File Changes for wong

v259_preview to v259_preview2 (2011-10-25 to 2011-11-01) v259

• python/lib/setup.py
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    removed execute flag on setup.py. it's now executable
• python/lib/ucscgenomics/mkChangeNotes.py
  • lines changed 57, context: html, text, full: html, text
    removed executable portion, fixed bug with special mdb
  • lines changed 0, context: html, text, full: html, text
    unsetting exectuable flag for these
  • lines changed 29, context: html, text, full: html, text
    moved a function out for cleanliness
  • lines changed 386, context: html, text, full: html, text
    refactored a bit, removed some random newlines in output
  • lines changed 12, context: html, text, full: html, text
    fix a reporting error in mkChangeNotes, added in fuctionality to show when newly revoked files go out as a result of a revoke and name change in one release
  • lines changed 8, context: html, text, full: html, text
    cleaned up output a little
  • lines changed 53, context: html, text, full: html, text
    pulled out functions that may be useful outside of mkChangeNotes
  • lines changed 78, context: html, text, full: html, text
    changed output a little, added in some some printing functions, prints out a missing tables list now also
  • lines changed 22, context: html, text, full: html, text
    declared some attributes earlier to bypass a qa check.
  • lines changed 3, context: html, text, full: html, text
    put in date notes file was generated
  • lines changed 7, context: html, text, full: html, text
    using correct path from dropped files
  • lines changed 26, context: html, text, full: html, text
    added some more human readable stuff, and put in a precheck for a condition that won't exist in release 1 mode.
• python/lib/ucscgenomics/qa.py
  • lines changed 111, context: html, text, full: html, text
    added some documentation, added in 2 new functions, and corrected some other stuff i noticed
  • lines changed 88, context: html, text, full: html, text
    reworked qa.py and separated out the executable portion into another app in encode
  • lines changed 0, context: html, text, full: html, text
    unsetting exectuable flag for these
  • lines changed 4, context: html, text, full: html, text
    added skipping of comment lines for label check
  • lines changed 1, context: html, text, full: html, text
    upped timeout to 20 seconds
  • lines changed 22, context: html, text, full: html, text
    added smarted filtering error messages
• python/lib/ucscgenomics/track.py
  • lines changed 16, context: html, text, full: html, text
    added in a property I needed in qaInit
  • lines changed 11, context: html, text, full: html, text
    added in ability to use a custom mdb
  • lines changed 10, context: html, text, full: html, text
    added qa test dir attribute
• python/lib/ucscgenomics/ucscUtils.py
  • lines changed 41, context: html, text, full: html, text
    pulled out functions that may be useful outside of mkChangeNotes
• src/hg/encode/encodeQaInit/encodeQaInit
  • lines changed 550, context: html, text, full: html, text
    made directory work with rename
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    changed program name in usage
• src/hg/encode/encodeQaInit/makefile
  • lines changed 27, context: html, text, full: html, text
    renamed directory qaInit > encodeQaInit
  • lines changed 1, context: html, text, full: html, text
    made directory work with rename
• src/hg/encode/encodeQaInit/qaInit
  • lines changed 550, context: html, text, full: html, text
    renamed directory qaInit > encodeQaInit
  • lines changed 550, context: html, text, full: html, text
    made directory work with rename
• src/hg/encode/encodeQaSqlRelease/encodeQaSqlRelease
  • lines changed 96, context: html, text, full: html, text
    first draft (still in perl, but it doesn't need library functions, so porting is not a priority) for qa's program to insert a row into the L queue
• src/hg/encode/encodeQaSqlRelease/makefile
  • lines changed 27, context: html, text, full: html, text
    first draft (still in perl, but it doesn't need library functions, so porting is not a priority) for qa's program to insert a row into the L queue
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 2, context: html, text, full: html, text
    corrected erroneously commented out line
• src/hg/encode/mkChangeNotes/makefile
  • lines changed 27, context: html, text, full: html, text
    fix a reporting error in mkChangeNotes, added in fuctionality to show when newly revoked files go out as a result of a revoke and name change in one release
• src/hg/encode/mkChangeNotes/mkChangeNotes
  • lines changed 7, context: html, text, full: html, text
    added in the ability to custom define a composite mdb
• src/hg/encode/mkChangeNotes/tests/CurrentMkChangeNotes.py
