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@@ -10,394 +10,597 @@ class OBOImporterTest extends TripalTestCase {
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// Uncomment to auto start and rollback db transactions per test method.
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use DBTransaction;
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-
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/**
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- * Tests that the Goslim ontology loads using a remote URL. Ensure subgroups
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- * load.
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+ * A helper function for loading any OBO.
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+ *
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+ * @param $name - ontology name. This goes in the tripal_cv_obo table.
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+ * @param $path - path to the OBO. this can be a file path or a URL.
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+ *
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+ * @throws \Exception
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+ */
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+ private function loadOBO($name, $path) {
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+
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+ $obo_id = db_select('public.tripal_cv_obo', 't')
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+ ->fields('t', ['obo_id'])
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+ ->condition('t.name', $name)
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+ ->execute()
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+ ->fetchField();
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+
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+ if (!$obo_id) {
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+
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+ $obo_id = db_insert('public.tripal_cv_obo')
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+ ->fields(['name' => $name, 'path' => $path])
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+ ->execute();
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+ }
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+
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+ $run_args = ['obo_id' => $obo_id];
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+
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+ module_load_include('inc', 'tripal_chado', 'includes/TripalImporter/OBOImporter');
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+ $importer = new \OBOImporter();
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+ $importer->create($run_args);
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+ $importer->prepareFiles();
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+ $importer->run();
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+ }
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+
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+
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+ /**
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+ * Tests that an OBO from a remote URL can be loaded.
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+ *
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+ * For this test we will use the GO Plant Slim.
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*
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* @group obo
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*/
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-
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- public function testGO_SLIM_load() {
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+ /* public function testRemoteOBO() {
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$name = 'core_test_goslim_plant';
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$path = 'http://www.geneontology.org/ontology/subsets/goslim_plant.obo';
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- $this->load_obo($name, $path);
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+ $this->loadOBO($name, $path);
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- $exists = db_select('chado.cv', 'c')
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+ // Test that we get all three vocabularies added: biological_process,
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+ // cellular_component and molecular_function.
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+ $bp_cv_id = db_select('chado.cv', 'c')
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->fields('c', ['cv_id'])
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->condition('name', 'biological_process')
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->execute()
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->fetchField();
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- $this->assertNotFalse($exists);
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+ $this->assertNotFalse($bp_cv_id,
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+ "Missing the 'biological_process' cv record after loading the GO plant slim.");
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- $exists = db_select('chado.cv', 'c')
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+ $cc_cv_id = db_select('chado.cv', 'c')
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->fields('c', ['cv_id'])
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->condition('name', 'cellular_component')
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->execute()
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->fetchField();
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- $this->assertNotFalse($exists);
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+ $this->assertNotFalse($cc_cv_id,
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+ "Missing the 'cellular_component' cv record after loading the GO plant slim.");
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- $exists = db_select('chado.cv', 'c')
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+ $mf_cv_id = db_select('chado.cv', 'c')
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->fields('c', ['cv_id'])
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->condition('name', 'molecular_function')
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->execute()
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->fetchField();
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- $this->assertNotFalse($exists);
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-
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-
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- $sql = "
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- SELECT DISTINCT CVTP.value
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- FROM {cvtermprop} CVTP
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- INNER JOIN {cvterm} CVTPT on CVTPT.cvterm_id = CVTP.type_id
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- INNER JOIN {cvterm} CVT on CVT.cvterm_id = CVTP.cvterm_id
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- INNER JOIN {dbxref} DBX on CVT.dbxref_id = DBX.dbxref_id
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- INNER JOIN {db} DB on DB.db_id = DBX.db_id
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- WHERE CVTPT.name = 'Subgroup' and DB.name = 'GO' and CVTP.value = 'goslim_plant'
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- ";
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- $exists = chado_query($sql)->fetchField();
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- $this->assertNotFalse($exists);
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- }
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-
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-
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+ $this->assertNotFalse($mf_cv_id,
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+ "Missing the 'molecular_function' cv record after loading the GO plant slim.");
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+
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+ // Make sure we have a proper database record.
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+ $go_db_id = db_select('chado.db', 'd')
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+ ->fields('d', ['db_id'])
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+ ->condition('name', 'GO')
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+ ->execute()
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+ ->fetchField();
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+ $this->assertNotFalse($go_db_id,
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+ "Missing the 'GO' database record after loading the GO plant slim.");
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+ } */
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+
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/**
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- * @param $name - ontology name. This goes in the tripal_cv_obo table.
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- * @param $path - path to the OBO. this can be a file path or a URL.
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+ * Tests that an OBO from a local path can be loaded.
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*
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- * @throws \Exception
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+ * For this test we will use a test ontology.
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+ *
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+ * @group obo
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*/
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-
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- private function load_obo($name, $path) {
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-
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- $obo_id = db_select('public.tripal_cv_obo', 't')
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- ->fields('t', ['obo_id'])
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- ->condition('t.name', $name)
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+ public function testLocalOBO() {
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+ $name = 'tripal_obo_test';
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+ $path = __DIR__ . '/../example_files/test.obo';
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+
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+ $this->loadOBO($name, $path);
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+
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+ // Make sure we have a proper vocabulary record.
