Add a record to a cvterm linking table (ie: feature_cvterm).

Parameters

$basetable: The base table to which the cvterm should be linked/associated. Thus to associate a cvterm to a feature the basetable=feature and cvterm_id is added to the feature_cvterm table.

$record_id: The primary key of the basetable to associate the cvterm with. This should be in integer.

$cvterm: An associative array describing the cvterm. Valid keys include:

• name: the name for the cvterm,
• cv_name: the name of the cv the cvterm belongs to.
• cv_id: the primary key of the cv the cvterm belongs to.

$options: An associative array of options. Valid keys include:

• insert_cvterm: Insert the cvterm if it doesn't already exist. FALSE is the default.

Related topics

File

tripal_chado/api/modules/tripal_chado.cv.api.inc, line 1532

Provides API functions specificially for managing controlled vocabulary records in Chado.

Code

function chado_associate_cvterm($basetable, $record_id, $cvterm, $options = array()) {
  $linking_table = $basetable . '_cvterm';
  $foreignkey_name = $basetable . '_id';

  // Default Values
  $options['insert_cvterm'] = (isset($options['insert_cvterm'])) ? $options['insert_cvterm'] : FALSE;

  // If the cvterm_id is not set then find the cvterm record using the name and 
  // cv_id.
  if (!isset($cvterm['cvterm_id'])) {
    $values = array(
      'name' => $cvterm['name'],
    );
    if (isset($cvterm['cv_id'])) {
      $values['cv_id'] = $cvterm['cv_id'];
    }
    elseif (isset($cvterm['cv_name'])) {
      $values['cv_id'] = array(
        'name' => $cvterm['cv_name']
      );
    }
    else {
      tripal_report_error('tripal_chado_api', TRIPAL_WARNING, 
      "chado_associate_cvterm: The cvterm needs to have either the cv_name or cv_id
          supplied. You were trying to associate a cvterm with the %base %record_id
          and supplied the cvterm values: %cvterm.", 
      array('%base' => $basetable, '%record_id' => $record_id, '%cvterm' => print_r($cvterm, TRUE))
      );
      return FALSE;
    }

    // Get the cvterm. If it doesn't exist then add it if the option
    // 'insert_cvterm' is set.
    $select = chado_select_record('cvterm', array('*'), $values);
    if ($select) {
      $cvterm['cvterm_id'] = $select[0]->cvterm_id;
    }
    elseif ($options['insert_cvterm']) {
      // Insert the cvterm
      $insert = chado_insert_cvterm($values);
      if (isset($insert->cvterm_id)) {
        $cvterm['cvterm_id'] = $insert->cvterm_id;
      }
      else {
        tripal_report_error('tripal_chado_api', TRIPAL_WARNING, 
        "chado_associate_cvterm: Unable to insert the cvterm using the cvterm values: %cvterm.", 
        array('%cvterm' => print_r($cvterm, TRUE))
        );
        return FALSE;
      }
    }
    else {
      tripal_report_error('tripal_api', TRIPAL_WARNING, 
      "chado_associate_cvterm: The cvterm doesn't already exist. You supplied the cvterm values: %cvterm.", 
      array('%cvterm' => print_r($cvterm, TRUE))
      );
      return FALSE;
    }
  }

  // Now add the link between the record & cvterm.
  if ($cvterm['cvterm_id'] > 0) {
    $values = array(
      'cvterm_id' => $cvterm['cvterm_id'],
      $foreignkey_name => $record_id,
      'pub_id' => 1,
    );

    // Check if the cvterm is already associated. If so, don't re-add it.
    $result = chado_select_record($linking_table, array('*'), $values);
    if (!$result) {
      $success = chado_insert_record($linking_table, $values);
      if (!$success) {
        tripal_report_error('tripal_api', TRIPAL_WARNING, 
        "Failed to insert the %base record %term", 
        array('%base' => $linking_table, '%term' => $cvterm['name'])
        );
        return FALSE;
      }
      $result = chado_select_record($linking_table, array('*'), $values);
    }

    if (isset($result[0])) {
      return $result[0];
    }
    else {
      return FALSE;
    }
  }

  return FALSE;
}