function getLoadedOntologies($structwsf, $queryExtension = NULL)
{
$ontologyRead = new OntologyReadQuery($structwsf);
$getLoadedOntologiesFunction = new GetLoadedOntologiesFunction();
$getLoadedOntologiesFunction->modeDescriptions();
$ontologyRead->getLoadedOntologies($getLoadedOntologiesFunction)->send($queryExtension !== NULL ? $queryExtension : NULL);
if ($ontologyRead->isSuccessful()) {
$resultset = $ontologyRead->getResultset()->getResultset();
$ontologies = array('local' => array(), 'reference' => array(), 'admin' => array());
foreach ($resultset['unspecified'] as $uri => $ontology) {
$onto = array('uri' => '', 'label' => '', 'modified' => false);
$ontologyType = 'local';
if (isset($ontology['http://purl.org/ontology/sco#ontologyType'])) {
switch ($ontology['http://purl.org/ontology/sco#ontologyType'][0]['uri']) {
case "http://purl.org/ontology/sco#referenceOntology":
$ontologyType = 'reference';
break;
case "http://purl.org/ontology/sco#administrativeOntology":
$ontologyType = 'admin';
break;
case "http://purl.org/ontology/sco#localOntology":
$ontologyType = 'local';
break;
}
}
$onto['uri'] = $uri;
$onto['label'] = $ontology['prefLabel'];
if (isset($ontology['http://purl.org/ontology/wsf#ontologyModified'])) {
$onto['modified'] = TRUE;
}
array_push($ontologies[$ontologyType], $onto);
}
return $ontologies;
} else {
$debugFile = md5(microtime()) . '.error';
file_put_contents('/tmp/' . $debugFile, var_export($ontologyRead, TRUE));
@cecho('Can\'t get loaded ontologies. ' . $ontologyRead->getStatusMessage() . $ontologyRead->getStatusMessageDescription() . "\nDebug file: /tmp/{$debugFile}\n", 'RED');
exit(1);
}
}
public function run()
{
cecho("\n\n");
cecho("Data validation test: " . $this->description . "...\n\n", 'LIGHT_BLUE');
// First, get the list of all the possible custom datatypes and their possible base datatype
$customDatatypes = $this->getCustomDatatypes();
// Check for universal restriction on Datatype Properties
$sparql = new SparqlQuery($this->network);
$from = '';
foreach ($this->checkOnDatasets as $dataset) {
$from .= 'from <' . $dataset . '> ';
}
foreach ($this->checkUsingOntologies as $ontology) {
$from .= 'from named <' . $ontology . '> ';
}
$sparql->mime("application/sparql-results+json")->query('select distinct ?restriction ?class ?onProperty ?dataRange
' . $from . '
where
{
?s a ?class.
graph ?g {
?class <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?restriction .
?restriction a <http://www.w3.org/2002/07/owl#Restriction> ;
<http://www.w3.org/2002/07/owl#onProperty> ?onProperty ;
<http://www.w3.org/2002/07/owl#allValuesFrom> ?dataRange .
?onProperty a <http://www.w3.org/2002/07/owl#DatatypeProperty> .
}
}')->send();
if ($sparql->isSuccessful()) {
$results = json_decode($sparql->getResultset(), TRUE);
if (isset($results['results']['bindings']) && count($results['results']['bindings']) > 0) {
cecho("Here is the list of all the OWL universal restrictions defined for the classes currently used in the target datasets applied on datatype properties:\n\n", 'LIGHT_BLUE');
$universals = array();
foreach ($results['results']['bindings'] as $result) {
$class = $result['class']['value'];
$dataRange = $result['dataRange']['value'];
$onProperty = $result['onProperty']['value'];
cecho(' -> Record of type "' . $class . '" has an universal restriction when using datatype property "' . $onProperty . '" with value type "' . $dataRange . '"' . "\n", 'LIGHT_BLUE');
if (!isset($universals[$class])) {
$universals[$class] = array();
}
$universals[$class][] = array('onProperty' => $onProperty, 'dataRange' => $dataRange);
}
cecho("\n\n");
foreach ($universals as $class => $univs) {
foreach ($univs as $universal) {
$sparql = new SparqlQuery($this->network);
$from = '';
foreach ($this->checkOnDatasets as $dataset) {
$from .= 'from <' . $dataset . '> ';
}
foreach ($this->checkUsingOntologies as $ontology) {
$from .= 'from <' . $ontology . '> ';
}
$datatypeFilter = '';
// Here, if rdfs:Literal is used, we have to filter for xsd:string also since it is the default
// used by Virtuoso...