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+ $tot_cv_id = db_select('chado.cv', 'c')
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+ ->fields('c', ['cv_id'])
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+ ->condition('name', 'tripal_obo_test')
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->execute()
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->fetchField();
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-
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- if (!$obo_id) {
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-
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- $obo_id = db_insert('public.tripal_cv_obo')
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- ->fields(['name' => $name, 'path' => $path])
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- ->execute();
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- }
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-
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- $run_args = ['obo_id' => $obo_id];
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-
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- module_load_include('inc', 'tripal_chado', 'includes/TripalImporter/OBOImporter');
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- $importer = new \OBOImporter();
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- $importer->create($run_args);
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- $importer->prepareFiles();
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- $importer->run();
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-
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+ $this->assertNotFalse($tot_cv_id,
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+ "Missing the 'tripal_obo_test' cv record after loading the test.obo file");
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+
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+ // Make sure we have a proper database record.
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+ $tot_db_id = db_select('chado.db', 'd')
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+ ->fields('d', ['db_id'])
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+ ->condition('name', 'TOT')
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+ ->execute()
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+ ->fetchField();
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+ $this->assertNotFalse($tot_db_id,
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+ "Missing the 'TOT' db record after loading the test.obo file");
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+
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+ return [[$tot_cv_id, $tot_db_id]];
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}
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/**
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- * Ensure SO can be loaded. Ensure that synonyms are set properly.
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- *
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+ * Test that all nodes in our test OBO are loaded.
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+ *
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* @group obo
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- * @ticket 525
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+ * @dataProvider testLocalOBO
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*/
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- public function test_relationships_in_SO_exist() {
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- // step 1: drop the SO CV and CASCADE.
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+ public function testCVterms($cv_id, $db_id) {
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- $result = chado_query("SET search_path to public, chado;
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- DELETE FROM {cv} WHERE name = 'sequence'");
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- $result = chado_query("SET search_path to public, chado;
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- DELETE FROM {db} WHERE name = 'SO'");
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-
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- // step 2: re-add SO.
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- $name = 'Sequence Ontology';
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- $path = 'http://purl.obolibrary.org/obo/so.obo';
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-
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- $this->load_obo($name, $path);
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-
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- $sql = "SELECT CVT.name, CVTSYN.synonym
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-FROM {cvterm} CVT
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- INNER JOIN {dbxref} DBX on DBX.dbxref_id = CVT.dbxref_id
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- INNER JOIN {db} on DB.db_id = DBX.db_id
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- LEFT JOIN {cvtermsynonym} CVTSYN on CVTSYN.cvterm_id = CVT.cvterm_id
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-WHERE DB.name = 'SO' and CVT.name = 'supercontig'
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-ORDER BY DBX.accession";
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-
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-
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- $results = chado_query($sql)->fetchAll();
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- $result = $results[0];
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+ // Our test OBO has 14 nodes.
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+ $nodes = [
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+ ['TOT:001' => 'node01'],
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+ ['TOT:002' => 'node02'],
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+ ['TOT:003' => 'node03'],
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+ ['TOT:004' => 'node04'],
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+ ['TOT:005' => 'node05'],
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+ ['TOT:006' => 'node06'],
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+ ['TOT:007' => 'node07'],
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+ ['TOT:008' => 'node08'],
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+ ['TOT:009' => 'node09'],
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+ ['TOT:010' => 'node10'],
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+ ['TOT:011' => 'node11'],
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+ ['TOT:012' => 'node12'],
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+ ['TOT:013' => 'node13'],
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+ ['TOT:014' => 'node14'],
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+ ];
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- $this->assertNotNull($result);
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- $this->assertNotEmpty($result);
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- $this->assertEquals("supercontig", $result->name);
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- $this->assertEquals("scaffold", $result->synonym);
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+ // Test that the proper records were added to identify the term.
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+ foreach ($nodes as $id => $node_name) {
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+
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+ // Check that cvterm record is inserted.
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+ $cvterm_id = db_select('chado.cvterm', 'cvt')
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+ ->fields('cvt', ['cvterm_id'])
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+ ->condition('cvt.name', $node_name)
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+ ->condition('cvt.cv_id', $cv_id)
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+ ->execute()
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+ ->fetchField();
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+ $this->assertNotFalse($cvterm_id,
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+ "Missing the cvterm record with name, '$node' after loading the test.obo file");
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+
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+ // Check that the dbxref record is inserted.
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+ $accession = preg_replace('/TOT:/', '', $id);
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+ $dbxref_id = db_select('chado.dbxref', 'dbx')
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+ ->fields('dbx', ['dbxref_id'])
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+ ->condition('accession', $accession)
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+ ->condition('db_id', $db_id);
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+ $this->assertNotFalse($cvterm_id,
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+ "Missing the dbxref record forid, '$id' after loading the test.obo file");
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+ }
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+
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+ // Test node 11 to make sure the definition was inserted correctly.
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+ // The definition for node11 has an extra colon and a comment. The colon
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+ // should not throw off the insertion of the full definition and
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+ // the comment should be excluded.
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+ $def = db_select('chado.cvterm', 'cvt')
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+ ->fields('cvt', ['definition'])
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+ ->condition('cvt.name', 'node11')
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+ ->condition('cvt.cv_id', $cv_id)
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+ ->execute()
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+ ->fetchField();
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+ $this->assertNotFalse($def,
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+ "The definition for node11 was not added.");
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+ $this->assertEquals('This is node 11 : Yo', $def,
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+ "The definition for node11 is incorrect. it was stored as \"$def\" but should be \"def: This is node 11 : Yo\".");
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+
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+ // Make sure that colons in term names don't screw up the term. This test
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+ // corresponds to the term with id CHEBI:132502 in the test.obo file.
