Created; base class for parsers that connect to databases.

misc-scripts/xref_mapping/XrefParser/DatabaseParser.pm

+package XrefParser::DatabaseParser;
+
+use strict;
+
+use DBI;
+use XrefParser::BaseParser;
+
+use vars qw(@ISA);
+@ISA = qw(XrefParser::BaseParser);
+
+# Base class for parsers that parse from databases rather than files
+
+# Format of $dsn (in populate_metadata.sql)
+# mysql:HOST:PORT:DATABASE:USERNAME:PASSWORD
+# e.g.
+# mysql:ecs4:3350:glenn_elegans_xrefs:ensro::
+
+my $db;
+
+# Parse the DSN.
+# Return hash with keys: host, port, database, user, pass
+
+sub parse_dsn {
+
+  my ($self,$dsn) = @_;
+
+  my %hash;
+
+  my @bits = split /:/, $dsn;
+
+  $hash{'host'} = $bits[1];
+  $hash{'port'} = $bits[2];
+  $hash{'database'} = $bits[3];
+  $hash{'user'} = $bits[4];
+  $hash{'pass'} = $bits[5];
+
+  return %hash;
+
+}
+
+# Connect to a database. Return DB connection.
+sub connect {
+
+  my ($self, $dsn) = @_;
+
+  my %dsn = $self->parse_dsn($dsn);
+
+  $db = DBI->connect( "DBI:mysql:host=" . $dsn{'host'} . ":port=" . $dsn{'port'} . ";database=" . $dsn{'database'}, $dsn{'user'}, $dsn{'pass'},
+		      {'RaiseError' => 1}) || die "Can't connect to database\n";
+
+  return $db;
+
+}
+
+sub db {
+
+  return $db;
+
+}
+
+sub new {
+
+  my $self = {};
+  bless $self, "XrefParser::DatabaseParser";
+  return $self;
+
+}
+
+1;
+