From a1098db4c5991b2e6c2c0f2c4fed6b6f96d1ff6c Mon Sep 17 00:00:00 2001
From: thomasmaurel <maurel@ebi.ac.uk>
Date: Thu, 8 Dec 2016 13:41:48 +0000
Subject: [PATCH] Updated script to work on both the EBI and Sanger MySQL
servers
---
misc-scripts/CopyDBoverServer.pl | 23 +++++++++++++----------
1 file changed, 13 insertions(+), 10 deletions(-)
diff --git a/misc-scripts/CopyDBoverServer.pl b/misc-scripts/CopyDBoverServer.pl
index eaa7c9e37a..60324fcdad 100755
--- a/misc-scripts/CopyDBoverServer.pl
+++ b/misc-scripts/CopyDBoverServer.pl
@@ -294,8 +294,8 @@ if ( defined($opt_skip_tables) ) {
%skip_tables = map( { $_ => 1 } split( /,/, $opt_skip_tables ) );
}
-if ( scalar( getpwuid($<) ) ne 'mysqlens' ) {
- warn("You are not running this script as the 'mysqlens' user.\n");
+if ( scalar( getpwuid($<) ) ne 'ensmysql' and scalar( getpwuid($<) ) ne 'mysqlens' ) {
+ warn("You are not running this script as the 'ensmysql' user at the EBI or as the 'mysqlens' at Sanger.\n");
}
if (!defined($opt_user))
@@ -321,7 +321,11 @@ foreach my $key (@executables) {
my $output = `which $key`;
my $rc = $? >> 8;
- if($rc != 0) {
+ if ( !$opt_check && $key eq 'myisamchk' ) {
+ print( "Can not find 'myisamchk' " .
+ "but --nocheck was specified so skipping\n" ),;
+ }
+ elsif($rc != 0) {
chomp $output;
die(
sprintf(
@@ -330,12 +334,6 @@ foreach my $key (@executables) {
$key, $key
) );
}
- else {
- if ( !$opt_check && $key eq 'myisamchk' ) {
- print( "Can not find 'myisamchk' " .
- "but --nocheck was specified so skipping\n" ),;
- }
- }
} ## end foreach my $key ( @executables...)
my $run_hostaddr = hostname_to_ip(hostname());
@@ -603,7 +601,12 @@ foreach my $spec (@todo) {
my $tmp_dir;
if ( defined($opt_tmpdir) ) { $tmp_dir = $opt_tmpdir }
else {
- $tmp_dir = canonpath( catdir( $target_dir, updir(), 'tmp' ) );
+ if ((scalar( getpwuid($<) ) eq 'mysqlens')) {
+ $tmp_dir = canonpath( catdir( $target_dir, updir(), 'tmp' ));
+ }
+ elsif ((scalar( getpwuid($<) ) eq 'ensmysql')){
+ $tmp_dir = canonpath( catdir( $target_dir, updir(), 'temp' ));
+ }
}
printf( "SOURCE 'datadir' = '%s'\n", $source_dir );
--
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