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+ $exists = db_select('chado.cv', 'c')
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+ ->fields('c', ['cv_id'])
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+ ->condition('name', 'fatty acid 18')
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+ ->execute()
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+ ->fetchField();
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+ $this->assertFalse($exists);
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+
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+
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+ // Node14 should be marked as obsolete.
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+ $sql = "
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+ SELECT CVT.is_obsolete
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+ FROM {cvterm} CVT
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+ INNER JOIN {dbxref} DBX on DBX.dbxref_id = CVT.dbxref_id
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+ INNER JOIN {db} DB on DB.db_id = DBX.db_id
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+ WHERE DB.name = 'TOT' and DBX.accession = '014'
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+ ";
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+ $is_obsolete = chado_query($sql)->fetchField();
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+ $this->assertEquals(1, $is_obsolete,
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+ "The term, node14, should be marked as obsolete after loading of the test.obo file.");
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+
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+ // Every vocabulary should have an is_a term added to support the is_a
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+ // relationships.
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+ $sql = "
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+ SELECT CVT.is_relationshiptype
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+ FROM {cvterm} CVT
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+ INNER JOIN {dbxref} DBX on DBX.dbxref_id = CVT.dbxref_id
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+ INNER JOIN {db} DB on DB.db_id = DBX.db_id
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+ WHERE CVT.name = 'is_a' and DB.name = 'TOT'
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+ ";
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+ $is_reltype = chado_query($sql)->fetchField();
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+ $this->assertNotFalse($is_reltype,
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+ "The cvterm record for, is_a, should have been added during loading of the test.obo file.");
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+ $this->assertEquals(1, $is_reltype,
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+ "The cvterm record, is_a, should be marked as a relationship type.");
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+
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}
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-
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-
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+
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/**
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- * Test simply that nodes are inserted.
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- ** @group obo
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+ * Test that insertion of synonyms works.
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+ *
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+ * The term 'node11' has a synonym:"crazy node" EXACT []
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+ *
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+ * @group obo
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+ * @dataProvider testLocalOBO
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+ */
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+ public function testSynonyms($cv_id, $db_id){
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+
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+ $query = db_select('chado.cvtermsynonym', 'cvts');
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+ $query->fields('cvts', ['synonym']);
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+ $query->join('chado.cvterm', 'cvt', 'cvts.cvterm_id = cvt.cvterm_id');
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+ $query->condition('cvt.name', 'node11');
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+ $synonym = $query->execute()->fetchField();
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+ $this->assertNotFalse($synonym,
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+ "Failed to find the 'crazy node' synonym record for node 11 after loading the test.obo file.");
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+
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+ $this->assertEquals("crazy node", $synonym,
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+ "Failed to properly add the 'crazy node' synonym for node 11 instead the following was loaded: $synonym");
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+ }
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+
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+ /**
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+ * Test that insertion of subset works.
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+ *
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+ * The term 'node11' belongs to the test_crazy subset. Everything else belongs
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+ * to the test_normal subset.
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+ *
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*
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+ * @group obo
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+ * @dataProvider testLocalOBO
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*/
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-
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- public function test_cvtermpath_cv_nodes_inserted() {
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-
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- $name = 'path_test_mini';
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- $path = __DIR__ . '/../example_files/cvtermpath_test.obo';
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- $this->load_obo($name, $path);
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-
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- //Check cvtermpath is sane.
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-
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- $cv_name = 'cvtermpath_test';
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-
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-
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- $nodes = [
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- 'node01',
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- 'node02',
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- 'node03',
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- 'node04',
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- 'node05',
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- 'node06',
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- 'node07',
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- 'node08',
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- 'node09',
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- 'node10',
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- 'node11',
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- 'node12',
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- 'node13',
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- 'node14',
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- ];
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-
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- //check nodes are inserted.
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- foreach ($nodes as $node) {
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-
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- $query = db_select('chado.cvterm', 'cvt')
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- ->fields('cvt', ['cvterm_id', 'cv_id'])
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- ->condition('cvt.name', $node);
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- $query->join('chado.cv', 'cv', 'cvt.cv_id = cv.cv_id');
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- $query->condition('cv.name', $cv_name);
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- $result = $query->execute()
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- ->fetchObject();
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- $this->assertNotFalse($result);
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-
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- }
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+ public function testSubset($cv_id, $db_id) {
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+
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+ $sql = "
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+ SELECT CVT.name
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+ FROM {cvtermprop} CVTP
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+ INNER JOIN {cvterm} CVTPT on CVTPT.cvterm_id = CVTP.type_id
|
|
|
+ INNER JOIN {cvterm} CVT on CVT.cvterm_id = CVTP.cvterm_id
|
|
|
+ INNER JOIN {dbxref} DBX on CVT.dbxref_id = DBX.dbxref_id
|
|
|
+ INNER JOIN {db} DB on DB.db_id = DBX.db_id
|
|
|
+ WHERE CVTPT.name = 'Subgroup' and DB.name = 'TOT' and CVTP.value = 'test_crazy'
|
|
|
+ ";
|
|
|
+ $term_name = chado_query($sql)->fetchField();
|
|
|
+ $this->assertNotFalse($term_name,
|
|
|
+ "This cvtermprop record for the subset 'test_crazy' is missing.");
|
|
|
+
|
|
|
+ $this->assertEquals('node11', $term_name,
|
|
|
+ "This cvtermprop record for the subset 'test_crazy' is assigned to term, $term_name, instead of node11.");
|
|
|
+
|
|
|
+ $sql = "
|
|
|
+ SELECT count(CVT.cvterm_id)
|
|
|
+ FROM {cvtermprop} CVTP
|
|
|
+ INNER JOIN {cvterm} CVTPT on CVTPT.cvterm_id = CVTP.type_id
|
|
|
+ INNER JOIN {cvterm} CVT on CVT.cvterm_id = CVTP.cvterm_id
|
|
|
+ INNER JOIN {dbxref} DBX on CVT.dbxref_id = DBX.dbxref_id
|
|
|
+ INNER JOIN {db} DB on DB.db_id = DBX.db_id
|
|
|
+ WHERE CVTPT.name = 'Subgroup' and DB.name = 'TOT' and CVTP.value = 'test_normal'
|
|
|
+ ";
|
|
|
+ $subset_count = chado_query($sql)->fetchField();
|
|
|
+
|
|
|
+ $this->assertNotFalse($subset_count,
|
|
|
+ "This cvtermprop record for the subset 'test_normal' are missing.");
|
|
|
+
|
|
|
+ // There should be 12 terms that belong to subset 'test_normal' as node14
|
|
|
+ // does not belong to a subset.
