function chado_insert_dbxref

3.x tripal_chado.db.api.inc chado_insert_dbxref($values)

Add a database reference.

Parameters

$values: An associative array of the values to be inserted including:

  • db_id: the database_id of the database the reference is from.
  • accession: the accession.
  • version: (Optional) The version of the database reference.
  • description: (Optional) A description of the database reference.

Return value

The newly inserted dbxref as an object, similar to that returned by the chado_select_record() function.

Related topics

Chado DB
External databases can be used to indicate the source for a variety of data. The most common use is with controlled vocabularies (CV). Chado expects that every CV have an external database record, where the database name must be the short name of the…
6 calls to chado_insert_dbxref()
chado_associate_dbxref in tripal_chado/api/modules/tripal_chado.db.api.inc
Add a record to a database reference linking table (ie: feature_dbxref).
chado_insert_cvterm in tripal_chado/api/modules/tripal_chado.cv.api.inc
Add's a controlled vocabulary term to Chado.
data__accession_widget::submit in tripal_chado/includes/TripalFields/data__accession/data__accession_widget.inc
TaxonomyImporter::addDbxref in tripal_chado/includes/TripalImporter/TaxonomyImporter.inc
tripal_insert_dbxref in tripal_chado/api/modules/tripal_chado.module.DEPRECATED.api.inc
Add a database reference.

... See full list

File

tripal_chado/api/modules/tripal_chado.db.api.inc, line 418
Provides API functions specificially for managing external database reference records in Chado.

Code

function chado_insert_dbxref($values) {

  $db_id = $values['db_id'];
  $accession = $values['accession'];
  $version = (isset($values['version'])) ? $values['version'] : '';
  $description = (isset($values['description'])) ? $values['description'] : '';

  $ins_values = array(
    'db_id' => $db_id,
    'accession' => $accession,
    'version' => $version,
    'description' => $description
  );

  // Check to see if the dbxref exists.
  $sel_values = array(
    'db_id' => $db_id,
    'accession' => $accession,
    'version' => $version
  );
  $result = chado_select_record('dbxref', array('*'), $sel_values);

  // If it doesn't already exist then add it.
  if (!$result) {
    $success = chado_insert_record('dbxref', $ins_values);
    if (!$success) {
      tripal_report_error('tripal_chado', TRIPAL_WARNING, "Failed to insert the dbxref record $accession", NULL);
      return 0;
    }
    $result = chado_select_record('dbxref', array('*'), $sel_values);
  }

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