From fc6f84e5a3127db6da5034aeb48b0e536b6c03ad Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Wed, 7 Aug 2013 23:04:51 +0000
Subject: [PATCH] reverting last change
---
.../Bio/EnsEMBL/DBSQL/Support/FullIdCache.pm | 233 +++---------------
modules/t/fullIdCaching.t | 58 +----
2 files changed, 34 insertions(+), 257 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/Support/FullIdCache.pm b/modules/Bio/EnsEMBL/DBSQL/Support/FullIdCache.pm
index a9f0cb7cfb..9d0b9f7edf 100644
--- a/modules/Bio/EnsEMBL/DBSQL/Support/FullIdCache.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/Support/FullIdCache.pm
@@ -33,8 +33,6 @@ An implementation of caching which uses a raw hash to hold all available
values from an adaptor. Useful for working with a controlled vocabulary
table where cardinality is low.
-Provides extra functionality to compute additional lookup keys.
-
=head1 METHODS
=cut
@@ -61,228 +59,63 @@ sub build_cache {
my ($self) = @_;
my $adaptor = $self->adaptor();
my %cache;
- my $objects = $adaptor->generic_fetch();
- my $support_additional_lookups = $self->support_additional_lookups();
- foreach my $object (@{$objects}) {
- my $key = $object->dbID();
- $cache{$key} = $object;
- #Add to additional lookup
- $self->add_to_additional_lookups($key, $object);
+ my $objs = $adaptor->generic_fetch();
+ foreach my $obj (@{$objs}) {
+ $cache{$obj->dbID()} = $obj;
}
return \%cache;
}
-########### Additional lookup code
+=head2 clear_cache
-sub put {
- my ($self, $key, $object) = @_;
- my $old = $self->SUPER::put($key, $object);
- #Add to additional lookup
- $self->add_to_additional_lookups($key, $object);
- return $old if $old;
- return;
-}
+ Description: Delegates to C<delete_cache()> in order to clear all values
+ and on the next cache request will force a C<build_cache()>
+ call
+ Returntype : None
+ Exceptions : None
+ Caller : BaseAdaptors
+ Status : Beta
-sub remove {
- my ($self, $key) = @_;
- my $old = $self->SUPER::remove($key);
- if($old) {
- #Remove it from the additional lookup
- $self->remove_from_additional_lookup($key, $old);
- return $old;
- }
- return;
-}
+=cut
sub clear_cache {
my ($self) = @_;
$self->delete_cache();
- #Remove the additional lookup hash contents
- delete $self->{_additional_lookup};
return;
}
-=head2 get_by_additional_lookup
-
- Arg [1] : String key of the lookup to search for the value in
- Arg [2] : String value to search for. We expect exact lookups in the hash
- Description : Returns the object linked to the value in the specified lookup.
- Example : my $analysis = $cache->get_by_additional_lookup('logic_name', 'xrefchecksum');
- Returntype : Object a single object
- Exceptions : Throws an exception if there are more than one ID linked to the
- value lookup. Also thrown if additional lookups are not supported
- Caller : BaseAdaptors
- Status : Beta
-
-=cut
-
-sub get_by_additional_lookup {
- my ($self, $key, $value) = @_;
- my $additional_lookup = $self->_additional_lookup();
- if(exists $additional_lookup->{$key}) {
- if(exists $additional_lookup->{$key}->{$value}) {
- my $ids = $additional_lookup->{$key}->{$value};
- my $size = scalar(@{$ids});
- if($size > 1) {
- throw "The lookup $key and search value $value has more than one value attached. Use get_all_by_additional_lookup() instead to fetch";
- }
- elsif($size == 1) {
- return $self->get($ids->[0]);
- }
- }
- }
- return;
-}
-
-=head2 get_all_by_additional_lookup
-
- Arg [1] : String key of the lookup to search for the value in
- Arg [2] : String value to search for. We expect exact lookups in the hash
- Description : Returns an array of all the objects linked to the value
- in the specified lookup.
- Example : my $array = $cache->get_all_by_additional_lookup('logic_name', 'xrefchecksum');
- Returntype : ArrayRef of objects keyed agains the second argument
- Exceptions : Throws an exception if there are more than one ID linked to the
- value lookup. Also thrown if additional lookups are not supported
- Caller : BaseAdaptors
- Status : Beta
-
-=cut
-
-sub get_all_by_additional_lookup {
- my ($self, $key, $value) = @_;
- my $additional_lookup = $self->_additional_lookup();
- if(exists $additional_lookup->{$key}) {
- if(exists $additional_lookup->{$key}->{$value}) {
- my $ids = $additional_lookup->{$key}->{$value};
- return $self->get_by_list($ids);
- }
- }
- return [];
-}
-
-=head2 remove_from_additional_lookup
+=head2 put
- Arg [1] : String The lookup key to remove from the additional lookup hash
- Arg [2] : Object The object to remove from the additional lookup hash
- Description : Re-computes the additional keys for this object
- Example : $cache->remove_Object_from_additional_lookup($lookup_key, $object);
- Returntype : None
- Exceptions : Thrown if we do not support additional lookups
- Caller : BaseAdaptors
- Status : Beta
+ Description: Unsupported operation since this cache is read only apart from
+ during the build process
+ Returntype : None
+ Exceptions : Thrown if ever called
+ Caller : BaseAdaptors
+ Status : Beta
=cut
-sub remove_from_additional_lookup {
- my ($self, $lookup_key, $object) = @_;
-
- my $additional_lookup = $self->_additional_lookup();
-
- # Compute the keys
- my $keys = $self->compute_keys($object);
-
- foreach my $key (keys %{$keys}) {
- my $value = $keys->{$key};
-
- #Only remove if we had originally stored this as an
- #additional lookup
- if(exists $additional_lookup->{$key}) {
- if(exists $additional_lookup->{$key}->{$value}) {
-
- #Get the object ID & lookup the array of DBIDs
- my $lookup_keys = $additional_lookup->{$key}->{$value};
- my $length = scalar(@{$lookup_keys});
- for(my $i = 0; $i < $length; $i++) {
- if($lookup_keys->[$i] == $lookup_key) {
- #remove the 1 lookup key from the array and then terminate the
- #loop as we found our value
- splice(@{$lookup_keys}, $i, 1);
- last;
- }
- }
-
- #If the size has hit 0 then delete the array
- if(scalar(@{$lookup_keys}) == 0) {
- delete $additional_lookup->{$key}->{$value};
- }
- }
- }
- }
-
+sub put {
+ my ($self) = @_;
+ throw 'Unsupported operation';
return;
}
-=head2 compute_keys
-
- Arg [1] : Object The object to compute keys from
- Description : Override to provide support for additional key lookup. The
- keys of the hash should represent the lookup name and the
- value is the computed key.
- Example : Example of returning hash not of its usage. Proposed Analysis encoding
- { logic_name => 'xrefalignment', display_label => 'Xref Alignment'}
- Returntype : HashRef key is the lookup name and value is the computed key
- Exceptions : none
- Caller : BaseAdaptors
- Status : Beta
-
-=cut
-
-sub compute_keys {
- my ($self, $object) = @_;
- return {};
-}
+=head2 remove
-=head2 add_to_additional_lookups
-
- Arg [1] : String The key used in the primary lookup hash. Normally
- a DB identifier
- Arg [2] : Object The object to add to the additional lookups
- Description : Internally calls the C<compute_keys()> method and adds
- the object to the C<_additional_lookup()> hash.
- Returntype : None
- Exceptions : Thrown if additional lookups are not supported
- Caller : BaseAdaptors
- Status : Beta
-
-=cut
-
-sub add_to_additional_lookups {
- my ($self, $lookup_key, $object) = @_;
- my $keys = $self->compute_keys($object);
- my $additional_lookup = $self->_additional_lookup();
- foreach my $key (keys %{$keys}) {
- my $value = $keys->{$key};
- push(@{$additional_lookup->{$key}->{$value}}, $lookup_key);
- }
- return;
-}
-
-=head2 _additional_lookup
-
- Description : Returns the additional lookup hash
- Example : Example of additional hash structure (key is
- lookup name, second key is value to search for
- and value is an array of dbIDs)
- {
- logic_name => {
- xrefalignment => [1]
- },
- display_label => {
- 'Xref Alignment' => [1]
- }
- }
- Returntype : HashRef
- Exceptions : none
