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sparql2s3db.php
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sparql2s3db.php
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<?php
#sparql serializer is an API that serializes a sparql query into an S3QL query
##HEADER: Read the file and include the functions for parsing the RDF
ini_set('display_errors',0);
if($_REQUEST['su3d']) {
ini_set('display_errors',1);
}
if(file_exists('config.inc.php')) {
include('config.inc.php');
} else {
Header('Location: index.php');
exit;
}
include('dbstruct.php');
@ini_set('allow_url_fopen', true);
@set_time_limit(0);
$x = ini_set('memory_limit', '500M');
#echo ini_get('memory_limit');exit;
@ini_set('upload_max_filesize', '128M');
@ini_set('post_max_size', '256M');
@ini_set('max_input_time', '-1');
@ini_set('max_execution_time', '3000');
@ini_set('expect.timeout', '-1');
@ini_set('default_socket_timeout', '-1');
ini_set('display_errors',0);
if($_REQUEST['su3d']) {
ini_set('display_errors',1);
}
define("RDFAPI_INCLUDE_DIR", S3DB_SERVER_ROOT."/pearlib/rdfapi-php/api/");
include(RDFAPI_INCLUDE_DIR . "RdfAPI.php");
include(RDFAPI_INCLUDE_DIR . "syntax/SyntaxN3.php");
include(RDFAPI_INCLUDE_DIR . "syntax/SyntaxRDF.php");
if(is_array($argv)) {
foreach ($argv as $argin) {
if(ereg('(format|url|noHTML)=(.*)', $argin, $zz)) {
$in[$zz[1]] = $zz[2];
}
}
} else {
$in = $_REQUEST;
}
$rdf = ($in['url']=='')?"http://ibl.mdanderson.org/TCGA/extras/NUavLcFy5fn6WsN/KfN1YnDBCN4dD6j.project126/TCGADATA.rdf":urldecode($in['url']);
$mysparql = '
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX : <http://ibl.mdanderson.org/TCGA/>
PREFIX s3db: <http://www.s3db.org/core#>
SELECT *
WHERE { ?x :R149 ?z FILTER regex(?z, "CGH") .
}';
//PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
//PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
//PREFIX : <http://http://ibl.mdanderson.org/TCGA/>
//PREFIX s3db: <http://www.s3db.org/core#>
//SELECT ?Item, ?Ilabel
//WHERE {?Item rdf:type :C186 .
// ?Item rdfs:label ?Ilabel .}
//
//";
//$mysparql = "
//PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
//PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
//PREFIX : <http://http://ibl.mdanderson.org/TCGA/>
//PREFIX s3db: <http://www.s3db.org/core#>
//SELECT ?R,?Rlabel
//WHERE {?R rdfs:subClassOf :P126 .
// ?R rdf:type s3db:s3dbRule .
// ?R rdfs:label ?Rlabel .
// ?R rdf:subject :C186 .}
//
//";
$sparql = ($in['sparql']=='')?$mysparql:urldecode($in['sparql']);
##Interpret the query
$parsed = s3db_parse($sparql);
exit;
$out = ($in['format']=='')?'HTML':strtoupper($in['format']);
##serialize the data so that is does not take very long to re-load it
$filename = md5($rdf);
$file_place = $GLOBALS['uploads'].'/';
if(!is_file($file_place.$filename)) {
#read the data into a model
$model = rdf2php($rdf);
if($model=='') {
echo "dataset could not be parsed";
} else {
$s_model = serialize($model);
file_put_contents($file_place.$filename, $s_model);
}
} else {
$model = file_get_contents($file_place.$filename);
$model = unserialize($model);
}
if(!$in['no_color']) {
echo '
<html>
<head>
</head>
<body>
<form method="GET" action="'.$_SERVER['PHP-SELF'].'" id="sparqlform">
<h5>URL</h5>
<input type = "text" id="url" size = "100%" value="'.$in['url'].'" name="url">
<h5>SPARQL <a href="http://www.w3.org/TR/rdf-sparql-query/" target="_blank">(help!!)</a></h5>
<br />
<textarea cols="100" id="sparql" rows="10" name = "sparql">'.stripslashes($sparql).'</textarea><br />
<input type="submit" value="SPARQL this!" id="submitsparql"></body>
</form>';
}
$sparqlQueryFile = md5(urlencode($sparql)).date('Gis');
if(!is_file($file_place.$sparqlQueryFile)) {
if(ereg('XML|HTML', $out)) {
#$incomingSparql = $sparql->_parseSparqlQuery($sparql);
$find=$model->sparqlQuery($sparql, $out);
echo $find;
} else {
$find=$model->sparqlQuery($sparql);
#echo '<pre>';print_r($find);
}
$s_find = serialize($find);
file_put_contents($file_place.$sparqlQueryFile, $s_find);
} else {
$s_find = file_get_contents($file_place.$sparqlQueryFile);
$find = unserialize($s_find);
if(ereg('XML|HTML', $out)) {
file_put_contents($GLOBALS['uploads'].'/sparqlResult.'.strtolower($out), $find);
echo $find;
} else {
echo '<pre>';print_r($find);
}
}
function rdf2php($doc) {
// Prepare RDF
$rdfInput = $data;
// Show the submitted RDF
// Create a new MemModel
$model = ModelFactory::getDefaultModel();
$model->load($doc);
return ($model);
}
function s3db_parse($queryString) {
if($queryString) {
$uncommentedQuery = s3db_uncomment($queryString);
$tokenized = s3db_tokenize($uncommentedQuery);
echo '<pre>';print_r($tokenized);exit;
$parsed = parseQuery($tokenized);
} else {
return ("Querystring is empty.");
}
}
function s3db_uncomment($queryString) {
// php appears to escape quotes, so unescape them
$queryString = str_replace('\"',"'",$queryString);
$queryString = str_replace("\'",'"',$queryString);
$regex ="/((\"[^\"]*\")|(\'[^\']*\')|(\<[^\>]*\>))|(#.*)/";
return preg_replace($regex,'\1',$queryString);
}
function s3db_tokenize($queryString) {
$queryString = trim($queryString);
$specialChars = array(" ", "\t", "\r", "\n", ",", "(", ")","{","}",'"',"'",";","[","]");
$len = strlen($queryString);
$this['tokens'][0]='';
$n = 0;
for ($i=0; $i<$len; ++$i) {
if (!in_array($queryString{$i}, $specialChars)) {
$this['tokens'][$n] .= $queryString{$i};
} else {
if ($this['tokens'][$n] != '') {
++$n;
}
$this['tokens'][$n] = $queryString{$i};
$this['tokens'][++$n] = '';
}
}
return ($this);
}
function parseQuery($tokenizedQuery) {
do {
switch(strtolower(current($tokenizedQuery['tokens']))) {
case "base":
$this->parseBase();
break;
case "prefix":
$this->parsePrefix();
break;
case "select":
$this->parseSelect();
break;
case "describe":
$this->parseDescribe();
break;
case "ask":
$this->parseAsk('ask');
break;
case "count":
$this->parseAsk('count');
break;
case "from":
$this->parseFrom();
break;
case "construct":
$this->parseConstruct();
break;
case "where":
$this->parseWhere();
$this->parseModifier();
break;
case "{":
prev($this->tokens);
$this->parseWhere();
$this->parseModifier();
break;
}
} while (next($this->tokens));
}
?>