t/unit_fixture/CXGN/Onto.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::Onto;
  10 use SGN::Model::Cvterm;
  11 use Test::WWW::Mechanize;
  12 use JSON;
  13
  14 my $mech = Test::WWW::Mechanize->new;
  15 my $json = JSON->new->allow_nonref;
  16
  17 my $t = SGN::Test::Fixture->new();
  18 my $schema = $t->bcs_schema();
  19
  20 my $onto = CXGN::Onto->new( { schema => $t->bcs_schema() });
  21
  22 my $cv_type = 'attribute_ontology';
  23 my @results = $onto->get_root_nodes($cv_type);
  24 #print STDERR "test 1 results " .Dumper @results;
  25
  26 is_deeply(@results, [
  27                59,
  28                'CHEBI:00000 chebi_compounds'
  29              ], 'onto get root nodes test');
  30
  31 =for comment
  32 my $cv_id = 58; # CASSTISS ontology with cvprop 'object'
  33 @results = $onto->get_terms($cv_id);
  34 print STDERR "test 2 results: @results";
  35 my @cass_tissues = ["[77181,'cass fibrous root|CASSTISS:0000011']",
  36                     "[77176,'cass lower leaf|CASSTISS:0000006']",
  37                     "[77171,'cass lower stem bark|CASSTISS:0000010']",
  38                     "[77174,'cass lower stem whole|CASSTISS:0000009']",
  39                     "[77178,'cass pre-storage root|CASSTISS:0000012']",
  40                     "[77180,'cass sink leaf|CASSTISS:0000004']",
  41                     "[77170,'cass source leaf|CASSTISS:0000005']",
  42                     "[77168,'cass storage root|CASSTISS:0000013']",
  43                     "[77172,'cass upper stem|CASSTISS:0000007']"];
  44                     # problem with this data structure
  45 is_deeply(@results, @cass_tissues, 'onto get terms test');
  46 =cut
  47
  48 my @allowed_composed_cvs = ('trait','toy');
  49 my $composable_cvterm_delimiter = '|';
  50 my $composable_cvterm_format = 'concise';
  51 my $traits1 = SGN::Model::Cvterm->get_traits_from_component_categories($t->bcs_schema(), \@allowed_composed_cvs, $composable_cvterm_delimiter, $composable_cvterm_format, {
  52     object => [],
  53     attribute => [],
  54     method => [],
  55     unit => [],
  56     trait => [70775,76555],
  57     tod => [],
  58     toy => [77526,77499],
  59     gen => [],
  60 });
  61 #print STDERR Dumper $traits1;
  62 is_deeply($traits1, {
  63           'existing_traits' => [],
  64           'new_traits' => [
  65                             [
  66                               [
  67                                 70775,
  68                                 77526
  69                               ],
  70                               'anthocyanin pigmentation visual rating 0-3|month 1'
  71                             ],
  72                             [
  73                               [
  74                                 70775,
  75                                 77499
  76                               ],
  77                               'anthocyanin pigmentation visual rating 0-3|month 10'
  78                             ],
  79                             [
  80                               [
  81                                 76555,
  82                                 77526
  83                               ],
  84                               'ease of harvest assessment 1-3|month 1'
  85                             ],
  86                             [
  87                               [
  88                                 76555,
  89                                 77499
  90                               ],
  91                               'ease of harvest assessment 1-3|month 10'
  92                             ]
  93                           ]
  94         }, 'check composed trait creation 1');
  95
  96 @allowed_composed_cvs = ('trait','toy','tod','object');
  97 $composable_cvterm_delimiter = '||';
  98 $composable_cvterm_format = 'concise';
  99 my $traits2 = SGN::Model::Cvterm->get_traits_from_component_categories($t->bcs_schema(), \@allowed_composed_cvs, $composable_cvterm_delimiter, $composable_cvterm_format, {
 100   object => [77176, 77180],
 101   attribute => [],
 102   method => [],
 103   unit => [],
 104   trait => [70775,76555],
 105   tod => [77536],
 106   toy => [77526,77499],
 107   gen => [],
 108 });
 109 #print STDERR Dumper $traits2;
 110 is_deeply($traits2, {
 111           'existing_traits' => [],
 112           'new_traits' => [
 113                             [
 114                               [
