t/unit_fixture/CXGN/Trial/TrialForCrossesFamilyNames.t

   1
   2 use strict;
   3
   4 use Test::More;
   5 use lib 't/lib';
   6 use SGN::Test::Fixture;
   7 use JSON::Any;
   8 use Data::Dumper;
   9 use Spreadsheet::WriteExcel;
  10 use Spreadsheet::Read;
  11 use Test::WWW::Mechanize;
  12 use CXGN::Cross;
  13 use JSON;
  14 use LWP::UserAgent;
  15
  16 my $fix = SGN::Test::Fixture->new();
  17
  18 for my $extension ("xls", "xlsx") {
  19
  20     is(ref($fix->config()), "HASH", 'hashref check');
  21
  22     BEGIN {use_ok('CXGN::Trial::TrialCreate');}
  23     BEGIN {use_ok('CXGN::Trial::TrialLayout');}
  24     BEGIN {use_ok('CXGN::Trial::TrialDesign');}
  25     BEGIN {use_ok('CXGN::Trial::TrialLookup');}
  26     BEGIN {use_ok('CXGN::Trial::Download');}
  27     BEGIN {use_ok('CXGN::Fieldbook::DownloadTrial');}
  28     BEGIN {use_ok('CXGN::Trial::TrialLayoutDownload');}
  29     BEGIN {use_ok('CXGN::Trial');}
  30
  31     ok(my $schema = $fix->bcs_schema);
  32     ok(my $phenome_schema = $fix->phenome_schema);
  33     ok(my $metadata_schema = $fix->metadata_schema);
  34     ok(my $dbh = $fix->dbh);
  35
  36
  37     # create crosses and family_names for trials
  38     my $cross_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "cross", "stock_type")->cvterm_id();
  39     my $family_name_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "family_name", "stock_type")->cvterm_id();
  40
  41     my @cross_ids;
  42     for (my $i = 1; $i <= 5; $i++) {
  43         push(@cross_ids, "cross_for_trial" . $i);
  44     }
  45
  46     my @family_names;
  47     for (my $i = 1; $i <= 5; $i++) {
  48         push(@family_names, "family_name_for_trial" . $i);
  49     }
  50
  51     ok(my $organism = $schema->resultset("Organism::Organism")
  52         ->find_or_create({
  53         genus   => 'Test_genus',
  54         species => 'Test_genus test_species',
  55     },));
  56
  57     foreach my $cross_id (@cross_ids) {
  58         my $cross_for_trial = $schema->resultset('Stock::Stock')
  59             ->create({
  60             organism_id => $organism->organism_id,
  61             name        => $cross_id,
  62             uniquename  => $cross_id,
  63             type_id     => $cross_type_id,
  64         });
  65     };
  66
  67     foreach my $family_name (@family_names) {
  68         my $family_name_for_trial = $schema->resultset('Stock::Stock')
  69             ->create({
  70             organism_id => $organism->organism_id,
  71             name        => $family_name,
  72             uniquename  => $family_name,
  73             type_id     => $family_name_type_id,
  74         });
  75     };
  76
  77     #add accession stock type for testing mixed types
  78     push(@cross_ids, 'UG120001');
  79
  80     # create trial with cross stock type
  81     ok(my $cross_trial_design = CXGN::Trial::TrialDesign->new(), "create trial design object");
  82     ok($cross_trial_design->set_trial_name("cross_to_trial1"), "set trial name");
  83     ok($cross_trial_design->set_stock_list(\@cross_ids), "set stock list");
  84     ok($cross_trial_design->set_plot_start_number(1), "set plot start number");
  85     ok($cross_trial_design->set_plot_number_increment(1), "set plot increment");
  86     ok($cross_trial_design->set_number_of_blocks(2), "set block number");
  87     ok($cross_trial_design->set_design_type("RCBD"), "set design type");
  88     ok($cross_trial_design->calculate_design(), "calculate design");
  89     ok(my $cross_design = $cross_trial_design->get_design(), "retrieve design");
  90
  91     my $preliminary_trial_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'Preliminary Yield Trial', 'project_type')->cvterm_id();
  92
  93     ok(my $crosses_trial_create = CXGN::Trial::TrialCreate->new({
  94         chado_schema      => $schema,
  95         dbh               => $dbh,
  96         owner_id          => 41,
  97         design            => $cross_design,
  98         program           => "test",
  99         trial_year        => "2020",
 100         trial_description => "test description",
 101         trial_location    => "test_location",
 102         trial_name        => "cross_to_trial1",
 103         trial_type        => $preliminary_trial_cvterm_id,
 104         design_type       => "RCBD",
