-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathsparql2s3db.php
283 lines (229 loc) · 7.23 KB
/
sparql2s3db.php
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
<?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));
}
?>