t/unit_fixture/CXGN/Uploading/UploadAndAddCrossesCrossingtrial.t

   1
   2 use strict;
   3 use warnings;
   4
   5 use lib 't/lib';
   6 use SGN::Test::Fixture;
   7 use Test::More;
   8 use Test::WWW::Mechanize;
   9 use LWP::UserAgent;
  10 use CXGN::Trial;
  11 use CXGN::Pedigree::AddCrossingtrial;
  12 use CXGN::Pedigree::AddCrosses;
  13 use CXGN::Pedigree::AddCrossInfo;
  14 use CXGN::Pedigree::AddProgeniesExistingAccessions;
  15 use CXGN::Pedigree::AddPedigrees;
  16 use Bio::GeneticRelationships::Individual;
  17 use Bio::GeneticRelationships::Pedigree;
  18 use CXGN::Cross;
  19 use CXGN::Pedigree::AddCrossTissueSamples;
  20 use LWP::UserAgent;
  21 use CXGN::Trial::Download;
  22 use Spreadsheet::WriteExcel;
  23 use Spreadsheet::Read;
  24
  25 #Needed to update IO::Socket::SSL
  26 use Data::Dumper;
  27 use JSON;
  28 local $Data::Dumper::Indent = 0;
  29
  30 my $f = SGN::Test::Fixture->new();
  31 my $schema = $f->bcs_schema;
  32 my $phenome_schema = $f->phenome_schema;
  33
  34 my $mech = Test::WWW::Mechanize->new;
  35
  36 for my $extension ("xls", "xlsx") {
  37
  38     # test adding crossing trial
  39     $mech->post_ok('http://localhost:3010/brapi/v1/token', [ "username" => "janedoe", "password" => "secretpw", "grant_type" => "password" ]);
  40     my $response = decode_json $mech->content;
  41     is($response->{'metadata'}->{'status'}->[2]->{'message'}, 'Login Successfull');
  42     my $sgn_session_id = $response->{access_token};
  43     print STDERR $sgn_session_id . "\n";
  44
  45     $mech->post_ok('http://localhost:3010/ajax/cross/add_crossingtrial', [ 'crossingtrial_name' => 'test_crossingtrial', 'crossingtrial_program_id' => 134,
  46         'crossingtrial_location'                                                                => 'test_location', 'year' => '2017', 'project_description' => 'test description' ]);
  47
  48     $response = decode_json $mech->content;
  49     is($response->{'success'}, '1');
  50
  51     $mech->post_ok('http://localhost:3010/ajax/cross/add_crossingtrial', [ 'crossingtrial_name' => 'test_crossingtrial2', 'crossingtrial_program_id' => 134,
  52         'crossingtrial_location'                                                                => 'test_location', 'year' => '2018', 'project_description' => 'test description2' ]);
  53
  54     $response = decode_json $mech->content;
  55     is($response->{'success'}, '1');
  56
  57     $mech->post_ok('http://localhost:3010/ajax/cross/add_crossingtrial', [ 'crossingtrial_name' => 'test_crossingtrial_deletion', 'crossingtrial_program_id' => 134,
  58         'crossingtrial_location'                                                                => 'test_location', 'year' => '2019', 'project_description' => 'test deletion' ]);
  59
  60     $response = decode_json $mech->content;
  61     is($response->{'success'}, '1');
  62
  63     #create populations for testing bulk and bulk_open cross types
  64     $mech->post_ok('http://localhost:3010/ajax/population/new', [ "population_name"=> 'test_population_A', "accessions[]"=> ['UG120001', 'UG120002'] ]);
  65     $response = decode_json $mech->content;
  66     is($response->{'success'}, "Success! Population test_population_A created");
  67     my $population_A_id = $response->{'population_id'};
  68
  69     $mech->post_ok('http://localhost:3010/ajax/population/new', [ "population_name"=> 'test_population_B', "accessions[]"=> ['UG120003', 'UG120004'] ]);
  70     $response = decode_json $mech->content;
  71     is($response->{'success'}, "Success! Population test_population_B created");
  72     my $population_B_id = $response->{'population_id'};
  73
  74     # test adding cross and info
  75     my $crossing_trial_rs = $schema->resultset('Project::Project')->find({ name => 'test_crossingtrial' });
  76     my $crossing_trial_id = $crossing_trial_rs->project_id();
  77     my $female_plot_id = $schema->resultset('Stock::Stock')->find({ name => 'KASESE_TP2013_842' })->stock_id();
  78     my $male_plot_id = $schema->resultset('Stock::Stock')->find({ name => 'KASESE_TP2013_1591' })->stock_id();
  79     my $cross_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "cross", "stock_type")->cvterm_id();
  80     my $cross_combination_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "cross_combination", "stock_property")->cvterm_id();
  81
  82     my $before_adding_cross = $schema->resultset("Stock::Stock")->search({ type_id => $cross_type_id })->count();
  83     my $before_adding_stocks = $schema->resultset("Stock::Stock")->search({})->count();
  84     my $before_adding_stockprop = $schema->resultset("Stock::Stockprop")->search({ type_id => $cross_combination_type_id })->count();
  85     my $before_adding_stockprop_all = $schema->resultset("Stock::Stockprop")->search({})->count();
  86     my $before_adding_relationship = $schema->resultset("Stock::StockRelationship")->search({})->count();
  87     my $before_adding_cross_in_experiment = $schema->resultset("NaturalDiversity::NdExperiment")->search({})->count();
  88     my $before_adding_cross_in_experiment_stock = $schema->resultset("NaturalDiversity::NdExperimentStock")->search({})->count();
  89
  90     $mech->post_ok('http://localhost:3010/ajax/cross/add_cross', [ 'crossing_trial_id' => $crossing_trial_id, 'cross_name' => 'test_add_cross', 'cross_combination' => 'UG120001xUG120002', 'cross_type' => 'biparental', 'maternal' => 'UG120001', 'paternal' => 'UG120002', 'female_plot' => $female_plot_id, 'male_plot' => $male_plot_id ]);
  91
  92     $response = decode_json $mech->content;
  93     is($response->{'success'}, '1');
  94
  95     my $after_adding_cross = $schema->resultset("Stock::Stock")->search({ type_id => $cross_type_id })->count();
  96     my $after_adding_stocks = $schema->resultset("Stock::Stock")->search({})->count();
  97     my $after_adding_stockprop = $schema->resultset("Stock::Stockprop")->search({ type_id => $cross_combination_type_id })->count();
  98     my $after_adding_stockprop_all = $schema->resultset("Stock::Stockprop")->search({})->count();
  99     my $after_adding_relationship = $schema->resultset("Stock::StockRelationship")->search({})->count();
 100     my $after_adding_cross_in_experiment = $schema->resultset("NaturalDiversity::NdExperiment")->search({})->count();
