/**
* Generate a new atom identifier for this concept
* @return string
*/
public function createNewAtomId()
{
static $prevTime = null;
if (strpos($this->name, '_AI') !== false && $this->isInteger()) {
$firstCol = current($this->mysqlConceptTable->getCols());
$query = "SELECT MAX(`{$firstCol->name}`) as `MAX` FROM `{$this->mysqlConceptTable->name}`";
$result = array_column((array) $this->database->Exe($query), 'MAX');
if (empty($result)) {
$atomId = 1;
} else {
$atomId = $result[0] + 1;
}
} else {
$now = explode(' ', microTime());
// yields ["microseconds", "seconds"] both in seconds, e.g. ["0.85629400", "1322761879"]
$time = $now[1] . substr($now[0], 2, 6);
// we drop the leading "0." and trailing "00" from the microseconds
// Guarantee that time is increased
if ($time <= $prevTime) {
$time = ++$prevTime;
} else {
$prevTime = $time;
}
$atomId = $this->name . '_' . $time;
}
return $atomId;
}
/**
*
* @throws Exception when segment type is unknown
* @throws Exception when segment expression return more that 1 tgt atom
* @return string
*/
public function getViolationMessage()
{
$database = Database::singleton();
$strArr = array();
foreach ($this->rule->violationSegments as $segment) {
// text segment
if ($segment['segmentType'] == 'Text') {
$strArr[] = $segment['Text'];
// expressie segment
} elseif ($segment['segmentType'] == 'Exp') {
// select starting atom depending on whether the segment uses the src of tgt atom.
$atom = $segment['srcOrTgt'] == 'Src' ? $this->src : $this->tgt;
// quering the expression
$query = "SELECT DISTINCT `tgt` FROM ({$segment['expSQL']}) AS `results` WHERE `src` = '{$atom->idEsc}'";
// SRC of TGT kunnen door een expressie gevolgd worden
$rows = $database->Exe($query);
// returning the result
if (count($rows) > 1) {
throw new Exception("Expression of pairview results in more than one tgt atom", 501);
}
// 501: Not implemented
$strArr[] = $rows[0]['tgt'];
// unknown segment
} else {
$errorMessage = "Unknown segmentType '{$segment['segmentType']}' in violationSegments of rule '{$this->rule->id}'";
throw new Exception($errorMessage, 501);
// 501: Not implemented
}
}
// If empty array of strings (i.e. no violation segments defined), use default violation representation: '<srcAtom>,<tgtAtom>'
$this->message = empty($strArr) ? "{$this->src->getLabel()},{$this->tgt->getLabel()}" : implode($strArr);
return $this->message;
}
/**
* Function to delete an atom from Concept collection
* @param array $options
* @throws Exception when delete is not allowed/possible
* @return void
*/
public function delete($options = array())
{
$this->logger->debug("delete() called on {$this->path}");
// CRUD check
if (!$this->parentIfc->crudD) {
throw new Exception("Delete not allowed for '{$this->path}'", 405);
}
if (!$this->parentIfc->tgtConcept->isObject) {
throw new Exception("Cannot delete non-object '{$this->__toString()}' in '{$this->path}'. Use PATCH remove operation instead", 405);
}
if ($this->parentIfc->isRef()) {
throw new Exception("Cannot delete on reference interface in '{$this->path}'. See #498", 501);
}
// Handle options
if (isset($options['requestType'])) {
$this->database->setRequestType($options['requestType']);
}
// Perform delete
$this->deleteAtom();
// Close transaction
$this->database->closeTransaction($this->concept . ' deleted');
return;
}
/**
* Return array with all links (pair of Atoms) in this relation
* @return array[]
*/
public function getAllLinks()
{
// Query all atoms in table
$query = "SELECT `{$this->mysqlTable->srcCol()->name}` as `src`, `{$this->mysqlTable->tgtCol()->name}` as `tgt` FROM `{$this->mysqlTable->name}`";
return (array) $this->db->Exe($query);
}
$allLinks = array();
foreach (Relation::getAllRelations() as $rel) {
$allLinks[$rel->signature] = $rel->getAllLinks();
}
$strFileContent = '<?php' . PHP_EOL . '$allAtoms = ' . var_export($allAtoms, true) . ';' . PHP_EOL . '$allLinks = ' . var_export($allLinks, true) . ';' . PHP_EOL . '?>';
file_put_contents(Config::get('absolutePath') . Config::get('logPath') . "export-" . date('Y-m-d_H-i-s') . ".php", $strFileContent);
});
$app->get('/admin/import', function () use($app) {
if (Config::get('productionEnv')) {
throw new Exception("Import not allowed in production environment", 403);
}
$file = $app->request->params('file');
if (is_null($file)) {
throw new Exception("Import file not specified", 500);
}
$database = Database::singleton();
include_once Config::get('absolutePath') . Config::get('logPath') . "{$file}";
// check if all concepts and relations are defined
foreach ((array) $allAtoms as $cpt => $atoms) {
if (!empty($atoms)) {
Concept::getConcept($cpt);
}
}
foreach ((array) $allLinks as $rel => $links) {
if (!empty($links)) {
Relation::getRelation($rel);
}
}
foreach ((array) $allAtoms as $cpt => $atoms) {
$concept = Concept::getConcept($cpt);
foreach ($atoms as $atomId) {
/**
* Function to create a new Atom at the given interface.
