t/unit_fixture/CXGN/Trial/TrialCreate.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
  10 my $fix = SGN::Test::Fixture->new();
  11
  12 is(ref($fix->config()), "HASH", 'hashref check');
  13
  14 BEGIN {use_ok('CXGN::Trial::TrialCreate');}
  15 BEGIN {use_ok('CXGN::Trial::TrialLayout');}
  16 BEGIN {use_ok('CXGN::Trial::TrialDesign');}
  17 BEGIN {use_ok('CXGN::Trial::TrialLookup');}
  18 ok(my $chado_schema = $fix->bcs_schema);
  19 ok(my $phenome_schema = $fix->phenome_schema);
  20 ok(my $dbh = $fix->dbh);
  21
  22 # create a location for the trial
  23 ok(my $trial_location = "test_location_for_trial");
  24 ok(my $location = $chado_schema->resultset('NaturalDiversity::NdGeolocation')
  25    ->new({
  26     description => $trial_location,
  27          }));
  28 ok($location->insert());
  29
  30 # create stocks for the trial
  31 ok(my $accession_cvterm = $chado_schema->resultset("Cv::Cvterm")
  32    ->create_with({
  33        name   => 'accession',
  34        cv     => 'stock_type',
  35
  36                  }));
  37 my @stock_names;
  38 for (my $i = 1; $i <= 10; $i++) {
  39     push(@stock_names, "test_stock_for_trial".$i);
  40 }
  41
  42 #create stocks for genotyping trial
  43 my @genotyping_stock_names;
  44 for (my $i = 1; $i <= 10; $i++) {
  45     push(@genotyping_stock_names, "test_stock_for_genotyping_trial".$i);
  46 }
  47
  48
  49 ok(my $organism = $chado_schema->resultset("Organism::Organism")
  50    ->find_or_create( {
  51        genus => 'Test_genus',
  52        species => 'Test_genus test_species',
  53                      }, ));
  54
  55 # create some test stocks
  56 foreach my $stock_name (@stock_names) {
  57     my $accession_stock = $chado_schema->resultset('Stock::Stock')
  58         ->create({
  59             organism_id => $organism->organism_id,
  60             name       => $stock_name,
  61             uniquename => $stock_name,
  62             type_id     => $accession_cvterm->cvterm_id,
  63                  });
  64 };
  65
  66 # create some genotyping test stocks
  67 foreach my $stock_name (@genotyping_stock_names) {
  68     my $accession_stock = $chado_schema->resultset('Stock::Stock')
  69         ->create({
  70             organism_id => $organism->organism_id,
  71             name       => $stock_name,
  72             uniquename => $stock_name,
  73             type_id     => $accession_cvterm->cvterm_id,
  74                  });
  75 };
  76
  77
  78 ok(my $trial_design = CXGN::Trial::TrialDesign->new(), "create trial design object");
  79 ok($trial_design->set_trial_name("test_trial"), "set trial name");
  80 ok($trial_design->set_stock_list(\@stock_names), "set stock list");
  81 ok($trial_design->set_plot_start_number(1), "set plot start number");
  82 ok($trial_design->set_plot_number_increment(1), "set plot increment");
  83 ok($trial_design->set_number_of_blocks(2), "set block number");
  84 ok($trial_design->set_design_type("RCBD"), "set design type");
  85 ok($trial_design->calculate_design(), "calculate design");
  86 ok(my $design = $trial_design->get_design(), "retrieve design");
  87
  88 my $ayt_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'Advanced Yield Trial', 'project_type')->cvterm_id();
  89
  90 ok(my $trial_create = CXGN::Trial::TrialCreate->new({
  91     chado_schema => $chado_schema,
  92     dbh => $dbh,
  93     user_name => "johndoe", #not implemented
  94     design => $design,
  95     program => "test",
  96     trial_year => "2015",
  97     trial_description => "test description",
  98     trial_location => "test_location_for_trial",
  99     trial_name => "new_test_trial_name",
 100     trial_type=>$ayt_cvterm_id,
 101     design_type => "RCBD",
 102     operator => "janedoe"
 103                                                     }), "create trial object");