 115                                 70775,
 116                                 77499,
 117                                 77536,
 118                                 77176
 119                               ],
 120                               'anthocyanin pigmentation visual rating 0-3||month 10||end of day||cass lower leaf'
 121                             ],
 122                             [
 123                               [
 124                                 70775,
 125                                 77499,
 126                                 77536,
 127                                 77180
 128                               ],
 129                               'anthocyanin pigmentation visual rating 0-3||month 10||end of day||cass sink leaf'
 130                             ],
 131                             [
 132                               [
 133                                 70775,
 134                                 77526,
 135                                 77536,
 136                                 77176
 137                               ],
 138                               'anthocyanin pigmentation visual rating 0-3||month 1||end of day||cass lower leaf'
 139                             ],
 140                             [
 141                               [
 142                                 70775,
 143                                 77526,
 144                                 77536,
 145                                 77180
 146                               ],
 147                               'anthocyanin pigmentation visual rating 0-3||month 1||end of day||cass sink leaf'
 148                             ],
 149                             [
 150                               [
 151                                 76555,
 152                                 77499,
 153                                 77536,
 154                                 77176
 155                               ],
 156                               'ease of harvest assessment 1-3||month 10||end of day||cass lower leaf'
 157                             ],
 158                             [
 159                               [
 160                                 76555,
 161                                 77499,
 162                                 77536,
 163                                 77180
 164                               ],
 165                               'ease of harvest assessment 1-3||month 10||end of day||cass sink leaf'
 166                             ],
 167                             [
 168                               [
 169                                 76555,
 170                                 77526,
 171                                 77536,
 172                                 77176
 173                               ],
 174                               'ease of harvest assessment 1-3||month 1||end of day||cass lower leaf'
 175                             ],
 176                             [
 177                               [
 178                                 76555,
 179                                 77526,
 180                                 77536,
 181                                 77180
 182                               ],
 183                               'ease of harvest assessment 1-3||month 1||end of day||cass sink leaf'
 184                             ]
 185                           ]
 186         }, 'check composed trait creation 2');
 187
 188 @allowed_composed_cvs = ('trait','toy','tod','object');
 189 $composable_cvterm_delimiter = '||';
 190 $composable_cvterm_format = 'extended';
 191 my $traits3 = SGN::Model::Cvterm->get_traits_from_component_categories($t->bcs_schema(), \@allowed_composed_cvs, $composable_cvterm_delimiter, $composable_cvterm_format, {
 192   object => [77171, 77174],
 193   attribute => [],
 194   method => [],
 195   unit => [],
 196   trait => [70775,76555],
 197   tod => [77536],
 198   toy => [77526,77499],
 199   gen => [],
 200 });
 201 #print STDERR Dumper $traits3;
 202 is_deeply($traits3, {
 203           'existing_traits' => [],
 204           'new_traits' => [
 205                             [
 206                               [
 207                                 70775,
 208                                 77499,
 209                                 77536,
 210                                 77171
 211                               ],