 101     my $after_adding_cross_in_experiment_stock = $schema->resultset("NaturalDiversity::NdExperimentStock")->search({})->count();
 102
 103     is($after_adding_cross, $before_adding_cross + 1);
 104     is($after_adding_stocks, $before_adding_stocks + 1);
 105     is($after_adding_stockprop, $before_adding_stockprop + 1);
 106     is($after_adding_stockprop_all, $before_adding_stockprop_all + 2);
 107     is($after_adding_relationship, $before_adding_relationship + 4);
 108     is($after_adding_cross_in_experiment, $before_adding_cross_in_experiment + 1);
 109     is($after_adding_cross_in_experiment_stock, $before_adding_cross_in_experiment_stock + 1);
 110
 111     #test adding a cross with backcross cross type
 112     my $crossing_trial2_rs = $schema->resultset('Project::Project')->find({ name => 'test_crossingtrial2' });
 113     my $crossing_trial2_id = $crossing_trial2_rs->project_id();
 114
 115     $mech->post_ok('http://localhost:3010/ajax/cross/add_cross', [ 'crossing_trial_id' => $crossing_trial2_id, 'cross_name' => 'test_backcross1', 'cross_combination' => 'test_add_crossxUG120001', 'cross_type' => 'backcross', 'maternal' => 'test_add_cross', 'paternal' => 'UG120001' ]);
 116
 117     $response = decode_json $mech->content;
 118     is($response->{'success'}, '1');
 119
 120     #test uploading crosses with backcross cross type
 121     my $file = $f->config->{basepath} . "/t/data/cross/backcross_upload.$extension";
 122     my $ua = LWP::UserAgent->new;
 123     $response = $ua->post(
 124         'http://localhost:3010/ajax/cross/upload_crosses_file',
 125         Content_Type => 'form-data',
 126         Content      => [
 127             "xls_crosses_simple_file"               => [
 128                 $file,
 129                 "backcross_upload.$extension",
 130                 Content_Type => ($extension eq "xls") ? 'application/vnd.ms-excel' : 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet',
 131             ],
 132             "upload_crosses_crossing_experiment_id" => $crossing_trial2_id,
 133             "sgn_session_id"                        => $sgn_session_id
 134         ]
 135     );
 136     ok($response->is_success);
 137     my $message = $response->decoded_content;
 138     my $message_hash = decode_json $message;
 139     is_deeply($message_hash, { 'success' => 1 });
 140
 141     # test uploading crosses with only accession info
 142
 143     my $before_uploading_cross_a = $schema->resultset("Stock::Stock")->search({ type_id => $cross_type_id })->count();
 144     my $before_uploading_stocks_a = $schema->resultset("Stock::Stock")->search({})->count();
 145     my $before_uploading_relationship_a = $schema->resultset("Stock::StockRelationship")->search({})->count();
 146
 147     my $file = $f->config->{basepath} . "/t/data/cross/crosses_simple_upload.$extension";
 148     my $ua = LWP::UserAgent->new;
 149     $response = $ua->post(
 150         'http://localhost:3010/ajax/cross/upload_crosses_file',
 151         Content_Type => 'form-data',
 152         Content      => [
 153             "xls_crosses_simple_file"               => [
 154                 $file,
 155                 "crosses_simple_upload.$extension",
 156                 Content_Type => ($extension eq "xls") ? 'application/vnd.ms-excel' : 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet',
 157             ],
 158             "upload_crosses_crossing_experiment_id" => $crossing_trial2_id,
 159             "sgn_session_id"                        => $sgn_session_id
 160         ]
 161     );
 162     ok($response->is_success);
 163     my $message = $response->decoded_content;
 164     my $message_hash = decode_json $message;
 165     is_deeply($message_hash, { 'success' => 1 });
 166
 167     my $after_uploading_cross_a = $schema->resultset("Stock::Stock")->search({ type_id => $cross_type_id })->count();
 168     my $after_uploading_stocks_a = $schema->resultset("Stock::Stock")->search({})->count();
 169     my $after_uploading_relationship_a = $schema->resultset("Stock::StockRelationship")->search({})->count();
 170
 171     is($after_uploading_cross_a, $before_uploading_cross_a + 4);
 172     is($after_uploading_stocks_a, $before_uploading_stocks_a + 4);
 173     is($after_uploading_relationship_a, $before_uploading_relationship_a + 8);
 174
 175     # test uploading crosses with plots
 176     my $female_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "female_parent", "stock_relationship")->cvterm_id();
 177     my $male_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "male_parent", "stock_relationship")->cvterm_id();
 178     my $female_plot_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "female_plot_of", "stock_relationship")->cvterm_id();
 179     my $male_plot_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "male_plot_of", "stock_relationship")->cvterm_id();
 180
 181     my $before_uploading_relationship_all = $schema->resultset("Stock::StockRelationship")->search({})->count();
 182     my $before_uploading_relationship_female = $schema->resultset("Stock::StockRelationship")->search({ type_id => $female_type_id })->count();
 183     my $before_uploading_relationship_male = $schema->resultset("Stock::StockRelationship")->search({ type_id => $male_type_id })->count();
 184     my $before_uploading_relationship_femaleplot = $schema->resultset("Stock::StockRelationship")->search({ type_id => $female_plot_type_id })->count();
 185     my $before_uploading_relationship_maleplot = $schema->resultset("Stock::StockRelationship")->search({ type_id => $male_plot_type_id })->count();
 186
 187     $file = $f->config->{basepath} . "/t/data/cross/crosses_plots_upload.$extension";
 188     $ua = LWP::UserAgent->new;
 189     $response = $ua->post(
 190         'http://localhost:3010/ajax/cross/upload_crosses_file',
 191         Content_Type => 'form-data',
 192         Content      => [
 193             "xls_crosses_plots_file"                => [
 194                 $file,
 195                 "crosses_plots_upload.$extension",
 196                 Content_Type => ($extension eq "xls") ? 'application/vnd.ms-excel' : 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet',
 197             ],
