class.tx_nG6_db.php 70 KB
Newer Older
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
<?php
/***************************************************************
*  Copyright notice
*
*  (c) 2009 PF bioinformatique de Toulouse <>
*  All rights reserved
*
*  This script is part of the TYPO3 project. The TYPO3 project is
*  free software; you can redistribute it and/or modify
*  it under the terms of the GNU General Public License as published by
*  the Free Software Foundation; either version 2 of the License, or
*  (at your option) any later version.
*
*  The GNU General Public License can be found at
*  http://www.gnu.org/copyleft/gpl.html.
*
*  This script is distributed in the hope that it will be useful,
*  but WITHOUT ANY WARRANTY; without even the implied warranty of
*  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
*  GNU General Public License for more details.
*
*  This copyright notice MUST APPEAR in all copies of the script!
***************************************************************/

require_once(t3lib_extMgm::extPath('nG6').'/lib/class.tx_nG6_utils.php');

/**
 * Class_nG6_db' for the 'nG6' extension.
 * This class is in charge of all communication with the database
 *
 * @author	PF bioinformatique de Toulouse <>
 */
class tx_nG6_db {
Penom Nom's avatar
Penom Nom committed
34
35
36
37
38
39
40
41
	
	/*
	 * Global functions
	*------------------------------------------------------------*/
	
	/**
	* Update the specified field of the table
	 *
42
	* @param	string  $table the entity to change
Penom Nom's avatar
Penom Nom committed
43
44
45
46
	* @param	string  $id     the element id to update
	* @param	string  $field  the field to change
	* @param	string  $value  the new value
	*/
47
	function update_field($table, $id, $field, $value) {
48
49
50
		if( $field == 'uid' ) {
			throw new Exception ("The function 'update_field' cannot change an id.") ;
		}	
51
		$GLOBALS['TYPO3_DB']-> exec_UPDATEquery ($table, 'uid='.$id, array($field => $value));
52
	}
Penom Nom's avatar
Penom Nom committed
53
	
Jerome Mariette's avatar
Jerome Mariette committed
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
	/**
     * Return the size used by ng6 datas from a starting date to a end date
     * 
     * @param int $usergroup		the usergroup
     * @param string $data_folder	the folder data
     * @param bool $get_analyzes	true if the admin wants to include analyzes
     * @param bool $cumul_values	true if the admin wants cumulatives values
     * @param int $step				the step (0 = one month, 1 = six months, 2 = one year)
     * @param int $date_start		the date start
     * @param int $date_end			the date end
     * @return array
     */
    function get_size($usergroup, $data_folder, $get_analyzes=false, $cumul_values=false, $step=2, $date_start=0, $date_end=0){
		
    	//const - tstamp is in seconds, nb of seconds in one day
    	$one_day_val = 24 * 3600;
    	
    	// init min max
    	if($date_start==0){ $date_start = intval(tx_nG6_db::get_run_min_date()); }
    	if($date_end==0){ $date_end = intval(tx_nG6_db::get_run_max_date()); }
  
    	$date_cursors = $date_start;
    	$res_tab = null;

		// get all users
Jerome Mariette's avatar
Jerome Mariette committed
79
80
81
82
83
84
85
86
87
88
		if ($usergroup != "0") {
			$users_in_group = tx_nG6_db::get_all_users_in_group($usergroup);
			$project_list_final = array();
			foreach($users_in_group as $list_current_user_id){
				// get all user projects
				$all_user_projects = tx_nG6_db::select_all_user_projects($list_current_user_id);
				foreach($all_user_projects as $p_val){
					if(!in_array($p_val['id'], $project_list_final)){
						$project_list_final[] = $p_val['id'];
					}
Jerome Mariette's avatar
Jerome Mariette committed
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
				}
			}
		}

		$cumulated_size = 0;
    	while($date_cursors < $date_end){
    		// increment step iterator
    		$total_day_count_tstamp = 0;
    		switch ($step) {
    			case 0:		// 1 month
    				$nb_days_in_month = date('t', $date_cursors);
    				$total_day_count_tstamp = $one_day_val * $nb_days_in_month;
    				break;
    			case 1:		// 6 months
    				$date_cursor_tmp = $date_cursors;
    				for($i = 0;$i < 6; $i++){
    					$nb_days_in_month = cal_days_in_month(CAL_GREGORIAN, date('n', $date_cursor_tmp), date('Y', $date_cursor_tmp));
    					$total_day_count_tstamp += $one_day_val * $nb_days_in_month;
    					// +1 month * 6
    					$date_cursor_tmp = strtotime('+1 month', $date_cursor_tmp);
    				}
    				break;
    			case 2:		// 1 year
    				$nb_days_in_year = date("z", mktime(0,0,0,12,31,date('Y', $date_cursors)));
    				$total_day_count_tstamp = $one_day_val * $nb_days_in_year;
    				break;
    		}
    		
    		$date_cursore = $date_cursors + $total_day_count_tstamp;
    		$current_size = 0;
Jerome Mariette's avatar
Jerome Mariette committed
119
120
121
122
123
124
    		
			if ($usergroup != "0") {
				$where = 'tx_nG6_project.uid IN ('.implode(",",$project_list_final).') AND tx_nG6_run.date BETWEEN '.$date_cursors.' AND '.$date_cursore;	
			} else {
				$where = 'tx_nG6_run.date BETWEEN '.$date_cursors.' AND '.$date_cursore;
			}
Jerome Mariette's avatar
Jerome Mariette committed
125
126
127
			
    		// get all runs the usergroup can access to
    		$queryParts = array(
Jerome Mariette's avatar
Jerome Mariette committed
128
    			'SELECT' 	=> 'tx_nG6_run.uid as run_id',
Jerome Mariette's avatar
Jerome Mariette committed
129
130
131
    			'FROM' 		=> 'tx_nG6_project '
    				.' INNER JOIN tx_nG6_project_run ON tx_nG6_project.uid=tx_nG6_project_run.project_id '
    				.' INNER JOIN tx_nG6_run ON tx_nG6_project_run.run_id=tx_nG6_run.uid ',
Jerome Mariette's avatar
Jerome Mariette committed
132
    			'WHERE' 	=> $where,
Jerome Mariette's avatar
Jerome Mariette committed
133
134
135
136
137
138
139
140
    			'GROUPBY' 	=> '',
    			'ORDERBY' 	=> '',
    			'LIMIT' 	=> ''
    		);
			$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
			while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
				$current_size += tx_nG6_db::get_run_size($res_row['run_id'], $data_folder, $get_analyzes);
			}
Jerome Mariette's avatar
Jerome Mariette committed
141
142
143
			
			// get all project analysis the usergroup can access to
			if ($get_analyzes) {
Jerome Mariette's avatar
Jerome Mariette committed
144
145
146
147
148
				if ($usergroup != "0") {
					$where = 'tx_nG6_project.uid IN ('.implode(",",$project_list_final).') AND tx_nG6_analyze.date BETWEEN '.$date_cursors.' AND '.$date_cursore;	
				} else {
					$where = 'tx_nG6_analyze.date BETWEEN '.$date_cursors.' AND '.$date_cursore;
				}
Jerome Mariette's avatar
Jerome Mariette committed
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
	    		$queryParts = array(
	    			'SELECT' 	=> 'tx_nG6_analyze.uid as analyze_id',
	    			'FROM' 		=> 'tx_nG6_project '
	    				.' INNER JOIN tx_nG6_project_analyze ON tx_nG6_project.uid=tx_nG6_project_analyze.project_id '
	    				.' INNER JOIN tx_nG6_analyze ON tx_nG6_project_analyze.analyze_id=tx_nG6_analyze.uid ',
	    			'WHERE' 	=> $where,
	    			'GROUPBY' 	=> '',
	    			'ORDERBY' 	=> '',
	    			'LIMIT' 	=> ''
	    		);
				$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
				while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
					$current_size += tx_nG6_db::get_analysis_size($res_row['analyze_id'], $data_folder);
				}
			}
Jerome Mariette's avatar
Jerome Mariette committed
164
165

    		$cumulated_size += $current_size;
Jerome Mariette's avatar
Jerome Mariette committed
166
167
168
169
170
    		if(!$cumul_values){
    	    	$res_tab[] = array($date_cursore*1000, $current_size);
    	    }else{
    	    	$res_tab[] = array($date_cursore*1000, $cumulated_size);
    	    }
Jerome Mariette's avatar
Jerome Mariette committed
171
172
173
174
175

    		$date_cursors = $date_cursore + 1;
    	}
    	return $res_tab;	
    }
Penom Nom's avatar
Penom Nom committed
176
	
177
178
179
180
181
182
	/*
	 * Project functions
	 *------------------------------------------------------------*/

