From 2dd70b3c3e9cc861e4e61c62152f9136c44402fe Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Wed, 2 Oct 2013 15:58:39 +0000
Subject: [PATCH] ENSCORESW-678: added special case for density feature unlike
other features, the related analysis is stored in the density type table
---
modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm | 41 +++++++++++++-------
1 file changed, 28 insertions(+), 13 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm
index b57471f541..f59d086a9c 100755
--- a/modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm
@@ -146,32 +146,47 @@ sub fetch_all {
sub fetch_all_by_feature_class {
my $self = shift;
- deprecate("Deprecated. Hard-coded logic is not supported");
my $feat_class = shift || throw( "Need a feature type, e.g. SimpleFeature" );
- my @feature_classes = $self->feature_classes; # List of all feature classes
- my %feat_table_map;
- foreach my $class( @feature_classes ){
- # Map e.g. DnaAlignFeature to dna_align_feature
- my $table = join( "_", map lc, ( $class =~ /([A-Z][a-z]+)/g ) );
- $feat_table_map{$class} = $table;
+ # Need a special case for density
+ # DensityFeature is the feature, but the analysis is linked to the DensityType
+ if ($feat_class =~ /Density/) {
+ $feat_class = 'DensityType';
+ }
+
+ my $adaptor = $self->db->get_adaptor($feat_class);
+ if (!$adaptor) {
+ throw("$feat_class is not a know feature. No adaptor found");
+ }
+
+ # Check that feature has an analysis
+ my $has_analysis = 0;
+ my @columns = $adaptor->_columns;
+ foreach my $column (@columns) {
+ if ($column =~ /analysis/) {
+ $has_analysis = 1;
+ last;
+ }
}
- $feat_table_map{DensityFeature}='density_type'; # analysis_id in diff table
- my $feat_table = $feat_table_map{$feat_class} ||
- ( warning( "No feature type corresponding to $feat_class" ) &&
- return [] );
+ if ($has_analysis == 0) {
+ throw("$feat_class does not have an analysis column");
+ }
+
+ # Retrieve the name of the table
+ my @tables = $adaptor->_tables();
+ my $table = $tables[0]->[0];
my $sql_t = qq|
SELECT DISTINCT analysis_id FROM %s |;
- my $sql = sprintf( $sql_t, $feat_table );
+ my $sql = sprintf( $sql_t, $table );
my $sth = $self->prepare( $sql );
my $rv = $sth->execute();
my $res = $sth->fetchall_arrayref;
my @analyses;
foreach my $r( @{$res} ){
my $analysis = $self->fetch_by_dbID($r->[0])
- || throw( "analysis_id $r->[0] from $feat_table table "
+ || throw( "analysis_id $r->[0] from $table table "
. "is not in the analysis table!" );
push @analyses, $analysis;
}
--
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