 198             "upload_crosses_crossing_experiment_id" => $crossing_trial2_id,
 199             "sgn_session_id"                        => $sgn_session_id
 200         ]
 201     );
 202     ok($response->is_success);
 203     $message = $response->decoded_content;
 204     $message_hash = decode_json $message;
 205     is_deeply($message_hash, { 'success' => 1 });
 206
 207     my $after_uploading_relationship_all = $schema->resultset("Stock::StockRelationship")->search({})->count();
 208     my $after_uploading_relationship_female = $schema->resultset("Stock::StockRelationship")->search({ type_id => $female_type_id })->count();
 209     my $after_uploading_relationship_male = $schema->resultset("Stock::StockRelationship")->search({ type_id => $male_type_id })->count();
 210     my $after_uploading_relationship_femaleplot = $schema->resultset("Stock::StockRelationship")->search({ type_id => $female_plot_type_id })->count();
 211     my $after_uploading_relationship_maleplot = $schema->resultset("Stock::StockRelationship")->search({ type_id => $male_plot_type_id })->count();
 212
 213     is($after_uploading_relationship_all, $before_uploading_relationship_all + 8);
 214     is($after_uploading_relationship_female, $before_uploading_relationship_female + 2);
 215     is($after_uploading_relationship_male, $before_uploading_relationship_male + 2);
 216     is($after_uploading_relationship_femaleplot, $before_uploading_relationship_femaleplot + 2);
 217     is($after_uploading_relationship_maleplot, $before_uploading_relationship_maleplot + 2);
 218
 219     #add plants for testing (a total of 38 entries)
 220     my $trial = CXGN::Trial->new({ bcs_schema => $schema, trial_id => 165 });
 221     $trial->create_plant_entities(2);
 222
 223     # test uploading crosses with plants
 224     my $female_plant_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "female_parent", "stock_relationship")->cvterm_id();
 225     my $male_plant_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "male_parent", "stock_relationship")->cvterm_id();
 226
 227     my $before_uploading_relationship_femaleplant = $schema->resultset("Stock::StockRelationship")->search({ type_id => $female_plant_type_id })->count();
 228     my $before_uploading_relationship_maleplant = $schema->resultset("Stock::StockRelationship")->search({ type_id => $male_plant_type_id })->count();
 229
 230     $file = $f->config->{basepath} . "/t/data/cross/crosses_plants_upload.$extension";
 231     $ua = LWP::UserAgent->new;
 232     $response = $ua->post(
 233         'http://localhost:3010/ajax/cross/upload_crosses_file',
 234         Content_Type => 'form-data',
 235         Content      => [
 236             "xls_crosses_plants_file"               => [
 237                 $file,
 238                 "crosses_plants_upload.$extension",
 239                 Content_Type => ($extension eq "xls") ? 'application/vnd.ms-excel' : 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet',
 240             ],
 241             "upload_crosses_crossing_experiment_id" => $crossing_trial2_id,
 242             "sgn_session_id"                        => $sgn_session_id
 243         ]
 244     );
 245     ok($response->is_success);
 246     $message = $response->decoded_content;
 247     $message_hash = decode_json $message;
 248     is_deeply($message_hash, { 'success' => 1 });
 249
 250     my $after_uploading_relationship_femaleplant = $schema->resultset("Stock::StockRelationship")->search({ type_id => $female_plant_type_id })->count();
 251     my $after_uploading_relationship_maleplant = $schema->resultset("Stock::StockRelationship")->search({ type_id => $male_plant_type_id })->count();
 252
 253     is($after_uploading_relationship_femaleplant, $before_uploading_relationship_femaleplant + 2);
 254     is($after_uploading_relationship_maleplant, $before_uploading_relationship_maleplant + 2);
 255
 256     # test uploading crosses with simplified parent info format
 257     my $before_uploading_cross_simplified_info = $schema->resultset("Stock::Stock")->search({ type_id => $cross_type_id })->count();
 258     my $before_uploading_stocks_simplified_info = $schema->resultset("Stock::Stock")->search({})->count();
 259     my $before_uploading_relationship_simplified_info = $schema->resultset("Stock::StockRelationship")->search({})->count();
 260
 261     my $file = $f->config->{basepath} . "/t/data/cross/crosses_simplified_parents_upload.$extension";
 262     my $ua = LWP::UserAgent->new;
 263     $response = $ua->post(
 264         'http://localhost:3010/ajax/cross/upload_crosses_file',
 265         Content_Type => 'form-data',
 266         Content      => [
 267             "xls_crosses_simplified_parents_file" => [
 268                 $file,
 269                 "crosses_simplified_parents_upload.$extension",
 270                 Content_Type => ($extension eq "xls") ? 'application/vnd.ms-excel' : 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet',
 271             ],
 272             "upload_crosses_crossing_experiment_id" => $crossing_trial2_id,
 273             "sgn_session_id"                        => $sgn_session_id
 274         ]
 275     );
 276     ok($response->is_success);
 277     my $message = $response->decoded_content;
 278     my $message_hash = decode_json $message;
 279     is_deeply($message_hash, { 'success' => 1 });
 280
 281     my $after_uploading_cross_simplified_info = $schema->resultset("Stock::Stock")->search({ type_id => $cross_type_id })->count();
 282     my $after_uploading_stocks_simplified_info = $schema->resultset("Stock::Stock")->search({})->count();
 283     my $after_uploading_relationship_simplified_info = $schema->resultset("Stock::StockRelationship")->search({})->count();
 284
 285     is($after_uploading_cross_simplified_info, $before_uploading_cross_simplified_info + 4);
 286     is($after_uploading_stocks_simplified_info, $before_uploading_stocks_simplified_info + 4);
 287     is($after_uploading_relationship_simplified_info, $before_uploading_relationship_simplified_info + 13);
 288
 289     # test retrieving crosses in a trial
 290     my $test_add_cross_rs = $schema->resultset('Stock::Stock')->find({ name => 'test_add_cross' });
 291     my $test_add_cross_id = $test_add_cross_rs->stock_id();
