class.tx_nG6_db.php 57.7 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
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
	/**
     * 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
		$users_in_group = tx_nG6_db::get_all_users_in_group($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'];
				}
			}
		}

		$cumulated_size = 0;
    	while($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;
			
    		// get all runs the usergroup can access to
    		$queryParts = array(
    			'SELECT' 	=> 'tx_nG6_run.uid as run_id, tx_nG6_run.name as name',
    			'FROM' 		=> 'tx_nG6_project '
    				.' INNER JOIN tx_nG6_project_run ON tx_nG6_project.uid=tx_nG6_project_run.project_id '
    				.' INNER JOIN tx_nG6_run ON tx_nG6_project_run.run_id=tx_nG6_run.uid ',
    			'WHERE' 	=> 'tx_nG6_project.uid IN ('.implode(",",$project_list_final).') AND tx_nG6_run.date BETWEEN '.$date_cursors.' AND '.$date_cursore,
    			'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);
			}

    		$cumulated_size += $current_size;
    		if ($date_cursore+$total_day_count_tstamp > $date_end) {
	    		if(!$cumul_values){
	    	    	$res_tab[] = array($date_end*1000, $current_size);
	    	    }else{
	    	    	$res_tab[] = array($date_end*1000, $cumulated_size);
	    	    }
    		} else {
	    		if(!$cumul_values){
	    	    	$res_tab[] = array($date_cursore*1000, $current_size);
	    	    }else{
	    	    	$res_tab[] = array($date_cursore*1000, $cumulated_size);
	    	    }
    		}

    		$date_cursors = $date_cursore + 1;
    	}
    	return $res_tab;	
    }
Penom Nom's avatar
Penom Nom committed
154
	
155
156
157
158
159
160
	/*
	 * Project functions
	 *------------------------------------------------------------*/

	/**
	 * Select all project for the current user
161
	 * 
162
	 * @param	string	$user_id	the user id
163
164
	 * @return	table with all projects
	 */
165
	function select_all_user_projects($user_id, $orderby='', $limit='') {		
166
		$projects = array();
Jerome Mariette's avatar
Jerome Mariette committed
167
		
168
		// If the user is not logged on display demonstration project
Jerome Mariette's avatar
Jerome Mariette committed
169
170
171
		if ($user_id == null) { $where = 'tx_nG6_project.public=0'; } 
		else { $where = 'fe_rights.fe_user_id='.$user_id; }
		
172
		//First, get the analyzis project-scale
173
		$queryParts = array(
174
175
176
			'SELECT' => 'tx_nG6_project.uid AS project_id, '.
						'tx_nG6_project.name AS project_name, '.
						'tx_nG6_project.description AS project_description, '.
177
						'tx_nG6_project.public AS project_public, '.
Jerome Mariette's avatar
Jerome Mariette committed
178
						'tx_nG6_project.crdate AS project_crdate, '.
179
180
						'tx_nG6_project.hidden AS project_hidden ',
			'FROM' => 'tx_nG6_project INNER JOIN fe_rights ON fe_rights.project_id=tx_nG6_project.uid',
181
182
			'WHERE' => $where,
			'GROUPBY' => '',
Jerome Mariette's avatar
Jerome Mariette committed
183
184
			'ORDERBY' => $orderby,
			'LIMIT' => $limit
185
		);
186
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);		
187
188
		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
			$project_id = $row['project_id'];
Jerome Mariette's avatar
Jerome Mariette committed
189
			if (!isset ($projects['project_'.$project_id])) {		
190
				$projects['project_'.$project_id] = array(
191
					'id'			=> $project_id,				
192
					'name'			=> $row['project_name'],
Jerome Mariette's avatar
Jerome Mariette committed
193
					'hidden'		=> $row['project_hidden'],
Jerome Mariette's avatar
Jerome Mariette committed
194
					'date'			=> $row['project_crdate'],
195
					'public'		=> $row['project_public'],
196
197
					'description'	=> $row['project_description']);
			}
198
						
199
		}		
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
		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
219
220
221
222
		$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
223
					 'date'			=> $vals['crdate'],
Jerome Mariette's avatar
Jerome Mariette committed
224
225
					 'public'		=> $vals['public'],
					 'description'	=> $vals['description']);
226
227
228
229
230
231
232
233
	}

	/**
	 * Select all runs linked to the specified project
	 *
	 * @param	string	$project_id	the project id
	 * @return	hash table with all runs information
	 */
Jerome Mariette's avatar
Jerome Mariette committed
234
    function get_project_runs($project_id, $orderby='', $limit='') {
235
    	
