galt: changes by file

branch to review (2009-05-12 to 2009-05-19) v206

• src/hg/encode/hgEncodeSubmit/config/environment.rb.sample
  • 1.4 lines changed: 1, context: html, text, full: html, text
    remove what does not work
  • 1.3 lines changed: 6, context: html, text, full: html, text
    Try to deal with lost Mysql connection after long waits for validate or load
• src/hg/encode/hgEncodeSubmit/lib/pipeline_background.rb
  • 1.13 lines changed: 4, context: html, text, full: html, text
    Try to deal with lost Mysql connection after long waits for validate or load
• src/hg/lib/customFactory.c
  • 1.97 lines changed: 26, context: html, text, full: html, text
    add touching of udc files in cache and reporting of names for the do-not-kill-list with verbose=4
• src/hg/makeDb/doc/aplCal1.txt
  • 1.3 lines changed: 50, context: html, text, full: html, text
    Initial Aplysia californica
  • 1.2 lines changed: 16, context: html, text, full: html, text
    Initial Aplysia californica
  • 1.1 lines changed: 52, context: html, text, full: html, text
    Initial Aplysia californica
• src/hg/makeDb/trackDb/makefile
  • 1.267 lines changed: 1, context: html, text, full: html, text
    Added aplCal1 to DBS.
• src/hg/utils/refreshNamedSessionCustomTracks/makeExclusionList.pl
  • 1.6 lines changed: 1, context: html, text, full: html, text
    fixed typo
  • 1.5 lines changed: 1, context: html, text, full: html, text
    tweak to handle udcCache location and process dataUrl setting to touch files in cache and report them for the do-not-kill list
• src/hg/utils/refreshNamedSessionCustomTracks/refreshNamedSessionCustomTracks.c
  • 1.9 lines changed: 3, context: html, text, full: html, text
    tweak to handle udcCache location and process dataUrl setting to touch files in cache and report them for the do-not-kill list
• src/hg/utils/refreshNamedSessionCustomTracks/refreshSledgeHammer.pl
  • 1.3 lines changed: 1, context: html, text, full: html, text
    handling udc cache files touching
• src/inc/udc.h
  • 1.10 lines changed: 3, context: html, text, full: html, text
    refactored to all udcFileCacheFiles to operate without requiring the url to be actually opened
• src/lib/udc.c
  • 1.17 lines changed: 71, context: html, text, full: html, text
    refactored to all udcFileCacheFiles to operate without requiring the url to be actually opened