Commits for rhead

v267_preview to v267_preview2 (2012-05-01 to 2012-05-08) v267

• Added getTrackType(), which uses tdbQuery to determine the track type for a table, if there is one.
  • python/lib/ucscgenomics/qa.py - lines changed 17, context: html, text, full: html, text
• Merge branch 'master' into rhead-pydev
• Start of qa package for analyzing tables.
  • python/lib/ucscgenomics/qa/__init__.py - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • python/lib/ucscgenomics/qa/tables/__init__.py - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • python/lib/ucscgenomics/qa/tables/factory.py - lines changed 41, context: html, text, full: html, text
  • python/lib/ucscgenomics/qa/tables/genePredQa.py - lines changed 12, context: html, text, full: html, text
  • python/lib/ucscgenomics/qa/tables/pointerQa.py - lines changed 8, context: html, text, full: html, text
  • python/lib/ucscgenomics/qa/tables/positionalQa.py - lines changed 21, context: html, text, full: html, text
  • python/lib/ucscgenomics/qa/tables/pslQa.py - lines changed 12, context: html, text, full: html, text
  • python/lib/ucscgenomics/qa/tables/tableQa.py - lines changed 30, context: html, text, full: html, text
• Merge branch 'master' into rhead-pydev
• Added import statements, fixed many indentation and syntax errors.
  • python/lib/ucscgenomics/qa/tables/factory.py - lines changed 13, context: html, text, full: html, text
  • python/lib/ucscgenomics/qa/tables/genePredQa.py - lines changed 4, context: html, text, full: html, text
  • python/lib/ucscgenomics/qa/tables/pointerQa.py - lines changed 3, context: html, text, full: html, text
  • python/lib/ucscgenomics/qa/tables/positionalQa.py - lines changed 3, context: html, text, full: html, text
  • python/lib/ucscgenomics/qa/tables/pslQa.py - lines changed 4, context: html, text, full: html, text
  • python/lib/ucscgenomics/qa/tables/tableQa.py - lines changed 2, context: html, text, full: html, text
• Merge branch 'master' into rhead-pydev
• Merge branch 'master' into rhead-pydev
• Added featureBits and statistics skeleton methods.
  • python/lib/ucscgenomics/qa/tables/positionalQa.py - lines changed 6, context: html, text, full: html, text
• Merge branch 'master' into rhead-pydev
  • python/lib/ucscgenomics/qa/encode/tableCheck.py - lines changed 316, context: html, text, full: html, text
• Added some new functions: getTrackType, tableExists, checkTablesExist, runCommand.
  • python/lib/ucscgenomics/qa/qaUtils.py - lines changed 37, context: html, text, full: html, text
• Made Reporter class for writing results of tests to a file. Wrote genePredCheck, pslCheck and tableDescriptionCheck funcitons using new class.
  • python/lib/ucscgenomics/qa/tables/factory.py - lines changed 9, context: html, text, full: html, text
  • python/lib/ucscgenomics/qa/tables/genePredQa.py - lines changed 12, context: html, text, full: html, text
  • python/lib/ucscgenomics/qa/tables/positionalQa.py - lines changed 2, context: html, text, full: html, text
  • python/lib/ucscgenomics/qa/tables/pslQa.py - lines changed 12, context: html, text, full: html, text
  • python/lib/ucscgenomics/qa/tables/reporter.py - lines changed 67, context: html, text, full: html, text
  • python/lib/ucscgenomics/qa/tables/tableQa.py - lines changed 15, context: html, text, full: html, text
• Started using new classes in ucscgenomics/qa/tables and started putting things into functions.
  • src/utils/qa/qaGbTracks - lines changed 76, context: html, text, full: html, text
• Removed colon from runCommand output. There is no error when using wait instead of communicate.
  • python/lib/ucscgenomics/qa/qaUtils.py - lines changed 1, context: html, text, full: html, text
• Got the validate methods mostly working. For calls to command-line programs, output is sent to the error log file and 'pass' or 'ERROR' is printed, depending on the return code. Still need to keep track of whether or not errors occurred for summary file.
  • python/lib/ucscgenomics/qa/tables/genePredQa.py - lines changed 12, context: html, text, full: html, text
  • python/lib/ucscgenomics/qa/tables/pointerQa.py - lines changed 1, context: html, text, full: html, text
  • python/lib/ucscgenomics/qa/tables/positionalQa.py - lines changed 30, context: html, text, full: html, text
  • python/lib/ucscgenomics/qa/tables/pslQa.py - lines changed 12, context: html, text, full: html, text
  • python/lib/ucscgenomics/qa/tables/reporter.py - lines changed 4, context: html, text, full: html, text
  • python/lib/ucscgenomics/qa/tables/tableQa.py - lines changed 19, context: html, text, full: html, text
  • src/utils/qa/qaGbTracks - lines changed 5, context: html, text, full: html, text
• Fixed calls to private parent class method.
  • python/lib/ucscgenomics/qa/tables/genePredQa.py - lines changed 6, context: html, text, full: html, text
  • python/lib/ucscgenomics/qa/tables/pslQa.py - lines changed 6, context: html, text, full: html, text
• Added summary module for making tab-separated summary output for table QA. Also made qaGbTracks make 3 different files. The .chrom output is just using the tableCheck countPerChrom function for now.
  • python/lib/ucscgenomics/qa/tables/factory.py - lines changed 6, context: html, text, full: html, text
  • python/lib/ucscgenomics/qa/tables/positionalQa.py - lines changed 5, context: html, text, full: html, text
  • python/lib/ucscgenomics/qa/tables/summary.py - lines changed 32, context: html, text, full: html, text
  • python/lib/ucscgenomics/qa/tables/tableQa.py - lines changed 7, context: html, text, full: html, text
  • src/utils/qa/qaGbTracks - lines changed 31, context: html, text, full: html, text
• Got greg to help make a floret for the preview machine that is easier on the eyes. Redmine #3834.
  • src/hg/htdocs/images/floretPreview.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• Merge branch 'master' into rhead-pydev
  • python/lib/ucscgenomics/qa/encode/tableCheck.py - lines changed 18, context: html, text, full: html, text
• Added several track types that are not documented in trackDb/README.
  • python/lib/ucscgenomics/qa/tables/factory.py - lines changed 3, context: html, text, full: html, text
• Made runCommand() use subprocess communicate(), and changed it to return stdout and stderr.
  • python/lib/ucscgenomics/qa/qaUtils.py - lines changed 7, context: html, text, full: html, text
• Tweaked description, changed outFile variable name, put delimter line in a variable.
  • src/utils/qa/qaGbTracks - lines changed 28, context: html, text, full: html, text
• Gave tableType and featureBits columns default values, added column for featureBits gap output, changed column headers.
  • python/lib/ucscgenomics/qa/tables/summary.py - lines changed 19, context: html, text, full: html, text
• Took extra information out of writeStepInfo().
  • python/lib/ucscgenomics/qa/tables/reporter.py - lines changed 1, context: html, text, full: html, text
• Added rowCount(), checkLabelLengths(), and featureBits() methods, and changed name of writePossOrFail() to recordPassOrError() and moved it from PositionalQa to TableQa class.
  • 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 47, 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 26, context: html, text, full: html, text
• Merge branch 'rhead-pydev'
• Added qaGbTracks.
  • src/utils/qa/makefile - lines changed 1, context: html, text, full: html, text