LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

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CONTACT

  Please email comments or questions to the public Ensembl
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  Questions may also be sent to the Ensembl help desk at
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NAME

Bio::EnsEMBL::Utils::CliHelper

VERSION

$Revision$

SYNOPSIS

  use Bio::EnsEMBL::Utils::CliHelper;

  my $cli = Bio::EnsEMBL::Utils::CliHelper->new();

  # get the basic options for connecting to a database server
  my $optsd = $cli->get_dba_opts();

  # add another option
  push(@$optsd,"print");

  # process the command line with the supplied options plus a reference to a help subroutine
  my $opts = $cli->process_args($optsd,\&usage);
  
  # use the command line options to get an array of database details
  for my $db_args (@{$cli->get_dba_args_for_opts($opts)}) {
    # use the args to create a DBA
    my $dba = new Bio::EnsEMBL::DBSQL::DBAdaptor(%{$db_args});
    ...
    if(defined $opts->{print}) {
        ...
    }
  }
  
  For adding secondary databases, a prefix can be supplied. For instance, to add a second set of
  db params prefixed with dna (-dnahost -dbport etc.) use the prefix argument with get_dba_opts and 
  get_dba_args_for_opts:
  # get the basic options for connecting to a database server
  my $optsd =
   [ @{ $cli_helper->get_dba_opts() }, @{ $cli_helper->get_dba_opts('gc') } ];
  # process the command line with the supplied options plus a help subroutine
  my $opts = $cli_helper->process_args( $optsd, \&usage );
  # get the dna details
  my ($dna_dba_details) =
    @{ $cli_helper->get_dba_args_for_opts( $opts, 1, 'dna' ) };
  my $dna_db =
    Bio::EnsEMBL::DBSQL::DBAdaptor->new( %{$dna_dba_details} ) );

DESCRIPTION

Utilities for a more consistent approach to parsing and handling EnsEMBL script command lines

METHODS

See subroutines.

new()

  Description : Construct a new instance of a CliHelper object
  Returntype  : Bio::EnsEMBL::Utils:CliHelper
  Status      : Under development

get_dba_opts()

  Arg [1]     : Optional prefix for dbnames e.g. dna
  Description : Retrieves the standard options for connecting to one or more Ensembl databases
  Returntype  : Arrayref of option definitions
  Status      : Under development

process_args()

    Arg [1]     : Arrayref of supported command line options (e.g. from get_dba_opts)
    Arg [2]     : Ref to subroutine to be invoked when -help or -? is supplied
    Description : Retrieves the standard options for connecting to one or more Ensembl databases
    Returntype  : Hashref of parsed options
    Status      : Under development

get_dba_args_for_opts()

    Arg [1]     : Hash of options (e.g. parsed from command line options by process_args())
    Arg [2]     : If set to 1, the databases are assumed to have a single species only. Default is 0 if database name matches collection, 1 otherwise.
    Arg [3]     : Optional prefix to use when parsing e.g. dna
    Description : Uses the parsed command line options to generate an array of DBAdaptor arguments 
                : (e.g. expands dbpattern, finds all species_ids for multispecies databases)
                : These can then be passed directly to Bio::EnsEMBL::DBSQL::DBAdaptor->new()
    Returntype  : Arrayref of DBA argument hash refs 
    Status      : Under development

get_dba_args_for_opts()

    Arg [1]     : Hash of options (e.g. parsed from command line options by process_args())
    Arg [2]     : If set to 1, the databases are assumed to have a single species only. Default is 0.
    Arg [3]     : Optional prefix to use when parsing e.g. dna
    Description : Uses the parsed command line options to generate an array DBAdaptors. 
                : Note this can overload connections on a server
    Returntype  : Arrayref of Bio::EnsEMBL::DBSQL::DBAdaptor
    Status      : Under development

load_registry_for_opts

  Arg [1]       : Hash of options (e.g. parsed from command line options by process_args()) 
  Arg [2]     : Optional prefix to use when parsing e.g. dna or master 
  Description   : Loads a Registry from the given options hash. If a C<registry> 
                option is given then the code will call C<load_all>. Otherwise
                we use the database parameters given to call 
                C<load_registry_from_db()>.
  Returntype  : Integer of the number of DBAdaptors loaded
  Status      : Under development