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Commit d25ee587 authored by Nick Langridge's avatar Nick Langridge
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added site_type param and removed dependency on load_plugins

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misc-scripts/ebi_search_dump/ebi_search_dump_generic.pl
+ 37
− 93
View file @ d25ee587
......@@ -18,10 +18,18 @@ use Getopt::Long;
use IO::Zlib;
use Data::Dumper;
BEGIN{
unshift @INC, "$Bin/../../../conf";
unshift @INC, "$Bin/../../..";
eval{ require utils::Tool };
if ($@){ warn "Can't use utils::Tool (required for ensemblgenomes)\n"; }
}
my (
$host, $user, $pass, $port, $species, $ind,
$release, $max_entries, $nogzip, $parallel, $dir, $inifile,
$skip_compara
$site_type
);
my %rHash = map { $_ } @ARGV;
......@@ -38,109 +46,44 @@ GetOptions(
"index=s", \$ind, "nogzip!", \$nogzip,
"max_entries=i", \$max_entries, "parallel", \$parallel,
"dir=s", \$dir, "help", \&usage,
"inifile=s", \$inifile
"inifile=s", \$inifile, "site_type=s", \$site_type,
);
#$site_type = $site_type ? lc($site_type) : 'ensembl';
$ind ||= 'ALL';
$dir ||= ".";
$release ||= 'LATEST';
$port ||= 3306;
usage() and exit unless ( $host && $port && $user );
BEGIN{
unshift @INC, "$Bin/../../../conf";
unshift @INC, "$Bin/../../..";
eval{ require SiteDefs };
if ($@){ die "Can't use SiteDefs.pm - $@\n"; }
map{ unshift @INC, $_ } @SiteDefs::ENSEMBL_LIB_DIRS;
}
use utils::Tool;
use EnsEMBL::Web::SpeciesDefs;
usage() and exit unless ( $host && $port && $user && $site_type);
my $SPECIES_DEFS = EnsEMBL::Web::SpeciesDefs->new();
print "Site type: $site_type\n";
#---- load plugins ---
my ($i, @plugins, @plugin_dirs);
my @lib_dirs = @{$SPECIES_DEFS->ENSEMBL_LIB_DIRS};
for (reverse @{$SPECIES_DEFS->ENSEMBL_PLUGINS||[]}) {
if (++$i % 2) {
push @plugin_dirs, "$_/modules" if -e "$_/modules";
} else {
unshift @plugins, $_;
}
}
unshift @INC, reverse @plugin_dirs; # Add plugin directories to INC so that EnsEMBL::PLUGIN modules can be used
find(\&load_plugins, @plugin_dirs);
# Loop through the plugin directories, requiring .pm files
# The effect of this is that any plugin with an EnsEMBL::Web:: namespace is used to extend that module in the core directory
# Functions that exist in both the core and the plugin will be overwritten, functions that exist only in the plugin will be added
sub load_plugins {
if (/\.pm$/ && !/MetaDataBlast\.pm/) {
my $dir = $File::Find::topdir;
my $file = $File::Find::name;
(my $relative_file = $file) =~ s/^$dir\///;
(my $package = $relative_file) =~ s/\//::/g;
$package =~ s/\.pm$//g;
# Regex matches all namespaces which are EnsEMBL:: but not EnsEMBL::Web
# Therefore the if statement is true for EnsEMBL::Web:: and Bio:: packages, which are the ones we need to overload
if ($package !~ /^EnsEMBL::(?!Web)/) {
no strict 'refs';
# Require the base module first, unless it already exists
if (!exists ${"$package\::"}{'ISA'}) {
foreach (@lib_dirs) {
eval "require '$_/$relative_file'";
warn $@ if $@ && $@ !~ /^Can't locate/;
last if exists ${"$package\::"}{'ISA'};
}
}
eval "require '$file'"; # Require the plugin module
warn $@ if $@;
}
}
}
#--- finished loading plugins ---
# what type of site is this?
my $sitetype = $SiteDefs::ENSEMBL_SITETYPE;
print "\nSite type: $sitetype\n";
# determine which species we are indexing
my @SPECIES = split ',', $species;
if( @SPECIES ) {
@SPECIES = @{ utils::Tool::check_species(\@SPECIES) };
} else {
@SPECIES = @{ utils::Tool::all_species() };
}
print "Species to process: \n " . join("\n ", @SPECIES) . "\n";
my $entry_count;
my $global_start_time = time;
my $total = 0;
my $FAMILY_DUMPED;
my $fh;
## HACK 1 - if the INDEX is set to all grab all dumper methods...
my @indexes = split ',', $ind;
@indexes = map { /dump(\w+)/ ? $1 : () } keys %ebi_search_dump::
if $ind eq 'ALL';
#warn Dumper \@indexes;
my $dbHash = get_databases();
#warn Dumper $dbHash;
print "*** No databases found ***\n" unless %{$dbHash};
my @species_list = split ',', $species;
if ($site_type eq 'ensemblgenomes') {
# restrict species to only those defined in the current eg site
@species_list = @species_list ? @{ utils::Tool::check_species(\@species_list) } : @{ utils::Tool::all_species() };
} else {
@species_list = @species_list ? @species_list : keys %{$dbHash};
}
print "Species to process: \n " . join("\n ", @species_list) . "\n";
print "*** No matching databases found ***\n" unless %{$dbHash};
my $entry_count;
my $global_start_time = time;
my $total = 0;
my $FAMILY_DUMPED;
my $fh;
foreach my $species ( @SPECIES ) {
foreach my $species ( @species_list ) {
my $conf = $dbHash->{lc($species)};
foreach my $index (@indexes) {
......@@ -200,13 +143,14 @@ sub usage {
print <<EOF; exit(0);
Usage: perl $0 <options>
-host Database host to connect to. Defaults to ens-staging.
-port Database port to connect to. Defaults to 3306.
-site_type REQUIRED. ensembl or ensemblgenomes.
-host REQUIRED. Database host to connect to.
-port REQUIRED. Database port to connect to.
-user Database username. Defaults to ensro.
-species Species name. Defaults to ALL.
-index Index to create. Defaults to ALL.
-release Release of the database to dump. Defaults to 'latest'.
-user Database username. Defaults to ensro.
-pass Password for user.
-dir Directory to write output to. Defaults to /lustre/scratch1/ensembl/gp1/xml.
-nogzip Don't compress output as it's written.
......@@ -281,13 +225,13 @@ sub footer {
sub header {
my ( $dbname, $dbspecies, $dbtype ) = @_;
my $sitetype_display_name = $sitetype =~/^ensembl[a-z]+$/i ? 'Ensembl Genomes' : $sitetype;
my $site_name = $site_type eq 'ensembl' ? 'Ensembl' : 'Ensembl Genomes';
p("<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>");
p("<!DOCTYPE database [ <!ENTITY auml \"&#228;\">]>");
p("<database>");
p("<name>$dbname</name>");
p("<description>$sitetype_display_name $dbspecies $dbtype database</description>");
p("<description>$site_name $dbspecies $dbtype database</description>");
p("<release>$release</release>");
p("");
p("<entries>");
......@@ -341,7 +285,7 @@ sub dumpGene {
my $want_species_orthologs;
my $ortholog_lookup;
if ($sitetype =~ /^Ensembl$/i) {
if ($site_type =~ /^Ensembl$/i) {
my $orth_target_species;
( $orth_target_species = lcfirst($dbspecies) ) =~ s/\s/_/;
if ( $want_species_orthologs =
......
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