Commits for angie

v336_base to v337_preview (2016-07-25 to 2016-08-01) v337

ca83404a952b1500d7bda386272dc5853b77895c Fri Jul 22 17:08:49 2016 -0700

• Updated snp147{,Common,Flagged,Mult,CodingDbSnp} after Chris Lee found incorrect assignment of cds-indel for noncoding transcripts. reds #17209 notes 25, 29-34, 37
  
  • src/hg/makeDb/doc/hg19.txt - lines changed 22, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/variation.txt - lines changed 23, context: html, text, full: html, text

7cba4825e2cdac43466409afe3507dd7da0245c9 Fri Jul 22 17:15:46 2016 -0700

• Special handling for tables that happen to include the bin column in their autoSql (e.g. pgSnp tables and oreganno): disable bin unless user explicitly enables it, to match UI behavior. refs #17748
  
  • src/hg/hgIntegrator/hgIntegrator.c - lines changed 17, context: html, text, full: html, text

3bae5ca22bf4695cff6eeb0988cc9708e1c83105 Mon Jul 25 12:20:15 2016 -0700

• Added missing SQL 'on' keyword -- triggered by joining snp147Mult with snp147ExceptionDesc (snp147Mult is a non-huge table and exceptions is comma-separated list).
  
  • src/hg/lib/annoStreamDb.c - lines changed 1, context: html, text, full: html, text

90a463516b1e9e6b4b942dda675c607e5c4fccf6 Mon Jul 25 14:15:46 2016 -0700

• chmod * will lead to errors if there are files owned by other users -- so run chmod only on owned files.
  
  • src/hg/utils/automation/doDbSnp.pl - lines changed 6, context: html, text, full: html, text

105193d3bc75ad4c8c5570cbd66286300c322bd3 Mon Jul 25 16:36:11 2016 -0700

• Always use https for hgLogin, even if returning to hgSession with http. refs #17778
  
  • src/hg/hgLogin/hgLogin.c - lines changed 8, context: html, text, full: html, text
  • src/hg/lib/wikiLink.c - lines changed 8, context: html, text, full: html, text

53bfcc23b47e1dab4dc8d0aa7bc2ca5c121ced2b Tue Jul 26 12:28:12 2016 -0700

• hgLogin's links to itself and form posts to itself also need to use https, even if hgLogin was loaded via http (e.g. from a static page, bookmark, etc). refs #17778
  
  • src/hg/hgLogin/hgLogin.c - lines changed 43, context: html, text, full: html, text

bb05b8e2c72fe5abb64e506f75eaf612e57ad1a9 Fri Jul 29 14:42:26 2016 -0700

• Use HTTPS for NCBI. refs #17793
  
  • src/hg/utils/automation/doDbSnp.pl - lines changed 2, context: html, text, full: html, text

d81a994fc5b713f0bafc32923e44d29c872c720b Fri Jul 29 16:18:55 2016 -0700

• Added a new hg.conf setting, login.https, so that mirror sites can turn off https for hgLogin if they don't support https (they really should). refs #17778 note-7
  
  • src/hg/hgLogin/hgLogin.c - lines changed 2, context: html, text, full: html, text
  • src/hg/inc/wikiLink.h - lines changed 4, context: html, text, full: html, text
  • src/hg/lib/wikiLink.c - lines changed 23, context: html, text, full: html, text

1cfb2e9463729a67e65fe5ecab8a7c9fa20399be Mon Aug 1 10:04:02 2016 -0700

• Rebuilt snp147 tables in hg19 and hg38 after fixing incorrect function codes in table from dbSNP and re-running the pipeline from ucscFunc onward. refs #17209
  
  • src/hg/makeDb/doc/hg19.txt - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/variation.txt - lines changed 24, context: html, text, full: html, text