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Commit 447168c3 authored by Leo Gordon's avatar Leo Gordon
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cleaned up the pipeline_create_commands a bit

parent 2da7e387
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modules/Bio/EnsEMBL/Hive/PipeConfig/HiveGeneric_conf.pm
+ 37
− 36
View file @ 447168c3
......@@ -112,36 +112,24 @@ sub pipeline_create_commands {
my $self = shift @_;
my $db_conn = shift @_ || 'pipeline_db';
return {
'sqlite' => [
$self->o('hive_force_init') ? ( 'rm -f '.$self->o($db_conn, '-dbname') ) : (),
# standard eHive tables, triggers and procedures:
$self->db_connect_command($db_conn).' <'.$self->o('hive_root_dir').'/sql/tables.sqlite',
$self->o('hive_use_triggers') ? ( $self->db_connect_command($db_conn).' <'.$self->o('hive_root_dir').'/sql/triggers.sqlite' ) : (),
$self->db_connect_command($db_conn).' <'.$self->o('hive_root_dir').'/sql/procedures.sqlite',
],
'mysql' => [
$self->o('hive_force_init') ? ( 'mysql '.$self->dbconn_2_mysql($db_conn, 0)." -e 'DROP DATABASE IF EXISTS `".$self->o($db_conn, '-dbname')."`'" ) : (),
'mysql '.$self->dbconn_2_mysql($db_conn, 0)." -e 'CREATE DATABASE `".$self->o($db_conn, '-dbname')."`'",
# standard eHive tables, triggers, foreign_keys and procedures:
$self->db_connect_command($db_conn).' <'.$self->o('hive_root_dir').'/sql/tables.mysql',
$self->o('hive_use_triggers') ? ( $self->db_connect_command($db_conn).' <'.$self->o('hive_root_dir').'/sql/triggers.mysql' ) : (),
$self->db_connect_command($db_conn).' <'.$self->o('hive_root_dir').'/sql/foreign_keys.sql',
$self->db_connect_command($db_conn).' <'.$self->o('hive_root_dir').'/sql/procedures.mysql',
],
'pgsql' => [
my $driver = $self->o($db_conn, '-driver');
return [
$self->o('hive_force_init') ? ( $self->db_execute_command($db_conn, 'DROP DATABASE IF EXISTS '.$self->o($db_conn, '-dbname'), 0 ) ) : (),
$self->db_execute_command($db_conn, 'CREATE DATABASE '.$self->o($db_conn, '-dbname'), 0 ),
# standard eHive tables, foreign_keys and procedures:
$self->db_connect_command($db_conn).' <'.$self->o('hive_root_dir').'/sql/tables.pgsql',
$self->db_connect_command($db_conn).' <'.$self->o('hive_root_dir').'/sql/foreign_keys.sql',
$self->db_connect_command($db_conn).' <'.$self->o('hive_root_dir').'/sql/procedures.pgsql',
],
}->{ $self->o($db_conn, '-driver') };
# we got table definitions for all drivers:
$self->db_connect_command($db_conn).' <'.$self->o('hive_root_dir').'/sql/tables.'.$driver,
# auto-sync'ing triggers are off by default and not yet available in pgsql:
$self->o('hive_use_triggers') && ($driver ne 'pgsql') ? ( $self->db_connect_command($db_conn).' <'.$self->o('hive_root_dir').'/sql/triggers.'.$driver ) : (),
# FOREIGN KEY constraints cannot be defined in sqlite separately from table definitions, so they are off there:
($driver ne 'sqlite') ? ( $self->db_connect_command($db_conn).' <'.$self->o('hive_root_dir').'/sql/foreign_keys.sql' ) : (),
# we got procedure definitions for all drivers:
$self->db_connect_command($db_conn).' <'.$self->o('hive_root_dir').'/sql/procedures.'.$driver,
];
}
......@@ -274,11 +262,13 @@ sub dbconn_2_pgsql { # will save you a lot of typing
sub db_connect_command {
my ($self, $db_conn) = @_;
my $driver = $self->o($db_conn, '-driver');
return {
'sqlite' => 'sqlite3 '.$self->o($db_conn, '-dbname'),
'mysql' => 'mysql '.$self->dbconn_2_mysql($db_conn, 1),
'pgsql' => 'env PGPASSWORD="'.$self->o($db_conn,'-pass').'" psql '.$self->dbconn_2_pgsql($db_conn, 1),
}->{ $self->o($db_conn, '-driver') };
'pgsql' => "env PGPASSWORD='".$self->o($db_conn,'-pass')."' psql ".$self->dbconn_2_pgsql($db_conn, 1),
}->{ $driver };
}
......@@ -293,11 +283,18 @@ sub db_execute_command {
$with_db = 1 unless(defined($with_db));
return {
'sqlite' => 'sqlite3 '.$self->o($db_conn, '-dbname')." '$sql_command'", # can't imagine an sqlite3 cmd without dbname
'mysql' => 'mysql '.$self->dbconn_2_mysql($db_conn, $with_db)." -e '$sql_command'",
'pgsql' => 'env PGPASSWORD="'.$self->o($db_conn,'-pass').'" psql '.$self->dbconn_2_pgsql($db_conn, 0)." --command='$sql_command' ".($with_db ? $self->o($db_conn, '-dbname') : ''),
}->{ $self->o($db_conn, '-driver') };
my $driver = $self->o($db_conn, '-driver');
if(($driver eq 'sqlite') && !$with_db) { # in these special cases we pretend sqlite can understand these commands
return "rm -f $1" if($sql_command=~/DROP\s+DATABASE\s+(?:IF\s+EXISTS\s+)?(\w+)/);
return "touch $1" if($sql_command=~/CREATE\s+DATABASE\s+(\w+)/);
} else {
return {
'sqlite' => 'sqlite3 '.$self->o($db_conn, '-dbname')." '$sql_command'",
'mysql' => 'mysql '.$self->dbconn_2_mysql($db_conn, $with_db)." -e '$sql_command'",
'pgsql' => "env PGPASSWORD='".$self->o($db_conn,'-pass')."' psql --command='$sql_command' ".$self->dbconn_2_pgsql($db_conn, $with_db),
}->{ $driver };
}
}
......@@ -310,17 +307,21 @@ sub db_execute_command {
sub dbconn_2_url {
my ($self, $db_conn) = @_;
return ($self->o($db_conn, '-driver') eq 'sqlite')
? $self->o($db_conn, '-driver').':///'.$self->o($db_conn,'-dbname')
: $self->o($db_conn, '-driver').'://'.$self->o($db_conn,'-user').':'.$self->o($db_conn,'-pass').'@'.$self->o($db_conn,'-host').':'.$self->o($db_conn,'-port').'/'.$self->o($db_conn,'-dbname');
my $driver = $self->o($db_conn, '-driver');
return ($driver eq 'sqlite')
? $driver.':///'.$self->o($db_conn,'-dbname')
: $driver.'://'.$self->o($db_conn,'-user').':'.$self->o($db_conn,'-pass').'@'.$self->o($db_conn,'-host').':'.$self->o($db_conn,'-port').'/'.$self->o($db_conn,'-dbname');
}
sub pipeline_url {
my $self = shift @_;
return $self->dbconn_2_url('pipeline_db'); # used to force vivification of the whole 'pipeline_db' structure (used in run() )
}
=head2 process_options
Description : The method that does all the parameter parsing magic.
......
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