|
|
|
+ $this->assertEquals(12, $subset_count,
|
|
|
+ "There are $subset_count cvtermprop record for the subset 'test_normal' but there should be 13.");
|
|
|
}
|
|
|
-
|
|
|
-
|
|
|
+
|
|
|
/**
|
|
|
- * This data provider currently returns an array of data in the following manner:
|
|
|
- * item[0] - the object node
|
|
|
- * item[1] - an array containing a list of subject nodes, ie, nodes that claim they have a "is_a" relationship with this node.
|
|
|
+ * Test that the insertion of xref works.
|
|
|
+ *
|
|
|
+ * The term 'node11' belongs to the test_crazy subset. Everything else belongs
|
|
|
+ * to the test_normal subset.
|
|
|
*
|
|
|
- * @return array
|
|
|
+ *
|
|
|
+ * @group obo
|
|
|
+ * @dataProvider testLocalOBO
|
|
|
*/
|
|
|
- public function node_data_provider() {
|
|
|
-
|
|
|
- $data = [
|
|
|
- [
|
|
|
- 'node01',// object
|
|
|
- [ //subjects
|
|
|
- 'node02',
|
|
|
- 'node03',
|
|
|
- 'node04',
|
|
|
- 'node05',
|
|
|
- 'node06',
|
|
|
- 'node07',
|
|
|
- 'node08',
|
|
|
- 'node09',
|
|
|
- 'node10',
|
|
|
- 'node11',
|
|
|
- 'node12',
|
|
|
- 'node13',
|
|
|
- // 'node14',
|
|
|
- //Node 14 is not connected!
|
|
|
- ],
|
|
|
- ],
|
|
|
-
|
|
|
- [
|
|
|
- 'node04',
|
|
|
- ['node09','node11'],
|
|
|
- ],
|
|
|
- [
|
|
|
- 'node11',
|
|
|
- ['node13',],
|
|
|
- ],
|
|
|
- ];
|
|
|
- return $data;
|
|
|
-
|
|
|
+ public function testXref($cv_id, $db_id) {
|
|
|
+
|
|
|
+ $sql = "
|
|
|
+ SELECT concat(DB2.name, ':', DBX2.accession)
|
|
|
+ FROM {cvterm} CVT
|
|
|
+ INNER JOIN {dbxref} DBX on DBX.dbxref_id = CVT.dbxref_id
|
|
|
+ INNER JOIN {db} on DB.db_id = DBX.db_id
|
|
|
+ INNER JOIN {cvterm_dbxref} CVTDBX on CVTDBX.cvterm_id = CVT.cvterm_id
|
|
|
+ INNER JOIN {dbxref} DBX2 on DBX2.dbxref_id = CVTDBX.dbxref_id
|
|
|
+ INNER JOIN {db} DB2 on DB2.db_id = DBX2.db_id
|
|
|
+ WHERE DB.name = 'TOT' and CVT.name = 'node11'
|
|
|
+ ORDER BY DBX.accession
|
|
|
+ ";
|
|
|
+ $xref_id = chado_query($sql)->fetchField();
|
|
|
+ $this->assertNotFalse($xref_id,
|
|
|
+ "This cvterm_dbxref record for the xref 'GO:0043226' is missing for node11.");
|
|
|
+
|
|
|
+ $this->assertEquals('GO:0043226', $xref_id,
|
|
|
+ "This cvterm_dbxref record for node 11 is, $xref_id, instead of GO:0043226.");
|
|
|
}
|
|
|
-
|
|
|
+
|
|
|
/**
|
|
|
+ * Test that the insertion of comments works.
|
|
|
+ *
|
|
|
+ * The term 'node11' contains a comment.
