When a new chado_feature node is created we also need to add information to our chado_feature table. This function is called on insert of a new node of type 'chado_feature' and inserts the necessary information.

Related topics

File

tripal_feature/tripal_feature.module, line 458

@todo Add file header description

Code

function chado_feature_insert($node) {
  // remove spaces, newlines from residues
  $residues = preg_replace("/[\n\r\s]/", "", $node->residues);
  $obsolete = 'FALSE';
  if ($node->is_obsolete) {
    $obsolete = 'TRUE';
  }

  // check to see if we are inserting a duplicate record.
  $values = array(
    'cv_id' => array(
      'name' => 'sequence'
    ),
    'name' => $node->feature_type
  );
  $type = tripal_core_chado_select('cvterm', array('cvterm_id'), $values);
  $values = array(
    'organism_id' => $node->organism_id,
    'name' => $node->fname,
    'uniquename' => $node->uniquename,
    'residues' => $residues,
    'seqlen' => drupal_strlen($residues),
    'is_obsolete' => $obsolete,
    'type_id' => $type[0]->cvterm_id,
    'md5checksum' => md5($residues)
  );
  $options = array('is_duplicate' => TRUE, 'has_record' => TRUE);
  $exists = tripal_core_chado_select('feature', array('*'), $values, $options);

  // if the record is not a duplicate then add it
  if (!$exists) {
    $istatus = tripal_core_chado_insert('feature', $values);
    if (!$istatus) {
      drupal_set_message(t('Unable to add feature.'), 'warning');
      watchdog('tripal_feature', 'Insert feature: Unable to create feature where values: %values', 
      array('%values' => print_r($values, TRUE)), WATCHDOG_WARNING);
    }
  }

  // now get the newly added record
  $values = array(
    'organism_id' => $node->organism_id,
    'uniquename' => $node->uniquename,
    'type_id' => $type[0]->cvterm_id,
  );
  $feature = tripal_core_chado_select('feature', array('feature_id'), $values);

  // add the genbank accession and synonyms
  chado_feature_add_synonyms($node->synonyms, $feature[0]->feature_id);

  // make sure the entry for this feature doesn't already exist in the chado_feature table
  // if it doesn't exist then we want to add it.
  $node_check_sql = "SELECT * FROM {chado_feature} " .
    "WHERE feature_id = '%s'";
  $node_check = db_fetch_object(db_query($node_check_sql, $feature[0]->feature_id));
  if (!$node_check) {
    // next add the item to the drupal table
    $sql = "INSERT INTO {chado_feature} (nid, vid, feature_id, sync_date) " .
      "VALUES (%d, %d, %d, " . time() . ")";
    db_query($sql, $node->nid, $node->vid, $feature[0]->feature_id);
  }
}