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Commit 6bfd5464 authored by Andy Yates's avatar Andy Yates
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Adding an option to remove meta keys which are deprecated

parent 1653f6b0
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......@@ -19,6 +19,7 @@ sub run {
$self->v( 'Processing %s', $db );
$self->_backup($db);
$self->_meta($db);
$self->_remove_deprecated($db);
$self->v('Done');
}
return;
......@@ -43,7 +44,9 @@ sub args {
# User database location (default values):
port => 3306,
backup => 1 #default backups on
backup => 1, #default backups on
removedeprecated => 0,
};
my @cmd_opts = qw/
......@@ -65,6 +68,7 @@ sub args {
pattern=s
verbose|v!
backup
removedeprecated!
help
man
/;
......@@ -232,6 +236,28 @@ sub _backup {
return;
}
sub _remove_deprecated {
my ($self, $db) = @_;
if(!$self->{opts}->{removedeprecated}) {
$self->v('Not removing deprecated meta keys');
return;
}
my $dba = $self->_core_dba($db);
my $mc = $dba->get_MetaContainer();
$self->v('Removing deprecated meta keys');
my @deprecated_keys = qw/species.ensembl_common_name species.ensembl_alias_name/;
foreach my $key (@deprecated_keys) {
$self->v('Deleting key "%s"', $key);
$mc->delete_key($key);
}
$self->v('Finished removing deprecated meta keys');
return;
}
sub _db_to_taxon {
my ( $self, $db ) = @_;
......@@ -416,6 +442,11 @@ Database name to search for. Can be a SQL like statement
If specified we will avoid performing backup of the meta table before
a run of the script.
=item B<--removedeprecated>
Deletes any key from the DB which is deemed to be deprecated. A temporary
option until we finish working with the latest set of meta key changes.
=item B<--verbose>
Make the script chatty
......
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