Inheritance diagram for Bio::EnsEMBL::Hive::DependentOptions:

Public Member Functions
public	new ()

public	use_cases ()

public	load_cmdline_options ()

public	root ()

public	is_fully_substituted_string ()

public	is_fully_substituted_structure ()

public	hash_leaves ()

public	o ()

public	substitute ()

public	merge_from_rules ()

public	process_options ()

Detailed Description

Description

    A parser for PipeConfig files that understands how and when to substitute $self->o() expressions.

Definition at line 11 of file DependentOptions.pm.

Member Function Documentation

◆ hash_leaves()

public Bio::EnsEMBL::Hive::DependentOptions::hash_leaves ( )

Undocumented method

Code:

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◆ is_fully_substituted_string()

public Bio::EnsEMBL::Hive::DependentOptions::is_fully_substituted_string ( )

Undocumented method

Code:

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◆ is_fully_substituted_structure()

public Bio::EnsEMBL::Hive::DependentOptions::is_fully_substituted_structure ( )

Undocumented method

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◆ load_cmdline_options()

public Bio::EnsEMBL::Hive::DependentOptions::load_cmdline_options ( )

Undocumented method

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◆ merge_from_rules()

public Bio::EnsEMBL::Hive::DependentOptions::merge_from_rules ( )

Undocumented method

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◆ new()

public Bio::EnsEMBL::Hive::DependentOptions::new ( )

Undocumented method

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◆ o()

public Bio::EnsEMBL::Hive::DependentOptions::o ( )

Undocumented method

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◆ process_options()

public Bio::EnsEMBL::Hive::DependentOptions::process_options ( )

Undocumented method

Code:

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sub process_options {
    my $self    = shift @_;
    my $definitely_used_options = $self->root();
        # dry-run of these methods allows us to collect definitely_used_options
    foreach my $method (@{ $self->use_cases() }) {
        $self->$method();
    }
    my $possibly_used_options = { 'ENV' => \%ENV };
    $self->root( $possibly_used_options );
        # the first run of this method allows us to collect possibly_used_options
    my $rules = $self->default_options();
    $self->load_cmdline_options( { %$definitely_used_options, %$possibly_used_options }, $rules, "check_extra" );
    $self->root( $definitely_used_options );
    my $rules_to_go;
    my $attempts = 32;
    do {
        $rules_to_go = 0;
        foreach my $key (keys %$definitely_used_options) {
            if(exists $rules->{$key}) {
                my $value = $self->substitute( \$rules->{$key} );
                    # it has to be intelligently (recursively, on by-element basis) merged back into the tree under $self->o($key):
                $self->merge_from_rules( $value, \$self->root->{$key} );
                if($self->is_fully_substituted_structure($value)) {
                    #warn "Resolved rule: $key -> ".stringify($value)."\n";
                } else {
                    #warn "Unresolved rule: $key -> ".stringify($value)."\n";
                    $rules_to_go++;
                }
            }
        }
        $attempts--;
        #warn "=======================[$rules_to_go rules to go; $attempts attempts to go]=================\n\n";
        #warn " definitely_used_options{} contains: ".stringify($definitely_used_options)."\n";
    } while($rules_to_go and $attempts);
    #warn "=======================[out of the substitution loop]=================\n\n";
    my $missing_options = $self->hash_leaves( {}, $self->root, '' );
    if(scalar(keys %$missing_options)) {
        my @missing_keys = grep {!defined $missing_options->{$_}} (keys %$missing_options);
        my @incomplete_keys = grep {defined $missing_options->{$_}} (keys %$missing_options);
        if (@missing_keys) {
            warn "The following options are missing:\n";
            print "\t$_\n" for sort @missing_keys;
        }
        if (@incomplete_keys) {
            warn "The following options are incomplete:\n";
            print "\t$_ needs '".($missing_options->{$_})."'\n" for sort @incomplete_keys;
        }
        exit(1);
    } else {
        #warn "Done parsing options!\n";
    }
}

◆ root()

public Bio::EnsEMBL::Hive::DependentOptions::root ( )

Undocumented method

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◆ substitute()

public Bio::EnsEMBL::Hive::DependentOptions::substitute ( )

Undocumented method

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◆ use_cases()

public Bio::EnsEMBL::Hive::DependentOptions::use_cases ( )

Undocumented method

Code:

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The documentation for this class was generated from the following file:

modules/Bio/EnsEMBL/Hive/DependentOptions.pm

Public Member Functions

Detailed Description

Description

Member Function Documentation

◆ hash_leaves()

◆ is_fully_substituted_string()

◆ is_fully_substituted_structure()

◆ load_cmdline_options()

◆ merge_from_rules()

◆ new()

◆ o()

◆ process_options()

◆ root()

◆ substitute()

◆ use_cases()