t/unit_fixture/CXGN/Uploading/UploadIntercrossData.t

   1 use strict;
   2 use warnings;
   3
   4 use lib 't/lib';
   5 use SGN::Test::Fixture;
   6 use Test::More;
   7 use Test::WWW::Mechanize;
   8 use LWP::UserAgent;
   9 use SGN::Model::Cvterm;
  10 use CXGN::Trial::Download;
  11 use Spreadsheet::WriteExcel;
  12 use Spreadsheet::Read;
  13 use Data::Dumper;
  14 use JSON;
  15 local $Data::Dumper::Indent = 0;
  16 my $f = SGN::Test::Fixture->new();
  17 my $schema = $f->bcs_schema;
  18
  19 my $mech = Test::WWW::Mechanize->new;
  20
  21 $mech->post_ok('http://localhost:3010/brapi/v1/token', [ "username"=> "janedoe", "password"=> "secretpw", "grant_type"=> "password" ]);
  22 my $response = decode_json $mech->content;
  23 is($response->{'metadata'}->{'status'}->[2]->{'message'}, 'Login Successfull');
  24 my $sgn_session_id = $response->{access_token};
  25 print STDERR $sgn_session_id."\n";
  26
  27 # adding a crossing experiment for intercross upload
  28 $mech->post_ok('http://localhost:3010/ajax/cross/add_crossingtrial', [ 'crossingtrial_name' => 'intercross_upload', 'crossingtrial_program_id' => 134 ,
  29     'crossingtrial_location' => 'test_location', 'year' => '2020', 'project_description' => 'test intercross upload' ]);
  30
  31 $response = decode_json $mech->content;
  32 is($response->{'success'}, '1');
  33
  34 my $crossing_experiment_rs = $schema->resultset('Project::Project')->find({name =>'intercross_upload'});
  35 my $crossing_experiment_id = $crossing_experiment_rs->project_id();
  36
  37 #test uploading target numbers
  38 my $target_numbers_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'target_numbers_json', 'project_property')->cvterm_id();
  39 my $before_uploading_target_numbers_all_projectprop = $schema->resultset("Project::Projectprop")->search({})->count();
  40 my $before_uploading_target_numbers = $schema->resultset("Project::Projectprop")->search({ project_id => $crossing_experiment_id, type_id => $target_numbers_type_id })->count();
  41
  42 for my $extension ("xls", "xlsx") {
  43     my $file = $f->config->{basepath} . "/t/data/cross/target_numbers.$extension";
  44     my $ua = LWP::UserAgent->new;
  45     my $response = $ua->post(
  46         'http://localhost:3010/ajax/crossing_experiment/upload_target_numbers',
  47         Content_Type => 'form-data',
  48         Content => [
  49             "target_numbers_file" => [
  50                 $file,
  51                 "target_numbers.$extension",
  52                 Content_Type => ($extension eq "xls") ? 'application/vnd.ms-excel' : 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet',
  53             ],
  54             "target_numbers_experiment_id" => $crossing_experiment_id,
  55             "sgn_session_id" => $sgn_session_id
  56         ]
  57     );
  58     ok($response->is_success);
  59     my $message = $response->decoded_content;
  60     my $message_hash = decode_json $message;
  61     is_deeply($message_hash, { 'success' => 1 });
  62 }
  63
  64 my $after_uploading_target_numbers_all_projectprop = $schema->resultset("Project::Projectprop")->search({})->count();
  65 my $after_uploading_target_numbers = $schema->resultset("Project::Projectprop")->search({ project_id => $crossing_experiment_id, type_id => $target_numbers_type_id })->count();
  66
  67 is($after_uploading_target_numbers_all_projectprop, $before_uploading_target_numbers_all_projectprop + 1);
  68 is($after_uploading_target_numbers, $before_uploading_target_numbers + 1);
