G5.13 Improvements to Germplasm Accession Synonyms Test

[laceysanderson]

Branch

g5.13-germplasmAccessionSynonymTests

Groups

Group 2 - Data Importing, Group 5 | Automated Testing | Performance

Describe

These suggestions came up in the review of #6. This issue makes sure we don't forget about them and allows us to merge that PR :-)

GermplasmAccessionImporterTest::testGermplasmAccessionImporterLoadSynonyms()

    // Check both synonyms are in chado.synonym
    $synonyms_semicolon_query = $this->connection->select('1:synonym', 's')
      ->fields('s', ['name']);
    $group = $synonyms_semicolon_query->orConditionGroup()
      ->condition('s.name', $syn3, '=')
      ->condition('s.name', $syn4, '=');
    $synonyms_semicolon_query->condition($group);
    $synonyms_semicolon_record = $synonyms_semicolon_query->execute()->fetchAll();
    $this->assertEquals($synonyms_semicolon_record[0]->name, $syn3, "The synonym table does not contain the expected synonym syn3");
    $this->assertEquals($synonyms_semicolon_record[1]->name, $syn4, "The synonym table does not contain the expected synonym syn4");

    // @todo: Test the case when a stock_relationship previously exists

    // Do my final queries to ensure everything we expect to be in the tables is there
    // stock table
    // $stock_table_query = $this->connection->select('1:stock', 'st')
    //   ->fields('st', ['stock_id', 'name', 'uniquename', 'organism_id']);
    // $stock_table_records = $stock_table_query->execute();
    // $stock_table_array_actual = $stock_table_records->fetchAllAssoc('stock_id');
    // print_r($stock_table_records->fetchAllAssoc('stock_id'));

Lacey: Might also be good to check that both synonyms are connected to the correct stock via the stock_synonym table here just as you have done with the other test cases above.

Carolyn: I didn't get to this in time sadly, but in commit 371d157 I added the check for a pre-existing stock_relationship and intended to also add a test to make sure duplicate stock_relationships indeed do not get added by the importer. All this to say that I plan to tackle your suggestion at the same time since both tests are synonym-focussed 😄