t/unit_fixture/CXGN/BreedersToolbox/Projects.t

   1 #test all functions in CXGN::BreedersToolbox::Projects
   2
   3 use strict;
   4
   5 use lib 't/lib';
   6
   7 use Test::More;
   8 use Data::Dumper;
   9 use SGN::Test::Fixture;
  10 use CXGN::BreedersToolbox::Projects;
  11
  12 my $f = SGN::Test::Fixture->new();
  13 my $schema = $f->bcs_schema();
  14
  15 my $p = CXGN::BreedersToolbox::Projects->new({schema=>$schema});
  16
  17 $f->get_db_stats();
  18
  19 my $trial_id = $schema->resultset('Project::Project')->find({name=>'test_trial'})->project_id();
  20 ok($p->trial_exists($trial_id));
  21
  22 my $projects = $p->get_breeding_programs();
  23 #print STDERR Dumper $projects;
  24 is_deeply($projects, [
  25           [
  26             134,
  27             'test',
  28             'test'
  29           ]
  30         ], 'test get bps');
  31
  32 my $bp_project_id = $p->get_breeding_program_by_name('test');
  33 ok($bp_project_id);
  34
  35 my ($field_trials, $cross_trials, $genotyping_trials) = $p->get_trials_by_breeding_program($bp_project_id->project_id);
  36 my @sorted_field_trials = sort {$a->[0] cmp $b->[0]} @$field_trials;
  37 print STDERR Dumper \@sorted_field_trials;
  38 is_deeply(\@sorted_field_trials, [
  39           [
  40             '137',
  41             'test_trial',
  42             'test trial'
  43           ],
  44           [
  45             '139',
  46             'Kasese solgs trial',
  47             'This trial was loaded into the fixture to test solgs.'
  48           ],
  49           [
  50             '141',
  51             'trial2 NaCRRI',
  52             'another trial for solGS'
  53           ],
  54           [
  55             '144',
  56             'test_t',
  57             'test tets'
  58           ],
  59           [
  60             '165',
  61             'CASS_6Genotypes_Sampling_2015',
  62             'Copy of trial with postcomposed phenotypes from cassbase.'
  63           ]
  64         ], 'test get trials');
  65 #print STDERR Dumper $cross_trials;
  66 =begin
  67 my @sorted_cross_trials = sort {$a->[0] cmp $b->[0]} @$cross_trials;
  68 #print STDERR Dumper \@sorted_cross_trials;
  69 is_deeply(\@sorted_cross_trials, [
  70           [
  71             '138',
  72             'test5',
  73             'test5'
  74           ],
  75           [
  76             '145',
  77             'cross_test1',
  78             'cross_test1'
  79           ],
  80           [
  81             '146',
  82             'cross_test4',
  83             'cross_test4'
  84           ],
  85           [
  86             '147',
  87             'cross_test5',
  88             'cross_test5'
  89           ],
  90           [
  91             '148',
  92             'cross_test6',
  93             'cross_test6'
  94           ],
  95           [
  96             '149',
  97             'cross_test2',
  98             'cross_test2'
  99           ],
 100           [
 101             '150',
 102             'cross_test3',
 103             'cross_test3'
 104           ],
 105           [
 106             '151',
 107             'TestCross1',
 108             'TestCross1'
 109           ],
 110           [
 111             '152',
 112             'TestCross2',
 113             'TestCross2'
 114           ],
 115           [
 116             '153',
 117             'TestCross3',
 118             'TestCross3'
 119           ],
 120           [
 121             '154',
 122             'TestCross4',
 123             'TestCross4'
 124           ],
 125           [
 126             '155',
 127             'TestCross5',
 128             'TestCross5'
 129           ],
 130           [
 131             '156',
 132             'TestCross6',
 133             'TestCross6'
 134           ],
 135           [
 136             '157',
 137             'TestCross7',
 138             'TestCross7'
 139           ],
 140           [
 141             '158',
 142             'TestCross8',
 143             'TestCross8'
 144           ],
 145           [
 146             '159',
 147             'TestCross9',
 148             'TestCross9'
 149           ],
 150           [
 151             '160',
 152             'TestCross10',
 153             'TestCross10'
 154           ],
 155           [
 156             '161',
 157             'TestCross11',
 158             'TestCross11'
 159           ],
 160           [
 161             '162',
 162             'TestCross12',
 163             'TestCross12'
 164           ],
 165           [
 166             '163',
 167             'TestCross13',
 168             'TestCross13'
 169           ],
 170           [
 171             '164',
 172             'TestCross14',
 173             'TestCross14'
 174           ]
 175         ], 'test get crosses');
 176 =end
 177
 178 =cut
 179
 180 #print STDERR Dumper $genotyping_trials;
 181 is_deeply($genotyping_trials, undef, 'test get geno trials');
 182
 183 my $locations = $p->get_location_geojson_data();
 184 print STDERR Dumper $locations;