	/**
	 * Select all project for the current user
183
	 * 
184
	 * @param	string	$user_id	the user id
185
186
	 * @return	table with all projects
	 */
187
	function select_all_user_projects($user_id, $orderby='', $limit='') {		
188
		$projects = array();
Jerome Mariette's avatar
Jerome Mariette committed
189
		
190
		// If the user is not logged on display demonstration project
Jerome Mariette's avatar
Jerome Mariette committed
191
192
193
		if ($user_id == null) { $where = 'tx_nG6_project.public=0'; } 
		else { $where = 'fe_rights.fe_user_id='.$user_id; }
		
194
		//First, get the analyzis project-scale
195
		$queryParts = array(
196
197
198
			'SELECT' => 'tx_nG6_project.uid AS project_id, '.
						'tx_nG6_project.name AS project_name, '.
						'tx_nG6_project.description AS project_description, '.
199
						'tx_nG6_project.public AS project_public, '.
Jerome Mariette's avatar
Jerome Mariette committed
200
						'tx_nG6_project.crdate AS project_crdate, '.
201
202
						'tx_nG6_project.hidden AS project_hidden ',
			'FROM' => 'tx_nG6_project INNER JOIN fe_rights ON fe_rights.project_id=tx_nG6_project.uid',
203
204
			'WHERE' => $where,
			'GROUPBY' => '',
Jerome Mariette's avatar
Jerome Mariette committed
205
206
			'ORDERBY' => $orderby,
			'LIMIT' => $limit
207
		);
208
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);		
209
210
		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
			$project_id = $row['project_id'];
Jerome Mariette's avatar
Jerome Mariette committed
211
			if (!isset ($projects['project_'.$project_id])) {		
212
				$projects['project_'.$project_id] = array(
213
					'id'			=> $project_id,				
214
					'name'			=> $row['project_name'],
Jerome Mariette's avatar
Jerome Mariette committed
215
					'hidden'		=> $row['project_hidden'],
Jerome Mariette's avatar
Jerome Mariette committed
216
					'date'			=> $row['project_crdate'],
217
					'public'		=> $row['project_public'],
218
219
					'description'	=> $row['project_description']);
			}
220
						
221
		}		
222
223
224
		return $projects;
	}

Penom Nom's avatar
Penom Nom committed
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
	/**
	* Select all project for the current user
	*
	* @param	string	$user_id	the user id
	* @return	table with all projects
	*/
	function get_user_projects($user_id, $orderby='', $limit='') {
		$projects = array();
	
		// If the user is not logged on display demonstration project
		if ($user_id == null) {
			$where = 'tx_nG6_project.public=0';
		}
		else { 
				$where = 'fe_rights.fe_user_id='.$user_id.' AND ((fe_rights.right_id<>2 AND tx_nG6_project.hidden=0) '
				.'OR fe_rights.right_id=2)' ;
		}
	
		//First, get the analyzis project-scale
		$queryParts = array(
				'SELECT' => 'tx_nG6_project.uid AS project_id, '.
							'tx_nG6_project.name AS project_name, '.
							'tx_nG6_project.description AS project_description, '.
							'tx_nG6_project.public AS project_public, '.
							'tx_nG6_project.crdate AS project_crdate, '.
							'tx_nG6_project.hidden AS project_hidden ',
				'FROM' => 'tx_nG6_project INNER JOIN fe_rights ON fe_rights.project_id=tx_nG6_project.uid',
				'WHERE' => $where,
				'GROUPBY' => '',
				'ORDERBY' => $orderby,
				'LIMIT' => $limit
		);
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
			$project_id = $row['project_id'];
			if (!isset ($projects['project_'.$project_id])) {
				$projects['project_'.$project_id] = array(
						'id'			=> $project_id,				
						'name'			=> $row['project_name'],
						'hidden'		=> $row['project_hidden'],
						'date'			=> $row['project_crdate'],
						'public'		=> $row['project_public'],
						'description'	=> $row['project_description']);
			}
	
		}
		return $projects;
	}

274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
	/**
	 * Select a run from the database
	 *
	 * @param	string	$project_id	the project id to return
	 * @return	hash table with all project information
	 */
	function select_project($project_id) {
		$queryParts = array(
			'SELECT' => '*',
			'FROM' => 'tx_nG6_project',
			'WHERE' => 'tx_nG6_project.uid = '.$project_id,
			'GROUPBY' => '',
			'ORDERBY' => '',
			'LIMIT' => ''
		);
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
Jerome Mariette's avatar
Jerome Mariette committed
290
291
292
293
		$vals = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res);
		return array('id'			=> $vals['uid'],				
					 'name'			=> $vals['name'],
					 'hidden'		=> $vals['hidden'],
Jerome Mariette's avatar
Jerome Mariette committed
294
					 'date'			=> $vals['crdate'],
Jerome Mariette's avatar
Jerome Mariette committed
295
296
					 'public'		=> $vals['public'],
					 'description'	=> $vals['description']);
297
298
299
300
301
302
303
304
	}

	/**
	 * Select all runs linked to the specified project
	 *
	 * @param	string	$project_id	the project id
	 * @return	hash table with all runs information
	 */
Jerome Mariette's avatar
Jerome Mariette committed
305
    function get_project_runs($project_id, $orderby='', $limit='') {
306
    	
307
		// First select all runs from the database
308
		$queryParts = Array( 
309
310
311
312
			'SELECT' => 'tx_nG6_run.uid AS run_id,'.
					 	'tx_nG6_run.directory AS run_directory,'.
					 	'tx_nG6_run.species AS run_species,'.
						'tx_nG6_run.description AS run_description, '.
Jerome Mariette's avatar
Jerome Mariette committed
313
314
315
						'tx_nG6_run.data_nature AS run_data_nature, '.
						'tx_nG6_run.sequencer AS run_sequencer, '.
						'tx_nG6_run.type AS run_type, '.
316
						'tx_nG6_run.name AS run_name, '.
Jerome Mariette's avatar
Jerome Mariette committed
317
318
						'tx_nG6_run.nb_sequences AS run_nb_sequences, '.
						'tx_nG6_run.full_seq_size AS run_full_seq_size, '.
319
320
						'tx_nG6_run.date AS run_date, '.
						'tx_nG6_run.hidden AS run_hidden, '.
321
322
						'tx_nG6_project.uid AS project_id, '.
						'tx_nG6_project.name AS project_name ',
Jerome Mariette's avatar
Jerome Mariette committed
323
			'FROM' => 'tx_nG6_project '.
324
325
  						'INNER JOIN tx_nG6_project_run ON  tx_nG6_project.uid=tx_nG6_project_run.project_id '.
  						'INNER JOIN tx_nG6_run ON tx_nG6_project_run.run_id=tx_nG6_run.uid ',
Jerome Mariette's avatar
Jerome Mariette committed
326
			'WHERE' => 'tx_nG6_project.uid='.$project_id,
327
			'GROUPBY' => '',
Jerome Mariette's avatar
Jerome Mariette committed
328
329
			'ORDERBY' => $orderby,
			'LIMIT' 	=> $limit
Penom Nom's avatar
Penom Nom committed
330
331
332
		);

	
333
334
335
336
		// Then create the result hash table
		$results = array();
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
Jerome Mariette's avatar
Jerome Mariette committed
337
338
			$run_id = $row['run_id'];				
			if (!isset($results['run_'.$run_id])) {				
339
				$results['run_'.$run_id] = array( 
Jerome Mariette's avatar
Jerome Mariette committed
340
					'id'			=> $run_id,
341
					'directory'		=> $row['run_directory'], 
342
					'name' 			=> $row['run_name'],
Jerome Mariette's avatar
Jerome Mariette committed
343
344
					'project_name' 	=> $row['project_name'],
					'hidden'		=> $row['run_hidden'],
345
					'species' 		=> $row['run_species'],
Jerome Mariette's avatar
Jerome Mariette committed
346
347
348
					'nb_sequences' 	=> $row['run_nb_sequences'],
					'full_seq_size' => $row['run_full_seq_size'],
					'project_id' 	=> $row['project_id'],
349
					'date'			=> $row['run_date'],
Jerome Mariette's avatar
Jerome Mariette committed
350
351
352
					'data_nature'	=> $row['run_data_nature'],
					'sequencer'		=> $row['run_sequencer'],
					'type'			=> $row['run_type'],
Jerome Mariette's avatar
Jerome Mariette committed
353
					'description' 	=> $row['run_description']
354
				);
355
			}						
356
357
358
359
		}
		return $results;
    }

Penom Nom's avatar
Penom Nom committed
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
    /**
     * Select all runs linked to the specified project for the user
     *
     * @param	string	$user_id	the user id
     * @param	string	$project_id	the project id
     * @return	hash table with all runs information
     */
     function get_user_project_runs($user_id, $project_id, $orderby='', $limit='') {
    	// If the user is not logged on display demonstration project
	    if ($user_id == null) {
	    	$where = 'tx_nG6_project.uid='.$project_id.' AND tx_nG6_project.public=0 AND tx_nG6_run.hidden=0';
	    }
	    else {
	    	$where = 'fe_users.uid='.$user_id.' AND '.'tx_nG6_project.uid='.$project_id.
	    		' AND ((fe_rights.right_id<>2 AND tx_nG6_run.hidden=0) OR fe_rights.right_id=2)' ;
	    }
    	
