File Changes for wong

v260_preview2 to v260_base (2011-11-22 to 2011-12-06) v260

• python/lib/ucscgenomics/mkChangeNotes.py
  • lines changed 27, context: html, text, full: html, text
    changes for TrackReport
  • lines changed 5, context: html, text, full: html, text
    changes the str output of printsize to be just the megabytes with no unit
  • lines changed 1, context: html, text, full: html, text
    made it so that tablesize also reprots an int
• python/lib/ucscgenomics/ra.py
  • lines changed 0, context: html, text, full: html, text
    rebalanced whitespace to use 4 spaces instead of tab
  • lines changed 190, context: html, text, full: html, text
    added in willy's changed to the ra.py library, only went over changeSummary and updateDiffFilter with him so far, the rest still need to be looked over
• python/lib/ucscgenomics/track.py
  • lines changed 2, context: html, text, full: html, text
    added line to ignore comments in trackDb.wgEncde.ra
  • lines changed 2, context: html, text, full: html, text
    patched in support to ignore folders in the release directory not named supplemental
  • lines changed 1, context: html, text, full: html, text
    corrected an incorrect exception, should be KeyError, FileError is not defined
  • lines changed 1, context: html, text, full: html, text
    fixed a bad regex for supplemental
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • lines changed 28, context: html, text, full: html, text
    get grants revomed
• src/hg/encode/encodeLoad/doEncodeUnload.pl
  • lines changed 2, context: html, text, full: html, text
    get grants revomed
  • lines changed 12, context: html, text, full: html, text
    took out the last remnant of tableSuffix in encodeUnload, missed it in the first pass
• src/hg/encode/encodeMkChangeNotes/test/CurrentMkChangeNotes.py
  • lines changed 34, context: html, text, full: html, text
    moving over mkChangeNotes to current one, passed all internal tests, failed expected end to ends (output changed due to bug fixes)
• src/hg/encode/encodeQaPrepareRelease/encodeQaPrepareRelease
  • lines changed 37, context: html, text, full: html, text
    changed it so that the lines aren't reordered in trackDb.wgEncode.ra by making the arrays be modified in place instead of a copy
  • lines changed 2, context: html, text, full: html, text
    added in line to remove trailing whitespace
• src/hg/encode/encodeQaSqlRelease/encodeQaSqlRelease
  • lines changed 1, context: html, text, full: html, text
    added in close statement for file handle
• src/hg/encode/encodeQaSqlRelease/makefile
  • lines changed 1, context: html, text, full: html, text
    added compilation check to makefile
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 18, context: html, text, full: html, text
    get grants revomed
• src/hg/encode/qaRaDiff/qaRaDiff
  • lines changed 25, context: html, text, full: html, text
    changed RaDiff to use the new ra.py library methods
  • lines changed 1, context: html, text, full: html, text
    had the comparison backwards
• src/hg/encode/qaUpdateMetadata/qaUpdateMetadata
  • lines changed 25, context: html, text, full: html, text
    changed to case insensitive sort of vars and added in magic number generation via a temp table in a database
  • lines changed 64, context: html, text, full: html, text
    rewrite to use library methods
  • lines changed 43, context: html, text, full: html, text
    fixed qaUpdateMetaData to use libraries and print back out a beta.ra with the magic number, and rebalanced whitespace
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwTfbs.release2.notes
  • lines changed 80, context: html, text, full: html, text
    put the cell lines without inputs as attic files
  • lines changed 5, context: html, text, full: html, text
    forgot README.txt
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 20, context: html, text, full: html, text
    first step of rename, renamed to have donor id
  • lines changed 73, context: html, text, full: html, text
    restored old trackDb and metaDb entries
  • lines changed 6, context: html, text, full: html, text
    fixed metadata to reflect renamed status for old objects
  • lines changed 4, context: html, text, full: html, text
    changed cell line to proper term
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 6, context: html, text, full: html, text
    fixed revoke message
  • lines changed 18, context: html, text, full: html, text
    added bai's in fileName
  • lines changed 109, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 5, context: html, text, full: html, text
    changed CD20+ > CD20+_RO01778
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
  • lines changed 2, context: html, text, full: html, text
    added in bai to fileName
  • lines changed 62, context: html, text, full: html, text
    made the cell lines missing inputs attic files
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeBroadHistone.ra
  • lines changed 920, context: html, text, full: html, text
    updated betaMdb with dccAccessions.
