t/unit_fixture/CXGN/Trial/EditFieldMap.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 BEGIN {use_ok('CXGN::Trial::FieldMap');}
  17 BEGIN {use_ok('CXGN::Trial');}
  18 ok(my $chado_schema = $fix->bcs_schema);
  19 ok(my $phenome_schema = $fix->phenome_schema);
  20 ok(my $dbh = $fix->dbh);
  21
  22 $chado_schema->txn_begin();
  23 # create a location for the trial
  24 ok(my $trial_location = "test_location_for_trial");
  25 ok(my $location = $chado_schema->resultset('NaturalDiversity::NdGeolocation')
  26    ->new({
  27     description => $trial_location,
  28          }));
  29 ok($location->insert());
  30
  31 # create stocks for the trial
  32 ok(my $accession_cvterm = $chado_schema->resultset("Cv::Cvterm")
  33    ->create_with({
  34        name   => 'accession',
  35        cv     => 'stock_type',
  36
  37                  }));
  38 my @stock_names;
  39 for (my $i = 1; $i <= 10; $i++) {
  40     push(@stock_names, "test_stock_for_trial".$i);
  41 }
  42
  43 # create a location for the trial
  44 ok(my $trial_location = "test_location_for_trial");
  45 ok(my $location = $chado_schema->resultset('NaturalDiversity::NdGeolocation')
  46    ->new({
  47     description => $trial_location,
  48          }));
  49 ok($location->insert());
  50
  51 # create stocks for the trial
  52 ok(my $accession_cvterm = $chado_schema->resultset("Cv::Cvterm")
  53    ->create_with({
  54        name   => 'accession',
  55        cv     => 'stock_type',
  56
  57                  }));
  58 my @stock_names;
  59 for (my $i = 1; $i <= 10; $i++) {
  60     push(@stock_names, "test_stock_for_fieldmap_trial".$i);
  61 }
  62
  63 ok(my $organism = $chado_schema->resultset("Organism::Organism")
  64    ->find_or_create( {
  65        genus => 'Test_genus',
  66        species => 'Test_genus test_species',
  67                      }, ));
  68
  69 # create some test stocks
  70 foreach my $stock_name (@stock_names) {
  71     my $accession_stock = $chado_schema->resultset('Stock::Stock')
  72         ->create({
  73             organism_id => $organism->organism_id,
  74             name       => $stock_name,
  75             uniquename => $stock_name,
  76             type_id     => $accession_cvterm->cvterm_id,
  77                  });
  78 };
  79
  80 ok(my $trial_design = CXGN::Trial::TrialDesign->new(), "create trial design object");
  81 ok($trial_design->set_trial_name("new_test_trial_fieldmap_name"), "set trial name");
  82 ok($trial_design->set_stock_list(\@stock_names), "set stock list");
  83 ok($trial_design->set_plot_start_number(1), "set plot start number");
  84 ok($trial_design->set_plot_number_increment(1), "set plot increment");
  85 ok($trial_design->set_number_of_blocks(2), "set block number");
  86 ok($trial_design->set_design_type("RCBD"), "set design type");
  87 ok($trial_design->set_plot_layout_format("serpentine"), "set plot layout format");
  88 ok($trial_design->calculate_design(), "calculate design");
  89 ok(my $design = $trial_design->get_design(), "retrieve design");
  90
  91 ok(my $trial_create = CXGN::Trial::TrialCreate->new({
  92     chado_schema => $chado_schema,
  93     dbh => $dbh,
  94     owner_id => 41,
  95     design => $design,
  96     program => "test",
  97     trial_year => "2015",
  98     trial_description => "test description",
  99     trial_location => "test_location_for_trial",
 100     trial_name => "new_test_trial_fieldmap_name",
 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_fieldmap_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 #replace trial accession
 121 ok(my $old_accession = "test_stock_for_fieldmap_trial1");
 122 ok(my $new_accession = "test_stock_for_fieldmap_trial2");
 123 ok(my $stock_id = $chado_schema->resultset('Stock::Stock')->find({'uniquename' => $old_accession})->stock_id(), "get stock id");
 124
 125 my $replace_accession_fieldmap = CXGN::Trial::FieldMap->new({
 126   bcs_schema => $chado_schema,
 127   trial_id => $trial_id,
 128   old_accession_id => $stock_id,
 129   new_accession => $new_accession,
 130 });
 131 ok(!$replace_accession_fieldmap->replace_trial_stock_fieldMap($new_accession, $stock_id), "replace trial accession");
 132
 133
 134 my $trial = CXGN::Trial->new( {
 135   bcs_schema => $chado_schema,
 136   trial_id => $trial_id
 137  });
 138
 139 #replace plot accession
 140 ok(my @data = $trial->get_plots(), "get plots");
 141 ok(my $old_plot_id = $data[0]->[0][0]);
 142 print STDERR Dumper($old_plot_id);
 143 my $plot_of_type_id = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'plot_of', 'stock_relationship')->cvterm_id();
 144 my $accession_id = $chado_schema->resultset('Stock::Stock')->find({'uniquename' => $new_accession})->stock_id(), "get stock id";
 145
 146 my $replace_plot_accession_fieldmap = CXGN::Trial::FieldMap->new({
 147   bcs_schema => $chado_schema,
 148   trial_id => $trial_id,
 149
 150 });
 151 ok(!$replace_plot_accession_fieldmap->replace_plot_accession_fieldMap($old_plot_id, $accession_id, $plot_of_type_id), "replace plot accession");
 152 # accessions substitution
 153 ok(my $plot_1_id = $data[0]->[0][0]);
 154 ok(my $plot_2_id = $data[0]->[1][0]);
 155 ok(my $accession_1 = "test_stock_for_fieldmap_trial1");
 156 ok(my $accession_2 = "test_stock_for_fieldmap_trial2");
 157 $chado_schema->txn_rollback();
 158 # my $fieldmap = CXGN::Trial::FieldMap->new({
 159 #   bcs_schema => $chado_schema,
 160 #   trial_id => $trial_id,
 161 #   first_plot_selected => $plot_1_id,
 162 #   second_plot_selected => $plot_2_id,
 163 #   first_accession_selected => $accession_1,
 164 #   second_accession_selected => $accession_2,
 165 # });
 166
 167 # ok(!$fieldmap->substitute_accession_fieldmap(), "substituting plots accessions");
 168
 169 done_testing();