	    // First select all runs from the database
	    $queryParts = Array(
		    'SELECT' => 'tx_nG6_run.uid AS run_id,'.
			    'tx_nG6_run.directory AS run_directory,'.
			    'tx_nG6_run.species AS run_species,'.
			    'tx_nG6_run.description AS run_description, '.
			    'tx_nG6_run.data_nature AS run_data_nature, '.
			    'tx_nG6_run.sequencer AS run_sequencer, '.
			    'tx_nG6_run.type AS run_type, '.
			    'tx_nG6_run.name AS run_name, '.
			    'tx_nG6_run.nb_sequences AS run_nb_sequences, '.
			    'tx_nG6_run.full_seq_size AS run_full_seq_size, '.
			    'tx_nG6_run.date AS run_date, '.
			    'tx_nG6_run.hidden AS run_hidden, '.
			    'tx_nG6_project.uid AS project_id, '.
			    'tx_nG6_project.name AS project_name ',
		    'FROM' => 'tx_nG6_run '.
			    'INNER JOIN tx_nG6_project_run ON tx_nG6_run.uid=tx_nG6_project_run.run_id '.
			    'INNER JOIN tx_nG6_project ON tx_nG6_project_run.project_id=tx_nG6_project.uid '.
			    'INNER JOIN fe_rights ON tx_nG6_project.uid=fe_rights.project_id '.
			    'INNER JOIN fe_users ON fe_rights.fe_user_id=fe_users.uid ',
		    'WHERE' => $where,
		    'GROUPBY' => '',
		    'ORDERBY' => $orderby,
		    'LIMIT' 	=> $limit
	    );
    
	    // Then create the result hash table
	    $results = array();
	    $res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
	    while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
	    	$run_id = $row['run_id'];
	    	if (!isset($results['run_'.$run_id])) {
			    $results['run_'.$run_id] = array(
			    'id'			=> $run_id,
			    'directory'		=> $row['run_directory'],
			    'name' 			=> $row['run_name'],
			    							'project_name' 	=> $row['project_name'],
			    'hidden'		=> $row['run_hidden'],
			    							'species' 		=> $row['run_species'],
			    'nb_sequences' 	=> $row['run_nb_sequences'],
			    							'full_seq_size' => $row['run_full_seq_size'],
			    							'project_id' 	=> $row['project_id'],
			    							'date'			=> $row['run_date'],
			    							'data_nature'	=> $row['run_data_nature'],
			    							'sequencer'		=> $row['run_sequencer'],
			    							'type'			=> $row['run_type'],
			    'description' 	=> $row['run_description']
			    				);
		    }
	    }
	    return $results;
    }

431
432
433
434
435
436
	/**
	 * Select all analysis linked to the specified project
	 *
	 * @param	string	$project_id	the project id
	 * @return	hash table with all analysis information
	 */
Jerome Mariette's avatar
Jerome Mariette committed
437
    function get_project_analysis($project_id, $orderby='', $limit='') {
438
439
    	
    	// First select all analysis from the database    	
440
    	$queryParts = array( 
441
442
			'SELECT' => 'tx_nG6_analyze.uid AS analyze_id,'. 
						'tx_nG6_analyze.directory AS analyze_directory,'. 
443
						'tx_nG6_analyze.name AS analyze_name, '.
444
						'tx_nG6_analyze.class AS analyze_class, '.
445
						'tx_nG6_analyze.date AS analyze_date, '.
Jerome Mariette's avatar
Jerome Mariette committed
446
447
						'tx_nG6_analyze.software AS analyze_software, '.
						'tx_nG6_analyze.version AS analyze_version, '.
448
						'tx_nG6_analyze.params AS analyze_params, '.
449
						'tx_nG6_analyze.description AS analyze_description, '.
Jerome Mariette's avatar
Jerome Mariette committed
450
						'tx_nG6_analyze.parent_uid AS analyze_parent_uid, '.
451
						'tx_nG6_analyze.hidden AS analyze_hidden ',
Jerome Mariette's avatar
Jerome Mariette committed
452
			'FROM' => 'tx_nG6_project '.
453
454
						'INNER JOIN tx_nG6_project_analyze ON tx_nG6_project.uid = tx_nG6_project_analyze.project_id '.
						'INNER JOIN tx_nG6_analyze ON tx_nG6_analyze.uid=tx_nG6_project_analyze.analyze_id ',
Jerome Mariette's avatar
Jerome Mariette committed
455
			'WHERE' => 'tx_nG6_project.uid='.$project_id,
456
			'GROUPBY' => '',
Jerome Mariette's avatar
Jerome Mariette committed
457
458
			'ORDERBY' => $orderby,
			'LIMIT' => $limit
459
460
461
462
463
464
		);
		// Then create the result hash table
		$results = array();
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
			$analyze_id = $row['analyze_id'];
Jerome Mariette's avatar
Jerome Mariette committed
465
			if (!isset ($results['analyse_'.$analyze_id])) {				
466
467
				$results['analyse_'.$analyze_id] = array( 
					'directory'		=> $row['analyze_directory'], 
468
					'name' 			=> $row['analyze_name'],
469
					'class'			=> $row['analyze_class'],
Jerome Mariette's avatar
Jerome Mariette committed
470
471
					'id' 			=> $row['analyze_id'],
					'hidden' 		=> $row['analyze_hidden'],
472
					'params' 		=> $row['analyze_params'],
Jerome Mariette's avatar
Jerome Mariette committed
473
474
					'software' 		=> $row['analyze_software'],
					'version' 		=> $row['analyze_version'],
475
					'date'			=> $row['analyze_date'],
Jerome Mariette's avatar
Jerome Mariette committed
476
477
					'description' 	=> $row['analyze_description'],
					'parent_id'		=> $row['analyze_parent_uid']	
478
				);
479
			}						
480
481
482
483
		}
		return $results;
    }

Penom Nom's avatar
Penom Nom committed
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
    /**
    * Select all analysis linked to the specified project for the user
    *
    * @param	string	$user_id	the user id
    * @param	string	$project_id	the project id
    * @return	hash table with all analysis information
    */
    function get_user_project_analysis($user_id, $project_id, $orderby='', $limit='') {
    	// If the user is not logged on display demonstration project
    	if ($user_id == null) {
    		$where = 'tx_nG6_project.uid='.$project_id.' AND tx_nG6_project.public=0 AND tx_nG6_run.hidden=0';
    	}
    	else {
    		$where = 'fe_users.uid='.$user_id.' AND tx_nG6_project.uid='.$project_id.
    					' AND ((fe_rights.right_id<>2 AND tx_nG6_analyze.hidden=0) OR fe_rights.right_id=2)' ;
    	}
    	
    	// First select all analysis from the database
    	$queryParts = array(
    			'SELECT' => 'tx_nG6_analyze.uid AS analyze_id,'. 
    						'tx_nG6_analyze.directory AS analyze_directory,'. 
    						'tx_nG6_analyze.name AS analyze_name, '.
    						'tx_nG6_analyze.class AS analyze_class, '.
    						'tx_nG6_analyze.date AS analyze_date, '.
    						'tx_nG6_analyze.software AS analyze_software, '.
    						'tx_nG6_analyze.version AS analyze_version, '.
    						'tx_nG6_analyze.params AS analyze_params, '.
    						'tx_nG6_analyze.description AS analyze_description, '.
    						'tx_nG6_analyze.parent_uid AS analyze_parent_uid, '.
    						'tx_nG6_analyze.hidden AS analyze_hidden ',
    			'FROM' => 'tx_nG6_analyze '.
    						'INNER JOIN tx_nG6_project_analyze ON tx_nG6_analyze.uid = tx_nG6_project_analyze.analyze_id '.
    						'INNER JOIN tx_nG6_project ON tx_nG6_project_analyze.project_id=tx_nG6_project.uid '.
							'INNER JOIN fe_rights ON tx_nG6_project.uid=fe_rights.project_id '.
					  		'INNER JOIN fe_users ON fe_rights.fe_user_id=fe_users.uid ',
    			'WHERE' => $where,
    			'GROUPBY' => '',
    			'ORDERBY' => $orderby,
    			'LIMIT' => $limit
    	);
    	// Then create the result hash table
    	$results = array();
    	$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
    	while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
    		$analyze_id = $row['analyze_id'];
    		if (!isset ($results['analyse_'.$analyze_id])) {
    			$results['analyse_'.$analyze_id] = array(
    					'directory'		=> $row['analyze_directory'], 
    					'name' 			=> $row['analyze_name'],
    					'class'			=> $row['analyze_class'],
    					'id' 			=> $row['analyze_id'],
    					'hidden' 		=> $row['analyze_hidden'],
    					'params' 		=> $row['analyze_params'],
    					'software' 		=> $row['analyze_software'],
    					'version' 		=> $row['analyze_version'],
    					'date'			=> $row['analyze_date'],
    					'description' 	=> $row['analyze_description'],
    					'parent_id'		=> $row['analyze_parent_uid']	
    			);
    		}
    	}
    	return $results;
    }

