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Commit 545d3b05 authored by Magali Ruffier's avatar Magali Ruffier
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a bit of text formatting 

methods are cleaner
added length check to decide if it is the same region
parent 923eea01
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misc-scripts/update_mapping_set.pl
+ 75
− 134
View file @ 545d3b05
......@@ -32,7 +32,7 @@ Optional arguments:
--port=port port (default: 3306)
--oldport=port old database server port (default: 5306)
--oldport=port old database server port (default: 3306)
--olduser=user old database server username
......@@ -89,21 +89,17 @@ 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 $host2 = 'ens-staging2';
my $oldhost = 'ensembldb.ensembl.org';
my $oldhost = 'ens-livemirror';
my $dbname = undef;
my $user = undef;
my $pass = undef;
my $port = 3306;
my $oldport = 5306;
my $olduser = "anonymous";
my $oldport = 3306;
my $olduser = "ensro";
my $oldpass = undef;
my $help = undef;
my $release = undef;
......@@ -132,8 +128,6 @@ my $old_dbh = DBI->connect("DBI:mysql:database=$database;host=$oldhost;port=$ol
foreach my $h ($host,$host2) {
my $dbh = DBI->connect("DBI:mysql:database=$database;host=$h;port=$port",$user,$pass);
my $status;
my $database_name;
#since there is no database defined, will run it agains all core databases
my $pattern;
......@@ -143,173 +137,121 @@ foreach my $h ($host,$host2) {
else{
$pattern = $dbname;
}
#fetch all databases matching the pattern
# print STDERR $pattern."\n";
my $sth = $dbh->prepare("SHOW DATABASES WHERE `database` REGEXP \'$pattern\'");
# Fetch all databases matching the pattern
my $sth = $dbh->prepare("SHOW DATABASES like \'%$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 = 1;
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(?,?)");
$schema_build = get_schema_and_build($db_name->[0]);
my $current_dbname = $db_name->[0];
print STDERR "Going to update mapping for $current_dbname....\n";
my $mapping_set_id = get_max_mapping_set_id($dbh, $current_dbname) + 1;
my $sth_seq_mapping = $dbh->prepare("INSERT INTO $current_dbname.seq_region_mapping VALUES(?,?,?)");
my $sth_mapping_set = $dbh->prepare("INSERT INTO $current_dbname.mapping_set VALUES(?,?)");
my $schema_build = get_schema_and_build($current_dbname);
my $current_assembly = get_assembly($dbh, $current_dbname) ;
my $current_assembly = get_assembly($dbh, $db_name->[0]) ;
my $previous_dbname = &get_previous_dbname($old_dbh,$db_name->[0],$release);
$sth_mapping_set->execute($mapping_set_id,$schema_build) unless $dry_run;
# If there is no previous database, no mapping needed
my $previous_dbname = &get_previous_dbname($old_dbh,$current_dbname,$release);
if (!defined($previous_dbname)) {
$sth_mapping_set->execute($mapping_set_id, $schema_build) unless $dry_run;
next;
print STDERR "First instance known for $current_dbname, no mapping needed\n";
next;
}
my $old_assembly = get_assembly($old_dbh, $previous_dbname);
# If it is a new assembly, no mapping needed
my $old_assembly = get_assembly($old_dbh, $previous_dbname);
if ($old_assembly ne $current_assembly) {
$sth_mapping_set->execute($mapping_set_id, $schema_build) unless $dry_run;
print STDERR "New assembly for $current_dbname, no mapping needed\n" ;
next;
}
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
$status = &mapping_status($dbh,$old_dbh, $db_name->[0],\$mapping_set_id,$release);
## prune newly added mapping_set entries
# $dbh->do(qq(delete from $db_name->[0].mapping_set where schema_build = '$schema_build'));
# next;
#add mapping_set information
if ($status == INITIAL_MAPPING){
#first time run the script, create new entry in mapping_set
$sth_mapping_set->execute($mapping_set_id,$schema_build) unless $dry_run;
# If there has been no change in seq_region, no mapping needed
my $cur_seq_region_checksum = &get_seq_region_checksum($dbh,$dbname);
my $previous_seq_region_checksum = &get_seq_region_checksum($old_dbh,$previous_dbname);
if ($cur_seq_region_checksum == $previous_seq_region_checksum) {
print STDERR "No change in seq_region for $current_dbname, no mapping needed\n";
next;
}
elsif ($status == SAME_MAPPING){
#seq_region_mapping has not change, just add a new entry for this version
$sth_mapping_set->execute($mapping_set_id,$schema_build) unless $dry_run;
}
elsif ($status == NEW_MAPPING){
$sth_mapping_set->execute($mapping_set_id,$schema_build) unless $dry_run;
#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
$current_seq_region = &read_seq_region($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) unless $dry_run;
$count++;
}
# There has been a seq_region change between releases, add the relation old_seq_region_id->new_seq_region_id
my $current_seq_region = &read_seq_region($dbh,$current_dbname);
