Notes from the weekly DAS/2 teleconference, 20 Nov 2006 $Id: das2-teleconf-2006-11-20.txt,v 1.1 2006/11/27 04:31:31 sac Exp $ Note taker: Steve Chervitz Attendees: Affy: Steve Chervitz, Gregg Helt, Ed Erwin Dalke Scientific: Andrew Dalke UCLA: Brian O'connor Action items are flagged with '[A]'. These notes are checked into the biodas.org CVS repository at das/das2/notes/2006. Instructions on how to access this repository are at http://biodas.org DISCLAIMER: The note taker aims for completeness and accuracy, but these goals are not always achievable, given the desire to get the notes out with a rapid turnaround. So don't consider these notes as complete minutes from the meeting, but rather abbreviated, summarized versions of what was discussed. There may be errors of commission and omission. Participants are welcome to post comments and/or corrections to these as they see fit. Agenda ------- * Spec discussion * Status reports Topic: Spec Discussion ----------------------- gh: has everyone reviewed steve's re-orged html doc of the retrieval spec? [To summarize the re-org: everything has been organized into three main sections: general, overview, and detailed. There's a table of contents and all sections and subsections are numbered a la W3C specs. The summary table at the top has been simplified, and in-page navigation has been fixed and improved.] consensus: no, haven't looked at in detail yet. [A] all give the new html retrieval spec doc a read through again. gh: need to add examples of alignments. I plan to announce in the next two weeks that it's ready. When reviewing, pay special attention to comments marked 'XXX' sc: esp in third para from the top, ambiguousness. ee: need commit privileges sc: sent email to support@open-bio.org. They are quick. Topic: Status reports --------------------- gh: First half of last week, getting affy das2 server up to snuff with spec changes and compliance with spec, had spotty compliance. correctly handle errors. email message about test server, different url than the public server. [A] gregg/steve to update public affy das2 server with new IGB release gh: lots of testing in last few days, ready to replace the existing server. ee: some zooming issues when switching servers. gh: worked on fixing bugs in das/2 client, problems w/ biopackages server due to problems in IGB, also w/r/t spec changes. also working on using das/2 in another context in igb, retrieving genomic locations. Expression console, recommended for processing affy chips (all expr), generates chp files. big request esp for whole exon folks, need igb to load these, but the chp files have no genomic location info, had to pre-load these in past. Now, when you load a chip file, igb automatically goes out via das2 and retrieves it. hardwired is what server to go to, based on genome + types from server, figures out what das request to make to load it. per-sequence basis, and lazy, doesn't load all locations for whole genome. big files: 1M probe sets, + 4 probes w diff locs. Also, igb gets it back in compact binary format (using alt format) -- new use of das in igb. not committed yet, but will be cool. ee: data? gh: yes. we need more bp2 files there. Will try and have igb prompt user for file if it can't look it up automatically. [A] gregg send ed a write up so he can get it in the release notes. gh: bottom line: efficient way to look at expr data in igb gh: Third thing: prepping for this release of igb. targetting wed. server change over tues, igb on wed. may cause a day of hassles. ee: I'll be working in Paris on Wed, will be Tues day for US.. gh: so I'll be done by noon wed or earlier. gh: happy with progress on affy client server now. ad: cleaning up code I did on validator while in EBI. will check into dasypus CVS on sf. ee: on vacation, but working now. sc: worked on affy das2 server set up for testing ( http://netaffxdas.affymetrix.com/das2/test ) and worked on the igb keystore update (digital signature for affy jars). Ran into issue with the error codes sent by the affy das2 server getting altered by apache into another error (502, I believe). Need to figure out how to get apache to not alter these error responses. [A] steve figure out how to prevent apache from changing das/2 error responses gh: would assume not doing redirection through apache. but plan b is to not use apache. [affy das2 server uses jetty servlet engine, and apache forwards request to it via a rewrite rule.] sc: quick load access now requires apache. gh: should be able to load and serve these through jetty running on port 80. need to get apache to stop mucking with the http headers. bo: no new progress, but will look into filtering issue this week. 'so:' stuff. either allen of I will look into it this week. gh: i get right feat response for some but not all request. wonder if the 'so:' is involved. that's the only remaining issue I know of. both servers are passing validation. this was a high priority. for brian gilman and lincoln to make use of the das/2 spec. ad: any more feedback from bg? gh: no. he was going to start working on a server as well. [A] gregg contact brian gilman to see how things are going. ee: good news, bug I reported about zooming out was not a bug, but cause by me pressing the wrong button. related to changing genome version. [A] steve set up jar signing cert today so Ed can use tomorrow. Wrap up: -------- [A] review and modify das/2 html retrieval docs over the next few days. [A] Next meeting in two weeks (4 Dec 06)