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Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute
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Questions may also be sent to the Ensembl help desk at
<http://www.ensembl.org/Help/Contact>.NAME
Bio::EnsEMBL::Utils::ConfParser - configuration parser for perl scripts
SYNOPSIS
my $conf = new Bio::EnsEMBL::Utils::ConfParser(
-SERVERROOT => "/path/to/ensembl",
-DEFAULT_CONF => "my.default.conf"
);
# parse options from configuration file and commandline
$conf->parse_options(
'mandatory_string_opt=s' => 1,
'optional_numeric_opt=n' => 0,
);
# get a paramter value
my $val = $conf->param('manadatory_string_op');DESCRIPTION
This module parses a configuration file and the commandline options passed to a script (the latter superseed the former). Configuration files contain ini-file style name-value pairs, and the commandline options are passed to Getopt::Long for parsing.
The parameter values are consequently accessible via the param() method. You can also create a commandline string of all current parameters and their values to pass to another script.
new
Arg [SERVERROOT] :
String $serverroot - root directory of your ensembl code
Arg [DEFAULT_CONF] :
String $default_conf - default configuration file
Example : my $conf = new Bio::EnsEMBL::Utils::ConfParser(
-SERVERROOT => '/path/to/ensembl',
-DEFAULT_CONF => 'my.default.conf'
);
Description : object constructor
Return type : Bio::EnsEMBL::Utils::ConfParser object
Exceptions : thrown if no serverroot is provided
Caller : general
Status : At Risk
: under developmentparse_options
Arg[1..n] : pairs of option definitions and mandatory flag (see below for
details)
Example : $conf->parse_options(
'mandatory_string_opt=s' => 1,
'optional_numeric_opt=n' => 0,
);
Description : This method reads options from an (optional) configuration file
and parses the commandline options supplied by the user.
Commandline options will superseed config file settings. The
string "$SERVERROOT" in the configuration entries will be
replaced by the appropriate value.
The arguments passed to this method are pairs of a Getopt::Long
style option definition (in fact it will be passed to
GetOptions() directly) and a flag indicating whether this
option is mandatory (1) or optional (0).
In addition to these user-defined options, a set of common
options is always parsed. See _common_options() for details.
If you run your script with --interactive the user will be
asked to confirm the parameters after parsing.
All parameters will then be accessible via $self->param('name').
Return type : true on success
Exceptions : thrown if configuration file can't be opened
thrown on missing mandatory parameters
Caller : general
Status : At Risk
: under developmentconfirm_params
Example : $conf->confirm_params;
Description : If the script is run with the --interactive switch, this method
prints a table of all parameters and their values and asks user
to confirm if he wants to proceed.
Return type : true on success
Exceptions : none
Caller : parse_options()
Status : At Risk
: under developmentparam
Arg[1] : Parameter name
Arg[2..n] : (optional) List of values to set
Example : # getter
my $dbname = $conf->param('dbname');
# setter
$conf->param('port', 3306);
$conf->param('chromosomes', 1, 6, 'X');
Description : Getter/setter for parameters. Accepts single-value params and
list params.
Return type : Scalar value for single-value parameters, array of values for
list parameters
Exceptions : thrown if no parameter name is supplied
Caller : general
Status : At Risk
: under developmentis_true
Arg[1] : Parameter name
Example : unless ($conf->is_true('upload')) {
print "Won't upload data.\n";
next;
}
Description : Checks whether a param value is set to 'true', which is defined
here as TRUE (in the Perl sense) but not the string 'no'.
Return type : Boolean
Exceptions : thrown if no parameter name is supplied
Caller : general
Status : At Risk
: under developmentlist_params
Example : print "Current parameter names:\n";
foreach my $param (@{ $conf->list_params }) {
print " $param\n";
}
Description : Returns a list of the currently available parameter names. The
list will be in the same order as option definitions were
passed to the new() method.
Return type : Arrayref of parameter names
Exceptions : none
Caller : list_param_values(), create_commandline_options()
Status : At Risk
: under developmentlist_param_values
Example : print LOG $conf->list_param_values;
Description : prints a table of the parameters used in the script
Return type : String - the table to print
Exceptions : none
Caller : general
Status : At Risk
: under developmentcreate_commandline_options
Arg[1..n] : param/value pairs which should be added to or override the
currently defined parameters
Example : $conf->create_commandline_options(
'dbname' => 'homo_sapiens_vega_33_35e',
'interactive' => 0
);
Description : Creates a commandline options string of all current paramters
that can be passed to another script.
Return type : String - commandline options string
Exceptions : none
Caller : general
Status : At Risk
: under developmentcomma_to_list
Arg[1..n] : list of parameter names to parse
Example : $conf->comma_to_list('chromosomes');
Description : Transparently converts comma-separated lists into arrays (to
allow different styles of commandline options, see perldoc
Getopt::Long for details). Parameters are converted in place
(accessible through $self->param('name')).
Return type : true on success
Exceptions : none
Caller : general
Status : At Risk
: under developmentlist_or_file
Arg[1] : Name of parameter to parse
Example : $conf->list_or_file('gene');
Description : Determines whether a parameter holds a list or it is a filename
to read the list entries from.
Return type : true on success
Exceptions : thrown if list file can't be opened
Caller : general
Status : At Risk
: under developmentserverroot
Arg[1] : (optional) String - root directory of your ensembl checkout
Example : my $serverroot = $conf->serverroot;
Description : Getter/setter for the root directory of your ensembl checkout.
Return type : String
Exceptions : none
Caller : new(), general
Status : At Risk
: under developmentdefault_conf
Arg[1] : (optional) String - default configuration file
Example : $conf->default_conf('my.default.conf');
Description : Getter/setter for the default configuration file.
Return type : String
Exceptions : none
Caller : new(), general
Status : At Risk
: under development