Commits for wong

v259_base to v260_preview (2011-11-07 to 2011-11-15) v260

• added information to an error to say that it is fatal
  • src/hg/encode/encodeQaInit/encodeQaInit - lines changed 1, context: html, text, full: html, text
• added more to error message
  • src/hg/encode/encodeQaInit/encodeQaInit - lines changed 4, context: html, text, full: html, text
• made other error message consistent
  • src/hg/encode/encodeQaInit/encodeQaInit - lines changed 5, context: html, text, full: html, text
• moved old version to .v09 and moved mkChangeNotes to encodeMkChangeNotes
  • src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes - lines changed 557, context: html, text, full: html, text
  • src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes.v09 - lines changed 565, context: html, text, full: html, text
  • src/hg/encode/mkChangeNotes/mkChangeNotes - lines changed 61, context: html, text, full: html, text
• changed mkChangeNotes test over to encodeMkChangeNotes and added README
  • src/hg/encode/encodeMkChangeNotes/test/CurrentMkChangeNotes.py - lines changed 637, context: html, text, full: html, text
  • src/hg/encode/encodeMkChangeNotes/test/CurrentMkChangeNotes.pyc - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/encode/encodeMkChangeNotes/test/README - lines changed 25, context: html, text, full: html, text
  • src/hg/encode/encodeMkChangeNotes/test/mkChangeTest - lines changed 83, context: html, text, full: html, text
  • src/hg/encode/encodeMkChangeNotes/test/testRunner - lines changed 61, 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 637, 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/testRunner - lines changed 61, context: html, text, full: html, text
• accidentally added the compiled library
  • src/hg/encode/encodeMkChangeNotes/test/CurrentMkChangeNotes.pyc - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• added in qaRaDiff first draft
  • src/hg/encode/qaRaDiff/makefile - lines changed 27, context: html, text, full: html, text
  • src/hg/encode/qaRaDiff/qaRaDiff - lines changed 75, context: html, text, full: html, text
• Revert "changed how encodeValidate and friends uses packages to allow for same directory location of the packages" This reverts commit 371b1e65141e2a3ef55220fee8a120e8fa90dc26.
  • src/hg/encode/encodeLoad/doEncodeLoad.pl - lines changed 13, context: html, text, full: html, text
  • src/hg/encode/encodeLoad/doEncodeUnload.pl - lines changed 13, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 14, context: html, text, full: html, text
• Revert "removed the need for labs.ra" This reverts commit 8dc382b443d003200c40eb60b1957d6bfcec5493.
  • src/hg/encode/encodeLoad/doEncodeLoad.pl - lines changed 7, context: html, text, full: html, text
  • src/hg/encode/encodeLoad/doEncodeUnload.pl - lines changed 2, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 28, context: html, text, full: html, text
  • src/hg/utils/automation/Encode.pm - lines changed 21, context: html, text, full: html, text
• Revert "removed the code for pi.ra" This reverts commit a8d2cd12a9005d8bb60f1c89c900ea5a76c145b6.
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/automation/Encode.pm - lines changed 13, context: html, text, full: html, text
• removed the need to labs.ra in encodeValidate only
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 2, context: html, text, full: html, text
• fixed some issues with tester. no long need a copy of doEncodeValidate.pl in the directory
  • src/hg/encode/encodeValidate/newtest/allGood/out/mdb.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/newtest/allGood/out/trackDb.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/newtest/badDdfDafs/invalidFiletype/notest.cfg - lines changed 49, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/newtest/baddafs/badDataVersion/out/mdb.txt - lines changed 2, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/newtest/baddafs/badDataVersion/out/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/newtest/baddafs/noDataVersionComment/test.cfg - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/newtest/list - lines changed 18, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/newtest/tester.pl - lines changed 19, context: html, text, full: html, text
• fleshed out test some more
  • src/hg/encode/encodeValidate/newtest/README - lines changed 14, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/newtest/badDdfDafs/invalidFiletype/test.cfg - lines changed 49, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/newtest/list - lines changed 18, context: html, text, full: html, text
• added comments to functions to be deprecated
  • src/hg/utils/automation/Encode.pm - lines changed 3, context: html, text, full: html, text
• fixed the Error: 1 error
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 9, context: html, text, full: html, text
• removed copy of doEncodeValidate
  • src/hg/encode/encodeValidate/newtest/doEncodeValidate.pl - lines changed 2409, context: html, text, full: html, text
• removed comment referencing pi.ra
  • src/hg/encode/encodeValidate/doEncodeValidate.pl - lines changed 2, context: html, text, full: html, text
• removed pi.ra from teste config directory
  • src/hg/encode/encodeValidate/newtest/config/pi.ra - lines changed 181, context: html, text, full: html, text
• fixed some error print in solo mode with errors
  • python/lib/ucscgenomics/mkChangeNotes.py - lines changed 4, context: html, text, full: html, text
• added test headers so you know what's up
  • src/hg/encode/encodeQaInit/encodeQaInit - lines changed 8, context: html, text, full: html, text
• first draft of qaPrepareRelease
  • src/hg/encode/encodeQaPrepareRelease/encodeQaPrepareRelease - lines changed 406, context: html, text, full: html, text
  • src/hg/encode/encodeQaPrepareRelease/makefile - lines changed 27, context: html, text, full: html, text
• removed hardcoded verbose output
  • src/hg/encode/encodeQaPrepareRelease/encodeQaPrepareRelease - lines changed 1, context: html, text, full: html, text
• made a check to see that you have a trackDb.ra in the trackDb dir
  • src/hg/encode/encodeQaPrepareRelease/encodeQaPrepareRelease - lines changed 14, context: html, text, full: html, text
• rebalanced whitespace, and made meta db diffs more descriptive
  • src/hg/encode/encodeQaPrepareRelease/encodeQaPrepareRelease - lines changed 3, context: html, text, full: html, text
• changed metaDb diff output again, alphabetizes and aggregates dropped and new stanzas
  • src/hg/encode/encodeQaPrepareRelease/encodeQaPrepareRelease - lines changed 31, context: html, text, full: html, text
• changed name in usage statement
  • src/hg/encode/encodeQaSqlRelease/encodeQaSqlRelease - lines changed 2, context: html, text, full: html, text
• revoked all the HEY1 entries, lab is not confident the antibody is binding to HEY1, looks like POL2 results
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 109, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.new.ra - lines changed 8921, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.ra - lines changed 8929, context: html, text, full: html, text
• changed visibility of hotspots to match the expected default behavior
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra - lines changed 1, context: html, text, full: html, text