236
		// First select all runs from the database
237
		$queryParts = Array( 
238
239
240
241
			'SELECT' => 'tx_nG6_run.uid AS run_id,'.
					 	'tx_nG6_run.directory AS run_directory,'.
					 	'tx_nG6_run.species AS run_species,'.
						'tx_nG6_run.description AS run_description, '.
Jerome Mariette's avatar
Jerome Mariette committed
242
243
244
						'tx_nG6_run.data_nature AS run_data_nature, '.
						'tx_nG6_run.sequencer AS run_sequencer, '.
						'tx_nG6_run.type AS run_type, '.
245
						'tx_nG6_run.name AS run_name, '.
Jerome Mariette's avatar
Jerome Mariette committed
246
247
						'tx_nG6_run.nb_sequences AS run_nb_sequences, '.
						'tx_nG6_run.full_seq_size AS run_full_seq_size, '.
248
249
						'tx_nG6_run.date AS run_date, '.
						'tx_nG6_run.hidden AS run_hidden, '.
250
251
						'tx_nG6_project.uid AS project_id, '.
						'tx_nG6_project.name AS project_name ',
Jerome Mariette's avatar
Jerome Mariette committed
252
			'FROM' => 'tx_nG6_project '.
253
254
  						'INNER JOIN tx_nG6_project_run ON  tx_nG6_project.uid=tx_nG6_project_run.project_id '.
  						'INNER JOIN tx_nG6_run ON tx_nG6_project_run.run_id=tx_nG6_run.uid ',
Jerome Mariette's avatar
Jerome Mariette committed
255
			'WHERE' => 'tx_nG6_project.uid='.$project_id,
256
			'GROUPBY' => '',
Jerome Mariette's avatar
Jerome Mariette committed
257
258
			'ORDERBY' => $orderby,
			'LIMIT' 	=> $limit
259
		); 
Jerome Mariette's avatar
Jerome Mariette committed
260
		
261
262
263
264
		// 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
265
266
			$run_id = $row['run_id'];				
			if (!isset($results['run_'.$run_id])) {				
267
				$results['run_'.$run_id] = array( 
Jerome Mariette's avatar
Jerome Mariette committed
268
					'id'			=> $run_id,
269
					'directory'		=> $row['run_directory'], 
270
					'name' 			=> $row['run_name'],
Jerome Mariette's avatar
Jerome Mariette committed
271
272
					'project_name' 	=> $row['project_name'],
					'hidden'		=> $row['run_hidden'],
273
					'species' 		=> $row['run_species'],
Jerome Mariette's avatar
Jerome Mariette committed
274
275
276
					'nb_sequences' 	=> $row['run_nb_sequences'],
					'full_seq_size' => $row['run_full_seq_size'],
					'project_id' 	=> $row['project_id'],
277
					'date'			=> $row['run_date'],
Jerome Mariette's avatar
Jerome Mariette committed
278
279
280
					'data_nature'	=> $row['run_data_nature'],
					'sequencer'		=> $row['run_sequencer'],
					'type'			=> $row['run_type'],
Jerome Mariette's avatar
Jerome Mariette committed
281
					'description' 	=> $row['run_description']
282
				);
283
			}						
284
285
286
287
288
289
290
291
292
293
		}
		return $results;
    }

	/**
	 * Select all analysis linked to the specified project
	 *
	 * @param	string	$project_id	the project id
	 * @return	hash table with all analysis information
	 */
Jerome Mariette's avatar
Jerome Mariette committed
294
    function get_project_analysis($project_id, $orderby='', $limit='') {
295
296
    	
