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Merge pull request #1498 from tripal/tv4g0-issue1485-port-pull-1244
Tripal 4 chado_unabbreviate_infraspecific_rank (port tripal 3 pull 1244) ported and tests now work with "correct" schema 馃榿
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tripal_chado/tests/src/Functional/api/ChadoOrganismAPITest.php
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| <?php | ||
|
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| namespace Drupal\Tests\tripal_chado; | ||
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| use Drupal\Core\Url; | ||
| use Drupal\Tests\tripal_chado\Functional\ChadoTestBrowserBase; | ||
| use Drupal\Core\Database\Database; | ||
| use Drupal\tripal_chado\api\ChadoSchema; | ||
|
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| /** | ||
| * Testing the tripal_chado/api/tripal_chado.organism.api.inc functions. | ||
| * | ||
| * @group Tripal | ||
| * @group Tripal Chado | ||
| * @group Tripal API | ||
| */ | ||
| class ChadoOrganismAPITest extends ChadoTestBrowserBase { | ||
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| protected $defaultTheme = 'stable'; | ||
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| /** | ||
| * Modules to enable. | ||
| * @var array | ||
| */ | ||
| protected static $modules = ['tripal', 'tripal_chado']; | ||
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| /** | ||
| * Schema to do testing out of. | ||
| * @var string | ||
| */ | ||
| protected $schemaName; | ||
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| /** | ||
| * Tests the following organism API functions: | ||
| * chado_get_organism() | ||
| * chado_get_organism_scientific_name() | ||
| * chado_get_organism_select_options() | ||
| * chado_abbreviate_infraspecific_rank() | ||
| * chado_unabbreviate_infraspecific_rank() | ||
| * @to-do: The following API functions do not have tests yet: | ||
| * chado_get_organism_image_url($organism) | ||
| * chado_autocomplete_organism($text) | ||
| * | ||
| * @group tripal-chado | ||
| * @group chado-organism | ||
| */ | ||
| public function test_chado_organism_api_functions() { | ||
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| putenv('TRIPAL_SUPPRESS_ERRORS=TRUE'); | ||
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| // Create a Test Chado schema which contains the expected cvterms added during the prepare step. | ||
| $connection = $this->createTestSchema(ChadoTestBrowserBase::PREPARE_TEST_CHADO); | ||
| $this->schemaName = $connection->getSchemaName(); | ||
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| // Lookup cvterm_id for 'subspecies' | ||
| $cvterm = chado_get_cvterm(['name' => 'subspecies'], [], $this->schemaName); | ||
| $this->assertNotNull($cvterm, 'Unable to retrieve cvterm for "subspecies" using chado_get_cvterm()'); | ||
| $subspecies_id = $cvterm->cvterm_id; | ||
|
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| // Create two test organisms of the same genus and species | ||
| $species = 'bogusii' . uniqid(); | ||
| $organism_ids = []; | ||
| $org = [ | ||
| 'genus' => 'Tripalus', | ||
| 'species' => $species, | ||
| 'type_id' => $subspecies_id, | ||
| 'infraspecific_name' => 'sativus', | ||
| 'common_name' => 'False Tripal', | ||
| 'abbreviation' => 'T. ' . $species . ' subsp. sativus', | ||
| ]; | ||
| $dbq = chado_insert_record('organism', $org, [], $this->schemaName); | ||
| $this->assertNotNull($dbq, 'Unable to insert test organism 1.'); | ||
| $organism_ids[0] = $dbq['organism_id']; | ||
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| $org['infraspecific_name'] = 'selvaticus'; | ||
| $org['abbreviation'] = 'T. ' . $species . ' subsp. selvaticus'; | ||
| $dbq = chado_insert_record('organism', $org, [], $this->schemaName); | ||
| $this->assertNotNull($dbq, 'Unable to insert test organism 2.'); | ||
| $organism_ids[1] = $dbq['organism_id']; | ||
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| // Test invalid $identifiers ($identifiers must be an array) = Should fail, and in fact causes an exception | ||
| $identifiers = 1; // not an array | ||
| try { | ||
| $org = chado_get_organism($identifiers, []); | ||
| } | ||
| catch (\Exception $e) { | ||
| $org = NULL; | ||
| } | ||
| $this->assertNull($org, 'Did not flag invalid $identifiers passed to chado_get_organism() (not an array)'); | ||
|
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| // Test using an empty array for $identifiers = Should fail | ||
| $identifiers = []; | ||
| $org = chado_get_organism($identifiers, [], $this->schemaName); | ||
| $this->assertNull($org, 'Did not flag invalid $identifiers passed to chado_get_organism() (empty array)'); | ||
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| // Test retrieving organism that does not exist = Should fail | ||
| $identifiers = ['genus' => 'Wrong', 'species' => 'incorrect']; | ||
| $org = chado_get_organism($identifiers, [], $this->schemaName); | ||
| $this->assertNull($org, 'Returned an organism from invalid $identifiers passed to chado_get_organism()'); | ||
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| // Get organism from organism_id = Should succeed | ||
| $identifiers = ['organism_id' => $organism_ids[0]]; | ||
| $org = chado_get_organism($identifiers, [], $this->schemaName); | ||
