Mercurial > repos > cpt > cpt_psm_comparison_table

comparison lib/CPT/GalaxyGetOpt.pm @ 1:f093e08f21f3 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:47:24 +0000
parents
children
comparison
equal deleted inserted replaced
0:b8b8b52904a5 1:f093e08f21f3
1 package CPT::GalaxyGetOpt;
2 use CPT::ParameterGroup;
3 use autodie;
4 use File::Spec::Functions qw[ catfile catdir ];
5 use Carp;
6 no warnings;
7 use Moose;
8
9 has 'appdesc' => ( is => 'rw', isa => 'Str', default => sub { 'No application description provided' } );
10 has 'appid' => ( is => 'rw', isa => 'Str', default => sub { "unknown_app_$0" } );
11 has 'appname' => ( is => 'rw', isa => 'Str', default => sub { "Unnamed application $0"} );
12 has 'appvers' => ( is => 'rw', isa => 'Str', default => sub { '0.0.1' } );
13 has 'registered_outputs' => ( is => 'rw', isa => 'HashRef' );
14 has 'opt' => ( is => 'rw', isa => 'Any');
15 has filetype_detector => (
16 is => 'rw',
17 isa => 'Any',
18 );
19
20
21 sub getOptions {
22 my ( $self, %passed_opts ) = @_;
23 require Getopt::Long::Descriptive;
24 # these get pushed through, thankfully. This way we can manually check for --genenrate_galaxy_export and exit slightly earlier.
25 my %args = map { $_ => 1 } @ARGV;
26 # Sections passed to us
27 my @script_args = @{ $passed_opts{'options'} };
28 my %defaults = @{ $passed_opts{'defaults'} };
29
30
31
32 # Output Files Stuff
33 my @getopt_formatted_outputs;
34 my %outputs;
35 # This is originally an array of output files. We transform to a hash for
36 # easier lookup
37 foreach(@{$passed_opts{'outputs'}}){
38 # Grab name/desc/opts
39 my ($name, $desc, $opts) = @{$_};
40 $outputs{$name} = {
41 description => $desc,
42 options => $opts,
43 required => 1,
44 };
45 my %tmp_opts_fix = %{$opts};
46 $tmp_opts_fix{required} = 1;
47 $tmp_opts_fix{validate} = 'File/Output';
48 push(@getopt_formatted_outputs, [$name, $desc, \%tmp_opts_fix]);
49
50 # Adds the {name}_files_path special parameter
51 my %fp_opts = %{$opts};
52 $fp_opts{hidden} = 1;
53 $fp_opts{value} = "${name}.files_path";
54 $fp_opts{default} = "${name}.files_path";
55 $fp_opts{required} = 1;
56 $fp_opts{_galaxy_specific} = 1;
57 $fp_opts{validate} = "String";
58 #$fp_opts{_show_in_galaxy} = 0;
59 my $desc2 = "Associated HTML files for $name";
60 my $name2 = "${name}_files_path";
61 my @files_path = ($name2, $desc2, \%fp_opts);
62 push(@getopt_formatted_outputs, \@files_path);
63
64 # Adds the {name}_format special parameter
65 my %fp_opts3 = %{$opts};
66 #$fp_opts3{hidden} = 1;
67 $fp_opts3{default} = $fp_opts3{"default_format"};
68 $fp_opts3{validate} = "File/OutputFormat";
69 $fp_opts{required} = 1;
70 #$fp_opts3{_galaxy_specific} = 1;
71 #$fp_opts3{_show_in_galaxy} = 0;
72 my $desc3 = "Associated Format for $name";
73 my $name3 = "${name}_format";
74 my @files_path3 = ($name3, $desc3, \%fp_opts3);
75 push(@getopt_formatted_outputs, \@files_path3);
76
77 # Adds the {name}_files_path special parameter
78 my %fp_opts4 = %{$opts};
79 $fp_opts4{hidden} = 1;
80 $fp_opts4{value} = "${name}.id";
81 $fp_opts4{default} = "${name}.id";
82 $fp_opts4{validate} = "String";
83 $fp_opts4{_galaxy_specific} = 1;
84 #$fp_opts4{_show_in_galaxy} = 0;
85 my $desc4 = "Associated ID Number for $name";
86 my $name4 = "${name}_id";
87 my @files_path4 = ($name4, $desc4, \%fp_opts4);
88 push(@getopt_formatted_outputs, \@files_path4);
89
90 }
91 $self->registered_outputs(\%outputs);
92
93
94 # Store the application's name and description
95 if($defaults{appdesc}){
96 $self->appdesc($defaults{appdesc});
97 }
98 if($defaults{appid}){
99 $self->appid($defaults{appid});
100 }
101 if($defaults{appname}){