  • lines changed 126, context: html, text, full: html, text
    new testing structure for mkChangeNotes, still needs full function testing
  • lines changed 411, context: html, text, full: html, text
    fleshed out function tests in mkChangeTest, added in runner for currentMkchangeNotes
  • lines changed 13, context: html, text, full: html, text
    fix a reporting error in mkChangeNotes, added in fuctionality to show when newly revoked files go out as a result of a revoke and name change in one release
  • lines changed 8, context: html, text, full: html, text
    updating test
  • lines changed 53, context: html, text, full: html, text
    pulled out functions that may be useful outside of mkChangeNotes
  • lines changed 123, context: html, text, full: html, text
    updated test to reflect newer version of mkChangenotes
• src/hg/encode/mkChangeNotes/tests/mkChangeTest
  • lines changed 83, context: html, text, full: html, text
    fleshed out function tests in mkChangeTest, added in runner for currentMkchangeNotes
• src/hg/encode/mkChangeNotes/tests/mkChangeTest.py
  • lines changed 36, context: html, text, full: html, text
    new testing structure for mkChangeNotes, still needs full function testing
  • lines changed 72, context: html, text, full: html, text
    fleshed out function tests in mkChangeTest, added in runner for currentMkchangeNotes
• src/hg/encode/mkChangeNotes/tests/release1test/wgEncodeTest.ra
  • lines changed 73, context: html, text, full: html, text
    fleshed out function tests in mkChangeTest, added in runner for currentMkchangeNotes
• src/hg/encode/mkChangeNotes/tests/release2test/wgEncodeTest.ra
  • lines changed 143, context: html, text, full: html, text
    fleshed out function tests in mkChangeTest, added in runner for currentMkchangeNotes
• src/hg/encode/mkChangeNotes/tests/release3test/wgEncodeTest.ra
  • lines changed 145, context: html, text, full: html, text
    fleshed out function tests in mkChangeTest, added in runner for currentMkchangeNotes
• src/hg/encode/mkChangeNotes/tests/release4test/wgEncodeTest.ra
  • lines changed 173, context: html, text, full: html, text
    fleshed out function tests in mkChangeTest, added in runner for currentMkchangeNotes
• src/hg/encode/mkChangeNotes/tests/testRunner
  • lines changed 61, context: html, text, full: html, text
    fleshed out function tests in mkChangeTest, added in runner for currentMkchangeNotes
• src/hg/encode/qaEncodeTracks2/qaEncodeTracks
  • lines changed 67, context: html, text, full: html, text
    reworked qa.py and separated out the executable portion into another app in encode
  • lines changed 14, context: html, text, full: html, text
    added in delimiters for human readibility in script output
  • lines changed 9, context: html, text, full: html, text
    put in better delimiters
• src/hg/encode/qaInit/makefile
  • lines changed 27, context: html, text, full: html, text
    fix a reporting error in mkChangeNotes, added in fuctionality to show when newly revoked files go out as a result of a revoke and name change in one release
  • lines changed 27, context: html, text, full: html, text
    renamed directory qaInit > encodeQaInit
• src/hg/encode/qaInit/qaInit
  • lines changed 60, context: html, text, full: html, text
    added in qa checks from ported qaEncodeTracks
  • lines changed 17, context: html, text, full: html, text
    bug fixes and added in ability to use custom mdb names
  • lines changed 3, context: html, text, full: html, text
    added in switch to take errors in local mkChangeNotes data into account
  • lines changed 1, context: html, text, full: html, text
    updated usage
  • lines changed 45, context: html, text, full: html, text
    last draft before reviewing for qaInit, added test mode, print out list of subIds
  • lines changed 23, context: html, text, full: html, text
    changed what initdate means, added function to keep it rolling along everytime init is run
  • lines changed 550, context: html, text, full: html, text
    renamed directory qaInit > encodeQaInit
• src/hg/encode/qaUpdateMetadata/qaUpdateMetadata
  • lines changed 2, context: html, text, full: html, text
    Updated description
• src/hg/makeDb/doc/encodeDccEncodetest/wgEncodeTest.release1.notes
  • lines changed 60, context: html, text, full: html, text
    notes location for encodeTest
• src/hg/makeDb/doc/encodeDccEncodetest/wgEncodeTest.release2.notes
  • lines changed 117, context: html, text, full: html, text
    notes location for encodeTest
• src/hg/makeDb/doc/encodeDccEncodetest/wgEncodeTest.release3.notes
  • lines changed 119, context: html, text, full: html, text
    notes location for encodeTest
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeCaltechRnaSeq.release2.notes
  • lines changed 1503, context: html, text, full: html, text
    added some more human readable stuff, and put in a precheck for a condition that won't exist in release 1 mode.