548
549
550
551
552
    /**
     * Hide a project and sublevels (runs & analyzes) datas from database project
     * 
     * @param	string	$p_id	the project id to hide
     */
Jerome Mariette's avatar
Jerome Mariette committed
553
	function hide_project($p_id) {
554
555
		
		// First change all project runs
Jerome Mariette's avatar
Jerome Mariette committed
556
		$project_runs = tx_nG6_db::get_project_runs($p_id);
557
		foreach($project_runs as $run_id => $run_values) {
Jerome Mariette's avatar
Jerome Mariette committed
558
			tx_nG6_db::hide_run($run_values['id']);
559
560
561
		}

		// Then all project analysis
Jerome Mariette's avatar
Jerome Mariette committed
562
    	$project_analysis = tx_nG6_db::get_project_analysis($p_id);
563
564
565
566
567
568
569
570
571
572
573
574
575
		foreach($project_analysis as $analysis_id => $analysis_values) {  
			tx_nG6_db::hide_analysis($analysis_values['id']);
		}
		
		// Finaly change the project itself
		$GLOBALS['TYPO3_DB']-> exec_UPDATEquery ('tx_nG6_project', 'uid='.$p_id, array('hidden' => '1'));
	}

    /**
     * Unhide a project and sublevels (runs & analyzes) datas
     * 
     * @param	string	$p_id	the project id to hide
     */
Jerome Mariette's avatar
Jerome Mariette committed
576
	function unhide_project($p_id) {
577
578
		
		// First change all project runs
Jerome Mariette's avatar
Jerome Mariette committed
579
		$project_runs = tx_nG6_db::get_project_runs($p_id);
580
		foreach($project_runs as $run_id => $run_values) {
Jerome Mariette's avatar
Jerome Mariette committed
581
			tx_nG6_db::unhide_run($run_values['id']);
582
583
584
		}

		// Then all project analysis
Jerome Mariette's avatar
Jerome Mariette committed
585
    	$project_analysis = tx_nG6_db::get_project_analysis($p_id);
586
587
588
589
590
591
592
593
594
595
596
597
598
		foreach($project_analysis as $analysis_id => $analysis_values) {  
			tx_nG6_db::unhide_analysis($analysis_values['id']);
		}
		
		// Finaly change the project itself
		$GLOBALS['TYPO3_DB']-> exec_UPDATEquery ('tx_nG6_project', 'uid='.$p_id, array('hidden' => '0'));
	}

    /**
     * Publish the project
     * 
     * @param	string	$p_id	the project id to publish
     */
Jerome Mariette's avatar
Jerome Mariette committed
599
	function publish_project($p_id) {
600
		// First unhide the project
Jerome Mariette's avatar
Jerome Mariette committed
601
		tx_nG6_db::unhide_project($p_id);
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
		// The set the project as visible
		$GLOBALS['TYPO3_DB']-> exec_UPDATEquery ('tx_nG6_project', 'uid='.$p_id, array('public' => '0'));
	}

    /**
     * Unpublish the project
     * 
     * @param	string	$p_id	the project id to publish
     */
	function unpublish_project($p_id) {
		$GLOBALS['TYPO3_DB']-> exec_UPDATEquery ('tx_nG6_project', 'uid='.$p_id, array('public' => '1'));
	}

    /**
     * Delete a project and sublevels (runs & analyzes) datas from database project
     * 
     * @param string $p_id			the project id
     * @param string $user_login	the user login
     * @param string $user_pwd		the user password
     * @param string $data_folder	the data folder
     */
Jerome Mariette's avatar
Jerome Mariette committed
623
	function delete_project($p_id, $user_login, $user_pwd, $data_folder) {
624
625
626
		
		$res = 0;
		// All runs
Jerome Mariette's avatar
Jerome Mariette committed
627
		$project_runs = tx_nG6_db::get_project_runs($p_id);
628
629
630
		foreach($project_runs as $run_id => $run_values) {
			if ($run_values['id'] != 'undefined' && $run_values['id'] != '') {
				//delete the run sublevels
Jerome Mariette's avatar
Jerome Mariette committed
631
				$res = tx_nG6_db::delete_run($run_values['id'], $user_login, $user_pwd, $data_folder);
632
633
634
635
636
637
				if ($res != 0) { break; }				
			}
		}
		
		// All project_analysis
		if ($res == 0) {
Jerome Mariette's avatar
Jerome Mariette committed
638
			$project_analysis = tx_nG6_db::get_project_analysis($p_id);
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
			foreach($project_analysis as $analyse_id => $analyze_values) {  
				if ($analyze_values['id'] != 'undefined' && $analyze_values['id'] != '') {
					// delete table 'analyze' entries
					$res = tx_nG6_db::delete_analysis($analyze_values['id'], $user_login, $user_pwd, $data_folder);
					if ($res != 0) { break; }
				}
			}
		}
		
		// Delete DB project entry
		if ($res == 0) {
			$table='tx_nG6_project';
			$where='tx_nG6_project.uid='.$p_id;
			$res1 = $GLOBALS['TYPO3_DB']-> exec_DELETEquery ($table, $where);
			if ($res1 != 1) {$res = 1;}
		}
		
		return $res;
	}

659
660
661
662
663
    /**
     * Return the size of the project
     * 
     * @param	string	$p_id	the project id to return the size
	 * @param	string	$data_folder	the data folder
Jerome Mariette's avatar
Jerome Mariette committed
664
	 * @param	boolean $get_analyzes	get analyzes size ? 
665
     */
Jerome Mariette's avatar
Jerome Mariette committed
666
	function get_project_size($p_id, $data_folder, $get_analyzes=false) {
667
668
669
		
		$full_size = 0;
		// All runs
Jerome Mariette's avatar
Jerome Mariette committed
670
		$project_runs = tx_nG6_db::get_project_runs($p_id);
671
		foreach($project_runs as $run_id => $run_values) {
Jerome Mariette's avatar
Jerome Mariette committed
672
			$full_size += tx_nG6_db::get_run_size($run_values['id'], $data_folder, $get_analyzes);
673
		}
Jerome Mariette's avatar
Jerome Mariette committed
674
675
676
677
678
679
		if ($get_analyzes) {
			// All analysis
			$project_analysis = tx_nG6_db::get_project_analysis($p_id);
			foreach($project_analysis as $analyse_id => $analyze_values) {  
				$full_size += tx_nG6_db::get_analysis_size($analyze_values['id'], $data_folder);
			}
680
681
682
683
		}
		return $full_size;
	}

684
685
686
687

	/*
	 * Run functions
	 *------------------------------------------------------------*/
688
689
	
	
Jerome Mariette's avatar
Jerome Mariette committed
690
691
	/**
	 * Select all run for the specified user
692
	 * 
693
	 * @param	string	$user_id	the user id
Jerome Mariette's avatar
Jerome Mariette committed
694
695
	 * @return	table with all projects
	 */
696
	function select_all_user_runs($user_id, $orderby='', $limit='') {
697

Jerome Mariette's avatar
Jerome Mariette committed
698
		// If the user is not logged on display demonstration project
Jerome Mariette's avatar
Jerome Mariette committed
699
700
701
		if ($user_id == null) { $where = 'tx_nG6_project.public=0'; } 
		else { $where = 'fe_rights.fe_user_id='.$user_id; }
		
