From 313dc75e17bd652344995a4efa6c7f434cc9ffee Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Fri, 27 Sep 2013 15:22:03 +0000
Subject: [PATCH] Deprecating a number of calls. Instead we want more API
compatible calls
---
modules/Bio/EnsEMBL/AltAlleleGroup.pm | 4 +-
.../EnsEMBL/DBSQL/AltAlleleGroupAdaptor.pm | 127 +++++++++++++-----
modules/t/altAlleleGroup.t | 24 ++--
3 files changed, 105 insertions(+), 50 deletions(-)
diff --git a/modules/Bio/EnsEMBL/AltAlleleGroup.pm b/modules/Bio/EnsEMBL/AltAlleleGroup.pm
index 3414eb0e1e..a908141db4 100644
--- a/modules/Bio/EnsEMBL/AltAlleleGroup.pm
+++ b/modules/Bio/EnsEMBL/AltAlleleGroup.pm
@@ -459,7 +459,7 @@ sub get_all_Genes {
}
-=head2 get_all_Gene_ids
+=head2 get_all_Genes_types
Arg[1] : Boolean - Do not include representative gene in list of ids.
Description : Fetches all the Gene objects within the allele group and their
@@ -516,4 +516,4 @@ sub get_all_members {
}
-1;
\ No newline at end of file
+1;
diff --git a/modules/Bio/EnsEMBL/DBSQL/AltAlleleGroupAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/AltAlleleGroupAdaptor.pm
index 056d71c056..9f72fc83ce 100644
--- a/modules/Bio/EnsEMBL/DBSQL/AltAlleleGroupAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/AltAlleleGroupAdaptor.pm
@@ -32,16 +32,16 @@ Alternative allele groupings
my $aag_adaptor = Bio::EnsEMBL::Registry->get_DBAdaptor("Human","core","AltAlleleGroup");
# For a known Gene, find the reference alternative allele
- my $aag = $aag_adaptor->fetch_Group_by_dbID($gene->dbID);
+ my $aag = $aag_adaptor->fetch_by_gene_id($gene->dbID);
my $reference_gene = $aag->get_ref_Gene;
# Get a list of AltAlleleGroups
- my $list = $aag_adaptor->fetch_all_Groups_by_type('IS_REPRESENTATIVE');
- $list = $aag_adaptor->fetch_all_Groups();
+ my $list = $aag_adaptor->fetch_all_('IS_REPRESENTATIVE');
+ $list = $aag_adaptor->fetch_all();
my $dbID = $aag_adaptor->store($aag);
- $aag = $aag_adaptor->fetch_Group_by_id($dbID);
+ $aag = $aag_adaptor->fetch_by_dbID($dbID);
$aag_adaptor->remove($aag);
=head1 DESCRIPTION
@@ -59,23 +59,41 @@ use warnings;
use base qw/Bio::EnsEMBL::DBSQL::BaseAdaptor/;
use Bio::EnsEMBL::AltAlleleGroup;
-use Bio::EnsEMBL::Utils::Exception qw/throw/;
+use Bio::EnsEMBL::Utils::Exception qw/throw deprecate/;
use Bio::EnsEMBL::Utils::Scalar qw/assert_ref/;
use DBI qw( :sql_types );
=head2 fetch_all_Groups
Arg[1] : (optional) String - type of group
+ Description : DEPRECATED. Please use fetch_all()
+ Returntype : ArrayRef of Bio::EnsEMBL::AltAlleleGroup
+
+=cut
+
+sub fetch_all_Groups {
+ my ($self, $type) = @_;
+ deprecate('Please use fetch_all()');
+ return $self->fetch_all($type);
+}
+
+=head2 fetch_all
+
+ Arg[1] : (optional) String - type of group
+ Restrict group fetches to just one type. Technically it selects
+ out mixed-annotation groups where a single member contains that type.
Description : Fetches all the alt-allele groups, creates objects to represent
- them and returns them in a list
+ them and returns them in a list. Specifying a group type
+ identifies all groups containing a member of this type. It
+ does not filter out the other members
+
Multispecies support is triggered by the is_multispecies flag
and species_id of the DBAdaptor.
- Specifying a group type identifies all groups containing a
- member of this type. It does not filter out the other members
- Returntype : Listref of Bio::EnsEMBL::AltAlleleGroup
+ Returntype : ArrayRef of Bio::EnsEMBL::AltAlleleGroup
+
=cut
-sub fetch_all_Groups {
+sub fetch_all {
my $self = shift;
my $type = shift;
@@ -103,16 +121,18 @@ sub fetch_all_Groups {
WHERE c.species_id = ? AND b.attrib = ?
