Commits for rhead

v267_preview2 to v267_base (2012-05-08 to 2012-05-15) v267

• Removed __ from __recordPassOrError() and got rid of calls to its name-mangled string, per Mark.
  • python/lib/ucscgenomics/qa/tables/genePredQa.py - lines changed 1, context: html, text, full: html, text
  • python/lib/ucscgenomics/qa/tables/positionalQa.py - lines changed 4, context: html, text, full: html, text
  • python/lib/ucscgenomics/qa/tables/pslQa.py - lines changed 1, context: html, text, full: html, text
  • python/lib/ucscgenomics/qa/tables/tableQa.py - lines changed 5, context: html, text, full: html, text
• Put in a special case for Chain/Net shortlabels, which are longer than the current shortLabel limit of 17 chars but are an exception to the rule.
  • python/lib/ucscgenomics/qa/tables/positionalQa.py - lines changed 3, context: html, text, full: html, text
• Added trackDb and hgFindSpec to pattern of exceptions for table name underscore check.
  • python/lib/ucscgenomics/qa/tables/tableQa.py - lines changed 2, context: html, text, full: html, text
• Changed and reordered help comment wording a little and added option to use the name of a single table at the command line rather than supply a list of tables.
  • src/utils/qa/qaGbTracks - lines changed 18, context: html, text, full: html, text
• Changed ucscgenomics to ucscGb in import statements to match reorganization.
  • src/utils/qa/qaGbTracks - lines changed 5, context: html, text, full: html, text
• Removed unused argument from validate(). Thanks, Greg.
  • python/lib/ucscGb/qa/tables/pointerQa.py - lines changed 1, context: html, text, full: html, text
• Moved two functions from qaUtils to qaGbTracks, and got rid of a duplicated function from qaUtils.
  • python/lib/ucscGb/qa/qaUtils.py - lines changed 28, context: html, text, full: html, text
  • src/utils/qa/qaGbTracks - lines changed 12, context: html, text, full: html, text
• Made getAttributeForTrack function check for the table setting in addition to the track setting, and made the getLabels function strip the on or off setting for parents so that they can be used to find more labels.
  • python/lib/ucscGb/qa/tables/positionalQa.py - lines changed 5, context: html, text, full: html, text
• Made PointerQa into a PositionalQa object instead of a generic TableQa object so that the check for label lengths can be done. Made validate and statistics methods mostly call TableQa methods plus the PositionalQa checkLabelLengths method. Also moved label length limits into a global variable.
  • python/lib/ucscGb/qa/tables/pointerQa.py - lines changed 9, context: html, text, full: html, text
  • python/lib/ucscGb/qa/tables/positionalQa.py - lines changed 6, context: html, text, full: html, text
• Made search for parent track labels look for deprecated subTrack setting in addition to parent setting; made it so that 'view' labels are not checked.
  • python/lib/ucscGb/qa/tables/positionalQa.py - lines changed 26, context: html, text, full: html, text
• Removed check for table descriptions from PointerQa types. See redmine #7896.
  • python/lib/ucscGb/qa/tables/pointerQa.py - lines changed 1, context: html, text, full: html, text
  • python/lib/ucscGb/qa/tables/tableQa.py - lines changed 4, context: html, text, full: html, text
• Excluded Genbank tables from positionalTblCheck. Also removed spaces from label printing.
  • python/lib/ucscGb/qa/tables/positionalQa.py - lines changed 24, context: html, text, full: html, text