t/unit_fixture/CXGN/Stock/AddStocks.t

   1 ## A test for adding stocks
   2 ## Jeremy D. Edwards (jde22@cornell.edu) 2015
   3 ##CXGN::Stock::AddStocks is DEPRECATED. Please use CXGN::Stock::Accession->store, which inherits from CXGN::Stock
   4
   5 use strict;
   6 use warnings;
   7
   8 use lib 't/lib';
   9
  10 use Test::More;
  11 use SGN::Test::Fixture;
  12 use CXGN::People::Person;
  13
  14 use Data::Dumper;
  15
  16 my $f = SGN::Test::Fixture->new();
  17 my $schema = $f->bcs_schema();
  18 my $phenome_schema = $f->phenome_schema();
  19 my $dbh = $f->dbh();
  20
  21 $f->get_db_stats();
  22
  23 BEGIN {use_ok('CXGN::Stock::AddStocks');}
  24 BEGIN {require_ok('Moose');}
  25
  26 my @stocks = qw( TestAddStock1 TestAddStock2 );
  27 my $species = "Solanum lycopersicum";
  28 my $owner_name = "johndoe"; #johndoe is a test user that exists in the fixture
  29
  30 ok(my $stock_add = CXGN::Stock::AddStocks
  31    ->new({
  32        schema => $schema,
  33        phenome_schema => $phenome_schema,
  34        dbh => $dbh,
  35        stocks => \@stocks,
  36        species => $species,
  37        owner_name => $owner_name,
  38          }),"Create AddStocks object");
  39
  40 is($stock_add->validate_stocks(), 1, "Validate new stocks don't already exist");  #is true when none of the stock names in the array exist in the database.
  41
  42 ok($stock_add->add_accessions(), "Add new stocks");
  43
  44 my $stock_search = $schema->resultset("Stock::Stock")
  45     ->search({
  46         uniquename => $stocks[0],
  47              } );
  48 ok($stock_search->first(), "Stock exists after adding");
  49
  50 my $stock_search_2 = $schema->resultset("Stock::Stock")
  51     ->search({
  52         uniquename => $stocks[1],
  53              } );
  54 ok($stock_search_2->first(), "Multiple stocks added");
  55
  56 my $organism = $schema->resultset("Organism::Organism")
  57     ->find({
  58         species => $species,
  59            } );
  60 my $organism_id = $organism->organism_id();
  61
  62 is($stock_search->first()->organism_id(), $organism_id, "Organism id on added stocks is correct");
  63
  64 is($stock_add->validate_stocks(), undef, "Stocks should not validate after being added");
  65
  66 my $owner_sp_person_id = CXGN::People::Person->get_person_by_username($dbh, $owner_name);
  67
  68 my $owner_search = $phenome_schema->resultset("StockOwner")
  69     ->find({
  70         stock_id     => $stock_search->first()->stock_id(),
  71            });
  72 is($owner_search->sp_person_id(), $owner_sp_person_id, "Stock owner attached to added stock");
  73
  74 is($stock_add->validate_organism(), 1, "Species name validation");
  75
  76 is($stock_add->validate_owner(), 1, "Stock owner name validation");
  77
  78 $stock_add->set_species("wrongname");
  79
  80 is($stock_add->validate_stocks(), undef, "Incorrect species should not validate");
  81
  82 $stock_add->set_owner_name("wrongowner");
  83
  84 is($stock_add->validate_owner(), undef, "Stock owner names that do not exist should not validate");
  85
  86 # Create a population
  87 my $population_cvterm = $schema->resultset("Cv::Cvterm")->create_with(
  88     { name   => 'population',
  89       cv     => 'stock_type',
  90
  91     });
  92
  93 my $population_name = "test_1_population";
  94
  95 my @populations_to_add = ( $population_name );
  96
  97 ok(my $add_population = CXGN::Stock::AddStocks
  98    ->new({
  99        schema => $schema,
 100        phenome_schema => $phenome_schema,
 101        dbh => $dbh,
 102        stocks => \@populations_to_add,
 103        species => $species,
 104        owner_name => $owner_name,
 105          }),"Create AddStocks object to add population");
 106
 107 ok($add_population->add_population(), "Add new population");
 108
 109 my @stocks_in_population = qw( GroupTestAddStock1 GroupTestAddStock2 );
 110 ok(my $stock_add_in_population = CXGN::Stock::AddStocks
 111    ->new({
 112        schema => $schema,
 113        phenome_schema => $phenome_schema,
 114        dbh => $dbh,
 115        stocks => \@stocks_in_population,
 116        species => $species,
 117        population_name => $population_name,
 118        owner_name => $owner_name,
 119          }),"Create AddStocks object");
 120
 121 is($stock_add_in_population->validate_population(), 1, "Stock population validation");
 122
 123 ok($stock_add_in_population->add_accessions(), "Add new stocks to a population");
 124
 125 my $accession_population_find = $schema->resultset("Stock::Stock")
 126       ->find({
 127           uniquename => $population_name,
 128           type_id => $population_cvterm->cvterm_id(),
 129                } );
 130
 131 my $population_member_cvterm = $schema->resultset("Cv::Cvterm")
 132     ->create_with({
 133         name   => 'member_of',
 134         cv     => 'stock_relationship',
 135
 136                   });
 137
 138 my $population_member = $schema->resultset("Stock::Stock")
 139     ->find({
 140         uniquename => $stocks_in_population[0],
 141         'object.uniquename'=> $population_name,
 142         'stock_relationship_subjects.type_id' => $population_member_cvterm->cvterm_id()
 143            }, {join => {'stock_relationship_subjects' => 'object'}});
 144
 145 is($population_member->uniquename(), $stocks_in_population[0], "Find members of population");
 146
 147 $f->clean_up_db();
 148
 149 done_testing();