Commits for wong

v263_base to v264_preview (2012-02-14 to 2012-02-21) v264

• md5sums for open chrom dnase
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra - lines changed 113, context: html, text, full: html, text
• changed it to complain and die upon subId setting to reviewing failure
  • src/hg/encode/encodeQaInit/encodeQaInit - lines changed 10, context: html, text, full: html, text
• some merge problem needs this
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 9, context: html, text, full: html, text
• more lab found errors
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 9, context: html, text, full: html, text
• added in provisional views for haib Bisulfite
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibBisulfate.ra - lines changed 115, context: html, text, full: html, text
• added in the rest of the bisulfate test track
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibBisulfate.html - lines changed 125, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibBisulfate.ra - lines changed 84, context: html, text, full: html, text
• forgot alpha tag
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 1, context: html, text, full: html, text
• flo's version of haib bisulfate
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibBisulfate.html - lines changed 74, context: html, text, full: html, text
• more fake stanzas
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibBisulfate.ra - lines changed 157, context: html, text, full: html, text
• I have no idea how that one got commented out
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release3.ra - lines changed 42, context: html, text, full: html, text
• for the merge
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 2, context: html, text, full: html, text
• removing temporary provisional views
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 16, context: html, text, full: html, text
• corrected notes, last time was premature
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwHistone.release3.notes - lines changed 30, context: html, text, full: html, text
• fixed tense
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release3.html - lines changed 1, context: html, text, full: html, text
• pre-qa fixes
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release3.html - lines changed 3, context: html, text, full: html, text
• pre=qa fixes and reformed references
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.html - lines changed 41, context: html, text, full: html, text
• renaming some files before they are released
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.ra - lines changed 8, context: html, text, full: html, text
• reverted a metaDB change, becuase hte objects already went out in release 1
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 9, context: html, text, full: html, text
• changing tag to conform to norm
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text
• renamed objects to now have antibody vendor id
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 191, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.ra - lines changed 64, context: html, text, full: html, text
• added in FoxM1 experiment
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 183, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.ra - lines changed 45, context: html, text, full: html, text
• the threading of the md5sums was causing problems with the database objects not being able to be clones, so i dosconnect fom the database, then reconnect after making the md5sums
  • src/hg/encode/encodeMkFilesList/encodeMkFilesList - lines changed 2, context: html, text, full: html, text
• added in md5sums
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 17, context: html, text, full: html, text
• updated notes again
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibTfbs.release2.notes - lines changed 135, context: html, text, full: html, text
• forgot to also remove revoked tables from the change table status set, possibly need to remove attic, but i'll do it if the problem comes up
  • python/lib/ucscgenomics/mkChangeNotes.py - lines changed 1, context: html, text, full: html, text
• fixed html and order of cells in list
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release3.html - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release3.ra - lines changed 1, context: html, text, full: html, text
• changed view limit according to lab
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra - lines changed 1, context: html, text, full: html, text
• expIds for haib
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 37, context: html, text, full: html, text
• expIds and other mdb fixes
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra - lines changed 271, context: html, text, full: html, text
• more metadata corrections
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra - lines changed 3, context: html, text, full: html, text
• added in antibody target to the decsription field (Willy)
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 95, context: html, text, full: html, text
• changed the gzip md5sum function to check internally for the contents, but report the external md5sum to the metaDb
  • src/hg/encode/encodeMkFilesList/encodeMkFilesList - lines changed 70, context: html, text, full: html, text
• changed filter to all for treatment
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.ra - lines changed 1, context: html, text, full: html, text
• fixed alphabetization
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release3.ra - lines changed 2, context: html, text, full: html, text
• this time for real on alphabetize
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release3.ra - lines changed 1, context: html, text, full: html, text
• fixed internal gzip md5sum
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra - lines changed 627, context: html, text, full: html, text
• fixed capitalization
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release3.ra - lines changed 1, context: html, text, full: html, text
• more internal gzip bug fixes
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra - lines changed 145, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 1076, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra - lines changed 409, context: html, text, full: html, text
• correcting for the gzip bug error in mkFilesList
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra - lines changed 687, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra - lines changed 98, context: html, text, full: html, text
• changed short labels according to lab
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra - lines changed 47, context: html, text, full: html, text
• expIds and accessions for rna seq
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibRnaSeq.ra - lines changed 21, context: html, text, full: html, text
• changed it to show the server and foldername onthe same line
  • src/hg/encode/encodeQaCheckHgdownloadFiles/encodeQaCheckHgdownloadFiles - lines changed 2, context: html, text, full: html, text
• correcting some errors
  • src/hg/utils/automation/HgDb.pm - lines changed 2, context: html, text, full: html, text
• removed line that was left from debugging
  • src/hg/utils/automation/HgDb.pm - lines changed 1, context: html, text, full: html, text
• uncomment parser line, and reomved Test \d: from test names
  • src/hg/encode/qaEncodeTracks2/qaEncodeTracks - lines changed 8, context: html, text, full: html, text
• changed the reporting of changed tables state to be a critical error
  • python/lib/ucscgenomics/mkChangeNotes.py - lines changed 17, context: html, text, full: html, text
• first draft of qaAddTrackReferences
  • src/hg/encode/qaAddTrackReferences/makefile - lines changed 28, context: html, text, full: html, text
  • src/hg/encode/qaAddTrackReferences/qaAddTrackReferences - lines changed 423, context: html, text, full: html, text
• removed unnecessary lines
  • src/hg/encode/qaAddTrackReferences/qaAddTrackReferences - lines changed 60, context: html, text, full: html, text
• changed how collective name is put in the author list. It's always put at the front now.
  • src/hg/encode/qaAddTrackReferences/qaAddTrackReferences - lines changed 17, context: html, text, full: html, text