diff --git a/misc-scripts/update_mapping_set.pl b/misc-scripts/update_mapping_set.pl
index aa324282adbbfad00b6b25500070a0643a35bf69..26c5337e9be01cd0e8b3a6a90fd1e7bffeda7867 100644
--- a/misc-scripts/update_mapping_set.pl
+++ b/misc-scripts/update_mapping_set.pl
@@ -130,7 +130,6 @@ my $database = 'information_schema';
my $old_dbh = DBI->connect("DBI:mysql:database=$database;host=$oldhost;port=$oldport",$olduser,$oldpass);
foreach my $h ($host,$host2) {
- my $error;
my $dbh = DBI->connect("DBI:mysql:database=$database;host=$h;port=$port",$user,$pass);
@@ -150,123 +149,134 @@ foreach my $h ($host,$host2) {
foreach my $db_name (@{$dbs}){
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 $sth_update_build = $dbh->prepare("UPDATE $current_dbname.mapping_set SET internal_schema_build = ?");
- my $sth_update_old = $dbh->prepare("UPDATE $current_dbname.seq_region_mapping SET internal_seq_region_id = ? WHERE internal_seq_region_id = ?");
- my $sth_remove_deprecated = $dbh->prepare("DELETE FROM $current_dbname.seq_region_mapping WHERE internal_seq_region_id = ?");
- my $latest_schema_build = get_latest_schema_build($dbh, $current_dbname);
+
my $schema_build = get_schema_and_build($current_dbname);
+ my $latest_schema_build = get_latest_schema_build($dbh, $current_dbname);
if ($latest_schema_build eq $schema_build) {
print STDERR "$current_dbname already has a mapping for $schema_build, skipping\n";
next;
}
- my $current_assembly = get_assembly($dbh,$current_dbname) ;
- my $count_removed = 0;
- my $count_updated = 0;
- my $count_added = 0;
- $sth_update_build->execute($schema_build) unless $dry_run;
if (!$compare_dbname) {
$previous_dbname = &get_previous_dbname($old_dbh,$current_dbname,$release);
} else {
$previous_dbname = $compare_dbname;
}
-# If there is no previous database, no mapping needed
- if (!defined($previous_dbname)) {
- print STDERR "First instance known for $current_dbname, no mapping needed\n";
- next;
- }
-
-# If it is a new assembly, no mapping needed
- my $old_assembly = get_assembly($old_dbh,$previous_dbname);
- if ($old_assembly ne $current_assembly) {
- print STDERR "New assembly $current_assembly for $current_dbname, no mapping needed\n" ;
- next;
- }
+ update_mapping($dbh, $current_dbname, $previous_dbname, $dry_run);
+ my $mapping_set_id = get_max_mapping_set_id($dbh,$current_dbname) + 1;
+ my $sth_mapping_set = $dbh->prepare("INSERT INTO $current_dbname.mapping_set VALUES(?,?,?)");
+ my $sth_update_build = $dbh->prepare("UPDATE $current_dbname.mapping_set SET internal_schema_build = ?");
my $previous_schema_build = get_schema_and_build($previous_dbname);
my $new_mapping = $sth_mapping_set->execute($mapping_set_id,$schema_build,$previous_schema_build) unless $dry_run;
+ $sth_update_build->execute($schema_build) unless $dry_run;
+ }
+}
- if (!$new_mapping && !$dry_run) {
- print STDERR "Mapping already run for this schema_build, please remove entry before proceeding\n" ;
- exit;
- }
+
+
+sub update_mapping {
+ my ($dbh, $current_dbname, $previous_dbname, $dry_run) = @_;
+ my $error;
+ 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_update_old = $dbh->prepare("UPDATE $current_dbname.seq_region_mapping SET internal_seq_region_id = ? WHERE internal_seq_region_id = ?");
+ my $sth_remove_deprecated = $dbh->prepare("DELETE FROM $current_dbname.seq_region_mapping WHERE internal_seq_region_id = ?");
+
+ my $current_assembly = get_assembly($dbh,$current_dbname) ;
+
+ my $count_removed = 0;
+ my $count_updated = 0;
+ my $count_added = 0;
+
+# If there is no previous database, no mapping needed
+ if (!defined($previous_dbname)) {
+ print STDERR "First instance known for $current_dbname, no mapping needed\n";
+ return;
+ }
+
+# If it is a new assembly, no mapping needed
+ my $old_assembly = get_assembly($old_dbh,$previous_dbname);
+ if ($old_assembly ne $current_assembly) {
+ print STDERR "New assembly $current_assembly for $current_dbname, no mapping needed\n" ;
+ return;
+ }
# If there has been no change in seq_region, no mapping needed
- my $cur_seq_region_checksum = &get_seq_region_checksum($dbh,$current_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;
- }
+ my $cur_seq_region_checksum = &get_seq_region_checksum($dbh,$current_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";
