Commits for tdreszer

v250_base to v251_preview (2011-04-19 to 2011-04-26) v251

• startsWithWordByDelimit failed when the line only contained the word.
  • src/lib/common.c - lines changed 4, context: html, text, full: html, text
• When in doubt, should always prefer the sandbox table.
  • src/hg/lib/mdb.c - lines changed 13, context: html, text, full: html, text
• Changed encodeExp option to take table name and diverged mdbPrint and mdbUpdate requirements for encodeExp as per Cricket's request.
  • src/hg/inc/mdb.h - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/mdbUpdate/mdbPrint.c - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/mdbUpdate/mdbUpdate.c - lines changed 21, context: html, text, full: html, text
• Adding CGI support for mdb fimeName being a comma delimited list. Also includes support for md5sum as comma delimited list.
  • src/hg/lib/fileUi.c - lines changed 313, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 16, context: html, text, full: html, text
• redmine 1411. One more tweek to martix CB graying. This was found by Katrina when already on beta.
  • src/hg/js/hui.js - lines changed 9, context: html, text, full: html, text
• Added expId's and dccAccessions to Broad Histone hg18 and hg19
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeBroadChipSeq.ra - lines changed 1099, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra - lines changed 1861, context: html, text, full: html, text
• Temprarily block experimentify from creating expId's in encodeExp table. Cricket will manage expId creation with Kate's tool for now. mdbUpdate can still create accessions in encodeExp table when expId already exists.
  • src/hg/lib/mdb.c - lines changed 4, context: html, text, full: html, text
• Changes so that -accession -test will work. Also made some experimentify errors more prominent.
  • src/hg/lib/mdb.c - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/mdbUpdate/mdbUpdate.c - lines changed 1, context: html, text, full: html, text
• Added expIds and dccAccessions for Open Chrom hg18 and hg19
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeChromatinMap.ra - lines changed 1067, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra - lines changed 555, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra - lines changed 657, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra - lines changed 363, context: html, text, full: html, text
• Added expIds and dccAccessions for Broad HMM hg18 and hg19
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeBroadHmm.ra - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHmm.ra - lines changed 19, context: html, text, full: html, text
• Extended typeOfTerm hidden var to hide from beta,public
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 5, context: html, text, full: html, text
• Support for cv.ra typeOfTerm hidden being alpha,beta,public
  • src/hg/inc/cv.h - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/cv.c - lines changed 42, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/mdb.c - lines changed 6, context: html, text, full: html, text
• Some old doc, and a lot of new stuff to get expIds and dccAccessions in
  • src/hg/makeDb/doc/encodeDccHg18/broadBernstein.txt - lines changed 75, context: html, text, full: html, text
  • src/hg/makeDb/doc/encodeDccHg18/dukeUtaUncCrawford.txt - lines changed 46, context: html, text, full: html, text
  • src/hg/makeDb/doc/encodeDccHg19/broadHistoneBernstein.hg19.txt - lines changed 76, context: html, text, full: html, text
  • src/hg/makeDb/doc/encodeDccHg19/openChromCrawford.hg19.txt - lines changed 194, context: html, text, full: html, text
• Simplified the encodeExp table option
  • src/hg/makeDb/mdbUpdate/mdbPrint.c - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/mdbUpdate/mdbUpdate.c - lines changed 9, context: html, text, full: html, text
• Four composites which are released but need fileSortOrder update for dccAccession
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.new.ra - lines changed 2767, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.new.ra - lines changed 1046, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.new.ra - lines changed 1225, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.new.ra - lines changed 695, context: html, text, full: html, text
• Added fileSortOrder to some hg18 tracks which will be reved some day with dccAccessions
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeq.new.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadHmm.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMap.new.ra - lines changed 2, context: html, text, full: html, text
• Updated fileSortOrder for dccAccession
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHmm.ra - lines changed 1, context: html, text, full: html, text
• Changed a wrong comment that Angie pointed out.
  • src/lib/ra.c - lines changed 1, context: html, text, full: html, text
• Removed a lot of ifdef'd out code. We are not going to revive fileSearch as a tab on trackSearch (unfortunately)
  • src/hg/hgTracks/searchTracks.c - lines changed 95, context: html, text, full: html, text
• Cleaned up some mesages in experimentify mdbPrint command
  • src/hg/lib/mdb.c - lines changed 30, context: html, text, full: html, text
• Hopefully fixed a bad regex on dccAccession
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text
• Added a validation level filter and changed coloring and wording to clarify the difference between OC code and validation level.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.html - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.ra - lines changed 24, context: html, text, full: html, text
• Checking in CGI usage of DOCTYPE 4.01 Transitional (instead of 3.2). Also removed some minor FONT tags that should be replaced by CSS.
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 3, context: html, text, full: html, text
  • src/hg/hgTracks/searchTracks.c - lines changed 2, context: html, text, full: html, text
  • src/hg/htdocs/style/HGStyle.css - lines changed 4, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 10, context: html, text, full: html, text
  • src/hg/lib/jsHelper.c - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/web.c - lines changed 130, context: html, text, full: html, text
  • src/lib/htmshell.c - lines changed 4, context: html, text, full: html, text
• Need the 'f' param for fput.
  • src/lib/htmshell.c - lines changed 1, context: html, text, full: html, text
• Changed antibody=Control to the standard antibody=Input. Removed expIds and dccAccessions for those as well.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra - lines changed 211, context: html, text, full: html, text
• 45 of 70 antobody=Input experiment objects got proper expId's matching hg18.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra - lines changed 91, context: html, text, full: html, text
• Revived the legitimate hg19 only antibody=Input experiments which had been screwed up by antibody=Control.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra - lines changed 41, context: html, text, full: html, text
• One more exp where antibody should not have been Control
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra - lines changed 11, context: html, text, full: html, text
• Removed a <P> tag to keep line spacing the same as when we used DOCTYPE 3.2.
  • src/hg/hgTables/usage.c - lines changed 1, context: html, text, full: html, text
• Insignificant change from FONT tags to CSS.
  • src/hg/hgTracks/hgTracks.c - lines changed 11, context: html, text, full: html, text
• Insignificant change from FONT tags to CSS.
  • src/hg/hgGateway/hgGateway.c - lines changed 3, context: html, text, full: html, text
• Insignificant change from FONT tags to CSS.
  • src/lib/seqOut.c - lines changed 4, context: html, text, full: html, text
• Added the common name of this cute little fellow.
  • src/hg/makeDb/trackDb/gibbon/nomLeu1/description.html - lines changed 1, context: html, text, full: html, text