Commits for angie

v267_preview to v267_preview2 (2012-05-01 to 2012-05-08) v267

• annoStreamDb now uses mysql server-side sorting in a couple of caseswhere table data may come out unsorted: 1) When a table e.g. knownGene
  has an index on txEnd, sometimes the mysql query optimizer uses that
  index and then rows come out not sorted by txStart.
  2) GenBank tables get ongoing updates, so although they are mostly
  sorted from initial load, they are not 100% sorted. (#6152)
  
  • src/hg/lib/annoStreamDb.c - lines changed 41, context: html, text, full: html, text
• hgVarAnnogrator now stores querySpec in the cart, and uses the cart'squerySpec (if exists) to draw the page. It also does a reload when the
  user hits the back button, because the web browser forgets all AJAX
  updates and the cart has the latest state. It does synchronous AJAX
  to lookup the position before executing a query; that causes failure
  of ajax.js's setCartVars async GET, so in order to avoid a warning
  about network error, we ignore errors for setCartVars. (#6152)
  
  • src/hg/hgVarAnnogrator/hgVarAnnogrator.c - lines changed 301, context: html, text, full: html, text
  • src/hg/js/ajax.js - lines changed 5, context: html, text, full: html, text
  • src/hg/js/hgVarAnnogrator.js - lines changed 35, context: html, text, full: html, text
• Make setCartVars optionally synchronous too -- page reload was interruptingsetCartVars in some cases. (#6152)
  
  • src/hg/js/ajax.js - lines changed 4, context: html, text, full: html, text
  • src/hg/js/hgVarAnnogrator.js - lines changed 1, context: html, text, full: html, text
• Use lastPosition cart variable (when present) when a position lookup fails. (#6152)
  • src/hg/hgVarAnnogrator/hgVarAnnogrator.c - lines changed 2, context: html, text, full: html, text
• Turns out that snp135 yields unsorted output for 'where chrom="...' --for now, just sort all queries that have a where clause. (#6152)
  
  • src/hg/lib/annoStreamDb.c - lines changed 12, context: html, text, full: html, text