if (!empty($universal['dataRange'])) {
if ($universal['dataRange'] == 'http://www.w3.org/2000/01/rdf-schema#Literal') {
$datatypeFilter = 'filter((str(datatype(?value)) != \'http://www.w3.org/2000/01/rdf-schema#Literal\' && str(datatype(?value)) != \'http://www.w3.org/2001/XMLSchema#string\') && ?onProperty in (<' . $universal['onProperty'] . '>))';
} else {
if (!empty($customDatatypes[$universal['dataRange']])) {
if ($customDatatypes[$universal['dataRange']] === 'http://www.w3.org/2001/XMLSchema#anySimpleType') {
$datatypeFilter = 'filter((str(datatype(?value)) = \'' . $universal['dataRange'] . '\' || str(datatype(?value)) = \'' . $customDatatypes[$universal['dataRange']] . '\' || str(datatype(?value)) = \'http://www.w3.org/2001/XMLSchema#string\') && ?onProperty in (<' . $universal['onProperty'] . '>))';
} else {
$datatypeFilter = 'filter((str(datatype(?value)) != \'' . $universal['dataRange'] . '\' && str(datatype(?value)) != \'' . $customDatatypes[$universal['dataRange']] . '\') && ?onProperty in (<' . $universal['onProperty'] . '>))';
}
} else {
$datatypeFilter = 'filter((str(datatype(?value)) != \'' . $universal['dataRange'] . '\') && ?onProperty in (<' . $universal['onProperty'] . '>))';
}
}
}
// With this query, we make sure that if we have a universal restriction for that property and class
// that all the values uses the specified datatype. Otherwise, we return the ones that doesn't.
$sparql->mime("application/sparql-results+json")->query('select ?s
' . $from . '
where
{
?s a <' . $class . '> .
?s ?onProperty ?value .
' . $datatypeFilter . '
}
')->send();
if ($sparql->isSuccessful()) {
$results = json_decode($sparql->getResultset(), TRUE);
if (isset($results['results']['bindings']) && count($results['results']['bindings']) > 0) {
foreach ($results['results']['bindings'] as $result) {
$subject = $result['s']['value'];
cecho(' -> record: ' . $subject . "\n", 'LIGHT_RED');
cecho(' -> property: ' . $universal['onProperty'] . "\n", 'LIGHT_RED');
$this->errors[] = array('id' => 'OWL-RESTRICTION-ONLY-100', 'type' => 'error', 'invalidRecordURI' => $subject, 'invalidPropertyURI' => $universal['onProperty'], 'dataRange' => $universal['dataRange']);
}
}
} else {
cecho("We couldn't get the number of properties per record from the structWSF instance\n", 'YELLOW');
// Error: can't get the number of properties used per record
$this->errors[] = array('id' => 'OWL-RESTRICTION-ONLY-51', 'type' => 'warning');
}
// Now let's make sure that there is at least one triple where the value belongs
// to the defined datatype
$values = array();
if (!empty($universal['dataRange'])) {
if ($universal['dataRange'] == 'http://www.w3.org/2000/01/rdf-schema#Literal') {
$datatypeFilter = 'filter(str(datatype(?value)) = \'http://www.w3.org/2000/01/rdf-schema#Literal\' || str(datatype(?value)) = \'http://www.w3.org/2001/XMLSchema#string\')';
} else {
if (!empty($customDatatypes[$universal['dataRange']])) {
if ($customDatatypes[$universal['dataRange']] === 'http://www.w3.org/2001/XMLSchema#anySimpleType') {
$datatypeFilter = 'filter(str(datatype(?value)) = \'' . $universal['dataRange'] . '\' || str(datatype(?value)) = \'' . $customDatatypes[$universal['dataRange']] . '\' || str(datatype(?value)) = \'http://www.w3.org/2001/XMLSchema#string\')';
} else {
$datatypeFilter = 'filter(str(datatype(?value)) = \'' . $universal['dataRange'] . '\' || str(datatype(?value)) = \'' . $customDatatypes[$universal['dataRange']] . '\' )';
}
} else {
$datatypeFilter = 'filter(str(datatype(?value)) = \'' . $universal['dataRange'] . '\')';
}
}
}
$sparql = new SparqlQuery($this->network);
$from = '';
foreach ($this->checkOnDatasets as $dataset) {
$from .= 'from <' . $dataset . '> ';
}
$sparql->mime("application/sparql-results+json")->query('select distinct ?value ?s
' . $from . '
where
{
?s a <' . $class . '> ;
<' . $universal['onProperty'] . '> ?value.
