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Summary

Bio::EnsEMBL::Funcgen::DBSQL::ExperimentAdaptor - A database adaptor for fetching and
storing Funcgen Experiment objects.

Package variables

Included modules

Inherit

Bio::EnsEMBL::Funcgen::DBSQL::BaseAdaptor

Synopsis

my $exp_a = $db->get_ExperimentAdaptor();
my $exp = $exp_a->fetch_by_name($name);

Description

The ExperimentAdaptor is a database adaptor for storing and retrieving
Funcgen Experiment objects.

Methods

Methods description

  Args       : None
  Example    : None
  Description: PROTECTED implementation of superclass abstract method.
               Returns a list of columns to use for queries.
  Returntype : List of strings
  Exceptions : None
  Caller     : Internal
  Status     : At Risk

  Arg [1]    : DBI statement handle object
  Example    : None
  Description: PROTECTED implementation of superclass abstract method.
               Creates Array objects from an executed DBI statement
			   handle.
  Returntype : Listref of Bio::EnsEMBL::Funcgen::Experiment objects
  Exceptions : None
  Caller     : Internal
  Status     : At Risk

  Args       : None
  Example    : None
  Description: PROTECTED implementation of superclass abstract method.
               Returns the names and aliases of the tables to use for queries.
  Returntype : List of listrefs of strings
  Exceptions : None
  Caller     : Internal
  Status     : At risk

  Arg [1]    : int - dbID of array_chip
  Example    : my $array = $oaa->fetch_by_array_chip_dbID($ac_dbid);
  Description: Retrieves a named Array object from the database.
  Returntype : listref of Bio::EnsEMBL::Funcgen::Experiment objects
  Exceptions : None
  Caller     : General
  Status     : At risk

  Arg [1]    : Bio::EnsEMBL::Funcgen::Experiment - array to fetch attributes for
  Example    : None
  Description: This function is solely intended to lazy load attributes into
               empty Experiment objects. You should not need to call this.
  Returntype : None
  Exceptions : None
  Caller     : Bio::EnsEMBL::Funcgen::Experiment getters
  Status     : Medium Risk

  Arg [1]    : string - name of an Experiment
  Example    : my $exp = $exp_a->fetch_by_name('Exp-1');
  Description: Retrieves a named Experiment object from the database.
  Returntype : Bio::EnsEMBL::Funcgen::Experiment
  Exceptions : Throws if no name defined or if more than one returned
  Caller     : General
  Status     : At Risk -replace with fetch_all_by_name and fetch_by_name_group

  Args       : Bio::EnsEMBL::Funcgen::Experiment
  Example    : my $xml = $exp_adaptor->fetch_mage_xml_by_Experiment($exp);
  Description: Gets the MAGE XML for this experiment
  Returntype : string
  Exceptions : throws if arg is not a valid stored Experiment
  Caller     : general
  Status     : at Risk

  Args       : 
  Example    : my $xml = $exp_adaptor->fetch_mage_xml_by_Experiment($exp);
  Description: Gets the MAGE XML for this experiment
  Returntype : string
  Exceptions : throws if no arg passed
  Caller     : general
  Status     : at Risk

  Arg [1]    : (optional) boolean - flag to denote whether experiment is flagged for web display
  Example    : my @names = @{$exp_a->get_all_experiment_names()};
  Description: Retrieves names of all experiments.
  Returntype : ARRAYREF
  Exceptions : none
  Caller     : General
  Status     : At Risk -rename fetch?

  Args       : None
  Example    : my @exp_ids = @{$exp_a->list_dbIDs()};
  Description: Gets an array of internal IDs for all Experiment objects in the
               current database.
  Returntype : List of ints
  Exceptions : None
  Caller     : ?
  Status     : Medium Risk

  Args       : List of Bio::EnsEMBL::Funcgen::Experiment objects
  Example    : $oaa->store($exp1, $exp2, $exp3);
  Description: Stores given Experiment objects in the database. 
  Returntype : ARRAYREF of Bio::EnsEMBL::Funcgen::Experiment objects
  Exceptions : Throws is group not present in DB
               Throws if object is not a Bio::EnsEMBL::Funcgen::Experiment
               Throws if object is already present in the DB but has no dbID
  Caller     : General
  Status     : At Risk