|
|
|
+ *
|
|
|
* @group obo
|
|
|
- * @dataProvider node_data_provider
|
|
|
+ * @dataProvider testLocalOBO
|
|
|
*/
|
|
|
- public function test_cvtermpath_correct($object, $subjects) {
|
|
|
-
|
|
|
- $name = 'path_test_mini';
|
|
|
- $path = __DIR__ . '/../example_files/cvtermpath_test.obo';
|
|
|
- $this->load_obo($name, $path);
|
|
|
-
|
|
|
-
|
|
|
- $cv_name = 'cvtermpath_test';
|
|
|
-
|
|
|
- $cv_id = chado_get_cv(['name' => $cv_name])->cv_id;
|
|
|
-
|
|
|
- //populate cvtermpath
|
|
|
- chado_update_cvtermpath($cv_id);
|
|
|
-
|
|
|
-
|
|
|
- $query = db_select('chado.cvtermpath', 'cp');
|
|
|
- $query->fields('cp', ['pathdistance']);
|
|
|
- $query->condition('cp.cv_id', $cv_id);
|
|
|
- $query->join('chado.cvterm', 'subject', 'cp.subject_id = subject.cvterm_id');
|
|
|
- $query->join('chado.cvterm', 'object', 'cp.object_id = object.cvterm_id');
|
|
|
- $query->condition('object.name', $object);
|
|
|
- $query->fields('subject', ['name']);
|
|
|
-
|
|
|
- //First, ensure that the number of relationships is correct
|
|
|
-
|
|
|
- $countquery = clone $query;
|
|
|
-
|
|
|
- $results = $countquery->execute()->fetchAll();
|
|
|
-
|
|
|
-
|
|
|
- $this->assertEquals(count($subjects), count($results));
|
|
|
-
|
|
|
-
|
|
|
-
|
|
|
- foreach ($subjects as $subject) {
|
|
|
-
|
|
|
- $query_copy = clone $query;
|
|
|
-
|
|
|
- $query_copy->condition('subject.name', $subject);
|
|
|
- $results = $query_copy->execute()->fetchObject();
|
|
|
-
|
|
|
- $this->assertNotFalse($results, "failed for {$object} as object and {$subject} as subject.");
|
|
|
-
|
|
|
- }
|
|
|
+ public function testComment($cv_id, $db_id) {
|
|
|
+
|
|
|
+ $sql = "
|
|
|
+ SELECT CVTP.value
|
|
|
+ FROM {cvterm} CVT
|
|
|
+ INNER JOIN {dbxref} DBX on DBX.dbxref_id = CVT.dbxref_id
|
|
|
+ INNER JOIN {db} on DB.db_id = DBX.db_id
|
|
|
+ INNER JOIN {cvtermprop} CVTP on CVTP.cvterm_id = CVT.cvterm_id
|
|
|
+ INNER JOIN {cvterm} CVTPT on CVTPT.cvterm_id = CVTP.type_id
|
|
|
+ WHERE DB.name = 'TOT' and CVTPT.name = 'comment' and CVT.name = 'node11'
|
|
|
+ ORDER BY DBX.accession
|
|
|
+ ";
|
|
|
+ $comment = chado_query($sql)->fetchField();
|
|
|
+ $this->assertNotFalse($xref_id,
|
|
|
+ "This cvterm_dbxref record for the xref 'This is a crazy node' is missing for node11.");
|
|
|
+
|
|
|
+ $this->assertEquals('This is a crazy node', $comment,
|
|
|
+ "This cvterm_dbxref record for node11 is, \"$comment\", instead of \"This is a crazy node\".");
|
|
|
}
|
|
|
-
|
|
|
+
|
|
|
/**
|
|
|
- * ONLY node 1 should be root for test OBO.
|
|
|
+ * Tests that the cvtermpath is properly loaded.
|
|
|
*
|
|
|
* @group obo
|
|
|
+ * @dataProvider testLocalOBO
|
|
|
*/
|
|
|
- public function test_cvtermpath_mview_root_terms_correct() {
|
|
|
-
|
|
|
- $name = 'path_test_mini';
|
|
|
- $path = __DIR__ . '/../example_files/cvtermpath_test.obo';
|
|
|
- $this->load_obo($name, $path);
|
|
|
-
|
|
|
- //populate mview
|
|
|
- chado_populate_mview(chado_get_mview_id('cv_root_mview'));
|
|
|
-
|
|
|
-
|
|
|
- $cv_name = 'cvtermpath_test';
|
|
|
-
|
|
|
- $roots = db_select('chado.cv_root_mview', 't')
|
|
|
- ->fields('t', ['name'])
|
|
|
- ->condition('cv_name', $cv_name)
|
|
|
- ->execute()
|
|
|
- ->fetchAll();
|
|
|
-
|
|
|
- $this->assertNotEmpty($roots);
|
|
|
-
|
|
|
- $this->assertLessThan(2, count($roots));
|
|
|
- $this->assertEquals("node01", $roots[0]->name);
|
|
|
-
|
|
|
+ public function testRelationships($cv_id, $db_id) {
|
|
|
+ $relationships = [
|
|
|
+ ['node02', 'is_a', 'node01'],
|
|
|
+ ['node03', 'is_a', 'node01'],
|
|
|
+ ['node04', 'is_a', 'node01'],
|
|
|
+ ['node04', 'has_part', 'node11'],
|
|
|
+ ['node05', 'is_a', 'node01'],
|
|
|
+ ['node06', 'is_a', 'node03'],
|
|
|
+ ['node07', 'is_a', 'node03'],
|
|
|
+ ['node08', 'is_a', 'node07'],
|
|
|
+ ['node09', 'is_a', 'node04'],
|
|
|
+ ['node09', 'is_a', 'node07'],
|
|
|
+ ['node10', 'is_a', 'node05'],
|
|
|
+ ['node11', 'is_a', 'node09'],
|
|
|
+ ['node11', 'is_a', 'node10'],
|
|
|
+ ['node12', 'is_a', 'node10'],
|
|
|
+ ['node13', 'is_a', 'node11'],
|
|
|
+ ];
|
|
|
+ foreach ($relationships as $relationship) {
|
|
|
+ $subject = $relationship[0];
|
|
|
+ $type = $relationship[1];
|
|
|
+ $object = $relationship[2];
|
|
|
+ $sql = "
|
|
|
+ SELECT CVTR.cvterm_relationship_id
|
|
|
+ FROM {cvterm} CVT
|
|
|
+ INNER JOIN {dbxref} DBX on DBX.dbxref_id = CVT.dbxref_id
|
|
|
+ INNER JOIN {db} on DB.db_id = DBX.db_id
|
|
|
+ INNER JOIN {cvterm_relationship} CVTR on CVTR.subject_id = CVT.cvterm_id
|
|
|
+ INNER JOIN {cvterm} CVT2 on CVT2.cvterm_id = CVTR.object_id
|
|
|
+ INNER JOIN {cvterm} CVT3 on CVT3.cvterm_id = CVTR.type_id
|
|
|
+ WHERE DB.name = 'TOT' AND CVT2.name = :object AND
|
|
|
+ CVT3.name = :type AND CVT.name = :subject
|
|
|
+ ";
|
|
|
+ $args = [':object' => $object, ':type' => $type, ':subject' => $subject];
|
|
|
+ $rel_id = chado_query($sql, $args)->fetchField();
|
|
|
+ $this->assertNotFalse($rel_id,
|
|
|
+ "The following relationship could not be found: $subect $type $object.");
|
|
|
+ }
|
|
|
+
|
|
|
+ // Now make sure we have no more relationships than what we are supposed
|
|
|
+ // to have.