    	// First select all analysis from the database    	
297
    	$queryParts = array( 
298
299
			'SELECT' => 'tx_nG6_analyze.uid AS analyze_id,'. 
						'tx_nG6_analyze.directory AS analyze_directory,'. 
300
						'tx_nG6_analyze.name AS analyze_name, '.
301
						'tx_nG6_analyze.class AS analyze_class, '.
302
						'tx_nG6_analyze.date AS analyze_date, '.
Jerome Mariette's avatar
Jerome Mariette committed
303
304
						'tx_nG6_analyze.software AS analyze_software, '.
						'tx_nG6_analyze.version AS analyze_version, '.
305
						'tx_nG6_analyze.params AS analyze_params, '.
306
						'tx_nG6_analyze.description AS analyze_description, '.
Jerome Mariette's avatar
Jerome Mariette committed
307
						'tx_nG6_analyze.parent_uid AS analyze_parent_uid, '.
308
						'tx_nG6_analyze.hidden AS analyze_hidden ',
Jerome Mariette's avatar
Jerome Mariette committed
309
			'FROM' => 'tx_nG6_project '.
310
311
						'INNER JOIN tx_nG6_project_analyze ON tx_nG6_project.uid = tx_nG6_project_analyze.project_id '.
						'INNER JOIN tx_nG6_analyze ON tx_nG6_analyze.uid=tx_nG6_project_analyze.analyze_id ',
Jerome Mariette's avatar
Jerome Mariette committed
312
			'WHERE' => 'tx_nG6_project.uid='.$project_id,
313
			'GROUPBY' => '',
Jerome Mariette's avatar
Jerome Mariette committed
314
315
			'ORDERBY' => $orderby,
			'LIMIT' => $limit
316
317
318
319
320
321
		);
		// 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 = $row['analyze_id'];
Jerome Mariette's avatar
Jerome Mariette committed
322
			if (!isset ($results['analyse_'.$analyze_id])) {				
323
324
				$results['analyse_'.$analyze_id] = array( 
					'directory'		=> $row['analyze_directory'], 
325
					'name' 			=> $row['analyze_name'],
326
					'class'			=> $row['analyze_class'],
Jerome Mariette's avatar
Jerome Mariette committed
327
328
					'id' 			=> $row['analyze_id'],
					'hidden' 		=> $row['analyze_hidden'],
329
					'params' 		=> $row['analyze_params'],
Jerome Mariette's avatar
Jerome Mariette committed
330
331
					'software' 		=> $row['analyze_software'],
					'version' 		=> $row['analyze_version'],
332
					'date'			=> $row['analyze_date'],
Jerome Mariette's avatar
Jerome Mariette committed
333
334
					'description' 	=> $row['analyze_description'],
					'parent_id'		=> $row['analyze_parent_uid']	
335
				);
336
			}						
337
338
339
340
		}
		return $results;
    }

341
342
343
344
345
    /**
     * Hide a project and sublevels (runs & analyzes) datas from database project
     * 
     * @param	string	$p_id	the project id to hide
     */
Jerome Mariette's avatar
Jerome Mariette committed
346
	function hide_project($p_id) {
347
348
		
		// First change all project runs
Jerome Mariette's avatar
Jerome Mariette committed
349
		$project_runs = tx_nG6_db::get_project_runs($p_id);
350
		foreach($project_runs as $run_id => $run_values) {
Jerome Mariette's avatar
Jerome Mariette committed
351
			tx_nG6_db::hide_run($run_values['id']);
352
353
354
		}

		// Then all project analysis
Jerome Mariette's avatar
Jerome Mariette committed
355
    	$project_analysis = tx_nG6_db::get_project_analysis($p_id);
356
357
358
359
360
361
362
363
364
365
366
367
368
		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	$p_id	the project id to hide
     */
Jerome Mariette's avatar
Jerome Mariette committed
369
	function unhide_project($p_id) {
370
371
		
		// First change all project runs
Jerome Mariette's avatar
Jerome Mariette committed
372
		$project_runs = tx_nG6_db::get_project_runs($p_id);
373
		foreach($project_runs as $run_id => $run_values) {
Jerome Mariette's avatar
Jerome Mariette committed
374
			tx_nG6_db::unhide_run($run_values['id']);
375
376
377
		}

		// Then all project analysis
Jerome Mariette's avatar
Jerome Mariette committed
378
    	$project_analysis = tx_nG6_db::get_project_analysis($p_id);
379
380
381
382
383
384
385
386
387
388
389
390
391
		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	$p_id	the project id to publish
     */
Jerome Mariette's avatar
Jerome Mariette committed
392
	function publish_project($p_id) {
393
		// First unhide the project
Jerome Mariette's avatar
Jerome Mariette committed
394
		tx_nG6_db::unhide_project($p_id);
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
		// 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 $data_folder	the data folder
     */
Jerome Mariette's avatar
Jerome Mariette committed
416
	function delete_project($p_id, $user_login, $user_pwd, $data_folder) {
417
418
419
		
		$res = 0;
		// All runs
Jerome Mariette's avatar
Jerome Mariette committed
420
		$project_runs = tx_nG6_db::get_project_runs($p_id);
421
422
423
		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
424
				$res = tx_nG6_db::delete_run($run_values['id'], $user_login, $user_pwd, $data_folder);
425
426
427
428
429
430
				if ($res != 0) { break; }				
			}
		}
		
		// All project_analysis
		if ($res == 0) {
Jerome Mariette's avatar
Jerome Mariette committed
431
			$project_analysis = tx_nG6_db::get_project_analysis($p_id);
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
			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;
	}

452
453
454
455
456
    /**
     * 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
457
	 * @param	boolean $get_analyzes	get analyzes size ? 
458
     */
Jerome Mariette's avatar
Jerome Mariette committed
459
	function get_project_size($p_id, $data_folder, $get_analyzes=false) {
460
461
462
		
