Commit 4b3a1051 authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
Browse files

Added new 'species' argument to load_registry_from_db():

Arg [SPECIES]:  (optional) string
                By default, all databases that are found on the server
                and that corresponds to the correct release are probed
                for aliases etc.  For some people, depending on where
                they are in the world, this might be a slow operation.
                With the '-species' argument, one may reduce the startup
                time by restricting the set of databases that are probed
                to those of a particular species.

                Note that the latin name of the species is required,
                e.g., 'homo sapiens', 'gallus gallus', 'callithrix
                jacchus' etc.  It may be the whole species name, or only
                the first part of the name, e.g. 'homo', 'gallus', or
                'callithrix'.  This will be used in matching against the
                name of the databases.
parent d10f6768
......@@ -1317,13 +1317,31 @@ sub load_registry_from_url {
Arg [VERBOSE]: (optional) boolean
Whether to print database messages.
Arg [SPECIES]: (optional) string
By default, all databases that are found on the
server and that corresponds to the correct release
are probed for aliases etc. For some people,
depending on where they are in the world, this might
be a slow operation. With the '-species' argument,
one may reduce the startup time by restricting the
set of databases that are probed to those of a
particular species.
Note that the latin name of the species is required,
e.g., 'homo sapiens', 'gallus gallus', 'callithrix
jacchus' etc. It may be the whole species name,
or only the first part of the name, e.g. 'homo',
'gallus', or 'callithrix'. This will be used in
matching against the name of the databases.
Arg [DB_VERSION]: (optional) integer
By default, only databases corresponding to this API
version are loaded. This allows the script to use
databases from another version although it might not
work properly. This option should only be used for
production or testing purposes and if you really
know what you are doing.
By default, only databases corresponding to the
current API version are loaded. This argument
allows the script to use databases from another
version although it might not work properly. This
argument should only be used for production or
testing purposes and if you really know what you are
doing.
Arg [WAIT_TIMEOUT]: (optional) integer
Time in seconds for the wait timeout to happen.
......@@ -1333,7 +1351,7 @@ sub load_registry_from_url {
getting deleted. Only set this if you are having
problems and know what you are doing.
Arg [-NO_CACHE]: (optional) int 1
Arg [-NO_CACHE]: (optional) boolean
This option will turn off caching for slice
features, so, every time a set of features is
retrieved, they will come from the database instead
......@@ -1351,7 +1369,7 @@ sub load_registry_from_url {
-verbose => '1'
);
Description: Will load the correct versions of the ensembl
Description: Will load the correct versions of the Ensembl
databases for the software release it can find on a
database instance into the registry. Also adds a set
of standard aliases.
......@@ -1364,14 +1382,20 @@ sub load_registry_from_url {
sub load_registry_from_db {
my ( $self, @args ) = @_;
my ( $host, $port, $user, $pass, $verbose, $db_version, $wait_timeout,
$no_cache )
= rearrange( [
'HOST', 'PORT', 'USER', 'PASS',
'VERBOSE', 'DB_VERSION', 'WAIT_TIMEOUT', 'NO_CACHE'
],
@args
);
my ( $host, $port, $user,
$pass, $verbose, $db_version,
$wait_timeout, $no_cache, $species )
= rearrange( [ 'HOST', 'PORT',
'USER', 'PASS',
'VERBOSE', 'DB_VERSION',
'WAIT_TIMEOUT', 'NO_CACHE',
'SPECIES' ],
@args );
if ( defined($species) ) {
$species = lc($species);
$species =~ tr/ -/__/;
}
my $go_version = 0;
my $ontology_version = 0;
......@@ -1431,9 +1455,16 @@ sub load_registry_from_db {
}
} elsif ( $db =~ /^([a-z]+_[a-z0-9]+_[a-z]+(?:_\d+)?)_(\d+)_(\w+)/ )
{
if ( $2 eq $software_version ) {
$temp{$1} = $2 . "_" . $3;
# Species specific databases (core, cdna, vega etc.)
my ( $one, $two, $three ) = ( $1, $2, $3 );
if ( !defined($species) || $one =~ /^$species/ ) {
if ( $two eq $software_version ) {
$temp{$one} = $two . "_" . $three;
}
}
} else {
# warn( sprintf( "Skipping database '%s'\n", $db ) );
}
......
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