From 5b379206dbaf3ca10feb4fc0afdc04cfcc984322 Mon Sep 17 00:00:00 2001
From: Leo Gordon <lg4@ebi.ac.uk>
Date: Fri, 17 Jan 2014 10:24:20 +0000
Subject: [PATCH] implemented input_column_mapping mechanism
---
modules/Bio/EnsEMBL/Hive/DBSQL/BaseAdaptor.pm | 32 +++++++++++++------
1 file changed, 23 insertions(+), 9 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Hive/DBSQL/BaseAdaptor.pm b/modules/Bio/EnsEMBL/Hive/DBSQL/BaseAdaptor.pm
index 8c9177b9b..7f03c5f41 100644
--- a/modules/Bio/EnsEMBL/Hive/DBSQL/BaseAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Hive/DBSQL/BaseAdaptor.pm
@@ -56,6 +56,15 @@ sub default_overflow_limit {
return {
# 'overflow_column1_name' => column1_size,
# 'overflow_column2_name' => column2_size,
+ # ...
+ };
+}
+
+sub default_input_column_mapping {
+ return {
+ # 'original_column1' => "original_column1*10 AS c1_times_ten",
+ # 'original_column2' => "original_column2+1 AS c2_plus_one",
+ # ...
};
}
@@ -70,6 +79,16 @@ sub overflow_limit {
}
+sub input_column_mapping {
+ my $self = shift @_;
+
+ if(@_) { # setter
+ $self->{_input_column_mapping} = shift @_;
+ }
+ return $self->{_input_column_mapping} || $self->default_input_column_mapping();
+}
+
+
sub table_name {
my $self = shift @_;
@@ -203,19 +222,14 @@ sub count_all {
sub fetch_all {
my ($self, $constraint, $one_per_key, $key_list, $value_column) = @_;
- my $table_name = $self->table_name();
+ my $table_name = $self->table_name();
+ my $input_column_mapping = $self->input_column_mapping();
- my $sql = 'SELECT ' . join(', ', keys %{$self->column_set()}) . " FROM $table_name";
+ my $sql = 'SELECT ' . join(', ', map { $input_column_mapping->{$_} // "$table_name.$_" } keys %{$self->column_set()}) . " FROM $table_name";
if($constraint) {
# in case $constraint contains any kind of JOIN (regular, LEFT, RIGHT, etc) do not put WHERE in front:
- if($constraint=~/\bJOIN\b/i) {
- $sql = 'SELECT ' . join(', ', map { "$table_name.$_" } keys %{$self->column_set()}) . " FROM $table_name $constraint";
- } elsif($constraint=~/^LIMIT|ORDER|GROUP/) {
- $sql .= ' '.$constraint;
- } else {
- $sql .= ' WHERE '.$constraint;
- }
+ $sql .= (($constraint=~/\bJOIN\b/i or $constraint=~/^LIMIT|ORDER|GROUP/) ? ' ' : ' WHERE ') . $constraint;
}
# warn "SQL: $sql\n";
--
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