diff --git a/misc-scripts/production_database/scripts/populate_analysis_description.pl b/misc-scripts/production_database/scripts/populate_analysis_description.pl
index 172d5142d7226aee7d5a1d4c0b87b341b53e1749..b43aa179cd2c27648659c48325bd645dab343c6e 100755
--- a/misc-scripts/production_database/scripts/populate_analysis_description.pl
+++ b/misc-scripts/production_database/scripts/populate_analysis_description.pl
@@ -7,7 +7,7 @@ use Data::Dumper;
use DBI qw( :sql_types );
use Getopt::Long qw( :config no_ignore_case );
-local $| = 1;
+my $timestamp = strftime( "%Y%m%d-%H%M%S", localtime() );
# Master database location:
my ( $mhost, $mport ) = ( 'ens-staging1', '3306' );
@@ -20,10 +20,9 @@ my ( $user, $pass );
my $dbname;
my $dbpattern;
-my $core = 0;
-my $verbose = 0;
+my $core = 0;
+my $verbose = 0;
my $dumppath;
-my $dbname_file;
# Do command line parsing.
if ( !GetOptions( 'mhost|mh=s' => \$mhost,
@@ -40,14 +39,14 @@ if ( !GetOptions( 'mhost|mh=s' => \$mhost,
'verbose|v!' => \$verbose,
'core=i' => \$core,
'dumppath|dp=s' => \$dumppath )
- || !(
- defined($host)
- && defined($user)
- && defined($pass)
- && ( defined($dbname) || defined($dbpattern) || defined($core) )
- && defined($mhost)
- && defined($muser)
- && defined($dumppath) ) )
+ ||
+ !( defined($host) &&
+ defined($user) &&
+ defined($pass) &&
+ ( defined($dbname) || defined($dbpattern) || defined($core) ) &&
+ defined($mhost) &&
+ defined($muser) &&
+ defined($dumppath) ) )
{
my $indent = ' ' x length($0);
print <<USAGE_END;
@@ -90,7 +89,8 @@ Usage:
-s / --species If the name of the database specified by -d (or
--database) is not in the standard format, this
flag is used to specify what species it is (e.g.,
- 'homo_sapiens', 'gallus_gallus' etc.).
+ 'homo_sapiens', 'gallus_gallus' etc., i.e. the
+ latin name).
-t / --type If the name of the database specified by -d (or
--database) is not in the standard format, this
@@ -113,10 +113,11 @@ Usage:
-v / --verbose Be verbose, display every SQL statement as they
are executed (on standard error).
+
USAGE_END
- die( "Need the following options: "
- . "-h -u -p -d (or --pattern) and -dp\n" );
+ die( "Need the following options: " .
+ "-h -u -p -d (or --pattern) and -dp\n" );
} ## end if ( !GetOptions( 'mhost|mh=s'...))
@@ -129,27 +130,6 @@ if ( defined($dbname) && defined($dbpattern) ) {
die("-d/--database and --pattern/--core are mutually exclusive\n");
}
-my %dbname_override;
-
-if ( defined($dbname_file) ) {
- if ( !-r $dbname_file ) {
- die(
- sprintf( "File '%s' not found or not readable", $dbname_file ) );
- }
-
- open( DBNAMEF, "<$dbname_file" );
-
- my @temp_array;
- while ( my $line = <DBNAMEF> ) {
- chomp $line;
- @temp_array = split( /\s+/, $line );
- $dbname_override{ $temp_array[0] } = $temp_array[1];
- }
-
- close(DBNAMEF);
-}
-
-
# Fetch all data from the master database.
my %data;
{
@@ -159,9 +139,9 @@ my %data;
{ 'PrintError' => 1, 'RaiseError' => 1 } );
my $sth =
- $dbh->prepare( 'SELECT full_db_name, logic_name, '
- . 'description, display_label, displayable, web_data '
- . 'FROM full_analysis_description' );
+ $dbh->prepare( 'SELECT full_db_name, logic_name, ' .
+ 'description, display_label, displayable, web_data ' .
+ 'FROM full_analysis_description' );
$sth->execute();
@@ -171,9 +151,6 @@ 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}{$logic_name} = { %{ \%hash } };
}
@@ -190,7 +167,8 @@ my %data;
if ( defined($dbname) ) {
$sth = $dbh->prepare('SHOW DATABASES LIKE ?');
$sth->bind_param( 1, $dbname, SQL_VARCHAR );
- } else {
+ }
+ else {
$sth = $dbh->prepare('SHOW DATABASES');
}
@@ -203,8 +181,8 @@ my %data;
my $dbdata = $data{$dbname};
if ( !defined($dbdata) ) {
- printf( "ERROR: Can not find data for database '%s' "
- . "(skipping it)!\n",
+ printf( "ERROR: Can not find data for database '%s' " .
