From 646d3d6003fe15844458c0f11d2a59181f37f1ae Mon Sep 17 00:00:00 2001
From: Alessandro Vullo <avullo@ebi.ac.uk>
Date: Mon, 8 Aug 2016 12:29:33 +0100
Subject: [PATCH] Changes to deal with connection to EBI mirror.
---
.../xref_mapping/XrefParser/ArrayExpressParser.pm | 7 ++-----
.../xref_mapping/XrefParser/CoreXrefParser.pm | 7 ++-----
.../XrefParser/InterproFromCoreParser.pm | 7 ++-----
misc-scripts/xref_mapping/XrefParser/RFAMParser.pm | 7 ++-----
.../XrefParser/RefSeqCoordinateParser.pm | 14 ++++----------
5 files changed, 12 insertions(+), 30 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/ArrayExpressParser.pm b/misc-scripts/xref_mapping/XrefParser/ArrayExpressParser.pm
index beb34a238d..6b59bdd3f2 100644
--- a/misc-scripts/xref_mapping/XrefParser/ArrayExpressParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/ArrayExpressParser.pm
@@ -103,13 +103,10 @@ sub run_script {
print "Loading the Registry\n" if $verbose;
$registry->load_registry_from_multiple_dbs(
{
- '-host' => 'ens-staging1',
+ '-host' => 'mysql-ensembl-mirror.ebi.ac.uk',
+ '-port' => 4240,
'-user' => 'ensro',
},
- {
- '-host' => 'ens-staging2',
- '-user' => 'ensro',
- }
);
$gene_adaptor = $registry->get_adaptor($species_name, 'core', 'Gene');
} elsif ($project eq 'ensemblgenomes') {
diff --git a/misc-scripts/xref_mapping/XrefParser/CoreXrefParser.pm b/misc-scripts/xref_mapping/XrefParser/CoreXrefParser.pm
index 5ef2408d65..c30fcfde09 100644
--- a/misc-scripts/xref_mapping/XrefParser/CoreXrefParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/CoreXrefParser.pm
@@ -71,13 +71,10 @@ sub run_script {
if ($project eq 'ensembl') {
$registry->load_registry_from_multiple_dbs(
{
- '-host' => 'ens-staging1',
+ '-host' => 'mysql-ensembl-mirror.ebi.ac.uk',
+ '-port' => 4240,
'-user' => 'ensro',
},
- {
- '-host' => 'ens-staging2',
- '-user' => 'ensro',
- },
);
} elsif ($project eq 'ensemblgenomes') {
diff --git a/misc-scripts/xref_mapping/XrefParser/InterproFromCoreParser.pm b/misc-scripts/xref_mapping/XrefParser/InterproFromCoreParser.pm
index 1d4e77ccd6..c687092fa7 100755
--- a/misc-scripts/xref_mapping/XrefParser/InterproFromCoreParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/InterproFromCoreParser.pm
@@ -50,11 +50,8 @@ sub run_script {
if ($project eq 'ensembl') {
$registry->load_registry_from_multiple_dbs(
{
- '-host' => 'ens-staging1',
- '-user' => 'ensro',
- },
- {
- '-host' => 'ens-staging2',
+ '-host' => 'mysql-ensembl-mirror.ebi.ac.uk',
+ '-port' => 4240,
'-user' => 'ensro',
},
);
diff --git a/misc-scripts/xref_mapping/XrefParser/RFAMParser.pm b/misc-scripts/xref_mapping/XrefParser/RFAMParser.pm
index 7b036fdb13..42556d5896 100644
--- a/misc-scripts/xref_mapping/XrefParser/RFAMParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/RFAMParser.pm
@@ -88,13 +88,10 @@ sub run_script {
} else {
$registry->load_registry_from_multiple_dbs(
{
- '-host' => 'ens-staging1',
+ '-host' => 'mysql-ensembl-mirror.ebi.ac.uk',
+ '-port' => 4240,
'-user' => 'ensro',
},
- {
- '-host' => 'ens-staging2',
- '-user' => 'ensro',
- },
);
$dba = $registry->get_DBAdaptor($species_name, 'core');
}
diff --git a/misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm b/misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm
index fdda1a9d2f..7349eda3be 100644
--- a/misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm
@@ -138,13 +138,10 @@ sub run_script {
# Else, database should be on staging
$registry->load_registry_from_multiple_dbs(
{
- -host => 'ens-staging1',
+ -host => 'mysql-ensembl-mirror.ebi.ac.uk',
+ '-port' => 4240,
-user => 'ensro',
},
- {
- -host => 'ens-staging2',
- -user => 'ensro',
- },
);
$core_dba = $registry->get_DBAdaptor($species_name,'core');
}
@@ -163,13 +160,10 @@ sub run_script {
# Else database should be on staging
$registry->load_registry_from_multiple_dbs(
{
- -host => 'ens-staging1',
+ -host => 'mysql-ensembl-mirror.ebi.ac.uk',
+ '-port' => 4240,
-user => 'ensro',
},
- {
- -host => 'ens-staging2',
- -user => 'ensro',
- },
);
$otherf_dba = $registry->get_DBAdaptor($species_name, 'otherfeatures') if !defined($ofhost);
if (defined $otherf_dba) { $otherf_dba->dnadb($core_dba); }
--
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