Commits for angie

v321_preview2 to v321_base (2015-08-17 to 2015-08-24) v321

• Updating DGV with new files after they fixed a couple bad names found by Matt.
  refs #15767
  
  • src/hg/makeDb/doc/hg18.txt - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/variation.txt - lines changed 6, context: html, text, full: html, text
• Concurrent POSTs by multiple ui event handlers were causing
  cart-saving race conditions like this: on the JS/client side, ui
  handler A sets a new cart var while sending a cartJson command, and
  concurrently ui handler B sends some other command. On the server
  side, if command B starts before command A finishes, and then B
  finishes after A finishes, then A's new cart var won't be in the cart
  that B closes out, and the new cart var will be lost.
  
  We still want concurrent POSTs so that we can fetch big old trackDb
  concurrently with smaller things that may arrive first. We can avoid
  losing cart vars by accumulating cart var settings from all cartJson
  commands, while queueing up the command objects. When all ui handlers
  have fired, the queue is flushed; it POSTs each command along with the
  accumulated set of cart vars, so that no matter which command finishes
  last, all of the cart var settings will be stored in the cart.
  
  The catch is that now we have to remember to cart.flush! ImModel
  takes care of it for ui handlers, but models that send out requests
  when initializing have to call it too.
  
  An ugly hack to manually merge cart vars has been removed from
  CladeOrgDbMixin and hgIntegrator -- cart.js merges them now.
  
  There could still be race conditions from conflicting or dependent
  commands running concurrently -- developers still need to prevent
  those.
  
  • src/hg/js/model/hgChooseDb/hgChooseDbModel.js - lines changed 1, context: html, text, full: html, text
  • src/hg/js/model/hgIntegrator/hgIntegratorModel.js - lines changed 5, context: html, text, full: html, text
  • src/hg/js/model/lib/CladeOrgDbMixin.js - lines changed 15, context: html, text, full: html, text
  • src/hg/js/model/lib/ImModel.js - lines changed 1, context: html, text, full: html, text
  • src/hg/js/model/lib/cart.js - lines changed 224, context: html, text, full: html, text
• Wrapping an errCatch around cartTrackDbInit so that if we switch to
  some database on hgwdev that is in dbDb but doesn't have a trackDb,
  we can return an empty groupedTrackDb instead of causing a JSON parse
  error.
  
  • src/hg/lib/cartJson.c - lines changed 19, context: html, text, full: html, text
• autoSql uses longblob not blob, but some .sql files have been tweaked
  to use blob; treat blob same as longblob.
  
  • src/lib/asParse.c - lines changed 2, context: html, text, full: html, text
• Watch out for another class of unsorted tables -- pubs*.
  
  • src/hg/lib/annoStreamDb.c - lines changed 9, context: html, text, full: html, text
• Make sure the #header line begins with a '#' and not a '\t' in the unlikely event that all fields of the primary streamer (or even of all streamers) are deselected.
  
  • src/lib/annoFormatTab.c - lines changed 11, context: html, text, full: html, text
• Fixing another entry where 'bed N .' should be 'bed N +'.
  
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 1, context: html, text, full: html, text