Parameters

$name: The name identfier to be used

$organism_id: The stock.organism_id of the stock to be selected

Return value

An array of stock node objects

See also

tripal_get_stock().

File

legacy/tripal_stock/api/tripal_stock.DEPRECATED.inc, line 146

Wrapper functions to provide backwards compatibility for the tripal stock api

Code

function tripal_stock_get_stock_by_name_identifier($name, $organism_id) {

  tripal_report_error(
  'tripal_deprecated', 
  TRIPAL_NOTICE, 
  "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.", 
  array(
    '%old_function' => 'tripal_stock_get_stock_by_name_identifier',
    '%new_function' => 'tripal_get_stock'
  )
  );

  $stock_ids = array();

  $options = array(
    'case_insensitive_columns' => array('name', 'uniquename', 'accession', 'value')
  );

  // where name_identifier = stock.name-------------------------------
  $current_stocks = chado_select_record('stock', array('stock_id'), 
  array(
    'name' => $name,
    'organism_id' => $organism_id,
  ), 
  array(
    'case_insensitive_columns' => array('name'),
  )
  );
  if (!empty($current_stocks)) {
    foreach ($current_stocks as $c) {
      $stock_ids[] = $c->stock_id;
    }
  }

  // where name_identifier = stock.uniquename-------------------------------
  $current_stocks = chado_select_record('stock', array('stock_id'), 
  array(
    'uniquename' => $name,
    'organism_id' => $organism_id,
  ), 
  array(
    'case_insensitive_columns' => array('uniquename'),
  )
  );
  if (!empty($current_stocks)) {
    foreach ($current_stocks as $c) {
      $stock_ids[] = $c->stock_id;
    }
  }

  // where name_identifier = dbxref.accession-------------------------------
  // linked to stock through stock.dbxref
  $current_stocks = chado_select_record('stock', array('stock_id'), 
  array(
    'dbxref_id' => array(
      'accession' => $name,
    ),
    'organism_id' => $organism_id,
  ), 
  array(
    'case_insensitive_columns' => array('accession'),
  )
  );
  if (!empty($current_stocks)) {
    foreach ($current_stocks as $c) {
      $stock_ids[] = $c->stock_id;
    }
  }

  // linked to stock through stock_dbxref?
  $current_stocks = chado_select_record('stock_dbxref', array('stock_id'), 
  array(
    'dbxref_id' => array(
      'accession' => $name,
    ),
    'stock_id' => array(
      'organism_id' => $organism_id,
    ),
  ), 
  array(
    'case_insensitive_columns' => array('accession'),
  )
  );
  if (!empty($current_stocks)) {
    foreach ($current_stocks as $c) {
      $stock_ids[] = $c->stock_id;
    }
  }

  // where name_identifier = stockprop.value-------------------------------
  // where type='synonym'
  $current_stocks = chado_select_record('stockprop', array('stock_id'), 
  array(
    'stock_id' => array(
      'organism_id' => $organism_id,
    ),
    'type_id' => array(
      'cv_id' => variable_get('chado_stock_prop_types_cv', 'null'),
      'name' => 'synonym',
    ),
    'value' => $name,
  ), 
  array(
    'case_insensitive_columns' => array('value'),
  )
  );
  if (!empty($current_stocks)) {
    foreach ($current_stocks as $c) {
      $stock_ids[] = $c->stock_id;
    }
  }

  // Change from stock_ids to nodes-----------------------------------
  $stock_ids = array_filter($stock_ids);
  $stock_ids = array_unique($stock_ids);

  $stocks = array();
  foreach ($stock_ids as $stock_id) {
    $node = tripal_stock_get_stock_by_stock_id($stock_id);
    if ($node) {
      $stocks[] = $node;
    }
  }

  return $stocks;
}