);
}
- $get_all_sql = q(
- SELECT DISTINCT alt_allele_group_id FROM alt_allele a
- JOIN (gene g, seq_region s, coord_system c)
- ON (
- c.coord_system_id = s.coord_system_id
- AND s.seq_region_id = g.seq_region_id
- AND g.gene_id = a.gene_id
- )
- WHERE c.species_id = ?
- );
+ else {
+ $get_all_sql = q(
+ SELECT DISTINCT alt_allele_group_id FROM alt_allele a
+ JOIN (gene g, seq_region s, coord_system c)
+ ON (
+ c.coord_system_id = s.coord_system_id
+ AND s.seq_region_id = g.seq_region_id
+ AND g.gene_id = a.gene_id
+ )
+ WHERE c.species_id = ?
+ );
+ }
} else {
if ($type) {
$get_all_sql = q(SELECT DISTINCT alt_allele_group_id
@@ -144,7 +164,7 @@ sub fetch_all_Groups {
$sth->bind_col(1, \$group_id );
while ( $sth->fetch() ) {
- my $aag = $self->fetch_Group_by_id($group_id);
+ my $aag = $self->fetch_by_dbID($group_id);
push @group_list, $aag;
}
$sth->finish;
@@ -154,22 +174,34 @@ sub fetch_all_Groups {
=head2 fetch_all_Groups_by_type
Arg[1] : String - type of group
- Description : Convenience method for restricting group fetches to just one
- type. Technically it selects out mixed-annotation groups where
- a single member contains that type.
- Returntype : Listref of Bio::EnsEMBL::AltAlleleGroup
+ Description : DEPRECATED. Please use fetch_all()
+ Returntype : ArrayRef of Bio::EnsEMBL::AltAlleleGroup
+
=cut
sub fetch_all_Groups_by_type {
- my $self = shift;
- my $type = shift; # refers to alt_allele_attrib type
-
- my $group_list = $self->fetch_all_Groups($type);
+ my ($self, $type) = @_;
+ deprecate('Please use fetch_all()');
+ my $group_list = $self->fetch_all($type);
return $group_list;
}
=head2 fetch_Group_by_id
+ Arg[1] : AltAlleleGroup dbID.
+ Description : DEPRECATED. Please use fetch_by_dbID
+ Returntype : Bio::EnsEMBL::AltAlleleGroup
+
+=cut
+
+sub fetch_Group_by_id {
+ my ($self, $group_id) = @_;
+ deprecate('Please use fetch_by_dbID()');
+ return $self->fetch_by_dbID($group_id);
+}
+
+=head2 fetch_by_dbID
+
Arg[1] : AltAlleleGroup dbID.
Description : Creates and returns an AltAlleleGroup for the given group id
@@ -177,7 +209,7 @@ sub fetch_all_Groups_by_type {
=cut
-sub fetch_Group_by_id {
+sub fetch_by_dbID {
my $self = shift;
my $group_id = shift;
@@ -225,10 +257,33 @@ sub fetch_Group_by_id {
return;
}
+=head2 fetch_Group_by_Gene_dbID
+
+ Arg[1] : Integer Gene ID of the member to query by
+ Description : DEPRECATED. Please use fetch_by_gene_id
+ Returntype : Bio::EnsEMBL::AltAlleleGroup
+
+=cut
+
+
sub fetch_Group_by_Gene_dbID {
- my $self = shift;
- my $gene_id = shift;
-
+ my ($self, $gene_id) = @_;
+ deprecate('Please use fetch_by_gene_id()');
+ return $self->fetch_by_gene_id($gene_id);
+}
+
+=head2 fetch_by_gene_id
+
+ Arg[1] : Integer Gene ID of the member to query by
+ Description : Creates and returns an AltAlleleGroup which contains
+ the specified gene member
+ Returntype : Bio::EnsEMBL::AltAlleleGroup
+
+=cut
+
+sub fetch_by_gene_id {
+ my ($self, $gene_id) = @_;
+
my $gene_id_sql = q(
SELECT alt_allele_group_id FROM alt_allele
WHERE gene_id = ?
@@ -242,14 +297,14 @@ sub fetch_Group_by_Gene_dbID {
$sth->fetch;
$sth->finish;
if (!$@ && $group_id) {
- return $self->fetch_Group_by_id($group_id);
+ return $self->fetch_by_dbID($group_id);
}
return;
}
=head2 store
- Arg[0] : Bio::EnsEMBL::AltAlleleGroup
+ Arg[1] : Bio::EnsEMBL::AltAlleleGroup
Description: Used for persisting new groups to the database.
