From e5f562c4483b763dc1bb9df9506278f00b1fbcd7 Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Wed, 9 Aug 2006 12:10:49 +0000
Subject: [PATCH] Slight change in procedure: a 'master' database must now be
specified. The external_dbs.txt file is loaded into this, and this in turn is
compared (id and name) with the contents of the external_db table in each of
the databases to be updated.
If the database to be updated has any extra rows, a warning is given and the database is skipped.
This should help avoid unilateral changes to external_db which haven't been commited to the external_dbs.txt file in CVS being silently overwritten and causing problems down the line.
---
.../external_db/update_external_dbs.pl | 107 ++++++++++++++----
1 file changed, 88 insertions(+), 19 deletions(-)
diff --git a/misc-scripts/external_db/update_external_dbs.pl b/misc-scripts/external_db/update_external_dbs.pl
index 96da96b55c..9793c32dea 100644
--- a/misc-scripts/external_db/update_external_dbs.pl
+++ b/misc-scripts/external_db/update_external_dbs.pl
@@ -9,22 +9,27 @@ use Getopt::Long;
use DBI;
use IO::File;
-my ( $host, $user, $pass, $port,@dbnames, $file, $release_num);
-
-GetOptions( "host=s", \$host,
- "user=s", \$user,
- "pass=s", \$pass,
- "port=i", \$port,
- "file=s", \$file,
- "dbnames=s@", \@dbnames,
- "release_num=i", \$release_num
+my ( $host, $user, $pass, $port,@dbnames, $file, $release_num, $master);
+
+GetOptions( "host=s", \$host,
+ "user=s", \$user,
+ "pass=s", \$pass,
+ "port=i", \$port,
+ "file=s", \$file,
+ "dbnames=s@", \@dbnames,
+ "release_num=i", \$release_num,
+ "master=s", \$master
);
#both host and file are required
usage() if(!$host || !$file);
+
#release num XOR dbname are required
usage() if(($release_num && @dbnames) || (!$release_num && !@dbnames));
+# master database is required
+usage() if (!$master);
+
$port ||= 3306;
my $dsn = "DBI:mysql:host=$host;port=$port";
@@ -33,7 +38,7 @@ my $db = DBI->connect( $dsn, $user, $pass, {RaiseError => 1} );
if($release_num) {
@dbnames = map {$_->[0] } @{ $db->selectall_arrayref( "show databases" ) };
-
+
#
# filter out all non-core databases
#
@@ -44,13 +49,13 @@ if($release_num) {
#
# make sure the user wishes to continue
#
-print STDERR "The following databases will be external_db updated:\n ";
+print STDERR "The following databases will have their external_db tables updated if necessary:\n ";
print join("\n ", @dbnames);
-print "\ncontinue with update (yes/no)> ";
+print "\nContinue with update (yes/no)> ";
my $input = lc(<STDIN>);
chomp($input);
-if($input ne 'yes') {
+if ($input ne 'yes') {
print "external_db conversion aborted\n";
exit();
}
@@ -59,10 +64,10 @@ if($input ne 'yes') {
# read all of the new external_db entries from the file
#
my $fh = IO::File->new();
-$fh->open($file) or die("could not open input file $file");
+$fh->open($file) or die("Could not open input file $file");
my @rows;
my $row;
-while($row = <$fh>) {
+while ($row = <$fh>) {
chomp($row);
my @a = split(/\t/, $row);
push @rows, {'external_db_id' => $a[0],
@@ -76,8 +81,38 @@ while($row = <$fh>) {
}
$fh->close();
+# Load into master database
+load_database($db, $master, @rows);
+
+# Check each other database in turn
+# Load if no extra rows in db that aren't in master
+# Warn and skip if there are
+
foreach my $dbname (@dbnames) {
- print STDERR "updating $dbname\n";
+
+ print STDERR "Looking at $dbname ... \n";
+
+ if (compare_external_db($db, $master, $dbname)) {
+
+ print STDERR "$dbname has no additional rows. Overwriting external_db table from $file\n";
+ load_database($db, $dbname, @rows);
+
+ } else {
+
+ print STDERR "$dbname has extra rows that are not in $file, skipping\n";
+
+ }
+
+}
+
+print STDERR "Updates complete\n";
+
+
+
+sub load_database {
+
+ my ($db, $dbname, @rows) = @_;
+
$db->do("use $dbname");
my $sth = $db->prepare('DELETE FROM external_db');
$sth->execute();
@@ -101,10 +136,40 @@ foreach my $dbname (@dbnames) {
}
$sth->finish();
+
}
-print STDERR "updates complete\n";
+# return true if the tables are the same, undef if not
+sub compare_external_db {
+
+ my ($db, $master, $dbname) = @_;
+
+ my $same = 1;
+
+ # check each row in $dbname against each row in $master
+ # only compare ID and name since we're only aiming to catch extra rows in $dbname
+ $db->do("use $dbname");
+
+ my $sth = $db->prepare(qq {SELECT d.external_db_id, d.db_name
+ FROM $dbname.external_db d
+ LEFT JOIN $master.external_db m
+ ON (d.external_db_id=m.external_db_id AND d.db_name=m.db_name)
+ WHERE m.external_db_id IS NULL OR m.db_name IS NULL });
+ $sth->execute();
+
+ while (my ($id, $external_db_name) = $sth->fetchrow_array) {
+
+ print "$dbname has external_db entry for $external_db_name (ID $id) which is not present in $master\n";
+ $same = undef;
+
+ }
+
+ $sth->finish();
+
+ return $same;
+
+}
sub usage {
print STDERR <<EOF
@@ -114,6 +179,7 @@ sub usage {
-user username
-pass password
-port port_of_server optional
+ -master the name of the master database to load the file into
-release the release of the database to update used to
match database names. e.g. 13
-file the path of the file containing the insert statements
@@ -127,12 +193,15 @@ sub usage {
E.g.:
- #update 2 databases
+ # update 2 databases
perl update_external_dbs.pl -host ecs1c -file external_dbs.txt -user ensadmin -pass secret -dbnames homo_sapiens_core_14_33 -dbnames mus_musculus_core_14_30
- #update all core databases for release 14
+ # update all core databases for release 14
perl update_external_dbs.pl -host ecs2d -file external_dbs.txt -user ensadmin -pass secret -release 14
+ If the databases to be updated contain rows that are not in the file, a warning will
+ be given and the database in question skipped.
+
EOF
;
exit;
--
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