  • lines changed 920, context: html, text, full: html, text
    Revert "updated betaMdb with dccAccessions." This reverts commit b3f4b90175570e64e2464c758d3b3dbf780769fb.
  • lines changed 920, context: html, text, full: html, text
    added dccAccessions to tracks that are missing them
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeCshlShortRnaSeq.ra
  • lines changed 54, context: html, text, full: html, text
    updated betaMdb with dccAccessions.
  • lines changed 54, context: html, text, full: html, text
    Revert "updated betaMdb with dccAccessions." This reverts commit b3f4b90175570e64e2464c758d3b3dbf780769fb.
  • lines changed 54, context: html, text, full: html, text
    added dccAccessions to tracks that are missing them
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeHaibTfbs.ra
  • lines changed 25, context: html, text, full: html, text
    revoking HEY1 and K562/BCL3 experiments in beta only
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromChip.ra
  • lines changed 271, context: html, text, full: html, text
    updated betaMdb with dccAccessions.
  • lines changed 271, context: html, text, full: html, text
    Revert "updated betaMdb with dccAccessions." This reverts commit b3f4b90175570e64e2464c758d3b3dbf780769fb.
  • lines changed 270, context: html, text, full: html, text
    added dccAccessions to tracks that are missing them
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromDnase.ra
  • lines changed 328, context: html, text, full: html, text
    updated betaMdb with dccAccessions.
  • lines changed 328, context: html, text, full: html, text
    Revert "updated betaMdb with dccAccessions." This reverts commit b3f4b90175570e64e2464c758d3b3dbf780769fb.
  • lines changed 328, context: html, text, full: html, text
    added dccAccessions to tracks that are missing them
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromFaire.ra
  • lines changed 179, context: html, text, full: html, text
    updated betaMdb with dccAccessions.
  • lines changed 179, context: html, text, full: html, text
    Revert "updated betaMdb with dccAccessions." This reverts commit b3f4b90175570e64e2464c758d3b3dbf780769fb.
  • lines changed 179, context: html, text, full: html, text
    added dccAccessions to tracks that are missing them
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeRikenCage.ra
  • lines changed 101, context: html, text, full: html, text
    updated betaMdb with dccAccessions.
  • lines changed 101, context: html, text, full: html, text
    Revert "updated betaMdb with dccAccessions." This reverts commit b3f4b90175570e64e2464c758d3b3dbf780769fb.
  • lines changed 102, context: html, text, full: html, text
    added dccAccessions to tracks that are missing them
  • lines changed 2, context: html, text, full: html, text
    restored order of var val pair
  • lines changed 100, context: html, text, full: html, text
    changed to case insensitive sort of vars and added in magic number generation via a temp table in a database
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSunyAlbanyTiling.ra
  • lines changed 8, context: html, text, full: html, text
    updated betaMdb with dccAccessions.
  • lines changed 8, context: html, text, full: html, text
    Revert "updated betaMdb with dccAccessions." This reverts commit b3f4b90175570e64e2464c758d3b3dbf780769fb.
  • lines changed 8, context: html, text, full: html, text
    added dccAccessions to tracks that are missing them
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwAffyExonArray.ra
  • lines changed 135, context: html, text, full: html, text
    updated betaMdb with dccAccessions.
  • lines changed 135, context: html, text, full: html, text
    Revert "updated betaMdb with dccAccessions." This reverts commit b3f4b90175570e64e2464c758d3b3dbf780769fb.
