class.tx_nG6_db.php 44.9 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
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
	
	/*
	 * Global functions
	*------------------------------------------------------------*/
	
	/**
	* Update the specified field of the table
	 *
	* @param	string  $entity the entity to change
	* @param	string  $id     the element id to update
	* @param	string  $field  the field to change
	* @param	string  $value  the new value
	*/
	function update_field($entity, $id, $field, $value) {
	
	if( $field == 'uid' )
		{
		throw new Exception ("The function 'update_field' cannot change an id.") ;
			}
	
			$GLOBALS['TYPO3_DB']-> exec_UPDATEquery ("tx_nG6_$entity", 'uid='.$id, array($field => $value));
	}
	
57
58
59
60
61
62
	/*
	 * Project functions
	 *------------------------------------------------------------*/

	/**
	 * Select all project for the current user
63
	 * 
64
65
66
	 * @param	string	$user_group	the user group
	 * @return	table with all projects
	 */
Jerome Mariette's avatar
Jerome Mariette committed
67
	function select_all_user_projects($user_group, $orderby='', $limit='') {
68
		
69
70
		$projects = array();
		// If the user is not logged on display demonstration project
71
		if (!$GLOBALS['TSFE']->loginUser) { 
72
			$where = 'public=0';
73
		} else {
74
			$where = 'fe_group IN ('.tx_nG6_db::get_user_groups($user_group).')';	
75
76
		}
		//First, get the analyzis project-scale
77
		$queryParts = array( 
78
79
80
81
			'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.fe_group AS project_fe_group, '.
82
						'tx_nG6_project.public AS project_public, '.
Jerome Mariette's avatar
Jerome Mariette committed
83
						'tx_nG6_project.crdate AS project_crdate, '.
84
85
86
87
						'tx_nG6_project.hidden AS project_hidden',
			'FROM' => 'tx_nG6_project',
			'WHERE' => $where,
			'GROUPBY' => '',
Jerome Mariette's avatar
Jerome Mariette committed
88
89
			'ORDERBY' => $orderby,
			'LIMIT' => $limit
90
91
92
93
94
		);
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
		$user_groups = t3lib_div::intExplode(',',tx_nG6_db::get_user_groups($user_group));
		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
			$project_id = $row['project_id'];
95
			
96
97
98
99
100
101
102
103
104
105
106
			// Is the user allowed to see this project
			$user_allowed = false;
			if ($row['project_hidden'] == 0) {
				$user_allowed = true;
			} else {
			    foreach(tx_nG6_db::get_super_groups_of($row['project_fe_group']) AS $valeur) {
					if (in_array($valeur, $user_groups)) {
						$user_allowed = true;
					}
			    }
			}
107
108
			
			if (!isset ($projects['project_'.$project_id]) and $user_allowed) {		
109
				$projects['project_'.$project_id] = array(
110
					'id'			=> $project_id,				
111
					'name'			=> $row['project_name'],
Jerome Mariette's avatar
Jerome Mariette committed
112
					'hidden'		=> $row['project_hidden'],
Jerome Mariette's avatar
Jerome Mariette committed
113
					'date'			=> $row['project_crdate'],
114
					'public'		=> $row['project_public'],
Jerome Mariette's avatar
Jerome Mariette committed
115
					'group'			=> $row['project_fe_group'],
116
117
					'description'	=> $row['project_description']);
			}
118
						
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
		}
		return $projects;
	}

	/**
	 * 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
139
140
141
142
		$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
143
					 'date'			=> $vals['crdate'],
Jerome Mariette's avatar
Jerome Mariette committed
144
145
146
					 'public'		=> $vals['public'],
					 'group'		=> $vals['fe_group'],
					 'description'	=> $vals['description']);
147
148
149
150
151
152
153
154
155
	}

	/**
	 * Select all runs linked to the specified project
	 *
	 * @param	string	$user_group	the user group
	 * @param	string	$project_id	the project id
	 * @return	hash table with all runs information
	 */
Jerome Mariette's avatar
Jerome Mariette committed
156
    function get_project_runs($user_group, $project_id, $orderby='', $limit='') {
157
		// First select all runs from the database
158
		$queryParts = Array( 
159
160
161
162
			'SELECT' => 'tx_nG6_run.uid AS run_id,'.
					 	'tx_nG6_run.directory AS run_directory,'.
					 	'tx_nG6_run.species AS run_species,'.
						'tx_nG6_run.description AS run_description, '.
Jerome Mariette's avatar
Jerome Mariette committed
163
164
165
						'tx_nG6_run.data_nature AS run_data_nature, '.
						'tx_nG6_run.sequencer AS run_sequencer, '.
						'tx_nG6_run.type AS run_type, '.
166
						'tx_nG6_run.name AS run_name, '.
Jerome Mariette's avatar
Jerome Mariette committed
167
168
169
						'tx_nG6_project.uid AS project_id, '.
						'tx_nG6_run.nb_sequences AS run_nb_sequences, '.
						'tx_nG6_run.full_seq_size AS run_full_seq_size, '.
170
171
						'tx_nG6_run.date AS run_date, '.
						'tx_nG6_run.hidden AS run_hidden, '.
Jerome Mariette's avatar
Jerome Mariette committed
172
						'tx_nG6_project.name AS project_name, '.
173
174
175
						'tx_nG6_project.fe_group AS project_fe_group',
			'FROM' => 'tx_nG6_project INNER JOIN ( tx_nG6_project_run INNER JOIN tx_nG6_run ON tx_nG6_project_run.run_id=tx_nG6_run.uid '.
					  ' ) ON tx_nG6_project.uid=tx_nG6_project_run.project_id',
176
			'WHERE' => 'tx_nG6_project.uid='.$project_id,
177
			'GROUPBY' => '',
Jerome Mariette's avatar
Jerome Mariette committed
178
179
			'ORDERBY' => $orderby,
			'LIMIT' 	=> $limit
180
		); 
181
182
183
184
185
186
		// Then create the result hash table
		$results = array();
		$user_groups = t3lib_div::intExplode(',',tx_nG6_db::get_user_groups($user_group));
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
			$run_id = $row['run_id'];
187
			
