This is the required update for tripal_pub when upgrading from Drupal core API 6.x.

File

legacy/tripal_pub/tripal_pub.install, line 223

Installation of the publication module

Code

function tripal_pub_update_7200() {


  // add the tripal_pub CV and set it to be the default for pub types and pub properties
  try {
    $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'tripal_pub'")->fetchField();
    if (!$cv_id) {
      // add the vocabulary
      $cv_id = db_insert('chado.cv')
        ->fields(array(
          'name' => 'tripal_pub',
          'definition' => 'A heirarchical set of terms for describing a publication. It is intended to be used as the default vocabularies in Tripal for publication types and contact properties.'
        ))
        ->execute();
    }
    // use the new pub_property CV we just added
    db_insert('tripal_cv_defaults')
      ->fields(array(
        'table_name' => 'pub',
        'field_name' => 'type_id',
        'cv_id' => $cv_id
      ))
      ->execute();
    // use the new pub_property CV we just added
    db_insert('tripal_cv_defaults')
      ->fields(array(
        'table_name' => 'pubprop',
        'field_name' => 'type_id',
        'cv_id' => $cv_id
      ))
      ->execute();
  }
  catch (\PDOException $e) {
    $error = $e->getMessage();
    throw new DrupalUpdateException('Failed to add pub_property vocabulary: ' . $error);
  }

  // add the pub_property CV
  try {
    $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'pub_property'")->fetchField();
    if (!$cv_id) {
      // add the vocabulary
      $cv_id = db_insert('chado.cv')
        ->fields(array(
          'name' => 'pub_property',
          'definition' => 'Contains properties for publications. This can be used if the tripal_pub vocabulary (which is default for publications in Tripal) is not desired.'
        ))
        ->execute();
    }
  }
  catch (\PDOException $e) {
    $error = $e->getMessage();
    throw new DrupalUpdateException('Failed to add pub_property vocabulary: ' . $error);
  }

  // add the pub_type CV
  try {
    $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'pub_type'")->fetchField();
    if (!$cv_id) {
      // add the vocabulary
      $cv_id = db_insert('chado.cv')
        ->fields(array(
          'name' => 'pub_type',
          'definition' => 'Contains types of publications. This can be used if the tripal_pub vocabulary (which is default for publications in Tripal) is not desired.'
        ))
        ->execute();
    }
  }
  catch (\PDOException $e) {
    $error = $e->getMessage();
    throw new DrupalUpdateException('Failed to add pub_type vocabulary: ' . $error);
  }

  // add the pub_relationship CV
  try {
    $cv_id = db_query("SELECT cv_id FROM chado.cv WHERE name = 'pub_relationship'")->fetchField();
    if (!$cv_id) {
      // add the vocabulary
      $cv_id = db_insert('chado.cv')
        ->fields(array(
          'name' => 'pub_relationship',
          'definition' => 'Contains types of relationships between publications.'
        ))
        ->execute();
    }
    // use the new pub_property CV we just added
    db_insert('tripal_cv_defaults')
      ->fields(array(
        'table_name' => 'pub_relationship',
        'field_name' => 'type_id',
        'cv_id' => $cv_id
      ))
      ->execute();
  }
  catch (\PDOException $e) {
    $error = $e->getMessage();
    throw new DrupalUpdateException('Failed to add pub_relationship vocabulary: ' . $error);
  }
}