File Changes for kent

v289_base to v290_preview (2013-09-09 to 2013-09-16) v290

• src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c
  • lines changed 19, context: html, text, full: html, text
    Controlling suffixes better so they come from format where possible, and only a limited number of double suffixes are allowed. Also check that .gz files have gzip signature at beginning.
• src/hg/encode3/encodeDataWarehouse/edwRunDaemon/edwRunDaemon.c
  • lines changed 21, context: html, text, full: html, text
    Making it so polls for new work every 30 seconds instead of every 60. Removing need for synchronization signals in FIFO to end with new line.
• src/hg/encode3/encodeDataWarehouse/edwRunOnIds/edwRunOnIds.c
  • lines changed 59, context: html, text, full: html, text
    Seems to work. Best used with edwTempJob.
• src/hg/encode3/encodeDataWarehouse/edwRunOnIds/makefile
  • lines changed 4, context: html, text, full: html, text
    Seems to work. Best used with edwTempJob.
• src/hg/encode3/encodeDataWarehouse/edwScriptSubmitStatus/edwScriptSubmitStatus.c
  • lines changed 1, context: html, text, full: html, text
    Coping with new parameter for edwLib routine.
• src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c
  • lines changed 8, context: html, text, full: html, text
    Controlling suffixes better so they come from format where possible, and only a limited number of double suffixes are allowed. Also check that .gz files have gzip signature at beginning.
  • lines changed 38, context: html, text, full: html, text
    First cut at putting in 'stop upload' button.
  • lines changed 5, context: html, text, full: html, text
    Doing clean up of temp files after user stops an upload early.
• src/hg/encode3/encodeDataWarehouse/edwWebBrowse/edwWebBrowse.c
  • lines changed 2, context: html, text, full: html, text
    Improving 'enriched in' display in case where it is not set in manifest.
• src/hg/encode3/encodeDataWarehouse/edwWebSubmit/edwWebSubmit.c
  • lines changed 54, context: html, text, full: html, text
    First cut at putting in 'stop upload' button.
• src/hg/encode3/encodeDataWarehouse/inc/edwLib.h
  • lines changed 3, context: html, text, full: html, text
    First cut at putting in 'stop upload' button.
• src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h
  • lines changed 2, context: html, text, full: html, text
    Making readSizeMin/Max be integers rather than doubles.
• src/hg/encode3/encodeDataWarehouse/lib/edwFastqFileFromRa.c
  • lines changed 142, context: html, text, full: html, text
    Redoing with improved parser generator.
• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
  • lines changed 3, context: html, text, full: html, text
    Controlling suffixes better so they come from format where possible, and only a limited number of double suffixes are allowed. Also check that .gz files have gzip signature at beginning.
  • lines changed 9, context: html, text, full: html, text
    First cut at putting in 'stop upload' button.
  • lines changed 1, context: html, text, full: html, text
    Fixed uninitialized variable warning.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as
  • lines changed 3, context: html, text, full: html, text
    Making readSizeMin/Max be integers rather than doubles.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c
  • lines changed 7, context: html, text, full: html, text
    Making readSizeMin/Max be integers rather than doubles.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql
  • lines changed 3, context: html, text, full: html, text
    Making readSizeMin/Max be integers rather than doubles.
• src/hg/encode3/encodeDataWarehouse/lib/resetEdw
  • lines changed 9, context: html, text, full: html, text
    Adding another email for Chin, and also some male & female specific assemblies for mouse and human.
• src/hg/inc/encode3/encode3Valid.h
  • lines changed 3, context: html, text, full: html, text
    Adding encode3IsGzip routine to see if a file starts with gzip signature.
• src/hg/lib/encode3/encode3Valid.c
  • lines changed 10, context: html, text, full: html, text
    Adding encode3IsGzip routine to see if a file starts with gzip signature.
• src/hg/oneShot/freen/freen.c
  • lines changed 6, context: html, text, full: html, text
    Adding encode3IsGzip routine to see if a file starts with gzip signature.
• src/inc/paraFetch.h
  • lines changed 7, context: html, text, full: html, text
    Adding parallelFetchInterruptable, which has a callback that checks for interrupt.
  • lines changed 5, context: html, text, full: html, text
    Adding parallelFetchRemovePartial clean up function.
• src/inc/raToStruct.h
  • lines changed 36, context: html, text, full: html, text
    Adding support for arrays, and also extraH option to raToStructGen.
• src/lib/paraFetch.c
  • lines changed 20, context: html, text, full: html, text
    Adding parallelFetchInterruptable, which has a callback that checks for interrupt.
  • lines changed 9, context: html, text, full: html, text
    Adding parallelFetchRemovePartial clean up function.
• src/lib/raToStruct.c
  • lines changed 104, context: html, text, full: html, text
    Adding support for arrays, and also extraH option to raToStructGen.
• src/utils/raToStructGen/raToStructGen.c
  • lines changed 110, context: html, text, full: html, text
    Pretty major reworking. Making an enum with symbolic names for the field offsets. Adding computed field option so not all fields need to be addressed by parser. Generating more functions. The code generated passes visual inspection but has not been compiled and tested.
  • lines changed 44, context: html, text, full: html, text
    Got output to compile. Added a test script.
  • lines changed 18, context: html, text, full: html, text
    Adding support for arrays, and also extraH option to raToStructGen.
• src/utils/raToStructGen/test.as
  • lines changed 33, context: html, text, full: html, text
    Starting to add test cases.
  • lines changed 33, context: html, text, full: html, text
    Streamlining unit test.
• src/utils/raToStructGen/testIt
  • lines changed 6, context: html, text, full: html, text
    Got output to compile. Added a test script.
  • lines changed 8, context: html, text, full: html, text
    Streamlining unit test.
• src/utils/raToStructGen/testOut/makefile
  • lines changed 3, context: html, text, full: html, text
    Got output to compile. Added a test script.
  • lines changed 1, context: html, text, full: html, text
    Streamlining unit test.
• src/utils/raToStructGen/testOut/test.as
  • lines changed 34, context: html, text, full: html, text
    Streamlining unit test.
• src/utils/raToStructGen/testOut/test.expected
  • lines changed 1, context: html, text, full: html, text
    Streamlining unit test.
• src/utils/raToStructGen/testOut/test.ra
  • lines changed 27, context: html, text, full: html, text
    Streamlining unit test.
• src/utils/raToStructGen/testOut/testRaToStruct.c
  • lines changed 301, context: html, text, full: html, text
    Streamlining unit test.
  • lines changed 14, context: html, text, full: html, text
    Adding support for arrays, and also extraH option to raToStructGen.