sparql2s3db.php | searchcode

/s3db3.5.10/sparql2s3db.php

https://github.com/drobbins/s3db
PHP | 283 lines | 199 code | 50 blank | 34 comment | 25 complexity | f107917ead55d6c502e1c9c5235c65eb MD5 | raw file

<?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);

	

}



#echo '<pre>';print_r($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));



    }





?>