		$full_size = 0;
		// All runs
Jerome Mariette's avatar
Jerome Mariette committed
463
		$project_runs = tx_nG6_db::get_project_runs($p_id);
464
		foreach($project_runs as $run_id => $run_values) {
Jerome Mariette's avatar
Jerome Mariette committed
465
			$full_size += tx_nG6_db::get_run_size($run_values['id'], $data_folder);
466
		}
Jerome Mariette's avatar
Jerome Mariette committed
467
468
469
470
471
472
		if ($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);
			}
473
474
475
476
		}
		return $full_size;
	}

477
478
479
480

	/*
	 * Run functions
	 *------------------------------------------------------------*/
481
482
	
	
Jerome Mariette's avatar
Jerome Mariette committed
483
484
	/**
	 * Select all run for the specified user
485
	 * 
486
	 * @param	string	$user_id	the user id
Jerome Mariette's avatar
Jerome Mariette committed
487
488
	 * @return	table with all projects
	 */
489
	function select_all_user_runs($user_id, $orderby='', $limit='') {
490

Jerome Mariette's avatar
Jerome Mariette committed
491
		// If the user is not logged on display demonstration project
Jerome Mariette's avatar
Jerome Mariette committed
492
493
494
		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
495
     	// Execute the request
496
		$queryParts = Array( 
Jerome Mariette's avatar
Jerome Mariette committed
497
498
499
500
			'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, '.
501
						'tx_nG6_run.data_nature AS run_data_nature, '. 
Jerome Mariette's avatar
Jerome Mariette committed
502
503
504
505
506
507
508
509
						'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, '.
510
511
512
513
514
						'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
515
516
517
518
			'WHERE' => $where,
			'GROUPBY' => '',
			'ORDERBY' => $orderby,
			'LIMIT' 	=> $limit
519
		); 
Jerome Mariette's avatar
Jerome Mariette committed
520
521
522
523
		// 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
524
525
			$run_id = $row['run_id'];	
			if (!isset($results['run_'.$run_id])) {				
Jerome Mariette's avatar
Jerome Mariette committed
526
				$results['run_'.$run_id] = array(
527
528
					'id'			=> $run_id,  
					'directory'		=> $row['run_directory'], 
Jerome Mariette's avatar
Jerome Mariette committed
529
530
531
532
533
534
535
536
537
538
539
					'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'],
540
					'description' 	=> $row['run_description']				
Jerome Mariette's avatar
Jerome Mariette committed
541
				);
542
			}						
Jerome Mariette's avatar
Jerome Mariette committed
543
544
545
546
547
		}
		return $results;

	}

548
549
550
551
552
553
	/**
	 * Select all information for the specified run
	 *
	 * @param	string	$run_id	the run id
	 * @return	hash table with all the run information
	 */
Jerome Mariette's avatar
Jerome Mariette committed
554
	function select_run($run_id) {
555
		
556
		// First select the run from the database
557
		$queryParts = Array( 
558
559
560
561
562
			'SELECT' => 'tx_nG6_project.uid AS project_id,'.
						'tx_nG6_project.name AS project_name,'.
						'tx_nG6_run.uid AS run_id,'.
					 	'tx_nG6_run.directory AS run_directory,'.
						'tx_nG6_run.description AS run_description, '.
Jerome Mariette's avatar
Jerome Mariette committed
563
						'tx_nG6_run.species AS run_species, '.
564
						'tx_nG6_run.name AS run_name, '.
Jerome Mariette's avatar
Jerome Mariette committed
565
566
567
568
						'tx_nG6_run.data_nature AS run_data_nature, '.
						'tx_nG6_run.sequencer AS run_sequencer, '.
						'tx_nG6_run.type AS run_type, '.
						'tx_nG6_run.full_seq_size, '.
Jerome Mariette's avatar
Jerome Mariette committed
569
						'tx_nG6_run.hidden AS run_hidden, '.
570
571
						'tx_nG6_run.nb_sequences, '.
						'tx_nG6_run.date AS run_date',
572
573
574
575
			'FROM' => 'fe_rights '.
						'INNER JOIN tx_nG6_project ON tx_nG6_project.uid=fe_rights.project_id '.
						'INNER JOIN tx_nG6_project_run ON tx_nG6_project.uid=tx_nG6_project_run.project_id '.
						'INNER JOIN tx_nG6_run ON tx_nG6_project_run.run_id=tx_nG6_run.uid ',
576
577
578
579
			'WHERE' => 'tx_nG6_run.uid='.$run_id,
			'GROUPBY' => '',
			'ORDERBY' => 'tx_nG6_run.date DESC',
			'LIMIT' 	=> ''
580
		); 
581
582
583
		// Then create the result hash table
		$result = array();
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
584
585
		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {			
			$result = array( 
Jerome Mariette's avatar
Jerome Mariette committed
586
				'id'			=> $row['run_id'],  
587
588
589
				'project_id'	=> $row['project_id'], 
				'project_name'	=> $row['project_name'], 
				'directory'		=> $row['run_directory'], 
Jerome Mariette's avatar
Jerome Mariette committed
590
				'name' 			=> $row['run_name'],
Jerome Mariette's avatar
Jerome Mariette committed
591
				'hidden'		=> $row['run_hidden'],
Jerome Mariette's avatar
Jerome Mariette committed
592
593
				'species' 		=> $row['run_species'],
				'nb_sequences' 	=> $row['nb_sequences'],
Jerome Mariette's avatar
Jerome Mariette committed
594
				'full_seq_size' => $row['full_seq_size'],
Jerome Mariette's avatar
Jerome Mariette committed
595
				'date'			=> $row['run_date'],
Jerome Mariette's avatar
Jerome Mariette committed
596
597
598
				'data_nature' 	=> $row['run_data_nature'],
				'sequencer' 	=> $row['run_sequencer'],
				'type' 			=> $row['run_type'],
599
600
				'description' 	=> $row['run_description']				
			);					
601
602
603
		}
		return $result;
    }
604