 104
 105 my $save = $trial_create->save_trial();
 106 ok($save->{'trial_id'}, "save trial");
 107
 108 ok(my $trial_lookup = CXGN::Trial::TrialLookup->new({
 109     schema => $chado_schema,
 110     trial_name => "new_test_trial_name",
 111                                                     }), "create trial lookup object");
 112 ok(my $trial = $trial_lookup->get_trial());
 113 ok(my $trial_id = $trial->project_id());
 114 ok(my $trial_layout = CXGN::Trial::TrialLayout->new({
 115     schema => $chado_schema,
 116     trial_id => $trial_id,
 117     experiment_type => 'field_layout'
 118                                                     }), "create trial layout object");
 119
 120 ok(my $accession_names = $trial_layout->get_accession_names(), "retrieve accession names1");
 121
 122 my %stocks = map { $_ => 1 } @stock_names;
 123
 124 foreach my $acc (@$accession_names) {
 125     ok(exists($stocks{$acc->{accession_name}}), "check accession names $acc->{accession_name}");
 126 }
 127
 128
 129
 130 #create RCBD trial with one accession
 131
 132 @stock_names;
 133 push @stock_names, "test_stock_for_trial1";
 134
 135 ok(my $trial_design = CXGN::Trial::TrialDesign->new(), "create trial design object");
 136 ok($trial_design->set_trial_name("new_test_trial_name_single"), "set trial name");
 137 ok($trial_design->set_stock_list(\@stock_names), "set stock list");
 138 ok($trial_design->set_plot_start_number(1), "set plot start number");
 139 ok($trial_design->set_plot_number_increment(1), "set plot increment");
 140 ok($trial_design->set_number_of_reps(2), "set rep number");
 141 ok($trial_design->set_design_type("CRD"), "set design type");
 142 ok($trial_design->calculate_design(), "calculate design");
 143 ok(my $design = $trial_design->get_design(), "retrieve design");
 144
 145 ok(my $trial_create = CXGN::Trial::TrialCreate->new({
 146     chado_schema => $chado_schema,
 147     dbh => $dbh,
 148     user_name => "johndoe", #not implemented
 149     design => $design,
 150     program => "test",
 151     trial_year => "2015",
 152     trial_description => "test description",
 153     trial_location => "test_location_for_trial",
 154     trial_name => "new_test_trial_name_single",
 155     design_type => "RCBD",
 156     operator => "janedoe"
 157                                                     }), "create trial object");
 158
 159 my $save = $trial_create->save_trial();
 160 ok($save->{'trial_id'}, "save trial");
 161
 162 ok(my $trial_lookup = CXGN::Trial::TrialLookup->new({
 163     schema => $chado_schema,
 164     trial_name => "new_test_trial_name_single",
 165                                                     }), "create trial lookup object");
 166 ok(my $trial = $trial_lookup->get_trial());
 167 ok(my $trial_id = $trial->project_id());
 168 ok(my $trial_layout = CXGN::Trial::TrialLayout->new({
 169     schema => $chado_schema,
 170     trial_id => $trial_id,
 171     experiment_type => 'field_layout'
 172                                                     }), "create trial layout object");
 173
 174 ok(my $accession_names = $trial_layout->get_accession_names(), "retrieve accession names2");
 175
 176 my %stocks = map { $_ => 1 } @stock_names;
 177
 178 foreach my $acc (@$accession_names) {
 179     ok(exists($stocks{$acc->{accession_name}}), "check accession names $acc->{accession_name}");
 180 }
 181
 182
 183 # layout for genotyping experiment
 184 # use data structure returned by brapi call for GDF:
 185 # plates:[ { 'project_id' : 'project x',
 186 #            'plate_name' : 'required',
 187 #            'plate_format': 'Plate_96' | 'tubes',
 188 #            'sample_type' : 'DNA' | 'RNA' | 'Tissue'
 189 #            'samples':[
 190 # {
 191 #               'name': 'sample_name1',
 192 #               'well': 'optional'
 193 #               'concentration:
