Commits for wong

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

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