Raw content of Bio::EnsEMBL::Funcgen::DBSQL::BaseAdaptor
<![CDATA[
#
# BioPerl module for Bio::EnsEMBL::Funcgen::DBSQL::BaseAdaptor
##
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::EnsEMBL::Funcgen::DBSQL::BaseAdaptor - Simple wrapper class for Funcgen StorableAdaptors
=head1 SYNOPSIS
$adaptor->store_states($storable);
=head1 DESCRIPTION
This is a simple wrapper class to hold common methods to all Funcgen StorableAdaptors.
Includes status methods.
Post questions to the EnsEMBL developer mailing list: <ensembl-dev@ebi.ac.uk>
=cut
package Bio::EnsEMBL::Funcgen::DBSQL::BaseAdaptor;
require Exporter;
use vars qw(@ISA @EXPORT);
use strict;
use Bio::EnsEMBL::Utils::Exception qw(throw deprecate);
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use DBI qw(:sql_types);
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor Exporter);
@EXPORT = (@{$DBI::EXPORT_TAGS{'sql_types'}});
#do we want to keep the IMPORTED_CS status for feature_sets/array_chips?
#rename to MAPPED_CS_N?
=head2 store_states
Arg [1] : Bio::EnsEMBL::Funcgen::Storable
Example : $rset_adaptor->store_states($result_set);
Description: Stores states of Storable in status table.
Returntype : None
Exceptions : Throws if Storable is not stored
Caller : General
Status : At Risk
=cut
sub store_states{
my ($self, $storable) = @_;
throw('Must pass a Bio::EnsEMBL::Funcgen::Storable') if(! $storable->isa("Bio::EnsEMBL::Funcgen::Storable"));
foreach my $state(@{$storable->get_all_states()}){
$self->store_status($state, $storable) if (! $self->has_stored_status($state, $storable));
}
return;
}
=head2 fetch_all
Arg[1] : string - optional status name e.g. 'DISPLAYABLE'
Example : my @dsets = @{$dsa->fetch_all()};
Description: Gets all available objects from the DB, which
might not be a good idea, shouldnt be called on
the BIG tables though
Returntype : ARRAYREF
Exceptions : None
Caller : General
Status : At Risk
=cut
sub fetch_all {
my ($self, $status) = @_;
my ($constraint);
#Can we throw here if we're trying to get all from known large tables
$constraint = $self->status_to_constraint($status) if $status;
if(defined $status && ! defined $constraint){
#warn "You have specifed a status($status) which is not present in the DB";
return undef;
}
return $self->generic_fetch($constraint);
}
=head2 fetch_all_diplayable
Example : my @displayable_dset = @{$dsa->fetch_all_displayable()};
Description: Gets all displayable DataSets
Returntype : ARRAYREF
Exceptions : None
Caller : General
Status : At Risk - can we just reimplement fetch_all with optional status arg
=cut
sub fetch_all_displayable{
my $self = shift;
return $self->fetch_all_by_status('DISPLAYABLE');
}
=head2 fetch_all_by_status
Arg [1] : string - status e.g. 'DISPLAYABLE'
Example : my @displayable_dset = @{$dsa->fetch_all_by_status('DISPLAYABLE')};
Description: Gets all DataSets with given status
Returntype : ARRAYREF
Exceptions : Throws is no status defined
Warns if
Caller : General
Status : At Risk - To be removed
=cut
sub fetch_all_by_status{
my ($self, $status) = @_;
deprecate('Use fetch_all($status) instead');
return $self->fetch_all($status);
}
#Can we not just re implement fetch_all here to have the optional status arg?
=head2 status_to_constraint
Arg [1] : string - status e.g. 'DISPLAYABLE'
Arg [2] : string - Constraint
Example : $sql = $self->status_to_constraint($self, $constraint, $status);
Description: Appends the appropriate status constraint dependant on the BaseAdaptor sub class.
Returntype : string - constraint
Exceptions : None
Caller : Bio::EnsEMBL::Funcgen::DBSQL::"BaseAdaptors"
Status : At risk
=cut
sub status_to_constraint{
my ($self, $status) = @_;
my $constraint;
#This will throw if status not valid, but still may be absent
my $status_id = $self->_get_status_name_id($status);
#THIS DOES NOT ACCOMODATE THE EXPEIRMENTAL_SUBSET ISSUE!!