|
|
|
+ $sql = "
|
|
|
+ SELECT count(CVTR.cvterm_relationship_id)
|
|
|
+ FROM {cvterm} CVT
|
|
|
+ INNER JOIN {dbxref} DBX on DBX.dbxref_id = CVT.dbxref_id
|
|
|
+ INNER JOIN {db} on DB.db_id = DBX.db_id
|
|
|
+ INNER JOIN {cvterm_relationship} CVTR on CVTR.object_id = CVT.cvterm_id
|
|
|
+ WHERE DB.name = 'TOT' AND CVT.is_relationshiptype = 0
|
|
|
+ ";
|
|
|
+ $rel_count = chado_query($sql)->fetchField();
|
|
|
+ $expected = count($relationships);
|
|
|
+ $this->assertEquals($expected, $rel_count,
|
|
|
+ "There are an incorrect number of relationships. There were $rel_count found but there should be $expected.");
|
|
|
}
|
|
|
|
|
|
/**
|
|
|
- * Test OBO has a synonym. check its inserted properly.
|
|
|
+ * Tests that the cvtermpath is properly loaded.
|
|
|
+ *
|
|
|
* @group obo
|
|
|
- * @group wip
|
|
|
+ * @dataProvider testLocalOBO
|
|
|
*/
|
|
|
- public function test_synonyms_are_loaded(){
|
|
|
- //node11 has a synonym:"crazy node" EXACT []
|
|
|
-
|
|
|
-
|
|
|
- $name = 'path_test_mini';
|
|
|
- $path = __DIR__ . '/../example_files/cvtermpath_test.obo';
|
|
|
- $this->load_obo($name, $path);
|
|
|
-
|
|
|
- $cv_name = 'cvtermpath_test';
|
|
|
-
|
|
|
- $query = db_select('chado.cvtermsynonym', 't')
|
|
|
- ->fields('t', ['synonym']);
|
|
|
- $query->join('chado.cvterm', 'cvt', 't.cvterm_id = cvt.cvterm_id');
|
|
|
- $query->condition('cvt.name', 'node11');
|
|
|
-
|
|
|
- $result = $query->execute()->fetchField();
|
|
|
-
|
|
|
- $this->assertNotFalse($result);
|
|
|
-
|
|
|
- $this->assertEquals("crazy node", $result);
|
|
|
-
|
|
|
-
|
|
|
+ public function testCVtermPath($cv_id, $db_id) {
|
|
|
+
|
|
|
+ // For now we won't include distance or type in the check because depending
|
|
|
+ // how the tree was loaded and if there are multiple paths to a node
|
|
|
+ // then there's no guarantee we'll always get the same path. Therefore the
|
|
|
+ // type and pathdistance may be different (althoug not incorrect).
|
|
|
+ $relationships = [
|
|
|
+ // Node01 as root: note that the root term always has a link to itself
|
|
|
+ // in the cvtermpath table.
|
|
|
+ ['node01', 'node01'],
|
|
|
+ ['node01', 'node02'],
|
|
|
+ ['node01', 'node03'],
|
|
|
+ ['node01', 'node04'],
|
|
|
+ ['node01', 'node05'],
|
|
|
+ ['node01', 'node06'],
|
|
|
+ ['node01', 'node07'],
|
|
|
+ ['node01', 'node08'],
|
|
|
+ ['node01', 'node09'],
|
|
|
+ ['node01', 'node10'],
|
|
|
+ ['node01', 'node11'],
|
|
|
+ ['node01', 'node12'],
|
|
|
+ ['node01', 'node13'],
|
|
|
+ // Node03 as root.
|
|
|
+ ['node03', 'node04'],
|
|
|
+ ['node03', 'node06'],
|
|
|
+ ['node03', 'node07'],
|
|
|
+ ['node03', 'node08'],
|
|
|
+ ['node03', 'node09'],
|
|
|
+ ['node03', 'node11'],
|
|
|
+ ['node03', 'node13'],
|
|
|
+ // Node04 as root.
|
|
|
+ ['node04', 'node09'],
|
|
|
+ ['node04', 'node11'],
|
|
|
+ ['node04', 'node13'],
|
|
|
+ // Node05 as root.
