added new utility methods for file and db access

modules/Bio/EnsEMBL/IdMapping/BaseObject.pm

@@ -35,6 +35,7 @@ no warnings 'uninitialized';
 
 use Bio::EnsEMBL::Utils::Exception qw(throw warning);
 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
+use Bio::EnsEMBL::Utils::ScriptUtils qw(path_append);
 
 
 =head2 new
@@ -78,6 +79,131 @@ sub new {
 }
 
 
+sub get_filehandle {
+  my $self = shift;
+  my $filename = shift;
+  my $path_append = shift;
+  my $mode = shift;
+
+  throw("Need a filename for this filehandle.") unless (defined($filename));
+  
+  my $path = $self->conf->param('dumppath');
+  $path = path_append($path, $path_append) if (defined($path_append));
+
+  $mode ||= '>';
+  
+  open(my $fh, $mode, "$path/$filename") or
+    throw("Unable to open $path/$filename: $!");
+
+  return $fh;
+}
+
+
+sub file_exists {
+  my $self = shift;
+  my $filename = shift;
+  my $path_append = shift;
+
+  my $path = $self->conf->param('dumppath');
+  $path = path_append($path, $path_append) if (defined($path_append));
+
+  return (-s "$path/$filename");
+}
+
+
+sub fetch_value_from_db {
+  my $self = shift;
+  my $dbh = shift;
+  my $sql = shift;
+
+  throw("Need a db handle.") unless ($dbh and $dbh->isa('DBI::db'));
+  throw("Need an SQL query to execute.") unless ($sql);
+
+  my $sth = $dbh->prepare($sql);
+  $sth->execute;
+  my ($retval) = $sth->fetchrow_array;
+
+  return $retval;
+}
+
+
+sub dump_table_to_file {
+  my $self = shift;
+  my $dbtype = shift;
+  my $table = shift;
+  my $filename = shift;
+
+  # argument check
+  unless (($dbtype eq 'source') or ($dbtype eq 'target')) {
+    throw("Missing or unknown db type: $dbtype.");
+  }
+  throw("Need a table name.") unless ($table);
+  throw("Need a filename.") unless ($filename);
+  
+  my $fh = $self->get_filehandle($filename, 'tables');
+
+  my $dba = $self->cache->get_DBAdaptor($dbtype);
+  my $dbh = $dba->dbc->db_handle;
+  my $sth = $dbh->prepare("SELECT * FROM $table");
+  $sth->execute;
+
+  my $i = 0;
+
+  while (my @row = $sth->fetchrow_array) {
+    $i++;
+
+    # use '\N' for NULL values
+    for (my $j = 0; $j < scalar(@row); $j++) {
+      $row[$j] = '\N' unless (defined($row[$j]));
+    }
+    
+    print $fh join("\t", @row);
+    print $fh "\n";
+  }
+
+  $sth->finish;
+  
+  return $i;
+}
+
+
+sub upload_file_into_table {
+  my $self = shift;
+  my $dbtype = shift;
+  my $table = shift;
+  my $filename = shift;
+
+  # argument check
+  unless (($dbtype eq 'source') or ($dbtype eq 'target')) {
+    throw("Missing or unknown db type: $dbtype.");
+  }
+  throw("Need a table name.") unless ($table);
+  throw("Need a filename.") unless ($filename);
+
+  # sanity check for dry run
+  if ($self->conf->param('dry_run')) {
+    $self->logger->warning("dry_run - skipping db upload for $filename.\n");
+    return;
+  }
+  
+  my $file = join('/', $self->conf->param('dumppath'), 'tables', $filename);
+  
+  if (-s $file) {
+    
+    my $dba = $self->cache->get_DBAdaptor($dbtype);
+    my $dbh = $dba->dbc->db_handle;
+    my $sql = qq(LOAD DATA LOCAL INFILE '$file' INTO TABLE $table);
+    my $sth = $dbh->prepare($sql);
+    $sth->execute;
+    $sth->finish;
+
+  } else {
+    $self->logger->warning("No data found in file $filename.\n", 1);
+  }
+
+}
+
+
 sub logger {
   my $self = shift;
   $self->{'_logger'} = shift if (@_);