From 1944569279ccf2b09c7ed2b2b944e1e1e935deff Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Mon, 19 May 2014 16:09:36 +0100
Subject: [PATCH] ENSCORESW-926: add update method for sliceAdaptor
---
modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm | 64 +++++++++++++++++++++++
modules/t/sliceAdaptor.t | 13 +++++
2 files changed, 77 insertions(+)
diff --git a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
index 5a45f724aa..87438e120d 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
@@ -2054,6 +2054,70 @@ sub store {
return $seq_region_id;
}
+
+sub update {
+ my $self = shift;
+ my $slice = shift;
+
+ #
+ # Get all of the sanity checks out of the way before storing anything
+ #
+
+ if(!ref($slice) || !($slice->isa('Bio::EnsEMBL::Slice') or $slice->isa('Bio::EnsEMBL::LRGSlice'))) {
+ throw('Slice argument is required');
+ }
+
+ my $cs = $slice->coord_system();
+ throw("Slice must have attached CoordSystem.") if(!$cs);
+
+ my $db = $self->db();
+
+ if($slice->start != 1 || $slice->strand != 1) {
+ throw("Slice must have start==1 and strand==1.");
+ }
+
+ if($slice->end() != $slice->seq_region_length()) {
+ throw("Slice must have end==seq_region_length");
+ }
+
+ my $sr_len = $slice->length();
+ my $sr_name = $slice->seq_region_name();
+
+ if(!$sr_name) {
+ throw("Slice must have valid seq region name.");
+ }
+
+ #update the seq_region
+
+ my $seq_region_id = $slice->get_seq_region_id();
+ my $update_sql = qq(
+ UPDATE seq_region
+ SET name = ?,
+ length = ?,
+ coord_system_id = ?
+ WHERE seq_region_id = ?
+ );
+
+ my $sth = $db->dbc->prepare($update_sql);
+
+ $sth->bind_param(1,$sr_name,SQL_VARCHAR);
+ $sth->bind_param(2,$sr_len,SQL_INTEGER);
+ $sth->bind_param(3,$cs->dbID,SQL_INTEGER);
+
+ $sth->bind_param(4, $seq_region_id, SQL_INTEGER);
+
+ $sth->execute();
+
+ #synonyms
+ if(defined($slice->{'synonym'})){
+ foreach my $syn (@{$slice->{'synonym'}} ){
+ $syn->seq_region_id($seq_region_id); # set the seq_region_id
+ my $syn_adaptor = $db->get_SeqRegionSynonymAdaptor();
+ $syn_adaptor->store($syn);
+ }
+ }
+}
+
=head2 remove
Arg [1] : Bio::EnsEMBL::Slice $slice
diff --git a/modules/t/sliceAdaptor.t b/modules/t/sliceAdaptor.t
index 1643fc16ee..9a1314e5ea 100644
--- a/modules/t/sliceAdaptor.t
+++ b/modules/t/sliceAdaptor.t
@@ -297,6 +297,19 @@ ok($chr_slice->length() == $chr_len);
ok($chr_slice->seq_region_length() == $chr_len);
ok($chr_slice->seq_region_name eq $name);
+#
+# Update a slice
+#
+
+$chr_slice->add_synonym('testregion3');
+$slice_adaptor->update($chr_slice);
+
+my $updated_slice = $slice_adaptor->fetch_by_region('chromosome', 'testregion3');
+ok($updated_slice->length() == $chr_len);
+ok($updated_slice->seq_region_length() == $chr_len);
+ok($updated_slice->seq_region_name eq $name);
+
+
#
# Store an assembly between the slices
#
--
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