Commits for galt

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

• initial commit for separating out the archive expansion
  • src/hg/encode/hgEncodeSubmit/app/controllers/pipeline_controller.rb - lines changed 2, context: html, text, full: html, text
  • src/hg/encode/hgEncodeSubmit/app/views/pipeline/show.rhtml - lines changed 2, context: html, text, full: html, text
  • src/hg/encode/hgEncodeSubmit/config/database.yml.sample - lines changed 4, context: html, text, full: html, text
  • src/hg/encode/hgEncodeSubmit/lib/pipeline_background.rb - lines changed 27, context: html, text, full: html, text
  • src/hg/encode/hgEncodeSubmit/pipeline_runner.rb - lines changed 21, context: html, text, full: html, text
• adding expand as a separate background step
  • src/hg/encode/hgEncodeSubmit/app/controllers/pipeline_controller.rb - lines changed 12, context: html, text, full: html, text
  • src/hg/encode/hgEncodeSubmit/app/views/pipeline/list.rhtml - lines changed 16, context: html, text, full: html, text
  • src/hg/encode/hgEncodeSubmit/app/views/pipeline/show.rhtml - lines changed 4, context: html, text, full: html, text
  • src/hg/encode/hgEncodeSubmit/lib/pipeline_background.rb - lines changed 61, context: html, text, full: html, text
• adding permissions compensation for oddness of ftpasswd utility that wants to change perms to 444 if it can
  • src/hg/encode/hgEncodeSubmit/app/models/user.rb - lines changed 10, context: html, text, full: html, text
• needs rescue if not owner
  • src/hg/encode/hgEncodeSubmit/app/models/user.rb - lines changed 2, context: html, text, full: html, text
• reducing duplicate project status messages in the log
  • src/hg/encode/hgEncodeSubmit/lib/pipeline_background.rb - lines changed 12, context: html, text, full: html, text
• cleaning up project.status for duplicate expanding messages
  • src/hg/encode/hgEncodeSubmit/lib/pipeline_background.rb - lines changed 2, 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/hg/visiGene/knownToVisiGene/knownToVisiGene.c - lines changed 36, 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/hgVisiGene/printCaption.c - lines changed 19, context: html, text, full: html, text
• fixed bug in handling translated psls
  • src/lib/basicBed.c - lines changed 13, context: html, text, full: html, text
• oops do not want commented out code
  • src/lib/basicBed.c - lines changed 1, context: html, text, full: html, text