Added -create option to (re)create database.

misc-scripts/xref_mapping/XrefParser/BaseParser.pm

@@ -19,7 +19,7 @@ my %dependent_sources;
 my %taxonomy2species_id;
 my %name2species_id;
 
-my ($host, $port, $dbname, $user, $pass);
+my ($host, $port, $dbname, $user, $pass, $create);
 my $skipdownload;
 
 # --------------------------------------------------------------------------------
@@ -27,11 +27,13 @@ my $skipdownload;
 
 sub run {
 
-  ($host, $port, $dbname, $user, $pass, my $speciesr, my $sourcesr, $skipdownload) = @_;
+  ($host, $port, $dbname, $user, $pass, my $speciesr, my $sourcesr, $skipdownload, $create) = @_;
 
   my @species = @$speciesr;
   my @sources = @$sourcesr;
 
+  create($host, $port, $user, $pass, $dbname) if ($create);
+
   my $dbi = dbi();
 
   # validate species names
@@ -771,5 +773,42 @@ sub sanitise {
 
 # --------------------------------------------------------------------------------
 
+# Create database if required. Assumes sql/table.sql and sql/populate_metadata.sql
+# are present.
+
+sub create {
+
+  my ($host, $port, $user, $pass, $dbname) = @_;
+
+  my $dbh = DBI->connect( "DBI:mysql:host=$host:port=$port", $user, $pass,
+                          {'RaiseError' => 1});
+
+  # check to see if the database already exists
+  my %dbs = map {$_->[0] => 1} @{$dbh->selectall_arrayref('SHOW DATABASES')};
+
+  if ($dbs{$dbname}) {
+    if ($create) {
+      $dbh->do( "DROP DATABASE $dbname" );
+      print "Removed existing database $dbname\n";
+    } else {
+      die("Database $dbname already exists. Use -create option to overwrite it.");
+    }
+  }
+
+  $dbh->do( "CREATE DATABASE " . $dbname );
+
+  print "Creating $dbname from sql/table.sql\n";
+  die "Cannot open sql/table.sql" if (! -e "sql/table.sql");
+  my $cmd = "mysql -u $user -p$pass -P $port -h $host $dbname < sql/table.sql";
+  system ($cmd);
+
+  print "Populating metadata in $dbname from sql/populate_metadata.sql\n";
+  die "Cannot open sql/populate_metadata.sql" if (! -e "sql/populate_metadata.sql");
+  $cmd = "mysql -u $user -p$pass -P $port -h $host $dbname < sql/populate_metadata.sql";
+  system($cmd);
+
+}
+
+# --------------------------------------------------------------------------------
 1;
 

misc-scripts/xref_mapping/xref_parser.pl

@@ -3,7 +3,7 @@ use strict;
 use Getopt::Long;
 use XrefParser::BaseParser;
 
-my ($host, $port, $dbname, $user, $pass, @species, @sources, $skipdownload);
+my ($host, $port, $dbname, $user, $pass, @species, @sources, $skipdownload, $create);
 
 GetOptions('user=s'       => \$user,
 	   'pass=s'       => \$pass,
@@ -13,6 +13,7 @@ GetOptions('user=s'       => \$user,
 	   'species=s'    => \@species,
 	   'source=s'     => \@sources,
 	   'skipdownload' => \$skipdownload,
+	   'create'       => \$create,
 	   'help'         => sub { usage(); exit(0); });
 
 @species = split(/,/,join(',',@species));
@@ -23,21 +24,21 @@ if (!$user || !$host || !$dbname) {
   usage();
   exit(1);
 
-
 }
 
-XrefParser::BaseParser::run($host, $port, $dbname, $user, $pass, \@species, \@sources, $skipdownload);
+XrefParser::BaseParser::run($host, $port, $dbname, $user, $pass, \@species, \@sources, $skipdownload, $create);
 
 # --------------------------------------------------------------------------------
 
+# TODO - better usage instructions
 sub usage {
 
   print << "EOF";
 
-  xref_parser.pm -user {user} -pass {password} -host {host} -port {port} -dbname {database} -species {species1,species2} -source {source1,source2} -skipdownload
+  xref_parser.pm -user {user} -pass {password} -host {host} -port {port} -dbname {database} -species {species1,species2} -source {source1,source2} -skipdownload -create
 
 EOF
 
 }
 
-# --------------------------------------------------------------------------------
+#--------------------------------------------------------------------------------