Jerome Mariette's avatar
Jerome Mariette committed
702
     	// Execute the request
703
		$queryParts = Array( 
Jerome Mariette's avatar
Jerome Mariette committed
704
705
706
707
			'SELECT' => 'tx_nG6_run.uid AS run_id,'.
					 	'tx_nG6_run.directory AS run_directory,'.
					 	'tx_nG6_run.species AS run_species,'.
						'tx_nG6_run.description AS run_description, '.
708
						'tx_nG6_run.data_nature AS run_data_nature, '. 
Jerome Mariette's avatar
Jerome Mariette committed
709
710
711
712
713
714
715
716
						'tx_nG6_run.sequencer AS run_sequencer, '.
						'tx_nG6_run.type AS run_type, '.
						'tx_nG6_run.name AS run_name, '.
						'tx_nG6_run.nb_sequences AS run_nb_sequences, '.
						'tx_nG6_run.full_seq_size AS run_full_seq_size, '.
						'tx_nG6_run.date AS run_date, '.
						'tx_nG6_run.hidden AS run_hidden, '.
						'tx_nG6_project.uid AS project_id, '.
717
718
719
720
721
						'tx_nG6_project.name AS project_name ',
			'FROM' => 'fe_rights '.
						'INNER JOIN tx_nG6_project ON tx_nG6_project.uid=fe_rights.project_id '.
						'INNER JOIN tx_nG6_project_run ON tx_nG6_project.uid=tx_nG6_project_run.project_id '.
						'INNER JOIN tx_nG6_run ON tx_nG6_project_run.run_id=tx_nG6_run.uid ',
Jerome Mariette's avatar
Jerome Mariette committed
722
723
724
725
			'WHERE' => $where,
			'GROUPBY' => '',
			'ORDERBY' => $orderby,
			'LIMIT' 	=> $limit
726
		); 
Jerome Mariette's avatar
Jerome Mariette committed
727
728
729
730
		// Then create the result hash table
		$results = array();
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
Jerome Mariette's avatar
Jerome Mariette committed
731
732
			$run_id = $row['run_id'];	
			if (!isset($results['run_'.$run_id])) {				
Jerome Mariette's avatar
Jerome Mariette committed
733
				$results['run_'.$run_id] = array(
734
735
					'id'			=> $run_id,  
					'directory'		=> $row['run_directory'], 
Jerome Mariette's avatar
Jerome Mariette committed
736
737
738
739
740
741
742
743
744
745
746
					'name' 			=> $row['run_name'],
					'project_name' 	=> $row['project_name'],
					'project_id' 	=> $row['project_id'],
					'hidden'		=> $row['run_hidden'],
					'species' 		=> $row['run_species'],
					'nb_sequences' 	=> $row['run_nb_sequences'],
					'full_seq_size' => $row['run_full_seq_size'],
					'date'			=> $row['run_date'],
					'data_nature'	=> $row['run_data_nature'],
					'sequencer'		=> $row['run_sequencer'],
					'type'			=> $row['run_type'],
747
					'description' 	=> $row['run_description']				
Jerome Mariette's avatar
Jerome Mariette committed
748
				);
749
			}						
Jerome Mariette's avatar
Jerome Mariette committed
750
751
752
753
754
		}
		return $results;

	}

755
756
757
758
759
760
	/**
	 * Select all information for the specified run
	 *
	 * @param	string	$run_id	the run id
	 * @return	hash table with all the run information
	 */
Jerome Mariette's avatar
Jerome Mariette committed
761
	function select_run($run_id) {
762
		
763
		// First select the run from the database
764
		$queryParts = Array( 
765
766
767
768
769
			'SELECT' => 'tx_nG6_project.uid AS project_id,'.
						'tx_nG6_project.name AS project_name,'.
						'tx_nG6_run.uid AS run_id,'.
					 	'tx_nG6_run.directory AS run_directory,'.
						'tx_nG6_run.description AS run_description, '.
Jerome Mariette's avatar
Jerome Mariette committed
770
						'tx_nG6_run.species AS run_species, '.
771
						'tx_nG6_run.name AS run_name, '.
Jerome Mariette's avatar
Jerome Mariette committed
772
773
774
775
						'tx_nG6_run.data_nature AS run_data_nature, '.
						'tx_nG6_run.sequencer AS run_sequencer, '.
						'tx_nG6_run.type AS run_type, '.
						'tx_nG6_run.full_seq_size, '.
Jerome Mariette's avatar
Jerome Mariette committed
776
						'tx_nG6_run.hidden AS run_hidden, '.
777
778
						'tx_nG6_run.nb_sequences, '.
						'tx_nG6_run.date AS run_date',
779
780
781
782
			'FROM' => 'fe_rights '.
						'INNER JOIN tx_nG6_project ON tx_nG6_project.uid=fe_rights.project_id '.
						'INNER JOIN tx_nG6_project_run ON tx_nG6_project.uid=tx_nG6_project_run.project_id '.
						'INNER JOIN tx_nG6_run ON tx_nG6_project_run.run_id=tx_nG6_run.uid ',
783
784
785
786
			'WHERE' => 'tx_nG6_run.uid='.$run_id,
			'GROUPBY' => '',
			'ORDERBY' => 'tx_nG6_run.date DESC',
			'LIMIT' 	=> ''
787
		); 
788
789
790
		// Then create the result hash table
		$result = array();
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
791
792
		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {			
			$result = array( 
Jerome Mariette's avatar
Jerome Mariette committed
793
				'id'			=> $row['run_id'],  
794
795
796
				'project_id'	=> $row['project_id'], 
				'project_name'	=> $row['project_name'], 
				'directory'		=> $row['run_directory'], 
Jerome Mariette's avatar
Jerome Mariette committed
797
				'name' 			=> $row['run_name'],
Jerome Mariette's avatar
Jerome Mariette committed
798
				'hidden'		=> $row['run_hidden'],
Jerome Mariette's avatar
Jerome Mariette committed
799
800
				'species' 		=> $row['run_species'],
				'nb_sequences' 	=> $row['nb_sequences'],
Jerome Mariette's avatar
Jerome Mariette committed
801
				'full_seq_size' => $row['full_seq_size'],
Jerome Mariette's avatar
Jerome Mariette committed
802
				'date'			=> $row['run_date'],
Jerome Mariette's avatar
Jerome Mariette committed
803
804
805
				'data_nature' 	=> $row['run_data_nature'],
				'sequencer' 	=> $row['run_sequencer'],
				'type' 			=> $row['run_type'],
806
807
				'description' 	=> $row['run_description']				
			);					
808
809
810
		}
		return $result;
    }
811

812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
	/**
	 * Select all mids linked to the specified run
	 *
	 * @param	string	$run_id	the run id
	 * @return	hash table with all mids description
	 */
	function select_mid_descriptions($run_id) {
		
		// First select all analysis from the database
		$queryParts = array( 
			'SELECT' => 'mid, description ',
			'FROM' => 'tx_nG6_sample ',
			'WHERE' => 'run_id='.$run_id,
			'GROUPBY' => '',
			'ORDERBY' => '',
			'LIMIT' => ''
		);
		
		$result = array();
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
			$result[$row["mid"]] = $row["description"];
		}
		return $result;
		
	}	

839
840
841
842
843
844
	/**
	 * Select all analysis linked to the specified run
	 *
	 * @param	string	$run_id	the run id
	 * @return	hash table with all analysis information
	 */
Jerome Mariette's avatar
Jerome Mariette committed
845
    function get_run_analysis($run_id, $orderby='', $limit='') {
846
		// First select all analysis from the database
847
848
849
		$queryParts = array( 
			'SELECT' => 'tx_nG6_analyze.uid AS analyze_id,'. 
						'tx_nG6_analyze.directory AS analyze_directory,'. 
850
						'tx_nG6_analyze.name AS analyze_name, '.
851
852
						'tx_nG6_analyze.params AS analyze_params, '.
						'tx_nG6_analyze.class AS analyze_class, '.
853
						'tx_nG6_analyze.date AS analyze_date, '.
Jerome Mariette's avatar
Jerome Mariette committed
854
855
						'tx_nG6_analyze.software AS analyze_software, '.
						'tx_nG6_analyze.version AS analyze_version, '.
856
857
						'tx_nG6_analyze.hidden AS analyze_hidden, '.
						'tx_nG6_analyze.description AS analyze_description, '.
858
						'tx_nG6_analyze.parent_uid AS analyze_parent_uid ',
Jerome Mariette's avatar
Jerome Mariette committed
859
			'FROM' => 'tx_nG6_run_analyze '.
860
						'INNER JOIN tx_nG6_analyze ON tx_nG6_analyze.uid = tx_nG6_run_analyze.analyze_id ',
Jerome Mariette's avatar
Jerome Mariette committed
861
			'WHERE' => 'tx_nG6_run_analyze.run_id='.$run_id,
862
			'GROUPBY' => '',
Jerome Mariette's avatar
Jerome Mariette committed
863
864
			'ORDERBY' => $orderby,
			'LIMIT' => $limit
865
866
867
868
869
870
		);
		// Then create the result hash table
		$results = array();
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
			$analyze_id = $row['analyze_id'];
Jerome Mariette's avatar
Jerome Mariette committed
871
			if (!isset ($results['analyse_'.$analyze_id])) {				
872
873
				$results['analyse_'.$analyze_id] = array( 
					'directory'		=> $row['analyze_directory'], 
Jerome Mariette's avatar
Jerome Mariette committed
874
					'name' 			=> $row['analyze_name'],
875
876
					'params' 		=> $row['analyze_params'],
					'class' 		=> $row['analyze_class'],
Jerome Mariette's avatar
Jerome Mariette committed
877
878
879
880
881
					'id' 			=> $row['analyze_id'],
					'hidden' 		=> $row['analyze_hidden'],
					'software' 		=> $row['analyze_software'],
					'version' 		=> $row['analyze_version'],
					'date'			=> $row['analyze_date'],
Jerome Mariette's avatar
Jerome Mariette committed
882
883
					'description' 	=> $row['analyze_description'],
					'parent_id'		=> $row['analyze_parent_uid']
884
				);
885
			}						
886
887
888
889
		}
		return $results;
    }