* @param array $data
* @param array $options
* @throws Exception
* @return mixed
*/
public function create($data, $options = array())
{
$this->logger->debug("create() called on {$this->path}");
// CRUD check
if (!$this->crudC) {
throw new Exception("Create not allowed for '{$this->path}'", 405);
}
if (!$this->tgtConcept->isObject) {
throw new Exception("Cannot create non-object '{$this->tgtConcept}' in '{$this->path}'. Use PATCH add operation instead", 405);
}
if ($this->isRef()) {
throw new Exception("Cannot create on reference interface in '{$this->path}'. See #498", 501);
}
// Handle options
if (isset($options['requestType'])) {
$this->database->setRequestType($options['requestType']);
}
// Perform create
$newAtom = $this->tgtConcept->createNewAtom();
// Special case for CREATE in I[Concept] interfaces
if ($this->srcAtom->id === '_NEW') {
$this->srcAtom->setId($newAtom->id);
$this->path = str_replace('_NEW', $newAtom->getJsonRepresentation(), $this->path);
}
// If interface expression is a relation, also add tuple(this, newAtom) in this relation
if ($this->relation) {
$this->relation()->addLink($this->srcAtom, $newAtom, $this->relationIsFlipped);
} else {
$newAtom->addAtom();
}
// Walk to new atom
$newAtom = $this->atom($newAtom->id);
// Set requested state (using patches)
$patches = is_array($data) ? $data['patches'] : array();
$newAtom->doPatches($patches);
// Special case for file upload. TODO: make extension with hooks
if ($this->tgtConcept->isFileObject()) {
$conceptFilePath = Concept::getConceptByLabel('FilePath');
$conceptFileName = Concept::getConceptByLabel('FileName');
if (is_uploaded_file($_FILES['file']['tmp_name'])) {
$tmp_name = $_FILES['file']['tmp_name'];
$new_name = time() . '_' . $_FILES['file']['name'];
$absolutePath = Config::get('absolutePath') . Config::get('uploadPath') . $new_name;
$relativePath = Config::get('uploadPath') . $new_name;
$result = move_uploaded_file($tmp_name, $absolutePath);
if ($result) {
Logger::getUserLogger()->notice("File '{$new_name}' uploaded");
} else {
throw new Exception("Error in file upload", 500);
}
// Populate filePath and originalFileName relations in database
$relFilePath = Relation::getRelation('filePath', $newAtom->concept, $conceptFilePath);
$relOriginalFileName = Relation::getRelation('originalFileName', $newAtom->concept, $conceptFileName);
$relFilePath->addLink($newAtom, new Atom($relativePath, $conceptFilePath));
$relOriginalFileName->addLink($newAtom, new Atom($_FILES['file']['name'], $conceptFileName));
} else {
throw new Exception("No file uploaded", 500);
}
}
// Close transaction
$this->database->closeTransaction($newAtom->concept . ' created', null, $newAtom);
// temp store content of $newAtom (also when not crudR)
// Return atom content (can be null)
return $newAtom->getStoredContent();
}
private function login($email)
{
if (empty($email)) {
throw new Exception("No emailaddress provided to login", 500);
}
$session = Session::singleton();
$db = Database::singleton();
$conceptUserID = Concept::getConceptByLabel('UserID');
$conceptDomain = Concept::getConceptByLabel('Domain');
$conceptDateTime = Concept::getConceptByLabel('DateTime');
$conceptOrg = Concept::getConceptByLabel('Organization');
$conceptAccount = Concept::getConceptByLabel('Account');
$conceptSession = Concept::getConceptByLabel('SESSION');
// Set sessionUser
$atom = new Atom($email, $conceptUserID);
$accounts = $atom->ifc('AccountForUserid')->getTgtAtoms();
// create new user
if (empty($accounts)) {