605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
	/**
	 * 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;
		
	}	

632
633
634
635
636
637
	/**
	 * Select all analysis linked to the specified run
	 *
	 * @param	string	$run_id	the run id
	 * @return	hash table with all analysis information
	 */
Jerome Mariette's avatar
Jerome Mariette committed
638
    function get_run_analysis($run_id, $orderby='', $limit='') {
639
		// First select all analysis from the database
640
641
642
		$queryParts = array( 
			'SELECT' => 'tx_nG6_analyze.uid AS analyze_id,'. 
						'tx_nG6_analyze.directory AS analyze_directory,'. 
643
						'tx_nG6_analyze.name AS analyze_name, '.
644
645
						'tx_nG6_analyze.params AS analyze_params, '.
						'tx_nG6_analyze.class AS analyze_class, '.
646
						'tx_nG6_analyze.date AS analyze_date, '.
Jerome Mariette's avatar
Jerome Mariette committed
647
648
						'tx_nG6_analyze.software AS analyze_software, '.
						'tx_nG6_analyze.version AS analyze_version, '.
649
650
						'tx_nG6_analyze.hidden AS analyze_hidden, '.
						'tx_nG6_analyze.description AS analyze_description, '.
651
						'tx_nG6_analyze.parent_uid AS analyze_parent_uid ',
Jerome Mariette's avatar
Jerome Mariette committed
652
			'FROM' => 'tx_nG6_run_analyze '.
653
						'INNER JOIN tx_nG6_analyze ON tx_nG6_analyze.uid = tx_nG6_run_analyze.analyze_id ',
Jerome Mariette's avatar
Jerome Mariette committed
654
			'WHERE' => 'tx_nG6_run_analyze.run_id='.$run_id,
655
			'GROUPBY' => '',
Jerome Mariette's avatar
Jerome Mariette committed
656
657
			'ORDERBY' => $orderby,
			'LIMIT' => $limit
658
659
660
661
662
663
		);
		// 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 = $row['analyze_id'];
Jerome Mariette's avatar
Jerome Mariette committed
664
			if (!isset ($results['analyse_'.$analyze_id])) {				
665
666
				$results['analyse_'.$analyze_id] = array( 
					'directory'		=> $row['analyze_directory'], 
Jerome Mariette's avatar
Jerome Mariette committed
667
					'name' 			=> $row['analyze_name'],
668
669
					'params' 		=> $row['analyze_params'],
					'class' 		=> $row['analyze_class'],
Jerome Mariette's avatar
Jerome Mariette committed
670
671
672
673
674
					'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
675
676
					'description' 	=> $row['analyze_description'],
					'parent_id'		=> $row['analyze_parent_uid']
677
				);
678
			}						
679
680
681
682
		}
		return $results;
    }

683
684
685
686
687
688
689
690
	/**
	 * 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 $data_folder	the data folder
	 */
Jerome Mariette's avatar
Jerome Mariette committed
691
	function delete_run($r_id, $user_login, $user_pwd, $data_folder) {		
692
693

		$res = 0;		
Jerome Mariette's avatar
Jerome Mariette committed
694
		$run_analysis = tx_nG6_db::get_run_analysis($r_id);
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
		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;
	}

