Commits for max
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v294_base to v295_preview (2014-01-13 to 2014-01-20) v295
- changing wording after code review rm #12486
- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 4, context: html, text, full: html, text
- adding intro to containers in trackDb doc, refs #12486
- src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html - lines changed 18, context: html, text, full: html, text
- src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html - lines changed 13, context: html, text, full: html, text
- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 5, context: html, text, full: html, text
- tiny change to readme file
- src/hg/htdocs/goldenPath/help/trackDb/README.txt - lines changed 1, context: html, text, full: html, text
- 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
- src/hg/hgGene/alleles.c - lines changed 1, context: html, text, full: html, text
- src/hg/hgMirror/hgMirror - lines changed 336, context: html, text, full: html, text
- src/hg/hgTracks/wigTrack.c - lines changed 25, context: html, text, full: html, text
- src/hg/lib/haplotypes.c - lines changed 5, context: html, text, full: html, text
- src/hg/lib/wigDataStream.c - lines changed 11, context: html, text, full: html, text
- addressing gcc warnings
- src/hg/lib/wigDataStream.c - lines changed 2, context: html, text, full: html, text
- fixing stray div, refs #12079
- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 2, context: html, text, full: html, text
- src/hg/lib/pubsBingBlat.sql - lines changed 13, context: html, text, full: html, text
- fiddling again with the trackDb container intro, adding examples
- src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html - lines changed 19, context: html, text, full: html, text
- src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html - lines changed 18, context: html, text, full: html, text
- adding .as files for publications track, ref #12212
- src/hg/lib/pubsArticle.as - lines changed 17, context: html, text, full: html, text
- src/hg/lib/pubsBingArticle.as - lines changed 17, context: html, text, full: html, text
- src/hg/lib/pubsBingArticle.sql - lines changed 5, context: html, text, full: html, text
- src/hg/lib/pubsBingBlat.as - lines changed 30, context: html, text, full: html, text
- src/hg/lib/pubsBingBlatPsl.as - lines changed 26, context: html, text, full: html, text
- src/hg/lib/pubsBingSequenceAnnot.as - lines changed 12, context: html, text, full: html, text
- src/hg/lib/pubsBlat.as - lines changed 19, context: html, text, full: html, text
- src/hg/lib/pubsBlatPsl.as - lines changed 26, context: html, text, full: html, text
- src/hg/lib/pubsBlatPsl.sql - lines changed 28, context: html, text, full: html, text
- src/hg/lib/pubsMarkerAnnot.as - lines changed 12, context: html, text, full: html, text
- src/hg/lib/pubsMarkerAnnot.sql - lines changed 1, context: html, text, full: html, text
- src/hg/lib/pubsMarkerBand.as - lines changed 9, context: html, text, full: html, text
- src/hg/lib/pubsMarkerBand.sql - lines changed 1, context: html, text, full: html, text
- src/hg/lib/pubsMarkerGene.as - lines changed 9, context: html, text, full: html, text
- src/hg/lib/pubsMarkerGene.sql - lines changed 1, context: html, text, full: html, text
- src/hg/lib/pubsMarkerSnp.as - lines changed 9, context: html, text, full: html, text
- src/hg/lib/pubsSequenceAnnot.as - lines changed 12, context: html, text, full: html, text
- fixing typo
- src/hg/lib/pubsBingBlat.as - lines changed 1, context: html, text, full: html, text
- fixed some more typos in pubs as/sql files
- src/hg/lib/pubsBingBlat.as - lines changed 3, context: html, text, full: html, text
- src/hg/lib/pubsBingBlat.sql - lines changed 2, context: html, text, full: html, text
- src/hg/lib/pubsBingBlatPsl.as - lines changed 1, context: html, text, full: html, text
- src/hg/lib/pubsBingBlatPsl.sql - lines changed 1, context: html, text, full: html, text
- src/hg/lib/pubsBingSequenceAnnot.as - lines changed 1, context: html, text, full: html, text
- src/hg/lib/pubsBingSequenceAnnot.sql - lines changed 1, context: html, text, full: html, text
- src/hg/lib/pubsBlat.as - lines changed 12, context: html, text, full: html, text
- src/hg/lib/pubsBlat.sql - lines changed 13, context: html, text, full: html, text
- a quick .sql to .as converter
- src/oneShot/sqlToAs/makefile - lines changed 7, context: html, text, full: html, text
- src/oneShot/sqlToAs/sqlToAs - lines changed 98, context: html, text, full: html, text
- fixing null pointer bug in jksql introduced with my last commit
- fixing a null pointer bug introduced in earlier commit today
- breaking long lines in fasta view of pubs tracks, adding better sequenceIDs (refs #12212)
- not adding failover connections to the connection pool, as they aremanaged by their "parent". This lead to invalid pointers when failover
was activated in the sqlCleanup step upon exit. Also fixing a debug
message.
- adding additional null pointer checks, just in case
- making sure that trackDb actually exists before changing it
- src/hg/hgMirror/hgMirror - lines changed 5, context: html, text, full: html, text
- forgot to always mirror the slowest table of all, trackDb.
- src/hg/hgMirror/hgMirror - lines changed 2, context: html, text, full: html, text
- not trying to parse rsync log anymore, just checking at-queue now
- src/hg/hgMirror/hgMirror - lines changed 15, context: html, text, full: html, text
- Changing handling of sqlConnect to allow a db that exists onlyon the failover server, not on the main one.
- handling the show table status command with failover connections
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