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Commit cee79387 authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
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Beautification of POD.

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modules/Bio/EnsEMBL/Registry.pm
+ 82
− 56
View file @ cee79387
......@@ -1165,22 +1165,29 @@ my $self = shift;
Arg [1] : string $url
Arg [2] : (optional) integer
If not 0, will print out all information.
If not 0, will print out all information.
Arg [3] : (optional) integer
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 of the cache. This option is only recommended
for advanced users, specially if you need to store and retrieve
features. It might reduce performance when querying the database if
not used properly. If in doubt, do not use it or ask in ensembl-dev
Example : load_registry_from_url(mysql://anonymous@ensembldb.ensembl.org:3306);
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. The url format is:
mysql://[[username][:password]@]hostname[:port].
You can also request a specific version for the databases by adding
a slash and the version number but your script may crash as the API
version won't match the DB version.
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 of the cache. This
option is only recommended for advanced users, specially
if you need to store and retrieve features. It might
reduce performance when querying the database if not used
properly. If in doubt, do not use it or ask in ensembl-dev
Example : load_registry_from_url(
'mysql://anonymous@ensembldb.ensembl.org:3306');
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. The url format is:
mysql://[[username][:password]@]hostname[:port]. You
can also request a specific version for the databases
by adding a slash and the version number but your
script may crash as the API version won't match the
DB version.
Exceptions : None.
Status : Stable
......@@ -1217,59 +1224,78 @@ sub load_registry_from_url {
=head2 load_registry_from_db
Arg [HOST] : The domain name of the database host to connect to.
Arg [HOST] : string
The domain name of the database host to connect to.
Arg [USER] : string
The name of the database user to connect with
The name of the database user to connect with.
Arg [PASS] : (optional) string
The password to be used to connect to the database
Arg [PORT] : int
The port to use when connecting to the database
Arg [VERBOSE]: (optional) Wether to print database messages
Arg [DB_VERSION]: (optional) 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.
Arg [WAIT_TIMEOUT]: (optional) integer
Time in seconds for the wait timeout to happen. Time after which
the connection is deleted if not used. By default this is 28800 (8 hours)
So set this to greater than this if your connection are getting deleted.
Only set this if you are having problems and know what you are doing.
Arg [-NO_CACHE]: (optional) int 1
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 of the cache. This option is only recommended
for advanced users, specially if you need to store and retrieve
features. It might reduce performance when querying the database if
not used properly. If in doubt, do not use it or ask in ensembl-dev
The password to be used to connect to the database.
Arg [PORT] : (optional) integer
The port to use when connecting to the database.
Example : load_registry_from_db( -host => 'ensembldb.ensembl.org',
-user => 'anonymous',
-verbose => "1" );
Arg [VERBOSE]: (optional) boolean
Whether to print database messages.
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.
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.
Arg [WAIT_TIMEOUT]: (optional) integer
Time in seconds for the wait timeout to happen.
Time after which the connection is deleted if not
used. By default this is 28800 (8 hours), so set
this to greater than this if your connection are
getting deleted. Only set this if you are having
problems and know what you are doing.
Arg [-NO_CACHE]: (optional) int 1
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
of the cache. This option is only recommended for
advanced users, specially if you need to store and
retrieve features. It might reduce performance when
querying the database if not used properly. If in
doubt, do not use it or ask in ensembl-dev.
Example : load_registry_from_db(
-host => 'ensembldb.ensembl.org',
-user => 'anonymous',
-verbose => '1'
);
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.
Exceptions : None.
Status : Stable
=cut
sub load_registry_from_db {
my ( $self, @args ) = @_;
my ( $host, $port, $user, $pass, $verbose, $db_version,
$wait_timeout, $no_cache ) =
rearrange(
[qw(HOST PORT USER PASS VERBOSE DB_VERSION WAIT_TIMEOUT NO_CACHE)],
@args );
my $go_version = 0;
my $compara_version =0;
my $ancestral_version =0;
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 $go_version = 0;
my $compara_version = 0;
my $ancestral_version = 0;
$user ||= "ensro";
if ( !defined($port) ) {
......
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