188
189
190
191
192
193
194
195
196
197
198
			// Is the user allowed to see this run
			$user_allowed = false;
			if ($row['run_hidden'] == 0) {
				$user_allowed = true;
			} else {
			    foreach(tx_nG6_db::get_super_groups_of($row['project_fe_group']) AS $valeur) {
					if (in_array($valeur, $user_groups)) {
						$user_allowed = true;
					}
			    }
			}
199
200
201
					
			if (!isset($results['run_'.$run_id]) and $user_allowed) {				
				$results['run_'.$run_id] = array( 
Jerome Mariette's avatar
Jerome Mariette committed
202
					'id'			=> $run_id,
203
					'directory'		=> $row['run_directory'], 
204
					'name' 			=> $row['run_name'],
Jerome Mariette's avatar
Jerome Mariette committed
205
206
207
					'project_name' 	=> $row['project_name'],
					'fe_group' 		=> $row['project_fe_group'],
					'hidden'		=> $row['run_hidden'],
208
					'species' 		=> $row['run_species'],
Jerome Mariette's avatar
Jerome Mariette committed
209
210
211
					'nb_sequences' 	=> $row['run_nb_sequences'],
					'full_seq_size' => $row['run_full_seq_size'],
					'project_id' 	=> $row['project_id'],
212
					'date'			=> $row['run_date'],
Jerome Mariette's avatar
Jerome Mariette committed
213
214
215
					'data_nature'	=> $row['run_data_nature'],
					'sequencer'		=> $row['run_sequencer'],
					'type'			=> $row['run_type'],
Jerome Mariette's avatar
Jerome Mariette committed
216
					'description' 	=> $row['run_description']
217
				);
218
			}						
219
220
221
222
223
224
225
226
227
228
229
		}
		return $results;
    }

	/**
	 * Select all analysis linked to the specified project
	 *
	 * @param	string	$user_group	the user group
	 * @param	string	$project_id	the project id
	 * @return	hash table with all analysis information
	 */
Jerome Mariette's avatar
Jerome Mariette committed
230
    function get_project_analysis($user_group, $project_id, $orderby='', $limit='') {
231
		// First select all analysis from the database
232
233
234
		$queryParts = array( 
			'SELECT' => 'tx_nG6_analyze.uid AS analyze_id,'. 
						'tx_nG6_analyze.directory AS analyze_directory,'. 
235
						'tx_nG6_analyze.name AS analyze_name, '.
236
						'tx_nG6_analyze.class AS analyze_class, '.
237
						'tx_nG6_analyze.date AS analyze_date, '.
Jerome Mariette's avatar
Jerome Mariette committed
238
239
						'tx_nG6_analyze.software AS analyze_software, '.
						'tx_nG6_analyze.version AS analyze_version, '.
240
						'tx_nG6_analyze.params AS analyze_params, '.
241
						'tx_nG6_analyze.description AS analyze_description, '.
Jerome Mariette's avatar
Jerome Mariette committed
242
						'tx_nG6_analyze.parent_uid AS analyze_parent_uid, '.
243
244
245
246
247
248
						'tx_nG6_analyze.hidden AS analyze_hidden, '.
						'tx_nG6_project.fe_group AS project_fe_group',
			'FROM' => 'tx_nG6_project INNER JOIN (tx_nG6_project_analyze INNER JOIN tx_nG6_analyze ON ' .
					  'tx_nG6_analyze.uid=tx_nG6_project_analyze.analyze_id) ON tx_nG6_project.uid = tx_nG6_project_analyze.project_id ',
			'WHERE' => 'tx_nG6_project_analyze.project_id='.$project_id,
			'GROUPBY' => '',
Jerome Mariette's avatar
Jerome Mariette committed
249
250
			'ORDERBY' => $orderby,
			'LIMIT' => $limit
251
252
253
254
255
256
257
		);
		// Then create the result hash table
		$results = array();
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
		$user_groups = t3lib_div::intExplode(',',tx_nG6_db::get_user_groups($user_group));
		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
			$analyze_id = $row['analyze_id'];
258
			
259
260
261
262
263
264
265
266
267
268
269
			// Is the user allowed to see this analyse
			$user_allowed = false;
			if ($row['analyze_hidden'] == 0) {
				$user_allowed = true;
			} else {
			    foreach(tx_nG6_db::get_super_groups_of($row['project_fe_group']) AS $valeur) {
					if (in_array($valeur, $user_groups)) {
						$user_allowed = true;
					}
			    }
			}
270
271
272
273
			
			if (!isset ($results['analyse_'.$analyze_id]) and $user_allowed) {				
				$results['analyse_'.$analyze_id] = array( 
					'directory'		=> $row['analyze_directory'], 
274
					'name' 			=> $row['analyze_name'],
275
					'class'			=> $row['analyze_class'],
Jerome Mariette's avatar
Jerome Mariette committed
276
277
					'id' 			=> $row['analyze_id'],
					'hidden' 		=> $row['analyze_hidden'],
278
					'params' 		=> $row['analyze_params'],
Jerome Mariette's avatar
Jerome Mariette committed
279
280
					'software' 		=> $row['analyze_software'],
					'version' 		=> $row['analyze_version'],
281
					'date'			=> $row['analyze_date'],
Jerome Mariette's avatar
Jerome Mariette committed
282
283
					'description' 	=> $row['analyze_description'],
					'parent_id'		=> $row['analyze_parent_uid']	
284
				);
285
			}						
286
287
288
289
		}
		return $results;
    }