 292     my $UG120001_id = $schema->resultset('Stock::Stock')->find({ name => 'UG120001' })->stock_id();
 293     my $UG120002_id = $schema->resultset('Stock::Stock')->find({ name => 'UG120002' })->stock_id();
 294
 295     $mech->post_ok("http://localhost:3010/ajax/breeders/trial/$crossing_trial_id/crosses_and_details_in_trial");
 296     $response = decode_json $mech->content;
 297
 298     is_deeply($response, { 'data' => [ {
 299         cross_id            => $test_add_cross_id,
 300         cross_name          => 'test_add_cross',
 301         cross_combination   => 'UG120001xUG120002',
 302         cross_type          => 'biparental',
 303         female_parent_id    => $UG120001_id,
 304         female_parent_name  => 'UG120001',
 305         female_ploidy_level => undef,
 306         male_parent_id      => $UG120002_id,
 307         male_parent_name    => 'UG120002',
 308         male_ploidy_level   => undef,
 309         female_plot_id      => $female_plot_id,
 310         female_plot_name    => 'KASESE_TP2013_842',
 311         male_plot_id        => $male_plot_id,
 312         male_plot_name      => 'KASESE_TP2013_1591',
 313         female_plant_id     => undef,
 314         female_plant_name   => undef,
 315         male_plant_id       => undef,
 316         male_plant_name     => undef
 317     } ] }, 'crosses in a trial');
 318
 319     # test uploading 6 progenies with new accessions
 320     my $offspring_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "offspring_of", "stock_relationship")->cvterm_id();
 321     my $accession_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "accession", "stock_type")->cvterm_id();
 322
 323     my $before_add_progenies_stock = $schema->resultset("Stock::Stock")->search({})->count();
 324     my $before_add_progenies_accession = $schema->resultset("Stock::Stock")->search({ type_id => $accession_type_id })->count();
 325     my $before_add_progenies_relationship_all = $schema->resultset("Stock::StockRelationship")->search({})->count();
 326     my $before_add_progenies_offspring = $schema->resultset("Stock::StockRelationship")->search({ type_id => $offspring_type_id })->count();
 327
 328     $file = $f->config->{basepath} . "/t/data/cross/update_progenies.$extension";
 329     $ua = LWP::UserAgent->new;
 330     $response = $ua->post(
 331         'http://localhost:3010/ajax/cross/upload_progenies',
 332         Content_Type => 'form-data',
 333         Content      => [
 334             progenies_new_upload_file => [
 335                 $file,
 336                 "update_progenies.$extension",
 337                 Content_Type => ($extension eq "xls") ? 'application/vnd.ms-excel' : 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet',
 338             ],
 339             "sgn_session_id"          => $sgn_session_id
 340         ]
 341     );
 342     ok($response->is_success);
 343     $message = $response->decoded_content;
 344     $message_hash = decode_json $message;
 345     is_deeply($message_hash, { 'success' => 1 });
 346
 347     my $after_add_progenies_stock = $schema->resultset("Stock::Stock")->search({})->count();
 348     my $after_add_progenies_accession = $schema->resultset("Stock::Stock")->search({ type_id => $accession_type_id })->count();
 349     my $after_add_progenies_relationship_all = $schema->resultset("Stock::StockRelationship")->search({})->count();
 350     my $after_add_progenies_offspring = $schema->resultset("Stock::StockRelationship")->search({ type_id => $offspring_type_id })->count();
 351
 352     is($after_add_progenies_stock, $before_add_progenies_stock + 6);
 353     is($after_add_progenies_accession, $before_add_progenies_accession + 6);
 354     is($after_add_progenies_relationship_all, $before_add_progenies_relationship_all + 18);
 355     is($after_add_progenies_offspring, $before_add_progenies_offspring + 6);
 356
 357
 358     #validate uploading 4 progenies using existing accessions (without previously stored pedigrees)
 359     $file = $f->config->{basepath} . "/t/data/cross/update_progenies_existing_accessions.$extension";
 360     $ua = LWP::UserAgent->new;
 361     $response = $ua->post(
 362         'http://localhost:3010/ajax/cross/validate_upload_existing_progenies',
 363         Content_Type => 'form-data',
 364         Content      => [
 365             progenies_exist_upload_file => [
 366                 $file,
 367                 "update_progenies_existing_accessions.$extension",
 368                 Content_Type => ($extension eq "xls") ? 'application/vnd.ms-excel' : 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet',
 369             ],
 370             "sgn_session_id"            => $sgn_session_id
 371         ]
 372     );
 373
 374     ok($response->is_success);
 375     $message = $response->decoded_content;
 376     $message_hash = decode_json $message;
 377     my %response_hash = %$message_hash;
 378     my $message1 = $response_hash{'error_string'};
 379     my $message2 = $response_hash{'existing_pedigrees'};
 380     ok($message1 eq '');
 381     ok($message2 eq '');
 382
 383
 384     #test storing 4 progenies using existing accessions (without previously stored pedigrees)
 385     my $cross_name = 'test_add_cross';
 386     my @existing_accessions = qw(XG120015 XG120021 XG120068 XG120073);
 387     my $overwrite_pedigrees = 'true';
 388     my $adding_progenies = CXGN::Pedigree::AddProgeniesExistingAccessions->new({
 389         chado_schema  => $schema,
 390         cross_name    => $cross_name,
 391         progeny_names => \@existing_accessions,
 392     });
 393
 394     ok(my $return = $adding_progenies->add_progenies_existing_accessions($overwrite_pedigrees));
 395     ok(!exists($return->{error}));
 396
 397     my $after_add_progenies_exist_stock = $schema->resultset("Stock::Stock")->search({})->count();
 398     my $after_add_progenies_exist_accession = $schema->resultset("Stock::Stock")->search({ type_id => $accession_type_id })->count();
 399     my $after_add_progenies_exist_relationship_all = $schema->resultset("Stock::StockRelationship")->search({})->count();
 400     my $after_add_progenies_exist_offspring = $schema->resultset("Stock::StockRelationship")->search({ type_id => $offspring_type_id })->count();
 401
