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File

tripal_feature/tripal_feature.module, line 688

@todo Add file header description

Code

function chado_feature_add_gbaccession($accession, $feature_id) {

  // use chado database

  // remove any old accession from genbank dbEST
  $fdbxref_dsql = "DELETE FROM {feature_dbxref} " .
    "WHERE feature_id = %d and dbxref_id IN " .
    "   (SELECT DBX.dbxref_id FROM {dbxref} DBX " .
    "    INNER JOIN DB  ON DB.db_id = DBX.db_id " .
    "    INNER JOIN feature_dbxref FDBX ON DBX.dbxref_id = FDBX.dbxref_id " .
    "    WHERE DB.name = 'DB:Genbank' and FDBX.feature_id = %d)";
  if (!chado_query($fdbxref_dsql, $feature_id, $feature_id)) {
    $error .= "Could not remove accession from feature. ";
  }

  // if we don't have an accession number to add then just return
  if (!$accession) {
    return;
  }
  // get the db_id
  $db_sql = "SELECT db_id FROM {DB} " .
    "WHERE name = 'DB:Genbank_est'";
  $db = db_fetch_object(chado_query($db_sql));

  // check to see if we have this accession number already in the database
  // if so then don't add it again. it messes up drupal if the insert fails.
  // It is possible for the accession number to be present and not the feature
  $dbxref_sql = "SELECT dbxref_id FROM {dbxref} " .
    "WHERE db_id = %d and accession = '%s'";
  $dbxref = db_fetch_object(chado_query($dbxref_sql, $db->db_id, $accession));
  if (!$dbxref) {
    // add the accession number
    $dbxref_isql = "INSERT INTO {dbxref} (db_id,accession) " .
      "  VALUES (%d, '%s') ";
    if (!chado_query($dbxref_isql, $db->db_id, $accession)) {
      $error .= 'Could not add accession as a database reference ';
    }
    // get the dbxref_id for the just added accession number
    $dbxref_sql = "SELECT dbxref_id FROM {dbxref} " .
      "WHERE db_id = %d and accession = '%s'";
    $dbxref = db_fetch_object(chado_query($dbxref_sql, $db->db_id, $accession));
  }


  // associate the accession number with the feature
  $feature_dbxref_isql = "INSERT INTO {feature_dbxref} (feature_id,dbxref_id) " .
    "  VALUES (%d, %d) ";
  if (!chado_query($feature_dbxref_isql, $feature_id, $dbxref->dbxref_id)) {
    $error .= 'Could not add feature database reference. ';
  }

  return $error;
}