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lib/Bio/EnsEMBL/IdMapping/Cache.pm  view on Meta::CPAN

  }
  
}


sub check_db_connection {
  my $self = shift;
  my $dbtype = shift;
  
  my $err = 0;
  
  eval {
    my $dba = $self->get_DBAdaptor($dbtype);
    $dba->dbc->connect;
  };
  
  if ($@) {
    $self->logger->warning("Can't connect to $dbtype db: $@\n");
    $err++;
  } else {
    $self->logger->debug("Connection to $dbtype db ok.\n");
    $self->{'_db_conn_ok'}->{$dbtype} = 1;
  }

  return $err;
}

  
sub check_db_read_permissions {
  my $self = shift;
  my $dbtype = shift;

  # skip this check if db connection failed (this prevents re-throwing
  # exceptions).
  return 1 unless ($self->{'_db_conn_ok'}->{$dbtype});
  
  my $err = 0;
  my %privs = %{ $self->get_db_privs($dbtype) };
  
  unless ($privs{'SELECT'} or $privs{'ALL PRIVILEGES'}) {
    $self->logger->warning("User doesn't have read permission on $dbtype db.\n");
    $err++;
  } else {
    $self->logger->debug("Read permission on $dbtype db ok.\n");
  }

  return $err;
}

  
sub check_db_write_permissions {
  my $self = shift;
  my $dbtype = shift;
  
  # skip this check if db connection failed (this prevents re-throwing
  # exceptions).
  return 1 unless ($self->{'_db_conn_ok'}->{$dbtype});
  
  my $err = 0;

  unless ($self->do_upload) {
    $self->logger->debug("No uploads, so write permission on $dbtype db not required.\n");
    return $err;
  }

  my %privs = %{ $self->get_db_privs($dbtype) };

  unless ($privs{'INSERT'} or $privs{'ALL PRIVILEGES'}) {
    $self->logger->warning("User doesn't have write permission on $dbtype db.\n");
    $err++;
  } else {
    $self->logger->debug("Write permission on $dbtype db ok.\n");
  }

  return $err;
}


sub do_upload {
  my $self = shift;

  if ($self->conf->param('dry_run') or
    ! ($self->conf->param('upload_events') or
       $self->conf->param('upload_stable_ids') or
       $self->conf->param('upload_archive'))) {
    return 0;
  } else {
    return 1;
  }
}   


sub get_db_privs {
  my ( $self, $dbtype ) = @_;

  my %privs = ();
  my $rs;

  # get privileges from mysql db
  eval {
    my $dbc = $self->get_DBAdaptor($dbtype)->dbc();
    my $sql = qq(SHOW GRANTS FOR ) . $dbc->username();
    my $sth = $dbc->prepare($sql);
    $sth->execute();
    $rs = $sth->fetchall_arrayref();
    #$sth->finish();
  };

  if ($@) {
    $self->logger->warning(
      "Error obtaining privileges from $dbtype db: $@\n");
    return {};
  }

  # parse the output
  foreach my $r ( map { $_->[0] } @{$rs} ) {
    $r =~ s/GRANT (.*) ON .*/$1/i;
    foreach my $p ( split( ',', $r ) ) {
      # trim leading and trailing whitespace
      $p =~ s/^\s+//;
      $p =~ s/\s+$//;
      $privs{ uc($p) } = 1;
    }
  }

  return \%privs;
} ## end sub get_db_privs


sub check_empty_tables {
  my $self = shift;
  my $dbtype = shift;
  
  # skip this check if db connection failed (this prevents re-throwing
  # exceptions).
  return 1 unless ($self->{'_db_conn_ok'}->{$dbtype});
  
  my $err = 0;
  my $c = 0;

  if ($self->conf->param('no_check_empty_tables') or !$self->do_upload) {
    $self->logger->debug("Won't check for empty stable ID and archive tables in $dbtype db.\n");
    return $err;
  }

  eval {
    my @tables =
      qw(
      gene_stable_id
      transcript_stable_id
      translation_stable_id
      exon_stable_id
      stable_id_event
      mapping_session
      gene_archive
      peptide_archive
    );

    my $dba = $self->get_DBAdaptor($dbtype);
    foreach my $table (@tables) {
      if ( $table =~ /^([^_]+)_stable_id/ ) {
        $table = $1;
        if ( $c =
             $self->fetch_value_from_db(
               $dba,
               "SELECT COUNT(*) FROM $table WHERE stable_id IS NOT NULL"
             ) )
        {
          $self->logger->warning(
                        "$table table in $dbtype db has $c stable IDs.\n");
          $err++;
        }
      }
      else {
        if ( $c =
             $self->fetch_value_from_db(
                                     $dba, "SELECT COUNT(*) FROM $table"
             ) )
        {
          $self->logger->warning(
                        "$table table in $dbtype db has $c entries.\n");
          $err++;
        }
      }
    } ## end foreach my $table (@tables)
  };

  if ($@) {
    $self->logger->warning(
"Error retrieving stable ID and archive table row counts from $dbtype db: $@\n"
    );
    $err++;
  }
  elsif ( !$err ) {
    $self->logger->debug(
         "All stable ID and archive tables in $dbtype db are empty.\n");
  }
  return $err;
}