Skip to content
Snippets Groups Projects
Commit 74abd522 authored by Monika Komorowska's avatar Monika Komorowska
Browse files

Dump table out to a file instead of creating a backup table. 

Added option to override db name.
parent 71319b7c
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
misc-scripts/production_database/scripts/populate_analysis_description.pl
+ 108
− 53
View file @ 74abd522
......@@ -21,9 +21,9 @@ my $dbname;
my $dbpattern;
my $core = 0;
my $drop_bak = 0;
my $verbose = 0;
my $cleanup = 0;
my $dumppath;
my $dbname_file;
# Do command line parsing.
if ( !GetOptions( 'mhost|mh=s' => \$mhost,
......@@ -37,17 +37,18 @@ if ( !GetOptions( 'mhost|mh=s' => \$mhost,
'pass|p=s' => \$pass,
'database|d=s' => \$dbname,
'pattern=s' => \$dbpattern,
'drop|D!' => \$drop_bak,
'verbose|v!' => \$verbose,
'core=i' => \$core,
'cleanup!' => \$cleanup )
'dumppath|dp=s' => \$dumppath,
'dbname_file|dbf=s' => \$dbname_file)
|| !(
defined($host)
&& defined($user)
&& defined($pass)
&& ( defined($dbname) || defined($dbpattern) || defined($core) )
&& defined($mhost)
&& defined($muser) ) )
&& defined($muser)
&& defined($dumppath) ) )
{
my $indent = ' ' x length($0);
print <<USAGE_END;
......@@ -59,54 +60,60 @@ Usage:
$0 -h host [-P port] \\
$indent -u user [-p password]
$indent -d database | --pattern pattern \\
$indent -dp dumppath
$indent [-dbf dbname override file]
$indent [-mh host] [-mP port] \\
$indent [-mu user] [-mp password] [-md database] \\
$indent [-D] [-v]
$indent [-v]
-h / --host User database server host
-P / --port User database server port (optional, default is 3306)
-h / --host User database server host
-P / --port User database server port (optional, default is 3306)
-u / --user User username (must have write-access)
-p / --pass User password
-u / --user User username (must have write-access)
-p / --pass User password
-d / --database User database name or SQL pattern
e.g. --database="homo_sapiens_rnaseq_62_37g"
or --database="%core_62%"
-d / --database User database name or SQL pattern
e.g. --database="homo_sapiens_rnaseq_62_37g"
or --database="%core_62%"
--pattern User database by Perl regular expression
e.g. --pattern="^homo.*(rnaseq|vega)_62"
-dp / --dumppath Dumpout path. Dump out table into the specified directory path
(-d/--database and --pattern are mutually exclusive)
--pattern User database by Perl regular expression
e.g. --pattern="^homo.*(rnaseq|vega)_62"
--core=NN Preset pattern for Core-like databases in relase NN
Specifying --core=62 is equivalent to using
--pattern="(cdna|core|otherfeatures|rnaseq|vega)_62"
(-d/--database and --pattern are mutually exclusive)
-mh / --mhost Production database server host
(optional, default is 'ens-staging1')
-mP / --mport Production database server port
(optional, default is 3306)
--core=NN Preset pattern for Core-like databases in relase NN
Specifying --core=62 is equivalent to using
--pattern="(cdna|core|otherfeatures|rnaseq|vega)_62"
-mu / --muser Production database username (no write-access required)
(optional, default is 'ensro')
-mp / --mpass Production database password
(optional, default is undefined)
-dbf / Override dbnames stored in the production database with
--dbname_file dbnames in the specified file. The file should have the following
tab delimited data on each line:
- db name stored in 'full_db_name' column 'db_list'
table in the production database
- new db name to use
-mh / --mhost Production database server host
(optional, default is 'ens-staging1')
-mP / --mport Production database server port
(optional, default is 3306)
-md / --mdatabase Production database name
(optional, default is 'ensembl_production')
-mu / --muser Production database username (no write-access required)
(optional, default is 'ensro')
-mp / --mpass Production database password
(optional, default is undefined)
-D / --drop Drop backup tables if they already exists in the
database from a previous run
-md / --mdatabase Production database name
(optional, default is 'ensembl_production')
--cleanup Just clean up backup tables, do nothing else
-v / --verbose Be verbose, display every SQL statement as they
are executed (on standard error)
-v / --verbose Be verbose, display every SQL statement as they
are executed (on standard error)
USAGE_END
die( "Need the following options: "
. "-h -u -p and -d (or --pattern)\n" );
. "-h -u -p -d (or --pattern) and -dp\n" );
} ## end if ( !GetOptions( 'mhost|mh=s'...))