|
|
|
+ ['node05', 'node04'],
|
|
|
+ ['node05', 'node09'],
|
|
|
+ ['node05', 'node10'],
|
|
|
+ ['node05', 'node11'],
|
|
|
+ ['node05', 'node12'],
|
|
|
+ ['node05', 'node13'],
|
|
|
+ // Node07 as root.
|
|
|
+ ['node07', 'node04'],
|
|
|
+ ['node07', 'node08'],
|
|
|
+ ['node07', 'node09'],
|
|
|
+ ['node07', 'node11'],
|
|
|
+ ['node07', 'node13'],
|
|
|
+ // Node09 as root.
|
|
|
+ ['node09', 'node04'],
|
|
|
+ ['node09', 'node11'],
|
|
|
+ ['node09', 'node13'],
|
|
|
+ // Node10 as root.
|
|
|
+ ['node10', 'node04'],
|
|
|
+ ['node10', 'node09'],
|
|
|
+ ['node10', 'node11'],
|
|
|
+ ['node10', 'node12'],
|
|
|
+ ['node10', 'node13'],
|
|
|
+ // Node11 as root.
|
|
|
+ ['node11', 'node04'],
|
|
|
+ ['node11', 'node09'],
|
|
|
+ ['node11', 'node13'],
|
|
|
+ ];
|
|
|
|
|
|
+ // Populate the cvtermpath for our test OBO.
|
|
|
+ chado_update_cvtermpath($cv_id);
|
|
|
+
|
|
|
+ foreach ($relationships as $relationship) {
|
|
|
+ $object = $relationship[0];
|
|
|
+ $subject = $relationship[1];
|
|
|
+ $sql = "
|
|
|
+ SELECT cvtermpath_id
|
|
|
+ FROM {cvtermpath} CVTP
|
|
|
+ INNER JOIN {cvterm} CVTO on CVTO.cvterm_id = CVTP.object_id
|
|
|
+ INNER JOIN {cvterm} CVTS on CVTS.cvterm_id = CVTP.subject_id
|
|
|
+ INNER JOIN {cvterm} CVTT on CVTT.cvterm_id = CVTP.type_id
|
|
|
+ WHERE CVTP.cv_id = :cv_id and CVTO.name = :object and
|
|
|
+ CVTS.name = :subject
|
|
|
+ ";
|
|
|
+ $args = [':cv_id' => $cv_id, ':object' => $object, ':subject' => $subject];
|
|
|
+ $cvtermpath_id = chado_query($sql, $args)->fetchField();
|
|
|
+ $this->assertNotFalse($cvtermpath_id,
|
|
|
+ "Cound not find the cvtermpath record for the relationship: $subject => $object.");
|
|
|
+ }
|
|
|
|
|
|
+ // Now make sure we have no additional entries.
|
|
|
+ $sql = "
|
|
|
+ SELECT count(cvtermpath_id)
|
|
|
+ FROM {cvtermpath} CVTP
|
|
|
+ INNER JOIN {cvterm} CVTO on CVTO.cvterm_id = CVTP.object_id
|
|
|
+ INNER JOIN {cvterm} CVTS on CVTS.cvterm_id = CVTP.subject_id
|
|
|
+ INNER JOIN {cvterm} CVTT on CVTT.cvterm_id = CVTP.type_id
|
|
|
+ WHERE CVTP.cv_id = :cv_id
|
|
|
+ ";
|
|
|
+ $args = [':cv_id' => $cv_id];
|
|
|
+ $rel_count = chado_query($sql, $args)->fetchField();
|
|
|
+ $expected = count($relationships);
|
|
|
+ $this->assertEquals($expected, $rel_count,
|
|
|
+ "There are an incorrect number of paths. There were $rel_count found but there should be $expected.");
|
|
|
}
|
|
|
-
|
|
|
-
|
|
|
-
|
|
|
+
|
|
|
/**
|
|
|
- * Test OBO has a xref. check its inserted properly.
|
|
|
+ * Tests that the EBI Lookup is properly working.
|
|
|
+ *
|
|
|
+ * The term CHEBI:132502 should have been loaded via EBI.
|
|
|
+ *
|
|
|
* @group obo
|
|
|
- * @group wip
|
|
|
+ * @dataProvider testLocalOBO
|
|
|
*/
|
|
|
- public function test_dbxref_loaded(){
|
|
|
- //node11 has a synonym:"crazy node" EXACT []
|
|
|
-
|
|
|
-
|
|
|
- $name = 'path_test_mini';
|
|
|
- $path = __DIR__ . '/../example_files/cvtermpath_test.obo';
|
|
|
- $this->load_obo($name, $path);
|
|
|
-
|
|
|
- $cv_name = 'cvtermpath_test';
|
|
|
-
|
|
|
- $query = db_select('chado.cvterm_dbxref', 't');
|
|
|
- $query->join('chado.cvterm', 'cvt', 't.cvterm_id = cvt.cvterm_id');
|
|
|
- $query->join('chado.dbxref', 'dbx', 'dbx.dbxref_id = t.dbxref_id');
|
|
|
- $query->fields('dbx', ['accession']);
|
|
|
- $query->condition('cvt.name', 'node11');
|
|
|
-
|
|
|
- $result = $query->execute()->fetchField();
|
|
|
-
|
|
|
- $this->assertNotFalse($result);
|
|
|
-
|
|
|
- $this->assertEquals("0043226", $result);
|
|
|
-
|
|
|
+ public function testEBILookup($cv_id, $db_id) {
|
|
|
+ $sql = "
|
|
|
+ SELECT CVT.cvterm_id
|
|
|
+ FROM {cvterm} CVT
|
|
|
+ INNER JOIN {dbxref} DBX on DBX.dbxref_id = CVT.dbxref_id
|
|
|
+ INNER JOIN {db} DB on DB.db_id = DBX.db_id
|
|
|
+ WHERE DB.name = 'CHEBI' and DBX.accession = '132502'
|
|
|
+ ";
|
|
|
+ $cvterm_id = chado_query($sql)->fetchField();
|
|
|
+ $this->assertNotFalse($cvterm_id,
|
|
|
+ "The term, CHEBI:132502, is not present the EBI OLS lookup must not have succeeded.");
|
|
|
}
|
|
|
-
|
|
|
+
|
|
|
/**
|
|
|
- * ensure that new CV's aren't accidentally created when term names have
|
|
|
- * colons in them.