 212                               'anthocyanin pigmentation visual rating 0-3|CO_334:0000103||month 10|TIME:0000069||end of day|TIME:0000003||cass lower stem bark|CASSTISS:0000010'
 213                             ],
 214                             [
 215                               [
 216                                 70775,
 217                                 77499,
 218                                 77536,
 219                                 77174
 220                               ],
 221                               'anthocyanin pigmentation visual rating 0-3|CO_334:0000103||month 10|TIME:0000069||end of day|TIME:0000003||cass lower stem whole|CASSTISS:0000009'
 222                             ],
 223                             [
 224                               [
 225                                 70775,
 226                                 77526,
 227                                 77536,
 228                                 77171
 229                               ],
 230                               'anthocyanin pigmentation visual rating 0-3|CO_334:0000103||month 1|TIME:0000060||end of day|TIME:0000003||cass lower stem bark|CASSTISS:0000010'
 231                             ],
 232                             [
 233                               [
 234                                 70775,
 235                                 77526,
 236                                 77536,
 237                                 77174
 238                               ],
 239                               'anthocyanin pigmentation visual rating 0-3|CO_334:0000103||month 1|TIME:0000060||end of day|TIME:0000003||cass lower stem whole|CASSTISS:0000009'
 240                             ],
 241                             [
 242                               [
 243                                 76555,
 244                                 77499,
 245                                 77536,
 246                                 77171
 247                               ],
 248                               'ease of harvest assessment 1-3|CO_334:0000225||month 10|TIME:0000069||end of day|TIME:0000003||cass lower stem bark|CASSTISS:0000010'
 249                             ],
 250                             [
 251                               [
 252                                 76555,
 253                                 77499,
 254                                 77536,
 255                                 77174
 256                               ],
 257                               'ease of harvest assessment 1-3|CO_334:0000225||month 10|TIME:0000069||end of day|TIME:0000003||cass lower stem whole|CASSTISS:0000009'
 258                             ],
 259                             [
 260                               [
 261                                 76555,
 262                                 77526,
 263                                 77536,
 264                                 77171
 265                               ],
 266                               'ease of harvest assessment 1-3|CO_334:0000225||month 1|TIME:0000060||end of day|TIME:0000003||cass lower stem bark|CASSTISS:0000010'
 267                             ],
 268                             [
 269                               [
 270                                 76555,
 271                                 77526,
 272                                 77536,
 273                                 77174
 274                               ],
 275                               'ease of harvest assessment 1-3|CO_334:0000225||month 1|TIME:0000060||end of day|TIME:0000003||cass lower stem whole|CASSTISS:0000009'
 276                             ]
 277                           ]
 278         }, 'check composed trait creation 3');
 279
 280 my $new_traits2 = $traits2->{new_traits};
 281 my %new_composed_terms2;
 282 foreach (@$new_traits2){
 283   $new_composed_terms2{$_->[1]} = join ',', @{$_->[0]};
 284 }
 285 my $results2 = $onto->store_composed_term(\%new_composed_terms2);
 286 #print STDERR Dumper $results2;
 287 my @results2_names;
 288 foreach (@$results2){
 289     ok($_->[0], 'check that cvterm_id saved');
 290     push @results2_names, $_->[1];
 291 }
 292 print STDERR Dumper \@results2_names;
 293 is_deeply(\@results2_names, [
 294           'anthocyanin pigmentation visual rating 0-3||month 10||end of day||cass lower leaf|COMP:0000014',
 295           'anthocyanin pigmentation visual rating 0-3||month 10||end of day||cass sink leaf|COMP:0000015',
