t/unit_fixture/CXGN/Trial/MultiTrialCreate.t

   1 use strict;
   2
   3 use Test::More;
   4 use lib 't/lib';
   5 use SGN::Test::Fixture;
   6 use Data::Dumper;
   7
   8 my $fix = SGN::Test::Fixture->new();
   9
  10 is(ref($fix->config()), "HASH", 'hashref check');
  11
  12 BEGIN {use_ok('CXGN::Trial::TrialCreate');}
  13 BEGIN {use_ok('CXGN::Trial::TrialLayout');}
  14 BEGIN {use_ok('CXGN::Trial::TrialDesign');}
  15 BEGIN {use_ok('CXGN::Trial::TrialLookup');}
  16 ok(my $chado_schema = $fix->bcs_schema);
  17 ok(my $phenome_schema = $fix->phenome_schema);
  18 ok(my $dbh = $fix->dbh);
  19
  20 # create locations for the trial
  21 my @multi_location;
  22 for (my $i = 1; $i <= 2; $i++) {
  23   ok(my $trial_location = "test_location_for_multi_trial".$i);
  24   push @multi_location, $trial_location;
  25 }
  26
  27 foreach my $multi_trial_loc (@multi_location) {
  28   ok(my $location = $chado_schema->resultset('NaturalDiversity::NdGeolocation')
  29      ->new({
  30       description => $multi_trial_loc,
  31          }));
  32   ok($location->insert());
  33 };
  34
  35 # create stocks for the trial
  36 ok(my $accession_cvterm = $chado_schema->resultset("Cv::Cvterm")
  37    ->create_with({
  38        name   => 'accession',
  39        cv     => 'stock_type',
  40
  41                  }));
  42
  43 my @stock_names;
  44 for (my $i = 1; $i <= 10; $i++) {
  45     push(@stock_names, "test_stock_for_multi_trial".$i);
  46 }
  47
  48 ok(my $organism = $chado_schema->resultset("Organism::Organism")
  49    ->find_or_create( {
  50        genus => 'Test_genus',
  51        species => 'Test_genus test_species',
  52                      }, ));
  53
  54 # create some test stocks
  55 foreach my $stock_name (@stock_names) {
  56     my $accession_stock = $chado_schema->resultset('Stock::Stock')
  57         ->create({
  58             organism_id => $organism->organism_id,
  59             name       => $stock_name,
  60             uniquename => $stock_name,
  61             type_id     => $accession_cvterm->cvterm_id,
  62                  });
  63 };
  64
  65 #create multilocation trial
  66 my @multi_design;
  67 my $design_index = 0;
  68 foreach my $trial_location (@multi_location) {
  69   ok(my $trial_design = CXGN::Trial::TrialDesign->new(), "create trial design object");
  70   ok($trial_design->set_trial_name("test_multi_trial_name".$trial_location), "set trial name");
  71   ok($trial_design->set_stock_list(\@stock_names), "set stock list");
  72   ok($trial_design->set_plot_start_number(1), "set plot start number");
  73   ok($trial_design->set_plot_number_increment(1), "set plot increment");
  74   ok($trial_design->set_number_of_blocks(2), "set block number");
  75   ok($trial_design->set_design_type("RCBD"), "set design type");
  76   ok($trial_design->calculate_design(), "calculate design");
  77   ok(my $design = $trial_design->get_design(), "retrieve design");
  78   push @multi_design, $design;
  79
  80     ok(my $trial_create = CXGN::Trial::TrialCreate->new({
  81         chado_schema => $chado_schema,
  82         dbh => $dbh,
  83         owner_id => 41,
  84         design => $multi_design[$design_index],
  85         program => "test",
  86         trial_year => "2016",
  87         trial_description => "multilocation test description",
  88         #trial_location => "test_location_for_trial",
  89         trial_location => $trial_location,
  90         trial_name => "test_multi_trial_name".$trial_location,
  91         design_type => "RCBD",
  92         operator => "janedoe"
  93                                                     }), "create trial object");
  94
  95     my $save = $trial_create->save_trial();
  96     ok($save->{'trial_id'}, "save trial");
  97
  98 $design_index++;
  99
 100 ok(my $trial_lookup = CXGN::Trial::TrialLookup->new({
 101     schema => $chado_schema,
 102     trial_name => "test_multi_trial_name".$trial_location,
 103                                                     }), "create trial lookup object");
 104 ok(my $trial = $trial_lookup->get_trial());
 105 ok(my $trial_id = $trial->project_id());
 106 ok(my $trial_layout = CXGN::Trial::TrialLayout->new({
 107     schema => $chado_schema,
 108     trial_id => $trial_id,
 109     experiment_type => 'field_layout'
 110                                                     }), "create trial layout object");
 111 print STDERR Dumper($trial_layout->get_design());
 112
 113 ok(my $accession_names = $trial_layout->get_accession_names(), "retrieve accession names2");
 114
 115 my %stocks = map { $_ => 1 } @stock_names;
 116
 117 foreach my $acc (@$accession_names) {
 118     ok(exists($stocks{$acc->{accession_name}}), "check accession names $acc->{accession_name}");
 119 }
 120
 121 }
 122
 123 done_testing();