t/unit_fixture/CXGN/Dataset.t

   1
   2 use strict;
   3
   4 use lib 't/lib';
   5
   6 use Test::More;
   7 use Data::Dumper;
   8 use SGN::Test::Fixture;
   9 use CXGN::Dataset;
  10 use CXGN::Dataset::File;
  11 use CXGN::Dataset::Cache;
  12
  13 my $t = SGN::Test::Fixture->new();
  14
  15 $t->dbh()->begin_work();
  16
  17 my $cache_root_dir = $t->config->{cache_file_path};
  18 my $cluster_shared_tempdir_config = $t->config->{cluster_shared_tempdir};
  19 my $backend_config = $t->config->{backend};
  20 my $cluster_host_config = $t->config->{cluster_host};
  21 my $web_cluster_queue_config = $t->config->{'web_cluster_queue'};
  22 my $basepath_config = $t->config->{basepath};
  23 my $forbid_cache = 0;
  24
  25 my $ds = CXGN::Dataset->new( people_schema => $t->people_schema(), schema => $t->bcs_schema());
  26 $ds->accessions( [ 38913, 38914, 38915 ]);
  27 $ds->years(['2012', '2013']);
  28 $ds->traits([ 70666, 70741 ]);
  29 $ds->trials([ 139, 144 ]);
  30 $ds->plots( [ 40034, 40035 ]);
  31 $ds->name("test");
  32 $ds->description("test description");
  33
  34 $ds->name("test");
  35 $ds->description("test description");
  36 $ds->sp_person_id(41);
  37
  38 my $sp_dataset_id = $ds->store();
  39
  40 print STDERR "Dataset_id = $sp_dataset_id\n";
  41
  42 my $new_ds = CXGN::Dataset->new( people_schema => $t->people_schema(), schema => $t->bcs_schema(), sp_dataset_id => $sp_dataset_id);
  43
  44 is_deeply($new_ds->accessions(), $ds->accessions(), "accession store");
  45 is_deeply($new_ds->years(), $ds->years(), "years store");
  46 is_deeply($new_ds->traits(), $ds->traits(), "traits store");
  47 is_deeply($new_ds->plots(), $ds->plots(), "plots store");
  48
  49 is($new_ds->name(), $ds->name(), "name store");
  50 is($new_ds->description(), $ds->description(), "desc store");
  51 is($new_ds->sp_person_id(), 41, "dataset owner");
  52
  53 my @datasets = (
  54     CXGN::Dataset->new( people_schema => $t->people_schema(), schema => $t->bcs_schema()),
  55     CXGN::Dataset::File->new( people_schema => $t->people_schema(), schema => $t->bcs_schema()),
  56     CXGN::Dataset::Cache->new( people_schema => $t->people_schema(), schema => $t->bcs_schema(), cache_root => '/tmp/dataset_cache_root'),
  57     );
  58
  59 foreach my $ds (@datasets) {
  60     if ($ds->can("cache")) { $ds->cache->clear(); }
  61     $ds->name("test");
  62     $ds->description("test description");
  63
  64     $ds->accessions( [ 38913, 38914, 38915 ] );
  65
  66     my $sp_dataset_id = $ds->store();
  67
  68     my $trials = $ds->retrieve_trials();
  69
  70     is_deeply($trials, [
  71                   [
  72                    139,
  73                    'Kasese solgs trial'
  74                   ],
  75                   [
  76                    144,
  77                    'test_t'
  78                   ],
  79                   [
  80                    141,
  81                    'trial2 NaCRRI'
  82                   ]
  83               ]
  84               , "trial retrieve test");
  85
  86     if ($ds->isa("CXGN::Dataset::File")) {
  87         ok(-e $ds->file_name()."_trials.txt", "trial file exists");
  88     }
  89
  90     my $traits = $ds->retrieve_traits();
  91
  92     print STDERR Dumper($traits);
  93
  94     is_deeply($traits, [
  95                   [
  96                    70741,
  97                    'dry matter content percentage|CO_334:0000092'
  98                   ],
  99                   [
 100                    70666,
 101                    'fresh root weight|CO_334:0000012'
 102                   ],
 103                   [
 104                    70773,
 105                    'fresh shoot weight measurement in kg|CO_334:0000016'
 106                   ],
 107                   [
 108                    70668,
 109                    'harvest index variable|CO_334:0000015'
 110                   ]
 111               ]
 112         );
 113
 114     my $phenotypes = $ds->retrieve_phenotypes();
 115
 116     if ($ds->isa("CXGN::Dataset::File")) {
 117         my$geno_filename = $ds->file_name()."_genotype.txt";
 118         my $genotypes = $ds->retrieve_genotypes(1,$geno_filename,$cache_root_dir,$cluster_shared_tempdir_config,$backend_config,$cluster_host_config,$web_cluster_queue_config,$basepath_config,$forbid_cache);
 119     } else {
 120         my $genotypes = $ds->retrieve_genotypes(1);
 121     }
 122
 123     my $years = $ds->retrieve_years();
 124
 125     is_deeply($years, [
 126           [
 127             '2014',
 128             '2014'
 129           ],
 130           [
 131             '2016',
 132             '2016'
 133           ]
 134         ], "Year retrieve test");
 135
 136     my $plots = $ds->retrieve_plots();
 137
 138     is_deeply($plots, [
 139                   [
 140                    39299,
 141                    'KASESE_TP2013_1029'
 142                   ],
 143                   [
 144                    39895,
 145                    'KASESE_TP2013_1590'
 146                   ],
 147                   [
 148                    39424,
 149                    'KASESE_TP2013_1717'
 150                   ],
 151                   [
 152                    39607,
 153                    'KASESE_TP2013_707'
 154                   ],
 155                   [
 156                    39733,
 157                    'KASESE_TP2013_880'
 158                   ],
 159                   [
 160                    40343,
 161                    'test_t113'
 162                   ],
 163                   [
 164                    40493,
 165                    'test_t249'
 166                   ],
 167                   [
 168                    40669,
 169                    'test_t407'
 170                   ],
 171                   [
 172                    40676,
 173                    'test_t413'
 174                   ],
 175                   [
 176                    40814,
 177                    'test_t538'
 178                   ],
 179                   [
 180                    40819,
 181                    'test_t542'
 182                   ],
 183                   [
 184                    40956,
 185                    'test_t666'
 186                   ],
 187                   [
 188                    41168,
 189                    'test_t857'
 190                   ],
 191                   [
 192                    41237,
 193                    'test_t919'
 194                   ],
 195                   [
 196                    40033,
 197                    'UG120036_block:2_plot:TP36_2012_NaCRRI'
 198                   ],
 199                   [
 200                    40034,
 201                    'UG120037_block:2_plot:TP37_2012_NaCRRI'
 202                   ],
 203                   [
 204                    40035,
 205                    'UG120038_block:2_plot:TP38_2012_NaCRRI'
 206                   ]
 207               ], "plot retrieve test");
 208
 209 }
 210
 211
 212
 213 print STDERR "DATA = ".$ds->data()."\n";
 214
 215 $ds->delete();
 216
 217
 218 $t->dbh->rollback();
 219
 220 done_testing();