#NO we need to handle this better
#can't just return as we'd then simply ignore the contraint
#can't throw??
return if (! $status_id);
my @tables = $self->_tables;
my ($table_name, $syn) = @{$tables[0]};
my @status_ids;
my $sql = "SELECT table_id from status where table_name='$table_name' and status_name_id='$status_id'";
@status_ids = map $_ = "@$_", @{$self->db->dbc->db_handle->selectall_arrayref($sql)};
#This is causing problems as we might get none, which will invalidate the sql
#Hence we return nothing
$constraint = " $syn.${table_name}_id IN (".join(',', @status_ids).")" if @status_ids;
return $constraint;
}
=head2 _test_funcgen_table
Arg [1] : Bio::EnsEMBL::"OBJECT"
Example : $status_a->_is_funcgen_object($experimental_chip)};
Description: Tests if the object is a valid funcgen object with an identifiable table_name
Returntype : string - table_name
Exceptions : Throws if argument if a Bio::EnsEMBL::Funcgen::"OBJECT" not supplied
Throws if not table name identified
Caller : general
Status : At risk
=cut
sub _test_funcgen_table{
my ($self, $obj) = @_;
if(! $obj ||
(ref($obj) !~ /Bio::EnsEMBL::Funcgen/) ||
(ref($obj) =~ /::DBSQL::/)){
throw("Need to specifiy a Bio::EnsEMBL::Funcgen::\"OBJECT\"");
}
throw("Cannot test state of unstored object: $obj") if (! $obj->is_stored($self->db()));
my @tables = $self->_tables;
my ($table) = @{$tables[0]};
#ExpreimetnalSubSet fix, as doesn't have own adaptor
$table = 'experimental_subset' if $obj->isa('Bio::EnsEMBL::Funcgen::ExperimentalSubset');
#my $table = ${$obj->adaptor->_tables()}[0];
return $table || $self->throw("Cannot identify table name from $obj adaptor");
}
=head2 fetch_all_states
Arg [1] : Bio::EnsEMBL::"OBJECT"
Arg [2...] : listref of states
Example : my @ec_states = @{$status_a->fetch_all_states($experimental_chip)};
Description: Retrieves all states associated with the given "OBJECT"
Returntype : ARRAYREF
Exceptions : None
Caller : general
Status : At risk
=cut
sub fetch_all_states{
my ($self, $obj) = @_;
my $table = $self->_test_funcgen_table($obj);
my $sql = "SELECT name FROM status_name sn, status s WHERE s.table_name='$table' AND s.table_id='".$obj->dbID()."' and s.status_name_id=sn.status_name_id";
my @states = map $_ = "@$_", @{$self->db->dbc->db_handle->selectall_arrayref($sql)};
return \@states;
}
=head2 has_stored_status
Arg [1] : string - status e.g. IMPORTED, DISPLAYABLE
Arg [2] : Bio::EnsEMBL::Storable
Example : if($status_a->has_stored_status('IMPORTED', $array){ ... skip import ... };
Description: Tests wether a given object has a given state
Returntype : BOOLEAN
Exceptions : Throws if Storable not passed or stored
Caller : Bio::EnsEMBL::Funcgen::BaseAdaptor
Status : At risk
=cut
sub has_stored_status{
my ($self, $state, $obj) = @_;
my (@row);
#Only used for set_status, merge with set_status?
my $status_id = $self->_get_status_name_id($state);
if (! (ref($obj) && $obj->isa("Bio::EnsEMBL::Funcgen::Storable") && $obj->dbID())){
throw("Must pass a stored Bio::EnsEMBL::Funcgen::Storable");
}
my $table = $self->_test_funcgen_table($obj);
if($status_id){
my $sql = "SELECT status_name_id FROM status WHERE table_name=\"$table\" AND table_id=\"".$obj->dbID()."\" AND status_name_id=\"$status_id\"";
#could just return the call directly?
@row = $self->db->dbc->db_handle->selectrow_array($sql);
}
return (@row) ? 1 : 0;
}
=head2 store_status
Arg [1] : string - status e.g. IMPORTED, DISPLAYABLE
Arg [2] : Bio::EnsEMBL::"OBJECT"
Example : $status_a->store_status('IMPORTED', $array_chip);
Description: Sets a state for a given object
Returntype : None
Exceptions : Warns if state already set
Throws is status name is not already stored.
Caller : general
Status : At risk - Move to Status
=cut
sub store_status{
my ($self, $state, $obj) = @_;
my $sql;
if($self->has_stored_status($state, $obj)){
warn("$obj with dbID ".$obj->dbID()." already has status $state set\n");
}else{
my $status_id = $self->_get_status_name_id($state);
if(! $status_id){
throw("$state is not a valid status_name for $obj:\t".$obj->dbID);
#$sql = "INSERT into status_name(name) values('$state')";
#$self->db->dbc->do($sql);
#$status_id = $self->_get_status_name_id($state);
}
my $table = $self->_test_funcgen_table($obj);
$sql = "INSERT into status(table_id, table_name, status_name_id) VALUES('".$obj->dbID()."', '$table', '$status_id')";
$self->db->dbc->do($sql);
#Should we not be setting it in the obj here too?
#No becasue we should have already added to the object.
}
return;
}
=head2 revoke_status
Arg [1] : string - status name e.g. 'IMPORTED'
Arg [2] : Bio::EnsEMBL::Funcgen::Storable
Example : $rset_adaptor->revoke_status('DAS DISPLAYABLE', $result_set);
Description: Revokes the given state of Storable in status table.
