Superclass for parsers containing common functionality

misc-scripts/xref_mapping/BaseParser.pm

+package BaseParser;
+
+my $host = "ecs1g";
+my $port = 3306;
+my $database = "glenn_test_xref";
+my $user = "ensadmin";
+my $password = "ensembl";
+
+my $dbi = DBI->connect("dbi:mysql:host=$host;port=$port;database=$database",
+		       "$user",
+		       "$password",
+		       {'RaiseError' => 1}) || die "Can't connect to database";
+
+# --------------------------------------------------------------------------------
+# Upload a source object to the source table.
+# Return the ID of the new row in the database.
+
+sub upload_source {
+
+  my ($self, $source) = @_;
+
+  my $sth = $dbi->prepare("INSERT INTO source (name,url,file_modified_date,upload_date,release) VALUES(?,?,?, NOW(),?)");
+  $sth->execute($source->{NAME},
+		$source->{URL},
+		$source->{FILE_MODIFIED_DATE}, "") || die $dbi->errstr;
+
+  $sth = $dbi->prepare("SELECT last_insert_id()");
+  $sth->execute();
+  my $id;
+  while(my @row = $sth->fetchrow_array()) {
+    $id = $row[0];
+  }
+
+  $sth->finish() if defined $sth;
+
+  return $id;
+
+}
+
+# --------------------------------------------------------------------------------
+# Upload xrefs to the database
+
+sub upload_xrefs {
+
+  my ($self, @xrefs) = @_;
+
+  my $sth;
+  foreach my $xref (@xrefs) {
+
+    # Create entry in xref table and note ID
+    $sth = $dbi->prepare("INSERT INTO xref (accession,label,source_id,species_id) VALUES(?,?,?,?)");
+    $sth->execute($xref->{ACCESSION},
+		  $xref->{LABEL},
+		  $xref->{SOURCE_ID},
+		  $xref->{SPECIES_ID}) || die $dbi->errstr;
+
+    # get ID of xref just inserted
+    $sth = $dbi->prepare("SELECT last_insert_id()");
+    $sth->execute();
+    my $id;
+    while(my @row = $sth->fetchrow_array()) {
+      $id = $row[0];
+    }
+
+    # create entry in primary_xref table with sequence
+    # TODO experimental/predicted????
+    $sth = $dbi->prepare("INSERT INTO primary_xref VALUES(?,?,?,?,?)");
+    $sth->execute($id,
+		  $xref->{SEQUENCE},
+		  'peptide',
+		  'experimental',
+		  $xref->{SOURCE_ID}) || die $dbi->errstr;
+
+  }
+
+  $sth->finish() if defined $sth;
+
+}
+
+# --------------------------------------------------------------------------------
+
+sub dbi {
+
+  my $self = shift;
+
+  return $dbi;
+
+}
+
+# --------------------------------------------------------------------------------
+
+1;