  Args       : Bio::EnsEMBL::Funcgen::Experiment
  Example    : my $xml = $exp_adaptor->fetch_mage_xml_by_Experiment($exp);
  Description: Gets the MAGE XML for this experiment
  Returntype : string
  Exceptions : throws if arg is not a valid stored Experiment
  Caller     : general
  Status     : at Risk

Methods code

sub _columns {

	my $self = shift;
	
	return qw( e.experiment_id e.name e.experimental_group_id e.date e.primary_design_type e.description e.mage_xml_id);

}

sub _objs_from_sth {

	my ($self, $sth) = @_;
	
	my (@result, $exp_id, $name, $group_id, $p_design_type, $date, $description, $xml_id);
	
	$sth->bind_columns(\$exp_id,\$ name,\$ group_id,\$ date,\$ p_design_type,\$ description,\$ xml_id);
	
	while ( $sth->fetch() ) {
	  my $exp = Bio::EnsEMBL::Funcgen::Experiment->new(
													   -DBID                => $exp_id,
													   -ADAPTOR             => $self,
													   -NAME                => $name,
													   -GROUP_ID            => $group_id,
													   -DATE                => $date,
													   -PRIMARY_DESIGN_TYPE => $p_design_type,
													   -DESCRIPTION         => $description,
													   -MAGE_XML_ID         => $xml_id,
													  );
	  
	  push @result, $exp;
	  
	}
	return\@ result;

}

sub _tables {

	my $self = shift;
	
	#should we add group, target, design_type, experimental_variable?

	return ['experiment', 'e'];

}

sub fetch_all_by_group {

    my $self = shift;

    throw("Not yet implemented");

    my $ac_dbid = shift;
    my $sth = $self->prepare("
		SELECT a.array_id
		FROM array a, array_chip ac
		WHERE a.array_id = ac.array_id
		AND ac.array_chip_id = $ac_dbid
	");


    $sth->execute();
    my ($array_id) = $sth->fetchrow();
    
    return $self->fetch_by_dbID($array_id);

}

sub fetch_attributes {

    my $self = shift;
    my $array = shift;

    my $tmp_array = $self->fetch_by_dbID( $array->dbID() );
    %$array = %$tmp_array;

}

sub fetch_by_name {

  my $self = shift;
  my $name = shift;
  
  throw("Need to specify and experiment name argument") if (! defined $name);

  my $result = $self->generic_fetch("e.name = '$name'");
  
  if (scalar @$result > 1) {
    throw("Experiment $name is not unique in the database, but only one result has been returned");
    #should have unique key of group_id and experiment_name
  } 
  return $result->[0];

}

sub fetch_mage_xml_by_Experiment {

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

  if(!($exp and $exp->isa('Bio::EnsEMBL::Funcgen::Experiment') && $exp->dbID())){
	throw('You must provide a valid stored Bio::EnsEMBL::Funcgen::Experiment');
  }

  return if ! $exp->mage_xml_id();

  my $sql = 'SELECT xml FROM mage_xml WHERE mage_xml_id='.$exp->mage_xml_id;
  
  return $self->db->dbc->db_handle->selectall_arrayref($sql)->[0];

}

sub fetch_mage_xml_by_experiment_name {

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

  if(! defined $exp_name){
	throw('You must provide an Experiment name argument');
  }

  my $sql = 'SELECT mx.xml FROM mage_xml mx, experiment e WHERE e.name="'.$exp_name.'" and e.mage_xml_id=mx.mage_xml_id';
  
  return $self->db->dbc->db_handle->selectall_arrayref($sql)->[0];

}

sub get_all_experiment_names {

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


  my ($constraint);

  my $sql = "SELECT e.name FROM experiment e";
  my @names = map $_ = "@$_", @{$self->db->dbc->db_handle->selectall_arrayref($sql)};

  $sql .= ", status s WHERE e.experiment_id =\"s.table_id\" AND s.table_name=\"experiment\" AND s.state=\"DISPLAYABLE\"" if($displayable);
  


  #can we do return [map $_ = "@$_", @{$self->db->dbc->db_handle->selectall_arrayref($sql)}];
  return\@ names;
}

#fetch_by_name_group


#=head2 fetch_all_by_design_type
#
#  Arg [1]    : List of strings - type(s) (e.g. AFFY or OLIGO)
#  Example    : my @arrays = @{$oaa->fetch_all_by_type('OLIGO')};
#  Description: Fetch all arrays of a particular type.
#  Returntype : Listref of Bio::EnsEMBL::Funcgen::Array objects
#  Exceptions : Throws if no type is provided
#  Caller     : General
#  Status     : Medium Risk

