From 6988020ba71a12446dbb6f1c6df546c0f1e9ce29 Mon Sep 17 00:00:00 2001
From: Kieron Taylor <ktaylor@ebi.ac.uk>
Date: Thu, 3 May 2012 14:24:39 +0000
Subject: [PATCH] Added proper support for limiting the back-catalogue of
patches that can be applied by --fix through the --oldest option.
---
misc-scripts/schema_patcher.pl | 27 +++++++++++++++++----------
1 file changed, 17 insertions(+), 10 deletions(-)
diff --git a/misc-scripts/schema_patcher.pl b/misc-scripts/schema_patcher.pl
index a63911fd53..9806ca927c 100755
--- a/misc-scripts/schema_patcher.pl
+++ b/misc-scripts/schema_patcher.pl
@@ -67,9 +67,10 @@ Usage:
patch (patching starts at release equal to the
oldest patch in the database) >>USE WITH CAUTION<<
- Can be used in conjunction with --from to limit the oldest
- release to search for patches. Useful for going from last
- release to current without missing anything out.
+ --oldest used in conjunction with --fix, this option allows control
+ over how many releases are included in the fix. This option
+ exists for users who have incomplete meta entries and
+ wish to bring their database automatically up to date.
--mysql specify the location of the mysql binary if it is not on
\$PATH. Otherwise we default this to mysql
@@ -173,6 +174,14 @@ sub about {
$0 -h host -u user -p password \\
-r 66 -d my_database --fix --dryrun
+
+ The genebuilder above has an evil twin who has mislayed their meta tables.
+ --fix threatens to apply ancient patches but they know their database
+ is correct until halfway through release 64. They wish to apply any
+ missing patches between release 64 and 66.
+
+ $0 -h host -u user -p password -r 66 \\
+ -d my_database --fix --oldest 64
ABOUT_END
} ## end sub about
@@ -187,6 +196,7 @@ my $opt_cvsdir;
my $opt_dryrun;
my $opt_from;
my $opt_fix;
+my $opt_oldest;
my $opt_mysql = 'mysql';
my $opt_interactive = 1;
@@ -204,6 +214,7 @@ if ( !GetOptions( 'host|h=s' => \$opt_host,
'cvsdir=s' => \$opt_cvsdir,
'dryrun|n!' => \$opt_dryrun,
'fix!' => \$opt_fix,
+ 'oldest=i' => \$opt_oldest,
'mysql=s' => \$opt_mysql,
'interactive|i!' => \$opt_interactive,
'verbose|v!' => \$opt_verbose,
@@ -231,7 +242,7 @@ my %patches;
# Get available patches.
-foreach my $thing ( [ 'ensembl', 'core', 'table.sql' ],
+foreach my $thing ( [ 'ensembl-core', 'core', 'table.sql' ],
[ 'ensembl-functgenomics', 'funcgen', 'efg.sql' ],
[ 'ensembl-variation', 'variation', 'table.sql' ] )
{
@@ -476,18 +487,14 @@ while ( $sth->fetch() ) {
my $start_version;
if ($opt_fix) {
- if ($opt_from) {
- $start_version = $opt_from;
- printf "Finding patches only as far back as user-selected version %s\n",$opt_from;
- }
- else {$start_version = ( sort { $a <=> $b } keys %dbpatches )[0];}
+ $start_version = $opt_oldest || ( sort { $a <=> $b } keys %dbpatches )[0];
if ( !defined($start_version) ) {
warn( sprintf( "No patches in database, " .
"beginning fix from release %d\n",
$schema_version ) );
$start_version = $schema_version;
}
- elsif (!$opt_fix) {
+ else {
printf( "Earliest patch in database '%s' is from release %d\n",
$database, $start_version );
}
--
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