/**
* Create a new, or update an existing entity based on the input RDF document.
*
* @param mixed $document
* @param mixed $advancedIndexation
*
* @author Frederick Giasson, Structured Dynamics LLC.
*/
public function createOrUpdateEntity($document, $advancedIndexation)
{
$this->initiateOwlBridgeSession();
$this->getOntologyReference();
if ($this->isValid()) {
// Now read the RDF file that we got as input to update the ontology with it.
// Basically, we list all the entities (classes, properties and instance)
// and we update each of them, one by one, in both the OWLAPI instance
// and structWSF if the advancedIndexation is enabled.
include_once "../../framework/arc2/ARC2.php";
$parser = ARC2::getRDFParser();
$parser->parse($this->ws->ontology->getBaseUri(), $document);
$rdfxmlSerializer = ARC2::getRDFXMLSerializer();
$resourceIndex = $parser->getSimpleIndex(0);
if (count($parser->getErrors()) > 0) {
$errorsOutput = "";
$errors = $parser->getErrors();
foreach ($errors as $key => $error) {
$errorsOutput .= "[Error #{$key}] {$error}\n";
}
$this->ws->conneg->setStatus(400);
$this->ws->conneg->setStatusMsg("Bad Request");
$this->ws->conneg->setError($this->ws->errorMessenger->_301->id, $this->ws->errorMessenger->ws, $this->ws->errorMessenger->_301->name, $this->ws->errorMessenger->_301->description, $errorsOutput, $this->ws->errorMessenger->_301->level);
return;
}
// Get all entities
foreach ($resourceIndex as $uri => $description) {
$types = array();
$literalValues = array();
$objectValues = array();
foreach ($description as $predicate => $values) {
switch ($predicate) {
case Namespaces::$rdf . "type":
foreach ($values as $value) {
array_push($types, $value["value"]);
}
break;
default:
foreach ($values as $value) {
if ($value["type"] == "literal") {
if (!is_array($literalValues[$predicate])) {
$literalValues[$predicate] = array();
}
array_push($literalValues[$predicate], $value["value"]);
} else {
if (!is_array($objectValues[$predicate])) {
$objectValues[$predicate] = array();
}
array_push($objectValues[$predicate], $value["value"]);
}
}
break;
}
}
// Call different API calls depending what we are manipulating
if ($this->in_array_r(Namespaces::$owl . "Ontology", $description[Namespaces::$rdf . "type"])) {
$this->ws->ontology->updateOntology($literalValues, $objectValues);
// Make sure advanced indexation is off when updating an ontology's description
$advancedIndexation = FALSE;
} elseif ($this->in_array_r(Namespaces::$owl . "Class", $description[Namespaces::$rdf . "type"])) {
$this->ws->ontology->updateClass($uri, $literalValues, $objectValues);
} elseif ($this->in_array_r(Namespaces::$owl . "DatatypeProperty", $description[Namespaces::$rdf . "type"]) || $this->in_array_r(Namespaces::$owl . "ObjectProperty", $description[Namespaces::$rdf . "type"]) || $this->in_array_r(Namespaces::$owl . "AnnotationProperty", $description[Namespaces::$rdf . "type"])) {
foreach ($types as $type) {
if (!is_array($objectValues[Namespaces::$rdf . "type"])) {
$objectValues[Namespaces::$rdf . "type"] = array();
}
array_push($objectValues[Namespaces::$rdf . "type"], $type);
}
$this->ws->ontology->updateProperty($uri, $literalValues, $objectValues);
} else {
$this->ws->ontology->updateNamedIndividual($uri, $types, $literalValues, $objectValues);
}
// Call different API calls depending what we are manipulating
if ($advancedIndexation == TRUE) {
include_once "../../framework/arc2/ARC2.php";
$rdfxmlParser = ARC2::getRDFParser();
$rdfxmlSerializer = ARC2::getRDFXMLSerializer();
$resourcesIndex = $rdfxmlParser->getSimpleIndex(0);
// Index the entity to update
$rdfxmlParser->parse($uri, $rdfxmlSerializer->getSerializedIndex(array($uri => $resourceIndex[$uri])));
$rIndex = $rdfxmlParser->getSimpleIndex(0);
$resourcesIndex = ARC2::getMergedIndex($resourcesIndex, $rIndex);
// Check if the entity got punned
$entities = $this->ws->ontology->_getEntities($uri);
if (count($entities) > 1) {
// The entity got punned.