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
Jerome Mariette's avatar
Jerome Mariette committed
738
	 * @param	boolean $get_analyzes	get analyzes size ? 
739
     */
Jerome Mariette's avatar
Jerome Mariette committed
740
	function get_run_size($r_id, $data_folder, $get_analyzes=false) {
741
		$full_size = 0;
Jerome Mariette's avatar
Jerome Mariette committed
742
743
744
745
746
		if($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);
			}
747
748
749
		}
		// Then select the run
		$my_run = tx_nG6_db::select_run($r_id);
Jerome Mariette's avatar
Jerome Mariette committed
750
		foreach(scandir($data_folder.$my_run['directory']) as $file) {			
751
752
753
			if (is_file($data_folder.$my_run['directory']."/".$file)) {
				$full_size += filesize($data_folder.$my_run['directory']."/".$file);
			}
Jerome Mariette's avatar
Jerome Mariette committed
754
		}		
755
756
757
		return $full_size;
	}

758
759
760
761
762
    /**
     * Hide a run and sublevels (analysis)
     * 
     * @param	string	$r_id	the run id to hide
     */
Jerome Mariette's avatar
Jerome Mariette committed
763
	function hide_run($r_id) {
764
765

		// First select all run analysis
Jerome Mariette's avatar
Jerome Mariette committed
766
    	$run_analysis = tx_nG6_db::get_run_analysis($r_id);
767
768
769
770
771
772
773
774
775
776
777
778
779
		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	$r_id	the run id to hide
     */
Jerome Mariette's avatar
Jerome Mariette committed
780
781
782
783
784
785
786
787
788
789
	function unhide_run($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')
			);
		}
790
791

		// Then all run analysis
Jerome Mariette's avatar
Jerome Mariette committed
792
    	$run_analysis = tx_nG6_db::get_run_analysis($r_id);
793
794
		foreach($run_analysis as $analysis_id => $analysis_values) {  
			tx_nG6_db::unhide_analysis($analysis_values['id']);
Jerome Mariette's avatar
Jerome Mariette committed
795
		}
796
797
798
799
		
		// Finaly change the run itself
		$GLOBALS['TYPO3_DB']-> exec_UPDATEquery ('tx_nG6_run', 'uid='.$r_id, array('hidden' => '0'));
	}
800

Jerome Mariette's avatar
Jerome Mariette committed
801
802
803
804
805
806
807
808
809
810
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
839
840
841
842
843
844
845
846
847
848
849
850
    /**
     * 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;
    }
    
851
	/*
852
	 * Analysis functions
853
	 *------------------------------------------------------------*/
854
	 
855
856
857
858
859
860
	/**
	 * Select all information on an analyse
	 *
	 * @param	string	$analyse_id	the analyse id
	 * @return	hash table with all analyse information
	 */
Jerome Mariette's avatar
Jerome Mariette committed
861
862
    function select_analyse($analyse_id) {

863
		// First select all analyse information
864
865
866
867
868
		$queryParts = array( 
			'SELECT' => 'tx_nG6_project.uid AS project_id,'. 
						'tx_nG6_project.name AS project_name,'. 
						'tx_nG6_analyze.uid AS analyze_id,'. 
						'tx_nG6_analyze.directory AS analyze_directory,'. 
869
						'tx_nG6_analyze.name AS analyze_name, '.
870
						'tx_nG6_analyze.params AS analyze_params, '.
Jerome Mariette's avatar
Jerome Mariette committed
871
						'tx_nG6_analyze.software AS analyze_software, '.
872
						'tx_nG6_analyze.class AS analyze_class, '.
873
						'tx_nG6_analyze.date AS analyze_date, '.
Jerome Mariette's avatar
Jerome Mariette committed
874
875
876
						'tx_nG6_analyze.description AS analyze_description, '.
						'tx_nG6_analyze.version AS analyze_version, '.
						'tx_nG6_analyze.parent_uid AS analyze_parent_uid ',
877
878
879
			'FROM' => 'tx_nG6_project '.
						'INNER JOIN tx_nG6_project_analyze ON tx_nG6_project.uid = tx_nG6_project_analyze.project_id '.
						'INNER JOIN tx_nG6_analyze ON tx_nG6_analyze.uid=tx_nG6_project_analyze.analyze_id ',
880
881
882
883
884
			'WHERE' => 'tx_nG6_analyze.uid='.$analyse_id,
			'GROUPBY' => '',
			'ORDERBY' => '',
			'LIMIT' => ''
		);
885
		
