t/unit_mech/AJAX/Heritability.t

   1
   2 use strict;
   3 use warnings;
   4
   5 use lib 't/lib';
   6 use SGN::Test::Fixture;
   7 use Test::More;
   8 use Test::WWW::Mechanize;
   9
  10 use Data::Dumper;
  11 use JSON;
  12 use Spreadsheet::Read;
  13
  14 use CXGN::Dataset;
  15 use Text::CSV ("csv");
  16
  17 my $f = SGN::Test::Fixture->new();
  18 my $schema = $f->bcs_schema;
  19 my $people_schema = $f->people_schema();
  20
  21 my $mech = Test::WWW::Mechanize->new;
  22 my $response;
  23
  24 # login
  25 #
  26 $mech->post_ok('http://localhost:3010/brapi/v1/token', [ "username"=> "janedoe", "password"=> "secretpw", "grant_type"=> "password" ], 'login with brapi call');
  27
  28 $response = decode_json $mech->content;
  29
  30 is($response->{'userDisplayName'}, 'Jane Doe', 'check login name');
  31
  32 # create a suitable dataset
  33 #
  34 my $ds = CXGN::Dataset->new( { schema=> $schema, people_schema => $people_schema });
  35
  36 $ds->trials( [ 139, 141 ]);
  37 $ds->store();
  38
  39 my $dataset_id = $ds->sp_dataset_id();
  40
  41 $mech->get_ok('http://localhost:3010/tools/heritability', 'load heritability input page');
  42
  43 $mech->get_ok('http://localhost:3010/ajax/heritability/shared_phenotypes?dataset_id='.$dataset_id, 'get common traits for dataset');
  44
  45 my $sp_data = JSON::Any->decode($mech->content());
  46
  47 my $trait_id = $sp_data->{options}->[0]->[0];
  48
  49 $mech->get_ok('http://localhost:3010/ajax/heritability/generate_results?dataset_id='.$dataset_id.'&trait_id='.$trait_id, 'run the heritability analysis');
  50
  51 my $rdata = JSON::Any->decode($mech->content());
  52
  53 print STDERR "RDATA: ".Dumper($rdata);
  54
  55 ok($rdata->{h2Table}, "h2TableJson returned");
  56 ok($rdata->{h2CsvTable}, "h2CsvTable returned");
  57
  58 # check if files were created
  59 ok( -e "static/".$rdata->{h2Table}, "table created");
  60 ok( -e "static/".$rdata->{h2CsvTable}, "csv table file created");
  61
  62 my $test_basic_h2_file = csv(in => "static/".$rdata->{h2CsvTable});
  63
  64 is(@$test_basic_h2_file[1]->[1], 'dry matter content percentage', "check value of row name in a table");
  65 is(@$test_basic_h2_file[1]->[5], '49.92', "check value of Vres fresh.root.weight in a table");
  66
  67 # run test for dataset with outliers but with false outliers parameter
  68 my $outliers_included_dataset_id = 1;
  69 my $outliers_included_trait_id = "fresh root weight";
  70 $mech->get_ok('http://localhost:3010/ajax/heritability/generate_results?dataset_id='.$outliers_included_dataset_id.'&trait_id='.$outliers_included_trait_id, 'run the heritability analysis');
  71
  72 my $rdata_full_set = JSON::Any->decode($mech->content());
  73 ok($rdata_full_set->{h2Table}, "h2TableJson returned");
  74 ok($rdata_full_set->{h2CsvTable}, "h2CsvTable returned");
  75
  76 my $test_included_h2_file = csv(in => "static/".$rdata_full_set->{h2CsvTable});
  77 is(@$test_included_h2_file[2]->[1], 'fresh root weight', "check value of row name in a table");
  78 is(@$test_included_h2_file[2]->[5], '15.542', "check value of Heritability fresh.root.weight in a table");
  79
  80 # run test for dataset with outliers but with false outliers parameter
  81 my $outliers_excluded_dataset_id = 1;
  82 my $outliers_excluded_trait_id = "dry matter content percentage";
  83
  84 # run test for dataset with outliers but with true outliers parameter
  85 $mech->get_ok('http://localhost:3010/ajax/heritability/generate_results?dataset_id='.$outliers_excluded_dataset_id.'&trait_id='.$outliers_excluded_trait_id.'&dataset_trait_outliers=1', 'run the heritability analysis');
  86 my $rdata_excluded_set = JSON::Any->decode($mech->content());
  87
  88 # check if names are created in jsn response
  89 ok($rdata_excluded_set->{h2Table}, "h2TableJson returned");
  90 ok($rdata_excluded_set->{h2CsvTable}, "h2CsvTable returned");
  91
  92 # check if files were created
  93 ok( -e "static/".$rdata_excluded_set->{h2Table}, "table created");
  94 ok( -e "static/".$rdata_excluded_set->{h2CsvTable}, "csv table file created");
  95
  96 # check if values are changed for set with outliers excluded
  97 my $test_excluded_h2_file = csv(in => "static/".$rdata_excluded_set->{h2CsvTable});
  98 is(@$test_excluded_h2_file[2]->[1], 'fresh root weight', "check value of row name in a table");
  99 is(@$test_excluded_h2_file[2]->[5], '8.864', "check value of Heritability fresh.root.weight in a table");
 100
 101 # remove changes to the database
 102 #
 103 $ds->delete();
 104
 105 done_testing();