102 $self->appname($defaults{appname});
103 }
104 if($defaults{appvers}){
105 $self->appvers($defaults{appvers});
106 }
107
108 my $usage_desc;
109 if ( $self->appname() && $self->appdesc() ) {
110 $usage_desc = sprintf( "%s: %s\n%s [options] <some-arg>", $self->appname(), $self->appdesc(), $0 );
111 }
112
113 # Individual parameter parsers
114 require CPT::Parameter;
115 # Which are stored in a collection of them
116 require CPT::ParameterCollection;
117
118
119 my $parameterCollection = CPT::ParameterCollection->new();
120
121 $parameterCollection->push_params(
122 [
123 #['Standard Options'],
124 #@extra_params,
125 #[],
126 ['outfile_supporting' , 'File or folder to output to, necessary when (class == Report || multiple calls to classyReturnResults || multiple standalone output files)' , { hidden => 1, validate => 'String', default => '__new_file_path__', _galaxy_specific => 1, _show_in_galaxy => 0 }],
127 ['galaxy' , 'Run with galaxy-specific overrides' , {validate => 'Flag' , hidden=>1, _galaxy_specific => 1, _show_in_galaxy => 0}],
128 ['generate_galaxy_xml' , 'Generate a compatible galaxy-xml file. May need editing' , {validate => 'Flag' , hidden=>1, _galaxy_specific => 1, _show_in_galaxy => 0}],
129 [],
130 ['Script Options'],
131 ]
132 );
133
134 # If there's a default specified, we should apply that.
135 foreach (@script_args) {
136 # If it's an array, push as is, because either it's old style/label/empty
137 # However, this doesn't allow setting defaults for things that aren't parameters
138 # and it won't set defaults for old style
139 if ( ref $_ eq 'ARRAY' ) {
140 $parameterCollection->push_param($_);
141 }elsif( ref $_ eq 'HASH'){
142 my $pG = CPT::ParameterGroup->new();
143 $pG->set_data($_);
144 $parameterCollection->push_group($pG);
145 }
146 }
147
148 # Our magic output files stuff
149 $parameterCollection->push_params(
150 [
151 [],
152 ['Output Files'],
153 @getopt_formatted_outputs,
154 ]
155 );
156
157 # Other standard options like verbosity/version/etc
158 $parameterCollection->push_params(
159 [
160 [],
161 ['Other Standard Options'],
162 ['verbose|v', 'Be more verbose', {validate => 'Flag', _show_in_galaxy => 0}],
163 ['version', 'Print version information', {validate => 'Flag', _show_in_galaxy => 0}],
164 ['help', 'Print usage message and exit', {validate => 'Flag', _show_in_galaxy => 0}],
165 ],
166 );
167
168 # If we want the galaxy_xml, do that before the reduction step is called.
169 if ( $args{'--version'} ) {
170 print $self->appvers() . "\n";
171 exit 1;
172 }
173
174 # If we want the galaxy_xml, do that before the reduction step is called.
175 if ( $args{'--generate_galaxy_xml'} ) {
176 require CPT::Galaxy;
177 my $galaxy_xml_generator = CPT::Galaxy->new();
178 $galaxy_xml_generator->gen(
179 full_options => $parameterCollection,
180 appdesc => $self->appdesc(),
181 appid => $self->appid(),
182 appname => $self->appname(),
183 appvers => $self->appvers(),
184 defaults => $passed_opts{'defaults'},
185 outputs => $passed_opts{'outputs'},
186 tests => $passed_opts{'tests'},
187 );
188 exit 1;
189 }
190
191 if( $args{'--gen_test'} ){
192 require CPT::GenerateTests;
193 my $tgen = CPT::GenerateTests->new();
194 if(defined $passed_opts{'tests'}){
195 print $tgen->gen(@{$passed_opts{'tests'}});
196 }else{
197 print $tgen->gen_empty();
198 }
199 exit 0;
200 }
201
202 # Now that the options_spec is complete, we reduce to something getopt will be happy with
203 my @getopt_spec = $parameterCollection->getopt();
204 #print STDERR Dumper \@getopt_spec;
205 #exit 1;
206
207 # It would be nice if there was a way to ensure that it didn't die here...