 402     is($after_add_progenies_exist_stock, $after_add_progenies_stock);
 403     is($after_add_progenies_exist_accession, $after_add_progenies_accession);
 404     is($after_add_progenies_exist_relationship_all, $after_add_progenies_relationship_all + 12);
 405     is($after_add_progenies_exist_offspring, $after_add_progenies_offspring + 4);
 406
 407
 408     #validate uploading 2 progenies using existing accessions (accessions have previously stored pedigrees)
 409     #adding pedigrees for testing
 410     my $female_parent = Bio::GeneticRelationships::Individual->new(name => 'TestAccession1');
 411     my $male_parent = Bio::GeneticRelationships::Individual->new(name => 'TestAccession2');
 412     my $pedigree1 = Bio::GeneticRelationships::Pedigree->new(name => 'TestAccession3', cross_type => 'biparental');
 413     $pedigree1->set_female_parent($female_parent);
 414     $pedigree1->set_male_parent($male_parent);
 415
 416     my $pedigree2 = Bio::GeneticRelationships::Pedigree->new(name => 'TestAccession4', cross_type => 'biparental');
 417     $pedigree2->set_female_parent($female_parent);
 418     $pedigree2->set_male_parent($male_parent);
 419
 420     my @pedigrees = ($pedigree1, $pedigree2);
 421     my $add_pedigrees = CXGN::Pedigree::AddPedigrees->new(schema => $schema, pedigrees => \@pedigrees);
 422     my $pedigree_return = $add_pedigrees->add_pedigrees();
 423
 424     my $after_add_pedigrees_relationship_all = $schema->resultset("Stock::StockRelationship")->search({})->count();
 425
 426     $file = $f->config->{basepath} . "/t/data/cross/update_progenies_overwrite_pedigrees.$extension";
 427     $ua = LWP::UserAgent->new;
 428     $response = $ua->post(
 429         'http://localhost:3010/ajax/cross/validate_upload_existing_progenies',
 430         Content_Type => 'form-data',
 431         Content      => [
 432             progenies_exist_upload_file => [
 433                 $file,
 434                 "update_progenies_overwrite_pedigrees.$extension",
 435                 Content_Type => ($extension eq "xls") ? 'application/vnd.ms-excel' : 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet',
 436             ],
 437             "sgn_session_id"            => $sgn_session_id
 438         ]
 439     );
 440
 441     ok($response->is_success);
 442     $message = $response->decoded_content;
 443     $message_hash = decode_json $message;
 444     %response_hash = %$message_hash;
 445     my $message3 = $response_hash{'error_string'};
 446     my $message4 = $response_hash{'existing_pedigrees'};
 447     ok($message3 eq '');
 448     ok($message4 ne '');
 449
 450
 451     #test storing 2 progenies using existing accessions (accessions have previously stored pedigrees)
 452     $cross_name = 'test_add_cross';
 453     @existing_accessions = qw(TestAccession3 TestAccession4);
 454     $overwrite_pedigrees = 'true';
 455     $adding_progenies = CXGN::Pedigree::AddProgeniesExistingAccessions->new({
 456         chado_schema  => $schema,
 457         cross_name    => $cross_name,
 458         progeny_names => \@existing_accessions,
 459     });
 460
 461     ok($return = $adding_progenies->add_progenies_existing_accessions($overwrite_pedigrees));
 462     ok(!exists($return->{error}));
 463
 464     my $after_add_progenies_overwrite_stock = $schema->resultset("Stock::Stock")->search({})->count();
 465     my $after_add_progenies_overwrite_accession = $schema->resultset("Stock::Stock")->search({ type_id => $accession_type_id })->count();
 466     my $after_add_progenies_overwrite_relationship_all = $schema->resultset("Stock::StockRelationship")->search({})->count();
 467     my $after_add_progenies_overwrite_offspring = $schema->resultset("Stock::StockRelationship")->search({ type_id => $offspring_type_id })->count();
 468
 469     is($after_add_progenies_overwrite_stock, $after_add_progenies_exist_stock);
 470     is($after_add_progenies_overwrite_accession, $after_add_progenies_exist_accession);
 471     is($after_add_progenies_overwrite_relationship_all, $after_add_pedigrees_relationship_all + 2);
 472     is($after_add_progenies_overwrite_offspring, $after_add_progenies_exist_offspring + 2);
 473
 474
 475     # test updating cross info by uploading
 476     my $before_updating_info_stocks = $schema->resultset("Stock::Stock")->search({})->count();
 477     my $before_updating_info_stockprop = $schema->resultset("Stock::Stockprop")->search({})->count();
 478     my $before_updating_info_relationship = $schema->resultset("Stock::StockRelationship")->search({})->count();
 479
 480     $file = $f->config->{basepath} . "/t/data/cross/update_crossinfo.$extension";
 481     $ua = LWP::UserAgent->new;
 482     $response = $ua->post(
 483         'http://localhost:3010/ajax/cross/upload_info',
 484         Content_Type => 'form-data',
 485         Content      => [
 486             crossinfo_upload_file => [
 487                 $file,
 488                 "update_crossinfo.$extension",
 489                 Content_Type => ($extension eq "xls") ? 'application/vnd.ms-excel' : 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet',
 490             ],
 491             "sgn_session_id"      => $sgn_session_id
 492         ]
 493     );
 494     ok($response->is_success);
 495     $message = $response->decoded_content;
 496     $message_hash = decode_json $message;
 497     is_deeply($message_hash, { 'success' => 1 });
 498
 499     my $after_updating_info_stocks = $schema->resultset("Stock::Stock")->search({})->count();
 500     my $after_updating_info_stockprop = $schema->resultset("Stock::Stockprop")->search({})->count();
 501     my $after_updating_info_relationship = $schema->resultset("Stock::StockRelationship")->search({})->count();
 502
 503     is($after_updating_info_stocks, $before_updating_info_stocks);
 504     is($after_updating_info_stockprop, $before_updating_info_stockprop + 3);
 505     is($after_updating_info_relationship, $before_updating_info_relationship);
 506
 507     # test uploading additional parent info
 508     $file = $f->config->{basepath} . "/t/data/cross/upload_additional_info.$extension";
 509     $ua = LWP::UserAgent->new;
 510     $response = $ua->post(
 511         'http://localhost:3010/ajax/cross/upload_info',
 512         Content_Type => 'form-data',
