From b106886f6ce152c8b23a58ca635db0c5cfb81c7e Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Tue, 17 Jan 2012 20:52:09 +0000
Subject: [PATCH] Program is now executable and also attempts to diagnose the
issues a user can face when setting up the API.
---
misc-scripts/ping_ensembl.pl | 59 ++++++++++++++++++++++++++++++++++++
1 file changed, 59 insertions(+)
create mode 100755 misc-scripts/ping_ensembl.pl
diff --git a/misc-scripts/ping_ensembl.pl b/misc-scripts/ping_ensembl.pl
new file mode 100755
index 0000000000..5297c0976e
--- /dev/null
+++ b/misc-scripts/ping_ensembl.pl
@@ -0,0 +1,59 @@
+#!/usr/bin/env perl
+
+#######################################################
+# This script is used to detect if you can contact the Ensembl database
+# server with your current setup. The program will attempt to print out
+# helpful hints about how to resolve your problems. If they still persist
+# then please contact helpdesk@ensembl.org.
+#######################################################
+
+use strict;
+use warnings;
+
+my $host = 'ensembldb.ensembl.org';
+my $user = 'anonymous';
+my $port = 5306;
+my $db_version = '-';
+
+eval {
+ require Bio::EnsEMBL::Registry;
+ require Bio::EnsEMBL::ApiVersion;
+ require Bio::Perl;
+ Bio::EnsEMBL::Registry->load_registry_from_db(
+ -host => $host,
+ -user => $user, -db_version => 65
+ );
+ $db_version = Bio::EnsEMBL::ApiVersion::software_version();
+ my $human = Bio::EnsEMBL::Registry->get_DBAdaptor('homo_sapiens', 'core');
+ my $name = $human->get_MetaContainer()->get_scientific_name();
+ if('Homo sapiens' eq $name) {
+ print "Installation is good. Connection to Ensembl works and you can query the human core database\n";
+ }
+ else {
+ print "Installation is good. Connection to Ensembl works but the species name '$name' was not as expected. Please contact the developers at dev\@ensembl.org to update this assertion\n";
+ }
+};
+
+if($@) {
+ print "ERROR: Cannot connect to Ensembl!\n";
+ if($@ =~ /Can't locate Bio\/E/) {
+ print "\tLooks like you need to setup your PERL5LIB with the Ensembl API. Please consult http://www.ensembl.org/info/docs/api/api_installation.html\n";
+ }
+ if($@ =~ /Can't locate Bio\/Perl/) {
+ print "\tLooks like you need to setup your PERL5LIB with BioPerl. Please consult http://www.ensembl.org/info/docs/api/api_installation.html\n";
+ }
+ if($@ =~ /Cannot connect to/) {
+ print "\tCannot seem to contact EnsemblDB at '$host' with the username '$user'. Try running 'ping $host' or asking your systems about firewalls against port $port\n";
+ }
+ if($@ =~ /internal name/) {
+ print "\tSpecies was not found. You may have accidentally download the HEAD API version (found API release $db_version). Please consult http://www.ensembl.org/info/docs/api/api_installation.html\n";
+ }
+ if($@ =~ /Species not defined/) {
+ print "\tSpecies was not found. You may have accidentally download the HEAD API version (found API release $db_version). Please consult http://www.ensembl.org/info/docs/api/api_installation.html\n";
+ }
+ print '='x80, "\n";
+ print "If the problem persists please send the following error message to helpdesk\@ensembl.org\n";
+ print $@;
+ print '='x80, "\n";
+ exit 1;
+}
\ No newline at end of file
--
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