+ "(skipping it)!\n",
$dbname );
next;
}
@@ -218,43 +196,29 @@ my %data;
my $full_table_name_bak = $dbh->quote_identifier( undef, $dbname,
'analysis_description_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 $dbname\n");
- next;
+ if ( defined($dumppath) ) {
+ # Backup the table on file.
+ my $filename = sprintf( "%s/%s.%s.%s.sql",
+ $dumppath, $dbname,
+ 'analysis_description', $timestamp );
+
+ if ( -e $filename ) {
+ die( sprintf( "File '%s' already exists.", $filename ) );
}
+ printf( "Backing up table %s on file.\n",
+ 'analysis_description' );
+ printf( "--> %s\n", $filename );
+
+ system( "mysqldump",
+ "--host=$host",
+ "--port=$port",
+ "--user=$user",
+ ( defined($pass) ? "--password=$pass" : "--opt" ),
+ "--result-file=$filename",
+ "$dbname",
+ 'analysis_description' );
+ }
$dbh->do(
sprintf( 'DROP TABLE IF EXISTS %s', $full_table_name_bak ) );
@@ -285,22 +249,23 @@ my %data;
# Insert into the empty analysis_description table.
$sth2 = $dbh->prepare(
- sprintf( 'INSERT INTO %s '
- . '(analysis_id, description, display_label, '
- . 'displayable, web_data) '
- . 'VALUES (?, ?, ?, ?, ?)',
- $full_table_name ) );
+ sprintf( 'INSERT INTO %s ' .
+ '(analysis_id, description, display_label, ' .
+ 'displayable, web_data) ' . 'VALUES (?, ?, ?, ?, ?)',
+ $full_table_name ) );
foreach my $logic_name ( keys( %{$dbdata} ) ) {
if ( !exists( $dbdata->{$logic_name}{'description'} ) ) {
- printf( "ERROR: Missing production database entry "
- . "for logic name '%s'\n",
+ printf( "ERROR: Missing production database entry " .
+ "for logic name '%s'\n",
$logic_name );
- } elsif ( !exists( $dbdata->{$logic_name}{'analysis_id'} ) ) {
- printf( "WARNING: Expected to find analysis entry "
- . "for logic name '%s'\n",
+ }
+ elsif ( !exists( $dbdata->{$logic_name}{'analysis_id'} ) ) {
+ printf( "WARNING: Expected to find analysis entry " .
+ "for logic name '%s'\n",
$logic_name );
- } else {
+ }
+ else {
$sth2->bind_param( 1, $dbdata->{$logic_name}{'analysis_id'},
SQL_INTEGER );
$sth2->bind_param( 2, $dbdata->{$logic_name}{'description'},
@@ -314,17 +279,15 @@ my %data;
$sth2->execute();
}
- }
+ } ## end foreach my $logic_name ( keys...)
print("Inserted data\n");
my $key_name = 'analysis_id';
{
- my $statement = sprintf( 'SELECT %s '
- . 'FROM %s '
- . 'LEFT JOIN %s t USING (%s) '
- . 'WHERE t.%s IS NULL '
- . 'ORDER BY %s',
+ my $statement = sprintf( 'SELECT %s ' . 'FROM %s ' .
+ 'LEFT JOIN %s t USING (%s) ' .
+ 'WHERE t.%s IS NULL ' . 'ORDER BY %s',
$key_name, $full_table_name,
$full_table_name_bak, $key_name,
$key_name, $key_name );
@@ -350,11 +313,9 @@ my %data;
}
}
{
- my $statement = sprintf( 'SELECT %s '
- . 'FROM %s '
- . 'LEFT JOIN %s t USING (%s) '
- . 'WHERE t.%s IS NULL '
- . 'ORDER BY %s',
+ my $statement = sprintf( 'SELECT %s ' . 'FROM %s ' .
+ 'LEFT JOIN %s t USING (%s) ' .
+ 'WHERE t.%s IS NULL ' . 'ORDER BY %s',
$key_name, $full_table_name_bak,
$full_table_name, $key_name,
$key_name, $key_name );
@@ -386,11 +347,15 @@ my %data;
$dbh->do(
sprintf( 'DROP TABLE IF EXISTS %s', $full_table_name_bak ) );
- } continue {
+ } ## end while ( $sth->fetch() )
+ continue {
print("\n");
}
$dbh->disconnect();
}
-print "To restore a table from dump login to the database and use command: source {dump file name};\n";
+print <<FINAL_END
+To restore a table from dump login to the database and use command:
+"source {dumpfile} or "\. {dumpfile}".
+FINAL_END