not workibng layout for attribute type loading system

misc-scripts/attribute_types/attrib_type.txt

+# this file is intended to hold all valid attrib_type
+# table entries for all ensembl databases that we release
+#
+# If you use the provided upload script, commentlines and 
+# emptry lines should be automatically removed, all
+# other lines should contain tab delimited database entries
+# for the attrib_type table
+
+# each attribute type should be preceeded with a comment that
+# describes its uses.
+
+
+
+

misc-scripts/attribute_types/upload_attributes.pl

+# Stolen from external db directory this script performs
+# the similar function of uploading all valid attribute types
+# into the attrib_type table of all databases that are going to
+# be released.
+
+
+use strict;
+
+use Getopt::Long;
+use DBI;
+use IO::File;
+use FindBin;
+
+
+my ( $host, $user, $pass, $port,@dbnames, $file, $release_num);
+
+GetOptions( "host=s", \$host,
+	    "user=s", \$user,
+	    "pass=s", \$pass,
+	    "port=i", \$port,
+	    "file=s", \$file,
+            "dbnames=s@", \@dbnames,
+	    "release_num=i", \$release_num
+	  );
+
+$file ||= $FindBin::Bin."/attrib_type.txt";
+usage() if(!$host);
+
+
+
+#release num XOR dbname are required
+usage() if(($release_num && @dbnames) || (!$release_num && !@dbnames));
+my $attribs = read_attrib_file( $file );
+
+$port ||= 3306;
+
+my $dsn = "DBI:mysql:host=$host;port=$port";
+
+my $db = DBI->connect( $dsn, $user, $pass, {RaiseError => 1} );
+
+if($release_num) {
+  @dbnames = map {$_->[0] } @{ $db->selectall_arrayref( "show databases" ) };
+  
+  #
+  # filter out all non-core databases
+  #
+  @dbnames = grep {/^[a-zA-Z]+\_[a-zA-Z]+\_(core|est|estgene|vega)\_${release_num}\_\d+[A-Za-z]?$/} @dbnames;
+}
+
+
+#
+# make sure the user wishes to continue
+#
+print STDERR "The following databases will be external_db updated:\n  ";
+print join("\n  ", @dbnames);
+print "\ncontinue with update (yes/no)>  ";
+
+my $input = lc(<STDIN>);
+chomp($input);
+if($input ne 'yes') {
+  print "Attrib_type loading aborted\n";
+  exit();
+}
+
+# if any attrib_types are loaded that are different from 
+# the file, a consistency problem is reported and the 
+# upload is not done.
+
+# alternatively consistency can be enforceed to a certain degree 
+sub check_consistency {
+  my $attribs = shift;
+  my $database_names = shift;
+  my $db = shift;
+
+}
+
+
+
+sub read_attrib_file {
+  my $file = shift;
+  #
+  # read all attrib_type entries from the file
+  #
+  my $fh = IO::File->new();
+  $fh->open($file) or die("could not open input file $file");
+  
+  my @rows;
+  my $row;
+  while($row = <$fh>) {
+    chomp($row);
+    next if( /^\S*$/ );
+    next if ( /^\#/ );
+
+    my @a = split(/\t/, $row);
+    
+    push @rows, {'attrib_type_id' => $a[0],
+		 'code' => $a[1],
+		 'name' => $a[2],
+		 'description'  => $a[3]};
+  }
+  $fh->close();
+  return \@rows;
+}
+
+