290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
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
    /**
     * Hide a project and sublevels (runs & analyzes) datas from database project
     * 
     * @param	string	$p_id	the project id to hide
     * @param	string	$user_group	the group of the current user
     */
	function hide_project($p_id, $user_group) {
		
		// First change all project runs
		$project_runs = tx_nG6_db::get_project_runs($user_group, $p_id);
		foreach($project_runs as $run_id => $run_values) {
			tx_nG6_db::hide_run($run_values['id'], $user_group);
		}

		// Then all project analysis
    	$project_analysis = tx_nG6_db::get_project_analysis($user_group, $p_id);
		foreach($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
     * @param	string	$user_group	the group of the current user
     */
	function unhide_project($p_id, $user_group) {
		
		// First change all project runs
		$project_runs = tx_nG6_db::get_project_runs($user_group, $p_id);
		foreach($project_runs as $run_id => $run_values) {
			tx_nG6_db::unhide_run($run_values['id'], $user_group);
		}

		// Then all project analysis
    	$project_analysis = tx_nG6_db::get_project_analysis($user_group, $p_id);
		foreach($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	$p_id	the project id to publish
     */
	function publish_project($p_id, $user_group) {
		// First unhide the project
		tx_nG6_db::unhide_project($p_id, $user_group);
		// 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 $user_group	the user group
     * @param string $p_id			the project id
     * @param string $user_login	the user login
     * @param string $user_pwd		the user password
     * @param string $data_folder	the data folder
     */
	function delete_project($user_group, $p_id, $user_login, $user_pwd, $data_folder) {
		
		$res = 0;
		// All runs
		$project_runs = tx_nG6_db::get_project_runs($user_group, $p_id);
		foreach($project_runs as $run_id => $run_values) {
			if ($run_values['id'] != 'undefined' && $run_values['id'] != '') {
				//delete the run sublevels
				$res = tx_nG6_db::delete_run($user_group, $run_values['id'], $user_login, $user_pwd, $data_folder);
				if ($res != 0) { break; }				
			}
		}
		
		// All project_analysis
		if ($res == 0) {
			$project_analysis = tx_nG6_db::get_project_analysis($user_group, $p_id);
			foreach($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;
	}

404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
    /**
     * Return the size of the project
     * 
     * @param	string	$p_id	the project id to return the size
	 * @param	string	$data_folder	the data folder
	 * @param	string	$user_group	the user group
     */
	function get_project_size($p_id, $data_folder, $user_group) {
		
		$full_size = 0;
		// All runs
		$project_runs = tx_nG6_db::get_project_runs($user_group, $p_id);
		foreach($project_runs as $run_id => $run_values) {
			$full_size += tx_nG6_db::get_run_size($run_values['id'], $data_folder, $user_group);
		}
		// All analysis
		$project_analysis = tx_nG6_db::get_project_analysis($user_group, $p_id);
		foreach($project_analysis as $analyse_id => $analyze_values) {  
			$full_size += tx_nG6_db::get_analysis_size($analyze_values['id'], $data_folder);
		}
		return $full_size;
	}

427
428
429
430
431

	/*
	 * Run functions
	 *------------------------------------------------------------*/

Jerome Mariette's avatar
Jerome Mariette committed
432
433
	/**
	 * Select all run for the specified user
434
	 * 
Jerome Mariette's avatar
Jerome Mariette committed
435
436
437
438
	 * @param	string	$user_group	the user group
	 * @return	table with all projects
	 */
	function select_all_user_runs($user_group, $orderby='', $limit='') {
439

Jerome Mariette's avatar
Jerome Mariette committed
440
		// If the user is not logged on display demonstration project
441
		if (!$GLOBALS['TSFE']->loginUser) { 
442
			$where = 'public=0';
Jerome Mariette's avatar
Jerome Mariette committed
443
		} else {
444
			$where = 'fe_group IN ('.tx_nG6_db::get_user_groups($user_group).')';	
Jerome Mariette's avatar
Jerome Mariette committed
445
446
		}
     	// Execute the request
447
		$queryParts = Array( 
Jerome Mariette's avatar
Jerome Mariette committed
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
			'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, '.
						'tx_nG6_project.fe_group AS project_fe_group',
			'FROM' => 'tx_nG6_project INNER JOIN ( tx_nG6_project_run INNER JOIN tx_nG6_run ON tx_nG6_project_run.run_id=tx_nG6_run.uid '.
					  ' ) ON tx_nG6_project.uid=tx_nG6_project_run.project_id',
			'WHERE' => $where,
			'GROUPBY' => '',
			'ORDERBY' => $orderby,
			'LIMIT' 	=> $limit
469
		); 
Jerome Mariette's avatar
Jerome Mariette committed
470
471
472
473
474
475
		// Then create the result hash table
		$results = array();
		$user_groups = t3lib_div::intExplode(',',tx_nG6_db::get_user_groups($user_group));
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
			$run_id = $row['run_id'];
476
			