 194 #'              'volume':
 195 #               'taxomony_id' :
 196 #               'tissue_type' :
 197 #               }
 198 # ]
 199
 200 my $plate_info = {
 201     elements => \@genotyping_stock_names,
 202     plate_format => 96,
 203     blank_well => 'A02',
 204     name => 'test_genotyping_trial_name',
 205     description => "test description",
 206     year => '2015',
 207     project_name => 'NextGenCassava',
 208     genotyping_facility_submit => 'no',
 209     genotyping_facility => 'igd',
 210     sample_type => 'DNA'
 211 };
 212
 213 my $gd = CXGN::Trial::TrialDesign->new( { schema => $chado_schema } );
 214 $gd->set_stock_list($plate_info->{elements});
 215 $gd->set_block_size($plate_info->{plate_format});
 216 $gd->set_blank($plate_info->{blank_well});
 217 $gd->set_trial_name($plate_info->{name});
 218 $gd->set_design_type("genotyping_plate");
 219 $gd->calculate_design();
 220 my $geno_design = $gd->get_design();
 221
 222 print STDERR Dumper $geno_design;
 223 is_deeply($geno_design, {
 224           'A09' => {
 225                      'row_number' => 'A',
 226                      'plot_name' => 'test_genotyping_trial_name_A09',
 227                      'stock_name' => 'test_stock_for_genotyping_trial8',
 228                      'col_number' => 9,
 229                      'is_blank' => 0,
 230                      'plot_number' => 'A09'
 231                    },
 232           'A07' => {
 233                      'is_blank' => 0,
 234                      'plot_number' => 'A07',
 235                      'plot_name' => 'test_genotyping_trial_name_A07',
 236                      'row_number' => 'A',
 237                      'col_number' => 7,
 238                      'stock_name' => 'test_stock_for_genotyping_trial6'
 239                    },
 240           'A02' => {
 241                      'is_blank' => 1,
 242                      'plot_number' => 'A02',
 243                      'row_number' => 'A',
 244                      'plot_name' => 'test_genotyping_trial_name_A02_BLANK',
 245                      'stock_name' => 'BLANK',
 246                      'col_number' => 2
 247                    },
 248           'A05' => {
 249                      'is_blank' => 0,
 250                      'plot_number' => 'A05',
 251                      'row_number' => 'A',
 252                      'plot_name' => 'test_genotyping_trial_name_A05',
 253                      'stock_name' => 'test_stock_for_genotyping_trial4',
 254                      'col_number' => 5
 255                    },
 256           'A08' => {
 257                      'plot_name' => 'test_genotyping_trial_name_A08',
 258                      'row_number' => 'A',
 259                      'col_number' => 8,
 260                      'stock_name' => 'test_stock_for_genotyping_trial7',
 261                      'is_blank' => 0,
 262                      'plot_number' => 'A08'
 263                    },
 264           'A04' => {
 265                      'plot_name' => 'test_genotyping_trial_name_A04',
 266                      'row_number' => 'A',
 267                      'stock_name' => 'test_stock_for_genotyping_trial3',
 268                      'col_number' => 4,
 269                      'is_blank' => 0,
 270                      'plot_number' => 'A04'
 271                    },
 272           'A01' => {
 273                      'is_blank' => 0,
 274                      'plot_number' => 'A01',
 275                      'plot_name' => 'test_genotyping_trial_name_A01',
 276                      'row_number' => 'A',
 277                      'stock_name' => 'test_stock_for_genotyping_trial1',
 278                      'col_number' => 1
 279                    },
 280           'A11' => {
 281                      'plot_name' => 'test_genotyping_trial_name_A11',