  69
  70 #retrieving target number
  71 $mech->post_ok("http://localhost:3010/ajax/crossing_experiment/target_numbers_and_progress/$crossing_experiment_id");
  72 $response = decode_json $mech->content;
  73 is_deeply($response, { 'data' => [
  74     ['UG120001','UG120002',50,undef,25,undef,''],
  75     ['UG120002','UG120003',40,undef,20,undef,'']
  76 ]}, 'target numbers');
  77
  78
  79 #uploading intercross data
  80 my $cross_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, "cross", "stock_type")->cvterm_id();
  81 my $before_uploading_cross = $schema->resultset("Stock::Stock")->search({ type_id => $cross_type_id})->count();
  82 my $before_uploading_stocks = $schema->resultset("Stock::Stock")->search({})->count();
  83 my $before_uploading_relationship = $schema->resultset("Stock::StockRelationship")->search({})->count();
  84 my $cross_identifier_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'cross_identifier', 'stock_property')->cvterm_id();
  85 my $before_upload_identifier_rows = $schema->resultset("Stock::Stockprop")->search({type_id => $cross_identifier_type_id})->count();
  86
  87 my $file = $f->config->{basepath}."/t/data/cross/intercross_upload.csv";
  88 my $ua = LWP::UserAgent->new;
  89 $response = $ua->post(
  90     'http://localhost:3010/ajax/cross/upload_intercross_file',
  91     Content_Type => 'form-data',
  92     Content => [
  93         "intercross_file" => [ $file, 'intercross_upload.csv', Content_Type => 'text/plain', ],
  94         "sgn_session_id" => $sgn_session_id,
  95         "cross_id_format_option" => 'auto_generated_id',
  96         "intercross_experiment_id" => $crossing_experiment_id
  97     ]
  98 );
  99 ok($response->is_success);
 100 my $message = $response->decoded_content;
 101 my $message_hash = decode_json $message;
 102 is_deeply($message_hash, {'success' => 1});
 103
 104 my $after_uploading_cross = $schema->resultset("Stock::Stock")->search({ type_id => $cross_type_id})->count();
 105 my $after_uploading_stocks = $schema->resultset("Stock::Stock")->search({})->count();
 106 my $after_uploading_relationship = $schema->resultset("Stock::StockRelationship")->search({})->count();
 107
 108 is($after_uploading_cross, $before_uploading_cross + 2);
 109 is($after_uploading_stocks, $before_uploading_stocks + 2);
 110 is($after_uploading_relationship, $before_uploading_relationship + 4);
 111
 112 #retrieving target number and progress
 113 $mech->post_ok("http://localhost:3010/ajax/crossing_experiment/target_numbers_and_progress/$crossing_experiment_id");
 114 $response = decode_json $mech->content;
 115 my $target_data = $response->{'data'};
 116
 117 is($target_data->[0]->[0], 'UG120001');
 118 is($target_data->[0]->[1], 'UG120002');
 119 is($target_data->[0]->[2], 50);
 120 is($target_data->[0]->[3], 35);
 121 is($target_data->[0]->[4], 25);
 122 is($target_data->[0]->[5], 0);
 123
 124 is($target_data->[1]->[0], 'UG120002');
 125 is($target_data->[1]->[1], 'UG120003');
 126 is($target_data->[1]->[2], 40);
 127 is($target_data->[1]->[3], 25);
 128 is($target_data->[1]->[4], 20);
 129 is($target_data->[1]->[5], 0);
 130
 131 # checking number of crosses in intercross_upload experiment
 132 $mech->post_ok("http://localhost:3010/ajax/breeders/trial/$crossing_experiment_id/crosses_and_details_in_trial");
 133 $response = decode_json $mech->content;
 134 my %data = %$response;
 135 my $crosses = $data{data};
 136 my $number_of_crosses = @$crosses;
 137 is($number_of_crosses, 2);
 138
