Commits for kent

v330_preview2.1 to v330_base (2016-03-14 to 2016-03-21) v330

• Changing paths in makefile so they work on cirm-01 as well as hgwdev.
  
  • src/hg/cirm/cdw/wrangle/addToStepTables/makefile - lines changed 2, context: html, text, full: html, text
• A file that attempts to give an overview of the CIRM Data Warehouse system.
  
  • src/hg/cirm/cdw/README - lines changed 106, context: html, text, full: html, text
• Updating to reflect how things work now.
  
  • src/hg/cirm/cdw/README - lines changed 81, context: html, text, full: html, text
• Adding verbose status message about copying a file.
  
  • src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c - lines changed 1, context: html, text, full: html, text
• Adding some program descriptions to README
  
  • src/hg/cirm/cdw/README - lines changed 283, context: html, text, full: html, text
• Adding isSymbolString function to common string library.
  
  • src/inc/common.h - lines changed 3, context: html, text, full: html, text
  • src/lib/common.c - lines changed 15, context: html, text, full: html, text
• Changing order of command line interpretation so that -flatten doesn't exclude -tab.
  
  • src/tagStorm/tagStormReformat/tagStormReformat.c - lines changed 5, context: html, text, full: html, text
• Adding array option.
  
  • src/utils/stringify/stringify.c - lines changed 20, context: html, text, full: html, text
• Starting to implement checking of tag values for controlled vocabularies.
  
  • src/hg/cirm/cdw/inc/cdwValid.h - lines changed 2, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdwValid.c - lines changed 153, context: html, text, full: html, text
• Adding -test option so it can look at meta and manifest files without updating database. In test mode it will currently also start checking controlled vocabs.
  
  • src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c - lines changed 14, context: html, text, full: html, text
• Removing some unused code. Making a sql command go through sql injection checking that was bypassing it.
  
  • src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c - lines changed 125, context: html, text, full: html, text
• Another little database fix utility. No longer need to include directory name in path, but forgot that.
  
  • src/hg/cirm/cdw/fix/cdwFixDoubleHivePath/cdwFixDoubleHivePath.c - lines changed 65, context: html, text, full: html, text
  • src/hg/cirm/cdw/fix/cdwFixDoubleHivePath/makefile - lines changed 3, context: html, text, full: html, text
• Adding submitId column to job table.
  
  • src/hg/cirm/cdw/inc/cdw.h - lines changed 4, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdw.as - lines changed 2, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdw.c - lines changed 20, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdw.sql - lines changed 2, context: html, text, full: html, text
• Adding submitId column to job table.
  
  • src/hg/cirm/cdw/inc/cdwLib.h - lines changed 3, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdwLib.c - lines changed 7, context: html, text, full: html, text
• Adding minimal support for Tabix validation. Making it avoid GEO_SAMPLE and GEO_SERIES tags, which should be lower case since they are ones we get even if the set is not wrangled out of GEO.
  
  • src/hg/cirm/cdw/inc/cdwValid.h - lines changed 3, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdwValid.c - lines changed 32, context: html, text, full: html, text
• Removing a set but not used symbol to get code to compile again with stricter warnings.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 5, context: html, text, full: html, text
• Adding submitId column to job table.
  
  • src/hg/cirm/cdw/cdwAddAssembly/cdwAddAssembly.c - lines changed 1, context: html, text, full: html, text
• Adding submitId column to job table.
  
  • src/hg/cirm/cdw/cdwAddQaEnrichTarget/cdwAddQaEnrichTarget.c - lines changed 1, context: html, text, full: html, text
• Adding submitId column to job table.
  
  • src/hg/cirm/cdw/cdwChangeFormat/cdwChangeFormat.c - lines changed 1, context: html, text, full: html, text
• Adding submitId column to job table.
  
  • src/hg/cirm/cdw/cdwCorrectFileTags/cdwCorrectFileTags.c - lines changed 1, context: html, text, full: html, text
• Adding minimal support for Tabix validation on vcf indices.
  
  • src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c - lines changed 5, context: html, text, full: html, text
• Adding submitId column to job table. Checking to make sure they don't put full path name in manifest file, which went from being a necessary hassle to being an error a few versions back.
  
  • src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c - lines changed 8, context: html, text, full: html, text
• Adding submitId column to job table. Checking to make sure they don't put full path name in manifest file, which went from being a necessary hassle to being an error a few versions back.
  
  • src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c - lines changed 2, context: html, text, full: html, text
• Slightly more robust error reporting if tags in database are messed up. Fixing up so that sqlDyStringPrintf is only used at start of command, since it is a bit overaggressive about flagging errors on partially built queries if you use it throughout a query build.
  
  • src/hg/cirm/cdw/cdwMakeFileTags/cdwMakeFileTags.c - lines changed 15, context: html, text, full: html, text
• Removing no longer used cdwSubmitJob table.
  
  • src/hg/cirm/cdw/inc/cdw.h - lines changed 73, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdw.as - lines changed 13, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdw.c - lines changed 179, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdw.sql - lines changed 14, context: html, text, full: html, text
• Fixing bug where browse tracks errored out when there were no chromosome tags.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 35, context: html, text, full: html, text