File Changes for mspeir

v343_base to v344_preview (2017-01-09 to 2017-01-16) v344

• python/lib/ucscGb/qa/qaUtils.py
  • lines changed 19, context: html, text, full: html, text
    c3aa94b6be83af4de2e755eaaf1e1294b795963e Tue Jan 10 09:46:49 2017 -0800
    Adding two new functions to qaUtils. Both are intended to be used to run various commands and manipulate the output beyond the original runCommand function. runCommandMergedOutErr combines both stdout and stderr into a single output and returns this. runCommandNoAbort skips the returncode check of the other versions of runCommand and instead returns the returncode to the user alongside the stdout and stderr of the command. Both added at the recommendation of Jonathan in CR, refs #18564
• python/lib/ucscGb/qa/tables/factory.py
  • lines changed 5, context: html, text, full: html, text
    853fb0e2d808a14d43a223ae7f19fdfd63e18869 Tue Jan 10 10:02:12 2017 -0800
    Changes to positionalQa.py include having it call new runCommandMergedOutErr function when running runBits. Also includes new runCommandNoAbort to replace Popen calls. Similar things was done in factory.py and genePredQa.py, Popen call were replaced with calls to new function runCommandNoAbort. Work to runBits done at Jonathan's request in CR, but other changes were made for the sake of consistency. refs #18564
• python/lib/ucscGb/qa/tables/genePredQa.py
  • lines changed 5, context: html, text, full: html, text
    853fb0e2d808a14d43a223ae7f19fdfd63e18869 Tue Jan 10 10:02:12 2017 -0800
    Changes to positionalQa.py include having it call new runCommandMergedOutErr function when running runBits. Also includes new runCommandNoAbort to replace Popen calls. Similar things was done in factory.py and genePredQa.py, Popen call were replaced with calls to new function runCommandNoAbort. Work to runBits done at Jonathan's request in CR, but other changes were made for the sake of consistency. refs #18564
• python/lib/ucscGb/qa/tables/positionalQa.py
  • lines changed 10, context: html, text, full: html, text
    853fb0e2d808a14d43a223ae7f19fdfd63e18869 Tue Jan 10 10:02:12 2017 -0800
    Changes to positionalQa.py include having it call new runCommandMergedOutErr function when running runBits. Also includes new runCommandNoAbort to replace Popen calls. Similar things was done in factory.py and genePredQa.py, Popen call were replaced with calls to new function runCommandNoAbort. Work to runBits done at Jonathan's request in CR, but other changes were made for the sake of consistency. refs #18564
• python/lib/ucscGb/qa/tables/pslQa.py
  • lines changed 18, context: html, text, full: html, text
    5b4eab4fd242caef8f8dd352d8f7f82b18cd4dba Tue Jan 10 09:55:40 2017 -0800
    Fixed error where qaGbTracks would crash if output from tdbQuery was empty. Included new runCommondNoAbort in the script. Instead of deleting db.sizes file created during process, will instead keep this and utilize it if it already exists which prevents the file from being created and deleted multiple times if qaGbTracks is run on multiple psl tracks. All added at Jonathan's recommendation in CR, refs #18564
  • lines changed 0, context: html, text, full: html, text
    e69aa3d527905a950a684ffc450ceed65b52368c Tue Jan 10 10:19:26 2017 -0800
    Correcting indentation on a few lines, no redmine
• src/hg/lib/ensGene.as
  • lines changed 6, context: html, text, full: html, text
    c257290253d707d2fc749e277f7a96c771accb80 Fri Jan 13 13:29:35 2017 -0800
    Adding more detail to transcription/coding/exons start/end columns, refs #18548
• src/hg/lib/genePred.as
  • lines changed 6, context: html, text, full: html, text
    c257290253d707d2fc749e277f7a96c771accb80 Fri Jan 13 13:29:35 2017 -0800