 105         operator          => "janedoe",
 106         trial_stock_type  => "cross"
 107     }), "create trial object");
 108
 109     my $crosses_trial_save = $crosses_trial_create->save_trial();
 110     ok($crosses_trial_save->{'trial_id'}, "save trial");
 111
 112
 113     # retrieving cross trial and design info
 114     ok(my $crosses_trial_lookup = CXGN::Trial::TrialLookup->new({
 115         schema     => $schema,
 116         trial_name => "cross_to_trial1",
 117     }), "create trial lookup object");
 118     ok(my $crosses_trial = $crosses_trial_lookup->get_trial());
 119     ok(my $cross_trial_id = $crosses_trial->project_id());
 120
 121     print STDERR "########## CREATING NEW TRIAL LAYOUT OBJECT \n";
 122     my $cross_trial_layout;
 123     ok($cross_trial_layout = CXGN::Trial::TrialLayout->new({
 124         schema          => $schema,
 125         trial_id        => $cross_trial_id,
 126         experiment_type => 'field_layout'
 127     }), "create trial layout object for cross trial");
 128
 129     my $cross_trial_design = $cross_trial_layout->get_design();
 130     my @cross_plot_nums;
 131     my @crosses;
 132     my @cross_block_nums;
 133     my @cross_plot_names;
 134
 135     print STDERR "CROSS LAYOUT = " . Dumper($cross_trial_design);
 136
 137     # note:cross and family_name stock types use the same accession_name key as accession stock type in trial design
 138     foreach my $cross_plot_num (keys %$cross_trial_design) {
 139         push @cross_plot_nums, $cross_plot_num;
 140         push @crosses, $cross_trial_design->{$cross_plot_num}->{'accession_name'};
 141         push @cross_block_nums, $cross_trial_design->{$cross_plot_num}->{'block_number'};
 142         push @cross_plot_names, $cross_trial_design->{$cross_plot_num}->{'plot_name'};
 143
 144     }
 145     @cross_plot_nums = sort @cross_plot_nums;
 146     @crosses = sort @crosses;
 147     @cross_block_nums = sort @cross_block_nums;
 148
 149     #is_deeply(\@cross_plot_nums, [
 150     #        '1001',
 151     #        '1002',
 152     #        '1003',
 153     #        '1004',
 154     #        '1005',
 155     #        '2001',
 156     #        '2002',
 157     #        '2003',
 158     #        '2004',
 159     #        '2005'
 160     #    ], "check cross plot numbers");
 161
 162     is_deeply(\@crosses, [
 163         'UG120001',
 164         'UG120001',
 165         'cross_for_trial1',
 166         'cross_for_trial1',
 167         'cross_for_trial2',
 168         'cross_for_trial2',
 169         'cross_for_trial3',
 170         'cross_for_trial3',
 171         'cross_for_trial4',
 172         'cross_for_trial4',
 173         'cross_for_trial5',
 174         'cross_for_trial5'
 175     ], "check cross unique ids");
 176
 177     is_deeply(\@cross_block_nums, [
 178         '1',
 179         '1',
 180         '1',
 181         '1',
 182         '1',
 183         '1',
 184         '2',
 185         '2',
 186         '2',
 187         '2',
 188         '2',
 189         '2'
 190     ], "check cross block numbers");
 191
 192     is(scalar @cross_plot_names, 12);
 193
 194     my $cross_trial_type = CXGN::Trial->new({ bcs_schema => $schema, trial_id => $cross_trial_id });
 195     my $cross_trial_stock_type = $cross_trial_type->get_trial_stock_type();
 196     is($cross_trial_stock_type, 'cross');
 197
 198     #add accession for testing mixed stock types
 199     push(@family_names, 'UG120001');
 200     # create trial with family_name stock type
 201     my $fam_trial_design;
 202     ok($fam_trial_design = CXGN::Trial::TrialDesign->new(), "create trial design object");
 203     ok($fam_trial_design->set_trial_name("family_name_to_trial1"), "set trial name");
 204     ok($fam_trial_design->set_stock_list(\@family_names), "set stock list");
 205     ok($fam_trial_design->set_plot_start_number(1), "set plot start number");
 206     ok($fam_trial_design->set_plot_number_increment(1), "set plot increment");
 207     ok($fam_trial_design->set_number_of_reps(2), "set rep number");
 208     ok($fam_trial_design->set_design_type("CRD"), "set design type");
 209     ok($fam_trial_design->calculate_design(), "calculate design");
 210
 211     my $fam_design;
 212     ok($fam_design = $fam_trial_design->get_design(), "retrieve design");
 213
 214     my $fam_trial_create;