' . $datatypeFilter . '
}')->send();
if ($sparql->isSuccessful()) {
$results = json_decode($sparql->getResultset(), TRUE);
$values = array();
if (isset($results['results']['bindings']) && count($results['results']['bindings']) > 0) {
foreach ($results['results']['bindings'] as $result) {
$value = $result['value']['value'];
$s = '';
if (isset($result['s'])) {
$s = $result['s']['value'];
}
$values[] = array('value' => $value, 'type' => $universal['dataRange'], 'affectedRecord' => $s);
}
}
// For each value/type(s), we do validate that the range is valid
// We just need to get one triple where the value comply with the defined datatype
// to have this check validated
foreach ($values as $value) {
// First, check if we have a type defined for the value. If not, then we infer it is rdfs:Literal
if (empty($value['type'])) {
$value['type'] = array('http://www.w3.org/2000/01/rdf-schema#Literal');
}
// If then match, then we make sure that the value is valid according to the
// internal Check datatype validation tests
$datatypeValidationError = FALSE;
switch ($value['type']) {
case "http://www.w3.org/2001/XMLSchema#anySimpleType":
if (!$this->validateAnySimpleType($value['value'])) {
$datatypeValidationError = TRUE;
}
break;
case "http://www.w3.org/2001/XMLSchema#base64Binary":
if (!$this->validateBase64Binary($value['value'])) {
$datatypeValidationError = TRUE;
}
break;
case "http://www.w3.org/2001/XMLSchema#boolean":
if (!$this->validateBoolean($value['value'])) {
$datatypeValidationError = TRUE;
}
break;
case "http://www.w3.org/2001/XMLSchema#byte":
if (!$this->validateByte($value['value'])) {
$datatypeValidationError = TRUE;
}
break;
case "http://www.w3.org/2001/XMLSchema#dateTimeStamp":
if (!$this->validateDateTimeStampISO8601($value['value'])) {
$datatypeValidationError = TRUE;
}
break;
case "http://www.w3.org/2001/XMLSchema#dateTime":
if (!$this->validateDateTimeISO8601($value['value'])) {
$datatypeValidationError = TRUE;
}
break;
case "http://www.w3.org/2001/XMLSchema#decimal":
if (!$this->validateDecimal($value['value'])) {
$datatypeValidationError = TRUE;
}
break;
case "http://www.w3.org/2001/XMLSchema#double":
if (!$this->validateDouble($value['value'])) {
$datatypeValidationError = TRUE;
}
break;
case "http://www.w3.org/2001/XMLSchema#float":
if (!$this->validateFloat($value['value'])) {
$datatypeValidationError = TRUE;
}
break;
case "http://www.w3.org/2001/XMLSchema#hexBinary":
if (!$this->validateHexBinary($value['value'])) {
$datatypeValidationError = TRUE;
}
break;
case "http://www.w3.org/2001/XMLSchema#int":
if (!$this->validateInt($value['value'])) {
$datatypeValidationError = TRUE;
}
break;
case "http://www.w3.org/2001/XMLSchema#integer":
if (!$this->validateInteger($value['value'])) {
$datatypeValidationError = TRUE;
}
break;
case "http://www.w3.org/2001/XMLSchema#language":
if (!$this->validateLanguage($value['value'])) {
$datatypeValidationError = TRUE;
}
break;
case "http://www.w3.org/2001/XMLSchema#long":
if (!$this->validateLong($value['value'])) {
$datatypeValidationError = TRUE;
}
break;
case "http://www.w3.org/2001/XMLSchema#Name":
if (!$this->validateName($value['value'])) {
$datatypeValidationError = TRUE;
}
break;
case "http://www.w3.org/2001/XMLSchema#NCName":
if (!$this->validateNCName($value['value'])) {
$datatypeValidationError = TRUE;
}
break;
case "http://www.w3.org/2001/XMLSchema#negativeInteger":
if (!$this->validateNegativeInteger($value['value'])) {
$datatypeValidationError = TRUE;
}
break;
case "http://www.w3.org/2001/XMLSchema#NMTOKEN":
if (!$this->validateNMTOKEN($value['value'])) {
$datatypeValidationError = TRUE;
}
break;
case "http://www.w3.org/2001/XMLSchema#nonNegativeInteger":
if (!$this->validateNonNegativeInteger($value['value'])) {
$datatypeValidationError = TRUE;
}
break;
case "http://www.w3.org/2001/XMLSchema#nonPositiveInteger":
if (!$this->validateNonPositiveInteger($value['value'])) {
$datatypeValidationError = TRUE;
}
break;
case "http://www.w3.org/2001/XMLSchema#normalizedString":
if (!$this->validateNormalizedString($value['value'])) {
$datatypeValidationError = TRUE;
}
break;
case "http://www.w3.org/1999/02/22-rdf-syntax-ns#PlainLiteral":
if (!$this->validatePlainLiteral($value['value'])) {
$datatypeValidationError = TRUE;
}
break;
case "http://www.w3.org/2001/XMLSchema#positiveInteger":
if (!$this->validatePositiveInteger($value['value'])) {
$datatypeValidationError = TRUE;
}
break;
case "http://www.w3.org/2001/XMLSchema#short":
if (!$this->validateShort($value['value'])) {
$datatypeValidationError = TRUE;
}
break;
case "http://www.w3.org/2001/XMLSchema#string":
if (!$this->validateString($value['value'])) {
$datatypeValidationError = TRUE;
}
break;
case "http://www.w3.org/2001/XMLSchema#token":
if (!$this->validateToken($value['value'])) {
$datatypeValidationError = TRUE;
}
break;
case "http://www.w3.org/2001/XMLSchema#unsignedByte":
if (!$this->validateUnsignedByte($value['value'])) {
$datatypeValidationError = TRUE;
}
break;
case "http://www.w3.org/2001/XMLSchema#unsignedInt":
if (!$this->validateUnsignedInt($value['value'])) {
$datatypeValidationError = TRUE;
}
break;
case "http://www.w3.org/2001/XMLSchema#unsignedLong":
if (!$this->validateUnsignedLong($value['value'])) {
$datatypeValidationError = TRUE;
}
break;
case "http://www.w3.org/2001/XMLSchema#unsignedShort":
if (!$this->validateUnsignedShort($value['value'])) {
$datatypeValidationError = TRUE;
}
break;
case "http://www.w3.org/1999/02/22-rdf-syntax-ns#XMLLiteral":
if (!$this->validateXMLLiteral($value['value'])) {
$datatypeValidationError = TRUE;
}
break;
case "http://www.w3.org/2001/XMLSchema#anyURI":
if (!$this->validateAnyURI($value['value'])) {
$datatypeValidationError = TRUE;
}
break;
default:
// Custom type, try to validate it according to the
// description of that custom datatype within the
// ontology
if (!$this->validateCustomDatatype($value['type'], $value['value'])) {
$datatypeValidationError = TRUE;
}
break;
}
if ($datatypeValidationError === TRUE) {
cecho(' -> Couldn\'t validate that this value: "' . $value['value'] . '" belong to the datatype "' . $universal['dataRange'] . '"' . "\n", 'LIGHT_RED');
cecho(' -> Affected record: "' . $value['affectedRecord'] . '"' . "\n", 'YELLOW');
// If it doesn't match, then we report an error directly
$this->errors[] = array('id' => 'OWL-RESTRICTION-ONLY-102', 'type' => 'error', 'datatypeProperty' => $universal['onProperty'], 'expectedDatatype' => $universal['dataRange'], 'invalidValue' => $value['value'], 'affectedRecord' => $value['affectedRecord']);
}
}
} else {
cecho("We couldn't get the list of values for the {$datatypePropety} property\n", 'YELLOW');
$this->errors[] = array('id' => 'OWL-RESTRICTION-ONLY-54', 'type' => 'warning');
}
}
}
if (count($this->errors) <= 0) {
cecho("\n\n All records respects the universal restrictions cardinality specified in the ontologies...\n\n\n", 'LIGHT_GREEN');
}
} else {
cecho("No classes have any universal restriction cardinality defined in any ontologies. Move on to the next check...\n\n\n", 'LIGHT_GREEN');
}
} else {
cecho("We couldn't get the list of universal restriction from the structWSF instance\n", 'YELLOW');
// Error: can't get the list of retrictions
$this->errors[] = array('id' => 'OWL-RESTRICTION-ONLY-50', 'type' => 'warning');
}
// Check for universal restriction on Object Properties
$sparql = new SparqlQuery($this->network);
$from = '';
foreach ($this->checkOnDatasets as $dataset) {
$from .= 'from <' . $dataset . '> ';
}
foreach ($this->checkUsingOntologies as $ontology) {
$from .= 'from named <' . $ontology . '> ';
}
$sparql->mime("application/sparql-results+json")->query('select distinct ?restriction ?class ?onProperty ?classExpression
' . $from . '
where
{
?s a ?class.
graph ?g {
?class <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?restriction .
?restriction a <http://www.w3.org/2002/07/owl#Restriction> ;
<http://www.w3.org/2002/07/owl#onProperty> ?onProperty ;
<http://www.w3.org/2002/07/owl#allValuesFrom> ?classExpression .
?onProperty a <http://www.w3.org/2002/07/owl#ObjectProperty> .
}
}')->send();
if ($sparql->isSuccessful()) {
$results = json_decode($sparql->getResultset(), TRUE);
if (isset($results['results']['bindings']) && count($results['results']['bindings']) > 0) {
cecho("Here is the list of all the OWL universal restrictions defined for the classes currently used in the target datasets applied on object properties:\n\n", 'LIGHT_BLUE');
$universals = array();
foreach ($results['results']['bindings'] as $result) {
$class = $result['class']['value'];
$onProperty = $result['onProperty']['value'];
$classExpression = $result['classExpression']['value'];
cecho(' -> Record of type "' . $class . '" have an universal restriction when using object property "' . $onProperty . '"' . "\n", 'LIGHT_BLUE');
if (!isset($universals[$class])) {
$universals[$class] = array();
}
$universals[$class][] = array('onProperty' => $onProperty, 'classExpression' => $classExpression);
}
cecho("\n\n");
foreach ($universals as $class => $univs) {
foreach ($univs as $universal) {
$sparql = new SparqlQuery($this->network);
$from = '';
foreach ($this->checkOnDatasets as $dataset) {
$from .= 'from <' . $dataset . '> ';
}
foreach ($this->checkUsingOntologies as $ontology) {
$from .= 'from <' . $ontology . '> ';
}
$classExpressionFilter = '';
if (!empty($universal['classExpression']) && $universal['classExpression'] != 'http://www.w3.org/2002/07/owl#Thing') {
$subClasses = array($universal['classExpression']);
// Get all the classes that belong to the class expression defined in this restriction
$getSubClassesFunction = new GetSubClassesFunction();
$getSubClassesFunction->getClassesUris()->allSubClasses()->uri($universal['classExpression']);
$ontologyRead = new OntologyReadQuery($this->network);
$ontologyRead->ontology($this->getClassOntology($universal['classExpression']))->getSubClasses($getSubClassesFunction)->enableReasoner()->mime('resultset')->send();
if ($ontologyRead->isSuccessful()) {
$resultset = $ontologyRead->getResultset()->getResultset();
$subClasses = array_merge($subClasses, array_keys($resultset['unspecified']));
if (!empty($subClasses)) {
$filter = '';
foreach ($subClasses as $subClass) {
$filter .= ' str(?value_type) = "' . $subClass . '" ||';
}
$classExpressionFilter .= " filter(" . trim(trim($filter, '||')) . ") \n";
}
} else {
cecho("We couldn't get sub-classes of class expression from the structWSF instance\n", 'YELLOW');
// Error: can't get the subclasses of a target ontology
$this->errors[] = array('id' => 'OWL-RESTRICTION-ONLY-53', 'type' => 'warning');
}
}
$sparql->mime("application/sparql-results+json")->query('select ?s
' . $from . '
where
{
?s a <' . $class . '> .
?s <' . $universal['onProperty'] . '> ?value .
filter not exists {
?value a ?value_type .
' . $classExpressionFilter . '
}
}
')->send();
if ($sparql->isSuccessful()) {
$results = json_decode($sparql->getResultset(), TRUE);
if (isset($results['results']['bindings']) && count($results['results']['bindings']) > 0) {
foreach ($results['results']['bindings'] as $result) {
$subject = $result['s']['value'];
cecho(' -> record: ' . $subject . "\n", 'LIGHT_RED');
cecho(' -> property: ' . $universal['onProperty'] . "\n", 'LIGHT_RED');
$this->errors[] = array('id' => 'OWL-RESTRICTION-ONLY-101', 'type' => 'error', 'invalidRecordURI' => $subject, 'invalidPropertyURI' => $universal['onProperty'], 'classExpression' => $universal['classExpression']);
}
}
} else {
cecho("We couldn't check if the universal restriction was respected from the structWSF instance\n", 'YELLOW');
$this->errors[] = array('id' => 'OWL-RESTRICTION-ONLY-53', 'type' => 'warning');
}
}
if (count($this->errors) <= 0) {
cecho("\n\n All records respects the universal restrictions specified in the ontologies...\n\n\n", 'LIGHT_GREEN');
}
}
}
} else {
cecho("We couldn't get the number of object properties used per record from the structWSF instance\n", 'YELLOW');
// Error: can't get the number of object properties used per record
$this->errors[] = array('id' => 'OWL-RESTRICTION-ONLY-52', 'type' => 'warning');
}
}
public function run()
{
cecho("\n\n");
cecho("Data validation test: " . $this->description . "...\n\n", 'LIGHT_BLUE');
$sparql = new SparqlQuery($this->network);
$from = '';
foreach ($this->checkOnDatasets as $dataset) {
$from .= 'from named <' . $dataset . '> ';
}
foreach ($this->checkUsingOntologies as $ontology) {
$from .= 'from <' . $ontology . '> ';
}
// Get the list of all the object properties used within the datasets
$sparql->mime("application/sparql-results+json")->query('select distinct ?p ?range
' . $from . '
where
{
graph ?g {
?s ?p ?o .
filter(isIRI(?o))
}
optional
{
?p <http://www.w3.org/2000/01/rdf-schema#range> ?range .
}
filter(str(?p) != "http://purl.org/dc/terms/isPartOf" && str(?p) != "http://www.w3.org/1999/02/22-rdf-syntax-ns#value" && str(?p) != "http://www.w3.org/1999/02/22-rdf-syntax-ns#type")
}')->send();
if ($sparql->isSuccessful()) {
$results = json_decode($sparql->getResultset(), TRUE);
if (isset($results['results']['bindings']) && count($results['results']['bindings']) > 0) {
$objectProperties = array();
$thereAreEmptyRanges = FALSE;
foreach ($results['results']['bindings'] as $result) {
$objectProperty = $result['p']['value'];
$objectProperties[$objectProperty] = '';
if (isset($result['range'])) {
$objectProperties[$objectProperty] = $result['range']['value'];
} else {
$thereAreEmptyRanges = TRUE;
}
}
// Display warnings
if ($thereAreEmptyRanges) {
cecho("The following object properties are used to describe records, but their range is not specified in the ontologies. owl:Thing is assumed as the range, but you may want to define it further and re-run this check:\n", 'YELLOW');
foreach ($objectProperties as $objectProperty => $range) {
if (empty($range)) {
cecho(' -> object property: ' . $objectProperty . "\n", 'YELLOW');
$this->errors[] = array('id' => 'OBJECT-PROPERTIES-RANGE-50', 'type' => 'warning', 'objectProperty' => $objectProperty);
}
}
}
// Now, for each object properties that have a range defined,
// we:
//
// (a) List all values used for a given property
// (b) For each of these values, make sure they comply with what is defined in the ontology as
// the range of the
foreach ($objectProperties as $objectProperty => $range) {
// If the range is empty, we consider it owl:Thing.
// If the range is owl:Thing, then we simply skip this check since everything is an owl:Thing
if (!empty($range) && $range != 'http://www.w3.org/2002/07/owl#Thing') {
$values = array();
$sparql = new SparqlQuery($this->network);
$from = '';
foreach ($this->checkOnDatasets as $dataset) {
$from .= 'from <' . $dataset . '> ';
$from .= 'from named <' . $dataset . '> ';
}
foreach ($this->checkUsingOntologies as $ontology) {
$from .= 'from <' . $ontology . '> ';
}
$sparql->mime("application/sparql-results+json")->query('select distinct ?value ?value_type
' . $from . '
where
{
graph ?g {
?s <' . $objectProperty . '> ?value.
filter(isIRI(?value))
}
optional
{
?value a ?value_type
}
}')->send();
if ($sparql->isSuccessful()) {
// Create the array of object-values/types
$results = json_decode($sparql->getResultset(), TRUE);
if (isset($results['results']['bindings']) && count($results['results']['bindings']) > 0) {
foreach ($results['results']['bindings'] as $result) {
$value = $result['value']['value'];
$type = '';
if (isset($result['value_type'])) {
$type = $result['value_type']['value'];
}
if (!isset($values[$value])) {
$values[$value] = array();
}
if (!empty($type) && !in_array($type, $values[$value])) {
$values[$value][] = $type;
}
}
}
// For each value/type(s), we do validate that the range is valid
foreach ($values as $value => $types) {
// First, check if we have a type defined for the value. If not, then we infer it is owl:Thing
if (empty($types)) {
$types = array('http://www.w3.org/2002/07/owl#Thing');
}
// Then, check if the $range and the $types directly match
if (in_array($range, $types)) {
continue;
} else {
// If they are not, then we check in the ontology to see if the range is not
// one of the super class of one of the type(s)
$superClasses = array();
foreach ($types as $type) {
$ontologyURI = $this->getTypeOntology($type);
if ($ontologyURI !== FALSE) {
$ontologyRead = new OntologyReadQuery($this->network);
$getSuperClassesFunc = new GetSuperClassesFunction();
$getSuperClassesFunc->allSuperClasses()->getClassesUris()->uri($type);
$ontologyRead->enableReasoner()->ontology($ontologyURI)->getSuperClasses($getSuperClassesFunc)->mime('resultset')->send();
if ($ontologyRead->isSuccessful()) {
$scs = $ontologyRead->getResultset()->getResultset();
// If empty, then there is no super-classes
if (!empty($scs)) {
$scs = $scs[key($scs)];
foreach ($scs as $superClass => $description) {
if (!in_array($superClass, $superClasses)) {
$superClasses[] = $superClass;
}
}
}
} else {
cecho("We couldn't get the list of super-classes of a target type from the structWSF instance\n", 'YELLOW');
// Log a warning
// Can't get the super classes of the target type
$this->errors[] = array('id' => 'OBJECT-PROPERTIES-RANGE-51', 'type' => 'warning', 'objectProperty' => $objectProperty);
}
} else {
cecho("We couldn't find the ontology where the {$type} is defined on the structWSF instance\n", 'YELLOW');
// Log a warning
// Can't find ontology where the type $type is defined
$this->errors[] = array('id' => 'OBJECT-PROPERTIES-RANGE-52', 'type' => 'warning', 'objectProperty' => $objectProperty);
}
}
$rangeMatch = FALSE;
foreach ($superClasses as $superClass) {
if ($superClass == $range) {
$rangeMatch = TRUE;
break;
}
}
if (!$rangeMatch) {
// Log an error
// Couldn't match one of the super classe with the specified range
cecho(' -> Object property "' . $objectProperty . '" doesn\'t match range "' . $range . '" for value "' . $value . '"' . "\n", 'LIGHT_RED');
$this->errors[] = array('id' => 'OBJECT-PROPERTIES-RANGE-100', 'type' => 'error', 'objectProperty' => $objectProperty, 'definedRange' => $range, 'value' => $value, 'valueTypes' => $types, 'valueSuperTypes' => $superClasses, 'affectedRecords' => $this->getAffectedRecords($objectProperty, $value));
}
}
}
} else {
cecho("We couldn't get the range of the {$objectProperty} object property from the structWSF instance\n", 'YELLOW');
$this->errors[] = array('id' => 'OBJECT-PROPERTIES-RANGE-54', 'type' => 'warning');
}
}
}
}
} else {
cecho("We couldn't get the list of object properties from the structWSF instance\n", 'YELLOW');
$this->errors[] = array('id' => 'OBJECT-PROPERTIES-RANGE-53', 'type' => 'warning');
}
}
function generateStructures($folder, $structwsf, $queryExtension = NULL)
{
include_once 'getLoadedOntologies.php';
cecho("Generating derivate ontological structures...\n", 'CYAN');
$ontologiesClustered = getLoadedOntologies($structwsf);
$ontologies = array();
$ontologies = array_merge($ontologies, $ontologiesClustered['local'], $ontologiesClustered['reference'], $ontologiesClustered['admin']);
// Generate the ironXML schemas
foreach ($ontologies as $ontology) {
cecho("Generating ironXML schema of the " . $ontology['label'] . " ontology...\n", 'CYAN');
$ontologyRead = new OntologyReadQuery($structwsf);
$ontologyRead->ontology($ontology['uri'])->getIronXMLSchema()->send($queryExtension !== NULL ? $queryExtension : NULL);
if ($ontologyRead->isSuccessful()) {
$resultset = $ontologyRead->getResultset()->getResultset();
$ironXML = $resultset['unspecified'][$ontology['uri']]['http://purl.org/ontology/wsf#serializedIronXMLSchema']['0']['value'];
cecho("Generated...\n", 'CYAN');
$filename = substr($ontology['uri'], strripos($ontology['uri'], "/") + 1);
$filename = substr($filename, 0, strripos($filename, "."));
file_put_contents(rtrim($folder, '/') . '/' . $filename . '.xml', $ironXML);
cecho("Saved to: " . rtrim($folder, '/') . '/' . $filename . '.xml' . "\n", 'CYAN');
} else {
$debugFile = md5(microtime()) . '.error';
file_put_contents('/tmp/' . $debugFile, var_export($ontologyRead, TRUE));
@cecho('Can\'t get the ironXML schema structure for this ontology: ' . $ontology . '. ' . $ontologyRead->getStatusMessage() . $ontologyRead->getStatusMessageDescription() . "\nDebug file: /tmp/{$debugFile}\n", 'RED');
continue;
}
}
// Generate the ironJSON schemas
foreach ($ontologies as $ontology) {
cecho("Generating ironJSON schema of the " . $ontology['label'] . " ontology...\n", 'CYAN');
$ontologyRead = new OntologyReadQuery($structwsf);
$ontologyRead->ontology($ontology['uri'])->getIronJsonSchema()->send($queryExtension !== NULL ? $queryExtension : NULL);
if ($ontologyRead->isSuccessful()) {
$resultset = $ontologyRead->getResultset()->getResultset();
$ironJSON = $resultset['unspecified'][$ontology['uri']]['http://purl.org/ontology/wsf#serializedIronJSONSchema']['0']['value'];
cecho("Generated...\n", 'CYAN');
$filename = substr($ontology['uri'], strripos($ontology['uri'], "/") + 1);
$filename = substr($filename, 0, strripos($filename, "."));
file_put_contents(rtrim($folder, '/') . '/' . $filename . '.json', $ironJSON);
cecho("Saved to: " . rtrim($folder, '/') . '/' . $filename . '.json' . "\n", 'CYAN');
// Create the pre-existing JS script to load that schema in a Schema object.
$ironJSONSchema = 'var ' . $filename . '_schema_srz = ' . $ironJSON . ";";
$ironJSONSchema .= 'var ' . $filename . '_schema = new Schema(' . $filename . '_schema_srz);';
// Special handling: make sure to convert all "%5C" characters into "\". This has to be done because
// of the way the ProcessorXML.php (so, the DOMDocument API) works, and how the xml-encoding currently
// works. Enventually, we should use the simplexml API in the processorXML script to properly
// manage the encoding, and decoding of the XML data, *AND* of the HTML entities (it is the HTML
// entities that are strangely manipulated in the DOMDocument API).
$ironJSONSchema = str_replace("%5C", '\\', $ironJSONSchema);
file_put_contents(rtrim($folder, "/") . "/" . $filename . ".js", $ironJSONSchema);
cecho("Saved to: " . rtrim($folder, '/') . '/' . $filename . '.js' . "\n", 'CYAN');
} else {
$debugFile = md5(microtime()) . '.error';
file_put_contents('/tmp/' . $debugFile, var_export($ontologyRead, TRUE));
@cecho('Can\'t get the ironJSON schema structure for this ontology: ' . $ontology . '. ' . $ontologyRead->getStatusMessage() . $ontologyRead->getStatusMessageDescription() . "\nDebug file: /tmp/{$debugFile}\n", 'RED');
continue;
}
}
// Create the JS schema file.
$schemaJS = ' /* List of attribute URIs that are generally used for labeling entities in different ontologies */
var prefLabelAttributes = [
"http://www.w3.org/2004/02/skos/core#prefLabel",
"http://purl.org/ontology/iron#prefLabel",
"http://umbel.org/umbel#prefLabel",
"http://purl.org/dc/terms/title",
"http://purl.org/dc/elements/1.1/title",
"http://xmlns.com/foaf/0.1/name",
"http://xmlns.com/foaf/0.1/givenName",
"http://xmlns.com/foaf/0.1/family_name",
"http://www.geonames.org/ontology#name",
"http://www.w3.org/2000/01/rdf-schema#label"
];
var altLabelAttributes = [
"http://www.w3.org/2004/02/skos/core#altLabel",
"http://purl.org/ontology/iron#altLabel",
"http://umbel.org/umbel#altLabel",
];
var descriptionAttributes = [
"http://purl.org/ontology/iron#description",
"http://www.w3.org/2000/01/rdf-schema#comment",
"http://purl.org/dc/terms/description",
"http://purl.org/dc/elements/1.1/description",
"http://www.w3.org/2004/02/skos/core#definition"
];
function Schema(sjson)
{
// Define all prefixes of this resultset
this.prefixes = sjson.schema.prefixList;
// Unprefixize all URIs of this Schema
var resultsetJsonText = JSON.stringify(sjson);
for(var prefix in this.prefixes)
{
if(this.prefixes.hasOwnProperty(prefix))
{
var pattern = new RegExp(prefix+"_", "igm");
resultsetJsonText = resultsetJsonText.replace(pattern, this.prefixes[prefix]);
}
}
sjson = JSON.parse(resultsetJsonText);
this.attributes = sjson.schema.attributeList;
this.types = sjson.schema.typeList;
// Extend all attributes of this schema with additional functions
for(var i = 0; i < this.attributes.length; i++)
{
this.attributes[i].prefixes = this.prefixes;
}
// Extend all types of this schema with additional functions
for(var i = 0; i < this.types.length; i++)
{
this.types[i].prefixes = this.prefixes;
}
}';
file_put_contents(rtrim($folder, "/") . "/schema.js", $schemaJS);
// Generate PHP serialized classes hierarchy
cecho("Generating PHP serialized classes hierarchy structure file...\n", 'CYAN');
$ontologyRead = new OntologyReadQuery($structwsf);
$ontologyRead->getSerializedClassHierarchy()->send($queryExtension !== NULL ? $queryExtension : NULL);
if ($ontologyRead->isSuccessful()) {
$resultset = $ontologyRead->getResultset()->getResultset();
$ironXML = $resultset['unspecified'][""]['http://purl.org/ontology/wsf#serializedClassHierarchy']['0']['value'];
cecho("Generated...\n", 'CYAN');
file_put_contents(rtrim($folder, '/') . '/classHierarchySerialized.srz', $ironXML);
cecho("Saved to: " . rtrim($folder, '/') . '/classHierarchySerialized.srz' . "\n", 'CYAN');
} else {
$debugFile = md5(microtime()) . '.error';
file_put_contents('/tmp/' . $debugFile, var_export($ontologyRead, TRUE));
@cecho('Can\'t get the PHP serialized classes hierarchy structure file' . $ontologyRead->getStatusMessage() . $ontologyRead->getStatusMessageDescription() . "\nDebug file: /tmp/{$debugFile}\n", 'RED');
}
// Generate PHP serialized properties hierarchy
cecho("Generating PHP serialized properties hierarchy structure file...\n", 'CYAN');
$ontologyRead = new OntologyReadQuery($structwsf);
$ontologyRead->getSerializedPropertyHierarchy()->send($queryExtension !== NULL ? $queryExtension : NULL);
if ($ontologyRead->isSuccessful()) {
$resultset = $ontologyRead->getResultset()->getResultset();
$ironXML = $resultset['unspecified'][""]['http://purl.org/ontology/wsf#serializedPropertyHierarchy']['0']['value'];
cecho("Generated...\n", 'CYAN');
file_put_contents(rtrim($folder, '/') . '/propertyHierarchySerialized.srz', $ironXML);
cecho("Saved to: " . rtrim($folder, '/') . '/propertyHierarchySerialized.srz' . "\n", 'CYAN');
} else {
$debugFile = md5(microtime()) . '.error';
file_put_contents('/tmp/' . $debugFile, var_export($ontologyRead, TRUE));
@cecho('Can\'t get the PHP serialized properties hierarchy structure file' . $ontologyRead->getStatusMessage() . $ontologyRead->getStatusMessageDescription() . "\nDebug file: /tmp/{$debugFile}\n", 'RED');
}
cecho("All structures generates!\n", 'CYAN');
}