$newAccount = Concept::getConceptByLabel('Account')->createNewAtom();
// Save email as accUserid
$relAccUserid = Relation::getRelation('accUserid', $newAccount->concept, $conceptUserID);
$relAccUserid->addLink($newAccount, new Atom($email, $conceptUserID), false, 'OAuthLoginExtension');
// If possible, add account to organization(s) based on domain name
$domain = explode('@', $email)[1];
$atom = new Atom($domain, $conceptDomain);
$orgs = $atom->ifc('DomainOrgs')->getTgtAtoms();
$relAccOrg = Relation::getRelation('accOrg', $newAccount->concept, $conceptOrg);
foreach ($orgs as $org) {
$relAccOrg->addLink($newAccount, $org, false, 'OAuthLoginExtension');
}
// Account created, add to $accounts list (used lateron)
$accounts[] = $newAccount;
}
if (count($accounts) > 1) {
throw new Exception("Multiple users registered with email {$email}", 401);
}
$relSessionAccount = Relation::getRelation('sessionAccount', $conceptSession, $conceptAccount);
$relAccMostRecentLogin = Relation::getRelation('accMostRecentLogin', $conceptAccount, $conceptDateTime);
$relAccLoginTimestamps = Relation::getRelation('accLoginTimestamps', $conceptAccount, $conceptDateTime);
foreach ($accounts as $account) {
// Set sessionAccount
$relSessionAccount->addLink($session->sessionAtom, $account, false, 'OAuthLoginExtension');
// Timestamps
$ts = new Atom(date(DATE_ISO8601), $conceptDateTime);
$relAccMostRecentLogin->addLink($account, $ts, false, 'OAuthLoginExtension');
$relAccLoginTimestamps->addLink($account, $ts, false, 'OAuthLoginExtension');
}
$db->closeTransaction('Login successfull', true);
}
global $app;
// Path to API is 'api/v1/excelimport/import'
$app->post('/excelimport/import', function () use($app) {
$session = Session::singleton();
$roleIds = $app->request->params('roleIds');
$session->activateRoles($roleIds);
// Check sessionRoles if allowedRolesForExcelImport is specified
$allowedRoles = Config::get('allowedRolesForExcelImport', 'excelImport');
if (!is_null($allowedRoles)) {
$ok = false;
foreach ($session->getSessionRoles() as $role) {
if (in_array($role->label, $allowedRoles)) {
$ok = true;
}
}
if (!$ok) {
throw new Exception("You do not have access to import excel files", 401);
}
}
if (is_uploaded_file($_FILES['file']['tmp_name'])) {
// Parse:
$parser = new ExcelImport();
$parser->ParseFile($_FILES['file']['tmp_name']);
Database::singleton()->closeTransaction("File {$_FILES['file']['tmp_name']} imported successfully", true);
unlink($_FILES['file']['tmp_name']);
} else {
Logger::getUserLogger()->error("No file uploaded");
}
$result = array('notifications' => Notifications::getAll(), 'files' => $_FILES);
print json_encode($result, JSON_PRETTY_PRINT | JSON_UNESCAPED_SLASHES);
});
/**
* Overwrites getViolationMessage() method from Violation class
* @throws Exception when segment type is unknown
* @throws Exception when segment expression return more that 1 tgt atom
* @return string
*/
public function getViolationMessage()
{
$database = Database::singleton();
$strArr = array();
foreach ($this->rule->violationSegments as $segment) {
// text segment
if ($segment['segmentType'] == 'Text') {
$strArr[] = $segment['Text'];
// expressie segment
} elseif ($segment['segmentType'] == 'Exp') {
// select starting atom depending on whether the segment uses the src of tgt atom.
$atom = $segment['srcOrTgt'] == 'Src' ? $this->src : $this->tgt;
$rows = array();
if ($segment['expIsIdent']) {
// when segment expression isIdent (i.e. SRC I or TGT I), we don't have to query the database.
