diff --git a/misc-scripts/production_database/scripts/populate_analysis_description.pl b/misc-scripts/production_database/scripts/populate_analysis_description.pl index 9ca0f6966669550ff941fd90bd0f83e9c8f8ef2b..172d5142d7226aee7d5a1d4c0b87b341b53e1749 100755 --- a/misc-scripts/production_database/scripts/populate_analysis_description.pl +++ b/misc-scripts/production_database/scripts/populate_analysis_description.pl @@ -26,21 +26,20 @@ my $dumppath; my $dbname_file; # Do command line parsing. -if ( !GetOptions( 'mhost|mh=s' => \$mhost, - 'mport|mP=i' => \$mport, - 'muser|mu=s' => \$muser, - 'mpass|mp=s' => \$mpass, - 'mdatabase|md=s' => \$mdbname, - 'host|h=s' => \$host, - 'port|P=i' => \$port, - 'user|u=s' => \$user, - 'pass|p=s' => \$pass, - 'database|d=s' => \$dbname, - 'pattern=s' => \$dbpattern, - 'verbose|v!' => \$verbose, - 'core=i' => \$core, - 'dumppath|dp=s' => \$dumppath, - 'dbname_file|dbf=s' => \$dbname_file ) +if ( !GetOptions( 'mhost|mh=s' => \$mhost, + 'mport|mP=i' => \$mport, + 'muser|mu=s' => \$muser, + 'mpass|mp=s' => \$mpass, + 'mdatabase|md=s' => \$mdbname, + 'host|h=s' => \$host, + 'port|P=i' => \$port, + 'user|u=s' => \$user, + 'pass|p=s' => \$pass, + 'database|d=s' => \$dbname, + 'pattern=s' => \$dbpattern, + 'verbose|v!' => \$verbose, + 'core=i' => \$core, + 'dumppath|dp=s' => \$dumppath ) || !( defined($host) && defined($user) @@ -60,59 +59,59 @@ 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 -dp dumppath \\ + $indent [-s species -t type] \\ $indent [-mh host] [-mP port] \\ $indent [-mu user] [-mp password] [-md database] \\ $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 + -d / --database User database name or SQL pattern, e.g. --database="homo_sapiens_rnaseq_62_37g" - or --database="%core_62%" + or --database="%core_62%". -dp / --dumppath Dump path. - Dump out table into the specified directory path. + Back-up table into the specified directory path. - --pattern User database by Perl regular expression - e.g. --pattern="^homo.*(rnaseq|vega)_62" + --pattern User database by Perl regular expressionm + e.g. --pattern="^homo.*(rnaseq|vega)_62". (-d/--database and --pattern are mutually exclusive) - --core=NN Preset pattern for Core-like databases in relase NN + --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" + --pattern="(cdna|core|otherfeatures|rnaseq|vega)_62". - -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: + -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.). - - database name stored in 'full_db_name' column - 'db_list' table in the production database. - - - new database name to use. + -t / --type If the name of the database specified by -d (or + --database) is not in the standard format, this + flag may be used to specify what type it is (e.g., + 'core', 'vega' etc.). -mh / --mhost Production database server host - (optional, default is 'ens-staging1') + (optional, default is 'ens-staging1'). -mP / --mport Production database server port - (optional, default is 3306) + (optional, default is 3306). -mu / --muser Production database username (no write-access required) - (optional, default is 'ensro') + (optional, default is 'ensro'). -mp / --mpass Production database password - (optional, default is undefined) + (optional, default is undefined). -md / --mdatabase Production database name - (optional, default is 'ensembl_production') + (optional, default is 'ensembl_production'). -v / --verbose Be verbose, display every SQL statement as they - are executed (on standard error) + are executed (on standard error). USAGE_END