File Changes for kate

v316_base to v317_preview (2015-05-11 to 2015-05-18) v317

• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 6, context: html, text, full: html, text
    Removed ifdef (BUTTONS_BY_CSS). No functional change. This code added in 2011 is unused. (no redmine)
    
• src/hg/hgTracks/config.c
  • lines changed 7, context: html, text, full: html, text
    Removed ifdef (BUTTONS_BY_CSS). No functional change. This code added in 2011 is unused. (no redmine)
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 7, context: html, text, full: html, text
    Removed ifdef (BUTTONS_BY_CSS). No functional change. This code added in 2011 is unused. (no redmine)
    
• src/hg/hgTracks/searchTracks.c
  • lines changed 7, context: html, text, full: html, text
    Removed ifdef (BUTTONS_BY_CSS). No functional change. This code added in 2011 is unused. (no redmine)
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.css
  • lines changed 5, context: html, text, full: html, text
    Extend trackDbHub doc to include version and support levels for settings. refs #10015
    
  • lines changed 1, context: html, text, full: html, text
    1. Change level-alpha to level-new (input from group review). Add -settings option to hubCheck (doesn't check, just shows settings and level). Add level to all settings (very initial proposed set based on input from Ensembl). refs #10015
    
  • lines changed 1, context: html, text, full: html, text
    Distinguish trackDb doc and hub doc. refs #10015
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.js
  • lines changed 59, context: html, text, full: html, text
    Extend trackDbHub doc to include version and support levels for settings. refs #10015
    
  • lines changed 1, context: html, text, full: html, text
    Add version check features to hubCheck (-version, -core, -extra, -settings). Initial coding, not yet functional. Also added levels (for testing only) to settings spec. refs #10015
    
  • lines changed 5, context: html, text, full: html, text
    1. Change level-alpha to level-new (input from group review). Add -settings option to hubCheck (doesn't check, just shows settings and level). Add level to all settings (very initial proposed set based on input from Ensembl). refs #10015
    
  • lines changed 13, context: html, text, full: html, text
    Remove unused function
    
  • lines changed 14, context: html, text, full: html, text
    Identify hub doc so it can be handled differently. refs #10015
    
  • lines changed 0, context: html, text, full: html, text
    whitespace++
    
  • lines changed 25, context: html, text, full: html, text
    Distinguish trackDb doc and hub doc. refs #10015
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html
  • lines changed 100, context: html, text, full: html, text
    Extend trackDbHub doc to include version and support levels for settings. refs #10015
    
  • lines changed 80, context: html, text, full: html, text
    Add version check features to hubCheck (-version, -core, -extra, -settings). Initial coding, not yet functional. Also added levels (for testing only) to settings spec. refs #10015
    
  • lines changed 115, context: html, text, full: html, text
    1. Change level-alpha to level-new (input from group review). Add -settings option to hubCheck (doesn't check, just shows settings and level). Add level to all settings (very initial proposed set based on input from Ensembl). refs #10015
    
  • lines changed 1, context: html, text, full: html, text
    HTML syntax fix. refs #10015
    
  • lines changed 7, context: html, text, full: html, text
    Distinguish trackDb doc and hub doc. refs #10015
    
  • lines changed 43, context: html, text, full: html, text
    Reorder settings so core are at the top of each section. refs #10015
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 1, context: html, text, full: html, text
    Extend trackDbHub doc to include version and support levels for settings. refs #10015
    
• src/hg/inc/trackHub.h
  • lines changed 27, context: html, text, full: html, text
    Cleanup hub check code and add new data structs to prep for hub versioning. refs #10015
    
  • lines changed 5, context: html, text, full: html, text
    Add version check features to hubCheck (-version, -core, -extra, -settings). Initial coding, not yet functional. Also added levels (for testing only) to settings spec. refs #10015
    
  • lines changed 3, context: html, text, full: html, text
    Add 'did you mean' suggestion to hubCheck settings check. Similarity test from JK based on axt alignment scoring. refs #10015
    
  • lines changed 3, context: html, text, full: html, text
    Add checkSettings option to hubCheck instead of having setting check be default. This is to maintain current behavior for initial release. Also hide version options for now (they are in additional -help). refs #10015
    
• src/hg/js/hui.js
  • lines changed 20, context: html, text, full: html, text
    Fix behavior of +/- buttons when used without a matrix. Detected during Q/A of hg38 track. refs #14732
    
