Raw content of Bio::EnsEMBL::KillList::KillList
<![CDATA[package Bio::EnsEMBL::KillList::KillList;
use strict;
use warnings;
use Bio::EnsEMBL::Analysis::Tools::Utilities;
use Bio::EnsEMBL::KillList::AnalysisLite;
use Bio::EnsEMBL::KillList::Comment;
use Bio::EnsEMBL::KillList::Filter;
use Bio::EnsEMBL::KillList::KillObject;
use Bio::EnsEMBL::KillList::Reason;
use Bio::EnsEMBL::KillList::Species;
use Bio::EnsEMBL::KillList::Team;
use Bio::EnsEMBL::KillList::User;
use Bio::EnsEMBL::KillList::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use vars qw (@ISA);
@ISA = qw();
=head2
Arg[1] :
Example :
Description :
Return type :
Exceptions :
Caller :
Status :
=cut
sub new {
my($class,@args) = @_;
my $self = bless {},$class;
my ($type, $db_params, $filter_params) =
rearrange([qw(TYPE
KILL_LIST_DB
FILTER_PARAMS
)],@args);
if (!defined($type)) {throw " ERROR: need to set -type\n";}
$self->type ( $type );
$self->db_params ( $db_params ) if ( defined $db_params );
$self->filter_params ( $filter_params ) if ( defined $filter_params );
return $self; # success - we hope!
}
=head2
Arg[1] :
Example :
Description :
Return type :
Exceptions :
Caller :
Status :
=cut
sub type {
my $self = shift;
$self->{'type'} = shift if ( @_ );
return $self->{'type'};
}
=head2
Arg[1] :
Example :
Description :
Return type :
Exceptions :
Caller :
Status :
=cut
sub db_params {
my ($self, $db_params) = @_;
if ( !$self->{'db_params'} ) {
$self->{'db_params'} = {};
}
if ( $db_params ) {
throw("Must pass KillList:db_params a hashref not a ".$db_params)
unless(ref($db_params) eq 'HASH');
$self->{'db_params'} = $db_params;
}
return $self->{'db_params'};
}
=head2
Arg[1] :
Example :
Description :
Return type :
Exceptions :
Caller :
Status :
=cut
sub filter_params {
my ($self, $filter_params) = @_;
if ( !$self->{'filter_params'} ) {
$self->{'filter_params'} = {};
}
if ( $filter_params ) {
throw("Must pass KillList:filter_params a hashref not a ".$filter_params)
unless(ref($filter_params) eq 'HASH');
$self->{'filter_params'} = $filter_params;
}
return $self->{'filter_params'};
}
=head2
Arg[1] :
Example :
Description :
Return type :
Exceptions :
Caller :
Status :
=cut
sub read_and_check_config {
my ($self, $var_hash) = @_;
parse_config($self, $var_hash, $self->type);
}
=head2
Arg[1] :
Example :
Description :
Return type :
Exceptions :
Caller :
Status :
=cut
sub make_filter {
my ($self, $hash) = @_;
my %filter = %$hash;
my $filter = $self->kill_list_filter->new(
%filter
);
return $filter;
}
=head2
Arg[1] : $db, the kill_list database
Arg[2] : $filter_options - an array
(maybe better as a hash or Filter obj)
specifying how to filter the kill_list.
Example : my %kill_list = %{Bio::EnsEMBL::Analysis::Tools::KillListUtils::get_kill_list($kill_list_db, $filter_options)};
Description :
Return type : Kill_list hash where keys = accession
and values = kill_objects
Exceptions :
Caller :
Status :
=cut
sub get_kill_list {
my ($self) = @_;
#connect to the db
my $db;
if ($self->db_params) {
if (!$self->db_params->dbname || !$self->db_params->dbhost ||
!$self->db_params->dbuser || !$self->db_params->dbport ||
!$self->db_params->dbpass ) {
throw("Some db parameters are not set");
}
$db = Bio::EnsEMBL::KillList::DBSQL::DBAdaptor->new(
'-dbname' => $self->db_params->dbname,
'-host' => $self->db_params->dbhost,
'-user' => $self->db_params->dbuser,
'-port' => $self->db_params->dbport,
'-pass' => $self->db_params->dbpass,
);
} else {
throw("Must set db connection parameters in config");
}
#get the kill_list filter
my $filter_params;
if($self->filter_params){
$filter_params = $self->filter_params;
} else {
throw("Must set filter parameters in config");
}
#now get all the filter parameters out of the hash
my $user_id = $filter_params->{user_id} if (exists( $filter_params->{user_id} ));
my $source_species = $filter_params->{source_species} if (exists( $filter_params->{source_species} ));
my $date = $filter_params->{date} if (exists( $filter_params->{date} ));
my $status = $filter_params->{status} if (exists( $filter_params->{status} ));
my $mol_type = $filter_params->{mol_type} if (exists( $filter_params->{mol_type} ));
my $reason_ids = $filter_params->{reason_ids} if (exists( $filter_params->{reason_ids} ));
my $analysis_ids = $filter_params->{analysis_ids} if (exists( $filter_params->{analysis_ids} ));
my $species_ids = $filter_params->{species_ids} if (exists( $filter_params->{species_ids} ));
my $external_db_ids = $filter_params->{external_db_ids} if (exists( $filter_params->{external_db_ids} ));
my (@reasons, @analyses, @species, @external_db_ids);
#make necessary objects
my $user = $db->get_UserAdaptor->fetch_by_dbID($user_id) if ($user_id);
my $source_spp = $db->get_SpeciesAdaptor->fetch_by_dbID($source_species) if ($source_species);
foreach my $id (@$reason_ids) {
push @reasons, $db->get_ReasonAdaptor->fetch_by_dbID($id);
}
foreach my $id (@$analysis_ids) {
push @analyses, $db->get_AnalysisLiteAdaptor->fetch_by_dbID($id);
}
foreach my $id (@$species_ids) {
push @species, $db->get_SpeciesAdaptor->fetch_by_dbID($id);
}
my $filter = Bio::EnsEMBL::KillList::Filter->new(
-user => $user,
-from_source_species => $source_spp,
-before_date => $date,
-having_status => $status,
-only_mol_type => $mol_type,
-reasons => \@reasons,
-for_analyses => \@analyses,
-for_species => \@species,
-for_external_db_ids => $external_db_ids,
);
# an array of kill_objects
my $kill_adaptor = $db->get_KillObjectAdaptor;
my $kill_objects = $kill_adaptor->fetch_KillObjects_by_Filter($filter);
my %kill_object_hash;
foreach my $ko (@{$kill_objects}) {
$kill_object_hash{$ko->accession} = $ko;
print STDERR "got ".$ko->dbID." accesssion ".$ko->accession."\n";
}
return \%kill_object_hash;
}
=head2
Arg[1] : $db, the reference database to be updated
Example :
Description : Deletes any previous similar entries in the
meta table and adds a new entry, with
meta_key = 'kill_list' and meta_value = now().
Return type : None
Exceptions : None
Caller :
Status :
=cut
sub update_meta_table {
my ($db) = @_;
my $sth = $db->dbc->prepare(
"DELETE FROM meta ".
"WHERE meta_key = 'kill_list'");
$sth->execute;
$sth->finish;
$sth = $db->dbc->prepare(
"INSERT INTO meta ".
"(meta_key, meta_value) ".
"VALUES ('kill_list', now())");
$sth->execute;
$sth->finish;
return;
}
1;
]]>