function chado_feature_update

2.x tripal_feature.chado_node.inc chado_feature_update($node)
3.x tripal_feature.chado_node.inc chado_feature_update($node)
1.x tripal_feature.module chado_feature_update($node)

Implements hook_update().

Related topics

File

tripal_feature/includes/tripal_feature.chado_node.inc, line 511
Implementation of hooks to create a feature content type

Code

function chado_feature_update($node) {

  $node->uniquename = trim($node->uniquename);
  $node->fname = trim($node->fname);
  $node->feature_type = trim($node->feature_type);
  $node->residues = trim($node->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);

  $feature_id = chado_get_id_from_nid('feature', $node->nid);

  if (sizeof($type) > 0) {
    $match = array(
      'feature_id' => $feature_id,
    );
    $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('return_record' => TRUE);
    $status = chado_update_record('feature', $match, $values, $options);

    // add the genbank 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 {
    drupal_set_message(t('Unable to update feature.'), 'warning');
    tripal_report_error('tripal_feature', TRIPAL_WARNING, 
    'Update feature: Unable to update feature where values: %values', 
    array('%values' => print_r($values, TRUE))
    );
  }


}