tripal/tests/tripal_chado/loaders/OBOImporterTest.php

<?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;

  /**
   * 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]);
//    }

}