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Commit 4e07076c authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
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Regarding dbname_file: don't require tab-delimited file, but allow for 

any whitespace.


Some reformatting.
parent 8242abd1
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misc-scripts/production_database/scripts/populate_analysis_description.pl
+ 65
− 57
View file @ 4e07076c
......@@ -26,28 +26,28 @@ my $dumppath;
my $dbname_file;
# Do command line parsing.
if ( !GetOptions( 'mhost|mh=s' => \$mhost,
'mport|mP=i' => \$mport,
'muser|mu=s' => \$muser,
'mpass|mp=s' => \$mpass,
'mdatabase|md=s' => \$mdbname,
'host|h=s' => \$host,
'port|P=i' => \$port,
'user|u=s' => \$user,
'pass|p=s' => \$pass,
'database|d=s' => \$dbname,
'pattern=s' => \$dbpattern,
'verbose|v!' => \$verbose,
'core=i' => \$core,
'dumppath|dp=s' => \$dumppath,
'dbname_file|dbf=s' => \$dbname_file)
if ( !GetOptions( 'mhost|mh=s' => \$mhost,
'mport|mP=i' => \$mport,
'muser|mu=s' => \$muser,
'mpass|mp=s' => \$mpass,
'mdatabase|md=s' => \$mdbname,
'host|h=s' => \$host,
'port|P=i' => \$port,
'user|u=s' => \$user,
'pass|p=s' => \$pass,
'database|d=s' => \$dbname,
'pattern=s' => \$dbpattern,
'verbose|v!' => \$verbose,
'core=i' => \$core,
'dumppath|dp=s' => \$dumppath,
'dbname_file|dbf=s' => \$dbname_file )
|| !(
defined($host)
&& defined($user)
&& defined($pass)
&& ( defined($dbname) || defined($dbpattern) || defined($core) )
&& defined($mhost)
&& defined($muser)
&& defined($muser)
&& defined($dumppath) ) )
{
my $indent = ' ' x length($0);
......@@ -76,7 +76,8 @@ Usage:
e.g. --database="homo_sapiens_rnaseq_62_37g"
or --database="%core_62%"
-dp / --dumppath Dumpout path. Dump out table into the specified directory path
-dp / --dumppath Dump path.
Dump out table into the specified directory path.
--pattern User database by Perl regular expression
e.g. --pattern="^homo.*(rnaseq|vega)_62"
......@@ -87,13 +88,16 @@ Usage:
Specifying --core=62 is equivalent to using
--pattern="(cdna|core|otherfeatures|rnaseq|vega)_62"
-dbf / Override dbnames stored in the production database with
--dbname_file dbnames in the specified file. The file should have the following
tab delimited data on each line:
- db name stored in 'full_db_name' column 'db_list'
table in the production database
- new db name to use
-dbf / --dbname_file Override database names stored in the production
database with database names in the specified
file. The file should have the following
tab/space delimited data on each line:
- database name stored in 'full_db_name' column
'db_list' table in the production database.
- new database name to use.
-mh / --mhost Production database server host
(optional, default is 'ens-staging1')
-mP / --mport Production database server port
......@@ -128,18 +132,22 @@ if ( defined($dbname) && defined($dbpattern) ) {
my %dbname_override;
if ($dbname_file) {
if( ! -r $dbname_file ) {
die ( "File $dbname_file not readable" );
if ( defined($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 $line;
@temp_array = split(/\t/,$line);
$dbname_override{$temp_array[0]} = $temp_array[1];
while ( my $line = <DBNAMEF> ) {
chomp $line;
@temp_array = split( /\s+/, $line );
$dbname_override{ $temp_array[0] } = $temp_array[1];
}
close(DBNAMEF);
}
......@@ -165,7 +173,7 @@ my %data;
while ( $sth->fetch() ) {
if ($dbname_override{$full_db_name}) {
$full_db_name = $dbname_override{$full_db_name};
$full_db_name = $dbname_override{$full_db_name};
}
$data{$full_db_name}{$logic_name} = { %{ \%hash } };
}
......@@ -218,33 +226,33 @@ my %data;
$test_sth->execute($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 {
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;
}
next;
}
} else {
print("table analysis_description does not exist in database $dbname\n");
print("table analysis_description does not exist in database $dbname\n");
next;
}
......
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