Jerome Mariette's avatar
Jerome Mariette committed
477
478
479
480
481
482
483
484
485
486
487
			// Is the user allowed to see this run
			$user_allowed = false;
			if ($row['run_hidden'] == 0) {
				$user_allowed = true;
			} else {
			    foreach(tx_nG6_db::get_super_groups_of($row['project_fe_group']) AS $valeur) {
					if (in_array($valeur, $user_groups)) {
						$user_allowed = true;
					}
			    }
			}
488
489
					
			if (!isset($results['run_'.$run_id]) and $user_allowed) {				
Jerome Mariette's avatar
Jerome Mariette committed
490
				$results['run_'.$run_id] = array(
491
492
					'id'			=> $run_id,  
					'directory'		=> $row['run_directory'], 
Jerome Mariette's avatar
Jerome Mariette committed
493
494
495
496
497
498
499
500
501
502
503
504
					'name' 			=> $row['run_name'],
					'project_name' 	=> $row['project_name'],
					'fe_group' 		=> $row['project_fe_group'],
					'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'],
505
					'description' 	=> $row['run_description']				
Jerome Mariette's avatar
Jerome Mariette committed
506
				);
507
			}						
Jerome Mariette's avatar
Jerome Mariette committed
508
509
510
511
512
		}
		return $results;

	}

513
514
515
516
517
518
	/**
	 * Select all information for the specified run
	 *
	 * @param	string	$run_id	the run id
	 * @return	hash table with all the run information
	 */
Jerome Mariette's avatar
Jerome Mariette committed
519
	function select_run($run_id) {
520
521
		
		
522
		// First select the run from the database
523
		$queryParts = Array( 
524
525
526
527
528
			'SELECT' => 'tx_nG6_project.uid AS project_id,'.
						'tx_nG6_project.name AS project_name,'.
						'tx_nG6_run.uid AS run_id,'.
					 	'tx_nG6_run.directory AS run_directory,'.
						'tx_nG6_run.description AS run_description, '.
Jerome Mariette's avatar
Jerome Mariette committed
529
						'tx_nG6_run.species AS run_species, '.
530
						'tx_nG6_run.name AS run_name, '.
Jerome Mariette's avatar
Jerome Mariette committed
531
532
533
534
						'tx_nG6_run.data_nature AS run_data_nature, '.
						'tx_nG6_run.sequencer AS run_sequencer, '.
						'tx_nG6_run.type AS run_type, '.
						'tx_nG6_run.full_seq_size, '.
Jerome Mariette's avatar
Jerome Mariette committed
535
						'tx_nG6_run.hidden AS run_hidden, '.
536
537
538
539
540
541
542
543
						'tx_nG6_run.nb_sequences, '.
						'tx_nG6_run.date AS run_date',
			'FROM' => 'tx_nG6_project INNER JOIN ( tx_nG6_project_run INNER JOIN tx_nG6_run ON tx_nG6_project_run.run_id=tx_nG6_run.uid '.
					  ' ) ON tx_nG6_project.uid=tx_nG6_project_run.project_id',
			'WHERE' => 'tx_nG6_run.uid='.$run_id,
			'GROUPBY' => '',
			'ORDERBY' => 'tx_nG6_run.date DESC',
			'LIMIT' 	=> ''
544
		); 
545
546
547
		// Then create the result hash table
		$result = array();
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
548
549
		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {			
			$result = array( 
Jerome Mariette's avatar
Jerome Mariette committed
550
				'id'			=> $row['run_id'],  
551
552
553
				'project_id'	=> $row['project_id'], 
				'project_name'	=> $row['project_name'], 
				'directory'		=> $row['run_directory'], 
Jerome Mariette's avatar
Jerome Mariette committed
554
				'name' 			=> $row['run_name'],
Jerome Mariette's avatar
Jerome Mariette committed
555
				'hidden'		=> $row['run_hidden'],
Jerome Mariette's avatar
Jerome Mariette committed
556
557
				'species' 		=> $row['run_species'],
				'nb_sequences' 	=> $row['nb_sequences'],
Jerome Mariette's avatar
Jerome Mariette committed
558
				'full_seq_size' => $row['full_seq_size'],
Jerome Mariette's avatar
Jerome Mariette committed
559
				'date'			=> $row['run_date'],
Jerome Mariette's avatar
Jerome Mariette committed
560
561
562
				'data_nature' 	=> $row['run_data_nature'],
				'sequencer' 	=> $row['run_sequencer'],
				'type' 			=> $row['run_type'],
563
564
				'description' 	=> $row['run_description']				
			);					
565
566
567
		}
		return $result;
    }
568

569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
	/**
	 * 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;
		