my $old_seq_region = &read_seq_region($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}){
my $current_name_hash = $current_seq_region->{$seq_region_name};
my $old_name_hash = $old_seq_region->{$seq_region_name};
# The seq_region might have disappeared
if (!defined $current_name_hash) {
next;
}
foreach my $coord_system_id (keys %{$old_name_hash}){
my $current_cs_hash = $current_name_hash->{$coord_system_id};
my $old_cs_hash = $old_name_hash->{$coord_system_id};
# The coord_system might have been removed in the current database
if (!defined $current_cs_hash) {
next;
}
foreach my $length (keys %{$old_cs_hash}) {
my $current_id = $current_cs_hash->{$length};
my $old_id = $old_cs_hash->{$length};
# If no change, no need to write out
if (!defined $current_id || $old_id == $current_id) {
next;
}
$sth_seq_mapping->execute($old_id, $current_id, $mapping_set_id) unless $dry_run;
$count++;
}
}
print STDERR "Added $count seq_region_mapping entry\n\n";
}
else{
throw("Mapping status not recognized by script: $status \n\n");
}
print STDERR "Added $count seq_region_mapping entry for $dbname\n\n";
}
}
#will for a given database, will return the seq_region_name->seq_region_id relation
# 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 $dbname.seq_region");
my ($seq_region_id, $seq_region_name, $coord_system_id, $length, $cs_name);
my $sth = $dbh->prepare("SELECT seq_region_id, name, length, 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);
$sth->bind_col(3,\$length);
$sth->bind_col(4,\$coord_system_id);
while ($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;
$seq_region_hash{$seq_region_name}{$coord_system_id}{$length} = $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 $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
my $previous_dbname = &get_previous_dbname($old_dbh,$dbname,$release);
if ($previous_dbname) {
my $old_sth_max_mapping = $old_dbh->prepare("select max(mapping_set_id) from $previous_dbname.mapping_set");
$old_sth_max_mapping->execute();
( $$mapping_set_id_ref ) = $old_sth_max_mapping->fetchrow_array();
if ($$mapping_set_id_ref) {
print (" There are mappings in the previous version of the database $dbname, need to do something with them ?\n");
}
else {
print " Previous version of the $dbname has no entries, this is wrong\n";
}
}
else {
print " This is the first version of a this database $dbname, so just creating a new entry\n";
$$mapping_set_id_ref = 1;
}
return INITIAL_MAPPING;
}
else{
#there is information, find out if it is the same mapping as previous release
my $previous_dbname = &get_previous_dbname($old_dbh,$dbname,$release);
if(!defined($previous_dbname)){
print " No previous database present for $dbname so cannot do diff so will initialise with this as the first version of the database\n";
$$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{
# For a given database, returns the size of the seq_region_table
sub get_seq_region_checksum{
my $dbh = shift;
my $dbname = shift;
my $sth_status = $dbh->prepare("show table status from $dbname like 'seq_region'") ;
my $sth_status = $dbh->prepare("checksum table $dbname.seq_region") ;
$sth_status->execute();
my @table_status = $sth_status->fetchrow_array();
return $table_status[6]; #return the size of the table
my $table_status = $sth_status->fetchrow_array();
return $table_status; #return the size of the table
}
#will return the max mapping_set_id being used in the mapping_set 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");
my $sth_mapping = $dbh->prepare("select max(mapping_set_id) from $dbname.mapping_set");
$sth_mapping->execute();
my ($max_mapping_set_id) = $sth_mapping->fetchrow_array();
if (!defined $max_mapping_set_id) { return 0; }
return $max_mapping_set_id;
}
#this method will return the name of the previous database to release for same species (assuming is present)
# 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;
......@@ -317,23 +259,22 @@ sub get_previous_dbname{
my $previous_dbname;
$dbname =~ /(^[a-z]+_[a-z]+_core_)/;
if (!$1) { throw("Database name $dbname is not in the right format"); }
my $previous_release_name = $1 . (--$release);
my $previous_sth = $dbh->prepare("show databases like \'%$previous_release_name%\'");
$previous_sth->execute();
($previous_dbname) = $previous_sth->fetchrow_array() ;
return $previous_dbname;
}
#for a standard ensembl database name, returns the release number and assembly
# For a standard ensembl database name, returns the release number and assembly
sub get_schema_and_build{
my ($dbname) = @_;
my @dbname = split/_/, $dbname;
return join "_",$dbname[($#dbname -1)], $dbname[($#dbname)];
}
# Returna the assembly name for a given database
sub get_assembly{
my ($dbh, $dbname) = @_;
my $sth = $dbh->prepare("select meta_value from $dbname.meta where meta_key = 'assembly.default'");
......
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