- Caller : BaseAdaptors
- Status : Beta
+ Description: Unsupported operation since this cache is read only apart from
+ during the build process
+ Returntype : None
+ Exceptions : Thrown if ever called
+ Caller : BaseAdaptors
+ Status : Beta
=cut
-sub _additional_lookup {
+sub remove {
my ($self) = @_;
- $self->{_additional_lookup} ||= {};
- return $self->{_additional_lookup};
+ throw 'Unsupported operation';
+ return;
}
-1;
\ No newline at end of file
+1;
diff --git a/modules/t/fullIdCaching.t b/modules/t/fullIdCaching.t
index acfc16512b..764b7819b0 100644
--- a/modules/t/fullIdCaching.t
+++ b/modules/t/fullIdCaching.t
@@ -1,26 +1,3 @@
-package TemporaryGeneCache;
-
-use base qw/Bio::EnsEMBL::DBSQL::Support::FullIdCache/;
-use strict;
-use warnings;
-
-sub support_additional_lookups {
- return 1;
-}
-
-sub compute_keys {
- my ($self, $object) = @_;
- return {
- biotype => $object->biotype(),
- logic_name => $object->analysis()->logic_name(),
- dbID => $object->dbID()
- };
-}
-
-1;
-
-#######################
-
package main;
use strict;
@@ -44,7 +21,7 @@ sub BEGIN {
no strict 'refs'; ## no critic
*Bio::EnsEMBL::DBSQL::GeneAdaptor::_build_id_cache = sub {
my ($self) = @_;
- return TemporaryGeneCache->new($self);
+ return Bio::EnsEMBL::DBSQL::Support::FullIdCache->new($self);
};
no warnings 'redefine';
my $original_store = \&Bio::EnsEMBL::DBSQL::GeneAdaptor::store;
@@ -87,39 +64,6 @@ sub BEGIN {
is_deeply($first_gene_refetch, $refetched_cached_ids->[0], 'fetch_by_dbID() should return the same object as fetch_all_by_dbID_list()');
ok(! defined $adaptor->fetch_by_dbID(1), 'Fetching with a bad ID returns nothing');
is(scalar(@{$adaptor->fetch_all_by_dbID_list([1])}), 0, 'Fetching with a bad ID returns an empty array');
-
- ############ Test additional lookup code
- {
- my $protein_coding_genes = $cache->get_all_by_additional_lookup('biotype', 'protein_coding');
- is_deeply([sort map { $_->dbID() } @{$protein_coding_genes} ], [sort map { $_->dbID() } @{$genes} ], 'Protein coding lookup returns all genes');
-
- my $wibble_genes = $cache->get_all_by_additional_lookup('biotype', 'wibble');
- is_deeply([], $wibble_genes, 'biotype is a valid lookup but wibble is a bad key. Empty array return');
-
- my $bad_lookup = $cache->get_all_by_additional_lookup('wibble', 'wibble');
- is_deeply([], $wibble_genes, 'wibble is a bad lookup. Empty array return');
-
- my $individual_gene = $cache->get_by_additional_lookup('dbID', $gene_ids->[0]);
- is($individual_gene->dbID, $gene_ids->[0], 'Lookup of dbID returns a single value');
- is($cache->get($gene_ids->[0]), $individual_gene, 'Same object is returned from the main get() method and the lookup');
-
- dies_ok { $cache->get_by_additional_lookup('biotype', 'protein_coding') } 'Expect to die as the query will return more than one value';
-
- $cache->remove($individual_gene->dbID());
- my $new_protein_coding_genes = $cache->get_all_by_additional_lookup('biotype', 'protein_coding');
-
- ok(! defined $cache->get_by_additional_lookup('dbID', $gene_ids->[0]), 'Removed gene so lookups can no longer return an object');
- ok(! exists $cache->_additional_lookup()->{dbID}->{$gene_ids->[0]}, 'Removed the resulting array from the lookup hash');
- ok(exists $cache->_additional_lookup()->{biotype}->{protein_coding}, 'Biotype lookup still exists for protein_coding');
- is(scalar(@{$new_protein_coding_genes}), (scalar(@{$protein_coding_genes}) -1), 'Reduced the returned number of protein coding genes by one');
-
- $cache->put($individual_gene->dbID(), $individual_gene);
- ok(defined $cache->get_by_additional_lookup('dbID', $gene_ids->[0]), 'Added the gene back in. Everything is OK again');
-
- #Checking DBSQL based lookup works
- my $sql_protein_coding_genes = $cache->get_by_sql('select gene_id from gene where biotype =?', ['protein_coding']);
- is_deeply([sort map { $_->dbID() } @{$sql_protein_coding_genes} ], [sort map { $_->dbID() } @{$protein_coding_genes} ], 'SQL based protein_coding lookup returns all genes');
- }
#Turn off caching; we should get a fresh object out of the cache
my $cached_obj = $adaptor->fetch_by_dbID($gene_ids->[0]);
--
GitLab