nid)) { return node_load($r->nid); } else { drupal_set_message("Function: triapl_stock_get_stock_by_stock_id() -no stock with that stock id sync'd with drupal", 'error'); } return 0; } /************************************************************************* * @section: Return Multiple Stocks *************************************************************************/ /************************************************************************* * Purpose: Returns all stocks currently sync'd with drupal * * @return array( * => * ) */ //function get_all_chado_stocks() { 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)) { $stocks[$r->stock_id] = node_load($r->nid); } return $stocks; } /************************************************************************* * Purpose: Return all stocks that match a given criteria * * @params Criteria = array( * => array( * 'value'=> , * 'regex' => , * 'type' => * ) * ) * column name can be any of those for the stock table * additional column names include: accession, synonym * if you don't know which column the value is from and want to match * the value against any of name, uniquename, dbxref accessions, and synonyms * use 'unknown' => array( * 'value' => , * 'columns' => array of columns to search * ) * where columns can be any combination of 'name', 'uniquename', 'stock','accession', or 'synonym' * @params match_type: can be either ALL or ANY * where ALL= mathcing stocks must match all criteria supplied * ANY= matching stock need only match ONE of the supplied criteria * @return an array of matching stock objects (produced using node_load) * matching the given criteria */ //function get_chado_stocks($criteria, $match_type, $organism_id = NULL, $error_checking = FALSE) { function tripal_stock_get_stocks($criteria, $match_type, $organism_id = NULL, $error_checking = FALSE) { //Deal with unknown column---------------------------- if (!empty($criteria['unknown'])) { if ($error_checking) { drupal_set_message('Uknown provided','warning');} $unknown_provided = TRUE; $new_criteria = array(); foreach ($criteria['unknown']['columns'] as $column_name) { if (in_array($column_name, array('stock_id','dbxref_id','organism_id','type_id') )) { if (preg_match('/^\d+$/',$criteria['unknown']['value'])) { $new_criteria[$column_name] = array('type'=>'INT','value' => $criteria['unknown']['value']); } } else { $new_criteria[$column_name] = array('type'=>'STRING','value' => $criteria['unknown']['value'], 'regex'=>TRUE); } } if ($error_checking) { drupal_set_message('Re-calling tripal_stock_get_stocks(

'.print_r($new_criteria,TRUE).'

, ANY, '.$organism_id.')','warning'); } $unknown_stocks = tripal_stock_get_stocks($new_criteria, 'ANY', $organism_id, $error_checking); if ($error_checking) { drupal_set_message(sizeof($unknown_stocks).' Unknown Stocks', 'warning'); } } unset($criteria['unknown']); //so it's not mistaken as a column in the stock table // Determine all criteria------------------------------ $where = array(); // parts of the where portion of the SQL query $joins = array(); //joins between the stock table and other tables foreach ($criteria as $column_name => $v) { if (preg_match("/accession/i",$column_name)) { if ($v['regex']) { $operator = '~'; } else { $operator = '='; } $where[] = 'dbxref.accession'.$operator."'".$v['value']."'"; $joins[] = 'LEFT JOIN stock_dbxref stock_dbxref ON stock_dbxref.stock_id=stock.stock_id'; $joins[] = 'LEFT JOIN dbxref dbxref ON dbxref.dbxref_id=stock_dbxref.dbxref_id'; } elseif (preg_match("/synonym/i",$column_name)) { if ($v['regex']) { $operator = '~'; } else { $operator = '='; } $synonym_cvterm = tripal_cv_get_cvterm_by_name('synonym', variable_get('chado_stock_prop_types_cv', 'null')); $where[] = '(stockprop.type_id='.$synonym_cvterm->cvterm_id.' AND stockprop.value'.$operator."'".$v['value']."')"; $joins[] = 'LEFT JOIN stockprop stockprop ON stockprop.stock_id=stock.stock_id'; } else { if ($v['regex']) { $operator = '~'; } else { $operator = '='; } if (preg_match('/INT/', $v['type'])) { $where[] = 'stock.'.$column_name.'='.$v['value']; } else { $where[] = 'stock.'.$column_name.$operator."'".$v['value']."'"; } } } if ($error_checking) { drupal_set_message('Where Conditions:

'.print_r($where,TRUE).'

', 'warning'); drupal_set_message('Left Joins:

'.print_r($joins,TRUE).'

', 'warning'); } //Build query----------------------------------------- if (preg_match('/ANY/', $match_type)) { $where_string = implode(' OR ',$where); if ($organism_id) { $where_string = '('.$where_string.') AND organism_id='.$organism_id; } } else { $where_string = implode(' AND ',$where); if ($organism_id) { $where_string .= ' AND organism_id='.$organism_id; } } if (sizeof($where) >= 1) { $execute_query = TRUE; $sql_query = 'SELECT stock.stock_id FROM stock '.implode(' ',$joins).' WHERE '.$where_string; //drupal_set_message('Query='.$sql_query); } elseif (!$unknown_provided) { $execute_query = TRUE; $sql_query = 'SELECT stock.stock_id FROM stock'; drupal_set_message('You did not enter any criteria during the stock selection process. All stocks will be returned.','warning'); } else { $execute_query = FALSE; } if ($error_checking) { drupal_set_message('Query: '.$sql_query, 'warning'); } if ($execute_query) { //Get stock_ids--------------------------------------- $previous_db = tripal_db_set_active('chado'); $resource = db_query($sql_query); tripal_db_set_active($previous_db); $stock_ids = array(); while ($r = db_fetch_object($resource)) { $stock_ids[] = $r->stock_id; } $stock_ids = array_unique($stock_ids); if ($error_checking) { drupal_set_message('Stock IDs:

'.print_r($stock_ids,TRUE).'

', 'warning'); } //Get Stocks------------------------------------------ if (!empty($stock_ids)) { $resource = db_query("SELECT nid FROM {chado_stock} WHERE stock_id IN (%s)",implode(',',$stock_ids)); $main_stocks = array(); while ($r = db_fetch_object($resource)) { $main_stocks[] = node_load($r->nid); } } } if (!empty($main_stocks)) { if(!empty($unknown_stocks)){ return array_merge($unknown_stocks,$main_stocks); } else { return $main_stocks; } } else { if(!empty($unknown_stocks)){ return $unknown_stocks; } else { //drupal_set_message('No Stocks matched the given criteria','warning'); return array(); } } }