+ return;
+ }
# 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);
+ my $current_seq_region = &read_seq_region($dbh,$current_dbname);
+ my $old_seq_region = &read_seq_region($old_dbh,$previous_dbname);
# Build a hash of currently used seq region ids to ensure we do not map to overlapping IDs
# i.e. a database has reused seq region IDs between releases
- my $current_seq_region_ids = get_seq_region_ids($dbh, $current_dbname);
+ my $current_seq_region_ids = get_seq_region_ids($dbh, $current_dbname);
# Update the seq_region_mapping table with the old->new seq_region_id relation
- 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};
+ 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};
# If the seq_region has disappeared, remove previous entries for that id
- if (!defined $current_name_hash) {
- my $id = get_seq_region_id($old_dbh,$previous_dbname, $seq_region_name);
- $count_removed += $sth_remove_deprecated->execute($id) unless $dry_run;
+ if (!defined $current_name_hash) {
+ my $id = get_seq_region_id($old_dbh,$previous_dbname, $seq_region_name);
+ $count_removed += $sth_remove_deprecated->execute($id) unless $dry_run;
+ next;
+ }
+# while ( my ($length, $hash_length) = each %{$old_name_hash})
+ foreach my $length (keys %{$old_name_hash}){
+ my $current_length_hash = $current_name_hash->{$length};
+ my $old_length_hash = $old_name_hash->{$length};
+
+# The seq_region might have a different length
+ if (!defined $current_length_hash) {
next;
}
- foreach my $length (keys %{$old_name_hash}){
- my $current_length_hash = $current_name_hash->{$length};
- my $old_length_hash = $old_name_hash->{$length};
+ foreach my $cs (keys %{$old_length_hash}) {
+ my $current_cs_hash = $current_length_hash->{$cs};
+ my $old_cs_hash = $old_length_hash->{$cs};
-# The seq_region might have a different length
- if (!defined $current_length_hash) {
+# The coord system might have changed
+ if (!defined $current_cs_hash) {
next;
}
- foreach my $cs (keys %{$old_length_hash}) {
- my $current_cs_hash = $current_length_hash->{$cs};
- my $old_cs_hash = $old_length_hash->{$cs};
+ foreach my $id (keys %{$old_cs_hash}) {
+ my $current_id = $current_cs_hash->{$id};
+ my $old_id = $old_cs_hash->{$id};
-# The coord system might have changed
- if (!defined $current_cs_hash) {
+# If no change, no need to write out
+ if (!defined $current_id || $old_id == $current_id) {
next;
}
- foreach my $id (keys %{$old_cs_hash}) {
- my $current_id = $current_cs_hash->{$id};
- my $old_id = $old_cs_hash->{$id};
-
-# If no change, no need to write out
- if (!defined $current_id || $old_id == $current_id) {
- next;
- }
- if(exists $current_seq_region_ids->{$old_id}) {
- printf STDERR "Skipping the mapping for old id %d to current id %d as the old ID is in use in the DB. This means IDs have been reused. Do not reused seq_region_id primary keys\n", $old_id, $current_id;
- $error = 1;
- next;
- }
+ if(exists $current_seq_region_ids->{$old_id}) {
+ printf STDERR "Skipping the mapping for old id %d to current id %d as the old ID is in use in the DB. This means IDs have been reused. Do not reused seq_region_id primary keys\n", $old_id, $current_id;
+ $error = 1;
+ next;
+ }
# If there is a change, update any existing entries for this seq_region to the new id
# Then, add a new entry to map said id to the old release
- $count_updated += $sth_update_old->execute($current_id,$old_id) unless $dry_run;
- $count_added += $sth_seq_mapping->execute($old_id,$current_id, $mapping_set_id) unless $dry_run;
- if($dry_run) {
- $count_updated++;
- $count_added++;
- }
+ $count_updated += $sth_update_old->execute($current_id,$old_id) unless $dry_run;
+ $count_added += $sth_seq_mapping->execute($old_id,$current_id, $mapping_set_id) unless $dry_run;
+ if($dry_run) {
+ $count_updated++;
+ $count_added++;
}
}
}
}
- print STDERR "For $current_dbname, removed $count_removed, added $count_added, updated $count_updated seq_region_mapping entries\n\n" ;
}
+ print STDERR "For $current_dbname, removed $count_removed, added $count_added, updated $count_updated seq_region_mapping entries\n\n" ;
+
if($error) {
die "Error detected when loading the mapping sets. Check STDERR for more information";