 296           'anthocyanin pigmentation visual rating 0-3||month 1||end of day||cass lower leaf|COMP:0000016',
 297           'anthocyanin pigmentation visual rating 0-3||month 1||end of day||cass sink leaf|COMP:0000017',
 298           'ease of harvest assessment 1-3||month 10||end of day||cass lower leaf|COMP:0000018',
 299           'ease of harvest assessment 1-3||month 10||end of day||cass sink leaf|COMP:0000019',
 300           'ease of harvest assessment 1-3||month 1||end of day||cass lower leaf|COMP:0000020',
 301           'ease of harvest assessment 1-3||month 1||end of day||cass sink leaf|COMP:0000021'
 302         ], 'check store composed terms 2');
 303
 304 my $new_traits3 = $traits3->{new_traits};
 305 my %new_composed_terms3;
 306 foreach (@$new_traits3){
 307     $new_composed_terms3{$_->[1]} = join ',', @{$_->[0]};
 308 }
 309 my $results3 = $onto->store_composed_term(\%new_composed_terms3);
 310 #print STDERR Dumper $results3;
 311 my @results3_names;
 312 foreach (@$results3){
 313     ok($_->[0], 'check that cvterm_id saved');
 314     push @results3_names, $_->[1];
 315 }
 316 print STDERR Dumper \@results3_names;
 317 is_deeply(\@results3_names, [
 318           'anthocyanin pigmentation visual rating 0-3|CO_334:0000103||month 10|TIME:0000069||end of day|TIME:0000003||cass lower stem bark|CASSTISS:0000010|COMP:0000022',
 319           'anthocyanin pigmentation visual rating 0-3|CO_334:0000103||month 10|TIME:0000069||end of day|TIME:0000003||cass lower stem whole|CASSTISS:0000009|COMP:0000023',
 320           'anthocyanin pigmentation visual rating 0-3|CO_334:0000103||month 1|TIME:0000060||end of day|TIME:0000003||cass lower stem bark|CASSTISS:0000010|COMP:0000024',
 321           'anthocyanin pigmentation visual rating 0-3|CO_334:0000103||month 1|TIME:0000060||end of day|TIME:0000003||cass lower stem whole|CASSTISS:0000009|COMP:0000025',
 322           'ease of harvest assessment 1-3|CO_334:0000225||month 10|TIME:0000069||end of day|TIME:0000003||cass lower stem bark|CASSTISS:0000010|COMP:0000026',
 323           'ease of harvest assessment 1-3|CO_334:0000225||month 10|TIME:0000069||end of day|TIME:0000003||cass lower stem whole|CASSTISS:0000009|COMP:0000027',
 324           'ease of harvest assessment 1-3|CO_334:0000225||month 1|TIME:0000060||end of day|TIME:0000003||cass lower stem bark|CASSTISS:0000010|COMP:0000028',
 325           'ease of harvest assessment 1-3|CO_334:0000225||month 1|TIME:0000060||end of day|TIME:0000003||cass lower stem whole|CASSTISS:0000009|COMP:0000029'
 326         ], 'test save composed terms 3');
 327
 328 my $traits3_duplicate = SGN::Model::Cvterm->get_traits_from_component_categories($t->bcs_schema(), \@allowed_composed_cvs, $composable_cvterm_delimiter, $composable_cvterm_format, {
 329   object => [77171, 77174],
 330   attribute => [],
 331   method => [],
 332   unit => [],
 333   trait => [70775,76555],
 334   tod => [77536],
 335   toy => [77526,77499],
 336   gen => [],
 337 });
 338 #print STDERR Dumper $traits3_duplicate;
 339 my $new_traits = $traits3_duplicate->{new_traits};
 340 my $existing_traits = $traits3_duplicate->{existing_traits};
 341 my @check_names;
 342 foreach (@$existing_traits){
 343     ok($_->[0], 'check that cvterm_id saved');
 344     push @check_names, $_->[1];
 345 }
 346 is_deeply($new_traits, [], 'check that duplicate traits are not added');
 347 print STDERR Dumper \@check_names;
 348 is_deeply(\@check_names, [
 349           'anthocyanin pigmentation visual rating 0-3|CO_334:0000103||month 10|TIME:0000069||end of day|TIME:0000003||cass lower stem bark|CASSTISS:0000010|COMP:0000022',
 350           'anthocyanin pigmentation visual rating 0-3|CO_334:0000103||month 10|TIME:0000069||end of day|TIME:0000003||cass lower stem whole|CASSTISS:0000009|COMP:0000023',
 351           'anthocyanin pigmentation visual rating 0-3|CO_334:0000103||month 1|TIME:0000060||end of day|TIME:0000003||cass lower stem bark|CASSTISS:0000010|COMP:0000024',
 352           'anthocyanin pigmentation visual rating 0-3|CO_334:0000103||month 1|TIME:0000060||end of day|TIME:0000003||cass lower stem whole|CASSTISS:0000009|COMP:0000025',
 353           'ease of harvest assessment 1-3|CO_334:0000225||month 10|TIME:0000069||end of day|TIME:0000003||cass lower stem bark|CASSTISS:0000010|COMP:0000026',
