Commits for galt

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

• taking out unneeded debugging info in verbose=2 which was messing up genbank logging anyway
  • src/hg/lib/jksql.c - lines changed 8, 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
  • src/hg/lib/jksql.c - lines changed 12, 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/hg/lib/jksql.c - lines changed 4, context: html, text, full: html, text
  • src/inc/common.h - lines changed 4, context: html, text, full: html, text
  • src/lib/errabort.c - lines changed 1, context: html, text, full: html, text
  • src/lib/osunix.c - lines changed 22, context: html, text, full: html, text
  • src/lib/pipeline.c - lines changed 1, context: html, text, full: html, text
• fixing callers of sqlGetField to use sqlSafeFrag
  • src/hg/dnaGene/dnaGene.c - lines changed 6, context: html, text, full: html, text
  • src/hg/gsid/pbGsid/pbGsid.c - lines changed 10, context: html, text, full: html, text
  • src/hg/hgGene/ctd.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hgGene/pathways.c - lines changed 4, context: html, text, full: html, text
  • src/hg/hgGene/pseudoGene.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hgGene/synonym.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hgTracks/retroGene.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgc/hgc.c - lines changed 102, context: html, text, full: html, text
  • src/hg/hgc/virusClick.c - lines changed 4, context: html, text, full: html, text
  • src/hg/lib/hdb.c - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/hgFind.c - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/spDb.c - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/hgCalStat/hgCalStat.c - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/hgKgMrna/hgKgMrna.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgBioCyc/hgBioCyc.c - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgJaxQtl/hgJaxQtl.c - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgKegg/hgKegg.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgKegg2/hgKegg2.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgKegg3/hgKegg3.c - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgSuperfam/hgSuperfam.c - lines changed 3, context: html, text, full: html, text
  • src/hg/oneShot/kgName/fbName.c - lines changed 1, context: html, text, full: html, text
  • src/hg/oneShot/kgName/kgName.c - lines changed 13, context: html, text, full: html, text
  • src/hg/pdbSP/pdbSP.c - lines changed 2, context: html, text, full: html, text
  • src/hg/protein/fixAgp/fixAgp.c - lines changed 9, context: html, text, full: html, text
  • src/hg/protein/kgAliasM/kgAliasM.c - lines changed 1, context: html, text, full: html, text
  • src/hg/protein/kgAliasP/kgAliasP.c - lines changed 1, context: html, text, full: html, text
  • src/hg/protein/kgBestMrna/kgPrepBestMrna.c - lines changed 6, context: html, text, full: html, text
  • src/hg/protein/kgBestMrna/kgPrepBestMrna2.c - lines changed 2, context: html, text, full: html, text
  • src/hg/protein/kgBestMrna/kgResultBestMrna.c - lines changed 3, context: html, text, full: html, text
  • src/hg/protein/kgBestMrna2/kgPrepBestMrna2.c - lines changed 2, context: html, text, full: html, text
  • src/hg/protein/kgBestMrna2/kgResultBestMrna2.c - lines changed 1, context: html, text, full: html, text
  • src/hg/protein/kgBestRef2/kgPrepBestRef2.c - lines changed 1, context: html, text, full: html, text
  • src/hg/protein/kgBestRef2/kgResultBestRef2.c - lines changed 1, context: html, text, full: html, text
  • src/hg/protein/kgCheck/kgCheck.c - lines changed 2, context: html, text, full: html, text
  • src/hg/protein/kgCheck2/kgCheck2.c - lines changed 8, context: html, text, full: html, text
  • src/hg/protein/kgGetCds/kgGetCds.c - lines changed 1, context: html, text, full: html, text
  • src/hg/protein/kgPepMrna/kgPepMrna.c - lines changed 4, context: html, text, full: html, text
  • src/hg/protein/kgPick/kgPick.c - lines changed 2, context: html, text, full: html, text
  • src/hg/protein/kgProtAlias/kgProtAlias.c - lines changed 2, context: html, text, full: html, text
  • src/hg/protein/kgProtAliasNCBI/kgProtAliasNCBI.c - lines changed 1, context: html, text, full: html, text
  • src/hg/protein/kgUniq/kgUniq.c - lines changed 7, context: html, text, full: html, text
  • src/hg/protein/kgXref/kgXref.c - lines changed 11, context: html, text, full: html, text
  • src/hg/protein/kgXref2/kgXref2.c - lines changed 11, context: html, text, full: html, text
  • src/hg/protein/lib/doSam.c - lines changed 2, context: html, text, full: html, text
  • src/hg/protein/lib/doStamps.c - lines changed 7, context: html, text, full: html, text
  • src/hg/protein/lib/doTracks.c - lines changed 11, context: html, text, full: html, text
  • src/hg/protein/lib/domains.c - lines changed 3, context: html, text, full: html, text
  • src/hg/protein/lib/pbUtil.c - lines changed 13, context: html, text, full: html, text
  • src/hg/protein/omimCheckAv/omimCheckAv.c - lines changed 2, context: html, text, full: html, text
  • src/hg/protein/pbCalDist/pbCalDist.c - lines changed 8, context: html, text, full: html, text
  • src/hg/protein/pbCalResStd/pbCalResStd.c - lines changed 4, context: html, text, full: html, text
  • src/hg/protein/pbGlobal/pbGlobal.c - lines changed 12, context: html, text, full: html, text
  • src/hg/protein/pbTracks/pbTracks.c - lines changed 7, context: html, text, full: html, text
  • src/hg/protein/pfamXref/pfamXref.c - lines changed 1, context: html, text, full: html, text
  • src/hg/protein/rmKGPepMrna/rmKGPepMrna.c - lines changed 5, context: html, text, full: html, text
  • src/hg/protein/spToProteins/spToProteins.c - lines changed 3, context: html, text, full: html, text
  • src/hg/protein/spToProteinsVar/spToProteinsVar.c - lines changed 1, context: html, text, full: html, text
  • src/hg/protein/spXref3/spXref3.c - lines changed 2, context: html, text, full: html, text
  • src/hg/protein/spm6/spm6.c - lines changed 2, context: html, text, full: html, text
  • src/hg/protein/spm7/spm7.c - lines changed 2, context: html, text, full: html, text
• increasing the size of a couple of query arrays
  • src/hg/lib/jksql.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
  • src/hg/hgGateway/hgGateway.c - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/web.c - lines changed 14, 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/memalloc.c - lines changed 21, context: html, text, full: html, text
• removing unneeded carefulCheckHeap calls since pushCarefulMemHandler was not being used and thus the check did absolutely nothing.
  • src/fuzzyFind/ffapp.c - lines changed 3, context: html, text, full: html, text
  • src/hg/pslReps/pslReps.c - lines changed 2, context: html, text, full: html, text
• oops.
  • src/hg/hgGateway/hgGateway.c - lines changed 1, context: html, text, full: html, text