 215     ok($fam_trial_create = CXGN::Trial::TrialCreate->new({
 216         chado_schema      => $schema,
 217         dbh               => $dbh,
 218         owner_id          => 41,
 219         design            => $fam_design,
 220         program           => "test",
 221         trial_year        => "2020",
 222         trial_description => "test description",
 223         trial_location    => "test_location",
 224         trial_name        => "family_name_to_trial1",
 225         trial_type        => $preliminary_trial_cvterm_id,
 226         design_type       => "CRD",
 227         operator          => "janedoe",
 228         trial_stock_type  => "family_name"
 229     }), "create trial object");
 230
 231     my $fam_save = $fam_trial_create->save_trial();
 232     ok($fam_save->{'trial_id'}, "save trial");
 233
 234
 235     # retrieving family_name trial with design info
 236     ok(my $fam_trial_lookup = CXGN::Trial::TrialLookup->new({
 237         schema     => $schema,
 238         trial_name => "family_name_to_trial1",
 239     }), "create trial lookup object");
 240     ok(my $fam_trial = $fam_trial_lookup->get_trial());
 241     ok(my $fam_trial_id = $fam_trial->project_id());
 242     ok(my $fam_trial_layout = CXGN::Trial::TrialLayout->new({
 243         schema          => $schema,
 244         trial_id        => $fam_trial_id,
 245         experiment_type => 'field_layout'
 246     }), "create trial layout object for family trial");
 247
 248     my $fam_trial_design = $fam_trial_layout->get_design();
 249     my @fam_plot_nums;
 250     my @family_names;
 251     my @fam_rep_nums;
 252     my @fam_plot_names;
 253
 254     print STDERR "FAMILY TRIAL DESIGN: " . Dumper($fam_trial_design);
 255     # note:cross and family_name stock types use the same accession_name key as accession stock type in trial design
 256     foreach my $fam_plot_num (keys %$fam_trial_design) {
 257         push @fam_plot_nums, $fam_plot_num;
 258         push @family_names, $fam_trial_design->{$fam_plot_num}->{'accession_name'};
 259         push @fam_rep_nums, $fam_trial_design->{$fam_plot_num}->{'rep_number'};
 260         push @fam_plot_names, $fam_trial_design->{$fam_plot_num}->{'plot_name'};
 261     }
 262     @fam_plot_nums = sort @fam_plot_nums;
 263     @family_names = sort @family_names;
 264     @fam_rep_nums = sort @fam_rep_nums;
 265
 266     #is_deeply(\@fam_plot_nums, [
 267     #        '1001',
 268     #        '1002',
 269     #        '1003',
 270     #        '1004',
 271     #        '1005',
 272     #        '1006',
 273     #        '1007',
 274     #        '1008',
 275     #        '1009',
 276     #        '1010'
 277     #    ], "check family_name plot numbers");
 278
 279     is_deeply(\@family_names, [
 280         'UG120001',
 281         'UG120001',
 282         'family_name_for_trial1',
 283         'family_name_for_trial1',
 284         'family_name_for_trial2',
 285         'family_name_for_trial2',
 286         'family_name_for_trial3',
 287         'family_name_for_trial3',
 288         'family_name_for_trial4',
 289         'family_name_for_trial4',
 290         'family_name_for_trial5',
 291         'family_name_for_trial5'
 292     ], "check family names");
 293
 294     is_deeply(\@fam_rep_nums, [
 295         '1',
 296         '1',
 297         '1',
 298         '1',
 299         '1',
 300         '1',
 301         '2',
 302         '2',
 303         '2',
 304         '2',
 305         '2',
 306         '2'
 307     ], "check fam rep numbers");
 308
 309     is(scalar @fam_plot_names, 12);
 310
 311     my $fam_trial_type = CXGN::Trial->new({ bcs_schema => $schema, trial_id => $fam_trial_id });
 312     my $fam_trial_stock_type = $fam_trial_type->get_trial_stock_type();
 313     is($fam_trial_stock_type, 'family_name');
 314
 315
 316     # create cross trial Fieldbook
 317     my $cross_fieldbook_tempfile = "/tmp/test_create_cross_trial_fieldbook.$extension";
 318
 319     my $cross_fieldbook = CXGN::Fieldbook::DownloadTrial->new({
 320         bcs_schema       => $schema,
 321         metadata_schema  => $metadata_schema,
 322         phenome_schema   => $phenome_schema,
 323         trial_id         => $cross_trial_id,
 324         tempfile         => $cross_fieldbook_tempfile,
