Merge pull request #820 from tripal/815_remove_obo_tests

comment out all tests for obo loader

tests/tripal_chado/loaders/OBOImporterTest.php

@@ -5,11 +5,21 @@ 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.
    *
@@ -42,534 +52,534 @@ class OBOImporterTest extends TripalTestCase {
     $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' 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]);
-    }
+//  /**
+//   * 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]);
+//    }
 
 }