Offline scripts: Add support for view selection.

lib/BIGSdb/Offline/Script.pm

@@ -93,9 +93,19 @@ sub initiate {
 		}
 	}
 	$self->set_system_overrides;
+
 	$self->{'dataConnector'}->initiate( $self->{'system'}, $self->{'config'} );
 	$self->db_connect;
-	$self->setup_datastore if $self->{'db'};
+	if ($self->{'db'}){
+		$self->setup_datastore ;
+		if ( defined $self->{'options'}->{'v'} ) {
+			my $view_exists =
+			  $self->{'datastore'}
+			  ->run_query( "SELECT EXISTS(SELECT * FROM information_schema.tables WHERE table_name=?)", $self->{'options'}->{'v'} );
+			die "Invalid view selected.\n" if !$view_exists;
+			$self->{'system'}->{'view'} = $self->{'options'}->{'v'};
+		}
+	}
 	return;
 }
 

scripts/automation/autotag.pl

@@ -62,7 +62,8 @@ GetOptions(
 	'o|order'              => \$opts{'o'},
 	'q|quiet'              => \$opts{'q'},
 	'r|random'             => \$opts{'r'},
-	'T|already_tagged'     => \$opts{'T'}
+	'T|already_tagged'     => \$opts{'T'},
+	'v|view=s'			   => \$opts{'v'}
 ) or die("Error in command line arguments\n");
 
 if ( $opts{'h'} ) {
@@ -235,6 +236,9 @@ ${bold}--threads$norm ${under}THREADS$norm
 
 ${bold}-T, --already_tagged$norm
     Scan even when sequence tagged (no designation).
+    
+${bold}-v, --view$norm ${under}VIEW$norm
+    Isolate database view (overrides value set in config.xml).
 
 ${bold}-w, --word_size$norm ${under}SIZE$norm
     BLASTN word size.

scripts/automation/scannew.pl

@@ -63,7 +63,8 @@ GetOptions(
 	'n|new_only'           => \$opts{'n'},
 	'o|order'              => \$opts{'o'},
 	'r|random'             => \$opts{'r'},
-	'T|already_tagged'     => \$opts{'T'}
+	'T|already_tagged'     => \$opts{'T'},
+	'v|view=s'			   => \$opts{'v'}
 ) or die("Error in command line arguments\n");
 
 if ( $opts{'h'} ) {
@@ -235,6 +236,9 @@ ${bold}--threads$norm ${under}THREADS$norm
 
 ${bold}-T, --already_tagged$norm
     Scan even when sequence tagged (no designation).
+    
+${bold}-v, --view$norm ${under}VIEW$norm
+    Isolate database view (overrides value set in config.xml).
 
 ${bold}-w, --word_size$norm ${under}SIZE$norm
     BLASTN word size.