37 - ben: seth, probably you and I should chat for a few minutes after ben: about systems issues sjcarbon: okay--no problem - gwg has joined the room sjcarbon: Well, I wanted to talk about the three graphs in the demo page, and maybe some problems with doing in through QuickGO. sjcarbon: but we don't really have the audience that we had last week... sjcarbon: Too bad I guess. - gwg has disconnected (Quit: Leaving.) sjcarbon: For the people who really liked the QG graph (any here?), could I ask you a question about it? - 08:42 - sjcarbon: Or for the smaller audience: do either of you prefer the QG graph? - gwg has joined the room ben: 3 looks cleaner than 2 ben: but of course, less informative j-lo: sorry - yes I liked the QG graph ben: the reality is that this is too small an example anyway sjcarbon: ben: i discovered that having labels in graphviz really messes the layout algorithm ben: you need a big ol nasty graph sjcarbon: yeah, I was hoping people could bring their favorites for show and tell. sjcarbon: here...I have one on the board...lemme see... j-lo: are there links we should be looking at seth? - 08:47 - sjcarbon: on the wiki, but if you have a convoluted area of the graph that you like, we can use that as a discussion point. sjcarbon: how about: sjcarbon: http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0034223 sjcarbon: http://amigo.berkeleybop.org/cgi-bin/amigo/amigo?mode=term_details4&term=GO:0034223 - pascale has joined the room j-lo: arggh - my client turning the :0 into smily faces so links don't work! j-lo: gottit now - 08:52 - sjcarbon: sjcarbon: unfortunately, my cache of the quickgo isn't working there (will debug later), so just follow the quickgo link for the comparison. j-lo: see, these are the cases where you would want the parent and child view only j-lo: all graphs are useless sjcarbon: personally, i'd say that the graphviz (non-quickgo one) is less useless here. what are the cases where the graph is complicated, but not useless? ben: lets just say they have equal value sjcarbon: besides some other reasons (like we'd have different graph formats in amigo because quickgo's is not general purpose), it seems to be better at showing neighborhood/rank, rather than structure. sjcarbon: i'm trying to get a feel for where the border sits. sjcarbon: and whether or not the main thing that people like about the quickgo one is the rank feel of it. - 08:57 - j-lo: I think it's quite compact j-lo: and it has a very visible key j-lo: and the boxes help with interpretation somehow ben: i agree that it's compact, that's a plus sjcarbon: i also find it easier to read, sjcarbon: but only when comparing ranks. ben: I find the "key" to be almost useless gwg: is it right that when I click on the QuickGO image link, I get a message saying "http://amigo.berkeleybop.org/cgi-bin/amigo/visualize?inline=false&mode=quickgo&beta=0&term=GO:0034223" ben: he just said that's a bug, you have to go directly to quickGO for now sjcarbon: yes--bug from earlier, use the quickgo link. gwg: sorry, that must have been when I dropped out of the chat sjcarbon: when the ontology jumps multiple "levels", it gets very confusing. sjcarbon: (to me.) sjcarbon: for example: - 09:03 - sjcarbon: http://amigo.berkeleybop.org/cgi-bin/amigo/amigo?mode=term_details4&term=GO:0021787 sjcarbon: (all tabs work in this one) ben: quick go is much better for this one, simply because it is more compact sjcarbon: i sense a compactness fixation. i guess that is the information i wanted. sjcarbon: i find the squiggly lines of quickgo maddening though. sjcarbon: i'll see if i can tease a more compact graphviz graph out, if not, i'll go with the quickgo. j-lo: I think the OE graph view is pretty nice too j-lo: v similar to QGO sjcarbon: that means though, that amigo will present different graphs in different places--the quickgo system isn't something we can use in the general case. sjcarbon: (it actually is quickgo.) sjcarbon: (we lifted the code a while back) sjcarbon: do y'all think people can deal with that? j-lo: yep - 09:08 - j-lo: (btw - it's the OE Graph Viewer) sjcarbon: for fun, on the wiki page there is also also a fully tabbed layout for term details. sjcarbon: also, there is a link to Sven's work--it is now folded in to experimental and should be getting regular updates. sjcarbon: I'm not sure how much outside comment hes taking yet though. sjcarbon: Pascale might know? gwg: the fully tabbed version looks good ben: brb sjcarbon: I found it a bit maddening, but that might just be me this week. gwg: it looks maddening with js turned off - 09:13 - sjcarbon: I'll keep that but of code dusted off so we can visit it all more seriously when we have a chance. gwg: I think all those graph views are enough to send anyone mad tho... sjcarbon: Gave me a headache... gwg: thank you for doing all the experimenting! sjcarbon: I see lines and boxes when I close my eyes... sjcarbon: No problem. This should be wrapped up this week, then onwards. sjcarbon: Anybody have anything else? ben: back sjcarbon: I think we're done then. I'll send out links to a "final" layout after I track down the caching bug and check for graphviz "compactness". - pascale has disconnected (Ping timeout) - pascale has joined the room - pascale has left the room - 09:20 - ben: seth - the tricks we tried with the load balancer didn't work last night sjcarbon: argh. ben: goweb2 still exploaded sjcarbon: should we disable that search? sjcarbon: or will the kill scripts be effective? ben: that might be best - or at least cripple it gwg: perhaps there should be some documentation about what dbxrefs exist in the GO DB ben: well, we tweaked the kill script, but not sure it's working still ben: gwg: no, the software should gracefully handle any input ben: not spin mysql for 2 minutes if someone uses a perfectly valid id ben: that we don't happen to cross index gwg: what do you suggest? gracefully killing their query? ben: the kill script was designed for REALLY long running queries - like 30 minutes. ben: like not running queries that take 2 minutes ben: maybe the problem is the %blah% ben: wild cards? sjcarbon: i'll see if i can get something temporary in to just get those, and die with a message to the lucene on experimental for now. ben: then at least we could use the indexes sjcarbon: i'll check both. ben: yeah, any bogo patch will work for now. I currently think there is something wrong at the hardware level as well ben: because it's always the SAME machine that blows up. goweb2 never goweb2 ben: sry never goweb1 gwg: can you try sending all those queries to goweb1 in that case? - 09:25 - ben: we are still messing with it here... but Stuart is really backlogged because he had pnumonia sjcarbon: okay. i'll work on that until around lunch, and then let you know what i've come up with. ben: gwg: well the stupid LOAD BALANCER is supposed to send queries to less loaded machine! gwg: but if one of the machines seems to handle them better... gwg: anyway, no point in arguing about it ben: the machines are supposed to be identical... ben: another issue is the sessions. ben: this forces us to make the IP address "sticky" so that a user always gets the same machine (which has it's session stored on it) ben: we suspect this stickyness might be part of the trouble, but I don't think amigo will even work without session ids currently sjcarbon: it should work...but it will be doing more work (no cached data). ben: what does it store? The filters, for sure. what else - 09:31 - sjcarbon: i think there's chewed search results in there as well sometime. as i recall, if it can't find the cache, it just soldiers on. sjcarbon: i don't thnk any of the production new stuff uses session/cache in any non-agnostic way. ben: hmmm... I recall that it redirects to the home page if you give it a bad session id... but that expereince from a few years ago gwg: it used to, but I don't know if it still does sjcarbon: lemme see... ben: I just tested by backspacing a few chars out of the session and it seems to work fine sjcarbon: that should be the behavior. ben: ok, I will suggest that we remove the stickyness and see how it goes sjcarbon: okay, i'll look at the queries, and see how easy catching them are. i'll contact you again around lunch. ben: kk ben: later