208 # Execute getopt
209 my ( $local_opt, $usage ) = Getopt::Long::Descriptive::describe_options( $usage_desc, @getopt_spec );
210 $self->opt($local_opt);
211
212 # Now that we've gotten the user's options, we need to copy their values back to our ParameterCollection
213 $parameterCollection->populate_from_getopt($self->opt());
214
215 # If they want help, print + exit
216 if ( $self->opt && $self->opt->help ) {
217 print $usage;
218 exit 1;
219 }
220 # Validate their choices
221 if ( $parameterCollection->validate($self->opt) ) {
222 return $self->opt;
223 # Easy access for the script, don't want them to have to deal with PC (just yet)
224 }
225 else {
226 # Some params failed to validate, so we die.
227 croak "Validation errors were found so cannot continue";
228 }
229 }
230
231 no Moose;
232 1;
233
234 __END__
235
236 =pod
237
238 =encoding UTF-8
239
240 =head1 NAME
241
242 CPT::GalaxyGetOpt
243
244 =head1 VERSION
245
246 version 1.99.4
247
248 =head2 getOptions
249
250 my $ggo = CPT::GalaxyGetOpt->new();
251 my $options = $ggo->getOptions(
252 'options' => [
253 [ 'file', 'Input file', { validate => 'File/Input' } ],
254 [
255 "option" => "Select an option!",
256 {
257 validate => 'Option',
258 options => \%options,
259 multiple => 1,
260 }
261 ],
262 [
263 "float" => "I'm a float",
264 { validate => 'Float' }
265 ],
266 [
267 "int" => "I'm an int",
268 { validate => 'Int', default => [42, 34], required => 1, multiple => 1 }
269 ],
270 [],
271 ['New section'],
272 [
273 "string" => "I'm a simple string",
274 { validate => 'String' }
275 ],
276 [
277 'flag' => 'This is a flag',
278 { validate => 'Flag' }
279 ],
280 ],
281 'outputs' => [
282 [
283 'my_output_data',
284 'Output TXT File',
285 {
286 validate => 'File/Output',
287 required => 1,
288 default => 'out',
289 data_format => 'text/plain',
290 default_format => 'TXT',
291 }
292 ],
293 ],
294 'defaults' => [
295 'appid' => 'TemplateScript',
296 'appname' => 'Template',
297 'appdesc' => 'A basic template for a new CPT application',
298 'appvers' => '1.94',
299 ],
300 'tests' => [
301 {
302 test_name => "Default",
303 params => {
304 },
305 outputs => {
306 'my_output_data' => ["out.txt", 'test-data/outputs/template.default.txt' ],
307 },
308 },
309 {
310 test_name => "Option A specified",
311 params => {
312 'int', '10000',
313 },
314 outputs => {
315 'my_output_data' => ["out.txt", 'test-data/outputs/template.A.txt' ],
316 },
317 },
318 ],
319 );
320
321 my @data;
322 foreach(qw(file int string option float flag)){
323 # Create a 2D array of all of our optoins
324 push(@data, [ $_, $options->{$_}]);
325 }
326
327 my %table = (
328 'Sheet1' => {
329 header => [qw(Key Value)],
330 data => \@data,
331 }
332 );
333
334 # And store it to file!
335 use CPT::OutputFiles;
336 my $crr_output = CPT::OutputFiles->new(
337 name => 'my_output_data',
338 GGO => $ggo,
339 );
340 $crr_output->CRR(data => \%table);
341
342 Gets command line options, and prints docs. Very convenient, removes the burden of writing any Getopt code from you.
343
344 =head3 Default Options Provided
345
346 =over 4
347
348 =item *
349
350 help, man - cause an early exit and printing of the POD for your script.
351
352 =item *
353
354 verbose - flag to make the script verbose. Will print everything that is sent to returnResults. Individual scripts should take advantage of this option
355
356 =back
357
358 =head3 Advanced Options Provided
359
360 =over 4
361
362 =item C<--generate_galaxy_xml>
363
364 Generates valid XML for the tool for use in Galaxy
365
366 =item C<--gen_test>
367
368 Generates code to test the script using specified test data
369
370 =back
371
372 =head1 AUTHOR
373
374 Eric Rasche <rasche.eric@yandex.ru>
375
376 =head1 COPYRIGHT AND LICENSE
377
378 This software is Copyright (c) 2014 by Eric Rasche.
379
380 This is free software, licensed under:
381
382 The GNU General Public License, Version 3, June 2007
383
384 =cut