 513         Content      => [
 514             additional_info_upload_file => [
 515                 $file,
 516                 "upload_additional_info.$extension",
 517                 Content_Type => ($extension eq "xls") ? 'application/vnd.ms-excel' : 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet',
 518             ],
 519             "sgn_session_id"            => $sgn_session_id
 520         ]
 521     );
 522     ok($response->is_success);
 523     $message = $response->decoded_content;
 524     $message_hash = decode_json $message;
 525     is_deeply($message_hash, { 'success' => 1 });
 526
 527     my $after_upload_additional_info_stocks = $schema->resultset("Stock::Stock")->search({})->count();
 528     my $after_upload_additional_info_stockprop = $schema->resultset("Stock::Stockprop")->search({})->count();
 529     my $after_upload_additional_info_relationship = $schema->resultset("Stock::StockRelationship")->search({})->count();
 530
 531     # note:added 3 more rows in stockprop table after uploading field crossing activities, then 3 more rows in stockprop table after uploading parent additional info
 532     is($after_upload_additional_info_stocks, $before_updating_info_stocks);
 533     is($after_upload_additional_info_stockprop, $before_updating_info_stockprop + 6);
 534     is($after_upload_additional_info_relationship, $before_updating_info_relationship);
 535
 536     # test retrieving crossing experimental info after updating
 537     $mech->post_ok("http://localhost:3010/ajax/breeders/trial/$crossing_trial_id/cross_properties_trial");
 538     $response = decode_json $mech->content;
 539
 540     is_deeply($response, { 'data' => [
 541         [ qq{<a href = "/cross/$test_add_cross_id">test_add_cross</a>}, 'UG120001xUG120002', "10", "2017/02/02", "10", "50", undef, undef ]
 542     ] }, 'crossing experiment info');
 543
 544
 545     # test uploading family names
 546     my $family_name_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "family_name", "stock_type")->cvterm_id();
 547     my $cross_member_of_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'cross_member_of', 'stock_relationship')->cvterm_id();
 548     my $family_female_parent_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'family_female_parent_of', 'stock_relationship')->cvterm_id();
 549     my $family_male_parent_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'family_male_parent_of', 'stock_relationship')->cvterm_id();
 550     my $family_type_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, "family_type", "stock_property")->cvterm_id();
 551
 552     my $before_family_name_stocks = $schema->resultset("Stock::Stock")->search({})->count();
 553     my $before_add_family_name = $schema->resultset("Stock::Stock")->search({ type_id => $family_name_type_id })->count();
 554     my $before_upload_family_relationship = $schema->resultset("Stock::StockRelationship")->search({})->count();
 555     my $before_upload_family_member = $schema->resultset("Stock::StockRelationship")->search({ type_id => $cross_member_of_cvterm_id })->count();
 556     my $before_upload_family_female = $schema->resultset("Stock::StockRelationship")->search({ type_id => $family_female_parent_cvterm_id })->count();
 557     my $before_upload_family_male = $schema->resultset("Stock::StockRelationship")->search({ type_id => $family_male_parent_cvterm_id })->count();
 558     my $before_upload_family_stockprop = $schema->resultset("Stock::Stockprop")->search({ type_id => $family_type_cvterm_id })->count();
 559
 560     $file = $f->config->{basepath} . "/t/data/cross/family_name_upload.$extension";
 561     $ua = LWP::UserAgent->new;
 562     $response = $ua->post(
 563         'http://localhost:3010/ajax/cross/upload_family_names',
 564         Content_Type => 'form-data',
 565         Content      => [
 566             same_parents_file => [
 567                 $file,
 568                 "family_name_upload.$extension",
 569                 Content_Type => ($extension eq "xls") ? 'application/vnd.ms-excel' : 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet',
 570             ],
 571             "sgn_session_id"  => $sgn_session_id
 572         ]
 573     );
 574     ok($response->is_success);
 575     $message = $response->decoded_content;
 576     $message_hash = decode_json $message;
 577     is_deeply($message_hash, { 'success' => 1 });
 578
 579     my $after_family_name_stocks = $schema->resultset("Stock::Stock")->search({})->count();
 580     my $after_add_family_name = $schema->resultset("Stock::Stock")->search({ type_id => $family_name_type_id })->count();
 581     my $after_upload_family_relationship = $schema->resultset("Stock::StockRelationship")->search({})->count();
 582     my $after_upload_family_member = $schema->resultset("Stock::StockRelationship")->search({ type_id => $cross_member_of_cvterm_id })->count();
 583     my $after_upload_family_female = $schema->resultset("Stock::StockRelationship")->search({ type_id => $family_female_parent_cvterm_id })->count();
 584     my $after_upload_family_male = $schema->resultset("Stock::StockRelationship")->search({ type_id => $family_male_parent_cvterm_id })->count();
 585     my $after_upload_family_stockprop = $schema->resultset("Stock::Stockprop")->search({ type_id => $family_type_cvterm_id })->count();
 586
 587     is($after_family_name_stocks, $before_family_name_stocks + 2);
 588     is($after_add_family_name, $before_add_family_name + 2);
 589     is($after_upload_family_relationship, $before_upload_family_relationship + 8);
 590     is($after_upload_family_member, $before_upload_family_member + 4);
 591     is($after_upload_family_female, $before_upload_family_female + 2);
 592     is($after_upload_family_male, $before_upload_family_male + 2);
 593     is($after_upload_family_stockprop, $before_upload_family_stockprop + 2);
 594
 595     #test retrieving family name info
 596     my $family_stock_rs = $schema->resultset("Stock::Stock")->find({ name => 'family1x2', type_id => $family_name_type_id });
 597     my $family_stock_id = $family_stock_rs->stock_id();
 598     my $family_type = $schema->resultset("Stock::Stockprop")->find({ stock_id => $family_stock_id, type_id => $family_type_cvterm_id })->value();
 599     is($family_type, 'same_parents');