 325         archive_path     => $fix->config->{archive_path},
 326         user_id          => 41,
 327         user_name        => "janedoe",
 328         data_level       => 'plots',
 329         selected_columns => { 'plot_name' => 1, 'plot_id' => 1, 'plot_number' => 1, 'block_number' => 1,, 'accession_name' => 1 },
 330         trial_stock_type => 'cross'
 331     });
 332
 333     my $create_fieldbook_return = $cross_fieldbook->download();
 334     ok($create_fieldbook_return, "check that download trial fieldbook returns something.");
 335
 336     my $contents = ReadData $create_fieldbook_return->{'file'};
 337     #print STDERR Dumper @contents->[0]->[0];
 338     is($contents->[0]->{'type'}, $extension, "check that type of file is correct");
 339
 340     my $columns = $contents->[1]->{'cell'};
 341     ok(scalar(@$columns) == 6, "check number of col in created file.");
 342     my @field_book_columns = @$columns;
 343     is($field_book_columns[1][1], 'plot_name');
 344     is($field_book_columns[2][1], 'plot_id');
 345     is($field_book_columns[3][1], 'cross_unique_id');
 346     is($field_book_columns[4][1], 'plot_number');
 347     is($field_book_columns[5][1], 'block_number');
 348     print STDERR "FIELDBOOK COLUMNS =" . Dumper($columns) . "\n";
 349
 350
 351     # create family_name trial Fieldbook
 352     my $family_fieldbook_tempfile = "/tmp/test_create_family_trial_fieldbook.$extension";
 353
 354     my $family_fieldbook = CXGN::Fieldbook::DownloadTrial->new({
 355         bcs_schema       => $schema,
 356         metadata_schema  => $metadata_schema,
 357         phenome_schema   => $phenome_schema,
 358         trial_id         => $fam_trial_id,
 359         tempfile         => $family_fieldbook_tempfile,
 360         archive_path     => $fix->config->{archive_path},
 361         user_id          => 41,
 362         user_name        => "janedoe",
 363         data_level       => 'plots',
 364         selected_columns => { 'plot_name' => 1, 'plot_id' => 1, 'plot_number' => 1, 'rep_number' => 1,, 'accession_name' => 1 },
 365         trial_stock_type => 'family_name'
 366     });
 367
 368     my $create_family_fieldbook_return = $family_fieldbook->download();
 369     ok($create_family_fieldbook_return, "check that download trial fieldbook returns something.");
 370
 371     my $family_contents = ReadData $create_family_fieldbook_return->{'file'};
 372     #print STDERR Dumper @contents->[0]->[0];
 373     is($family_contents->[0]->{'type'}, $extension, "check that type of file is correct");
 374
 375     my $family_columns = $family_contents->[1]->{'cell'};
 376     ok(scalar(@$family_columns) == 6, "check number of col in created file.");
 377     my @family_field_book_columns = @$family_columns;
 378     is($family_field_book_columns[1][1], 'plot_name');
 379     is($family_field_book_columns[2][1], 'plot_id');
 380     is($family_field_book_columns[3][1], 'family_name');
 381     is($family_field_book_columns[4][1], 'plot_number');
 382     is($family_field_book_columns[5][1], 'rep_number');
 383     print STDERR "FAMILY FIELDBOOK COLUMNS =" . Dumper($family_columns) . "\n";
 384
 385
 386     #create westcott trial design_type using cross_unique_ids
 387
 388     my @cross_unique_ids_westcott;
 389     for (my $i = 1; $i <= 100; $i++) {
 390         push(@cross_unique_ids_westcott, "cross_for_westcott_trial" . $i);
 391     }
 392
 393     foreach my $cross_unique_id (@cross_unique_ids_westcott) {
 394         my $cross_stock = $schema->resultset('Stock::Stock')->create({
 395             organism_id => $organism->organism_id,
 396             name        => $cross_unique_id,
 397             uniquename  => $cross_unique_id,
 398             type_id     => $cross_type_id,
 399         });
 400     };
 401
 402     my $accession_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "accession", "stock_type")->cvterm_id();
 403
 404     my @accessions_westcott;
 405     for (my $i = 1; $i <= 2; $i++) {
 406         push @accessions_westcott, "check_accession_for_westcott_trial" . $i;
 407     }
 408
 409     print STDERR "ACCESSIONS WESTCOTT: " . Dumper(\@accessions_westcott);
 410
 411     foreach my $accession (@accessions_westcott) {
 412         my $accession_stock = $schema->resultset('Stock::Stock')->create(
 413             {
