File Changes for galt

v243_base to v244_preview (2010-11-02 to 2010-11-16) v244

• src/hg/encode/hgEncodeSubmit/app/controllers/pipeline_controller.rb
  • lines changed 2, context: html, text, full: html, text
    initial commit for separating out the archive expansion
  • lines changed 12, context: html, text, full: html, text
    adding expand as a separate background step
• src/hg/encode/hgEncodeSubmit/app/models/user.rb
  • lines changed 10, context: html, text, full: html, text
    adding permissions compensation for oddness of ftpasswd utility that wants to change perms to 444 if it can
  • lines changed 2, context: html, text, full: html, text
    needs rescue if not owner
• src/hg/encode/hgEncodeSubmit/app/views/pipeline/list.rhtml
  • lines changed 16, context: html, text, full: html, text
    adding expand as a separate background step
• src/hg/encode/hgEncodeSubmit/app/views/pipeline/show.rhtml
  • lines changed 2, context: html, text, full: html, text
    initial commit for separating out the archive expansion
  • lines changed 4, context: html, text, full: html, text
    adding expand as a separate background step
• src/hg/encode/hgEncodeSubmit/config/database.yml.sample
  • lines changed 4, context: html, text, full: html, text
    initial commit for separating out the archive expansion
• src/hg/encode/hgEncodeSubmit/lib/pipeline_background.rb
  • lines changed 27, context: html, text, full: html, text
    initial commit for separating out the archive expansion
  • lines changed 61, context: html, text, full: html, text
    adding expand as a separate background step
  • lines changed 12, context: html, text, full: html, text
    reducing duplicate project status messages in the log
  • lines changed 2, context: html, text, full: html, text
    cleaning up project.status for duplicate expanding messages
• src/hg/encode/hgEncodeSubmit/pipeline_runner.rb
  • lines changed 21, context: html, text, full: html, text
    initial commit for separating out the archive expansion
• src/hg/visiGene/hgVisiGene/printCaption.c
  • lines changed 19, context: html, text, full: html, text
    using a new field geneId in knownToVisiGene table so that links going back to hgGene will correctly function when there happens to be a panel that has multiple genes/probes including yours but the others mess it up: example nkx2-2 used to take you to Ctnna2
• src/hg/visiGene/knownToVisiGene/knownToVisiGene.c
  • lines changed 36, context: html, text, full: html, text
    adding a new field geneId to knownToVisiGene table so that links going back to hgGene will correctly function when there happens to be a panel that has multiple genes/probes including yours but the others mess it up: example nkx2-2 used to take you to Ctnna2
• src/lib/basicBed.c
  • lines changed 13, context: html, text, full: html, text
    fixed bug in handling translated psls
  • lines changed 1, context: html, text, full: html, text
    oops do not want commented out code