	}	

596
597
598
599
600
601
602
	/**
	 * Select all analysis linked to the specified run
	 *
	 * @param	string	$user_group	the user group
	 * @param	string	$run_id	the run id
	 * @return	hash table with all analysis information
	 */
Jerome Mariette's avatar
Jerome Mariette committed
603
    function get_run_analysis($user_group, $run_id, $orderby='', $limit='') {
604
		// First select all analysis from the database
605
606
607
		$queryParts = array( 
			'SELECT' => 'tx_nG6_analyze.uid AS analyze_id,'. 
						'tx_nG6_analyze.directory AS analyze_directory,'. 
608
						'tx_nG6_analyze.name AS analyze_name, '.
609
610
						'tx_nG6_analyze.params AS analyze_params, '.
						'tx_nG6_analyze.class AS analyze_class, '.
611
						'tx_nG6_analyze.date AS analyze_date, '.
Jerome Mariette's avatar
Jerome Mariette committed
612
613
						'tx_nG6_analyze.software AS analyze_software, '.
						'tx_nG6_analyze.version AS analyze_version, '.
614
615
						'tx_nG6_analyze.hidden AS analyze_hidden, '.
						'tx_nG6_analyze.description AS analyze_description, '.
Jerome Mariette's avatar
Jerome Mariette committed
616
						'tx_nG6_analyze.parent_uid AS analyze_parent_uid, '.
617
618
619
620
621
622
						'tx_nG6_project.fe_group AS project_fe_group',
			'FROM' => 'tx_nG6_project INNER JOIN ( tx_nG6_project_run INNER JOIN ( tx_nG6_run INNER JOIN ( tx_nG6_run_analyze INNER JOIN '.
					  'tx_nG6_analyze ON tx_nG6_analyze.uid = tx_nG6_run_analyze.analyze_id) ON tx_nG6_run_analyze.run_id = tx_nG6_run.uid '.
					  ') ON tx_nG6_run.uid = tx_nG6_project_run.run_id) ON tx_nG6_project_run.project_id = tx_nG6_project.uid ',
			'WHERE' => 'tx_nG6_run_analyze.run_id='.$run_id,
			'GROUPBY' => '',
Jerome Mariette's avatar
Jerome Mariette committed
623
624
			'ORDERBY' => $orderby,
			'LIMIT' => $limit
625
626
627
628
629
630
631
		);
		// Then create the result hash table
		$results = array();
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
		$user_groups = t3lib_div::intExplode(',',tx_nG6_db::get_user_groups($user_group));
		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
			$analyze_id = $row['analyze_id'];
632
			
633
634
635
636
637
638
639
640
641
642
643
			// Is the user allowed to see this analyse
			$user_allowed = false;
			if ($row['analyze_hidden'] == 0) {
				$user_allowed = true;
			} else {
			    foreach(tx_nG6_db::get_super_groups_of($row['project_fe_group']) AS $valeur) {
					if (in_array($valeur, $user_groups)) {
						$user_allowed = true;
					}
			    }
			}
644
645
646
647
			
			if (!isset ($results['analyse_'.$analyze_id]) and $user_allowed) {				
				$results['analyse_'.$analyze_id] = array( 
					'directory'		=> $row['analyze_directory'], 
Jerome Mariette's avatar
Jerome Mariette committed
648
					'name' 			=> $row['analyze_name'],
649
650
					'params' 		=> $row['analyze_params'],
					'class' 		=> $row['analyze_class'],
Jerome Mariette's avatar
Jerome Mariette committed
651
652
653
654
655
					'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
656
657
					'description' 	=> $row['analyze_description'],
					'parent_id'		=> $row['analyze_parent_uid']
658
				);
659
			}						
660
661
662
663
		}
		return $results;
    }

664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
	/**
	 * Delete a run, sample and sublevel (analyzes) datas from database project
	 * 
	 * @param string $user_group	the user group
	 * @param string $r_id			the run id
	 * @param string $user_login	the user login
	 * @param string $user_pwd		the user password
	 * @param string $data_folder	the data folder
	 */
	function delete_run($user_group, $r_id, $user_login, $user_pwd, $data_folder) {		

		$res = 0;		
		$run_analysis = tx_nG6_db::get_run_analysis($user_group, $r_id);
		foreach($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;
	}

715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
    /**
     * Return the size of the run
     * 
     * @param	string	$r_id	the run id to return the size
	 * @param	string	$data_folder	the data folder
	 * @param	string	$user_group	the user group
     */
	function get_run_size($r_id, $data_folder, $user_group) {
		$full_size = 0;
		$run_analysis = tx_nG6_db::get_run_analysis($user_group, $r_id);
		foreach($run_analysis as $analyse_id => $analyze_values) {
			$full_size += tx_nG6_db::get_analysis_size($analyze_values['id'], $data_folder);
		}
		// Then select the run
		$my_run = tx_nG6_db::select_run($r_id);
		foreach(scandir($data_folder.$my_run['directory']) as $file) {
			if (is_file($data_folder.$my_run['directory']."/".$file)) {
				$full_size += filesize($data_folder.$my_run['directory']."/".$file);
			}
		}
		return $full_size;
	}

738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
    /**
     * Hide a run and sublevels (analysis)
     * 
     * @param	string	$r_id	the run id to hide
     * @param	string	$user_group	the group of the current user
     */
	function hide_run($r_id, $user_group) {

		// First select all run analysis
    	$run_analysis = tx_nG6_db::get_run_analysis($user_group, $r_id);
		foreach($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
     * @param	string	$user_group	the group of the current user
     */
	function unhide_run($r_id, $user_group) {

		// Then all run analysis
    	$run_analysis = tx_nG6_db::get_run_analysis($user_group, $r_id);
		foreach($run_analysis as $analysis_id => $analysis_values) {  
			tx_nG6_db::unhide_analysis($analysis_values['id']);
768
769
770
771
772
773
774
775
		}		
		
		// 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')
		) ;
776
777
778
779
		
		// Finaly change the run itself
		$GLOBALS['TYPO3_DB']-> exec_UPDATEquery ('tx_nG6_run', 'uid='.$r_id, array('hidden' => '0'));
	}
780
781

	/*
782
	 * Analysis functions
783
	 *------------------------------------------------------------*/
784
	 
785
786
787
788
789
790
	/**
	 * Select all information on an analyse
	 *
	 * @param	string	$analyse_id	the analyse id
	 * @return	hash table with all analyse information
	 */
Jerome Mariette's avatar
Jerome Mariette committed
791
792
    function select_analyse($analyse_id) {

