Merge branch 'master' of github.com:EnsemblGenomes/eg-web-common

conf/ini-files/DEFAULTS.ini

@@ -1199,6 +1199,12 @@ enterococcus_faecalis_v583_asm778v1 = Enterococcus faecalis V583 (ASM778v1)
 paramecium_tetraurelia = Paramecium tetraurelia
 guillardia_theta =  Guillardia theta
 giardia_lamblia = Giardia lamblia
+pythium_aphanidermatum = Pythium aphanidermatum
+pythium_arrhenomanes = Pythium arrhenomanes
+pythium_irregulare = Pythium irregulare
+pythium_iwayamai = Pythium iwayamai
+pythium_vexans = Pythium vexans
+bigelowiella_natans = Bigelowiella natans
 plasmodium_berghei = Plasmodium berghei
 plasmodium_chabaudi = Plasmodium chabaudi
 plasmodium_falciparum = Plasmodium falciparum
@@ -1561,6 +1567,11 @@ yarrowia_lipolytica = fungi
 paramecium_tetraurelia = protists
 guillardia_theta = protists
 giardia_lamblia = protists
+pythium_aphanidermatum = protists
+pythium_arrhenomanes = protists
+pythium_irregulare = protists
+pythium_iwayamai = protists
+pythium_vexans = protists
 d_discoideum = protists
 dictyostelium_discoideum = protists
 p_tricornutum = protists
@@ -1590,6 +1601,7 @@ tetrahymena_thermophila = protists
 hyaloperonospora_arabidopsidis = protists
 emiliania_huxleyi = protists
 tribolium_castaneum = protists
+bigelowiella_natans = protists
 
 ;Bacteria (only pan compara)
 methanothermobacter_thermautotrophicus_str_delta_h = bacteria