 600     #print STDERR "FAMILY ID =".Dumper($family_stock_id)."\n";
 601     $mech->post_ok('http://localhost:3010/ajax/family/members/' . $family_stock_id);
 602     $response = decode_json $mech->content;
 603     my %data = %$response;
 604     my $members = $data{data};
 605     my $number_of_members = @$members;
 606     is($number_of_members, 2);
 607
 608     $mech->post_ok('http://localhost:3010/ajax/family/all_progenies/' . $family_stock_id);
 609     $response = decode_json $mech->content;
 610     my %data = %$response;
 611     my $progenies = $data{data};
 612     my $number_of_progenies = @$progenies;
 613     is($number_of_progenies, 2);
 614
 615     #test adding tissue culture samples
 616     my $before_adding_samples_stockprop = $schema->resultset("Stock::Stockprop")->search({})->count();
 617
 618     my $cross_unique_id = 'test_add_cross';
 619     my $sample_type = 'Embryo IDs';
 620     my @ids = qw(test_embryo_1 test_embryo_2 test_embryo_3 test_embryo_4);
 621     my $cross_add_samples = CXGN::Pedigree::AddCrossTissueSamples->new({
 622         chado_schema => $schema,
 623         cross_name   => $cross_unique_id,
 624         key          => $sample_type,
 625         value        => \@ids,
 626     });
 627
 628     ok(my $return = $cross_add_samples->add_samples());
 629
 630     my $after_adding_samples_stockprop = $schema->resultset("Stock::Stockprop")->search({})->count();
 631     is($after_adding_samples_stockprop, $before_adding_samples_stockprop + 1);
 632
 633     #test retrieving tissue culture samples
 634     my $cross_id = $schema->resultset('Stock::Stock')->find({ name => 'test_add_cross' })->stock_id();
 635     my $cross_samples_obj = CXGN::Cross->new({ schema => $schema, cross_stock_id => $cross_id });
 636     my $cross_sample_data = $cross_samples_obj->get_cross_tissue_culture_samples();
 637     my $embryo_ids_ref = $cross_sample_data->{'Embryo IDs'};
 638     my $number_of_embryo_samples = @$embryo_ids_ref;
 639     is($number_of_embryo_samples, 4);
 640
 641
 642     #test search crosses using female parent
 643     $mech->post_ok('http://localhost:3010/ajax/search/crosses', [ 'female_parent' => 'TMEB419' ]);
 644     $response = decode_json $mech->content;
 645     my %data1 = %$response;
 646     my $result1 = $data1{data};
 647     my $number_of_result1 = @$result1;
 648     is($number_of_result1, 3);
 649
 650     #test search crosses using both female and male parents
 651     $mech->post_ok('http://localhost:3010/ajax/search/crosses', [ 'female_parent' => 'TMEB419', 'male_parent' => 'TMEB693' ]);
 652     $response = decode_json $mech->content;
 653     my %data2 = %$response;
 654     my $result2 = $data2{data};
 655     my $number_of_result2 = @$result2;
 656     is($number_of_result2, 2);
 657
 658     #test search crosses using male parent
 659     $mech->post_ok('http://localhost:3010/ajax/search/crosses', [ 'male_parent' => 'TMEB693' ]);
 660     $response = decode_json $mech->content;
 661     my %data3 = %$response;
 662     my $result3 = $data3{data};
 663     my $number_of_result3 = @$result3;
 664     is($number_of_result3, 2);
 665
 666     #test crossing experiment download
 667     my @cross_properties = ("Tag Number", "Pollination Date", "Number of Bags", "Number of Flowers", "Number of Fruits", "Number of Seeds");
 668     my $tempfile = "/tmp/test_download_crossing_experiment.$extension";
 669     my $format = 'CrossingExperimentXLS';
 670     my $create_spreadsheet = CXGN::Trial::Download->new({
 671         bcs_schema                => $f->bcs_schema,
 672         trial_list                => [ $crossing_trial2_id ],
 673         filename                  => $tempfile,
 674         format                    => $format,
 675         field_crossing_data_order => \@cross_properties
 676     });
 677
 678     $create_spreadsheet->download();
 679     my $contents = ReadData $tempfile;
 680
 681     my $columns = $contents->[1]->{'cell'};
 682     my @column_array = @$columns;
 683     my $number_of_columns = scalar @column_array;
 684     print STDERR "COLUMNS =".Dumper ($columns)."\n";
 685
 686     ok(scalar($number_of_columns) == 22, "check number of columns.");
 687     is_deeply($contents->[1]->{'cell'}->[1], [
 688         undef,
 689         'Cross Unique ID',
 690         'test_backcross1',
 691         'test_backcross2',
 692         'test_backcross3',
 693         'test_cross_upload1',
 694         'test_cross_upload2',
 695         'test_bulk_cross',
 696         'test_bulk_open_cross',
 697         'test_cross_upload3',
 698         'test_cross_upload4',
 699         'test_cross_upload5',
 700         'test_cross_upload6',
 701         'test_cross_simplified_parents_1',
 702         'test_cross_simplified_parents_2',
 703         'test_cross_simplified_parents_3',
 704         'test_cross_simplified_parents_4'
 705     ], "check column 1");
 706
 707     is_deeply($contents->[1]->{'cell'}->[3], [
 708         undef,
 709         'Cross Type',
 710         'backcross',
 711         'backcross',
 712         'backcross',
 713         'biparental',
 714         'self',
 715         'bulk',
 716         'bulk_open',
 717         'biparental',
 718         'self',
 719         'biparental',
 720         'self',
 721         'biparental',
 722         'biparental',
 723         'biparental',
 724         'biparental'
 725     ], "check column 3");
 726
 727     is_deeply($contents->[1]->{'cell'}->[4], [
 728         undef,
 729         'Female Parent',
 730         'test_add_cross',
 731         'test_add_cross',
 732         'test_add_cross',
 733         'UG120001',
 734         'UG120001',
 735         'test_population_A',
 736         'test_population_A',
 737         'UG120001',
 738         'UG120001',
 739         'TMEB419',
 740         'TMEB419',
 741         'UG120001',
 742         'UG120001',
 743         'UG120001',
 744         'TMEB419'
 745     ], "check column 4");
 746
 747
 748     # test retrieving all cross entries
 749     my $crosses = CXGN::Cross->new({ schema => $schema });
 750     my $result = $crosses->get_all_cross_entries();
 751     my @all_cross_entries = @$result;
 752     my $first_cross = $all_cross_entries[0];
 753     is(scalar @all_cross_entries, 16);