    Adding more detail to transcription/coding/exons start/end columns, refs #18548
• src/hg/lib/genePredExt.as
  • lines changed 6, context: html, text, full: html, text
    c257290253d707d2fc749e277f7a96c771accb80 Fri Jan 13 13:29:35 2017 -0800
    Adding more detail to transcription/coding/exons start/end columns, refs #18548
• src/hg/lib/knownGene.as
  • lines changed 7, context: html, text, full: html, text
    c257290253d707d2fc749e277f7a96c771accb80 Fri Jan 13 13:29:35 2017 -0800
    Adding more detail to transcription/coding/exons start/end columns, refs #18548
• src/hg/lib/refFlat.as
  • lines changed 6, context: html, text, full: html, text
    c257290253d707d2fc749e277f7a96c771accb80 Fri Jan 13 13:29:35 2017 -0800
    Adding more detail to transcription/coding/exons start/end columns, refs #18548
• src/hg/lib/sangerGene.as
  • lines changed 6, context: html, text, full: html, text
    c257290253d707d2fc749e277f7a96c771accb80 Fri Jan 13 13:29:35 2017 -0800
    Adding more detail to transcription/coding/exons start/end columns, refs #18548
• src/utils/qa/checkMachineName.csh
  • lines changed 1, context: html, text, full: html, text
    9b1eb09e57cf432a1efe4fae3a240c66babfc2cc Tue Jan 10 13:06:05 2017 -0800
    Adding genome-asia to machine name list. Part of work to make genome-asia show up in updateTimes output, refs #18617
• src/utils/qa/getTableStatus.csh
  • lines changed 1, context: html, text, full: html, text
    38e8bc506420f5605d5fd8a0b0ccc813b68f5b7b Tue Jan 10 13:19:11 2017 -0800
    Adding exception for genome-asia to and if statement. Part of work to make genome-asia show up in updateTimes output, refs #18617
• src/utils/qa/getVersion.csh
  • lines changed 1, context: html, text, full: html, text
    ef05cfa9b2b4b0c8d24e1d7e1f8fefaf53a9afa0 Tue Jan 10 14:08:35 2017 -0800
    Making script aware of genome-asia, refs #18646
• src/utils/qa/makefile
  • lines changed 1, context: html, text, full: html, text
    22341d9f9e935e2adb290488f5321fee77e770c3 Fri Jan 13 11:18:00 2017 -0800
    Adding helper script that runs qaAutoTrack.sh for all current autopushed tracks. Updating makefile so that this new script will be copied when make is run. refs #12561
• src/utils/qa/qaAutoTrack.sh
  • lines changed 21, context: html, text, full: html, text
    df0b2815a68268581da0984e2de1d718a9dcb661 Wed Jan 11 15:54:16 2017 -0800
    Changes based on CR. Added new variables for previous log time and current runtime. Changed log file name format, now includes current runtime in name. Changed way previous log file was found, now can compare to previous logs from the same day. Simplified checks for newLogDir and overwriteLogUrl. refs #18632
• src/utils/qa/realTime.csh
  • lines changed 4, context: html, text, full: html, text
    d3f13ad7ba599c99681f0c5924eff738971ea97e Tue Jan 10 13:51:08 2017 -0800
    Adding genome-asia to output for both scripts, refs #18617
• src/utils/qa/runQaAutoTrack.sh
  • lines changed 114, context: html, text, full: html, text
    22341d9f9e935e2adb290488f5321fee77e770c3 Fri Jan 13 11:18:00 2017 -0800
    Adding helper script that runs qaAutoTrack.sh for all current autopushed tracks. Updating makefile so that this new script will be copied when make is run. refs #12561
  • lines changed 8, context: html, text, full: html, text
    f6c2a19a73b7f191470115d4c5c6bf8ea9f24895 Fri Jan 13 11:30:29 2017 -0800
    Minor tweak to usage message for runQaAutoTrack.sh, refs #12561
• src/utils/qa/updateTimes.csh
  • lines changed 20, context: html, text, full: html, text
    d3f13ad7ba599c99681f0c5924eff738971ea97e Tue Jan 10 13:51:08 2017 -0800
    Adding genome-asia to output for both scripts, refs #18617