From 0799dabab7cad62992b681bb7418002eb5e1bb5c Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Wed, 17 Oct 2018 17:21:53 +0100
Subject: [PATCH] ENSCORESW-2903: remove default 0 analysis_id, should be NULL
---
modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm | 2 --
modules/t/dbEntries.t | 8 +++++++-
2 files changed, 7 insertions(+), 3 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
index 29942c95f5..d19ed7c534 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
@@ -790,8 +790,6 @@ sub _store_object_xref_mapping {
my $analysis_id;
if ( $dbEntry->analysis() ) {
$analysis_id = $self->db()->get_AnalysisAdaptor->store( $dbEntry->analysis() );
- } else {
- $analysis_id = 0; ## This used to be undef, but uniqueness in mysql requires a value
}
my $insert_ignore = $self->insert_ignore_clause();
diff --git a/modules/t/dbEntries.t b/modules/t/dbEntries.t
index 5e7968a6c9..174a230094 100644
--- a/modules/t/dbEntries.t
+++ b/modules/t/dbEntries.t
@@ -554,12 +554,18 @@ $multi->restore();
my $no_desc_id_again = $dbEntryAdaptor->store($entry_no_desc, $gene->dbID(), 'Gene');
is($no_desc_id_again, $no_desc_id, 'Checking the ID is consistent between store() invocations');
is_rows(1, $db, 'xref', 'where description = ?', [q{}]);
- is_rows(1, $db, 'object_xref');
+ is_rows(2, $db, 'object_xref');
is_rows(0, $db, 'object_xref', 'where xref_id =?', [0]);
$multi->restore('core', 'xref', 'object_xref');
}
+# Test storing with no analysis
+
+my $dbentry = Bio::EnsEMBL::DBEntry->new(-PRIMARY_ID => 'my_id', -DBNAME => 'EntrezGene', -RELEASE => 1);
+$xref_id = $dbEntryAdaptor->store($dbentry, $gene->dbID(), 'Gene');
+is_rows("1", $db, "object_xref", "where xref_id = $xref_id and analysis_id is null");
+
# Test for external DB ids
{
is($dbEntryAdaptor->get_external_db_id('RFAM', 1), 4200, 'RFAM ID as expected');
--
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