$isClass = FALSE;
$isProperty = FALSE;
$isNamedEntity = FALSE;
foreach ($entities as $entity) {
if ((bool) java_values($entity->isOWLClass())) {
$isClass = TRUE;
}
if ((bool) java_values($entity->isOWLDataProperty()) || (bool) java_values($entity->isOWLObjectProperty()) || (bool) java_values($entity->isOWLAnnotationProperty())) {
$isProperty = TRUE;
}
if ((bool) java_values($entity->isOWLNamedIndividual())) {
$isNamedEntity = TRUE;
}
}
$queries = array();
if ($description[Namespaces::$rdf . "type"][0]["value"] != Namespaces::$owl . "Class" && $isClass) {
array_push($queries, array("function" => "getClass", "params" => "uri=" . $uri));
}
if ($description[Namespaces::$rdf . "type"][0]["value"] != Namespaces::$owl . "DatatypeProperty" && $description[Namespaces::$rdf . "type"][0]["value"] != Namespaces::$owl . "ObjectProperty" && $description[Namespaces::$rdf . "type"][0]["value"] != Namespaces::$owl . "AnnotationProperty" && $isProperty) {
array_push($queries, array("function" => "getProperty", "params" => "uri=" . $uri));
}
if ($description[Namespaces::$rdf . "type"][0]["value"] != Namespaces::$owl . "NamedIndividual" && $isNamedEntity) {
array_push($queries, array("function" => "getNamedIndividual", "params" => "uri=" . $uri));
}
foreach ($queries as $query) {
// Get the class description of the current punned entity
$ontologyRead = new OntologyRead($this->ws->ontologyUri, $query["function"], $query["params"], $this->ws->registered_ip, $this->ws->requester_ip);
// Since we are in pipeline mode, we have to set the owlapisession using the current one.
// otherwise the java bridge will return an error
$ontologyRead->setOwlApiSession($this->OwlApiSession);
$ontologyRead->ws_conneg("application/rdf+xml", $_SERVER['HTTP_ACCEPT_CHARSET'], $_SERVER['HTTP_ACCEPT_ENCODING'], $_SERVER['HTTP_ACCEPT_LANGUAGE']);
if ($this->ws->reasoner) {
$ontologyRead->useReasoner();
} else {
$ontologyRead->stopUsingReasoner();
}
$ontologyRead->process();
if ($ontologyRead->pipeline_getResponseHeaderStatus() != 200) {
$this->ws->conneg->setStatus($ontologyRead->pipeline_getResponseHeaderStatus());
$this->ws->conneg->setStatusMsg($ontologyRead->pipeline_getResponseHeaderStatusMsg());
$this->ws->conneg->setStatusMsgExt($ontologyRead->pipeline_getResponseHeaderStatusMsgExt());
$this->ws->conneg->setError($ontologyRead->pipeline_getError()->id, $ontologyRead->pipeline_getError()->webservice, $ontologyRead->pipeline_getError()->name, $ontologyRead->pipeline_getError()->description, $ontologyRead->pipeline_getError()->debugInfo, $ontologyRead->pipeline_getError()->level);
return;
}
$entitySerialized = $ontologyRead->pipeline_serialize();
$rdfxmlParser->parse($uri, $entitySerialized);
$rIndex = $rdfxmlParser->getSimpleIndex(0);
$resourcesIndex = ARC2::getMergedIndex($resourcesIndex, $rIndex);
unset($ontologyRead);
}
}
switch ($description[Namespaces::$rdf . "type"][0]["value"]) {
case Namespaces::$owl . "Class":
case Namespaces::$owl . "DatatypeProperty":
case Namespaces::$owl . "ObjectProperty":
case Namespaces::$owl . "AnnotationProperty":
case Namespaces::$owl . "NamedIndividual":
default:
// We have to check if this entity to update is punned. If yes, we have to merge all the
// punned descriptison together before updating them in structWSF (Virtuoso and Solr).
// otherwise we will loose information in these other systems.
// Once we start the ontology creation process, we have to make sure that even if the server
// loose the connection with the user the process will still finish.
ignore_user_abort(true);
// However, maybe there is an issue with the server handling that file tht lead to some kind of infinite or near
// infinite loop; so we have to limit the execution time of this procedure to 45 mins.
set_time_limit(2700);
$serializedResource = $rdfxmlSerializer->getSerializedIndex($resourcesIndex);
// Update the classes and properties into the Solr index
$crudUpdate = new CrudUpdate($serializedResource, "application/rdf+xml", $this->ws->ontologyUri, $this->ws->registered_ip, $this->ws->requester_ip);
$crudUpdate->ws_conneg($_SERVER['HTTP_ACCEPT'], $_SERVER['HTTP_ACCEPT_CHARSET'], $_SERVER['HTTP_ACCEPT_ENCODING'], $_SERVER['HTTP_ACCEPT_LANGUAGE']);
$crudUpdate->process();
if ($crudUpdate->pipeline_getResponseHeaderStatus() != 200) {
$this->ws->conneg->setStatus($crudUpdate->pipeline_getResponseHeaderStatus());
$this->ws->conneg->setStatusMsg($crudUpdate->pipeline_getResponseHeaderStatusMsg());
$this->ws->conneg->setStatusMsgExt($crudUpdate->pipeline_getResponseHeaderStatusMsgExt());
$this->ws->conneg->setError($crudUpdate->pipeline_getError()->id, $crudUpdate->pipeline_getError()->webservice, $crudUpdate->pipeline_getError()->name, $crudUpdate->pipeline_getError()->description, $crudUpdate->pipeline_getError()->debugInfo, $crudUpdate->pipeline_getError()->level);
return;
}
unset($crudUpdate);
/*
// Once we start the ontology creation process, we have to make sure that even if the server
// loose the connection with the user the process will still finish.
