t/unit_fixture/CXGN/Trial/DeriveTrait.t

   1
   2 use strict;
   3
   4 use Test::More;
   5 use lib 't/lib';
   6 use SGN::Test::Fixture;
   7 use Data::Dumper;
   8 use CXGN::Phenotypes::StorePhenotypes;
   9 use CXGN::BreedersToolbox::DeriveTrait;
  10 use SGN::Model::Cvterm;
  11
  12 my $fix = SGN::Test::Fixture->new();
  13
  14 is(ref($fix->config()), "HASH", 'hashref check');
  15
  16 BEGIN {use_ok('CXGN::Trial::TrialCreate');}
  17 BEGIN {use_ok('CXGN::Trial::TrialLayout');}
  18 BEGIN {use_ok('CXGN::Trial::TrialDesign');}
  19 BEGIN {use_ok('CXGN::Trial::TrialLookup');}
  20 ok(my $chado_schema = $fix->bcs_schema);
  21 ok(my $phenome_schema = $fix->phenome_schema);
  22 ok(my $dbh = $fix->dbh);
  23
  24 # create a location for the trial
  25 ok(my $trial_location = "test_location_for_trial_derive_trait");
  26 ok(my $location = $chado_schema->resultset('NaturalDiversity::NdGeolocation')
  27    ->new({
  28     description => $trial_location,
  29          }));
  30 ok($location->insert());
  31
  32 # create stocks for the trial
  33 ok(my $accession_cvterm = $chado_schema->resultset("Cv::Cvterm")
  34    ->create_with({
  35        name   => 'accession',
  36        cv     => 'stock_type',
  37 }));
  38 my @stock_names;
  39 for (my $i = 1; $i <= 10; $i++) {
  40     push(@stock_names, "test_stock_for_trial_derive_trait".$i);
  41 }
  42
  43 ok(my $organism = $chado_schema->resultset("Organism::Organism")
  44    ->find_or_create( {
  45        genus => 'Test_genus',
  46        species => 'Test_genus test_species',
  47 }, ));
  48
  49 # create some test stocks
  50 foreach my $stock_name (@stock_names) {
  51     my $accession_stock = $chado_schema->resultset('Stock::Stock')
  52         ->create({
  53             organism_id => $organism->organism_id,
  54             name       => $stock_name,
  55             uniquename => $stock_name,
  56             type_id     => $accession_cvterm->cvterm_id,
  57                  });
  58 };
  59
  60
  61 ok(my $trial_design = CXGN::Trial::TrialDesign->new(), "create trial design object");
  62 ok($trial_design->set_trial_name("test_trial_derive_trait"), "set trial name");
  63 ok($trial_design->set_stock_list(\@stock_names), "set stock list");
  64 ok($trial_design->set_plot_start_number(1), "set plot start number");
  65 ok($trial_design->set_plot_number_increment(1), "set plot increment");
  66 ok($trial_design->set_number_of_blocks(2), "set block number");
  67 ok($trial_design->set_design_type("RCBD"), "set design type");
  68 ok($trial_design->calculate_design(), "calculate design");
  69 ok(my $design = $trial_design->get_design(), "retrieve design");
  70
  71 print STDERR Dumper $design;
  72
  73 ok(my $trial_create = CXGN::Trial::TrialCreate->new({
  74     chado_schema => $chado_schema,
  75     dbh => $dbh,
  76     owner_id => 41,
  77     design => $design,
  78     program => "test",
  79     trial_year => "2016",
  80     trial_description => "test_trial_derive_trait description",
  81     trial_location => "test_location_for_trial_derive_trait",
  82     trial_name => "test_trial_derive_trait",
  83     design_type => "RCBD",
  84     operator => "janedoe"
  85 }), "create trial object");
  86
  87 ok(my $save = $trial_create->save_trial(), "save trial");
  88 my $trial_id = $save->{'trial_id'};
  89 my $trial = CXGN::Trial->new({ bcs_schema => $fix->bcs_schema(), trial_id => $trial_id });
  90
