Update scripts to use new LibDirs module

EnsemblGenomes · Mar 6, 2014 · 2058a7d · 2058a7d
1 parent 500e66f
commit 2058a7d
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Showing 7 changed files with 12 additions and 61 deletions.
diff --git a/utils/check_atlas_species.pl b/utils/check_atlas_species.pl
@@ -19,13 +19,7 @@
 use Data::Dumper;
 use DBI;
 use Net::FTP;
-
-BEGIN {
-  unshift @INC, "$Bin/../../../conf";
-  unshift @INC, "$Bin/../../../";
-  require SiteDefs;
-  unshift @INC, $_ for @SiteDefs::ENSEMBL_LIB_DIRS;
-}
+use LibDirs;
 
 use LoadPlugins;
 use EnsEMBL::Web::SpeciesDefs;
@@ -53,7 +47,7 @@ BEGIN
 (my $plugin = lc($SiteDefs::ENSEMBL_SITETYPE)) =~ s/^ensembl\s*//;
 
 # crude check to see which ini files already have pride configured
-my $grep = `grep "S4_EXPRESSION\\s*=\\s*1" $Bin/../../$plugin/conf/ini-files/*`;
+my $grep = `grep "S4_EXPRESSION\\s*=\\s*1" $Bin/../../eg-web-$plugin/conf/ini-files/*`;
 
 print "\nIt looks like Expression Atlas is already configured in these ini files:\n";
 print "$grep\n";

diff --git a/utils/check_pride_species.pl b/utils/check_pride_species.pl
@@ -25,20 +25,14 @@
 
 my $REGISTRY_URL  = 'http://www.ebi.ac.uk/pride/biomart/martservice?type=registry';
 
-BEGIN {
-  unshift @INC, "$Bin/../../../conf";
-  unshift @INC, "$Bin/../../../";
-  require SiteDefs;
-  unshift @INC, $_ for @SiteDefs::ENSEMBL_LIB_DIRS;
-}
-
+use LibDirs;
 use LoadPlugins;
 use EnsEMBL::Web::SpeciesDefs;
 my $species_defs = EnsEMBL::Web::SpeciesDefs->new;
 
 # crude check to see which ini files in this plugin already have pride configured
 (my $plugin = lc($SiteDefs::ENSEMBL_SITETYPE)) =~ s/^ensembl\s*//;
-my $grep = `grep "DS_1436\\s*=" $Bin/../../$plugin/conf/ini-files/*`;
+my $grep = `grep "DS_1436\\s*=" $Bin/../../eg-web-$plugin/conf/ini-files/*`;
 
 my %site_tax  = map {$species_defs->get_config($_, 'TAXONOMY_ID') => $_} $species_defs->valid_species;
 

diff --git a/utils/compress_web_assets.pl b/utils/compress_web_assets.pl
@@ -28,7 +28,7 @@
   "v" => \$verbose,
 ) || die "Invalid options\n";
 
-die "Please specify the plugin dir (example: --plugin_dir=eg-plugins/fungi)\n" if !$plugin_dir;
+die "Please specify the plugin dir (example: --plugin_dir=eg-web-fungi)\n" if !$plugin_dir;
 die "Plugin dir does not exist\n" if !-e $plugin_dir;
 $plugin_dir =~ s/\/$//; # strip trailing slash
 

diff --git a/utils/make_docsearch_index.pl b/utils/make_docsearch_index.pl
@@ -20,14 +20,7 @@
 use File::Find;
 use Lucy::Simple;
 use File::Path qw(make_path remove_tree);
-#use File::Copy qw(move);
-
-BEGIN {
-  unshift @INC, "$Bin/../../../conf";
-  unshift @INC, "$Bin/../../../";
-  require SiteDefs;
-  unshift @INC, $_ for @SiteDefs::ENSEMBL_LIB_DIRS;
-}
+use LibDirs;
 
 my $index_dir = $SiteDefs::DOCSEARCH_INDEX_DIR || die '$SiteDefs::DOCSEARCH_INDEX_DIR is not set';
 

diff --git a/utils/meta_sample_healthch.pl b/utils/meta_sample_healthch.pl
@@ -31,19 +31,7 @@ package example_links_healthcheck;
 use Config::Tiny;
 use File::Basename;
 use Time::Local;
-
-# Load libraries needed for reading config -----------------------------------                                                                                                                                    
-use vars qw( $SERVERROOT );
-
-BEGIN {
-    my $dirname = dirname("$Bin");
-    $SERVERROOT = "$dirname/../../";
-    unshift @INC, "$SERVERROOT/conf";
-    unshift @INC, "$SERVERROOT";
-    eval { require SiteDefs };
-    if ($@) { die "Can't use SiteDefs.pm - $@\n"; }
-    map { unshift @INC, $_ } @SiteDefs::ENSEMBL_LIB_DIRS;
-}
+use LibDirs;
 
 use Bio::EnsEMBL::DBLoader;
 use EnsEMBL::Web::DBSQL::DBConnection;

diff --git a/utils/search_dump_extra.pl b/utils/search_dump_extra.pl
@@ -15,19 +15,12 @@
 
 use strict;
 use warnings;
-use FindBin qw($Bin);
 use Getopt::Long;
 use XML::Generator;
 use Data::Dumper;
 use HTML::Entities;
-
-BEGIN {
-  unshift @INC, "$Bin/../../conf";
-  unshift @INC, "$Bin/../../";
-  require SiteDefs;
-  unshift @INC, $_ for @SiteDefs::ENSEMBL_LIB_DIRS;
-  require EnsEMBL::Web::Hub; 
-}
+use LibDirs;
+use EnsEMBL::Web::Hub; 
 
 my $dir  = '.';
 my $index_list;

diff --git a/utils/update_website_db.pl b/utils/update_website_db.pl
@@ -19,20 +19,9 @@
 use File::Basename qw(dirname);
 use FindBin qw($Bin);
 use Data::Dumper;
-
-# Comment; this script will create a copy of the help link for every ontology graph in EG
-
-BEGIN {
-  my $serverroot = dirname($Bin) . "/../../";
-  unshift @INC, "$serverroot/conf", $serverroot;
-
-  require SiteDefs;
-
-  unshift @INC, $_ for @SiteDefs::ENSEMBL_LIB_DIRS;
-
-  require EnsEMBL::Web::DBSQL::WebsiteAdaptor;
-  require EnsEMBL::Web::Hub;  
-}
+use LibDirs;
+use EnsEMBL::Web::DBSQL::WebsiteAdaptor;
+use EnsEMBL::Web::Hub;  
 
 my $hub = new EnsEMBL::Web::Hub;
 my $dbh = new EnsEMBL::Web::DBSQL::WebsiteAdaptor($hub)->db;