/**
* Function is called to load the requested page, check permissions and set up global Smarty variables.
*
* @param string $request p_page_name to find in database
* @return RoutingEngine
*/
public function initialize($request)
{
$request = strtolower($request);
if (substr($request, 0, 1) == "/") {
$request = substr($request, 1);
}
if (substr($request, -1, 1) == "/") {
$request = substr($request, 0, -1);
}
$this->_request_path = $request;
$paths = explode("/", $this->_request_path);
if (in_array($paths[0], self::$controllers)) {
$this->controller = $paths[0];
$action = array_safe($paths, 1);
$params = array_slice($paths, 2);
} else {
$this->controller = "home";
$action = $paths[0];
$params = array_slice($paths, 1);
}
$this->controller_full = "Controller_" . $this->controller;
if (!empty($action) && $this->_checkAction($action)) {
$this->action = $action;
$this->_request_path = $this->controller . "/{$this->action}";
} else {
$this->action = "index";
$this->_request_path = $this->controller . "/index";
}
//$this->page = Page::getPage($this->_request_path);
$this->page = new Page();
$this->page->page_name = $this->_request_path;
$this->_processParamters($params);
$this->start_time = $_SERVER["TIME_START"];
return $this;
}
function smarty_function_modules($params, &$smarty)
{
$mod_con = new Controller_Module($params, RoutingEngine::getSmarty());
$mod_names = array_safe($params, "list");
$mod_list = explode(",", $mod_names);
$modules = array();
$unplaced_modules = array();
$counts = array("3" => 0, "4" => 0, "5" => 0);
foreach ($mod_list as $mod_code) {
$mod_name = Module::$hash[$mod_code];
if (!method_exists($mod_con, $mod_name)) {
continue;
}
$module = $mod_con->{$mod_name}();
if ($module->size) {
$modules[$module->size][] = $module;
$counts[$module->size]++;
} else {
$unplaced_modules[] = $module;
}
}
foreach ($unplaced_modules as $module) {
asort($counts);
current($counts);
$modules[key($counts)][] = $module;
$counts[key($counts)]++;
}
RoutingEngine::getSmarty()->assign("modules", $modules);
return RoutingEngine::getSmarty()->fetch("modules/module_master.tpl");
}
function handleNewBlock($tag)
{
//TODO: Consider moving modifiers to their own system.
$command = $tag->command;
//looks for the | (pipe) in order to determine modifier.
$mod_regex = "/^(.*)[|](.*?)(?::(.*))?\$/";
$count = preg_match($mod_regex, $tag->command, $matches);
if ($count) {
$var = array_safe($matches, 1);
$mod = array_safe($matches, 2);
$param = array_safe($matches, 3);
if (substr($mod, 0, 1) == "@") {
$mod = substr($mod, 1);
$command = $mod . "(" . $var . ")";
$allowed = false;
} else {
$allowed = $this->_compiler->addFunctionToSource($mod, "modifier");
if ($allowed) {
if ($param) {
$command = "template_modifier_" . $mod . "({$var}, {$param})";
} else {
$command = "template_modifier_" . $mod . "({$var})";
}
} else {
$command = $var;
}
}
}
return "<?php echo {$command}; ?>";
}
/**
* Function to get the directory of a template.
*
* @param string $template_name Template name.
* @return string Resolved directory name.
*/
public function getTemplateDir($template_name)
{
//removes the ending backslash
$regex = "/(.*(?:\\/|\\\\)).*\\..*\$/";
$matches = array();
preg_match($regex, $template_name, $matches);
$dir = array_safe($matches, 1, "");
return $this->_template->compile_dir . "/" . $dir;
}
public function update()
{
RoutingEngine::setPage("runnDAILY User Update", "PV__300");
$format = array_safe($_POST, "format", "html");
$user = new User($_POST);
if ($user->updateUserInDB()) {
if ($format == "ajax") {
exit("success");
}
}
Page::redirect("/admin/user");
}
public function action_elevation_add_packed()
{
if ($_FILES["packed_hdr"]) {
move_uploaded_file($_FILES["packed_hdr"]["tmp_name"], SYSTEM_ROOT . "/elev_packed.hdr");
}
if ($_FILES["packed_flt"]) {
move_uploaded_file($_FILES["packed_flt"]["tmp_name"], SYSTEM_ROOT . "/elev_packed.flt");
}
$region = array_safe($_POST, "region_name", "Elevation data");
Elevation::addElevationToDatabase(SYSTEM_ROOT . "/elev_packed", 1, $region);
unlink(SYSTEM_ROOT . "/elev_packed.hdr");
unlink(SYSTEM_ROOT . "/elev_packed.flt");
Notification::add("Elevation data has been added");
Page::redirect("/admin/elevation");
}
public function action_save()
{
RoutingEngine::setPage("runnDAILY Training Save", "PV__300");
$t_item = new TrainingLog($_POST);
if (array_safe($_POST, "t_rid") == "") {
$t_item->rid = null;
}
if ($t_item->createItem()) {
$affected_goals = Goal::getGoalIdsForUserInRange(User::$current_user->uid, $t_item->date);
if ($affected_goals) {
Goal::updatePercentForList($affected_goals);
}
Page::redirect("/training/");
}
Page::redirect("/training/");
}
/**
* Constructor is the entry point to generate tag parts.
*
* @param string $tag The stuff inside {{here}}.
* @return Template_TagData Returns itself.
