Implements hook_update().

Related topics

File

tripal_organism/includes/tripal_organism.chado_node.inc, line 469

Implements the organims node content type

Code

function chado_organism_update($node) {

  $chado_version = chado_get_version(TRUE);

  // remove any white space around values
  $node->genus = trim($node->genus);
  $node->species = trim($node->species);
  $node->abbreviation = trim($node->abbreviation);
  $node->common_name = trim($node->common_name);
  $node->description = trim($node->description['value']);
  if ($chado_version > 1.2) {
    $node->type_id = trim($node->type_id);
    $node->infraspecific_name = trim($node->infraspecific_name);
  }

  $organism_id = chado_get_id_from_nid('organism', $node->nid);

  if ($node->revision) {
    // there is no way to handle revisions in Chado but leave
    // this here just to make not we've addressed it.
  }
  $match = array(
    'organism_id' => $organism_id,
  );
  $values = array(
    'genus' => $node->genus,
    'species' => $node->species,
    'abbreviation' => $node->abbreviation,
    'common_name' => $node->common_name,
    'comment' => $node->description
  );
  if ($chado_version > 1.2) {
    if ($node->type_id) {
      $values['type_id'] = $node->type_id;
    }
    else {
      $values['type_id'] = '__NULL__';
    }
    if ($node->infraspecific_name) {
      $values['infraspecific_name'] = $node->infraspecific_name;
    }
    else {
      $values['infraspecific_name'] = '__NULL__';
    }
  }

  $org_status = chado_update_record('organism', $match, $values);
  if ($node->organism_image != '') {
    chado_organism_add_image($node);
  }

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

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