  91 my $trial_plots = $trial->get_plots();
  92 my @trial_plot_names;
  93 foreach (@$trial_plots){
  94     push @trial_plot_names, $_->[1];
  95 }
  96 @trial_plot_names = sort @trial_plot_names;
  97 is(scalar(@trial_plot_names), 20, "check num plots saved");
  98
  99 my $num_plants_add = 2;
 100 $trial->create_plant_entities($num_plants_add);
 101
 102 my %phenotype_metadata;
 103 $phenotype_metadata{'operator'}="janedoe";
 104 $phenotype_metadata{'date'}="2017-02-16_01:10:56";
 105 my @plots = sort ( $trial_plot_names[0], $trial_plot_names[1], $trial_plot_names[2] );
 106 my @plants = sort ( $trial_plot_names[0]."_plant_2", $trial_plot_names[1]."_plant_2", $trial_plot_names[2]."_plant_2" );
 107 print STDERR Dumper \@plots;
 108
 109 my $parsed_data = {
 110             $plants[0] => {
 111                                 'dry matter content|CO_334:0000092' => [
 112                                                                      '23',
 113                                                                      '2017-02-11 11:12:20-0500'
 114                                                                    ]
 115                                                    },
 116             $plants[1] => {
 117                                'dry matter content|CO_334:0000092' => [
 118                                                                     '28',
 119                                                                     '2017-02-11 11:13:20-0500'
 120                                                                   ]
 121                                                   },
 122             $plants[2] => {
 123                               'dry matter content|CO_334:0000092' => [
 124                                                                    '30',
 125                                                                    '2017-02-11 11:15:20-0500'
 126                                                                  ]
 127                                                  },
 128             };
 129
 130 my @traits = ( 'dry matter content|CO_334:0000092' );
 131
 132 my $store_phenotypes = CXGN::Phenotypes::StorePhenotypes->new(
 133     basepath=>$fix->config->{basepath},
 134     dbhost=>$fix->config->{dbhost},
 135     dbname=>$fix->config->{dbname},
 136     dbuser=>$fix->config->{dbuser},
 137     dbpass=>$fix->config->{dbpass},
 138     temp_file_nd_experiment_id=>$fix->config->{cluster_shared_tempdir}."/test_temp_nd_experiment_id_delete",
 139     bcs_schema=>$fix->bcs_schema,
 140     metadata_schema=>$fix->metadata_schema,
 141     phenome_schema=>$fix->phenome_schema,
 142     user_id=>41,
 143     stock_list=>\@plants,
 144     trait_list=>\@traits,
 145     values_hash=>$parsed_data,
 146     has_timestamps=>1,
 147     overwrite_values=>0,
 148     metadata_hash=>\%phenotype_metadata,
 149     composable_validation_check_name=>$fix->config->{composable_validation_check_name}
 150 );
 151
 152 my ($stored_phenotype_error_msg, $stored_phenotype_success) = $store_phenotypes->store();
 153 ok(!$stored_phenotype_error_msg, "check that store pheno spreadsheet works");
 154
 155 my $tn = CXGN::Trial->new( { bcs_schema => $fix->bcs_schema(),
 156                                 trial_id => $trial_id });
 157 my $traits_assayed  = $tn->get_traits_assayed();
 158 my @traits_assayed_sorted = sort {$a->[0] cmp $b->[0]} @$traits_assayed;
 159 print STDERR Dumper \@traits_assayed_sorted;