$rows[] = array('tgt' => $atom->id);
} else {
// quering the expression
$query = "SELECT DISTINCT `tgt` FROM ({$segment['expSQL']}) AS `results` WHERE `src` = '{$atom->idEsc}'";
// SRC of TGT kunnen door een expressie gevolgd worden
$rows = $database->Exe($query);
}
// returning the result
if (count($rows) == 0) {
$strArr[] = '_NULL';
} else {
$str = '';
foreach ($rows as $row) {
$str .= $row['tgt'] . '_AND';
}
$str = substr($str, 0, -4);
// strip the last _AND
$strArr[] = str_replace(array('{EX}', '{php}'), '', $str);
// prevent php interpreter by user input. Only allowed as Text segments specified in &-script
}
// unknown segment
} else {
$errorMessage = "Unknown segmentType '{$segment['segmentType']}' in violationSegments of rule '{$this->rule->id}'";
throw new Exception($errorMessage, 501);
// 501: Not implemented
}
}
return $this->message = implode($strArr);
}
function OverwritePopulation($rArray, $relationName, $conceptName)
{
try {
$database = Database::singleton();
$concept = Concept::getConceptByLabel($conceptName);
$relation = Relation::getRelation($relationName, $concept, $concept);
$relationTable = $relation->getMysqlTable();
$srcCol = $relationTable->srcCol();
$tgtCol = $relationTable->tgtCol();
$query = "DELETE FROM `{$relationTable->name}`";
// Do not use TRUNCATE statement, this causes an implicit commit
$database->Exe($query);
foreach ($rArray as $src => $tgtArray) {
foreach ($tgtArray as $tgt => $bool) {
if ($bool) {
$query = "INSERT INTO `{$relationTable->name}` (`{$srcCol->name}`, `{$tgtCol->name}`) VALUES ('{$src}','{$tgt}')";
$database->Exe($query);
}
}
}
} catch (Exception $e) {
throw new Exception('OverwritePopulation: ' . $e->getMessage(), 500);
}
}
/**
* Function to evaluate conjunct
* @param boolean $cacheConjuncts
* @return array[] array(array('src' => '<srcAtomId>', 'tgt' => '<tgtAtomId>'))
*/
public function evaluateConjunct($cacheConjuncts = true)
{
$this->logger->debug("Checking conjunct '{$this->id}' cache:" . var_export($cacheConjuncts, true));
try {
// If conjunct is already evaluated and conjunctCach may be used -> return violations
if (isset($this->conjunctViolations) && $cacheConjuncts) {
$this->logger->debug("Conjunct is already evaluated, getting violations from cache");
return $this->conjunctViolations;
// Otherwise evaluate conjunct, cache and return violations
} else {
$db = Database::singleton();
$dbsignalTableName = Config::get('dbsignalTableName', 'mysqlDatabase');
$violations = array();
// Execute conjunct query
$violations = (array) $db->Exe($this->query);
// Cache violations in php Conjunct object
if ($cacheConjuncts) {
$this->conjunctViolations = $violations;
}
if (count($violations) == 0) {
$this->logger->debug("Conjunct '{$this->id}' holds");
// Remove "old" conjunct violations from database
$query = "DELETE FROM `{$dbsignalTableName}` WHERE `conjId` = '{$this->id}'";
$db->Exe($query);
} else {
$this->logger->debug("Conjunct '{$this->id}' broken, updating violations in database");
// Remove "old" conjunct violations from database
$query = "DELETE FROM `{$dbsignalTableName}` WHERE `conjId` = '{$this->id}'";
$db->Exe($query);
// Add new conjunct violation to database
$query = "INSERT IGNORE INTO `{$dbsignalTableName}` (`conjId`, `src`, `tgt`) VALUES ";
$values = array();
foreach ($violations as $violation) {
$values[] = "('{$this->id}', '" . $db->escape($violation['src']) . "', '" . $db->escape($violation['tgt']) . "')";
}
$query .= implode(',', $values);
$db->Exe($query);
}
return $violations;
}
} catch (Exception $e) {
Logger::getUserLogger()->error("While checking conjunct '{$this->id}': " . $e->getMessage());
return array();
}
}
/**
* Function to return the database instance
* @return Database
*/
public static function singleton()
{
try {
if (!is_object(self::$_instance)) {
self::$_instance = new Database();
}
} catch (Exception $e) {
// Convert mysqli_sql_exceptions into 500 errors
if (!Config::get('productionEnv')) {
switch ($e->getCode()) {
case 1049:
// Error: 1049 SQLSTATE: 42000 (ER_BAD_DB_ERROR)
// throw new Exception("Please <a href=\"#/admin/installer\" class=\"alert-link\">install database</a>",500);
self::createDB();
self::$_instance = new Database();
self::$_instance->logger->info("Automatically installing database for the first time");
self::$_instance->reinstallDB();
break;
default:
throw new Exception("{$e->getCode()}: {$e->getMessage()}", 500);
}
} else {
throw new Exception("Cannot connect to database", 500);
}
}
return self::$_instance;
}
function ClearConcept($concept, $atom)
{
Logger::getLogger('EXECENGINE')->info("ClearConcept({$concept},{$atom})");
if (func_num_args() != 2) {
throw new Exception("Wrong number of arguments supplied for function ClearConcept(): " . func_num_args() . " arguments", 500);
}
try {
$database = Database::singleton();
$atom = new Atom($atom, Concept::getConceptByLabel($concept));
$database->atomClearConcept($atom);
Logger::getLogger('EXECENGINE')->debug("Atom '{$atom->__toString()}' removed as member from concept '{$concept}'");
} catch (Exception $e) {
Logger::getUserLogger()->error('ClearConcept: ' . $e->getMessage());
}
}
/**
* Returns if session refresh is adviced in frontend
* True when
* - session variable is affected (otherwise nothing to update)
* - AND transaction request is 'promise' (otherwise rollback)
* - AND invariant rules hold (otherwise rollback)
* False otherwise
* @return boolean
*/
public function getSessionRefreshAdvice()
{
return $this->getSessionVarAffected() && $this->database->getRequestType() == 'promise' && $this->database->getInvariantRulesHold();
}
