225c0d55992aefae478461bba278644bdfdda3c5
max
  Wed Jan 15 08:33:57 2014 -0800
library changes for the browser box: This changes mostly hdb and jksql,plus - to a smaller extent - various other places in the code that deal
with /gbdb/ files.  The overall aim is to make it possible to have the
data remote at UCSC while having the CGIs on a machine far away. At up to
180msecs distance from UCSC (Europe,Japan), each query can get slow. So
I tried to reduce the number of queries sent to UCSC while allowing to
keep some mysql tables on localhost.

I changed four things:
- extend larry's table cache to include field names. The code uses
"describe" very often, which is slow from remote. With a table name
cache these queries can be handled locally. This is configured in
hg.conf
- mysql "failover" connections: a mysql connection can have a 2nd
connection that is used if a query fails, configured in hg.conf
(I didn't call it "remote" connections, because we use that term already
in the code)
- mysql lazy connects: don't connect a sqlConnection right away, but
only when needed. a mysql connect takes >500msecs from across the
atlantic.
- move gbdb: patch various places that use absolute "/gbdb/" pathnames
to go through a central function that can change the filename of
gbdb files to something else, as configured in hg.conf

Plus patch 1 or 2 lines for more speed + update the hgMirror script

diff --git src/hg/hgGene/alleles.c src/hg/hgGene/alleles.c
index 66b5a1e..6254e3f 100644
--- src/hg/hgGene/alleles.c
+++ src/hg/hgGene/alleles.c
@@ -1,96 +1,97 @@
 // alleles - common Gene haplotype alleles. */
 
 #include "common.h"
 #include "web.h"
 #include "genePredReader.h"
 #include "vcf.h"
 #include "haplotypes.h"
 #include "hgGene.h"
 
 static boolean allelesExists(struct section *section,
         struct sqlConnection *conn, char *geneId)
 // Return TRUE if common haplotype alleles exist.
 {
 // If there was a reset then clear out settings
 if (cartUsualBoolean(cart, HAPLO_RESET_ALL, FALSE))
     cartRemovePrefix(cart,HAPLO_TABLE "_" );
 
 // Start with the default variables for haplotype retrieval
 struct haploExtras *he = haplotypeExtrasDefault(database, 0);
 section->extras = he;
 
 // Need to get genePred struct from geneId
 char where[128];
 safef(where,sizeof(where),"name = '%s'",geneId);
 struct genePred *gp = genePredReaderLoadQuery(conn,he->geneTable, where);
 if (gp == NULL || gp->cdsStart == gp->cdsEnd)  // Ain't interested in non-protein coding genes
     {
     haplotypeExtrasFree(&he);
     return FALSE;
     }
 
 he->chrom = gp->chrom; // Probably not needed
 he->justModel = lmCloneString(he->lm,geneId);
 //he->growTree = FALSE; // Tree growing not needed here
 
 // Need to determine the correct vcf file and open it
 if (haplotypesDiscoverVcfFile(he, gp->chrom) == NULL)
     {
     haplotypeExtrasFree(&he);
     return FALSE;
     }
+
 struct vcfFile *vcff = vcfTabixFileMayOpen(he->inFile, NULL, 0, 0,VCF_IGNORE_ERRS, 0);
 if (vcff == NULL)
     {
     haplotypeExtrasFree(&he);
     return FALSE;
     }
 vcfFileMakeReusePool(vcff,1024 * 1024);
 
 // All or Limit to the 99%
 boolean rareVars =  cartUsualBoolean(cart, HAPLO_RARE_VAR, FALSE);
 if (rareVars)
     he->synonymous = TRUE;
 else
     he->variantMinPct = HAPLO_COMMON_VARIANT_MIN_PCT;
 
 // Lets show the population distribution
 he->populationsToo   = cartUsualBoolean(cart, HAPLO_MAJOR_DIST, FALSE);
 he->populationsMinor = cartUsualBoolean(cart, HAPLO_MINOR_DIST, FALSE);
 if (he->populationsToo)
     he->populationMinPct = 5;
 else if (he->populationsMinor)
     {
     he->populationsMinor = FALSE;
     cartRemove(cart, HAPLO_MINOR_DIST );
     }
 
 // Need to generate haplotypes
 section->items = geneHapSetForOneModel(he,vcff,gp,TRUE);
 
 return TRUE;// (section->items != NULL);
 }
 
 static void allelesPrint(struct section *section,
 	struct sqlConnection *conn, char *geneId)
 // Print out common gene haplotype alleles.
 {
 struct haploExtras *he = section->extras;
 struct haplotypeSet *hapSet = section->items;
 geneAllelesTableAndControls(cart, geneId, he, hapSet);
 
 haplotypeExtrasFree(&he);
 }
 
 struct section *allelesSection(struct sqlConnection *conn, struct hash *sectionRa)
 // Create UCSC KG Method section.
 {
 struct section *section = sectionNew(sectionRa, HGG_GENE_ALLELES);
 if (section != NULL)
     {
     section->exists = allelesExists;
     section->print = allelesPrint;
     }
 return section;
 }