Penom Nom's avatar
Penom Nom committed
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
    /**
    * Select all analysis linked to the specified run for the user
    *
    * @param	string	$user_id	the user id
    * @param	string	$run_id	the run id
    * @return	hash table with all analysis information
    */
    function get_user_run_analysis($user_id, $run_id, $orderby='', $limit='') {
    	// If the user is not logged on display demonstration project
    	if ($user_id == null) {
    		$where = 'tx_nG6_run_analyze.run_id='.$run_id.' AND tx_nG6_project.public=0 AND tx_nG6_analyze.hidden=0' ;
    	}
    	else {
    		$where = 'fe_users.uid='.$user_id.' AND '.'tx_nG6_run_analyze.run_id='.$run_id.
    	    					' AND ((fe_rights.right_id<>2 AND tx_nG6_analyze.hidden=0) OR fe_rights.right_id=2)' ;
    	}
    	
    	// First select all analysis from the database
    	$queryParts = array(
    			'SELECT' => 'tx_nG6_analyze.uid AS analyze_id,'. 
    						'tx_nG6_analyze.directory AS analyze_directory,'. 
    						'tx_nG6_analyze.name AS analyze_name, '.
    						'tx_nG6_analyze.params AS analyze_params, '.
    						'tx_nG6_analyze.class AS analyze_class, '.
    						'tx_nG6_analyze.date AS analyze_date, '.
    						'tx_nG6_analyze.software AS analyze_software, '.
    						'tx_nG6_analyze.version AS analyze_version, '.
    						'tx_nG6_analyze.hidden AS analyze_hidden, '.
    						'tx_nG6_analyze.description AS analyze_description, '.
    						'tx_nG6_analyze.parent_uid AS analyze_parent_uid ',
    			'FROM' => 'tx_nG6_analyze '.
							'INNER JOIN tx_nG6_run_analyze ON tx_nG6_analyze.uid = tx_nG6_run_analyze.analyze_id '.
							'INNER JOIN tx_nG6_run ON tx_nG6_run_analyze.run_id = tx_nG6_run.uid '.
							'INNER JOIN tx_nG6_project_run ON tx_nG6_run.uid = tx_nG6_project_run.run_id '.
							'INNER JOIN tx_nG6_project ON tx_nG6_project_run.project_id = tx_nG6_project.uid '. 
							'INNER JOIN fe_rights ON tx_nG6_project.uid=fe_rights.project_id '.
							'INNER JOIN fe_users ON fe_rights.fe_user_id=fe_users.uid ',
    			'WHERE' => $where,
    			'GROUPBY' => '',
    			'ORDERBY' => $orderby,
    			'LIMIT' => $limit
    	);
    	// Then create the result hash table
    	$results = array();
    	$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
    	while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
    		$analyze_id = $row['analyze_id'];
    		if (!isset ($results['analyse_'.$analyze_id])) {
    			$results['analyse_'.$analyze_id] = array(
    					'directory'		=> $row['analyze_directory'], 
    					'name' 			=> $row['analyze_name'],
    					'params' 		=> $row['analyze_params'],
    					'class' 		=> $row['analyze_class'],
    					'id' 			=> $row['analyze_id'],
    					'hidden' 		=> $row['analyze_hidden'],
    					'software' 		=> $row['analyze_software'],
    					'version' 		=> $row['analyze_version'],
    					'date'			=> $row['analyze_date'],
    					'description' 	=> $row['analyze_description'],
    					'parent_id'		=> $row['analyze_parent_uid']
    			);
    		}
    	}
    	return $results;
    }

956
957
958
959
960
961
962
963
	/**
	 * Delete a run, sample and sublevel (analyzes) datas from database project
	 * 
	 * @param string $r_id			the run id
	 * @param string $user_login	the user login
	 * @param string $user_pwd		the user password
	 * @param string $data_folder	the data folder
	 */
Jerome Mariette's avatar
Jerome Mariette committed
964
	function delete_run($r_id, $user_login, $user_pwd, $data_folder) {		
965
966

		$res = 0;		
Jerome Mariette's avatar
Jerome Mariette committed
967
		$run_analysis = tx_nG6_db::get_run_analysis($r_id);
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
		foreach($run_analysis as $analyse_id => $analyze_values) {
			if ($analyze_values['id'] != 'undefined' && $analyze_values['id'] != '') {				
				// delete table 'analyze' entries
				$res = tx_nG6_db::delete_analysis($analyze_values['id'], $user_login, $user_pwd, $data_folder);
				if ($res != 0) { break; }
			}
		}
		
		// First select the run
		$my_run = tx_nG6_db::select_run($r_id);
		
		// delete run
		if ($res == 0) {
			$table='tx_nG6_project_run';
			$where='run_id='.$r_id;
			$GLOBALS['TYPO3_DB']-> exec_DELETEquery ($table, $where);
			
			$table='tx_nG6_run';
			$where='tx_nG6_run.uid='.$r_id;
			$res1 = $GLOBALS['TYPO3_DB']-> exec_DELETEquery ($table, $where);
			if ($res1 != 1) {$res = 1;}
		}
			
		// delete run samples
		if ($res == 0) {
			$table='tx_nG6_sample';
			$where='tx_nG6_sample.run_id='.$r_id;
			$GLOBALS['TYPO3_DB']-> exec_DELETEquery ($table, $where);
		}
		
		if ($res == 0) {
			// Delete the run directory
			$res = tx_nG6_utils::delete_directory($user_login, $user_pwd, $data_folder.$my_run['directory']);
		}
		
		return $res;
	}

1006
1007
1008
1009
1010
    /**
     * Return the size of the run
     * 
     * @param	string	$r_id	the run id to return the size
	 * @param	string	$data_folder	the data folder
Jerome Mariette's avatar
Jerome Mariette committed
1011
	 * @param	boolean $get_analyzes	get analyzes size ? 
1012
     */
Jerome Mariette's avatar
Jerome Mariette committed
1013
	function get_run_size($r_id, $data_folder, $get_analyzes=false) {
1014
		$full_size = 0;
Jerome Mariette's avatar
Jerome Mariette committed
1015
1016
1017
1018
1019
		if($get_analyzes){
			$run_analysis = tx_nG6_db::get_run_analysis($r_id);
			foreach($run_analysis as $analyse_id => $analyze_values) {
				$full_size += tx_nG6_db::get_analysis_size($analyze_values['id'], $data_folder);
			}
1020
1021
1022
		}
		// Then select the run
		$my_run = tx_nG6_db::select_run($r_id);
Jerome Mariette's avatar
Jerome Mariette committed
1023
		foreach(scandir($data_folder.$my_run['directory']) as $file) {			
1024
1025
1026
			if (is_file($data_folder.$my_run['directory']."/".$file)) {
				$full_size += filesize($data_folder.$my_run['directory']."/".$file);
			}
Jerome Mariette's avatar
Jerome Mariette committed
1027
		}		
1028
1029
1030
		return $full_size;
	}

1031
1032
1033
1034
1035
    /**
     * Hide a run and sublevels (analysis)
     * 
     * @param	string	$r_id	the run id to hide
     */
Jerome Mariette's avatar
Jerome Mariette committed
1036
	function hide_run($r_id) {
1037
1038

		// First select all run analysis
Jerome Mariette's avatar
Jerome Mariette committed
1039
    	$run_analysis = tx_nG6_db::get_run_analysis($r_id);
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
		foreach($run_analysis as $analysis_id => $analysis_values) {  
			tx_nG6_db::hide_analysis($analysis_values['id']);
		}
		
		// Finaly change the project itself
		$GLOBALS['TYPO3_DB']-> exec_UPDATEquery ('tx_nG6_run', 'uid='.$r_id, array('hidden' => '1'));
	}

    /**
     * Unhide a run and sublevels (analysis)
     * 
     * @param	string	$r_id	the run id to hide
     */
Jerome Mariette's avatar
Jerome Mariette committed
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
	function unhide_run($r_id, $unhide_up=false) {
	
		if ($unhide_up) {
			// Unhide the project
			$GLOBALS['TYPO3_DB']-> exec_UPDATEquery (
				'tx_nG6_project, tx_nG6_project_run',
				'tx_nG6_project.uid = tx_nG6_project_run.project_id AND tx_nG6_project_run.run_id = '.$r_id ,
				array('tx_nG6_project.hidden' => '0')
			);
		}
1063
1064