#=cut

#sub fetch_all_by_design_type {
#	my ($self, @types) = @_;
	
#	throw('Need type as parameter') if !@types;
	
#	my $constraint;
#	if (scalar @types == 1) {
#		$constraint = qq( oa.type = '$types[0]' );
#	} else {
#		$constraint = join q(','), @types;
#		$constraint = qq( oa.type IN ('$constraint') );
#	}

#	return $self->generic_fetch($constraint);
#

}

sub list_dbIDs {

    my ($self) = @_;
	
    return $self->_list_dbIDs('experiment');
}


#Need to add lazy load methods
#experimental_variables
#group


1;

}

sub store {

    my $self = shift;
    my @args = @_;
	
	my ($s_exp);
   	
	my $sth = $self->prepare('INSERT INTO experiment
                                 (name, experimental_group_id, date, primary_design_type, description, mage_xml_id)
                                 VALUES (?, ?, ?, ?, ?, ?)');

    foreach my $exp (@args) {
	  throw('Can only store Experiment objects') 	if ( ! $exp->isa('Bio::EnsEMBL::Funcgen::Experiment'));
	  
	  if (!( $exp->dbID() && $exp->adaptor() == $self )){
		
		
		my ($g_dbid) = $self->db->fetch_group_details($exp->group());
		throw("Group specified does, not exist.  Use Importer(group, location, contact)") if(! $g_dbid);
		
		$s_exp = $self->fetch_by_name($exp->name());#validate on group too!
		throw("Experimental already exists in the database with dbID:".$s_exp->dbID().
			  "\nTo reuse/update this Experimental you must retrieve it using the ExperimentalAdaptor".
			  "\nMaybe you want to use the -recover option?") if $s_exp;
		
		
		$exp = $self->update_mage_xml_by_Experiment($exp) if(defined $exp->mage_xml());
			
		$sth->bind_param(1, $exp->name(),                SQL_VARCHAR);
		$sth->bind_param(2, $g_dbid,                     SQL_INTEGER);
		$sth->bind_param(3, $exp->date(),                SQL_VARCHAR);#date?
		$sth->bind_param(4, $exp->primary_design_type(), SQL_VARCHAR);
		$sth->bind_param(5, $exp->description(),         SQL_VARCHAR);
		$sth->bind_param(6, $exp->mage_xml_id(),         SQL_INTEGER);
		
		$sth->execute();
		$exp->dbID($sth->{'mysql_insertid'});
		$exp->adaptor($self);
		
			
			#do we need to set egroup, target, design_type, experimentall_variable here?
			#}
			#else{
			#	warn("Experiment already exists in DB, using previously stored Experiment\n");
			#	$exp = $s_exp;
			#}
		}else{
			#assume we want to update the states
			warn('You may want to use $exp->adaptor->store_states($exp)');
			$self->store_states($exp);
		}
	}
		
    return\@ args;

}

sub update_mage_xml_by_Experiment {

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


  if(!($exp and $exp->isa('Bio::EnsEMBL::Funcgen::Experiment'))){
	throw('You must provide a valid Bio::EnsEMBL::Funcgen::Experiment');
  }

  if($exp->mage_xml_id()){
	#potentially calling dbID on a un-stored obj, implicit that it
	warn('Overwriting mage_xml entry for Experiment:    '.$exp->name);
	my $sql = "UPDATE mage_xml set xml='".$exp->mage_xml()."'";
	$self->db->dbc->do($sql);

  }else{
	my $sql = "INSERT INTO mage_xml (xml) VALUES('".$exp->mage_xml()."')";
	#need to get a statement handle to retrieve insert id
	my $sth = $self->prepare($sql);
	$sth->execute();
	$exp->mage_xml_id($sth->{'mysql_insertid'});

	$sql = "UPDATE experiment set mage_xml_id=".$exp->mage_xml_id()." where experiment_id =".$exp->dbID();
	$sth = $self->prepare($sql);
	$sth->execute();
  }

  return $exp;

}

General documentation

This module was created by Nathan Johnson.
This module is part of the Ensembl project: /

Post comments or questions to the Ensembl development list: ensembl-dev@ebi.ac.uk