Commits for kate

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

• Extend trackDbHub doc to include version and support levels for settings. refs #10015
  
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.css - lines changed 5, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.js - lines changed 59, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html - lines changed 100, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 1, 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/hgTrackUi/hgTrackUi.c - lines changed 6, context: html, text, full: html, text
  • src/hg/hgTracks/config.c - lines changed 7, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c - lines changed 7, context: html, text, full: html, text
  • src/hg/hgTracks/searchTracks.c - lines changed 7, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 44, context: html, text, full: html, text
  • src/hg/lib/jsHelper.c - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/search.c - lines changed 7, 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/js/hui.js - lines changed 20, context: html, text, full: html, text
• Tweak filter setting. refs #14732
  
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeRegDnase.ra - lines changed 1, context: html, text, full: html, text
• Merge branch 'dnase38'
  
• Fix broken URLs from ScienCell (in wgEncodeCell table). refs #14353
  
  • src/hg/makeDb/doc/hg38/reg.txt - lines changed 38, context: html, text, full: html, text
• Merge branch 'dnase38'
  
• Cleanup hub check code and add new data structs to prep for hub versioning. refs #10015
  
  • src/hg/inc/trackHub.h - lines changed 27, context: html, text, full: html, text
  • src/hg/lib/trackHubCheck.c - lines changed 148, context: html, text, full: html, text
  • src/hg/utils/hubCheck/hubCheck.c - lines changed 68, 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/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
  
  • 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
  
  • src/hg/utils/checkUrlsInTable/checkUrlsInTable.c - lines changed 22, context: html, text, full: html, text
  • src/hg/utils/checkUrlsInTable/makefile - lines changed 2, context: html, text, full: html, text
• Merge branch 'master' into tdbVersion
  
• 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/htdocs/goldenPath/help/trackDb/trackDbDoc.js - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html - lines changed 80, context: html, text, full: html, text
  • src/hg/inc/trackHub.h - lines changed 5, context: html, text, full: html, text
  • src/hg/lib/trackHub.c - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/trackHubCheck.c - lines changed 126, context: html, text, full: html, text
  • src/hg/utils/hubCheck/hubCheck.c - lines changed 60, 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
  
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.css - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.js - lines changed 5, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html - lines changed 115, context: html, text, full: html, text
  • src/hg/lib/trackHubCheck.c - lines changed 72, context: html, text, full: html, text
  • src/hg/utils/hubCheck/hubCheck.c - lines changed 1, context: html, text, full: html, text
• Finish -core and -extra options to hubCheck. refs #10015
  
  • src/hg/lib/trackHubCheck.c - lines changed 75, context: html, text, full: html, text
  • src/hg/utils/hubCheck/hubCheck.c - lines changed 15, context: html, text, full: html, text
• HTML syntax fix. refs #10015
  
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html - lines changed 1, 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
  
  • src/hg/inc/trackHub.h - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/trackHubCheck.c - lines changed 101, context: html, text, full: html, text
• Lower verbosity of this low-level module
  
  • src/lib/udc.c - lines changed 16, context: html, text, full: html, text
• Remove unused function
  
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.js - lines changed 13, context: html, text, full: html, text
• Identify hub doc so it can be handled differently. refs #10015
  
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.js - lines changed 14, context: html, text, full: html, text
• whitespace++
  
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.js - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• Distinguish trackDb doc and hub doc. refs #10015
  
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.css - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.js - lines changed 25, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html - lines changed 7, 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/trackDbHub.html - lines changed 43, 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/inc/trackHub.h - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/trackHubCheck.c - lines changed 80, context: html, text, full: html, text
  • src/hg/utils/hubCheck/hubCheck.c - lines changed 32, context: html, text, full: html, text
• Merge branch 'tdbVersion'