From fc2098b8f50745c28e730257bea398bb68168b3e Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Fri, 4 Mar 2011 09:52:59 +0000
Subject: [PATCH] dbentries MUST have an analysis now due to INSERT IGNORE in
dbentrie cahnged to just INSERT
---
modules/t/dbEntries.t | 12 ++++++++----
modules/t/gene.t | 5 ++++-
2 files changed, 12 insertions(+), 5 deletions(-)
diff --git a/modules/t/dbEntries.t b/modules/t/dbEntries.t
index ffab63c3d3..0b2c081cf0 100644
--- a/modules/t/dbEntries.t
+++ b/modules/t/dbEntries.t
@@ -77,6 +77,8 @@ debug( "GoXrefs and IdentityXrefs: ".$goxref_count . " " . $ident_count);
ok( $goxref_count == 48 );
ok( $ident_count == 32 );
+my $analysis_adap = $db->get_AnalysisAdaptor();
+my $analysis = $analysis_adap->fetch_by_logic_name("RepeatMask");
# try storing and retrieval
@@ -92,7 +94,8 @@ my $xref = Bio::EnsEMBL::DBEntry->new
-db_display_name => "Nice friendly name",
-info_type => "PROJECTION",
-info_text => "from human gene ENSG0000011111",
- -type => "ARRAY"
+ -type => "ARRAY",
+ -analysis => $analysis
);
@@ -104,8 +107,8 @@ my $ident_xref = Bio::EnsEMBL::IdentityXref->new
-primary_id => "1",
-dbname => "Uniprot/SPTREMBL",
-release => "1",
- -display_id => "Ens related Ident"
- );
+ -display_id => "Ens related Ident",
+ -analysis => $analysis );
$ident_xref->xref_identity( 100 );
$ident_xref->ensembl_identity( 95 );
@@ -115,7 +118,8 @@ my $goref = Bio::EnsEMBL::OntologyXref->new
-primary_id => "1",
-dbname => "GO",
-release => "1",
- -display_id => "Ens related GO"
+ -display_id => "Ens related GO",
+ -analysis => $analysis
);
$goref->add_linkage_type( "IC" ); # Linkage type on own
$goref->add_linkage_type( "ISS", $goref ); # Linkage type with source xref
diff --git a/modules/t/gene.t b/modules/t/gene.t
index 3566231d2a..f676157b8d 100644
--- a/modules/t/gene.t
+++ b/modules/t/gene.t
@@ -613,12 +613,15 @@ $multi->hide( "core", "gene", "transcript", "exon", 'xref', 'object_xref',
"exon_transcript", "translation" );
$gene->analysis($analysis);
+my $analysis_adap = $db->get_AnalysisAdaptor();
+my $analysis = $analysis_adap->fetch_by_logic_name("ensembl");
my $dbe = Bio::EnsEMBL::DBEntry->new(-primary_id => 'test_id',
-version => 1,
-dbname => 'EMBL',
-release => 1,
- -display_id => 'test_id');
+ -display_id => 'test_id',
+ -analysis => $analysis);
$gene->add_DBEntry($dbe);
--
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