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwAffyExonArray.release2.notes
  • lines changed 395, context: html, text, full: html, text
    added some more human readable stuff, and put in a precheck for a condition that won't exist in release 1 mode.
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeCaltechHist.release1.notes
  • lines changed 35, context: html, text, full: html, text
    added some more human readable stuff, and put in a precheck for a condition that won't exist in release 1 mode.
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeCaltechTfbs.release1.notes
  • lines changed 49, context: html, text, full: html, text
    added some more human readable stuff, and put in a precheck for a condition that won't exist in release 1 mode.
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/alpha/makefile
  • lines changed 7, context: html, text, full: html, text
    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/alpha/wgEncodeTest1.ra
  • lines changed 72, context: html, text, full: html, text
    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/alpha/wgEncodeTest2.ra
  • lines changed 143, context: html, text, full: html, text
    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/alpha/wgEncodeTest3.ra
  • lines changed 145, context: html, text, full: html, text
    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/alpha/wgEncodeTest4.ra
  • lines changed 173, context: html, text, full: html, text
    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/beta/makefile
  • lines changed 7, context: html, text, full: html, text
    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/beta/wgEncodeTest1.ra
  • lines changed 0, context: html, text, full: html, text
    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/beta/wgEncodeTest2.ra
  • lines changed 73, context: html, text, full: html, text
    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/beta/wgEncodeTest3.ra
  • lines changed 143, context: html, text, full: html, text
    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/beta/wgEncodeTest4.ra
  • lines changed 145, context: html, text, full: html, text
    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/public/makefile
  • lines changed 7, context: html, text, full: html, text
    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/public/wgEncodeTest.ra
  • lines changed 145, context: html, text, full: html, text
    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/public/wgEncodeTest1.ra
  • lines changed 0, context: html, text, full: html, text
    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/public/wgEncodeTest2.ra
  • lines changed 73, context: html, text, full: html, text
    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/public/wgEncodeTest3.ra
  • lines changed 143, context: html, text, full: html, text
    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/public/wgEncodeTest4.ra
  • lines changed 145, context: html, text, full: html, text
    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/testRelease1/wgEncodeTest.ra
  • lines changed 73, context: html, text, full: html, text
    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/testRelease2/wgEncodeTest.ra
  • lines changed 143, context: html, text, full: html, text
    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/testRelease3/wgEncodeTest.ra
  • lines changed 145, context: html, text, full: html, text
    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/testRelease4/wgEncodeTest.ra
  • lines changed 173, context: html, text, full: html, text
    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/wgEncodeTest.html
  • lines changed 0, context: html, text, full: html, text
    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/wgEncodeTest.ra
  • lines changed 0, context: html, text, full: html, text
    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/wgEncodeTest1.html
  • lines changed 0, context: html, text, full: html, text
    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/wgEncodeTest1.ra
  • lines changed 0, context: html, text, full: html, text
    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/wgEncodeTest2.html
  • lines changed 0, context: html, text, full: html, text
    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/wgEncodeTest2.ra
  • lines changed 0, context: html, text, full: html, text
    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/wgEncodeTest3.html
  • lines changed 0, context: html, text, full: html, text
    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/wgEncodeTest3.ra
  • lines changed 0, context: html, text, full: html, text
    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra
  • lines changed 253, context: html, text, full: html, text
    removed 12 objects - Willy via Cricket
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 301, context: html, text, full: html, text
    added in geo accessions - Willy
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 73, context: html, text, full: html, text
    added in SKMC control
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
  • lines changed 83, context: html, text, full: html, text
    fixed control metadata terms
  • lines changed 742, context: html, text, full: html, text
    added treatment = None for items that needed it
  • lines changed 741, context: html, text, full: html, text
    added in None for treatment field in controlId
  • lines changed 73, context: html, text, full: html, text
    added in SKMC control
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra
  • lines changed 8, context: html, text, full: html, text
    added in SKMC control
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.ra
  • lines changed 9, context: html, text, full: html, text
    added in SKMC control