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- <?php
- namespace Tests;
- use StatonLab\TripalTestSuite\DBTransaction;
- use StatonLab\TripalTestSuite\TripalTestCase;
- class OBOImporterTest extends TripalTestCase {
- // Uncomment to auto start and rollback db transactions per test method.
- use DBTransaction;
- /**
- * Dummy test to prevent warnings until the below tests are uncommented.
- */
- public function testDummy() {
- $this->assertTrue(TRUE);
- }
- /**
- * A helper function for loading any OBO.
- *
- * @param $name - ontology name. This goes in the tripal_cv_obo table.
- * @param $path - path to the OBO. this can be a file path or a URL.
- *
- * @throws \Exception
- */
- private function loadOBO($name, $path) {
- $obo_id = db_select('public.tripal_cv_obo', 't')
- ->fields('t', ['obo_id'])
- ->condition('t.name', $name)
- ->execute()
- ->fetchField();
- if (!$obo_id) {
- $obo_id = db_insert('public.tripal_cv_obo')
- ->fields(['name' => $name, 'path' => $path])
- ->execute();
- }
- $run_args = ['obo_id' => $obo_id];
- module_load_include('inc', 'tripal_chado', 'includes/TripalImporter/OBOImporter');
- $importer = new \OBOImporter();
- $importer->create($run_args);
- $importer->prepareFiles();
- $importer->run();
- }
- // /**
- // * Tests that an OBO from a local path can be loaded.
- // *
- // * For this test we will use a test ontology.
- // *
- // * @group obo
- // */
- // public function testLocalOBO() {
- // $name = 'tripal_obo_test';
- // $path = __DIR__ . '/../example_files/test.obo';
- //
- // $this->loadOBO($name, $path);
- //
- // // Make sure we have a proper vocabulary record.
- // $tot_cv_id = db_select('chado.cv', 'c')
- // ->fields('c', ['cv_id'])
- // ->condition('name', 'tripal_obo_test')
- // ->execute()
- // ->fetchField();
- // $this->assertNotFalse($tot_cv_id,
- // "Missing the 'tripal_obo_test' cv record after loading the test.obo file");
- //
- // // Make sure we have a proper database record.
- // $tot_db_id = db_select('chado.db', 'd')
- // ->fields('d', ['db_id'])
- // ->condition('name', 'TOT')
- // ->execute()
- // ->fetchField();
- // $this->assertNotFalse($tot_db_id,
- // "Missing the 'TOT' db record after loading the test.obo file");
- //
- // return [[$tot_cv_id, $tot_db_id]];
- // }
- //
- // /**
- // * Test that all nodes in our test OBO are loaded.
- // *
- // * @group obo
- // * @dataProvider testLocalOBO
- // */
- //
- // public function testCVterms($cv_id, $db_id) {
- //
- // // Our test OBO has 14 nodes.
- // $nodes = [
- // ['TOT:001' => 'node01'],
- // ['TOT:002' => 'node02'],
- // ['TOT:003' => 'node03'],
- // ['TOT:004' => 'node04'],
- // ['TOT:005' => 'node05'],
- // ['TOT:006' => 'node06'],
- // ['TOT:007' => 'node07'],
- // ['TOT:008' => 'node08'],
- // ['TOT:009' => 'node09'],
- // ['TOT:010' => 'node10'],
- // ['TOT:011' => 'node11'],
- // ['TOT:012' => 'node12'],
- // ['TOT:013' => 'node13'],
- // ['TOT:014' => 'node14'],
- // ];
- //
- // // Test that the proper records were added to identify the term.
- // foreach ($nodes as $id => $node_name) {
- //
- // // Check that cvterm record is inserted.
- // $cvterm_id = db_select('chado.cvterm', 'cvt')
- // ->fields('cvt', ['cvterm_id'])
- // ->condition('cvt.name', $node_name)
- // ->condition('cvt.cv_id', $cv_id)
- // ->execute()
- // ->fetchField();
- // $this->assertNotFalse($cvterm_id,
- // "Missing the cvterm record with name, ' $node_name ' after loading the test.obo file");
- //
- // // Check that the dbxref record is inserted.
- // $accession = preg_replace('/TOT:/', '', $id);
- // $dbxref_id = db_select('chado.dbxref', 'dbx')
- // ->fields('dbx', ['dbxref_id'])
- // ->condition('accession', $accession)
- // ->condition('db_id', $db_id);
- // $this->assertNotFalse($cvterm_id,
- // "Missing the dbxref record forid, '$id' after loading the test.obo file");
- // }
- //
- // // Test node 11 to make sure the definition was inserted correctly.
- // // The definition for node11 has an extra colon and a comment. The colon
- // // should not throw off the insertion of the full definition and
- // // the comment should be excluded.
