Implements hook_insert().

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/includes/tripal_feature.chado_node.inc, line 414

Implementation of hooks to create a feature content type

Code

function chado_feature_insert($node) {

  $feature_id = '';

  // if there is a feature_id in the $node object then this must be a sync so
  // we can skip adding the feature as it is already there, although
  // we do need to proceed with insertion into the chado/drupal linking table.
  if (!property_exists($node, 'feature_id')) {
    $node->uniquename = trim($node->uniquename);
    $node->fname = trim($node->fname);
    $node->feature_type = trim($node->feature_type);
    $node->residues = trim($node->residues);

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

    // get the feature type id
    $values = array(
      'cv_id' => array(
        'name' => 'sequence'
      ),
      'name' => $node->feature_type
    );
    $type = chado_select_record('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)
    );
    $feature = chado_insert_record('feature', $values);
    if (!$feature) {
      drupal_set_message(t('Unable to add feature.'), 'warning');
      tripal_report_error('tripal_feature', TRIPAL_WARNING, 'Insert feature: Unable to create feature where values: %values', 
      array('%values' => print_r($values, TRUE)));
      return;
    }
    $feature_id = $feature['feature_id'];

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

    // * Properties Form *
    $details = array(
      'property_table' => 'featureprop', // the name of the prop table
      'base_table' => 'feature', // the name of your chado base table
      'foreignkey_name' => 'feature_id', // the name of the key in your base table
      'foreignkey_value' => $feature_id // the value of the feature_id key
    );
    chado_update_node_form_properties($node, $details);

    // * Additional DBxrefs Form *
    $details = array(
      'linking_table' => 'feature_dbxref', // the name of your _dbxref table
      'foreignkey_name' => 'feature_id', // the name of the key in your base table
      'foreignkey_value' => $feature_id // the value of the feature_id key
    );
    chado_update_node_form_dbxrefs($node, $details);

    // * Relationships Form *
    $details = array(
      'relationship_table' => 'feature_relationship',
      'foreignkey_value' => $feature_id
    );
    chado_update_node_form_relationships($node, $details);

  }
  else {
    $feature_id = $node->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.
  $check_org_id = chado_get_id_from_nid('feature', $node->nid);
  if (!$check_org_id) {
    $record = new stdClass();
    $record->nid = $node->nid;
    $record->vid = $node->vid;
    $record->feature_id = $feature_id;
    drupal_write_record('chado_feature', $record);
  }
}