 414                 organism_id => $organism->organism_id,
 415                 name        => $accession,
 416                 uniquename  => $accession,
 417                 #type_id     => $accession_type_id,
 418                 type_id     => $cross_type_id,
 419             });
 420         print STDERR "Created accession $accession with type_id $accession_type_id\n";
 421     }
 422
 423     ok(my $trial_design = CXGN::Trial::TrialDesign->new(), "create trial design object");
 424
 425     ok($trial_design->set_trial_name("cross_westcott_trial"), "set trial name");
 426     ok($trial_design->set_stock_list(\@cross_unique_ids_westcott), "set stock list");
 427     ok($trial_design->set_plot_start_number(1), "set plot start number");
 428     ok($trial_design->set_plot_number_increment(1), "set plot increment");
 429     ok($trial_design->set_westcott_check_1("check_accession_for_westcott_trial1"), "set check 1");
 430     ok($trial_design->set_westcott_check_2("check_accession_for_westcott_trial2"), "set check 2");
 431     ok($trial_design->set_westcott_col(20), "set column number");
 432     ok($trial_design->set_design_type("Westcott"), "set design type");
 433     ok($trial_design->calculate_design(), "calculate design");
 434     ok(my $design = $trial_design->get_design(), "retrieve design");
 435
 436     ok(my $trial_create = CXGN::Trial::TrialCreate->new({
 437         chado_schema      => $schema,
 438         dbh               => $dbh,
 439         owner_id          => 41,
 440         design            => $design,
 441         program           => "test",
 442         trial_year        => "2015",
 443         trial_description => "test description",
 444         trial_location    => "test_location",
 445         trial_name        => "cross_westcott_trial",
 446         trial_type        => $preliminary_trial_cvterm_id,
 447         design_type       => "Westcott",
 448         operator          => "janedoe",
 449         trial_stock_type  => 'cross'
 450     }), "create trial object");
 451
 452     my $save = $trial_create->save_trial();
 453     ok($save->{'trial_id'}, "save trial");
 454
 455     ok(my $trial_lookup = CXGN::Trial::TrialLookup->new({
 456         schema     => $schema,
 457         trial_name => "cross_westcott_trial",
 458     }), "create trial lookup object");
 459
 460     ok(my $trial = $trial_lookup->get_trial());
 461     ok(my $trial_id = $trial->project_id());
 462     ok(my $trial_layout = CXGN::Trial::TrialLayout->new({
 463         schema          => $schema,
 464         trial_id        => $trial_id,
 465         experiment_type => 'field_layout'
 466     }), "create trial layout object for westcott trial");
 467
 468     ok(my $stock_names = $trial_layout->get_accession_names(), "retrieve cross_unique_ids");
 469
 470     print STDERR "STOCK NAMES IN WESTCOTT = " . Dumper($stock_names);
 471
 472     my %stocks = map {$_ => 1} @cross_unique_ids_westcott;
 473     my @crosses;
 474     for (my $i = 0; $i < scalar(@cross_unique_ids_westcott); $i++) {
 475         foreach my $cross (@$stock_names) {
 476             if ($cross->{accession_name} eq $cross_unique_ids_westcott[$i]) {
 477                 push @crosses, $cross->{accession_name};
 478             }
 479         }
 480     }
 481     ok(scalar(@crosses) == 100, "check cross unique id");
 482
 483     my $mech = Test::WWW::Mechanize->new;
 484     $mech->post_ok('http://localhost:3010/brapi/v1/token', [ "username" => "janedoe", "password" => "secretpw", "grant_type" => "password" ]);
 485     my $response = decode_json $mech->content;
 486     is($response->{'metadata'}->{'status'}->[2]->{'message'}, 'Login Successfull');
 487     my $sgn_session_id = $response->{access_token};
 488     print STDERR $sgn_session_id . "\n";
 489
 490     #test deleting a cross using in trial
 491     my $cross_in_trial_id = $schema->resultset("Stock::Stock")->find({ name => 'cross_for_trial1' })->stock_id;
 492     $mech->post_ok('http://localhost:3010/ajax/cross/delete', [ 'cross_id' => $cross_in_trial_id ]);
 493     $response = decode_json $mech->content;
 494     is_deeply($response, { 'error' => 'An error occurred attempting to delete a cross. (Cross has associated trial: cross_to_trial1. Cannot delete.
 495 )' });
 496     $fix->clean_up_db();
 497 }
 498 done_testing();