		// Then all run analysis
Jerome Mariette's avatar
Jerome Mariette committed
1065
    	$run_analysis = tx_nG6_db::get_run_analysis($r_id);
1066
1067
		foreach($run_analysis as $analysis_id => $analysis_values) {  
			tx_nG6_db::unhide_analysis($analysis_values['id']);
Jerome Mariette's avatar
Jerome Mariette committed
1068
		}
1069
1070
1071
1072
		
		// Finaly change the run itself
		$GLOBALS['TYPO3_DB']-> exec_UPDATEquery ('tx_nG6_run', 'uid='.$r_id, array('hidden' => '0'));
	}
1073

Jerome Mariette's avatar
Jerome Mariette committed
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
    /**
     * Get the run min date
     * 
     * @return int timestamp
     */
    function get_run_min_date(){
    	$queryParts = Array(
    		'SELECT' 	=> 'MIN(tx_nG6_run.date) as min_date ',
    		'FROM' 		=> 'tx_nG6_run',
    		'WHERE' 	=> 'tx_nG6_run.date!=0',
    		'GROUPBY' 	=> '',
    		'ORDERBY' 	=> '',
    		'LIMIT' 	=> ''
    	);
    	$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
   		$min_date = 0;
    	if($GLOBALS['TYPO3_DB']->sql_num_rows($res) == 1) {
    		$tab = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res);
    		$min_date = intval($tab['min_date']);
    	}else{
    		$min_date = -1;
    	}
    	return $min_date;
    }
    
    /**
    * Get the run max date
    *
    * @return int timestamp
    */
    function get_run_max_date(){
    	$queryParts = Array(
        		'SELECT' 	=> 'MAX(tx_nG6_run.date) as max_date ',
        		'FROM' 		=> 'tx_nG6_run',
        		'WHERE' 	=> 'tx_nG6_run.date!=0',
        		'GROUPBY' 	=> '',
        		'ORDERBY' 	=> '',
        		'LIMIT' 	=> ''
    	);
    	$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
    	$max_date = 0;
    	if($GLOBALS['TYPO3_DB']->sql_num_rows($res) == 1) {
    		$tab = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res);
    		$max_date = intval($tab['max_date']);
    	}else{
    		$max_date = -1;
    	}
    	return $max_date;
    }
    
1124
	/*
1125
	 * Analysis functions
1126
	 *------------------------------------------------------------*/
1127
	 
1128
1129
1130
1131
1132
1133
	/**
	 * Select all information on an analyse
	 *
	 * @param	string	$analyse_id	the analyse id
	 * @return	hash table with all analyse information
	 */
Jerome Mariette's avatar
Jerome Mariette committed
1134
1135
    function select_analyse($analyse_id) {

1136
		// First select all analyse information
1137
1138
1139
1140
1141
		$queryParts = array( 
			'SELECT' => 'tx_nG6_project.uid AS project_id,'. 
						'tx_nG6_project.name AS project_name,'. 
						'tx_nG6_analyze.uid AS analyze_id,'. 
						'tx_nG6_analyze.directory AS analyze_directory,'. 
1142
						'tx_nG6_analyze.name AS analyze_name, '.
1143
						'tx_nG6_analyze.params AS analyze_params, '.
Jerome Mariette's avatar
Jerome Mariette committed
1144
						'tx_nG6_analyze.software AS analyze_software, '.
1145
						'tx_nG6_analyze.class AS analyze_class, '.
1146
						'tx_nG6_analyze.date AS analyze_date, '.
Jerome Mariette's avatar
Jerome Mariette committed
1147
1148
1149
						'tx_nG6_analyze.description AS analyze_description, '.
						'tx_nG6_analyze.version AS analyze_version, '.
						'tx_nG6_analyze.parent_uid AS analyze_parent_uid ',
1150
1151
1152
			'FROM' => 'tx_nG6_project '.
						'INNER JOIN tx_nG6_project_analyze ON tx_nG6_project.uid = tx_nG6_project_analyze.project_id '.
						'INNER JOIN tx_nG6_analyze ON tx_nG6_analyze.uid=tx_nG6_project_analyze.analyze_id ',
1153
1154
1155
1156
1157
			'WHERE' => 'tx_nG6_analyze.uid='.$analyse_id,
			'GROUPBY' => '',
			'ORDERBY' => '',
			'LIMIT' => ''
		);
1158
		
1159
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
1160
		
1161
1162
1163
		// If it's a project analyse, add project information
		if ($GLOBALS['TYPO3_DB']->sql_num_rows($res) > 0) {
			$result = array();
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
			while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {	
				$result = array( 
					'project_name'	=> $row['project_name'], 
					'project_id'	=> $row['project_id'],
					'run_name'		=> 'None', 
					'run_id'		=> 'None',					 
					'directory'		=> $row['analyze_directory'], 
					'name' 			=> $row['analyze_name'],
					'class'			=> $row['analyze_class'],
					'params'		=> $row['analyze_params'],
					'date'			=> $row['analyze_date'],
Jerome Mariette's avatar
Jerome Mariette committed
1175
1176
1177
1178
					'description' 	=> $row['analyze_description'],
					'parent_id'		=> $row['analyze_parent_uid'],
					'software'		=> $row['analyze_software'],
					'version'		=> $row['analyze_version']				
1179
				);				
1180
1181
1182
			}
			return $result;
		} else { // If it's a run analyse, add run information
1183
			$queryParts = array( 
1184
1185
				'SELECT' => 'tx_nG6_project.name AS project_name,'.
							'tx_nG6_project.uid AS project_id,'.
1186
							'tx_nG6_run.uid AS run_id,'. 
1187
							'tx_nG6_run.name AS run_name,'.
1188
1189
							'tx_nG6_analyze.uid AS analyze_id,'. 
							'tx_nG6_analyze.directory AS analyze_directory,'. 
1190
							'tx_nG6_analyze.name AS analyze_name, '.
1191
1192
							'tx_nG6_analyze.params AS analyze_params, '.
							'tx_nG6_analyze.class AS analyze_class, '.
1193
							'tx_nG6_analyze.date AS analyze_date, '.
Jerome Mariette's avatar
Jerome Mariette committed
1194
1195
1196
1197
							'tx_nG6_analyze.software AS analyze_software, '.
							'tx_nG6_analyze.version AS analyze_version, '.
							'tx_nG6_analyze.description AS analyze_description,'.
							'tx_nG6_analyze.parent_uid AS analyze_parent_uid ',
1198
				'FROM' => 'tx_nG6_project '.
Jerome Mariette's avatar
Jerome Mariette committed
1199
							'INNER JOIN tx_nG6_project_run ON tx_nG6_project_run.project_id = tx_nG6_project.uid '.
1200
1201
1202
							'INNER JOIN tx_nG6_run ON tx_nG6_run.uid = tx_nG6_project_run.run_id '.
							'INNER JOIN tx_nG6_run_analyze ON tx_nG6_run_analyze.run_id = tx_nG6_run.uid '.
							'INNER JOIN tx_nG6_analyze ON tx_nG6_analyze.uid = tx_nG6_run_analyze.analyze_id ',
1203
1204
1205
1206
1207
1208
1209
				'WHERE' => 'tx_nG6_analyze.uid='.$analyse_id,
				'GROUPBY' => '',
				'ORDERBY' => 'tx_nG6_analyze.name',
				'LIMIT' => ''
			);
			$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
			$result = array();
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
			while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {	
				$result = array( 
					'project_name'	=> $row['project_name'], 
					'project_id'	=> $row['project_id'],
					'run_name'		=> $row['run_name'], 
					'run_id'		=> $row['run_id'], 			 
					'directory'		=> $row['analyze_directory'], 
					'name' 			=> $row['analyze_name'],
					'params'		=> $row['analyze_params'],
					'class' 		=> $row['analyze_class'],
					'date'			=> $row['analyze_date'],
Jerome Mariette's avatar
Jerome Mariette committed
1221
1222
1223
1224
					'description' 	=> $row['analyze_description'],
					'software'		=> $row['analyze_software'],
					'parent_id'		=> $row['analyze_parent_uid'],
					'version'		=> $row['analyze_version']			
1225
				);				
1226
1227
1228
1229
			}
			return $result;
		}
    }
1230

1231
1232
1233
1234
1235
1236
1237
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247
1248
1249
1250
1251
1252
1253
1254
1255
1256
1257
1258
1259
1260
1261
1262
1263
	/**
	 * Select all results of an analyse
	 *
	 * @param	string	$analyse_id	the analyse id
	 * @return	hash table with all analyse results
	 */
    function select_analyse_results($analyse_id) {

		// First select all analyse information
		$queryParts = array( 
			'SELECT' => 'uid,file,rkey,rvalue,rgroup ',
			'FROM' => 'tx_nG6_result ',
			'WHERE' => 'analyze_id='.$analyse_id,
			'GROUPBY' => '',
			'ORDERBY' => '',
			'LIMIT' => ''
		);
		