793
		// First select all analyse information
794
795
796
797
798
		$queryParts = array( 
			'SELECT' => 'tx_nG6_project.uid AS project_id,'. 
						'tx_nG6_project.name AS project_name,'. 
						'tx_nG6_analyze.uid AS analyze_id,'. 
						'tx_nG6_analyze.directory AS analyze_directory,'. 
799
						'tx_nG6_analyze.name AS analyze_name, '.
800
						'tx_nG6_analyze.params AS analyze_params, '.
Jerome Mariette's avatar
Jerome Mariette committed
801
						'tx_nG6_analyze.software AS analyze_software, '.
802
						'tx_nG6_analyze.class AS analyze_class, '.
803
						'tx_nG6_analyze.date AS analyze_date, '.
Jerome Mariette's avatar
Jerome Mariette committed
804
805
806
						'tx_nG6_analyze.description AS analyze_description, '.
						'tx_nG6_analyze.version AS analyze_version, '.
						'tx_nG6_analyze.parent_uid AS analyze_parent_uid ',
807
808
809
810
811
812
813
			'FROM' => 'tx_nG6_project INNER JOIN (tx_nG6_project_analyze INNER JOIN tx_nG6_analyze ON ' .
					  'tx_nG6_analyze.uid=tx_nG6_project_analyze.analyze_id) ON tx_nG6_project.uid = tx_nG6_project_analyze.project_id ',
			'WHERE' => 'tx_nG6_analyze.uid='.$analyse_id,
			'GROUPBY' => '',
			'ORDERBY' => '',
			'LIMIT' => ''
		);
814
		
815
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
816
		
817
818
819
		// If it's a project analyse, add project information
		if ($GLOBALS['TYPO3_DB']->sql_num_rows($res) > 0) {
			$result = array();
820
821
822
823
824
825
826
827
828
829
830
			while($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
831
832
833
834
					'description' 	=> $row['analyze_description'],
					'parent_id'		=> $row['analyze_parent_uid'],
					'software'		=> $row['analyze_software'],
					'version'		=> $row['analyze_version']				
835
				);				
836
837
838
			}
			return $result;
		} else { // If it's a run analyse, add run information
839
			$queryParts = array( 
840
841
				'SELECT' => 'tx_nG6_project.name AS project_name,'.
							'tx_nG6_project.uid AS project_id,'.
842
							'tx_nG6_run.uid AS run_id,'. 
843
							'tx_nG6_run.name AS run_name,'.
844
845
							'tx_nG6_analyze.uid AS analyze_id,'. 
							'tx_nG6_analyze.directory AS analyze_directory,'. 
846
							'tx_nG6_analyze.name AS analyze_name, '.
847
848
							'tx_nG6_analyze.params AS analyze_params, '.
							'tx_nG6_analyze.class AS analyze_class, '.
849
							'tx_nG6_analyze.date AS analyze_date, '.
Jerome Mariette's avatar
Jerome Mariette committed
850
851
852
853
							'tx_nG6_analyze.software AS analyze_software, '.
							'tx_nG6_analyze.version AS analyze_version, '.
							'tx_nG6_analyze.description AS analyze_description,'.
							'tx_nG6_analyze.parent_uid AS analyze_parent_uid ',
854
855
856
857
858
859
860
861
862
863
				'FROM' => 'tx_nG6_project INNER JOIN ( tx_nG6_project_run INNER JOIN ( tx_nG6_run INNER JOIN ( tx_nG6_run_analyze INNER JOIN '.
						  'tx_nG6_analyze ON tx_nG6_analyze.uid = tx_nG6_run_analyze.analyze_id) ON tx_nG6_run_analyze.run_id = tx_nG6_run.uid '.
						  ') ON tx_nG6_run.uid = tx_nG6_project_run.run_id) ON tx_nG6_project_run.project_id = tx_nG6_project.uid ',
				'WHERE' => 'tx_nG6_analyze.uid='.$analyse_id,
				'GROUPBY' => '',
				'ORDERBY' => 'tx_nG6_analyze.name',
				'LIMIT' => ''
			);
			$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
			$result = array();
864
865
866
867
868
869
870
871
872
873
874
			while($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
875
876
877
878
					'description' 	=> $row['analyze_description'],
					'software'		=> $row['analyze_software'],
					'parent_id'		=> $row['analyze_parent_uid'],
					'version'		=> $row['analyze_version']			
879
				);				
880
881
882
883
			}
			return $result;
		}
    }
884

885
886
887
888
889
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
	/**
	 * 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;
    }
918

919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
    /**
     * 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;
	}

937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
    /**
     * 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
     * @param	string	$user_group	the group of the current user
     */
	function unhide_analysis($a_id) {
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
		$queryParts = array(
					'SELECT'  => 'tx_nG6_project_analyze.uid',
					'FROM'    => 'tx_nG6_project_analyze',
					'WHERE'   => 'tx_nG6_project_analyze.analyze_id = '.$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')
			) ;
		}

986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
		// 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;
	}

1033
1034
1035
1036
1037
1038
1039

	/*
	 * User functions
	 *------------------------------------------------------------*/

    /**
    * Return the supergroups list of the specified group
1040
    * 
1041
1042
    * @param string	$group	the group
    * @return array
1043
    */ 
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
	function get_super_groups_of ($group) {
		// First get the super group of the given group
		$queryParts = array(
			'SELECT' => 'uid, subgroup',
			'FROM' => 'fe_groups',
			'WHERE' => '',
			'GROUPBY' => '',
			'ORDERBY' => '',
			'LIMIT' => ''
		);
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
		$reslist = array();
		$i = 0;
Jerome Mariette's avatar
Jerome Mariette committed
1057
1058
		