*/
function __construct($tag)
{
//check for echo only
$_echo = "/^((?:[\$].*)|(?:\\w::.*))/";
$echo = preg_match($_echo, $tag, $_echo_match);
if ($echo) {
$this->_special = '$';
$_nonBlock = $_echo_match[1];
$this->block = "echo";
} else {
//parses out the tag parts.
$_specialRegex = "/^(\\W)?\\s*(\\S+)(?:\\s+(.*?))?\\s*\$/s";
$_matches = array();
$_isSpecial = preg_match($_specialRegex, $tag, $_matches);
$this->_special = array_safe($_matches, 1, "");
$this->block = array_safe($_matches, 2, "");
$_nonBlock = array_safe($_matches, 3, "");
}
$this->_parseCommandAndParams($_nonBlock);
return $this;
}
error_reporting(E_ALL);
ini_set('display_errors', '1');
require_once 'mysql.php';
require_once 'search_chemicalDatabase.php';
require_once 'getNames.php';
require_once 'getDatabaseIDs.php';
// $_POST['query'] contains the raw query here, split it process it boil it salt it serve it
$queryString = trim(strtoupper($_POST['query']), " \t,");
$queryString = preg_replace('/;\\s+/', ';', $queryString);
$queryString = preg_replace('/\\s+;/', ';', $queryString);
$query = explode(";", $queryString);
// Find where chemicals, genes and GOterms are in Query
$chemicals = array_safe(array_intersect($query, array_map('strtoupper', getChemicalList())));
$genes = array_safe(array_intersect($query, array_map('strtoupper', getGeneList())));
$GOterms = array_safe(array_intersect($query, array_map('strtoupper', getGOList())));
$databaseIDs_chemicals = getChemicalDatabaseIDs($chemicals);
$databaseIDs_genes = getGeneDatabaseIDs($genes);
$databaseIDs_GOs = getGeneOntologyDatabaseIDs($GOterms);
$results = array(0 => search_info_chemicals($databaseIDs_chemicals), 1 => search_info_genes($databaseIDs_genes), 2 => search_info_GO_terms($databaseIDs_GOs));
//echo $queryString;
if ($queryString == "" || $queryString == "NAME OF CHEMICALS TO SEARCH GOES HERE, SEPARATED BY;") {
echo "NO_SEARCH";
} else {
if (count($chemicals) == 0 && count($genes) == 0 && count($GOterms) == 0) {
echo "INVALID_SEARCH";
} else {
if (count($results[0]) == 0 && count($results[1]) == 0 && count($results[2]) == 0) {
echo "EMPTY";
} else {
echo json_encode($results);
/**
* Gets the permissions for the current user.
* This searches the page perm code first.
* Then it search for permission groups.
* Finally it gets things from the user_roles table.
* It does not handle do_not_allow yet.
*
* @return array
*/
function getPermissions()
{
$this->permissions = array();
$this->_addPermission($this->page_perm);
//get the groups table first
$stmt = Database::getDB()->prepare("\r\n\t\t\tSELECT pr_code, g_gid, pgr_allow\r\n\t\t\tFROM users_permission_groups\r\n\t\t\tLEFT JOIN permission_groups_roles USING(pg_id)\r\n\t\t\tWHERE\r\n\t\t\t\tu_uid = ?\r\n\t\t");
$stmt->bind_param("i", User::$current_user->uid);
$stmt->execute();
$stmt->store_result();
while ($row = $stmt->fetch_assoc()) {
$this->_addPermission($row["pr_code"], array_safe($row, "g_gid"));
}
$stmt->close();
//get the user individual ones
$stmt = Database::getDB()->prepare("\r\n\t\t\tSELECT pr_code, g_gid, ur_allow\r\n\t\t\tFROM users_roles\r\n\t\t\tWHERE\r\n\t\t\t\tu_uid = ?\r\n\t\t");
$stmt->bind_param("i", User::$current_user->uid);
$stmt->execute();
$stmt->store_result();
while ($row = $stmt->fetch_assoc()) {
$this->_addPermission($row["pr_code"], array_safe($row, "g_gid"));
}
$stmt->close();
return $this->permissions;
}
public static function addElevationToFile($filename, $skip = 4)
{
$ini = self::_readConfigFile($filename);
$rows = $ini["nrows"];
$cols = $ini["ncols"];
$xll_corner = $ini["xllcorner"];
$yll_corner = $ini["yllcorner"];
$size = $ini["cellsize"];
$top = array_safe($ini, "top", $yll_corner + $size * ($rows + 1));
$left = array_safe($ini, "left", $xll_corner);
//read the data file
$handle = fopen("{$filename}.flt", "rb");
$handle_out = fopen("{$filename}_out.txt", "w+");
$lat = $top;
$lng = $left;
$elev = 0;
fwrite($handle_out, "lat\tlng\telev\r\n");
set_time_limit(120);
for ($i = 0; $i < $rows; $i++) {
$contents = fread($handle, $cols * 4);
if ($i % $skip) {
continue;
}
//unpack is 1-indexed
$arr = unpack("f*", $contents);
$lng = $left;
for ($j = 0; $j < $cols; $j += $skip) {
$elev = round($arr[$j + 1], 5);
//moving to the right on the map
fwrite($handle_out, "{$lat}\t{$lng}\t{$elev}\r\n");
$lng += $size * $skip;
}
//moving down the map
$lat -= $size * $skip;
}
fclose($handle);
fclose($handle_out);
return true;
}
