script to populate the seq_region_mapping and mapping_set tables to allow user upload data

misc-scripts/update_mapping_set.pl

+#!/software/bin/perl
+
+=head1 NAME
+
+update_mapping_set.pl - script to update 2 tables: mapping_set and seq_region_id mapping.
+                        These tables are supposed to store different mapping of seq_region_id
+                        between releases
+
+=head1 SYNOPSIS
+
+update_mapping_set.pl [arguments]
+
+Required arguments:
+
+    --user=user                        username for the database
+
+    --pass=pass                        password for the database
+
+    --release=num_release              release we want to run the updating
+
+Optional arguments:
+
+    --host=host                        server where the core databases are stored (default: ens-staging)
+
+    --dbname=dbname                    if you want a single database to update the mapping_set information
+                                       (all databases by default)
+
+    --port=port                        port (default=3306)
+
+    --help                             print help (this message)
+
+=head1 DESCRIPTION
+
+This script will update the mapping_set table with the current schema_build information and indicate if the seq_region
+table has changed from previous release. If it has, the table seq_region_mapping will contain the relation between old
+(external_seq_region_id) and the current (internal_seq_region_id). If it hasn't, a single entry in the mapping_set table
+with the same mapping_set_id as the previous release will be stored
+
+=head1 EXAMPLES
+
+Update mapping_set information for all databases in ens-staging in release 50(usual use case in release process)
+
+   $ ./update_mapping_set.pl --user ensadmin --pass password --release 50
+
+Update mapping_set information only for pig database in ens-genomics1
+
+   $ ./update_mapping_set.pl --host ens-genomics1 --user ensadmin --pass password --dbname my_pig_db --release 52
+
+=head1 LICENCE
+
+This code is distributed under an Apache style licence. Please see
+http://www.ensembl.org/info/about/code_licence.html for details.
+
+=head1 AUTHOR
+
+Daniel Rios <dani@ebi.ac.uk>, Ensembl core API team
+
+=head1 CONTACT
+
+=cut
+
+use strict;
+use warnings;
+
+use Getopt::Long;
+use Pod::Usage;
+
+use DBI qw(:sql_types);
+
+use Bio::EnsEMBL::Utils::Exception qw(throw);
+
+use constant INITIAL_MAPPING => 1;
+use constant SAME_MAPPING => 2;
+use constant NEW_MAPPING => 3;
+
+## Command line options
+
+my $host = 'ens-staging';
+my $dbname = undef;
+my $user = undef;
+my $pass = undef;
+my $port = 3306;
+my $help = undef;
+my $release = undef;
+
+GetOptions('host=s'    => \$host,
+	   'dbname=s'  => \$dbname,
+	   'user=s'    => \$user,
+	   'pass=s'    => \$pass,
+	   'port=s'    => \$port,
+           'release=i' => \$release,
+	   'help'    => \$help
+	   );
+
+pod2usage(1) if($help);
+throw("--user argument required") if (!defined($user));
+throw("--pass argument required") if (!defined($pass));
+throw("--release argument required") if(!defined($release));
+
+my $database = 'information_schema';
+my $dbh = DBI->connect("DBI:mysql:database=$database;host=$host;port=$port",$user,$pass);
+my $status;
+my $database_name;
+
+#since there is no database defined, will run it agains all core databases
+my $pattern;
+if (!defined ($dbname)){
+    $pattern = '_core_\$release_';
+}
+else{
+$pattern = $dbname;
+}
+#fetch all databases matching the pattern
+my $sth = $dbh->prepare("SHOW DATABASES WHERE `database` REGEXP \'$pattern\'");
+$sth->execute();
+my $dbs = $sth->fetchall_arrayref();
+my $schema_build;
+foreach my $db_name (@{$dbs}){
+    print STDERR "Going to update mapping for $db_name->[0]....\n";
+     my $mapping_set_id;
+     my $current_seq_region = (); # hash containing the relation seq_region_name->seq_region_id for the current database
+     my $old_seq_region = (); #hash containing the previous database relation seq_region_name->seq_region_id
+     my $sth_seq_mapping = $dbh->prepare("INSERT INTO $db_name->[0].seq_region_mapping VALUES(?,?,?)");
+     my $sth_mapping_set = $dbh->prepare("INSERT INTO $db_name->[0].mapping_set VALUES(?,?)");
+     $status = &mapping_status($dbh,$db_name->[0],\$mapping_set_id,$release);
+     $schema_build = get_schema_and_build($db_name->[0]);
+     #add mapping_set information
+     $sth_mapping_set->execute($mapping_set_id,$schema_build);
+     if ($status == INITIAL_MAPPING){
+     #first time run the script, create new entry in mapping_set and copy seq_region entries in seq_region_mapping
+        $current_seq_region =  &read_seq_region($dbh,$db_name->[0]);
+        #copy the seq_region_id in the seq_region_mapping
+        foreach my $seq_region_name (keys %{$current_seq_region}){
+            #when copying there won't be any ambiguity with coord_systems
+            foreach my $region_id (values %{$current_seq_region->{$seq_region_name}}){
+                $sth_seq_mapping->execute($region_id,$region_id,$mapping_set_id);
+            }
+        }       
+     }
+     elsif ($status == SAME_MAPPING){
+     #seq_region_mapping has not change, nothing to do for the moment....