 354           'ease of harvest assessment 1-3|CO_334:0000225||month 10|TIME:0000069||end of day|TIME:0000003||cass lower stem whole|CASSTISS:0000009|COMP:0000027',
 355           'ease of harvest assessment 1-3|CO_334:0000225||month 1|TIME:0000060||end of day|TIME:0000003||cass lower stem bark|CASSTISS:0000010|COMP:0000028',
 356           'ease of harvest assessment 1-3|CO_334:0000225||month 1|TIME:0000060||end of day|TIME:0000003||cass lower stem whole|CASSTISS:0000009|COMP:0000029'
 357         ], 'check that duplicate traits are separated from new_traits');
 358
 359
 360 ## Test adding observation variables, traits, methods, scales
 361
 362 my $response;
 363 $mech->post_ok('http://localhost:3010/brapi/v1/token', [ "username"=> "janedoe", "password"=> "secretpw", "grant_type"=> "password" ]);
 364 $response = decode_json $mech->content;
 365 print STDERR Dumper $response;
 366 my $sgn_session_id = $response->{access_token};
 367 print STDERR $sgn_session_id."\n";
 368
 369 my $q = "Select db_id FROM db where name = 'CO_334';";
 370 my $sth = $schema->storage->dbh->prepare($q);
 371 $sth->execute();
 372 my ($db_id) = $sth->fetchrow_array();
 373
 374 $mech->post_ok('http://localhost:3010/ajax/onto/store_trait_method_scale_observation_variable',
 375     [
 376         "sgn_session_id"=>$sgn_session_id,
 377         "selected_observation_variable_db_id"=> $db_id,
 378         "new_observation_variable_name"=> "new observation variable name",
 379         "new_observation_variable_definition"=> "new observation variable definition",
 380         "selected_trait_db_id"=> $db_id,
 381         "selected_trait_cvterm_id"=> undef,
 382         "new_trait_name"=> "new trait name",
 383         "new_trait_definition"=> "new trait definition",
 384         "selected_method_db_id"=> $db_id,
 385         "selected_method_cvterm_id"=> undef,
 386         "new_method_name"=> "new method name",
 387         "new_method_definition"=> "new method definition",
 388         "selected_scale_db_id"=> $db_id,
 389         "selected_scale_cvterm_id"=> undef,
 390         "new_scale_name"=> "new scale name",
 391         "new_scale_definition"=> "new scale definition",
 392         "new_scale_format"=> "",
 393         "new_scale_minimum"=> "",
 394         "new_scale_maximum"=> "",
 395         "new_scale_default"=> "",
 396         "new_scale_categories"=> ""
 397     ]
 398 );
 399 $response = decode_json $mech->content;
 400 print STDERR Dumper $response;
 401 ok($response->{success});
 402
 403 $q = "Select cvterm_id FROM cvterm where name = 'new trait name';";
 404 $sth = $schema->storage->dbh->prepare($q);
 405 $sth->execute();
 406 my ($trait_cvterm_id) = $sth->fetchrow_array();
 407
 408 $mech->post_ok('http://localhost:3010/ajax/onto/store_trait_method_scale_observation_variable',
 409     [
 410         "selected_observation_variable_db_id"=> $db_id,
 411         "new_observation_variable_name"=> "new observation variable name 2",
 412         "new_observation_variable_definition"=> "new observation variable definition 2",
 413         "selected_trait_db_id"=> $db_id,
 414         "selected_trait_cvterm_id"=> $trait_cvterm_id,
 415         "new_trait_name"=> "",
 416         "new_trait_definition"=> "",
 417         "selected_method_db_id"=> $db_id,
 418         "selected_method_cvterm_id"=> "",
 419         "new_method_name"=> "new method name 2",
 420         "new_method_definition"=> "new method definition 2",
 421         "selected_scale_db_id"=> $db_id,
 422         "selected_scale_cvterm_id"=> "",
 423         "new_scale_name"=> "new scale name 2",
 424         "new_scale_definition"=> "new scale definition 2",
 425         "new_scale_format"=> "",
 426         "new_scale_minimum"=> "",
 427         "new_scale_maximum"=> "",
 428         "new_scale_default"=> "",
 429         "new_scale_categories"=> ""
 430     ]
 431 );
 432 $response = decode_json $mech->content;
 433 print STDERR Dumper $response;
 434 ok($response->{success});
 435
 436 $mech->post_ok('http://localhost:3010/ajax/onto/store_ontology_identifier',
 437     [
 438         "sgn_session_id"=>$sgn_session_id,
 439         "ontology_name"=> "NewOntology1",
 440         "ontology_description"=> "new ontology",
 441         "ontology_identifier"=> "NOO1",
 442         "ontology_type"=> "method_ontology",
 443     ]
 444 );
 445 $response = decode_json $mech->content;
 446 print STDERR Dumper $response;
 447 ok($response->{success});
 448
 449 done_testing();