<commit_before>#!/usr/bin/env perl
# $Source$
# $Revision$
# $Date$
# $Author$
#
# script to execute the specified healthcheck module
#
use warnings;
use strict;
use Getopt::Long;
use Log::Log4perl qw(:easy);
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Utils::ScriptUtils qw(inject);
use Carp;

my ( $host, $user, $pass, $port, $dbname, $species_id, $module );

GetOptions(
	"host=s",       \$host,   
	"user=s",       \$user,
	"pass:s",       \$pass,   
	"port=i",       \$port,
	"dbname=s",     \$dbname, 
	"species_id=s", \$species_id,
	"module=s",     \$module
);

if (   !defined $host
	|| !defined $port
	|| !defined $user
	|| !defined $module
	|| !defined $dbname ) {
	croak (
		"Usage: $0 -host host -port port -user user [-pass password] -dbname db [-species_id species_id] -module module"
	);
}
my %args = (
	-HOST   => $host,
	-USER   => $user,
	-PORT   => $port,<commit_msg>Allow password to be passed by setting the environment variable 'pass'.<commit_after>#!/usr/bin/env perl
# $Source$
# $Revision$
# $Date$
# $Author$
#
# script to execute the specified healthcheck module
#
use warnings;
use strict;
use Getopt::Long;
use Log::Log4perl qw(:easy);
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Utils::ScriptUtils qw(inject);
use Carp;

my ( $host, $user, $pass, $port, $dbname, $species_id, $module );

# Allow password to be passed by setting the environment variable 'pass'.
#
$pass = $ENV{'pass'};

GetOptions(
	"host=s",       \$host,
	"user=s",       \$user,
	"pass:s",       \$pass,
	"port=i",       \$port,
	"dbname=s",     \$dbname,
	"species_id=s", \$species_id,
	"module=s",     \$module
);

if (   !defined $host
	|| !defined $port
	|| !defined $user
	|| !defined $module
	|| !defined $dbname ) {
	croak (
		"Usage: $0 -host host -port port -user user [-pass password] -dbname db [-species_id species_id] -module module"
	);
}

my %args = (
	-HOST   => $host,
	-USER   => $user,
	-PORT   => $port,
{'fraction_non_alphanumeric': 0.1893978383942357, 'fraction_numerical': 0.002058672156459084, 'mean_word_length': 3.5849056603773586, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 9, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '777061', 'n_tokens_mistral': 787, 'n_tokens_neox': 751, 'n_words': 198}