  • lines changed 135, context: html, text, full: html, text
    added dccAccessions to tracks that are missing them
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwDgf.ra
  • lines changed 114, context: html, text, full: html, text
    updated betaMdb with dccAccessions.
  • lines changed 114, context: html, text, full: html, text
    Revert "updated betaMdb with dccAccessions." This reverts commit b3f4b90175570e64e2464c758d3b3dbf780769fb.
  • lines changed 114, context: html, text, full: html, text
    added dccAccessions to tracks that are missing them
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwTfbs.ra
  • lines changed 483, context: html, text, full: html, text
    updated betaMdb with dccAccessions.
  • lines changed 483, context: html, text, full: html, text
    Revert "updated betaMdb with dccAccessions." This reverts commit b3f4b90175570e64e2464c758d3b3dbf780769fb.
  • lines changed 483, context: html, text, full: html, text
    added dccAccessions to tracks that are missing them
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.html
  • lines changed 1, context: html, text, full: html, text
    added in line about metadata location to html descriptions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHmm.html
  • lines changed 1, context: html, text, full: html, text
    added in line about metadata location to html descriptions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.html
  • lines changed 2, context: html, text, full: html, text
    fixed a spelling error
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.html
  • lines changed 1, context: html, text, full: html, text
    added in line about metadata location to html descriptions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.new.html
  • lines changed 1, context: html, text, full: html, text
    added in line about metadata location to html descriptions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.html
  • lines changed 2, context: html, text, full: html, text
    added in line about metadata location to html descriptions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
  • lines changed 64, context: html, text, full: html, text
    revokeing HEY1 tracks in trackDb, this will leak out at the the of the week.
  • lines changed 28, context: html, text, full: html, text
    the K562/BCL3 objects need to be revoke also
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.html
  • lines changed 2, context: html, text, full: html, text
    added in line about metadata location to html descriptions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.new.ra
  • lines changed 2, context: html, text, full: html, text
    checking trackDb changes for rename
  • lines changed 9, context: html, text, full: html, text
    restored old trackDb and metaDb entries
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.html
  • lines changed 2, context: html, text, full: html, text
    added in line about metadata location to html descriptions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.html
  • lines changed 2, context: html, text, full: html, text
    added in line about metadata location to html descriptions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.html
  • lines changed 2, context: html, text, full: html, text
    added in line about metadata location to html descriptions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.html
  • lines changed 1, context: html, text, full: html, text
    added in line about metadata location to html descriptions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.new.html
  • lines changed 1, context: html, text, full: html, text
    added in line about metadata location to html descriptions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhNsome.html
  • lines changed 1, context: html, text, full: html, text
    added in line about metadata location to html descriptions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.html
  • lines changed 1, context: html, text, full: html, text
    added in line about metadata location to html descriptions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.html
  • lines changed 2, context: html, text, full: html, text
    added in line about metadata location to html descriptions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.new.html
  • lines changed 2, context: html, text, full: html, text
    added in line about metadata location to html descriptions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.html
  • lines changed 1, context: html, text, full: html, text
    added in line about metadata location to html descriptions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.html
  • lines changed 2, context: html, text, full: html, text
    added in line about metadata location to html descriptions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.html
  • lines changed 2, context: html, text, full: html, text
    added in line about metadata location to html descriptions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.html
  • lines changed 2, context: html, text, full: html, text
    added in line about metadata location to html descriptions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra
  • lines changed 1, context: html, text, full: html, text
    reordered cell lines to be alphabetical
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.ra
  • lines changed 1, context: html, text, full: html, text
    reordered cell lines to be alphabetical
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.html
  • lines changed 2, context: html, text, full: html, text
    added in line about metadata location to html descriptions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.html
  • lines changed 2, context: html, text, full: html, text
    added in line about metadata location to html descriptions
• src/hg/utils/automation/Encode.pm
  • lines changed 6, context: html, text, full: html, text
    get grants revomed
• src/hg/utils/automation/makefile
  • lines changed 3, context: html, text, full: html, text
    added development target