Commits for tdreszer

v248_preview to v248_preview2 (2011-02-22 to 2011-03-01) v248

• Added mdbObjsEncodeExperimentify() which will organize objects into experiments and allow the expId to be updated into the mdb
  • src/hg/inc/mdb.h - lines changed 33, context: html, text, full: html, text
  • src/hg/lib/mdb.c - lines changed 789, context: html, text, full: html, text
• Added -encodeExp options to mdbPrint and mdbUpdate allowing organizing objects into experiments and possibly updating the expId
  • src/hg/makeDb/mdbUpdate/mdbPrint.c - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/mdbUpdate/mdbUpdate.c - lines changed 46, context: html, text, full: html, text
• Always print composite summary msg in mdbObjsEncodeExperimentify()
  • src/hg/lib/mdb.c - lines changed 2, context: html, text, full: html, text
• Changed a bunch of labels as per QA and Kate. I have not removed Base Overlap signals and consequently the labels still distinglushe between those signals and f-Seq Density signals. However I have gone back to FD and BO used in the hg18 short labels and have made the longLabels more explicit.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.html - lines changed 25, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.ra - lines changed 196, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.html - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.ra - lines changed 230, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.html - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.ra - lines changed 126, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.ra - lines changed 22, context: html, text, full: html, text
• Minor changes to composite long label to further identify lab
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.ra - lines changed 1, context: html, text, full: html, text
• Further fine-tuning as per QA
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.html - lines changed 56, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.html - lines changed 49, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.html - lines changed 53, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.ra - lines changed 1, context: html, text, full: html, text
• Further fine-tuning as per QA
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.html - lines changed 52, context: html, text, full: html, text
• Base Overlap is not 'raw'
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.ra - lines changed 1, context: html, text, full: html, text
• Fixed redmine 2911. 'No tracks found' message was lost but now is found.
  • src/hg/hgTracks/searchTracks.c - lines changed 15, context: html, text, full: html, text
• Standardizing tier 1 and 2 labels
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.ra - lines changed 1, context: html, text, full: html, text
• Back to the new style 'Dnesity Signal' and 'Overlap Signal' labelling
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.ra - lines changed 177, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.ra - lines changed 219, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.ra - lines changed 128, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.ra - lines changed 2, context: html, text, full: html, text
• Back and forth 'Density Signal' and 'Overlap Signal' labelling
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.ra - lines changed 1, context: html, text, full: html, text
• Beginning to support mutiSelects for cv.ra searchables
  • src/hg/lib/mdb.c - lines changed 23, context: html, text, full: html, text
• File search can get terribly slow with too many files. Limit to 1000.
  • src/hg/lib/fileUi.c - lines changed 15, context: html, text, full: html, text
• Another step towards supporting multi-selects in track search and file search
  • src/hg/hgApi/hgApi.c - lines changed 27, context: html, text, full: html, text
• Moved code from 'hgTracks.js' to common 'utils.js' and added support for multi-selects in file and track search
  • src/hg/js/hgTracks.js - lines changed 446, context: html, text, full: html, text
  • src/hg/js/utils.js - lines changed 466, context: html, text, full: html, text
• Support for multi-selects for mdb searches on advanced tab. Requires cv.ra change to be active.
  • src/hg/hgTracks/searchTracks.c - lines changed 91, context: html, text, full: html, text
• Working on file search as a stand alone CGI. Not ready yet, but it does work.
  • src/hg/hgFileSearch/hgFileSearch.c - lines changed 750, context: html, text, full: html, text
  • src/hg/hgFileSearch/makefile - lines changed 15, context: html, text, full: html, text
• Go ahead and make the new hgFileSearch cgi
  • src/hg/makefile - lines changed 1, context: html, text, full: html, text
• Now that multiSelect is supported in track search and file search, turn in on in cv.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 27, context: html, text, full: html, text
• Need to change cv.ra white list to include multiSelects.
  • src/hg/lib/mdb.c - lines changed 1, context: html, text, full: html, text
• Brooke suggests 'is amung' instead of 'is (any of)'.
  • src/hg/hgFileSearch/hgFileSearch.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTracks/searchTracks.c - lines changed 1, context: html, text, full: html, text
  • src/hg/js/utils.js - lines changed 1, context: html, text, full: html, text
• Kate wrangles
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUmassDekker5C.ra - lines changed 137, context: html, text, full: html, text
• Kate missed this step - shame
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile - lines changed 1, context: html, text, full: html, text
• Mdb vars for files, not tables
  • src/hg/hgFileSearch/hgFileSearch.c - lines changed 1, context: html, text, full: html, text
• Changed the comment for submittedDataVersion validation to be more clear (I hope).
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text
• Removed erroneous text from the methods section
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.html - lines changed 11, context: html, text, full: html, text
• Oops. Added paragraph back in.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.html - lines changed 5, context: html, text, full: html, text
• Cleaned up a little code to make track search not dependent upon var=tableName being set.
  • src/hg/lib/mdb.c - lines changed 16, context: html, text, full: html, text