ignore_user_abort(true);
// However, maybe there is an issue with the server handling that file tht lead to some kind of infinite or near
// infinite loop; so we have to limit the execution time of this procedure to 45 mins.
set_time_limit(2700);
$ser = ARC2::getTurtleSerializer();
$serializedResource = $ser->getSerializedIndex(array($uri => $resourceIndex[$uri]));
// Update the classes and properties into the Solr index
$crudUpdate = new CrudUpdate($serializedResource, "application/rdf+n3", $this->ws->ontologyUri,
$this->ws->registered_ip, $this->ws->requester_ip);
$crudUpdate->ws_conneg($_SERVER['HTTP_ACCEPT'], $_SERVER['HTTP_ACCEPT_CHARSET'], $_SERVER['HTTP_ACCEPT_ENCODING'],
$_SERVER['HTTP_ACCEPT_LANGUAGE']);
$crudUpdate->process();
if($crudUpdate->pipeline_getResponseHeaderStatus() != 200)
{
$this->ws->conneg->setStatus($crudUpdate->pipeline_getResponseHeaderStatus());
$this->ws->conneg->setStatusMsg($crudUpdate->pipeline_getResponseHeaderStatusMsg());
$this->ws->conneg->setStatusMsgExt($crudUpdate->pipeline_getResponseHeaderStatusMsgExt());
$this->ws->conneg->setError($crudUpdate->pipeline_getError()->id, $crudUpdate->pipeline_getError()->webservice,
$crudUpdate->pipeline_getError()->name, $crudUpdate->pipeline_getError()->description,
$crudUpdate->pipeline_getError()->debugInfo, $crudUpdate->pipeline_getError()->level);
return;
}
unset($crudUpdate);
*/
break;
}
}
}
// Update the name of the file of the ontology to mark it as "changed"
$this->ws->ontology->addOntologyAnnotation("http://purl.org/ontology/wsf#ontologyModified", "true");
}
}
$mtime = $mtime[1] + $mtime[0];
$starttime = $mtime;
$start_datetime = date("Y-m-d h:i:s");
$requester_ip = "0.0.0.0";
if (isset($_SERVER['REMOTE_ADDR'])) {
$requester_ip = $_SERVER['REMOTE_ADDR'];
}
$parameters = "";
if (isset($_SERVER['REQUEST_URI'])) {
$parameters = $_SERVER['REQUEST_URI'];
$pos = strpos($parameters, "?");
if ($pos !== FALSE) {
$parameters = substr($parameters, $pos, strlen($parameters) - $pos);
}
} elseif (isset($_SERVER['PHP_SELF'])) {
$parameters = $_SERVER['PHP_SELF'];
}
$ws_crudupdate = new CrudUpdate($document, $mime, $dataset, $registered_ip, $requester_ip, $interface, $version);
$ws_crudupdate->ws_conneg(isset($_SERVER['HTTP_ACCEPT']) ? $_SERVER['HTTP_ACCEPT'] : "", isset($_SERVER['HTTP_ACCEPT_CHARSET']) ? $_SERVER['HTTP_ACCEPT_CHARSET'] : "", isset($_SERVER['HTTP_ACCEPT_ENCODING']) ? $_SERVER['HTTP_ACCEPT_ENCODING'] : "", isset($_SERVER['HTTP_ACCEPT_LANGUAGE']) ? $_SERVER['HTTP_ACCEPT_LANGUAGE'] : "");
$ws_crudupdate->process();
$ws_crudupdate->ws_respond($ws_crudupdate->ws_serialize());
$mtime = microtime();
$mtime = explode(" ", $mtime);
$mtime = $mtime[1] + $mtime[0];
$endtime = $mtime;
$totaltime = $endtime - $starttime;
//echo $totaltime."ms\n";
if ($ws_crudupdate->isLoggingEnabled()) {
$logger = new Logger("crud_update", $requester_ip, "?document=" . substr($document, 0, 64) . "&mime=" . $mime . "&dataset=" . $dataset . "®istered_ip=" . $registered_ip . "&requester_ip={$requester_ip}", isset($_SERVER['HTTP_ACCEPT']) ? $_SERVER['HTTP_ACCEPT'] : "", $start_datetime, $totaltime, $ws_crudupdate->pipeline_getResponseHeaderStatus(), isset($_SERVER['HTTP_USER_AGENT']) ? $_SERVER['HTTP_USER_AGENT'] : "");
}
//@}