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
		$result = array();
		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
			if (array_key_exists($row['file'], $result)) {
				if (array_key_exists($row['rgroup'], $result[$row['file']])) {
					$result[$row['file']][$row['rgroup']][$row['rkey']] = $row['rvalue'];
				} else {
					$result[$row['file']][$row['rgroup']] = array($row['rkey'] => $row['rvalue']);
				}
			} else {
				$result[$row['file']] = array($row['rgroup'] => array($row['rkey'] => $row['rvalue']));
			}			
		}
		return $result;
    }
1264

1265
1266
1267
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
    /**
     * Return the size of the analysis
     * 
     * @param	string	$a_id	the analysis id to return the size
	 * @param	string	$data_folder	the data folder
     */
	function get_analysis_size($a_id, $data_folder) {
		// First select the analyse
		$my_analysis = tx_nG6_db::select_analyse($a_id);
		$full_size = 0;
		foreach(scandir($data_folder.$my_analysis['directory']) as $file) {
			if (is_file($data_folder.$my_analysis['directory']."/".$file)) {
				$full_size += filesize($data_folder.$my_analysis['directory']."/".$file);
			}
		}
		return $full_size;
	}

1283
1284
1285
1286
1287
1288
1289
1290
1291
1292
1293
1294
1295
1296
1297
    /**
     * Hide an analysis
     * 
     * @param	string	$a_id	the analysis id to hide
     */
	function hide_analysis($a_id) {
		// Change the analysis itself
		$GLOBALS['TYPO3_DB']-> exec_UPDATEquery ('tx_nG6_analyze', 'uid='.$a_id, array('hidden' => '1'));
	}

    /**
     * Unhide an analysis
     * 
     * @param	string	$a_id	the analysis id to hide
     */
Jerome Mariette's avatar
Jerome Mariette committed
1298
1299
1300
1301
1302
1303
1304
1305
1306
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
1324
1325
1326
1327
1328
1329
1330
1331
1332
1333
1334
	function unhide_analysis($a_id, $unhide_up=false) {
	
		if ($unhide_up) {
			$queryParts = array(
				'SELECT'  => 'tx_nG6_project_analyze.uid',
				'FROM'    => 'tx_nG6_project_analyze',
				'WHERE'   => 'tx_nG6_project_analyze.analyze_id = '.$a_id,
				'GROUPBY' => '',
				'ORDERBY' => '',
				'LIMIT'   => ''
			);
			$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts) ;
			$is_project_analyze = $GLOBALS['TYPO3_DB']->sql_num_rows( $res ) ;
			
			// If the analyse isn't link to run
			if( $is_project_analyze ) 
			{
				// unhide the project
				$GLOBALS['TYPO3_DB']-> exec_UPDATEquery (
					'tx_nG6_project, tx_nG6_project_analyze',
					'tx_nG6_project.uid = tx_nG6_project_analyze.project_id AND tx_nG6_project_analyze.analyze_id = '.$a_id ,
					array('tx_nG6_project.hidden' => '0')
				) ;
			}
			// If the analyse is link to run
			else
			{
				// unhide the project and the run
				$GLOBALS['TYPO3_DB']->exec_UPDATEquery (
					'tx_nG6_project, tx_nG6_project_run, tx_nG6_run, tx_nG6_run_analyze', 
					'tx_nG6_project.uid = tx_nG6_project_run.project_id '.
						'AND tx_nG6_project_run.run_id = tx_nG6_run.uid '.
						'AND tx_nG6_run.uid = tx_nG6_run_analyze.run_id '.
						'AND tx_nG6_run_analyze.analyze_id = '.$a_id ,
					array('tx_nG6_project.hidden' => '0', 'tx_nG6_run.hidden' => '0')
				) ;
			}
1335
1336
		}

1337
1338
1339
1340
1341
1342
1343
1344
1345
1346
1347
1348
1349
1350
1351
1352
1353
1354
1355
1356
1357
1358
1359
1360
1361
1362
1363
1364
1365
1366
1367
1368
1369
1370
1371
1372
1373
1374
1375
1376
1377
1378
1379
1380
1381
1382
1383
		// Change the analysis itself
		$GLOBALS['TYPO3_DB']-> exec_UPDATEquery ('tx_nG6_analyze', 'uid='.$a_id, array('hidden' => '0'));
	}

	/**
	 * Delete an analyze and results from database project
	 * 
	 * @param string $a_id			the analyze id
	 * @param string $user_login	the user login
	 * @param string $user_pwd		the user password
	 * @param string $data_folder	the data folder
	 * @return	0=>everything ok, 1=>user right problem, 2=>wrong authentification, 3=>connection error
	 */
	function delete_analysis($a_id, $user_login, $user_pwd, $data_folder) {

		$res = 0;

		// First select the analyse
		$my_analysis = tx_nG6_db::select_analyse($a_id);
		
		// Delete the analysis results from the database
		$table='tx_nG6_result';
		$where='tx_nG6_result.analyze_id='.$a_id;
		$GLOBALS['TYPO3_DB']-> exec_DELETEquery ($table, $where);

		// Intermediate tables
		$table='tx_nG6_project_analyze';
		$where='analyze_id='.$a_id;
		$GLOBALS['TYPO3_DB']-> exec_DELETEquery ($table, $where);
		$table='tx_nG6_run_analyze';
		$where='analyze_id='.$a_id;
		$GLOBALS['TYPO3_DB']-> exec_DELETEquery ($table, $where);
		
		// Finaly the analysis itself
		$table='tx_nG6_analyze';
		$where='tx_nG6_analyze.uid='.$a_id;
		$res1 = $GLOBALS['TYPO3_DB']-> exec_DELETEquery ($table, $where);
		if ($res1 != 1) { $res = 1; } 
		
		if ($res == 0) {
			// Delete the analyse directory
			$res = tx_nG6_utils::delete_directory($user_login, $user_pwd, $data_folder.$my_analysis['directory']);
		}

		return $res;
	}

1384
1385
1386
1387

	/*
	 * User functions
	 *------------------------------------------------------------*/
1388
	
1389
1390
1391
	/**
	 * Return if the user is authorized or not to access the specified project and run
	 *
1392
	 * @param	int	$user_id	the user id
1393
1394
1395
1396
	 * @param	string	$project_id	the project id
	 * @param	string	$project_id	the run id
	 * @return	boolean
	 */
1397
	function user_is_authorized ($user_id, $project_id, $run_id) {
1398
		$authorized = false;
1399
1400
1401
1402
1403
1404
1405
1406
1407
1408
1409
1410
1411
1412
1413
1414
1415
1416
1417
1418
1419
1420
1421
1422
1423
1424
1425
1426
1427
1428
1429
1430
1431
1432
1433
1434
1435
1436
1437
1438
1439
1440
1441
1442
1443
1444
1445
1446
1447
1448
1449
1450
1451
1452
		
		// public project ?
		$queryParts = array(
			'SELECT' => 'public',
			'FROM' => 'tx_nG6_project',
			'WHERE' => 'uid='.$project_id,
			'GROUPBY' => '',
			'ORDERBY' => '',
			'LIMIT' => ''
		);
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
		$val = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res);
		$authorized = ($val['public'] == 0);
		
		// not a public project
		if(!$authorized){
		
			// authorized in project ?
			if ($project_id) {			
				$queryParts = array(
					'SELECT' => 'fe_rights.right_id ',
					'FROM' => 'fe_rights INNER JOIN tx_nG6_project ON tx_nG6_project.uid=fe_rights.project_id ',
					'WHERE' => 'fe_rights.fe_user_id='.$user_id.' AND tx_nG6_project.uid='.$project_id,
					'GROUPBY' => '',
					'ORDERBY' => '',
					'LIMIT' => ''
				);
				$res1 = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
				$val = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res1);
				
				if(isset($val['right_id'])){
					$authorized = true;
				}
				
			// authorized in run ?
			} elseif ($run_id) {
				$queryParts = array(
					'SELECT' => 'fe_rights.right_id ',
					'FROM' => 'fe_rights '.
							'INNER JOIN tx_nG6_project ON tx_nG6_project.uid=fe_rights.project_id '.
							'INNER JOIN tx_nG6_project_run ON tx_nG6_project.uid=tx_nG6_project_run.project_id ',
					'WHERE' => 'fe_rights.fe_user_id='.$user_id.' AND tx_nG6_project_run.uid='.$run_id,
					'GROUPBY' => '',
					'ORDERBY' => '',
					'LIMIT' => ''
				);
				$res1 = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
				$val = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res1);
				
				if(isset($val['right_id'])){
					$authorized = true;
				}
				
			} 
1453
		}
1454
		return $authorized;
1455
	}
Jerome Mariette's avatar
Jerome Mariette committed
1456
1457

	/**
1458
	 * Return if the user is a superuser (administrator) for the specified project/run/analyse