- // $def = db_select('chado.cvterm', 'cvt')
- // ->fields('cvt', ['definition'])
- // ->condition('cvt.name', 'node11')
- // ->condition('cvt.cv_id', $cv_id)
- // ->execute()
- // ->fetchField();
- // $this->assertNotFalse($def,
- // "The definition for node11 was not added.");
- // $this->assertEquals('This is node 11 : Yo', $def,
- // "The definition for node11 is incorrect. it was stored as \"$def\" but should be \"def: This is node 11 : Yo\".");
- //
- // // Make sure that colons in term names don't screw up the term. This test
- // // corresponds to the term with id CHEBI:132502 in the test.obo file.
- // $exists = db_select('chado.cv', 'c')
- // ->fields('c', ['cv_id'])
- // ->condition('name', 'fatty acid 18')
- // ->execute()
- // ->fetchField();
- // $this->assertFalse($exists);
- //
- //
- // // Node14 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 = '014'
- // ";
- // $is_obsolete = chado_query($sql)->fetchField();
- // $this->assertEquals(1, $is_obsolete,
- // "The term, node14, should be marked as obsolete after loading of the test.obo file.");
- //
- // // Every vocabulary should have an is_a term added to support the is_a
- // // relationships.
- // $sql = "
- // SELECT CVT.is_relationshiptype
- // 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 CVT.name = 'is_a' and DB.name = 'TOT'
- // ";
- // $is_reltype = chado_query($sql)->fetchField();
- // $this->assertNotFalse($is_reltype,
- // "The cvterm record for, is_a, should have been added during loading of the test.obo file.");
- // $this->assertEquals(1, $is_reltype,
- // "The cvterm record, is_a, should be marked as a relationship type.");
- //
- // }
- // /**
- // * Test that insertion of synonyms works.
- // *
- // * The term 'node11' has a synonym:"crazy node" EXACT []
- // *
- // * @group obo
- // * @dataProvider testLocalOBO
- // */
- // public function testSynonyms($cv_id, $db_id) {
- //
- // $query = db_select('chado.cvtermsynonym', 'cvts');
- // $query->fields('cvts', ['synonym']);
- // $query->join('chado.cvterm', 'cvt', 'cvts.cvterm_id = cvt.cvterm_id');
- // $query->condition('cvt.name', 'node11');
- // $synonym = $query->execute()->fetchField();
- // $this->assertNotFalse($synonym,
- // "Failed to find the 'crazy node' synonym record for node 11 after loading the test.obo file.");
- //
- // $this->assertEquals("crazy node", $synonym,
- // "Failed to properly add the 'crazy node' synonym for node 11 instead the following was loaded: $synonym");
- // }
- // /**
- // * Test that insertion of subset works.
- // *
- // * The term 'node11' belongs to the test_crazy subset. Everything else belongs
- // * to the test_normal subset.
- // *
- // *
- // * @group obo
- // * @dataProvider testLocalOBO
- // */
- // public function testSubset($cv_id, $db_id) {
- //
- // $sql = "
- // SELECT CVT.name
- // 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_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 $subset_count cvtermprop record for the subset 'test_normal' but there should be 13.");
- // }
- // /**
- // * Test that the insertion of xref works.
- // *
- // * The term 'node11' belongs to the test_crazy subset. Everything else belongs
- // * to the test_normal subset.
- // *
- // *
- // * @group obo
- // * @dataProvider testLocalOBO
- // */
- // public function testXref($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, $xref_id, instead of GO:0043226.");
- // }
- // /**
- // * Test that the insertion of comments works.
- // *
- // * The term 'node11' contains a comment.
- // *
- // * @group obo
- // * @dataProvider testLocalOBO
- // */
- // public function testComment($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\".");
- // }
- //
- // /**
- // * Tests that the cvtermpath is properly loaded.
- // *
- // * @group obo
- // * @dataProvider testLocalOBO
- // */
- // 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 $expected.");
- // }
- //
- // /**
- // * Tests that the cvtermpath is properly loaded.
- // *
- // * @group obo
- // * @dataProvider testLocalOBO
- // */
- // public function testCVtermPath($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 $expected.");
- // }
- //
- // /**
- // * Tests that the EBI Lookup is properly working.
- // *
- // * The term CHEBI:132502 should have been loaded via EBI.
- // *
- // * @group obo
- // * @dataProvider testLocalOBO
- // */
- // public function testEBILookup($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.");
- // }
- // /**
- // * 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
- // * @dataProvider testLocalOBO
- // */
- // 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.");
- // }
- //
- // /**
- // * @group obo
- // * @group chado
- // */
- // public function testfindEBITerm_finder_retrieves_term() {
- //
- // module_load_include('inc', 'tripal_chado', 'includes/TripalImporter/OBOImporter');
- // $importer_private = new \OBOImporter();
- // $importer = reflect($importer_private);
- // $id = 'PECO:0007085';
- // $result = $importer->findEBITerm($id);
- // $this->assertNotEmpty($result);
- // $this->assertEquals('fertilizer exposure', $result['name'][0]);
- // }
- }
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