From 2058a7d762794494c8041ac1e04840d2ded0f139 Mon Sep 17 00:00:00 2001 From: Nick Langridge Date: Thu, 6 Mar 2014 14:23:07 +0000 Subject: [PATCH] Update scripts to use new LibDirs module --- utils/check_atlas_species.pl | 10 ++-------- utils/check_pride_species.pl | 10 ++-------- utils/compress_web_assets.pl | 2 +- utils/make_docsearch_index.pl | 9 +-------- utils/meta_sample_healthch.pl | 14 +------------- utils/search_dump_extra.pl | 11 ++--------- utils/update_website_db.pl | 17 +++-------------- 7 files changed, 12 insertions(+), 61 deletions(-) mode change 100644 => 100755 utils/meta_sample_healthch.pl mode change 100644 => 100755 utils/update_website_db.pl diff --git a/utils/check_atlas_species.pl b/utils/check_atlas_species.pl index f95beb72..aefe5a89 100755 --- 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 index 90180774..dfea24b4 100755 --- 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') => $_} $species_defs->valid_species; diff --git a/utils/compress_web_assets.pl b/utils/compress_web_assets.pl index affe33cb..7059b986 100755 --- a/utils/compress_web_assets.pl +++ b/utils/compress_web_assets.pl @@ -28,7 +28,7 @@ "v" => \$verbose, ) || die "Invalid options\n"; -die "Please specify the plugin dir (example: --plugin_dir=eg-plugins/fungi)\n" if !$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 index e13e8c87..76243e92 100755 --- 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 old mode 100644 new mode 100755 index db22d4a2..cb994617 --- 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, $_ } @SiteDefs::ENSEMBL_LIB_DIRS; -} +use LibDirs; use Bio::EnsEMBL::DBLoader; use EnsEMBL::Web::DBSQL::DBConnection; diff --git a/utils/search_dump_extra.pl b/utils/search_dump_extra.pl index 7d167254..00037674 100755 --- a/utils/search_dump_extra.pl +++ b/utils/search_dump_extra.pl @@ -15,19 +15,12 @@ use strict; use warnings; -use FindBin qw($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 $index_list; diff --git a/utils/update_website_db.pl b/utils/update_website_db.pl old mode 100644 new mode 100755 index ff21e4d4..80ca4d87 --- a/utils/update_website_db.pl +++ b/utils/update_website_db.pl @@ -19,20 +19,9 @@ use File::Basename qw(dirname); use FindBin qw($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;