886
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
887
		
888
889
890
		// If it's a project analyse, add project information
		if ($GLOBALS['TYPO3_DB']->sql_num_rows($res) > 0) {
			$result = array();
891
892
893
894
895
896
897
898
899
900
901
			while($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
902
903
904
905
					'description' 	=> $row['analyze_description'],
					'parent_id'		=> $row['analyze_parent_uid'],
					'software'		=> $row['analyze_software'],
					'version'		=> $row['analyze_version']				
906
				);				
907
908
909
			}
			return $result;
		} else { // If it's a run analyse, add run information
910
			$queryParts = array( 
911
912
				'SELECT' => 'tx_nG6_project.name AS project_name,'.
							'tx_nG6_project.uid AS project_id,'.
913
							'tx_nG6_run.uid AS run_id,'. 
914
							'tx_nG6_run.name AS run_name,'.
915
916
							'tx_nG6_analyze.uid AS analyze_id,'. 
							'tx_nG6_analyze.directory AS analyze_directory,'. 
917
							'tx_nG6_analyze.name AS analyze_name, '.
918
919
							'tx_nG6_analyze.params AS analyze_params, '.
							'tx_nG6_analyze.class AS analyze_class, '.
920
							'tx_nG6_analyze.date AS analyze_date, '.
Jerome Mariette's avatar
Jerome Mariette committed
921
922
923
924
							'tx_nG6_analyze.software AS analyze_software, '.
							'tx_nG6_analyze.version AS analyze_version, '.
							'tx_nG6_analyze.description AS analyze_description,'.
							'tx_nG6_analyze.parent_uid AS analyze_parent_uid ',
925
926
927
928
929
				'FROM' => 'tx_nG6_project '.
							'INNER JOIN tx_nG6_project_run ON tx_nG6_project_run.project_id = pro.uid '.
							'INNER JOIN tx_nG6_run ON tx_nG6_run.uid = tx_nG6_project_run.run_id '.
							'INNER JOIN tx_nG6_run_analyze ON tx_nG6_run_analyze.run_id = tx_nG6_run.uid '.
							'INNER JOIN tx_nG6_analyze ON tx_nG6_analyze.uid = tx_nG6_run_analyze.analyze_id ',
930
931
932
933
934
935
936
				'WHERE' => 'tx_nG6_analyze.uid='.$analyse_id,
				'GROUPBY' => '',
				'ORDERBY' => 'tx_nG6_analyze.name',
				'LIMIT' => ''
			);
			$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
			$result = array();
937
938
939
940
941
942
943
944
945
946
947
			while($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
948
949
950
951
					'description' 	=> $row['analyze_description'],
					'software'		=> $row['analyze_software'],
					'parent_id'		=> $row['analyze_parent_uid'],
					'version'		=> $row['analyze_version']			
952
				);				
953
954
955
956
			}
			return $result;
		}
    }
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
986
987
988
989
990
	/**
	 * 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;
    }
991

992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
    /**
     * 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;
	}

1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
    /**
     * 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	$a_id	the analysis id to hide
     */
Jerome Mariette's avatar
Jerome Mariette committed
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
	function unhide_analysis($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')
				) ;
			}
1062
1063
		}

1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
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
		// 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;
	}

1111
1112
1113
1114

	/*
	 * User functions
	 *------------------------------------------------------------*/
1115
	
1116
1117
1118
	/**
	 * Return if the user is authorized or not to access the specified project and run
	 *
1119
	 * @param	int	$user_id	the user id
1120
1121
1122
1123
	 * @param	string	$project_id	the project id
	 * @param	string	$project_id	the run id
	 * @return	boolean
	 */
1124
	function user_is_authorized ($user_id, $project_id, $run_id) {
1125
		$authorized = false;
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
		
		// 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;
				}
				
			} 
1180
		}
1181
		return $authorized;
1182
	}
Jerome Mariette's avatar
Jerome Mariette committed
1183
1184

	/**
1185
	 * Return if the user is a superuser (administrator) for the specified project/run/analyse
Jerome Mariette's avatar
Jerome Mariette committed
1186
	 *
1187
	 * @param	string	$user_id		the user id
Jerome Mariette's avatar
Jerome Mariette committed
1188
	 * @param	string	$type			can be project/run/analyse
1189
	 * @param	string	$uid			the [project/run/analyse]'s uid
Jerome Mariette's avatar
Jerome Mariette committed
1190
1191
	 * @return	boolean {1 = ok, 0 = nok}
	 */
1192
    function is_administrator($user_id, $type, $uid) {
Jerome Mariette's avatar
Jerome Mariette committed
1193
    	
1194
1195
    	$is_admin = false;
    	
Jerome Mariette's avatar
Jerome Mariette committed
1196
    	if(!$user_id == null){
1197
1198
1199
1200
    	