 139 # checking transactions in intercross_upload_1
 140 my $intercross_upload_1_id = $schema->resultset('Stock::Stock')->find({ name => 'intercross_upload_1' })->stock_id();
 141 $mech->post_ok("http://localhost:3010/ajax/cross/transactions/$intercross_upload_1_id");
 142 $response = decode_json $mech->content;
 143 my %result = %$response;
 144 my $transactions = $result{data};
 145 my $number_of_transactions = @$transactions;
 146 is($number_of_transactions, 2);
 147
 148 #checking stockprop
 149 my $cross_transaction_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'cross_transaction_json', 'stock_property')->cvterm_id();
 150 my $transaction_rows = $schema->resultset("Stock::Stockprop")->search({type_id => $cross_transaction_type_id})->count();
 151 is($transaction_rows, 2);
 152
 153 my $after_upload_identifier_rows = $schema->resultset("Stock::Stockprop")->search({type_id => $cross_identifier_type_id})->count();
 154 is($after_upload_identifier_rows, $before_upload_identifier_rows + 2);
 155
 156 #test crossing experiment download with transaction info
 157 my @cross_properties = ("Tag Number", "Pollination Date", "Number of Bags", "Number of Flowers", "Number of Fruits", "Number of Seeds");
 158 my $tempfile = "/tmp/test_download_crossing_experiment.xls";
 159 my $format = 'CrossingExperimentXLS';
 160 my $create_spreadsheet = CXGN::Trial::Download->new({
 161     bcs_schema => $f->bcs_schema,
 162     trial_list => [$crossing_experiment_id],
 163     filename => $tempfile,
 164     format => $format,
 165     field_crossing_data_order => \@cross_properties
 166 });
 167
 168 $create_spreadsheet->download();
 169 my $contents = ReadData $tempfile;
 170
 171 my $columns = $contents->[1]->{'cell'};
 172 my @column_array = @$columns;
 173 my $number_of_columns = scalar @column_array;
 174 ok(scalar($number_of_columns) == 22, "check number of columns.");
 175
 176 is_deeply($contents->[1]->{'cell'}->[1], [
 177     undef,
 178     'Cross Unique ID',
 179     'intercross_upload_1',
 180     'intercross_upload_2'
 181 ], "check cross unique ids column");
 182
 183 my $transaction_column = $contents->[1]->{'cell'}->[21];
 184 my @transaction_array = @$transaction_column;
 185 my $correct_grouping_1;
 186 my $correct_grouping_2;
 187
 188 if ('transaction_id_0001,transaction_id_0004' ~~ @transaction_array){
 189     $correct_grouping_1 = 1;
 190 } else {
 191     $correct_grouping_1 = 0
 192 }
 193
 194 if ('transaction_id_0002,transaction_id_0003' ~~ @transaction_array){
 195     $correct_grouping_2 = 1;
 196 } else {
 197     $correct_grouping_2 = 0
 198 }
 199
 200 is($correct_grouping_1, 1);
 201 is($correct_grouping_2, 1);
 202
 203 #deleting crosses and crossing experiment after testing
 204 $mech->post_ok('http://localhost:3010/ajax/cross/delete', [ 'cross_id' => $intercross_upload_1_id]);
 205 $response = decode_json $mech->content;
 206 is_deeply($message_hash, {'success' => 1});
 207
 208 my $intercross_upload_2_id = $schema->resultset('Stock::Stock')->find({name =>'intercross_upload_2'})->stock_id();
 209 $mech->post_ok('http://localhost:3010/ajax/cross/delete', [ 'cross_id' => $intercross_upload_2_id]);
 210 $response = decode_json $mech->content;
 211 is_deeply($message_hash, {'success' => 1});
 212
 213 $mech->get_ok('http://localhost:3010/ajax/breeders/trial/'.$crossing_experiment_id.'/delete/crossing_experiment');
 214 $response = decode_json $mech->content;
 215 is_deeply($message_hash, {'success' => 1});
 216
 217 $f->clean_up_db();
 218
 219
 220 done_testing();