File Changes for rhead

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

• python/lib/ucscgenomics/qa.py
  • lines changed 17, context: html, text, full: html, text
    Added getTrackType(), which uses tdbQuery to determine the track type for a table, if there is one.
• python/lib/ucscgenomics/qa/__init__.py
  • lines changed 0, context: html, text, full: html, text
    Start of qa package for analyzing tables.
• python/lib/ucscgenomics/qa/encode/tableCheck.py
  • lines changed 316, context: html, text, full: html, text
    Merge branch 'master' into rhead-pydev
  • lines changed 18, context: html, text, full: html, text
    Merge branch 'master' into rhead-pydev
• python/lib/ucscgenomics/qa/qaUtils.py
  • lines changed 37, context: html, text, full: html, text
    Added some new functions: getTrackType, tableExists, checkTablesExist, runCommand.
  • lines changed 1, context: html, text, full: html, text
    Removed colon from runCommand output. There is no error when using wait instead of communicate.
  • lines changed 7, context: html, text, full: html, text
    Made runCommand() use subprocess communicate(), and changed it to return stdout and stderr.
• python/lib/ucscgenomics/qa/tables/__init__.py
  • lines changed 0, context: html, text, full: html, text
    Start of qa package for analyzing tables.
• python/lib/ucscgenomics/qa/tables/factory.py
  • lines changed 41, context: html, text, full: html, text
    Start of qa package for analyzing tables.
  • lines changed 13, context: html, text, full: html, text
    Added import statements, fixed many indentation and syntax errors.
  • lines changed 9, 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.
  • 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.
  • lines changed 3, context: html, text, full: html, text
    Added several track types that are not documented in trackDb/README.
• python/lib/ucscgenomics/qa/tables/genePredQa.py
  • lines changed 12, context: html, text, full: html, text
    Start of qa package for analyzing tables.
  • lines changed 4, context: html, text, full: html, text
    Added import statements, fixed many indentation and syntax errors.
  • lines changed 12, 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.
  • lines changed 12, 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.
  • lines changed 6, context: html, text, full: html, text
    Fixed calls to private parent class method.
  • 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/pointerQa.py
  • lines changed 8, context: html, text, full: html, text
    Start of qa package for analyzing tables.
  • lines changed 3, context: html, text, full: html, text
    Added import statements, fixed many indentation and syntax errors.
  • 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/positionalQa.py
  • lines changed 21, context: html, text, full: html, text
    Start of qa package for analyzing tables.
  • lines changed 3, context: html, text, full: html, text
    Added import statements, fixed many indentation and syntax errors.
  • lines changed 6, context: html, text, full: html, text
    Added featureBits and statistics skeleton methods.
  • lines changed 2, 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.
  • lines changed 30, 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.
  • lines changed 5, 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.
  • lines changed 47, 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/pslQa.py
  • lines changed 12, context: html, text, full: html, text
    Start of qa package for analyzing tables.
  • lines changed 4, context: html, text, full: html, text
    Added import statements, fixed many indentation and syntax errors.
  • lines changed 12, 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.
  • lines changed 12, 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.
  • lines changed 6, context: html, text, full: html, text
    Fixed calls to private parent class method.
  • 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/reporter.py
  • lines changed 67, 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.
  • lines changed 4, 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.
  • lines changed 1, context: html, text, full: html, text
    Took extra information out of writeStepInfo().
• python/lib/ucscgenomics/qa/tables/summary.py
  • lines changed 32, 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.
  • lines changed 19, 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/tableQa.py
  • lines changed 30, context: html, text, full: html, text
    Start of qa package for analyzing tables.
  • lines changed 2, context: html, text, full: html, text
    Added import statements, fixed many indentation and syntax errors.
  • lines changed 15, 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.
  • lines changed 19, 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.
  • lines changed 7, 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.
  • lines changed 26, 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.
• src/hg/htdocs/images/floretPreview.jpg
  • lines changed 0, 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/utils/qa/makefile
  • lines changed 1, context: html, text, full: html, text
    Added qaGbTracks.
• src/utils/qa/qaGbTracks
  • lines changed 76, context: html, text, full: html, text
    Started using new classes in ucscgenomics/qa/tables and started putting things into functions.
  • lines changed 5, 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.
  • lines changed 31, 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.
  • lines changed 28, context: html, text, full: html, text
    Tweaked description, changed outFile variable name, put delimter line in a variable.