	    	// Project
	   		if ($type == 'project') {
				$is_admin = tx_nG6_db::is_project_administrator($user_id, $uid);
Jerome Mariette's avatar
Jerome Mariette committed
1201
			
1202
1203
			// Run
			} elseif ($type == 'run') {
1204
1205
1206
				$queryParts = array(
					'SELECT' => 'project_id',
					'FROM' => 'tx_nG6_project_run',
1207
					'WHERE' => 'run_id='.$uid,
1208
1209
1210
1211
					'GROUPBY' => '',
					'ORDERBY' => '',
					'LIMIT' => ''
				);
1212
1213
1214
1215
1216
1217
				$res1 = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
				$val = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res1);
				$is_admin = tx_nG6_db::is_project_administrator($user_id, $val['project_id']);
			
			// Analyze
			} elseif ($type == 'analyze') {
1218
				$queryParts = array(
1219
1220
					'SELECT' => 'run_id',
					'FROM' => 'tx_nG6_run_analyze',
1221
1222
1223
1224
1225
1226
					'WHERE' => 'analyze_id='.$uid,
					'GROUPBY' => '',
					'ORDERBY' => '',
					'LIMIT' => ''
				);
				$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
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
1256
1257
1258
1259
				
				// Run_analyze
				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);
					$is_admin = tx_nG6_db::is_project_administrator($user_id, $val['project_id']);
				
				// project_analyze
				} else {
					$queryParts = array(
						'SELECT' => 'project_id',
						'FROM' => 'tx_nG6_project_analyze',
						'WHERE' => 'analyze_id='.$uid,
						'GROUPBY' => '',
						'ORDERBY' => '',
						'LIMIT' => ''
					);
					$res2 = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
					$val = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res2);
					$is_admin = tx_nG6_db::is_project_administrator($user_id, $val['project_id']);
				}
				
			} 
    	}
Jerome Mariette's avatar
Jerome Mariette committed
1260
		
1261
1262
		return $is_admin; 
    }
Jerome Mariette's avatar
Jerome Mariette committed
1263

1264
1265
1266
1267
1268
1269
1270
    /**
    * Get user's rights on project.
    *
    * @param int $project_id the project id
    * @param int $user_id the user id
    */
    function get_user_right_on_project($user_id, $project_id) {
1271
    	$right_id = -1;
1272
    	$queryParts = array(
1273
1274
    		'SELECT' => 'fe_rights.right_id AS right_id ',
    		'FROM' => 'fe_rights',
1275
1276
1277
1278
    		'WHERE' => 'fe_rights.fe_user_id='. $user_id .' AND fe_rights.project_id='.$project_id
    	);
    	$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
    	while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
1279
1280
1281
    		$right_id = $row['right_id'];
    	}    	
    	return $right_id;
Jerome Mariette's avatar
Jerome Mariette committed
1282
    }
1283
1284
    
    /**
1285
     * Return true if the user is a member on the project
1286
1287
1288
1289
     *
     * @param int $user_id the user id
     * @param int $project_id ths project id
     */
1290
1291
1292
1293
1294
    function is_project_member($user_id, $project_id){
    	$is_member = false;
    	$right = tx_nG6_db::get_user_right_on_project($user_id, $project_id);
    	if ($right == 0) {
    		$is_member = true;
Jerome Mariette's avatar
Jerome Mariette committed
1295
    	}
1296
    	return $is_member;
1297
1298
1299
1300
1301
1302
1303
1304
1305
1306
    }
    
    /**
     * Return true if the user is a manager on the project
     *
     * @param int $user_id the user id
     * @param int $project_id ths project id
     */
    function is_project_manager($user_id, $project_id){
    	$is_manager = false;
1307
1308
    	$right = tx_nG6_db::get_user_right_on_project($user_id, $project_id);
    	if ($right == 1) {
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
    		$is_manager = true;
    	}
    	return $is_manager;
    }
    
    /**
     * Return true if the user is an administrator on the project
     *
     * @param int $user_id the user id
     * @param int $project_id ths project id
     */
    function is_project_administrator($user_id, $project_id){
    	$is_admin = false;
1322
1323
    	$right = tx_nG6_db::get_user_right_on_project($user_id, $project_id);
    	if ($right == 2) {
1324
1325
1326
    		$is_admin = true;
    	}
    	return $is_admin;
1327
1328
    }

1329
1330
    
    
Jerome Mariette's avatar
Jerome Mariette committed
1331
1332
1333
1334
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
1384
1385
1386
1387
1388
1389
1390
1391
1392
1393
1394
1395
1396
1397
1398