		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
1059
1060
1061
1062
1063
			if (in_array($group, t3lib_div::intExplode(',',$row['subgroup']))) {
				$reslist[$i] = $row['uid'];
				$i++;
			}
		}
Jerome Mariette's avatar
Jerome Mariette committed
1064
		
1065
1066
		return $reslist;
	}
1067
    
Jerome Mariette's avatar
Jerome Mariette committed
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
	/**
     * Return the recursive supergroups list of the specified group
     *
     * @param string $group the group id
     * @param string $level the search depth, can be 'all' or 'first' (default)
     * @return array
     */
    function get_all_super_groups_of ($group, $level = 'first') {
        
        if ($level == 'all') {
            // return the recursive list of all $group super groups
            $first_list = tx_nG6_db::get_super_groups_of($group);
            $super_list = $first_list;
        
            foreach ($first_list as $first_list_group_id) {
                $next_list = tx_nG6_db::get_all_super_groups_of($first_list_group_id, $level);
                $super_list = array_merge($super_list,$next_list);
            }
	        return $super_list;
        } else {
            return tx_nG6_db::get_super_groups_of($group);
        }
    }
    
1092
1093
	/**
	 * Returns a string with user groups separated by comas
1094
	 * 
1095
1096
1097
1098
1099
1100
1101
1102
     * @param	string	$user_group	the user group
	 * @return	string	list of user groups splited by a coma
	 */
	function get_user_groups($user_group) {
		$tab_groups = array();
		tx_nG6_db::get_sub_groups($user_group, '', $tab_groups);
		$groups = '';
		foreach($tab_groups as $valeur) { $groups .= $valeur.','; }
1103
		return substr($groups, 0, -1);	
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
	}

	/**
	 * Fetches subgroups of groups. Function is called recursively for each subgroup.
	 * Function was previously copied from t3lib_userAuthGroup->fetchGroups and has been slightly modified.
	 *
	 * @param	string	$grList	commalist of fe_groups uid numbers
	 * @param	string	$idList	list of already processed fe_groups-uids so the function will not fall into a eternal recursion.
	 * @return	array
	 */
	function get_sub_groups($grList, $idList='', &$groups)	{

		// Fetching records of the groups in $grList (which are not blocked by lockedToDomain either):
		$lockToDomain_SQL = ' AND (lockToDomain=\'\' OR lockToDomain IS NULL)';
		$res = $GLOBALS['TYPO3_DB']->exec_SELECTquery('uid,subgroup', 'fe_groups', 'deleted=0 AND hidden=0 AND uid IN ('.$grList.')'.$lockToDomain_SQL);

		$groupRows = array();	// Internal group record storage
		// The groups array is filled
		while ($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res))	{
			if(!in_array($row['uid'], $groups))	{ $groups[] = $row['uid']; }
			$groupRows[$row['uid']] = $row;
		}

		// Traversing records in the correct order
		$include_staticArr = t3lib_div::intExplode(',', $grList);
		foreach($include_staticArr as $uid)	{	// traversing list
			// Get row:
			$row=$groupRows[$uid];
			if (is_array($row) && !t3lib_div::inList($idList,$uid))	{	// Must be an array and $uid should not be in the idList, because then it is somewhere previously in the grouplist
				// Include sub groups
				if (trim($row['subgroup']))	{
					$theList = implode(',',t3lib_div::intExplode(',',$row['subgroup']));	// Make integer list
					tx_nG6_db::get_sub_groups($theList, $idList.','.$uid, $groups);		// Call recursively, pass along list of already processed groups so they are not recursed again.
				}
			}
		}
	}
1141
	
1142
1143
1144
1145
1146
1147
1148
1149
1150
	/**
	 * Return if the user is authorized or not to access the specified project and run
	 *
	 * @param	string	$user_group	the user group
	 * @param	string	$project_id	the project id
	 * @param	string	$project_id	the run id
	 * @return	boolean
	 */
	function user_is_authorized ($user_group, $project_id, $run_id) {
1151
		$authorized = false;
1152
1153
		if ($project_id) {
			$queryParts = array(
1154
				'SELECT' => 'fe_group,public',
1155
1156
1157
1158
1159
1160
1161
1162
				'FROM' => 'tx_nG6_project',
				'WHERE' => 'uid='.$project_id,
				'GROUPBY' => '',
				'ORDERBY' => '',
				'LIMIT' => ''
			);
			$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
			$val = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res);
1163
1164
1165
1166
1167
			if ($GLOBALS['TSFE']->loginUser) {
				$authorized = in_array($val['fe_group'], preg_split("/,/", tx_nG6_db::get_user_groups($user_group)));
			} else {
				$authorized = ($val['public'] == 0);
			}
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
		} elseif ($run_id) {
			$queryParts = array(
				'SELECT' => 'project_id',
				'FROM' => 'tx_nG6_project_run',
				'WHERE' => 'run_id='.$run_id,
				'GROUPBY' => '',
				'ORDERBY' => '',
				'LIMIT' => ''
			);
			$res1 = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
			$val = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res1);
			$queryParts = array(
1180
				'SELECT' => 'fe_group,public',
1181
1182
1183
1184
1185
1186
1187
1188
				'FROM' => 'tx_nG6_project',
				'WHERE' => 'uid='.$val['project_id'],
				'GROUPBY' => '',
				'ORDERBY' => '',
				'LIMIT' => ''
			);
			$res2 = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
			$val = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res2);
1189
1190
1191
1192
1193
			if ($GLOBALS['TSFE']->loginUser) {
				$authorized = in_array($val['fe_group'], preg_split("/,/", tx_nG6_db::get_user_groups($user_group)));
			} else {
				$authorized = ($val['public'] == 0);
			}
1194
		} else {
1195
			$authorized = true;
1196
		}
1197
		return $authorized;
1198
	}
Jerome Mariette's avatar
Jerome Mariette committed
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
1225
1226
1227
1228
1229
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