utils/add_species.pl

@@ -0,0 +1,170 @@
+use DBI;
+use strict;
+use warnings;
+use Config::Tiny;
+
+############################################################################
+# Script can be used for fungi and protists.
+# To use for bacteria sample bacteria species needs to be added
+# to %sample_species hash.
+# Before running the script, check if $dir is correct.
+#
+# How to run:
+# ./add_species.pl Trichoderma_reesei fungi eg-hx-staging-2 
+###########################################################################
+
+
+die "You should provide arguments: species_name and site. Ex: ./add_species.pl Trichoderma_reesei fungi eg-hx-staging-2"
+        if (!$ARGV[0] || !$ARGV[1] || !$ARGV[2]);
+
+my ($sp, $site, $server) = @ARGV;
+
+# preconfigure this
+my $dir = "/nfs/public/rw/ensembl/ensembl-genomes/release-22/$site";
+my $dir = "/homes/jk/ensembl/master";
+
+# sample species used to copy over a config file and to add new species
+# in the config files after these.
+# bacteria and others should be added here.
+my %sample_species = (
+        fungi    => 'Aspergillus_fumigatus',
+        protists => 'Giardia_lamblia',
+        metazoa  => 'Daphnia_pulex',
+);
+
+#ensembl-webcode/eg-web-ensembl-configs/
+my $file=  -e $dir.'/ensembl-webcode/eg-web-ensembl-configs/'.$server.'/conf/ini-files/MULTI.ini' ?
+        $dir.'/ensembl-webcode/eg-web-ensembl-configs/'.$server.'/conf/ini-files/MULTI.ini' :
+        $dir.'/ebi-plugins/'.$server.'/conf/ini-files/MULTI.ini';
+
+# cheking if database for a new species exists
+
+my $conf = Config::Tiny->read($file);
+use Data::Dumper;
+#print "conf=".Dumper($conf);
+
+my $dbh = DBI->connect('dbi:mysql:information_schema;host='
+        .$conf->{DATABASE_WEBSITE}->{HOST}.';port='.$conf->{DATABASE_WEBSITE}->{PORT},
+        $conf->{DATABASE_WEBSITE}->{USER}, $conf->{DATABASE_WEBSITE}->{PASS}, { 'RaiseError' => 1 } )
+        or die "Can't connect to db host".$conf->{DATABASE_WEBSITE}->{HOST};
+
+my $databases = $dbh->selectcol_arrayref('show databases');
+
+my $core_db = lc($sp);
+my @db = grep { $_ =~ /$core_db/ } @$databases;
+
+if ($db[0]) {
+        print "Database $db[0] exists","\n";
+}
+else {
+        print "Database $db[0] doesn't exist","\n";
+}
+
+print "Checking if species.classification matches species.production_name\n";
+
+$dbh->do("use $db[0]") or die $dbh->errstr;
+
+$sp =~ m/(\w+)\_/;
+my $short_name = substr($1,1);
+
+my $query = qq{ select meta_key, meta_value from meta where
+        (meta_key='species.classification' or meta_key='species.production_name')
+        && meta_value like "%$short_name%"
+};
+
+my $array_ref = $dbh->selectall_arrayref($query);
+map { print "$_->[0] => $_->[1]\n"; } @$array_ref;
+
+$dbh->disconnect;
+
+# copying a sample config file
+my $new_species_config_name = "$dir/eg-web-$site/conf/ini-files/$sp.ini";
+print "New species config name=".$new_species_config_name."\n";
+
+if (-e $new_species_config_name){
+        print "Config file for the species already exists: $new_species_config_name. Exiting. \n";
+        exit;
+}
+
+# create a config file for species based on some example
+my $sample_config = "$dir/eg-web-$site/conf/ini-files/".$sample_species{$site}.".ini";
+print "Sample config file=".$sample_config;
+`cp $sample_config $new_species_config_name`;
+
+# check if ini file for new species has been created
+unless (-e $new_species_config_name){
+        print "Species ini file $new_species_config_name hasn't been created. Exiting.\n";
+        exit;
+}
+
+# creating a config file for a new species
+$conf = Config::Tiny->read($new_species_config_name);
+$db[0] =~ /\_(\d+)$/;
+warn "\nrelease verion=".$1;
+my $species_release_version =  $1;
+
+$conf->{general}->{SPECIES_RELEASE_VERSION} = $species_release_version;     # Change a value
+$conf->{databases}->{DATABASE_USERDATA} = $core_db."_userdata";
+
+delete $conf->{general}->{ONTOLOGY_SUBSETS};                        # Delete a value or section
+
+# Saving config
+$conf->write($new_species_config_name);
+
+my $file2 =  -e $dir.'/ensembl-webcode/eg-web-ensembl-configs/eg-hx/conf/ini-files/DEFAULTS.ini' ?
+        $dir.'/ensembl-webcode/eg-web-ensembl-configs/eg-hx/conf/ini-files/DEFAULTS.ini' :
+        $dir.'/ebi-plugins/eg-hx/conf/ini-files/DEFAULTS.ini';
+
+$conf = Config::Tiny->read($file2);
+
+unless ($conf) {
+        print "Can't get DB connect details from $file2\n";
+        exit;
+}
+
+my $db_host = $conf->{DATABASE_USERDATA}->{HOST};
+my $db_port = $conf->{DATABASE_USERDATA}->{PORT};
+my $db_user = $conf->{DATABASE_USERDATA}->{USER};
+my $db_pass = $conf->{DATABASE_USERDATA}->{PASS};
+my $db_name = lc($sp)."_userdata";
+
+warn "Userdata=".Dumper($conf->{DATABASE_USERDATA});
+`mysqldump --single_transaction -d -h $db_host -P $db_port -u ensro zea_mays_userdata>/tmp/userdata.sql`;
+
+# creating userdata database for a new species
+$dbh = DBI->connect('dbi:mysql:information_schema;host='
+        .$db_host.';port='.$db_port, $db_user, $db_pass, { 'RaiseError' => 1 } );
+warn "CREATE DATABASE IF NOT EXIST $db_name";
+$dbh->do("CREATE DATABASE IF NOT EXISTS $db_name");
+
+$dbh->do("use $db_name") or die $dbh->errstr;
+`mysql -h $db_host -P $db_port -u $db_user --password=$db_pass $db_name < /tmp/userdata.sql`; # add an error handler here
+
+# check if tables exist
+my $tables_exists = $dbh->selectcol_arrayref('show tables');
+
+$dbh->disconnect;
+
+unless (@$tables_exists) {
+        print "Tables structure wasn't loaded into $db_name. Exiting\n";
+}
+
+`rm /tmp/userdata.sql`;
+
+# add species alias and restart apache.
+my $line_to_add = '    $SiteDefs::__species_aliases{'."'".$sp."'} = [qw($sp)];";
+
+`sed -i '/$sample_species{$site}/a $line_to_add' $dir/eg-web-$site/conf/SiteDefs.pm`;
+
+my $sample_sp_lowcase = lc($sample_species{$site});
+`sed -i '/$sample_sp_lowcase = $site/a $core_db = $site' $dir/eg-web-common/conf/ini-files/DEFAULTS.ini`;
+
+my $sp_name = $sp;
+$sp_name =~ s/_/ /g;
+my $sample_sp_nounderscore = $sample_species{$site};
+$sample_sp_nounderscore =~ s/_/ /g;
+
+`sed -i '/$sample_sp_lowcase = $sample_sp_nounderscore/a $core_db = $sp_name' $dir/eg-web-common/conf/ini-files/DEFAULTS.ini`;
+#`ctrl_scripts/restart_server -r`;
+print "Done. Now restart apache and check the species page.\n";
+