......@@ -119,6 +126,23 @@ if ( defined($dbname) && defined($dbpattern) ) {
die("-d/--database and --pattern/--core are mutually exclusive\n");
}
my %dbname_override;
if ($dbname_file) {
if( ! -r $dbname_file ) {
die ( "File $dbname_file not readable" );
}
open( DBNAMEF, "<$dbname_file" );
my @temp_array;
while( my $line = <DBNAMEF> ) {
chomp $line;
@temp_array = split(/\t/,$line);
$dbname_override{$temp_array[0]} = $temp_array[1];
}
}
# Fetch all data from the master database.
my %data;
{
......@@ -140,6 +164,9 @@ my %data;
$hash{'displayable'}, $hash{'web_data'} ) );
while ( $sth->fetch() ) {
if ($dbname_override{$full_db_name}) {
$full_db_name = $dbname_override{$full_db_name};
}
$data{$full_db_name}{$logic_name} = { %{ \%hash } };
}
......@@ -184,21 +211,52 @@ my %data;
my $full_table_name_bak = $dbh->quote_identifier( undef, $dbname,
'analysis_description_bak' );
# Drop backup table if it exists and if asked to do so.
if ( $cleanup || $drop_bak ) {
$dbh->do(
sprintf( 'DROP TABLE IF EXISTS %s', $full_table_name_bak ) );
# check if table exists
my $test_sql = "select count(1) from information_schema.tables where table_schema = ? and table_name = 'analysis_description'";
my $test_sth = $dbh->prepare($test_sql);
$test_sth->execute($dbname);
my ($table_exists) = $test_sth->fetchrow_array();
if ($table_exists) {
my $file_path = $dumppath . "/" . $dbname . 'analysis_description.sql';
my $file_exists = 0;
my $response;
if (-e $file_path) {
print("file $file_path already exists, overwrite? (y/n)\n");
$file_exists = 1;
$response = <>;
chomp $response;
}
if ( !$file_exists or $response eq 'y') {
open(BKUPFILE, ">$file_path") or die("Failed to open file $file_path for writing\n");
my $cmd = "mysqldump -h $host -u $user -p$pass $dbname analysis_description";
my $result = `$cmd`;
print BKUPFILE $result;
close BKUPFILE;
if ($result !~ /Dump completed/) {
print("back up failed, check file $file_path for details\n");
next;
} else {
print("$full_table_name dumped out to file $file_path\n");
}
} else {
print("skipping update for table analysis_description\n");
next;
}
} else {
print("table analysis_description does not exist in database $dbname\n");
next;
}
print("Dropped old backup table\n");
if ($cleanup) { next }
}
$dbh->do(
sprintf( 'DROP TABLE IF EXISTS %s', $full_table_name_bak ) );
# Make a backup of any existing data.
$dbh->do( sprintf( 'CREATE TABLE %s LIKE %s',
$full_table_name_bak, $full_table_name ) );
$dbh->do( sprintf( 'INSERT INTO %s SELECT * FROM %s',
$full_table_name_bak, $full_table_name ) );
print("Created new backup table\n");
# Truncate (empty) the table before inserting new data into it.
$dbh->do( sprintf( 'TRUNCATE TABLE %s', $full_table_name ) );
......@@ -316,19 +374,16 @@ my %data;
print("\n");
}
print("To undo:\n");
printf( " DROP TABLE %s;\n", $full_table_name );
printf( " RENAME TABLE %s TO %s;\n",
$full_table_name_bak, $full_table_name );
}
#delete the backup table
$dbh->do(
sprintf( 'DROP TABLE IF EXISTS %s', $full_table_name_bak ) );
} continue {
print("\n");
}
if ( !$cleanup ) {
print("Remember to drop the backup tables!\n\n");
}
$dbh->disconnect();
}
print "To restore a table from dump login to the database and use command: source {dump file name};\n";
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment