/**
* Perform the load.
*
* @param EasyRdf_Graph $chunk
* @return void
*/
public function execute(&$chunk)
{
if (!$chunk->isEmpty()) {
// Don't use EasyRdf's ntriple serializer, as something might be wrong with its unicode byte characters
// After serializing with semsol/arc and easyrdf, the output looks the same (with unicode characters), but after a
// binary utf-8 conversion (see $this->serialize()) the outcome is very different, leaving easyrdf's encoding completely different
// from the original utf-8 characters, and the semsol/arc encoding correct as the original.
$ttl = $chunk->serialise('turtle');
$arc_parser = \ARC2::getTurtleParser();
$ser = \ARC2::getNTriplesSerializer();
$arc_parser->parse('', $ttl);
$triples = $ser->getSerializedTriples($arc_parser->getTriples());
preg_match_all("/(<.*\\.)/", $triples, $matches);
if ($matches[0]) {
$this->buffer = array_merge($this->buffer, $matches[0]);
}
$triple_count = count($matches[0]);
$this->log("Added {$triple_count} triples to the load buffer.");
while (count($this->buffer) >= $this->loader->buffer_size) {
// Log the time it takes to load the triples into the store
$start = microtime(true);
$buffer_size = $this->loader->buffer_size;
$triples_to_send = array_slice($this->buffer, 0, $buffer_size);
$this->addTriples($triples_to_send);
$this->buffer = array_slice($this->buffer, $buffer_size);
$duration = round((microtime(true) - $start) * 1000, 2);
$this->log("Took {$buffer_size} triples from the load buffer, loading them took {$duration} ms.");
}
}
}
function extractLinkedData($link, $origin)
{
global $ep;
// Wenn es die URL im Graph schon gibt, nichts machen, TODO besser updaten?
if (graphContainsUrl($link)) {
$res = new Response(null, "URL {$link} already visited, skip indexing");
return res;
} else {
$parser = ARC2::getTurtleParser();
//$data = $_POST['turtle'];
$parser->parse($link);
$triples = $parser->getTriples();
// print_r($triples);
// Wenn keine Tripel gefunden wurden
if (count($triples) < 1) {
$res = new Response(null, "URL {$link} contains no triples");
} else {
// in Datenbank einfügen
$ep->insert($triples, $origin);
//echo "<pre>";
//print_r($triples);
//echo "</pre>";
$res = new Response(null, "URL {$link}: added " . count($triples) . " triples");
}
return $res;
}
}
public function __construct($a = '')
{
parent::__construct();
$this->a = $a;
/* parse the before and after graphs if necessary*/
foreach (array('before', 'after', 'before_rdfxml', 'after_rdfxml') as $rdf) {
if (!empty($a[$rdf])) {
if (is_string($a[$rdf])) {
/** @var \ARC2_RDFParser $parser */
$parser = \ARC2::getRDFParser();
$parser->parse(false, $a[$rdf]);
$a[$rdf] = $parser->getSimpleIndex(0);
} else {
if (is_array($a[$rdf]) and isset($a[$rdf][0]) and isset($a[$rdf][0]['s'])) {
//triples array
/** @var \ARC2_RDFSerializer $ser */
$ser = \ARC2::getTurtleSerializer();
/** @var string $turtle */
$turtle = $ser->getSerializedTriples($a[$rdf]);
/** @var \ARC2_RDFParser $parser */
$parser = \ARC2::getTurtleParser();
$parser->parse(false, $turtle);
$a[$rdf] = $parser->getSimpleIndex(0);
}
}
$nrdf = str_replace('_rdfxml', '', $rdf);
$this->{$nrdf} = $a[$rdf];
}
}
$this->__init();
}
function __construct( $importdata, $dataformat ) {
global $rdfiogExtraNSPrefixes,
$rdfiogPropertiesToUseAsWikiTitle,
$rdfiogUseNSPrefixInWikiTitleForProperties,
$rdfiogUseNSPrefixInWikiTitleForEntities;
if ( $dataformat == 'triples_array' ) {
$this->m_triples = $importdata;
} else {
$this->m_unparseddata = $importdata;
}
$this->m_dataformat = $dataformat;
$this->m_haserrors = false;
$this->m_delete = false;
if ( $this->m_dataformat == 'rdfxml' ) {
$this->m_unparseddata = $this->cleanupXML( $this->m_unparseddata );
$this->m_parser = ARC2::getRDFXMLParser();
$this->parse();
} elseif ( $this->m_dataformat == 'turtle' ) {
$this->m_unparseddata = $wgRequest->getText( 'importdata' );
$this->m_parser = ARC2::getTurtleParser();
$this->parse();
}
$this->extractTripleIndex();
$this->m_nsprefixes = $this->getNSPrefixMappingFromParser();
if ( $rdfiogExtraNSPrefixes != '' ) {
$this->addNamespacePrefixes( $rdfiogExtraNSPrefixes );
}
$nsprefixes = $this->m_nsprefixes;
$this->setNSPrefixes( $nsprefixes );
$this->setTripleIndex( $this->m_tripleindex );
// Previously in Equiv URI Class
if ( isset($rdfiogUsePseudoNamespacesForProperties) ) { // TODO: Change to check options from import screen
// use parameter set in LocalSettings.php
$this->m_usenspintitles_properties = $rdfiogUsePseudoNamespacesForProperties;
}
if ( isset($rdfiogUsePseudoNamespacesForEntities) ) {
// use parameter set in LocalSettings.php
$this->m_usenspintitles_entities = $rdfiogUsePseudoNamespacesForEntities;
}
if ( !empty( $rdfiogPropertiesToUseAsWikiTitle ) ) {
$this->m_wikititlepropertyuris = $rdfiogPropertiesToUseAsWikiTitle;
} else {
$this->m_wikititlepropertyuris = array(
'http://semantic-mediawiki.org/swivt/1.0#page', // Suggestion for new property
'http://www.w3.org/2000/01/rdf-schema#label',
'http://purl.org/dc/elements/1.1/title',
'http://www.w3.org/2004/02/skos/core#preferredLabel',
'http://xmlns.com/foaf/0.1/name'
);
}
$this->m_store = new RDFIOStore();
}
/**
* Import RDF/XML, e.g. from the RDF Import Special Page.
* @param string $importData
*/
public function importTurtle($importData)
{
// Parse RDF/XML to triples
$arc2turtleparser = ARC2::getTurtleParser($importData);
$arc2turtleparser->parseData($importData);
// Receive the data
$triples = $arc2turtleparser->triples;
$tripleIndex = $arc2turtleparser->getSimpleIndex();
$namespaces = $arc2turtleparser->nsp;
/* DEBUGGING
echo "*** Triples ***";
echo( print_r( $triples, true ));
echo "*** Triple index ***";
echo( print_r( $tripleIndex, true ));
echo "*** Namespaces ***";
echo( print_r( $namespaces, true ));
*/
$this->importFromArc2Data($triples, $tripleIndex, $namespaces);
return $output = array('triples' => $triples, 'tripleIndex' => $tripleIndex, 'namespaces' => $namespaces);
}
public function load($uri, $aliases = array(), $map = array())
{
$this->forceString($uri);
$uri = $this->expandURI($uri);
if (substr($uri, 0, 5) == "data:") {
$data = urldecode(preg_replace("/^data:[^,]*,/", "", $uri));
$parser = ARC2::getTurtleParser();
$parser->parse($uri, $data);
} else {
if (isset($this->loaded[$uri])) {
return $this->loaded[$uri];
}
if (isset($this->cacheDir)) {
$filename = $this->cacheDir . "/" . md5($uri);
if (!file_exists($filename) || filemtime($filename) + $this->cacheAge < time()) {
# decache if out of date, even if we fail to re cache.
if (file_exists($filename)) {
unlink($filename);
}
$url = $uri;
$ttl = 16;
$mime = "";
$old_user_agent = ini_get('user_agent');
ini_set('user_agent', "PHP\r\nAccept: application/rdf+xml");
while ($ttl > 0) {
# dirty hack to set the accept header without using curl
if (!($rdf_fp = fopen($url, 'r'))) {
break;
}
$meta_data = stream_get_meta_data($rdf_fp);
$redir = 0;
foreach ($meta_data['wrapper_data'] as $response) {
if (substr(strtolower($response), 0, 10) == 'location: ') {
$newurl = substr($response, 10);
if (substr($newurl, 0, 1) == "/") {
$parts = preg_split("/\\//", $url);
$newurl = $parts[0] . "//" . $parts[2] . $newurl;
}
$url = $newurl;
$redir = 1;
}
if (substr(strtolower($response), 0, 14) == 'content-type: ') {
$mime = preg_replace("/\\s*;.*\$/", "", substr($response, 14));
}
}
if (!$redir) {
break;
}
$ttl--;
fclose($rdf_fp);
}
ini_set('user_agent', $old_user_agent);
if ($ttl > 0 && $mime == "application/rdf+xml" && $rdf_fp) {
# candidate for caching!
if (!($cache_fp = fopen($filename, 'w'))) {
echo "Cannot write file ({$filename})";
exit;
}
while (!feof($rdf_fp)) {
fwrite($cache_fp, fread($rdf_fp, 8192));
}
fclose($cache_fp);
}
fclose($rdf_fp);
}
}
if (isset($filename) && file_exists($filename)) {
$parser = ARC2::getRDFXMLParser();
$parser->parse($filename);
} else {
$parser = ARC2::getRDFParser();
# Don't try to load the same URI twice!
if (!isset($this->firstGraphURI)) {
$this->firstGraphURI = $uri;
}
$parser->parse($uri);
}
}
$errors = $parser->getErrors();
$parser->resetErrors();
if (sizeof($errors)) {
if ($this->debug) {
print "<h3>Error loading: {$uri}</h3>";
print "<ul><li>" . join("</li><li>", $errors) . "</li></ul>";
}
return 0;
}
$triples = $parser->getTriples();
foreach ($triples as $t) {
$t["s"] = $this->cleanURI($t["s"]);
if (!isset($map[$t["s"]])) {
continue;
}
$t["p"] = $this->cleanURI($t["p"]);
if ($t["p"] != "http://www.w3.org/2002/07/owl#sameAs") {
continue;
}
$aliases[$t["o"]] = $t["s"];
}
foreach ($triples as $t) {
$t["s"] = $this->cleanURI($t["s"]);
$t["p"] = $this->cleanURI($t["p"]);
/*
if( $t["o_type"]=="literal" )
{
$t["o_dataype"] = $this->cleanURI($t["o_datatype"]);
$this->t["sp"][$t["s"]][$t["p"]][] = array(
"v"=>$t["o"],
"d"=>$t["o_datatype"],
"l"=>$t["o_lang"] );
}
else
{
$t["o"] = $this->cleanURI($t["o"]);
$this->t["sp"][$t["s"]][$t["p"]][] = $t["o"];
}
$this->t["op"][$t["o"]][$t["p"]][] = $t["s"];
if( $alias )
{
*/
$mod = 0;
if (isset($aliases[$t["s"]])) {
$t["s"] = $aliases[$t["s"]];
}
if (isset($aliases[$t["p"]])) {
$t["p"] = $aliases[$t["p"]];
}
if (isset($aliases[$t["o"]])) {
$t["o"] = $aliases[$t["o"]];
}
// if( $mod )
// {
if ($t["o_type"] == "literal") {
$this->t["sp"][$t["s"]][$t["p"]][] = array("v" => $t["o"], "d" => $t["o_datatype"], "l" => $t["o_lang"]);
} else {
$this->t["sp"][$t["s"]][$t["p"]][] = $t["o"];
}
$this->t["op"][$t["o"]][$t["p"]][] = $t["s"];
// }
// }
}
$this->loaded[$uri] = sizeof($triples);
return $this->loaded[$uri];
}
function getFilledTemplate($t, $vals, $g = '')
{
$parser = ARC2::getTurtleParser();
$parser->parse($g, $this->getTurtleHead() . $t);
return $parser->getSimpleIndex(0, $vals);
}
public function run()
{
set_time_limit(0);
error_reporting(E_ERROR);
if (is_file(FILE)) {
echo "There is an existing " . FILE . " file on this installation. Please remove it before importing a new one";
exit(0);
}
if (!isset($_GET['import']) && !isset($_POST['importtext'])) {
$this->showInterface();
exit(0);
}
if (!is_writable('.')) {
echo 'The webserver needs write permissions in "lodspeakr/" "lodspeakr/models/" and "lodspeakr/views/" dirs to import settings.';
exit(0);
}
echo $this->external_basedir;
include_once 'lib/arc2/ARC2.php';
$parser = ARC2::getTurtleParser();
if (isset($_GET['import'])) {
$parser->parse($_GET['import']);
$this->external_basedir = str_replace('export', '', $_GET['import']);
} elseif (isset($_POST['importtext'])) {
$parser->parse(RDF, $_POST['importtext']);
} else {
HTTPStatus::send500();
exit(0);
}
$triples = $parser->getTriples();
$appArr = $this->search($triples, null, RDF . 'type', LS . 'Application');
if (!(sizeof($appArr) > 0)) {
echo "I can't find an application from the URL given";
exit(0);
}
$app = $appArr[0]['s'];
$this->external_basedir = $app;
$compArr = $this->search($triples, null, SKOS . 'broader', $app);
$content = "<?\n\$conf['debug'] = false;\n\$conf['mirror_external_uris'] = true;\n\n";
$this->basedir = preg_replace('/import$/', '', !empty($_SERVER['HTTPS']) ? "https://" . $_SERVER['SERVER_NAME'] . $_SERVER['REQUEST_URI'] : "http://" . $_SERVER['SERVER_NAME'] . $_SERVER['REQUEST_URI']);
//$arr = explode("lodspeakr/benegesserit", $this->basedir);
//$this->basedir = $arr[0];
$content .= "\$conf['basedir'] = \"{$this->basedir}\";\n";
$content .= "\$conf['parentApp'] = \"{$app}\";\n";
$pwd = getcwd();
$content .= "\$conf['home'] = \"{$pwd}/\";\n";
//App params
$q = $this->search($triples, $app, LS . 'usedParameter', null);
$appParams = array();
foreach ($q as $p) {
$param = $p['o'];
$labelArr = $this->search($triples, $param, RDFS . 'label', null);
$label = $labelArr[0]['o'];
$format = $this->search($triples, $param, DC . 'hasFormat', null);
$cntArr = $this->search($triples, $format[0]['o'], CNT . 'chars', null);
$cnt = $cntArr[0]['o'];
$appParams[$label] = $cnt;
}
foreach ($appParams as $k => $v) {
$content .= "\$conf['{$k}'] = \"{$v}\";\n";
}
$content .= "/*ATTENTION: By default this application is available to\n * be exported and copied (its configuration)\n * by others. If you do not want that, \n * turn the next option as false\n */ \n\$conf['export'] = true;\n\n";
//Components
foreach ($compArr as $v) {
$component = $v['s'];
$componentTypeArr = $this->search($triples, $component, RDF . 'type', null);
$compType = $componentTypeArr[0]['o'];
$params = array();
$q = $this->search($triples, $component, LS . 'usedParameter', null);
foreach ($q as $p) {
$param = $p['o'];
$labelArr = $this->search($triples, $param, RDFS . 'label', null);
$label = $labelArr[0]['o'];
$format = $this->search($triples, $param, DC . 'hasFormat', null);
$cntArr = $this->search($triples, $format[0]['o'], CNT . 'chars', null);
$cnt = $cntArr[0]['o'];
$params[$label] = $cnt;
}
$inputs = array();
$q = $this->search($triples, $component, LS . 'usedInput', null);
foreach ($q as $p) {
$param = $p['o'];
$labelArr = $this->search($triples, $param, RDFS . 'label', null);
if (sizeof($labelArr) > 0) {
$label = $labelArr[0]['o'];
$format = $this->search($triples, $param, DC . 'hasFormat', null);
$cntArr = $this->search($triples, $format[0]['o'], CNT . 'chars', null);
$cnt = $cntArr[0]['o'];
$inputs[$label] = $cnt;
}
}
if ($compType == LS . "LodspeakrEndpointManagerComponent") {
$content .= $this->createEndpoints($params);
} elseif ($compType == LS . "LodspeakrNamespaceManagerComponent") {
$content .= $this->createNamespaces($params);
} elseif ($compType == LS . "LodspeakrSparqlEndpointRetriever") {
$this->createModels($inputs);
} elseif ($compType == LS . "LodspeakrStaticElementsComponent") {
$this->createStatics($inputs);
} elseif ($compType == LS . "LodspeakrVisualComponent") {
$this->createViews($inputs);
} else {
if ($conf['debug']) {
Logging::log("Component '{$component}' (of type {$compType}) not supported", E_USER_WARNING);
}
}
}
$content .= "?>\n";
try {
$fh = fopen(FILE, 'a');
fwrite($fh, $content);
fclose($fh);
} catch (Exception $e) {
echo 'Caught exception while writing settings: ', $e->getMessage(), "\n";
exit(1);
}
$this->showFinishing();
}
/**
* Store triples into our local store
*
* @param integer $id The id of the configured semantic source
* @param array $config The configuration needed to extract the triples
*/
public function cacheTriples($id, array $config)
{
// Fetch the ARC2 triplestore
$store = $this->setUpArc2Store();
// Fetch the data extractor for the given type
$type = $config['type'];
$source_type = strtolower($type);
$graph = '';
$caching_necessary = true;
switch ($source_type) {
case 'turtle':
$rdf_reader = \App::make('\\Tdt\\Core\\DataControllers\\RDFController');
$configuration = array('uri' => $config['uri'], 'format' => 'turtle');
$data = $rdf_reader->readData($configuration, array());
$graph = $data->data;
break;
case 'rdf':
$rdf_reader = \App::make('\\Tdt\\Core\\DataControllers\\RDFController');
$configuration = array('uri' => $config['uri'], 'format' => 'xml');
$data = $rdf_reader->readData($configuration, array());
$graph = $data->data;
break;
case 'sparql':
// Do nothing, the sparql endpoint is already optimized for read operations
$caching_necessary = false;
break;
case 'ldf':
// Do nothing the ldf endpoint is a queryable endpoint itself
$caching_necessary = false;
break;
default:
\App::abort(400, "The source type, {$source_type}, was configured, but no reader has been found\n to extract semantic data from it.");
break;
}
// If the semantic source needs caching in our local store@
if ($caching_necessary) {
// Make the graph name to cache the triples into
$graph_name = self::$graph_name . $id;
// Serialise the triples into a turtle string
$ttl = $graph->serialise('turtle');
// Parse the turtle into an ARC graph
$arc_parser = \ARC2::getTurtleParser();
$ser = \ARC2::getNTriplesSerializer();
// Parse the turtle string
$arc_parser->parse('', $ttl);
// Serialize the triples again, this is because an EasyRdf_Graph has
// troubles with serializing some unicode characters. The underlying bytes are
// not properly converted to utf8
// A dump shows that all unicode encodings through serialization are the same (in easyrdf and arc)
// however when we convert the string (binary) into a utf8, only the arc2 serialization
// comes out correctly, hence something beneath the encoding (byte sequences?) must hold some wrongs in the EasyRdf library.
$triples = $ser->getSerializedTriples($arc_parser->getTriples());
preg_match_all("/(<.*\\.)/", $triples, $matches);
$triples_buffer = array();
if ($matches[0]) {
$triples_buffer = $matches[0];
}
\Log::info("--------------- CACHING TRIPLES -------------------------");
\Log::info("Starting insertion of triples into the ARC2 RDF Store into the graph with the name " . $graph_name);
// Insert the triples in a chunked manner (not all triples at once)
$buffer_size = 20;
while (count($triples_buffer) >= $buffer_size) {
$triples_to_cache = array_slice($triples_buffer, 0, $buffer_size);
\Log::info("Caching " . count($triples_to_cache) . " triples into the store.");
$this->addTriples($graph_name, $triples_to_cache, $store);
$triples_buffer = array_slice($triples_buffer, $buffer_size);
}
// Insert the last triples in the buffer
\Log::info("Caching " . count($triples_buffer) . " triples into the store.");
$this->addTriples($graph_name, $triples_buffer, $store);
\Log::info("--------------- DONE CACHING TRIPLES -------------------");
}
}
//this is a workaround while its being fixed in ARC2
$ch = curl_init();
curl_setopt($ch, CURLOPT_URL, $u);
curl_setopt($ch, CURLOPT_FOLLOWLOCATION, true);
curl_setopt($ch, CURLOPT_MAXREDIRS, 10);
curl_setopt($ch, CURLOPT_HTTPHEADER, array("Accept: text/turtle, text/n3; q=0.9, application/turtle; q=0.8, application/n-triples; q=0.7, application/rdf+xml; q=0.6, application/json; q=0.4, */*; q=0.1"));
curl_setopt($ch, CURLOPT_RETURNTRANSFER, 1);
$data = curl_exec($ch);
$_aux = curl_getinfo($ch, CURLINFO_CONTENT_TYPE);
$_aux2 = explode(";", $_aux);
$content_type = array_shift($_aux2);
curl_close($ch);
$parser = NULL;
$parsers = array();
$parsers[0]['formats'] = array('text/n3', 'application/x-turtle', 'application/turtle', 'text/turtle');
$parsers[0]['parser'] = ARC2::getTurtleParser();
$parsers[1]['formats'] = array('application/rdf+xml');
$parsers[1]['parser'] = ARC2::getRDFXMLParser();
$parsers[2]['formats'] = array('application/json', 'application/x-javascript', 'text/javascript', 'text/x-javascript', 'text/x-json');
$parsers[2]['parser'] = ARC2::getJSONParser();
foreach ($parsers as $v) {
if (in_array($content_type, $v['formats'])) {
$parser = $v['parser'];
}
}
//If nothing fits, pray to your favorite god that this can be detected and parsed correctly by ARC2.
$parser = ARC2::getRDFParser();
//end of workaround
$parser->parse($u, $data);
//Since IDK which namespace the documents contains, lets use the uri requested
$triples = $parser->getTriples();
/**
* Take a base URI and a string of turtle RDF and load the new triples into the graph. Return the number of triples loaded.
*/
function addTurtle($base, $data)
{
$parser = ARC2::getTurtleParser($this->arc2config);
$parser->parse($base, $data);
$errors = $parser->getErrors();
$parser->resetErrors();
if (sizeof($errors)) {
if ($this->debug) {
print "<h3>Error loading turtle string</h3>";
print "<ul><li>" . join("</li><li>", $errors) . "</li></ul>";
}
return 0;
}
return $this->addTriples($parser->getTriples());
}
protected function readScaffold($scaffold, $serviceArgs)
{
global $conf;
require_once $conf['home'] . 'lib/arc2/ARC2.php';
$parser = ARC2::getTurtleParser();
$parser->parse($scaffold);
$triples = $parser->getTriples();
$aux = Utils::filterTriples($triples, array(null, "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", "http://lodspeakr.org/vocab/ScaffoldedService"));
$scaffoldUri = $aux[0][0];
$aux = Utils::filterTriples($triples, array($scaffoldUri, "http://lodspeakr.org/vocab/scaffold", null));
foreach ($aux as $r) {
$patterns = Utils::filterTriples($triples, array($r[2], "http://lodspeakr.org/vocab/uriPattern", null));
$pattern = stripcslashes($patterns[0][2]);
if (preg_match("|{$pattern}|", $serviceArgs) > 0) {
// echo "match ! \n ".$pattern."\n";
$patternDir = Utils::filterTriples($triples, array($r[2], "http://lodspeakr.org/vocab/subComponent", null));
return $patternDir[0][2];
}
}
// exit(0);
return "";
}
public function oldCrapForTesting(&$node)
{
$node->content['rdfnodeproxy_uri'] = array('#value' => "<h3>Node URI = '" . $node->rdfnodeproxy_uri . "'</h3>", '#weight' => -2);
// $client = new SimpleSparqlClient("http://localhost:8080/openrdf-sesame/repositories/scfnat/");
$client = new SimpleSparqlClient("http://sparql.neurocommons.org:8890/sparql/");
/*
$qs = "PREFIX sc: <http://purl.org/science/owl/sciencecommons/>\n";
$qs .= "SELECT ?s ?p ?o\n";
$qs .= "FROM <http://purl.org/commons/hcls/gene>\n";
$qs .= "WHERE { ?s rdf:type sc:gene_record . ?s ?p ?o }\n";
$qs .= "LIMIT 10";
*/
$qs = "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n";
$qs .= "PREFIX sc: <http://purl.org/science/owl/sciencecommons/>\n";
$qs .= "PREFIX dc: <http://purl.org/dc/elements/1.1/>\n";
$qs .= "CONSTRUCT {\n";
$qs .= " ?s ?pl ?lit .\n";
// $qs .= " ?s ?pr ?res .\n";
$qs .= "}\n";
$qs .= "FROM <http://purl.org/commons/hcls/gene>\n";
$qs .= "WHERE {\n";
$qs .= " ?s ?pl ?lit .\n";
$qs .= " ?s a sc:gene_record .\n";
$qs .= " ?s dc:identifier ?id .\n";
$qs .= " filter(isLiteral(?lit)) .\n";
$qs .= " filter(xsd:integer(?id) > 11286 && xsd:integer(?id) < 11299) .\n";
/*
$qs .= " optional {\n";
$qs .= " ?s ?pr ?res .\n";
$qs .= " ?res ?p2 ?o2 .\n";
$qs .= " }\n";
*/
$qs .= "}\n";
$qs .= "LIMIT 1";
$result = $client->query($qs);
dvm($result);
// arc2_include();
// $parser = arc2_parse_sparql_results($result);
$parser = ARC2::getTurtleParser();
$parser->parse('', $result);
$triples = $parser->getTriples();
/*
$structure = $parser->getStructure();
*/
$node->content['rdfnodeproxy_results'] = array('#value' => dpr($triples, TRUE), '#weight' => -1);
/*
$cols = $client->cols($result);
$rows = $client->rows($result, TRUE);
// $tree = $client->tree($result);
$node->content['rdfnodeproxy_results'] = array(
'#value' => theme('table', $cols, $rows),
'#weight' => -1
);
*/
}
/**
* Add the triples parsed from the supplied Turtle to the graph
* @see http://www.dajobe.org/2004/01/turtle/
* @param string $turtle the Turtle to parse
* @param string $base the base URI against which relative URIs in the Turtle document will be resolved
*/
public function add_turtle($turtle, $base = '')
{
if ($turtle) {
/** @var \ARC2_TurtleParser $parser */
$parser = \ARC2::getTurtleParser();
$parser->parse($base, $turtle);
$triples = $parser->getTriples();
$this->_add_arc2_triple_list($triples);
unset($parser);
}
}
$time_start = microtime(true);
// $uri = $service . "?input-type=text&nif=true&prefix=" . urlencode ( $prefix ) . "&urirecipe=$urirecipe&input=" . urlencode ( $_REQUEST ['text'] );
$uri = $service . "?f=text&prefix=" . urlencode($prefix) . "&input=" . urlencode($_REQUEST['text']);
// case opennlp was chosen we need add &modelFolder=model in order to se the defauld model folder
if (strstr($uri, "opennlp")) {
$uri = $uri . "&modelFolder=model";
}
if (strstr($uri, "spotlight")) {
$uri = $uri . "&confidence=" . $_REQUEST['confidence'];
}
$data = file_get_contents($uri);
$time_end = microtime(true);
$time_service_needed = round($time_end - $time_start, 2);
// parsing
$time_start = microtime(true);
$parser = ARC2::getTurtleParser();
$parser->parse($prefix, $data);
$triples = $parser->getTriples();
$alltriples = array_merge($alltriples, $triples);
$time_end = microtime(true);
$time_arc2_needed = round($time_end - $time_start, 2);
$meta .= "\n\t<p>Sevice was {$service}:</p>\n\t<ul class=\"checks\">\n\t <li>NLP component needed: {$time_service_needed} seconds.</li>\n\t <li>ARC2 RDF Parser overhead: {$time_arc2_needed} seconds.</li>\n\t <li><a href=\"{$uri}\" >request url</a> </li>\n\t <li>Text size: " . strlen($_REQUEST['text']) . "</li>\n\t <li>Triples: " . count($triples) . "</li>\n\t</ul>";
}
$ns = array('p' => trim($prefix), 'rdf' => 'http://www.w3.org/1999/02/22-rdf-syntax-ns#', 'rdfs' => 'http://www.w3.org/2000/01/rdf-schema#', 'owl' => 'http://www.w3.org/2002/07/owl#', 'sso' => 'http://nlp2rdf.lod2.eu/schema/sso/', 'str' => 'http://nlp2rdf.lod2.eu/schema/string/', 'topic' => 'http://nlp2rdf.lod2.eu/schema/topic/', 'error' => 'http://nlp2rdf.lod2.eu/schema/error/', 'olia' => 'http://purl.org/olia/olia.owl#', 'olia-top' => 'http://purl.org/olia/olia-top.owl#', 'olia_system' => 'http://purl.org/olia/system.owl#', 'penn' => 'http://purl.org/olia/penn.owl#', 'penn-syntax' => 'http://purl.org/olia/penn-syntax.owl#', 'stanford' => 'http://purl.org/olia/stanford.owl#', 'brown' => 'http://purl.org/olia/brown.owl#', 'dbo' => 'http://dbpedia.org/ontology/', 'dbpedia' => 'http://dbpedia.org/resource/', 'nerd' => 'http://nerd.eurecom.fr/ontology#', 'scms' => 'http://ns.aksw.org/scms/', 'spotlight' => 'http://dbpedia.org/spotlight/', 'nif' => "http://persistence.uni-leipzig.org/nlp2rdf/ontologies/nif-core#", 'rlog' => "http://persistence.uni-leipzig.org/nlp2rdf/ontologies/rlog#", 'dc' => "http://purl.org/dc/elements/1.1/", 'stanford' => "http://persistence.uni-leipzig.org/nlp2rdf/ontologies/vm/dep/stanford#", 'itsrdf' => "http://www.w3.org/2005/11/its/rdf#");
if ($format == "turtle") {
$ser = ARC2::getTurtleSerializer(array('ns' => $ns));
$output = $ser->getSerializedTriples($alltriples);
header("Content-Type: text/turtle");
echo $output;
} else {
if ($format == "rdfxml") {
function turtle2xml($file)
{
//Andrea Mazzocchi
//Includo le librerie necessarie per gestire Turtle
include_once "semsol-arc2-c7c03da/ARC2.php";
//Instanziazione del parser...
$parser = ARC2::getTurtleParser();
$parser->parse($file);
//...parsing delle triple
$triples = $parser->getSimpleIndex();
//Inizializzo nuovo documento DOM (con versione, codifica e DTD)
$doc = new DOMDocument("1.0", "UTF-8");
$imple = new DOMImplementation();
$dtd = $imple->createDocumentType('locations', '', 'http://vitali.web.cs.unibo.it/twiki/pub/TechWeb12/DTDs/locations.dtd');
$doc = $imple->createDocument('', '', $dtd);
$doc->formatOutput = true;
//Inializzo il nodo radice "locations"
$root = $doc->appendChild($doc->createElement("locations"));
//Prelevo le chiavi dell'array associativo
$index = array_keys($triples);
//Eseguo un ciclo su quante sono le chiavi
for ($i = 0; $i < count($index); $i++) {
//Separo l'URL secondo gli "/"
$temp = explode("/", $index[$i]);
$a = count($temp) - 1;
$id = $temp[$a];
//Codice per il riempimento del tag "metadata"
if (stristr($id, '.ttl') == true) {
//"metadata" viene riconosciuto con ".ttl" al termine del prefix "this"
$root2 = $root->appendChild($doc->createElement("metadata"));
$temp1 = $index[$i];
//Secondo le direttive del DTD, un database XML non ha il tag
//"description" ("version" dell'XML corrisponde a "description"
//del Turtle), quindi sostituisco "description" (dal Turtle)
//in "version" (per XML)
foreach ($triples[$temp1] as $deep1 => $deep2) {
if (stristr($temp1, "description") == true) {
$temp1 = "version";
} else {
$b = explode("/", $deep1);
}
//Costruisco i "metadata" nel DOM
$root30 = $root2->appendChild($doc->createElement($b[count($b) - 1]));
$root30->appendChild($doc->createTextNode($deep2[0]));
}
} else {
$root3 = $root->appendChild($doc->createElement("location"));
$id = $temp[$a];
//"id" deve essere attributo di "location"
$root3->setAttribute("id", $id);
$temp2 = $index[$i];
//Costruisco le varie "location"
foreach ($triples[$temp2] as $key => $value) {
if (stristr($key, "fn") == true) {
$key = "name";
}
if (stristr($key, "extended-address") == true) {
$key = "address";
}
//anche "latitude" e "longitude" devono essere attributi di "location"
if (stristr($key, "latitude") == true) {
$root3->setAttribute("lat", $value[0]);
unset($value);
}
if (stristr($key, "longitude") == true) {
$root3->setAttribute("long", $value[0]);
unset($value);
}
if (stristr($key, "opening") == true or stristr($key, "closing") == true) {
$b = explode("/", $key);
} else {
$b = explode("ns#", $key);
}
foreach ($value as $deep1 => $deep2) {
$root30 = $root3->appendChild($doc->createElement($b[count($b) - 1]));
$root30->appendChild($doc->createTextNode($deep2));
}
}
}
}
//Salvo il documento DOM in XML
echo $doc->saveXML();
}
/**
* Add the triples parsed from the supplied Turtle to the graph
* @see http://www.dajobe.org/2004/01/turtle/
* @param string turtle the Turtle to parse
* @param string base the base URI against which relative URIs in the Turtle document will be resolved
*/
function add_turtle($turtle, $base = '')
{
if ($turtle) {
$parser = ARC2::getTurtleParser();
$parser->parse($base, $turtle);
$this->_add_arc2_triple_list($parser->getTriples());
unset($parser);
}
}