It updates the dbID of the object handed to it to match the
database.
@@ -373,4 +428,4 @@ sub _tables {
return (['alt_allele', 'a'], ['alt_allele_group', 'g'], ['alt_allele_attrib', 'b']);
}
-1;
\ No newline at end of file
+1;
diff --git a/modules/t/altAlleleGroup.t b/modules/t/altAlleleGroup.t
index 6169376b6f..fea128be57 100644
--- a/modules/t/altAlleleGroup.t
+++ b/modules/t/altAlleleGroup.t
@@ -86,7 +86,7 @@ ok($db, 'DB was retrieved');
my $aaga = $db->get_adaptor('AltAlleleGroup');
# Test data consists of a single group, of type AUTOMATIC, with a reference Allele and 3 others
-my $group_list = $aaga->fetch_all_Groups;
+my $group_list = $aaga->fetch_all;
my $aag = $group_list->[0];
is($aag->rep_Gene_id, 18256,"Check for correct selection of allele");
@@ -101,26 +101,26 @@ $gene = $gene_list->[0];
is (ref($gene),'Bio::EnsEMBL::Gene',"Returned object type from get_all_Genes");
ok ($gene->dbID == 18256,"Ensure Gene objects acquire correct information");
-# test fetch_all_Groups_by_type
-$group_list = $aaga->fetch_all_Groups_by_type('UNLIKELY STRING');
+# test fetch_all
+$group_list = $aaga->fetch_all('UNLIKELY STRING');
ok(scalar(@{$group_list}) == 0,"Try outlandish typed group lookup");
-$group_list = $aaga->fetch_all_Groups_by_type('HAS_CODING_POTENTIAL');
+$group_list = $aaga->fetch_all('HAS_CODING_POTENTIAL');
ok(scalar(@$group_list) == 1,"Try known group type lookup");
# fetch_Group_by_id
$aag = $group_list->[0];
my $group_id = $aag->dbID;
-my $new_aag = $aaga->fetch_Group_by_id($group_id);
+my $new_aag = $aaga->fetch_by_dbID($group_id);
is_deeply($aag, $new_aag, "Compare previously fetched group with group found by using the dbID");
-$aag = $aaga->fetch_Group_by_id(undef);
+$aag = $aaga->fetch_by_dbID(undef);
ok(!defined($aag), "See what happens if no argument is given");
# fetch_Group_by_Gene_dbID
-$aag = $aaga->fetch_all_Groups->[0];
-$new_aag = $aaga->fetch_Group_by_Gene_dbID(18257);
+$aag = $aaga->fetch_all->[0];
+$new_aag = $aaga->fetch_by_gene_id(18257);
is_deeply($new_aag,$aag,"Check single gene ID returns entire group correctly");
# check store method
@@ -128,7 +128,7 @@ my $dbID = $aaga->store($group);
ok($dbID, 'A dbID was returned from the store method');
{
- my $aag2 = $aaga->fetch_Group_by_id($dbID);
+ my $aag2 = $aaga->fetch_by_dbID($dbID);
is_deeply($aag2->get_all_members,$group->get_all_members,"Compare stored with original");
$group->add_member(4, {});
my $update_dbID = $aaga->update($group);
@@ -137,11 +137,11 @@ ok($dbID, 'A dbID was returned from the store method');
$group->remove_member(4);
$aaga->remove($group);
-ok(! defined $aaga->fetch_Group_by_id($dbID), 'Using a deleted ID means no group returned');
+ok(! defined $aaga->fetch_by_dbID($dbID), 'Using a deleted ID means no group returned');
my $new_dbID = $aaga->store($group);
cmp_ok($new_dbID, '!=', $dbID, 'Should have been assgined a new ID');
-my $aag2 = $aaga->fetch_Group_by_id($new_dbID);
+my $aag2 = $aaga->fetch_by_dbID($new_dbID);
my $gene_ids = $aag2->get_all_Gene_ids();
eq_or_diff($gene_ids,[1,2,3], "Update and re-retrieve the same AltAlleleGroup") or diag explain $gene_ids;
@@ -149,7 +149,7 @@ eq_or_diff($gene_ids,[1,2,3], "Update and re-retrieve the same AltAlleleGroup")
# Proper test data is hard to fabricate and no samples exist.
$aaga->db->is_multispecies(1);
-$group_list = $aaga->fetch_all_Groups;
+$group_list = $aaga->fetch_all;
$aag = $group_list->[0];
ok(scalar(@$group_list) == 1, "Pretend multi-species fetch returns same groups as normal.");
--
GitLab