	/**
	 * Return if the user is a superuser for the specified project/run/analyse
	 *
	 * @param	string	$user_group		the user group
	 * @param	string	$type			can be project/run/analyse
	 * @param	string	$uid			the uid
	 * @return	boolean {1 = ok, 0 = nok}
	 */
    function is_super_user($user_group, $type, $uid) {
    	
   		if ($type == 'project') {
			$queryParts = array(
				'SELECT' => 'fe_group',
				'FROM' => 'tx_nG6_project',
				'WHERE' => 'uid='.$uid,
				'GROUPBY' => '',
				'ORDERBY' => '',
				'LIMIT' => ''
			);
			$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
			$val = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res);
			$authorized_group = $val['fe_group'];
			
		} elseif ($type == 'run') {
			$queryParts = array(
				'SELECT' => 'project_id',
				'FROM' => 'tx_nG6_project_run',
				'WHERE' => 'run_id='.$uid,
				'GROUPBY' => '',
				'ORDERBY' => '',
				'LIMIT' => ''
			);
			$res1 = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
			$val = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res1);
			$queryParts = array(
				'SELECT' => 'fe_group',
				'FROM' => 'tx_nG6_project',
				'WHERE' => 'uid='.$val['project_id'],
				'GROUPBY' => '',
				'ORDERBY' => '',
				'LIMIT' => ''
			);
			$res2 = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
			$val = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res2);
			$authorized_group = $val['fe_group'];
			
		} elseif ($type == 'analyze') {
			$queryParts = array(
				'SELECT' => 'run_id',
				'FROM' => 'tx_nG6_run_analyze',
				'WHERE' => 'analyze_id='.$uid,
				'GROUPBY' => '',
				'ORDERBY' => '',
				'LIMIT' => ''
			);
			$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
1256
1257
1258
1259
1260
1261
1262
1263
1264
1265
1266
1267
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
1285
1286
1287
1288
1289
1290
1291
1292
1293
1294
1295
1296
1297
1298
1299
1300
1301
			if ($GLOBALS['TYPO3_DB']->sql_num_rows($res) > 0) {
				$val = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res);
				$queryParts = array(
					'SELECT' => 'project_id',
					'FROM' => 'tx_nG6_project_run',
					'WHERE' => 'run_id='.$val['run_id'],
					'GROUPBY' => '',
					'ORDERBY' => '',
					'LIMIT' => ''
				);
				$res2 = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
				$val = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res2);
				$queryParts = array(
					'SELECT' => 'fe_group',
					'FROM' => 'tx_nG6_project',
					'WHERE' => 'uid='.$val['project_id'],
					'GROUPBY' => '',
					'ORDERBY' => '',
					'LIMIT' => ''
				);
				$res3 = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
				$val = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res3);
				$authorized_group = $val['fe_group'];
			} else {
				$queryParts = array(
					'SELECT' => 'project_id',
					'FROM' => 'tx_nG6_project_analyze',
					'WHERE' => 'analyze_id='.$uid,
					'GROUPBY' => '',
					'ORDERBY' => '',
					'LIMIT' => ''
				);
				$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
				$val = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res);
				$queryParts = array(
					'SELECT' => 'fe_group',
					'FROM' => 'tx_nG6_project',
					'WHERE' => 'uid='.$val['project_id'],
					'GROUPBY' => '',
					'ORDERBY' => '',
					'LIMIT' => ''
				);
				$res2 = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
				$val = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res2);
				$authorized_group = $val['fe_group'];
			}
Jerome Mariette's avatar
Jerome Mariette committed
1302
1303
1304
1305
1306
1307
			
		} else {
			return true;
		}
		
		if (!$GLOBALS['TSFE']->loginUser) { // If the user is not logged on
1308
			return false;
Jerome Mariette's avatar
Jerome Mariette committed
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
		} else {
			
			// super groups string => supergroup1,supergroup2,...
			$all_list = tx_nG6_db::get_all_super_groups_of($authorized_group,'all');
			$groups_str='';
			foreach ($all_list as $asd) { $groups_str .= $asd.','; }
			$effective_supergroups = substr($groups_str, 0, -1); //delete the last comma
			
			
			if (strlen($effective_supergroups) == 0) {
				$is_super_user = true; 		// means : current user is a super user (no super groups exists)
			} else {
				$is_super_user = in_array($user_group, preg_split("/,/", $effective_supergroups));
			}
Jerome Mariette's avatar
Jerome Mariette committed
1323

Jerome Mariette's avatar
Jerome Mariette committed
1324
1325
1326
1327
			return $is_super_user;
		}
    }

1328
1329
1330
1331
1332
1333
1334
}

if (defined('TYPO3_MODE') && $TYPO3_CONF_VARS[TYPO3_MODE]['XCLASS']['ext/nG6/class.tx_nG6_db.php']) {
    include_once($TYPO3_CONF_VARS[TYPO3_MODE]['XCLASS']['ext/nG6/class.tx_nG6_db.php']);
}

?>