Returntype : None
Exceptions : Warns if storable does not have state
Throws is status name is not valid
Throws if not state passed
Throws if Storable is not valid and stored
Caller : General
Status : At Risk
=cut
sub revoke_status{
my ($self, $state, $storable) = @_;
throw('Must provide a status name') if(! defined $state);
throw('Must pass a Bio::EnsEMBL::Funcgen::Storable') if(! $storable->isa("Bio::EnsEMBL::Funcgen::Storable"));
my $status_id = $self->_get_status_name_id($state);
my $table_name = $self->_test_funcgen_table($storable);
#hardcode for ExperimentalSubset as this uses the ExperimentalSetAdaptor
$table_name = 'experimental_subset' if $storable->isa('Bio::Ensembl::Funcgen:ExperimentalSubset');
if(! $self->has_store_status($state, $storable)){
warn $storable.' '.$storable->dbID()." does not have status $state to revoke\n";
return;
}
#do sanity checks on table to ensure that IMPORTED does not get revoke before data deleted?
#how would we test this easily?
my $sql = "delete from status where table_name='${table_name}'".
" and status_name_id=${status_id} and table_id=".$storable->dbID();
$self->db->dbc->db_handle->do($sql);
#now splice from status array;
#splice in loop should work as we will only see 1
#Just hash this?
for my $i(0..$#{$storable->{'states'}}){
if($storable->{'states'}->[0] eq $state){
splice @{$storable->{'states'}}, $i, 1;
last;
}
}
return;
}
=head2 revoke_states
Arg [1] : Bio::EnsEMBL::Funcgen::Storable
Example : $rset_adaptor->revoke_status($result_set);
Description: Revokes all states of Storable in status table.
Returntype : Bio::EnsEMBL::Funcgen::Storable
Exceptions : None
Caller : General + Helper rollback methods
Status : At Risk
=cut
sub revoke_states{
my ($self, $storable) = @_;
$self->db->is_stored_and_valid('Bio::EnsEMBL::Funcgen::Storable', $storable);
my $table_name = $self->_test_funcgen_table($storable);
#hardcode for ExperimentalSubset as this uses the ExperimentalSetAdaptor
$table_name = 'experimental_subset' if $storable->isa('Bio::Ensembl::Funcgen:ExperimentalSubset');
my $sql = "delete from status where table_name='${table_name}'".
" and table_id=".$storable->dbID();
$self->db->dbc->db_handle->do($sql);
#Clear stored states
undef $storable->{'states'};
return $storable;
}
=head2 status_filter
Arg [1] : string - status e.g. IMPORTED, DISPLAYABLE
Arg [2] : string - table name e.g. experimental_chip
Arg [3] : list - table dbIDs
Exmaple : my @displayable_ec_ids = @{$ec_adaptor->status_filter('DISPLAYABLE',
'experimental_chip',
(map $_->dbID, @echips))};
Description: Quick method for filtering dbIDs based on their table and and status
Returntype : ARRAYREF
Exceptions : Warns if state already set
Throws is status name is not already stored.
Caller : general - ResultSetAdaptor->fetch_Resultfeatures_by_Slice
Status : At risk - Move to Status?
=cut
sub status_filter{
my ($self, $status, $table_name, @table_ids) = @_;
my @status_ids;
my $status_id = $self->_get_status_name_id($status);
return \@status_ids if(! $status_id);
throw("Must provide a table_name and table_ids to filter non-displayable ids") if(! ($table_name && @table_ids));
my $sql = "SELECT table_id from status where table_name='$table_name' and table_id in (".join(", ", @table_ids).") and status.status_name_id='$status_id'";
@status_ids = map $_ = "@$_", @{$self->db->dbc->db_handle->selectall_arrayref($sql)};
return \@status_ids;
}
=head2 _get_status_name_id
Arg [1] : string - status e.g. IMPORTED, DISPLAYABLE
Example : my $status_id = $self->_get_status_name_id('IMPORTED');
Description: Retrieves the dbID of a given status_name
Returntype : INT
Exceptions : None
Caller : Bio::EnsEMBL::Funcgen::BaseAdaptor
Status : At risk - Move to Status?
=cut
sub _get_status_name_id{
my ($self, $status) = @_;
#$self->_validate_status($status);
my $sql = "SELECT status_name_id from status_name where name='$status'";
my $ref = $self->db->dbc->db_handle->selectrow_arrayref($sql);
my ($status_id) = @$ref if $ref;
#we should throw here?
#To force manual addition of the status_name
#need to make sure all status_names which are explicitly used by API
#are stored in all DBs, else we could find ourselves with broken code
#for sparsely populated DBs
throw("Status name $status is not valid. Maybe you need to add it using update_status_name.pl?") if ! $status_id;
return $status_id;
}
1;
]]>