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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:48:47 +0000
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0:54c7a3ea81e2 1:8691c1c61a8e
1 package CPT::ParameterGroup;
2 use Moose;
3 use strict;
4 use warnings;
5 use autodie;
6
7 # A special type of a ParameterCollection (could probably be a child...ohwell)
8 use Moose::Util::TypeConstraints;
9 #subtype 'TypeStr', as 'Str', where { $_ eq 'xor' || $_ eq 'or' || $_ eq 'and' };
10 # Replaced with the enum
11
12 has 'name' => ( is => 'rw', isa => 'Str');
13 has 'description' => ( is => 'rw', isa => 'Str');
14 has 'validator' => ( is => 'rw', isa => enum([qw(xor or and)]));
15 has 'options' => ( is => 'rw', isa => 'ArrayRef[HashRef]' );
16
17
18 sub validate {
19 die 'Unimplemented';
20 }
21
22
23
24 sub set_data {
25 my ($self, $hash_ref) = @_;
26 my %d = %{$hash_ref};
27 $self->name($d{name});
28 $self->description($d{description});
29 $self->validator($d{validator});
30 $self->options($d{options});
31 }
32
33
34
35 sub getopt {
36 my ($self) = @_;
37 die 'unimplemented';
38 }
39
40 sub flattenOptionsArray{
41 my ($self) = @_;
42 my @opts;
43 push(@opts, [sprintf("Option Group: %s\n%s\n[%s]", $self->name(), $self->description(), $self->_formatted_choice_str)]);
44 require CPT::ParameterCollection;
45 my $pC = CPT::ParameterCollection->new();
46 foreach(@{$self->options()}){
47 my %z = %{$_};
48 my $group_name = $z{group};
49 my @group_opts = @{$z{options}};
50 push(@opts, [sprintf("Subgroup: %s", $group_name)]);
51 foreach(@group_opts){
52 my $p = $pC->_coerce_param($_);
53 push(@opts, $p->getOptionsArray());
54 }
55 }
56 return \@opts;
57 }
58
59 sub _formatted_choice_str{
60 my ($self) = @_;
61 if($self->validator() eq 'xor'){
62 return 'Please only use options from ONE of the groups below, and no more';
63 }elsif($self->validator() eq 'or'){
64 return 'Please only use options from at least ONE of the groups below';
65 }elsif($self->validator() eq 'and'){
66 return 'Please ensure values/defaults are specified for ALL of the options in the groups below';
67 }
68 return undef;
69 }
70
71
72 sub populate_from_getopt {
73 my ( $self, $opt ) = @_;
74 die 'unimplemented';
75 }
76
77 no Moose;
78 1;
79
80 __END__
81
82 =pod
83
84 =encoding UTF-8
85
86 =head1 NAME
87
88 CPT::ParameterGroup
89
90 =head1 VERSION
91
92 version 1.99.4
93
94 =head2 validate
95
96 $pC->validate();
97
98 calls the validate method, which loops through and checks that user values line up with the validate method in each and every slot.
99
100 Currently unimplemented!
101
102 =head2 getopt
103
104 my @getopt_compatible_array = $pC->getopt()
105
106 Returns a getopt compatible array by looping through the array and simply returning array objects, and calling the getOptionsArray method on CPT::Parameter::* objects
107
108 =head2 populate_from_getopt
109
110 $parameterCollection->populate_from_getopt($opt);
111
112 Populate the ->value() from getopt. This is the special sauce of this portion of the module.
113 Our test case for this function is the connector choice problem.
114
115 {
116 name => 'Data Source #1',
117 description => "FASTA data source for our script",
118 type => 'xor', # must select only from one subgroup
119 options => [
120 {
121 group => 'Chado Custom',
122 options => [
123 [ 'host' => 'Hostname', { required => 1, validate => 'Str' } ],
124 [ 'user' => 'Username', { required => 1, validate => 'Str' } ],
125 [ 'pass' => 'Password', { required => 1, validate => 'Str' } ],
126 [ 'name' => 'Database name', { required => 1, validate => 'Str' } ],
127 [ 'organism' => 'organism name', { required => 1, validate => 'Str' } ],
128 [ 'landmark' => 'landmark name', { required => 1, validate => 'Str' } ],
129 ]
130 },
131 {
132 group => 'Chado GMOD pre-defined connector',
133 options => [
134 [ 'conn=s' => 'Connection Nickname', { required => 1, validate => 'Str' } ],
135 ]
136 },
137 {
138 group => 'File',
139 options => [
140 [ 'file|f=' => 'Input file', { required => 1, validate => 'File/Input' } ],
141 ]
142 },
143
144 ]
145 },
146
147 This should intelligently set parameters in $opt based on the passed data. The real question is how to handle password....
148
149 =head1 AUTHOR
150
151 Eric Rasche <rasche.eric@yandex.ru>
152
153 =head1 COPYRIGHT AND LICENSE
154
155 This software is Copyright (c) 2014 by Eric Rasche.
156
157 This is free software, licensed under:
158
159 The GNU General Public License, Version 3, June 2007
160
161 =cut