Commits for galt

v320_base to v321_preview (2015-08-03 to 2015-08-21) v321

• Initial check-in for Add-SSL-Support-Options to jksql.c and to hgsql-and-family functions.
  
  • src/hg/hgsql/hgsql.c - lines changed 2, context: html, text, full: html, text
  • src/hg/inc/jksql.h - lines changed 25, context: html, text, full: html, text
  • src/hg/lib/jksql.c - lines changed 234, context: html, text, full: html, text
  • src/hg/lib/sqlProg.c - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/schema/dbSnoop/dbSnoop.c - lines changed 6, context: html, text, full: html, text
  • src/lib/common.c - lines changed 1, context: html, text, full: html, text
• adding ssl params crl and crlPath. also more cleanup, got rid of a separate function sqlProfileNew() since it was no longer needed.
  
  • src/hg/lib/jksql.c - lines changed 83, context: html, text, full: html, text
• adding db field to sqlProfile just in case it is useful.
  
  • src/hg/lib/jksql.c - lines changed 10, context: html, text, full: html, text
• adding -profile option to dbSnoop
  
  • src/hg/makeDb/schema/dbSnoop/dbSnoop.c - lines changed 26, context: html, text, full: html, text
• oops
  
  • src/hg/lib/jksql.c - lines changed 1, context: html, text, full: html, text
• Added -profile=<profileName> option to hg/lib/sqlProg.c
  so now all of the hgsql-family of utils can login via
  ANY profile in their hg.conf. Seems to work quite well.
  Might be a lot easier in many cases to add a new profile
  to the existing ~/.hg.conf, instead of trying to use
  environment vars to point to some other hg.conf file.
  
  • src/hg/lib/sqlProg.c - lines changed 5, context: html, text, full: html, text
• adding setting HGDB_PROF which can over-ride the default profile value of "db" for any utility using jksql.
  
  • src/hg/inc/jksql.h - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/jksql.c - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/ccds/ccdsImport.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/schema/dbSnoop/dbSnoop.c - lines changed 1, context: html, text, full: html, text
• allow hgsql to use HGDB_PROF env setting to override default profile
  
  • src/hg/lib/sqlProg.c - lines changed 1, context: html, text, full: html, text
• Fixes bugs related to RM#15751
  
  • src/hg/lib/hgFind.c - lines changed 11, context: html, text, full: html, text
• Merge branch 'master' into addSslOptions
  
• Merge branch 'addSslOptions'
  
• adding documentation for the new SSL settings in hg.conf, and configuring mysql for SSL connections to the database.
  
  • src/product/README.mysql.setup - lines changed 141, context: html, text, full: html, text