 185 is_deeply($locations, [{"geometry"=>{"coordinates"=>[-115.86428,32.61359],"type"=>"Point"},"properties"=>{"Abbreviation"=>undef,"Altitude"=>109,"Code"=>"USA","Country"=>"United States","Id"=>"23","Latitude"=>32.61359,"Longitude"=>-115.86428,"NOAAStationID"=>undef,"Name"=>"test_location","Program"=>"test","Trials"=>"<a href=\"/search/trials?location_id=23\">5 trials</a>","Type"=>undef},"type"=>"Feature"},{"geometry"=>{"coordinates"=>[-76.4735,42.45345],"type"=>"Point"},"properties"=>{"Abbreviation"=>undef,"Altitude"=>274,"Code"=>"USA","Country"=>"United States","Id"=>"24","Latitude"=>42.45345,"Longitude"=>-76.4735,"NOAAStationID"=>undef,"Name"=>"Cornell Biotech","Program"=>"test","Trials"=>"<a href=\"/search/trials?location_id=24\">0 trials</a>","Type"=>undef},"type"=>"Feature"},{"geometry"=>{"coordinates"=>[undef,undef],"type"=>"Point"},"properties"=>{"Abbreviation"=>undef,"Altitude"=>undef,"Code"=>undef,"Country"=>undef,"Id"=>"25","Latitude"=>undef,"Longitude"=>undef,"NOAAStationID"=>undef,"Name"=>"NA","Program"=>undef,"Trials"=>"<a href=\"/search/trials?location_id=25\">0 trials</a>","Type"=>undef},"type"=>"Feature"},{"geometry"=>{"coordinates"=>[undef,undef],"type"=>"Point"},"properties"=>{"Abbreviation"=>undef,"Altitude"=>undef,"Code"=>undef,"Country"=>undef,"Id"=>"26","Latitude"=>undef,"Longitude"=>undef,"NOAAStationID"=>undef,"Name"=>"[Computation]","Program"=>undef,"Trials"=>"<a href=\"/search/trials?location_id=26\">0 trials</a>","Type"=>undef},"type"=>"Feature"}]);
 186
 187
 188
 189 #'[{"geometry":{"coordinates":[-115.864,32.6136],"type":"Point"},"properties":{"Abbreviation":null,"Altitude":109,"Code":"USA","Country":"United States","Id":"23","Latitude":32.6136,"Longitude":-115.864,"NOAAStationID":null,"Name":"test_location","Program":"test","Trials":"<a href=\"/search/trials?location_id=23\">5 trials</a>","Type":null},"type":"Feature"},{"geometry":{"coordinates":[-76.4735,42.4534],"type":"Point"},"properties":{"Abbreviation":null,"Altitude":274,"Code":"USA","Country":"United States","Id":"24","Latitude":42.4534,"Longitude":-76.4735,"NOAAStationID":null,"Name":"Cornell Biotech","Program":"test","Trials":"<a href=\"/search/trials?location_id=24\">0 trials</a>","Type":null},"type":"Feature"},{"geometry":{"coordinates":[null,null],"type":"Point"},"properties":{"Abbreviation":null,"Altitude":null,"Code":null,"Country":null,"Id":"25","Latitude":null,"Longitude":null,"NOAAStationID":null,"Name":"NA","Program":null,"Trials":"<a href=\"/search/trials?location_id=25\">0 trials</a>","Type":null},"type":"Feature"}]', 'get locations by bp');
 190
 191 my $all_locations = $p->get_all_locations();
 192 print STDERR Dumper $all_locations;
 193 is(scalar(@$all_locations), 4);
 194 is_deeply($all_locations,[
 195               [ 26,
 196                 '[Computation]',
 197                 ],
 198           [
 199             24,
 200             'Cornell Biotech'
 201           ],
 202           [
 203             25,
 204             'NA'
 205           ],
 206           [
 207             23,
 208             'test_location'
 209           ]
 210         ], 'get all locations');
 211
 212 my $all_locations = $p->get_locations();
 213 print STDERR Dumper $all_locations;
 214 is_deeply($all_locations, [
 215           [
 216             24,
 217             'Cornell Biotech',
 218             '42.45345',
 219             '-76.4735',
 220             '274',
 221             0
 222           ],
 223           [
 224             23,
 225             'test_location',
 226             '32.61359',
 227             '-115.86428',
 228             '109',
 229             5456
 230           ],
 231           [
 232             25,
 233             'NA',
 234             undef,
 235             undef,
 236             undef,
 237             0
 238           ],
 239           [
 240             26,
 241             '[Computation]',
 242             undef,
 243             undef,
 244             undef,
 245             0
 246           ]
 247         ], 'get all locations');
 248
 249 my @all_years = $p->get_all_years();
 250 print STDERR Dumper \@all_years;
 251 is_deeply(\@all_years, [
 252           '2017',
 253           '2016',
 254           '2015',
 255           '2014'
 256         ], 'get all years');
 257
 258 my $new_bp = CXGN::BreedersToolbox::Projects->new({
 259     schema=>$schema,
 260     name => 'test_new_bp_to_edit',
 261     description => 'test_new_bp_desc_to_edit',
 262 });
 263 my $new_bp_result = $new_bp->store_breeding_program();
 264 print STDERR Dumper $new_bp_result;
 265 ok($new_bp_result->{success});
 266
 267 my $edit_bp = CXGN::BreedersToolbox::Projects->new({
 268     schema=>$schema,
 269     id => $new_bp_result->{id},
 270     name => 'test_new_bp',
 271     description => 'test_new_bp_desc',
 272 });
 273 my $edit_bp_result = $edit_bp->store_breeding_program();
 274 print STDERR Dumper $edit_bp_result;
 275 ok($edit_bp_result->{success});
 276
 277 my $bp_projects = $p->get_breeding_program_with_trial($trial_id);
 278 #print STDERR Dumper $bp_projects;
 279 is_deeply($bp_projects, [
 280           [
 281             134,
 282             'test',
 283             'test'
 284           ]
 285         ], 'get bps');
 286
 287 my $gt_protocols = $p->get_gt_protocols();
 288 #print STDERR Dumper $gt_protocols;
 289 is_deeply($gt_protocols, [
 290           [
 291             1,
 292             'GBS ApeKI genotyping v4'
 293           ]
 294         ], 'get gt protocols');
 295
 296 my $program_id = $schema->resultset('Project::Project')->find({name=>'test_new_bp'})->project_id();
 297 ok($p->delete_breeding_program($program_id));
 298
 299 $f->clean_up_db();
 300
 301 done_testing;