Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor

  $dataflowRuleAdaptor = $db_adaptor->get_DataflowRuleAdaptor;
  $dataflowRuleAdaptor = $dataflowRuleObj->adaptor;

  Module to encapsulate all db access for persistent class DataflowRule.
  There should be just one per application and database connection.

  my $self = shift;

  return qw (r.dataflow_rule_id
             r.from_analysis_id
             r.to_analysis_url
             r.branch_code
            );

  my $self = shift;
  return '';

  my $self = shift;
  return '';
}

###############################################################################
#
# General access methods that could be moved
# into a superclass
#
###############################################################################

  my ($self, $constraint, $join) = @_;

  my @tables = $self->_tables;
  my $columns = join(', ', $self->_columns());

  if ($join) {
    foreach my $single_join (@{$join}) {
      my ($tablename, $condition, $extra_columns) = @{$single_join};
      if ($tablename && $condition) {
        push @tables, $tablename;

        if($constraint) {
          $constraint .= " AND $condition";
        } else {
          $constraint = " $condition";
        }
      }
      if ($extra_columns) {
        $columns .= ", " . join(', ', @{$extra_columns});
      }
    }
  }

  #construct a nice table string like 'table1 t1, table2 t2'
  my $tablenames = join(', ', map({ join(' ', @$_) } @tables));

  my $sql = "SELECT $columns FROM $tablenames";

  my $default_where = $self->_default_where_clause;
  my $final_clause = $self->_final_clause;

  #append a where clause if it was defined
  if($constraint) {
    $sql .= " WHERE $constraint ";
    if($default_where) {
      $sql .= " AND $default_where ";
    }
  } elsif($default_where) {
    $sql .= " WHERE $default_where ";
  }

  #append additional clauses which may have been defined
  $sql .= " $final_clause";

  my $sth = $self->prepare($sql);
  $sth->execute;

#  print STDERR $sql,"\n";

  return $self->_objs_from_sth($sth);
}


1;

  my ($self, $sth) = @_;
  my @rules = ();

  my ($dataflow_rule_id, $from_analysis_id, $to_analysis_url, $branch_code);
  $sth->bind_columns(\$dataflow_rule_id,\$ from_analysis_id,\$ to_analysis_url,\$ branch_code);

  while ($sth->fetch()) {
    my $rule = Bio::EnsEMBL::Hive::DataflowRule->new;
    $rule->adaptor($self);
    $rule->dbID($dataflow_rule_id);
    $rule->from_analysis_id($from_analysis_id);
    $rule->to_analysis_url($to_analysis_url);
    $rule->branch_code($branch_code);
    push @rules, $rule;
  }
  return\@ rules;

  my $self = shift;

  return (['dataflow_rule', 'r']);

  my ($self, $fromAnalysis, $toAnalysis, $branchCode) = @_;

  return unless($fromAnalysis and $toAnalysis);
  
  my $rule = Bio::EnsEMBL::Hive::DataflowRule->new();
  $rule->from_analysis($fromAnalysis);
  $rule->to_analysis($toAnalysis);
  $rule->branch_code($branchCode) if(defined($branchCode));
  
  return $self->store($rule);
}

############################
#
# INTERNAL METHODS
# (pseudo subclass methods)
#
############################

#internal method used in multiple calls above to build objects from table data

  my $self = shift;
  return $self->_generic_fetch();

  my ($self,$id) = @_;

  unless(defined $id) {
    throw("fetch_by_dbID must have an id");
  }

  my @tabs = $self->_tables;

  my ($name, $syn) = @{$tabs[0]};

  #construct a constraint like 't1.table1_id = 1'
  my $constraint = "${syn}.${name}_id = $id";

  #return first element of _generic_fetch list
  my ($obj) = @{$self->_generic_fetch($constraint)};
  return $obj;

  my $self = shift;
  my $fromAnalysisJob = shift;
  
  throw("arg is required\n") unless($fromAnalysisJob);
  throw("arg must be a [Bio::EnsEMBL::Hive::AnalysisJob] not a $fromAnalysisJob")
    unless ($fromAnalysisJob->isa('Bio::EnsEMBL::Hive::AnalysisJob'));
  return [] unless($fromAnalysisJob->analysis_id);
      
  my $constraint = "r.from_analysis_id = '".$fromAnalysisJob->analysis_id."'"
                  ." AND r.branch_code=". $fromAnalysisJob->branch_code;

  return $self->_generic_fetch($constraint);

  my ( $self, $rule ) = @_;

  my $dbID = $rule->dbID;
  if( !defined $dbID ) {
    throw( "DataflowRuleAdaptor->remove called with non persistent DataflowRule" );
  }

  my $sth = $self->prepare("DELETE FROM dataflow_rule WHERE dataflow_rule_id = $dbID");
  $sth->execute;

  my ( $self, $rule ) = @_;

  #print("\nDataflowRuleAdaptor->store()\n");
  my $dataflow_rule_id;
  my $newly_inserted_rule = 0;
  
  my $sth = $self->prepare( q{INSERT ignore INTO dataflow_rule
       (from_analysis_id, to_analysis_url, branch_code) VALUES (?,?,?) } );
  my $rtnCode = $sth->execute($rule->from_analysis_id, $rule->to_analysis_url, $rule->branch_code);
  if($rtnCode and $rtnCode != 0E0) {
    $dataflow_rule_id = $sth->{'mysql_insertid'};
    $sth->finish();
    $rule->dbID($dataflow_rule_id);
    $newly_inserted_rule = 1;
    #print("  stored with dbID = $dataflow_rule_id\n");
  } else {
    #print("  already inserted -> need to get dbID\n");
    $sth->finish();
    $sth = $self->prepare(q{SELECT dataflow_rule_id FROM dataflow_rule WHERE
         from_analysis_id = ? AND to_analysis_url = ? } );
    $sth->execute($rule->from_analysis_id, $rule->to_analysis_url);
    $sth->bind_columns(\$dataflow_rule_id);
    if($sth->fetch()) {
      $rule->dbID($dataflow_rule_id);
    }
    $sth->finish;
  }
  #print("  dataflow_rule_id = '".$rule->dbID."'\n");
  $rule->adaptor( $self );
  return $newly_inserted_rule;

  Contact Jessica Severin on implemetation/design detail: jessica@ebi.ac.uk
  Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk

  The rest of the documentation details each of the object methods.
  Internal methods are usually preceded with a _