|
|
|
+ * Tests when changes are made between OBO loads.
|
|
|
+ *
|
|
|
+ * Sometimes an ontology can change the names of it's terms, or set some
|
|
|
+ * as obsolete, etc. We need to makes sure that when changes are made and
|
|
|
+ * the OBO is reloaded that the terms are properly update.
|
|
|
*
|
|
|
* @group obo
|
|
|
- * @ticket 525
|
|
|
+ * @dataProvider testLocalOBO
|
|
|
*/
|
|
|
- public function test_PTO_loads_colon_issue() {
|
|
|
-
|
|
|
- $name = 'core_test_PTO_mini';
|
|
|
- $path = __DIR__ . '/../example_files/pto_colon.obo';
|
|
|
-
|
|
|
- $this->load_obo($name, $path);
|
|
|
-
|
|
|
- $exists = db_select('chado.cv', 'c')
|
|
|
- ->fields('c', ['cv_id'])
|
|
|
- ->condition('name', 'core_test_PTO_mini')
|
|
|
- ->execute()
|
|
|
- ->fetchField();
|
|
|
- $this->assertNotFalse($exists);
|
|
|
-
|
|
|
- //hte colon splitting issue: a new CV will created named fatty acid 18
|
|
|
- $exists = db_select('chado.cv', 'c')
|
|
|
- ->fields('c', ['cv_id'])
|
|
|
- ->condition('name', 'fatty acid 18')
|
|
|
- ->execute()
|
|
|
- ->fetchField();
|
|
|
- $this->assertFalse($exists);
|
|
|
-
|
|
|
+ public function testOBOChanges($cv_id, $db_id) {
|
|
|
+ $name = 'tripal_obo_test_update';
|
|
|
+ $path = __DIR__ . '/../example_files/test.update.obo';
|
|
|
+
|
|
|
+ $this->loadOBO($name, $path);
|
|
|
+
|
|
|
+ // Did the name of term 13 change?
|
|
|
+ $sql = "
|
|
|
+ SELECT CVT.name
|
|
|
+ FROM {cvterm} CVT
|
|
|
+ INNER JOIN {dbxref} DBX on DBX.dbxref_id = CVT.dbxref_id
|
|
|
+ INNER JOIN {db} DB on DB.db_id = DBX.db_id
|
|
|
+ WHERE DB.name = 'TOT' and DBX.accession = '013'
|
|
|
+ ";
|
|
|
+ $name = chado_query($sql)->fetchField();
|
|
|
+ $this->assertEquals('New name 13.', $name,
|
|
|
+ "The name for node13 (TOT:013) failed to update to 'New name 13'.");
|
|
|
+
|
|
|
+ // Node15 is new, and node02 got removed. Node15 now uses node02's name and
|
|
|
+ // has TOT:002 as an alt_id. So, node02 should be marked as obsolete
|
|
|
+ $sql = "
|
|
|
+ SELECT CVT.is_obsolete
|
|
|
+ FROM {cvterm} CVT
|
|
|
+ INNER JOIN {dbxref} DBX on DBX.dbxref_id = CVT.dbxref_id
|
|
|
+ INNER JOIN {db} DB on DB.db_id = DBX.db_id
|
|
|
+ WHERE DB.name = 'TOT' and DBX.accession = '002'
|
|
|
+ ";
|
|
|
+ $is_obsolete = chado_query($sql)->fetchField();
|
|
|
+ $this->assertEquals(1, $is_obsolete,
|
|
|
+ "The node02 (TOT:002) should be marked as obsolete after update.");
|
|
|
+
|
|
|
+ // Node16 is new, and node08 is now obsolete. Node16 now uses node08's name,
|
|
|
+ // so, node08 should be marked as obsolete and have the word '(obsolete)'
|
|
|
+ // added to prevent future conflicts.
|
|
|
+ $sql = "
|
|
|
+ SELECT CVT.name
|
|
|
+ FROM {cvterm} CVT
|
|
|
+ INNER JOIN {dbxref} DBX on DBX.dbxref_id = CVT.dbxref_id
|
|
|
+ INNER JOIN {db} DB on DB.db_id = DBX.db_id
|
|
|
+ WHERE DB.name = 'TOT' and DBX.accession = '008'
|
|
|
+ ";
|
|
|
+ $name = chado_query($sql)->fetchField();
|
|
|
+ $this->assertEquals("node08 (obsolete)", $name,
|
|
|
+ "The node08 (TOT:008) should be marked as obsolete after update.");
|
|
|
}
|
|
|
-
|
|
|
-
|
|
|
}
|
Stephen Ficklin