File Changes for galt

v286_preview to v286_preview2 (2013-06-24 to 2013-07-02) v286

• src/fuzzyFind/ffapp.c
  • lines changed 3, context: html, text, full: html, text
    removing unneeded carefulCheckHeap calls since pushCarefulMemHandler was not being used and thus the check did absolutely nothing.
• src/hg/dnaGene/dnaGene.c
  • lines changed 6, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/gsid/pbGsid/pbGsid.c
  • lines changed 10, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/hgGateway/hgGateway.c
  • lines changed 2, context: html, text, full: html, text
    fixes #11192 -- handling https in redirects between ucsc and other official mirror sites like genome-euro
  • lines changed 1, context: html, text, full: html, text
    oops.
• src/hg/hgGene/ctd.c
  • lines changed 2, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/hgGene/pathways.c
  • lines changed 4, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/hgGene/pseudoGene.c
  • lines changed 2, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/hgGene/synonym.c
  • lines changed 2, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/hgTracks/retroGene.c
  • lines changed 2, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/hgc/hgc.c
  • lines changed 102, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/hgc/virusClick.c
  • lines changed 4, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/lib/hdb.c
  • lines changed 2, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/lib/hgFind.c
  • lines changed 2, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/lib/jksql.c
  • lines changed 8, context: html, text, full: html, text
    taking out unneeded debugging info in verbose=2 which was messing up genbank logging anyway
  • lines changed 12, context: html, text, full: html, text
    making the output a little safer for ignore situations so logs will not fill up with messages no one cares about
  • lines changed 4, context: html, text, full: html, text
    fixing dumpstack to use _exit instead of exit so that the child cleanup will not close the mysql connections that are shared with the parent process.
  • lines changed 2, context: html, text, full: html, text
    increasing the size of a couple of query arrays
• src/hg/lib/spDb.c
  • lines changed 2, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/lib/web.c
  • lines changed 14, context: html, text, full: html, text
    fixes #11192 -- handling https in redirects between ucsc and other official mirror sites like genome-euro
• src/hg/makeDb/hgCalStat/hgCalStat.c
  • lines changed 9, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/makeDb/hgKgMrna/hgKgMrna.c
  • lines changed 1, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/makeDb/outside/hgBioCyc/hgBioCyc.c
  • lines changed 3, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/makeDb/outside/hgJaxQtl/hgJaxQtl.c
  • lines changed 3, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/makeDb/outside/hgKegg/hgKegg.c
  • lines changed 1, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/makeDb/outside/hgKegg2/hgKegg2.c
  • lines changed 1, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/makeDb/outside/hgKegg3/hgKegg3.c
  • lines changed 4, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/makeDb/outside/hgSuperfam/hgSuperfam.c
  • lines changed 3, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/oneShot/kgName/fbName.c
  • lines changed 1, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/oneShot/kgName/kgName.c
  • lines changed 13, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/pdbSP/pdbSP.c
  • lines changed 2, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/fixAgp/fixAgp.c
  • lines changed 9, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgAliasM/kgAliasM.c
  • lines changed 1, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgAliasP/kgAliasP.c
  • lines changed 1, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgBestMrna/kgPrepBestMrna.c
  • lines changed 6, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgBestMrna/kgPrepBestMrna2.c
  • lines changed 2, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgBestMrna/kgResultBestMrna.c
  • lines changed 3, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgBestMrna2/kgPrepBestMrna2.c
  • lines changed 2, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgBestMrna2/kgResultBestMrna2.c
  • lines changed 1, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgBestRef2/kgPrepBestRef2.c
  • lines changed 1, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgBestRef2/kgResultBestRef2.c
  • lines changed 1, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgCheck/kgCheck.c
  • lines changed 2, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgCheck2/kgCheck2.c
  • lines changed 8, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgGetCds/kgGetCds.c
  • lines changed 1, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgPepMrna/kgPepMrna.c
  • lines changed 4, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgPick/kgPick.c
  • lines changed 2, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgProtAlias/kgProtAlias.c
  • lines changed 2, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgProtAliasNCBI/kgProtAliasNCBI.c
  • lines changed 1, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgUniq/kgUniq.c
  • lines changed 7, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgXref/kgXref.c
  • lines changed 11, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgXref2/kgXref2.c
  • lines changed 11, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/lib/doSam.c
  • lines changed 2, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/lib/doStamps.c
  • lines changed 7, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/lib/doTracks.c
  • lines changed 11, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/lib/domains.c
  • lines changed 3, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/lib/pbUtil.c
  • lines changed 13, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/omimCheckAv/omimCheckAv.c
  • lines changed 2, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/pbCalDist/pbCalDist.c
  • lines changed 8, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/pbCalResStd/pbCalResStd.c
  • lines changed 4, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/pbGlobal/pbGlobal.c
  • lines changed 12, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/pbTracks/pbTracks.c
  • lines changed 7, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/pfamXref/pfamXref.c
  • lines changed 1, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/rmKGPepMrna/rmKGPepMrna.c
  • lines changed 5, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/spToProteins/spToProteins.c
  • lines changed 3, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/spToProteinsVar/spToProteinsVar.c
  • lines changed 1, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/spXref3/spXref3.c
  • lines changed 2, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/spm6/spm6.c
  • lines changed 2, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/spm7/spm7.c
  • lines changed 2, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/pslReps/pslReps.c
  • lines changed 2, context: html, text, full: html, text
    removing unneeded carefulCheckHeap calls since pushCarefulMemHandler was not being used and thus the check did absolutely nothing.
• src/inc/common.h
  • lines changed 4, context: html, text, full: html, text
    fixing dumpstack to use _exit instead of exit so that the child cleanup will not close the mysql connections that are shared with the parent process.
• src/lib/errabort.c
  • lines changed 1, context: html, text, full: html, text
    fixing dumpstack to use _exit instead of exit so that the child cleanup will not close the mysql connections that are shared with the parent process.
• src/lib/memalloc.c
  • lines changed 21, context: html, text, full: html, text
    fixing bug in unlocking. There were too many places where returns and errAbort were leaving the routine without unlocking. It was easy to fix. Now I understand that if the user does not call pushCarefulMemHandler, then carefulParent is NULL and carefulCheckHeap exits early without doing anything. So only for routines that did NOT call pushCarefulMemHandler, but did call carefulCheckHeap multiple times was there a problem, and only pslReps util met those criteria
• src/lib/osunix.c
  • lines changed 22, context: html, text, full: html, text
    fixing dumpstack to use _exit instead of exit so that the child cleanup will not close the mysql connections that are shared with the parent process.
• src/lib/pipeline.c
  • lines changed 1, context: html, text, full: html, text
    fixing dumpstack to use _exit instead of exit so that the child cleanup will not close the mysql connections that are shared with the parent process.