• src/hg/lib/hui.c
  • lines changed 44, context: html, text, full: html, text
    Removed ifdef (BUTTONS_BY_CSS). No functional change. This code added in 2011 is unused. (no redmine)
    
• src/hg/lib/jsHelper.c
  • lines changed 6, context: html, text, full: html, text
    Removed ifdef (BUTTONS_BY_CSS). No functional change. This code added in 2011 is unused. (no redmine)
    
• src/hg/lib/search.c
  • lines changed 7, context: html, text, full: html, text
    Removed ifdef (BUTTONS_BY_CSS). No functional change. This code added in 2011 is unused. (no redmine)
    
• src/hg/lib/trackHub.c
  • lines changed 2, context: html, text, full: html, text
    Add version check features to hubCheck (-version, -core, -extra, -settings). Initial coding, not yet functional. Also added levels (for testing only) to settings spec. refs #10015
    
• src/hg/lib/trackHubCheck.c
  • lines changed 148, context: html, text, full: html, text
    Cleanup hub check code and add new data structs to prep for hub versioning. refs #10015
    
  • lines changed 126, context: html, text, full: html, text
    Add version check features to hubCheck (-version, -core, -extra, -settings). Initial coding, not yet functional. Also added levels (for testing only) to settings spec. refs #10015
    
  • lines changed 72, context: html, text, full: html, text
    1. Change level-alpha to level-new (input from group review). Add -settings option to hubCheck (doesn't check, just shows settings and level). Add level to all settings (very initial proposed set based on input from Ensembl). refs #10015
    
  • lines changed 75, context: html, text, full: html, text
    Finish -core and -extra options to hubCheck. refs #10015
    
  • lines changed 101, context: html, text, full: html, text
    Add 'did you mean' suggestion to hubCheck settings check. Similarity test from JK based on axt alignment scoring. refs #10015
    
  • lines changed 80, context: html, text, full: html, text
    Add checkSettings option to hubCheck instead of having setting check be default. This is to maintain current behavior for initial release. Also hide version options for now (they are in additional -help). refs #10015
    
• src/hg/makeDb/doc/hg38/reg.txt
  • lines changed 38, context: html, text, full: html, text
    Fix broken URLs from ScienCell (in wgEncodeCell table). refs #14353
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegDnase.ra
  • lines changed 1, context: html, text, full: html, text
    Tweak filter setting. refs #14732
    
• src/hg/utils/checkUrlsInTable/checkUrlsInTable.c
  • lines changed 16, context: html, text, full: html, text
    Add -strict option. Suppress 302 (Temp redirect) errors unless strict is on. Sometimes redirects work, sometimes not... refs #14353
    
  • lines changed 22, context: html, text, full: html, text
    Add -strict option. Suppress 302 (Temp redirect) errors unless strict is on. Sometimes redirects work, sometimes not... refs #14353
    
• src/hg/utils/checkUrlsInTable/makefile
  • lines changed 3, context: html, text, full: html, text
    Add -strict option. Suppress 302 (Temp redirect) errors unless strict is on. Sometimes redirects work, sometimes not... refs #14353
    
  • lines changed 2, context: html, text, full: html, text
    Add -strict option. Suppress 302 (Temp redirect) errors unless strict is on. Sometimes redirects work, sometimes not... refs #14353
    
• src/hg/utils/hubCheck/hubCheck.c
  • lines changed 68, context: html, text, full: html, text
    Cleanup hub check code and add new data structs to prep for hub versioning. refs #10015
    
  • lines changed 60, context: html, text, full: html, text
    Add version check features to hubCheck (-version, -core, -extra, -settings). Initial coding, not yet functional. Also added levels (for testing only) to settings spec. refs #10015
    
  • lines changed 1, context: html, text, full: html, text
    1. Change level-alpha to level-new (input from group review). Add -settings option to hubCheck (doesn't check, just shows settings and level). Add level to all settings (very initial proposed set based on input from Ensembl). refs #10015
    
  • lines changed 15, context: html, text, full: html, text
    Finish -core and -extra options to hubCheck. refs #10015
    
  • lines changed 32, context: html, text, full: html, text
    Add checkSettings option to hubCheck instead of having setting check be default. This is to maintain current behavior for initial release. Also hide version options for now (they are in additional -help). refs #10015
    
• src/lib/udc.c
  • lines changed 16, context: html, text, full: html, text
    Lower verbosity of this low-level module