 160 is_deeply(\@traits_assayed_sorted, [
 161           [
 162             70741,
 163             'dry matter content percentage|CO_334:0000092', [], 3, undef, undef
 164           ]
 165         ], "check upload worked");
 166
 167
 168 my $method = 'arithmetic_mean';
 169 my $rounding = 'round';
 170 my $trait_name = 'dry matter content|CO_334:0000092';
 171 my $derive_trait = CXGN::BreedersToolbox::DeriveTrait->new({bcs_schema=>$fix->bcs_schema, trait_name=>$trait_name, trial_id=>$trial_id, method=>$method, rounding=>$rounding});
 172 my ($info, $plots_ret, $traits, $store_hash) = $derive_trait->generate_plot_phenotypes();
 173 #print STDERR Dumper $info;
 174
 175 my @sorted_plots_ret = sort @$plots_ret;
 176 is_deeply(\@plots, \@sorted_plots_ret, 'check generated plots');
 177
 178 my @values_to_store;
 179 foreach my $info_n (@$info) {
 180     push @values_to_store, $info_n->{'value_to_store'};
 181 }
 182 @values_to_store = sort @values_to_store;
 183 print STDERR Dumper \@values_to_store;
 184 is_deeply(\@values_to_store, [23,28,30], "check returned values");
 185
 186 print STDERR Dumper $store_hash;
 187
 188 my %phenotype_metadata;
 189 $phenotype_metadata{'operator'}='janedoe';
 190 $phenotype_metadata{'date'}="2017-02-16_03:10:59";
 191 my $store_phenotypes = CXGN::Phenotypes::StorePhenotypes->new(
 192     basepath=>$fix->config->{basepath},
 193     dbhost=>$fix->config->{dbhost},
 194     dbname=>$fix->config->{dbname},
 195     dbuser=>$fix->config->{dbuser},
 196     dbpass=>$fix->config->{dbpass},
 197     temp_file_nd_experiment_id=>$fix->config->{cluster_shared_tempdir}."/test_temp_nd_experiment_id_delete",
 198     bcs_schema=>$fix->bcs_schema,
 199     metadata_schema=>$fix->metadata_schema,
 200     phenome_schema=>$fix->phenome_schema,
 201     user_id=>41,
 202     stock_list=>$plots_ret,
 203     trait_list=>$traits,
 204     values_hash=>$store_hash,
 205     has_timestamps=>0,
 206     overwrite_values=>1,
 207     metadata_hash=>\%phenotype_metadata,
 208     composable_validation_check_name=>$fix->config->{composable_validation_check_name}
 209 );
 210
 211 my ($store_error, $store_success) = $store_phenotypes->store();
 212 ok(!$store_error, "check that store pheno spreadsheet works");
 213
 214 my $trait_id = SGN::Model::Cvterm->get_cvterm_row_from_trait_name($fix->bcs_schema, 'dry matter content|CO_334:0000092')->cvterm_id();
 215 my $all_stock_phenotypes_for_dry_matter_content = $tn->get_stock_phenotypes_for_traits([$trait_id], 'all', ['plot_of','plant_of'], 'accession', 'subject');
 216 #print STDERR Dumper $all_stock_phenotypes_for_dry_matter_content;
 217 ok(scalar(@$all_stock_phenotypes_for_dry_matter_content) == 6, "check if num phenotype saved is correct");
 218 my $plant_phenotypes_for_dry_matter_content = $tn->get_stock_phenotypes_for_traits([$trait_id], 'plant', ['plant_of'], 'accession', 'subject');
 219 #print STDERR Dumper $plant_phenotypes_for_dry_matter_content;
 220 ok(scalar(@$plant_phenotypes_for_dry_matter_content) == 3, "check num phenotype for plant is correct");
 221 my $plot_phenotypes_for_dry_matter_content = $tn->get_stock_phenotypes_for_traits([$trait_id], 'plot', ['plot_of'], 'accession', 'subject');
 222 #print STDERR Dumper $plot_phenotypes_for_dry_matter_content;
 223 ok(scalar(@$plot_phenotypes_for_dry_matter_content) == 3, "check num phenotype for plot is correct");
 224
 225 done_testing();