 282                      'row_number' => 'A',
 283                      'stock_name' => 'test_stock_for_genotyping_trial10',
 284                      'col_number' => 11,
 285                      'is_blank' => 0,
 286                      'plot_number' => 'A11'
 287                    },
 288           'A06' => {
 289                      'plot_number' => 'A06',
 290                      'is_blank' => 0,
 291                      'stock_name' => 'test_stock_for_genotyping_trial5',
 292                      'col_number' => 6,
 293                      'row_number' => 'A',
 294                      'plot_name' => 'test_genotyping_trial_name_A06'
 295                    },
 296           'A10' => {
 297                      'is_blank' => 0,
 298                      'plot_number' => 'A10',
 299                      'plot_name' => 'test_genotyping_trial_name_A10',
 300                      'row_number' => 'A',
 301                      'col_number' => 10,
 302                      'stock_name' => 'test_stock_for_genotyping_trial9'
 303                    },
 304           'A03' => {
 305                      'plot_name' => 'test_genotyping_trial_name_A03',
 306                      'row_number' => 'A',
 307                      'stock_name' => 'test_stock_for_genotyping_trial2',
 308                      'col_number' => 3,
 309                      'is_blank' => 0,
 310                      'plot_number' => 'A03'
 311                    }
 312         }, 'check genotyping trial design');
 313
 314 my $genotyping_trial_create;
 315 ok($genotyping_trial_create = CXGN::Trial::TrialCreate->new({
 316     chado_schema => $chado_schema,
 317     dbh => $dbh,
 318     user_name => "johndoe", #not implemented
 319     program => "test",
 320     trial_location => "test_location_for_trial",
 321     operator => "janedoe",
 322     trial_year => $plate_info->{year},
 323     trial_description => $plate_info->{description},
 324     design_type => 'genotyping_plate',
 325     design => $geno_design,
 326     trial_name => $plate_info->{name},
 327     is_genotyping => 1,
 328     genotyping_user_id => 41,
 329     genotyping_project_name => $plate_info->{project_name},
 330     genotyping_facility_submitted => $plate_info->{genotyping_facility_submit},
 331     genotyping_facility => $plate_info->{genotyping_facility},
 332     genotyping_plate_format => $plate_info->{plate_format},
 333     genotyping_plate_sample_type => $plate_info->{sample_type},
 334     }), "create genotyping trial");
 335
 336 my $save = $genotyping_trial_create->save_trial();
 337 ok($save->{'trial_id'}, "save genotyping trial");
 338
 339 ok(my $genotyping_trial_lookup = CXGN::Trial::TrialLookup->new({
 340     schema => $chado_schema,
 341     trial_name => "test_genotyping_trial_name",
 342                                                     }), "lookup genotyping trial");
 343 ok(my $genotyping_trial = $genotyping_trial_lookup->get_trial(), "retrieve genotyping trial");
 344 ok(my $genotyping_trial_id = $genotyping_trial->project_id(), "retrive genotyping trial id");
 345 ok(my $genotyping_trial_layout = CXGN::Trial::TrialLayout->new({
 346     schema => $chado_schema,
 347     trial_id => $genotyping_trial_id,
 348     experiment_type => 'genotyping_layout'
 349                                                     }), "create trial layout object for genotyping trial");
 350 ok(my $genotyping_accession_names = $genotyping_trial_layout->get_accession_names(), "retrieve accession names3");
 351 my %genotyping_stocks = map { $_ => 1 } @genotyping_stock_names;
 352 $genotyping_stocks{'BLANK'} = 1;
 353 foreach my $acc (@$genotyping_accession_names) {
 354     ok(exists($genotyping_stocks{$acc->{accession_name}}), "check existence of accession names $acc->{accession_name}");
 355 }
 356
 357 done_testing();