ping_ensembl.pl

Go to the documentation of this file.

#!/usr/bin/env perl
# See the NOTICE file distributed with this work for additional information
# regarding copyright ownership.
# 
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# 
#      http://www.apache.org/licenses/LICENSE-2.0
# 
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
 
=head1 CONTACT
 
  Please email comments or questions to the Ensembl help desk
  <http://www.ensembl.org/Help/Contact>.
 
=head1 NAME
 
  ping_ensembl.pl
 
=head1 SYNOPSIS
 
  # print usage 
  $ ping_ensembl.pl -h 
 
  # ping Ensembl with default species (Human)
  $ ping_ensembl.pl
 
  # ping Ensembl with user provided species
  $ ping_ensembl.pl -s "dog"
 
  # ping Ensembl with a different version (Human)
  $ ping_ensembl.pl -db_version 70
 
  # ping the US Ensembl mirror
  $ ping_ensembl.pl -ue
 
  # ping Ensembl Genomes with default species (arabidopsis thaliana)
  $ ping_ensembl.pl -eg
 
  # ping Ensembl Genomes with user provided species 
  $ ping_ensembl.pl -eg -s "oryza sativa japonica"
 
=head1 DESCRIPTION
 
  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 http://www.ensembl.org/Help/Contact.
 
=head1 SUBROUTINES
 
=cut
 
use strict;
use warnings;
 
use File::Temp qw/tempfile/;
use Net::FTP;
use Getopt::Long;
 
#
# Default option values
#
my $help = 0;
my $host = 'ensembldb.ensembl.org';
my $user = 'anonymous';
my $port = 3306;
my $verbose = 0;
my $db_version = -1;
my $grch37;
 
my $useast = 0;
my $ensembl_genomes = 0;
my $species = undef;
my $api_version = -1;
 
#
# Parse command-line arguments
#
my $options_ok = 
  GetOptions(
    "ue"            => \$useast,
    "eg"            => \$ensembl_genomes,
    "species=s"     => \$species,
    "db_version=i"  => \$db_version,
    "verbose"       => \$verbose,
    "grch37"        => \$grch37,
    "help"          => \$help);
($help or !$options_ok) && usage();
 
$useast and $ensembl_genomes and
 die "Cannot test Ensembl Genomes on the US mirror.\n" .
  "Options \"ue\" and \"eg\" are mutually exclusive\n";
 
$useast and $host = "useastdb.ensembl.org";
 
$verbose and $verbose = 1;
 
$grch37 and $port = 3337;
 
if ($ensembl_genomes) {
  $host = "mysql-eg-publicsql.ebi.ac.uk";
  $port = 4157;
  $species = "arabidopsis thaliana"
    unless defined $species;
}
 
eval {
  require DBI;
  require DBD::mysql;
  require Bio::Perl;
  require Bio::EnsEMBL::Registry;
  require Bio::EnsEMBL::ApiVersion;
  require Bio::EnsEMBL::LookUp if $ensembl_genomes;
  $api_version = Bio::EnsEMBL::ApiVersion::software_version();
  $db_version = $api_version if $db_version == -1; #if it was still -1 then it wasn't set. Default is current API version
  Bio::EnsEMBL::Registry->load_registry_from_db(
    -host       => $host,
    -port       => $port,
    -user       => $user,
    -db_version => $db_version,
    -verbose    => $verbose,
  );
  $species = "human" unless defined $species;
  my $species_adaptor = Bio::EnsEMBL::Registry->get_DBAdaptor("$species", 'core');  
  print "Installation is good. Connection to Ensembl works and you can query the $species core database\n";
};
my $error = $@;
 
# If no error found then see if we've got all of our external modules available
if(!$error) {
  $error = '';
  eval {
    foreach my $module (qw/Compara Variation Funcgen/) {
      my $full_module = "Bio::EnsEMBL::${module}::DBSQL::DBAdaptor";
      eval "require $full_module;";
      if($@) {
        $error .= "\tMissing the checkout $module\n"; 
      }
    }
  };
}
 
# Check the current release of datafiles from the FTP site
my $ftp_version = -1;
eval {
  my $ftp = Net::FTP->new('ftp.ensembl.org', Debug => 0);
  $ftp->login("anonymous",'-anonymous@');
  $ftp->cwd('/pub');
  my ($fh, $filename) = tempfile();
  close($fh);
  $ftp->get('current_README', $filename);
  $ftp->quit();
  open($fh, '<', $filename);
  local $/ = undef;
  my $ftp_readme = <$fh>;
  close($fh);
  ($ftp_version) = $ftp_readme =~ /Ensembl Release (\d+) Databases/;
};
 
# Print all the errors which could have occured 
if($error) {
  print "ERROR: Error detected when connecting to Ensembl!\n";
  
  if($error =~ /Can't connect to MySQL server on /) {
    print "\tPlease check if your connection with mysql client works fine. \n";
  } elsif ($error =~ /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 $port\n";
  } elsif ($error =~ /DBI/) {
    print "\tCannot find the DBI perl module. Please install this using your package management system, cpan or cpanm. Please consult http://www.ensembl.org/info/docs/api/api_installation.html\n";
  }
  if($error =~ /mysql/) {
    print "\tCannot find the DBD::mysql perl module. Please install this using your package management system, cpan or cpanm. Also install the mysql libs. Please consult http://www.ensembl.org/info/docs/api/api_installation.html\n";
  }
  if($error =~ /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($error =~ /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($error =~ /internal name/) {
    print "\tSpecies was not found. You may have accidentally download the HEAD API version (found API release $db_version & public FTP release is $ftp_version). Please consult http://www.ensembl.org/info/docs/api/api_installation.html\n";
  }
  if($error =~ /Species not defined/) {
    print "\tSpecies was not found. You may have accidentally download the HEAD API version (told to load release $db_version, API version is $api_version & public FTP release is $ftp_version). Please consult http://www.ensembl.org/info/docs/api/api_installation.html\n";
  }
  if($error =~ /Missing the checkout/) {
    print "\tYour core installation was good but supplementary modules cannot be found. If you wish to access these other Ensembl resources add the libraries to your PERL5LIB:\n";
    print $error;
    #bail early
    exit 0;
  }
  print '='x80, "\n";
  print "If the problem persists please send the following error message to helpdesk\@ensembl.org\n";
  print $error;
  print '='x80, "\n";
  exit 1;
}
 
 
=head2 usage
 
  Arg []         : None
  Returntype     : None
  Example        :
  Description    : Print script usage string
  Exceptions     : None
  Caller         : General
 
=cut
 
sub usage {
  my $prog = `basename $0`; chomp($prog);
    
  print "Usage: $prog [OPTIONS]\n\n";
  print "Options:\n";
  print "  -ue                    Ping Ensembl US mirror\n";
  print "  -eg                    Ping Ensembl Genomes (can't be used together with \"ue\")\n";
  print "  -species <species>     Use species <species> (use double quotes if species name contains spaces)\n";
  print "  -db_version <version>  Use the specified version of Ensembl not the API version\n";
  print "  -grch37                Use human assembly GRCh37 rather than the default GRCh38 version\n";
  print "  -verbose               Ping output is more verbose. Not recommended for Ensembl genomes\n";
  print "  -help                  Print this message\n";
  print "\n\n";
 
  exit 1;
}