 754     is($first_cross->[1], 'test_add_cross');
 755     is($first_cross->[2], 'biparental');
 756     is($first_cross->[4], 'UG120001');
 757     is($first_cross->[8], 'UG120002');
 758     is($first_cross->[11], '2017/02/02');
 759     is($first_cross->[13], 8);
 760     is($first_cross->[15], 'test_crossingtrial');
 761
 762     #test deleting cross
 763     my $before_deleting_crosses = $schema->resultset("Stock::Stock")->search({ type_id => $cross_type_id })->count();
 764     my $before_deleting_accessions = $schema->resultset("Stock::Stock")->search({ type_id => $accession_type_id })->count();
 765     my $before_deleting_stocks = $schema->resultset("Stock::Stock")->search({})->count();
 766     my $before_deleting_relationship = $schema->resultset("Stock::StockRelationship")->search({})->count();
 767     my $experiment_before_deleting_cross = $schema->resultset("NaturalDiversity::NdExperiment")->search({})->count();
 768     my $experiment_stock_before_deleting_cross = $schema->resultset("NaturalDiversity::NdExperimentStock")->search({})->count();
 769
 770     # test_cross_upload1 has 2 progenies and has family name
 771     my $deleting_cross_id = $schema->resultset("Stock::Stock")->find({ name => 'test_cross_upload1' })->stock_id;
 772     $mech->post_ok('http://localhost:3010/ajax/cross/delete', [ 'cross_id' => $deleting_cross_id ]);
 773     $response = decode_json $mech->content;
 774     is($response->{'success'}, '1');
 775
 776     my $after_deleting_crosses = $schema->resultset("Stock::Stock")->search({ type_id => $cross_type_id })->count();
 777     my $after_deleting_accessions = $schema->resultset("Stock::Stock")->search({ type_id => $accession_type_id })->count();
 778     my $after_deleting_stocks = $schema->resultset("Stock::Stock")->search({})->count();
 779     my $after_deleting_relationship = $schema->resultset("Stock::StockRelationship")->search({})->count();
 780     my $experiment_after_deleting_cross = $schema->resultset("NaturalDiversity::NdExperiment")->search({})->count();
 781     my $experiment_stock_after_deleting_cross = $schema->resultset("NaturalDiversity::NdExperimentStock")->search({})->count();
 782
 783     is($after_deleting_crosses, $before_deleting_crosses - 1);
 784     is($after_deleting_accessions, $before_deleting_accessions - 2);
 785     is($after_deleting_stocks, $before_deleting_stocks - 3);
 786     is($after_deleting_relationship, $before_deleting_relationship - 9);
 787     is($experiment_after_deleting_cross, $experiment_before_deleting_cross - 1);
 788     is($experiment_stock_after_deleting_cross, $experiment_stock_before_deleting_cross - 1);
 789
 790     # test deleting empty crossing experiment
 791     my $before_deleting_empty_experiment = $schema->resultset("Project::Project")->search({})->count();
 792
 793     my $crossing_experiment_id = $schema->resultset("Project::Project")->find({ name => 'test_crossingtrial_deletion' })->project_id;
 794     $mech->get_ok('http://localhost:3010/ajax/breeders/trial/' . $crossing_experiment_id . '/delete/crossing_experiment');
 795     $response = decode_json $mech->content;
 796     is($response->{'success'}, '1');
 797
 798     my $after_deleting_empty_experiment = $schema->resultset("Project::Project")->search({})->count();
 799
 800     is($after_deleting_empty_experiment, $before_deleting_empty_experiment - 1);
 801
 802     # test deleting crossing experiment with crosses
 803     my $before_deleting_experiment = $schema->resultset("Project::Project")->search({})->count();
 804
 805     my $crossing_experiment_id_2 = $schema->resultset("Project::Project")->find({ name => 'test_crossingtrial' })->project_id;
 806     $mech->get_ok('http://localhost:3010/ajax/breeders/trial/' . $crossing_experiment_id_2 . '/delete/crossing_experiment');
 807     $response = decode_json $mech->content;
 808     ok($response->{'error'});
 809
 810     my $after_deleting_experiment = $schema->resultset("Project::Project")->search({})->count();
 811
 812     is($after_deleting_experiment, $before_deleting_experiment);
 813
 814     #test deleting all crosses in test_crossingtrial and test_crossingtrial2
 815     $mech->get_ok('http://localhost:3010/ajax/breeders/trial/' . $crossing_trial2_id . '/delete_all_crosses_in_crossingtrial');
 816     $mech->get_ok('http://localhost:3010/ajax/breeders/trial/' . $crossing_trial_id . '/delete_all_crosses_in_crossingtrial');
 817
 818     my $after_delete_all_crosses = $schema->resultset("Stock::Stock")->search({ type_id => $cross_type_id })->count();
 819     my $after_delete_all_crosses_in_experiment = $schema->resultset("NaturalDiversity::NdExperiment")->search({})->count();
 820     my $after_delete_all_crosses_in_experiment_stock = $schema->resultset("NaturalDiversity::NdExperimentStock")->search({})->count();
 821     my $stocks_after_delete_all_crosses = $schema->resultset("Stock::Stock")->search({})->count();
 822
 823     is($after_delete_all_crosses, $before_adding_cross + 1);                             #one cross cannot be deleted because progenies have associated data
 824     is($after_delete_all_crosses_in_experiment, $before_adding_cross_in_experiment + 1); #one cross cannot be deleted because progenies have associated data
 825
 826     # nd_experiment_stock has 38 more rows after adding plants for testing uploading crosses with plant info
 827     is($after_delete_all_crosses_in_experiment_stock, $before_adding_cross_in_experiment_stock + 39);
 828
 829     # stock table has 43 more rows after adding family names and plants, one cross with two new accessions cannot be deleted
 830     is($stocks_after_delete_all_crosses, $before_adding_stocks + 43);
 831
 832     # remove added crossing trials after test so that they don't affect downstream tests
 833     my $project_owner_row_1 = $phenome_schema->resultset('ProjectOwner')->find({ project_id => $crossing_trial_rs->project_id() });
 834     $project_owner_row_1->delete();
 835     $crossing_trial_rs->delete();
 836
 837     my $project_owner_row_2 = $phenome_schema->resultset('ProjectOwner')->find({ project_id => $crossing_trial2_rs->project_id() });
 838     $project_owner_row_2->delete();
 839     $crossing_trial2_rs->delete();
 840
 841     $f->clean_up_db();
 842 }
 843
 844 done_testing();