Commit 78b1069f authored by Ian Longden's avatar Ian Longden
Browse files

many changes but the most important is to only add seq_region mapping if the...

many changes but the most important is to only add seq_region mapping if the seq_region_ids are different
parent bb674e0b
......@@ -24,12 +24,20 @@ Optional arguments:
--host=host server where the core databases are stored
(default: ens-staging)
--oldhost = oldhost server where the old release databases are stored
--dbname=dbname if you want a single database to update
the mapping_set information (default: all
databases)
--port=port port (default: 3306)
--oldport=port old database server port (default: 5306)
--olduser=user old database server username
--oldpass=pass password for old database server
--help print help (this message)
=head1 DESCRIPTION
......@@ -51,7 +59,7 @@ Update mapping_set information for all databases in ens-staging in
release NN (the usual use case in release process):
$ ./update_mapping_set.pl --user ensadmin \
--pass password --release NN
--pass password --release NN --old_host ensembldb-ensembl.org
Update mapping_set information only for pig database in ens-genomics1:
......@@ -88,10 +96,14 @@ use constant NEW_MAPPING => 3;
## Command line options
my $host = 'ens-staging';
my $oldhost = 'ensembldb.ensembl.org';
my $dbname = undef;
my $user = undef;
my $pass = undef;
my $port = 3306;
my $oldport = 5306;
my $olduser = "anonymous";
my $oldpass = undef;
my $help = undef;
my $release = undef;
......@@ -101,7 +113,11 @@ GetOptions('host=s' => \$host,
'pass=s' => \$pass,
'port=s' => \$port,
'release=i' => \$release,
'help' => \$help
'oldhost=s' => \$oldhost,
'oldport=s' => \$oldport,
'olduser=s' => \$olduser,
'oldpass=s' => \$oldpass,
'help' => \$help
);
pod2usage(1) if($help);
......@@ -111,65 +127,78 @@ 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 $old_dbh = DBI->connect("DBI:mysql:database=$database;host=$oldhost;port=$oldport",$olduser,$oldpass);
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_';
$pattern = "_core_".$release."_";
}
else{
$pattern = $dbname;
}
#fetch all databases matching the pattern
print STDERR $pattern."\n";
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");
}
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,$old_dbh, $db_name->[0],\$mapping_set_id,$release);
$schema_build = get_schema_and_build($db_name->[0]);
#add mapping_set information
if ($status == INITIAL_MAPPING){
$sth_mapping_set->execute($mapping_set_id,$schema_build);
#first time run the script, create new entry in mapping_set and copy seq_region entries in seq_region_mapping
############
#Actually NO only store the differences so for the initial one it is NONE.
############
# $current_seq_region = &read_seq_region($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){
$sth_mapping_set->execute($mapping_set_id,$schema_build);
#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 $previous_dbname = &get_previous_dbname($old_dbh,$db_name->[0],$release);
$current_seq_region = &read_seq_region($dbh,$db_name->[0]);
$old_seq_region = &read_seq_region($old_dbh,$previous_dbname);
#update the seq_region_mapping table with the old->new seq_region_id relation
my $count = 0;
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}->{$coord_system_id}); #the coord_system might have been removed in current database
next if ($old_seq_region->{$seq_region_name}->{$coord_system_id} == $current_seq_region->{$seq_region_name}->{$coord_system_id}); # if no change no need to write out
$sth_seq_mapping->execute($old_seq_region->{$seq_region_name}->{$coord_system_id},$current_seq_region->{$seq_region_name}->{$coord_system_id},$mapping_set_id);
$count++;
}
}
print STDERR "Added $count seq_region_mapping entry\n\n";
}
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
......@@ -194,43 +223,48 @@ sub read_seq_region{
#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;
}
}
my $dbh = shift;
my $old_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
# $$mapping_set_id_ref = 1;
# return INITIAL_MAPPING;
# }
# else{
#there is information, find out if it is the same mapping as previous release
my $previous_dbname = &get_previous_dbname($old_dbh,$dbname,$release);
if(!defined($previous_dbname)){
print "No previous database present for $dbname so cannot do diff so will initialise with this as the first version of the database\n";
$$mapping_set_id_ref = 1;
return INITIAL_MAPPING;
}
my $cur_seq_region_size = &get_seq_region_size($dbh,$dbname);
my $previous_seq_region_size = &get_seq_region_size($old_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'");
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
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment