tripal_stock.api.inc

Go to the documentation of this file.

<?php
function tripal_stock_get_stock_by_nid($nid) {

  return node_load($nid);

}

function tripal_stock_get_stock_by_stock_id($stock_id) {

  $sql = "SELECT nid FROM {chado_stock} WHERE stock_id=%d";
  $r = db_fetch_object(db_query($sql, $stock_id));
  if (!empty($r->nid)) {
    return node_load($r->nid);
  }
  else {
    watchdog('tripal_stock', 'tripal_stock_get_stock_by_stock_id(!stock_id): no stock with that stock_id is sync\'d with drupal', array('!stock_id' => $stock_id), WATCHDOG_WARNING);
  }

  return 0;

}

function tripal_stock_get_all_stocks() {
  $sql = "SELECT stock_id, nid from {chado_stock}";
  $resource = db_query($sql);
  $stocks = array();
  while ($r = db_fetch_object($resource)) {
    $node = node_load($r->nid);
    if ($node) {
      $stocks[$r->stock_id] = $node;
    }
  }
  return $stocks;
}

function tripal_stock_get_stocks($values) {

  $stock_ids = tripal_core_chado_select('stock', array('stock_id'), $values);

  // 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->stock_id);
    if ($node) {
      $stocks[] = $node;
    }
  }

  return $stocks;
}

function tripal_stock_get_stocks_by_stockprop($stockprop_values, $stock_values) {

  //add stock values to stockprop values
  if (!empty($stock_values)) {
    $stockprop_values['stock_id'] = $stock_values;
  }

  //get stock_ids from stockprop table
  $stock_ids = tripal_core_chado_select('stockprop', array('stock_id'), $stockprop_values);

  // 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->stock_id);
    if ($node) {
      $stocks[] = $node;
    }
  }

  return $stocks;
}

function tripal_stock_get_stock_by_name_identifier($name, $organism_id) {
  $stock_ids = array();

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

  // where name_identifier = stock.name-------------------------------
  $current_stocks = tripal_core_chado_select('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 = tripal_core_chado_select('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 = tripal_core_chado_select('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 = tripal_core_chado_select('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 = tripal_core_chado_select('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;
}