| $this->assertIsObject($org, 'Did not return the organism with organism_id=' | ||
| . $organism_ids[0] . ' using chado_get_organism()'); | ||
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| // Test ambiguous $identifiers = Should fail | ||
| $identifiers = ['genus' => 'Tripalus', 'species' => $species]; // subspecies not specified, thus ambiguous | ||
| $org = chado_get_organism($identifiers, [], $this->schemaName); | ||
| $this->assertNull($org, 'Returned an organism from ambiguous $identifiers passed to chado_get_organism()'); | ||
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| // Test unambiguous $identifiers = Should succeed | ||
| $identifiers = ['genus' => 'Tripalus', 'species' => $species, 'type_id' => $subspecies_id, 'infraspecific_name' => 'selvaticus']; | ||
| $org = chado_get_organism($identifiers, [], $this->schemaName); | ||
| $this->assertIsObject($org, 'Did not return an organism from unambiguous $identifiers passed to chado_get_organism()'); | ||
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| // Test getting scientific name = Should succeed | ||
| $name = chado_get_organism_scientific_name($org, $this->schemaName); | ||
| $expect = 'Tripalus ' . $species . ' subsp. selvaticus'; | ||
| $this->assertEquals($name, $expect, 'Did not return the expected scientific name ' . $expect | ||
| . ' instead returned ' . $name . ' using chado_get_organism_scientific_name()'); | ||
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| // Test organism select options with default parameters, and test that an array is returned = should succeed | ||
| $select_options = chado_get_organism_select_options(FALSE, FALSE, $this->schemaName); | ||
| $this->assertIsArray($select_options, 'Did not return an array from chado_get_organism_select_options()'); | ||
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| // Test that the array contains at least the two test organisms = should succeed | ||
| $count = count($select_options); | ||
| $this->assertGreaterThanOrEqual(2, $count, 'Did not return at least two organisms from chado_get_organism_select_options()'); | ||
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| // Test that both of the test organisms are in the returned array = should succeed | ||
| $expect = 'Tripalus ' . $species . ' subsp. sativus'; | ||
| $this->assertArrayHasKey($organism_ids[0], $select_options, 'Returned array does not contain the expected organism id ' | ||
| . $organism_ids[0] . ' using chado_get_organism_select_options()'); | ||
| $this->assertEquals($expect, $select_options[$organism_ids[0]], 'Array element 0 does not contain the expected organism text ' | ||
| . $expect . ' using chado_get_organism_select_options()'); | ||
| $expect = 'Tripalus ' . $species . ' subsp. selvaticus'; | ||
| $this->assertArrayHasKey($organism_ids[1], $select_options, 'Returned array does not contain the expected organism id ' | ||
| . $organism_ids[1] . ' using chado_get_organism_select_options()'); | ||
| $this->assertEquals($expect, $select_options[$organism_ids[1]], 'Array element 1 does not contain the expected organism text ' | ||
| . $expect . ' using chado_get_organism_select_options()'); | ||
|
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| // Data to test abbreviation of infraspecific rank | ||
| $expected_abbreviated = [ | ||
| 'no_rank' => '', | ||
| 'subspecies' => 'subsp.', | ||
| 'varietas' => 'var.', | ||
| 'subvarietas' => 'subvar.', | ||
| 'cultivar' => 'cv.', | ||
| 'forma' => 'f.', | ||
| 'subforma' => 'subf.', | ||
| 'anything_else' => 'anything_else', | ||
| ]; | ||
|
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| // Data to test unabbreviation of infraspecific rank | ||
| $expected_unabbreviated = [ | ||
| '' => '', | ||
| 'subsp' => 'subspecies', | ||
| 'subsp.' => 'subspecies', | ||
| 'ssp' => 'subspecies', | ||
| 'ssp.' => 'subspecies', | ||
| 'var' => 'varietas', | ||
| 'var.' => 'varietas', | ||
| 'subvar' => 'subvarietas', | ||
| 'subvar.' => 'subvarietas', | ||
| 'cv' => 'cultivar', | ||
| 'cv.' => 'cultivar', | ||
| 'f' => 'forma', | ||
| 'f.' => 'forma', | ||
| 'subf' => 'subforma', | ||
| 'subf.' => 'subforma', | ||
| 'anything_else' => 'anything_else', | ||
| 'anything_else.' => 'anything_else.', | ||
| ]; | ||
|
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| // Test abbreviation of infraspecific rank | ||
| foreach ($expected_abbreviated as $full => $abbreviation) { | ||
| $result = chado_abbreviate_infraspecific_rank($full); | ||
| $this->assertEqual($result, $abbreviation, 'Did not properly abbreviate ' . $full | ||
| . ' returned ' . $result . ' using chado_abbreviate_infraspecific_rank()'); | ||
| } | ||
|
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| // Test unabbreviation of infraspecific rank | ||
| foreach ($expected_unabbreviated as $abbreviation => $full) { | ||
| $result = chado_unabbreviate_infraspecific_rank($full); | ||
| $this->assertEqual($result, $full, 'Did not properly unabbreviate ' . $abbreviation | ||
| . ' returned ' . $result . ' using chado_unabbreviate_infraspecific_rank()'); | ||
| } | ||
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| putenv('TRIPAL_SUPPRESS_ERRORS=FALSE'); | ||
| } | ||
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| } |