Related topics

File

tripal_feature/includes/tripal_feature.admin.inc, line 633

@todo Add file header description

Code

function tripal_feature_set_vocabulary() {

  //include the file containing the required functions for adding taxonomy vocabs
  module_load_include('inc', 'taxonomy', 'taxonomy.admin');

  // get the vocabularies so that we make sure we don't recreate
  // the vocabs that already exist
  $vocabularies = taxonomy_get_vocabularies();
  $ft_vid = NULL;
  $op_vid = NULL;
  $lb_vid = NULL;
  $an_vid = NULL;

  // These taxonomic terms are hard coded because we
  // konw we have these relationships in the chado tables
  // through foreign key relationships.  The tripal
  // modules that correspond to these chado "modules" don't
  // need to be installed for the taxonomy to work.
  foreach ($vocabularies as $vocab) {
    if ($vocab->name == 'Feature Type') {
      $ft_vid = $vocab->vid;
    }
    if ($vocab->name == 'Organism') {
      $op_vid = $vocab->vid;
    }
    if ($vocab->name == 'Library') {
      $lb_vid = $vocab->vid;
    }
    if ($vocab->name == 'Analysis') {
      $an_vid = $vocab->vid;
    }
  }

  if (!$ft_vid) {
    $form_state = array();
    $values = array(
      'name' => t('Feature Type'),
      'nodes' => array('chado_feature' => 'chado_feature'),
      'description' => t('The feature type (or SO cvterm for this feature).'),
      'help' => t('Select the term that matches the feature'),
      'tags' => 0,
      'hierarchy' => 1,
      'relations' => 1,
      'multiple' => 0,
      'required' => 0,
      'weight' => 1,
    );
    drupal_execute('taxonomy_form_vocabulary', $form_state, $values);
    drupal_execute('taxonomy_form_vocabulary', $form_state);
  }

  if (!$op_vid) {
    $form_state = array();
    $values = array(
      'name' => t('Organism'),
      'nodes' => array('chado_feature' => 'chado_feature'),
      'description' => t('The organism to which this feature belongs.'),
      'help' => t('Select the term that matches the feature'),
      'tags' => 0,
      'hierarchy' => 1,
      'relations' => 1,
      'multiple' => 0,
      'required' => 0,
      'weight' => 2,
    );
    drupal_execute('taxonomy_form_vocabulary', $form_state, $values);
    drupal_execute('taxonomy_form_vocabulary', $form_state);
  }

  if (!$lb_vid) {
    $form_state = array();
    $values = array(
      'name' => t('Library'),
      'nodes' => array('chado_feature' => 'chado_feature'),
      'description' => t('Chado features associated with a library are assigned the term associated with the library'),
      'help' => t('Select the term that matches the feature'),
      'tags' => 0,
      'hierarchy' => 1,
      'relations' => 1,
      'multiple' => 0,
      'required' => 0,
      'weight' => 3,
    );
    drupal_execute('taxonomy_form_vocabulary', $form_state, $values);
    drupal_execute('taxonomy_form_vocabulary', $form_state);
  }

  if (!$an_vid) {
    $form_state = array();
    $values = array(
      'name' => t('Analysis'),
      'nodes' => array('chado_feature' => 'chado_feature'),
      'description' => t('Any analysis to which this feature belongs.'),
      'help' => t('Select the term that matches the feature'),
      'tags' => 0,
      'hierarchy' => 1,
      'relations' => 1,
      'multiple' => 1,
      'required' => 0,
      'weight' => 4,
    );
    drupal_execute('taxonomy_form_vocabulary', $form_state, $values);
    drupal_execute('taxonomy_form_vocabulary', $form_state);
  }
}