+
+     }
+     elsif ($status == NEW_MAPPING){
+     #there has been a seq_region change between releases, add a new mapping_set and the relation old_seq_region_id->new_seq_region_id
+	my $previous_dbname = &get_previous_dbname($dbh,$db_name->[0],$release);
+        $current_seq_region =  &read_seq_region($dbh,$db_name->[0]);
+        $old_seq_region = &read_seq_region($dbh,$previous_dbname);
+        #update the seq_region_mapping table with the old->new seq_region_id relation
+        foreach my $seq_region_name (keys %{$old_seq_region}){
+            next if (!defined $current_seq_region->{$seq_region_name}); #the seq_region might have disappeared
+            foreach my $coord_system_id (keys %{$old_seq_region->{$seq_region_name}}){
+		next if (!defined $current_seq_region->{$seq_region_name}->{$coord_system_id}); #the coord_system might have been removed in current database
+                $sth_seq_mapping->execute($old_seq_region->{$seq_region_name}->{$coord_system_id},$current_seq_region->{$seq_region_name}->{$coord_system_id},$mapping_set_id);
+            }
+        }       
+     }
+     else{
+         throw("Mapping status not recognized by script: $status \n\n");
+     } 
+}
+
+#will for a given database, will return the seq_region_name->seq_region_id relation
+sub read_seq_region{
+    my $dbh = shift;
+    my $dbname = shift;
+    my %seq_region_hash;
+    my $seq_region_id;
+    my $seq_region_name;
+    my $coord_system_id;
+    my $sth = $dbh->prepare("SELECT seq_region_id, name, coord_system_id FROM $dbname.seq_region");
+    $sth->execute();
+    $sth->bind_col(1,\$seq_region_id);
+    $sth->bind_col(2,\$seq_region_name);
+    $sth->bind_col(3,\$coord_system_id);
+    while ($sth->fetch){
+	#there might be more than one assembly in the core database, thus we need the coord_system_id to remove ambiguity
+	$seq_region_hash{$seq_region_name}{$coord_system_id} = $seq_region_id;
+    }
+    return \%seq_region_hash;
+}
+
+#method to check the status of the current core database: INITIAL_MAPPING, SAME_MAPPING and NEW_MAPPING are the possible states
+sub mapping_status{
+    my $dbh = shift;
+    my $dbname = shift;
+    my $mapping_set_id_ref = shift;
+    my $release = shift;
+
+    my $sth_max_mapping = $dbh->prepare("select max(mapping_set_id) from $dbname.mapping_set");
+    $sth_max_mapping->execute();
+    ( $$mapping_set_id_ref ) = $sth_max_mapping->fetchrow_array();
+    if (! $$mapping_set_id_ref){
+	#the table is empty, first mapping
+	$$mapping_set_id_ref = 1;
+	return INITIAL_MAPPING;
+    }
+    else{
+	#there is information, find out if it is the same mapping as previous release
+	my $previous_dbname = &get_previous_dbname($dbh,$dbname,$release);
+	throw("No previous database present for $dbname\n") if (!defined $previous_dbname);
+	my $cur_seq_region_size = &get_seq_region_size($dbh,$dbname);
+	my $previous_seq_region_size = &get_seq_region_size($dbh,$previous_dbname);
+	if ($cur_seq_region_size == $previous_seq_region_size){
+	    #if both tables have same size, SAME_MAPPING
+	    return SAME_MAPPING;
+	}
+	else{
+	    #if tables have different size, NEW_MAPPING
+	    $$mapping_set_id_ref++;
+	    return NEW_MAPPING;
+	}	
+    }
+}
+
+
+#for a given database, returns the size of the seq_region_table
+sub get_seq_region_size{
+    my $dbh = shift;
+    my $dbname = shift;
+    my $sth_status = $dbh->prepare("show table status from $dbname like 'seq_region'");
+    $sth_status->execute();
+    my @table_status = $sth_status->fetchrow_array();
+    return $table_status[6]; #return the size of the table
+}
+
+#will return the max mapping_set_id being used in the mapping_set table
+sub get_max_mapping_set_id{
+    my $dbh = shift;
+    my $dbname = shift;
+
+    my $sth_mapping = $dbh->prepare("select max(mapping_set_id) from mapping_set");
+    $sth_mapping->execute();
+    my ($max_mapping_set_id) = $sth_mapping->fetchrow_array();
+    return $max_mapping_set_id;
+}
+
+#this method will return the name of the previous database to release for same species (assuming is present)
+sub get_previous_dbname{
+    my $dbh = shift;
+    my $dbname = shift;
+    my $release = shift;
+
+    $dbname =~ /(^[a-z]+_[a-z]+_core_)/;
+
+    my $previous_release_name = $1 . (--$release);
+    my $previous_sth = $dbh->prepare("show databases like \'%$previous_release_name%\'");
+    $previous_sth->execute();
+    my ($previous_dbname) = $previous_sth->fetchrow_array();
+    return $previous_dbname;
+    
+}
+
+#for a standard ensembl database name, returns the release number and assembly
+sub get_schema_and_build{
+  my ($dbname) = @_;
+  my @dbname = split/_/, $dbname;
+  return join "_",$dbname[($#dbname -1)], $dbname[($#dbname)];
+}