class.tx_nG6_db.php 123 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  $value  the new value
	*/
Celine Noirot's avatar
Celine Noirot committed
47
        function update_field($table, $id, $field, $value,$no_quote_fields) {
48
49
50
51
52
53
54
55
56
57
58
59
            if( $field == 'uid' ) {
                throw new Exception ("The function 'update_field' cannot change an id.") ;
            }
            $array=array();
            if( is_array($field) ){
                    for($i =0; $i<count($field);$i++){
                            $array[$field[$i]]=$value[$i];
                    }
            }else{
                     $array=array($field => $value);
            }
            if ( is_array($id) ){
Celine Noirot's avatar
Celine Noirot committed
60
                $GLOBALS['TYPO3_DB']-> exec_UPDATEquery ($table, 'uid IN ('.implode(',',$id).')', $array,$no_quote_fields);
61
            }else{ 
Celine Noirot's avatar
Celine Noirot committed
62
                $GLOBALS['TYPO3_DB']-> exec_UPDATEquery ($table, 'uid='.$id, $array,$no_quote_fields);
63
64
            }
	}
65
66
	
	function select_all_in_view($view, $where) {
67
		$queryParts = array(
68
69
70
					'SELECT' 	=> '*',
					'FROM' 		=> $view,
					'WHERE' 	=> $where ,
71
					'GROUPBY' 	=> '',
Gerald Salin's avatar
Gerald Salin committed
72
73
					'ORDERBY' 	=> '',
					'LIMIT' 	=> ''
74
			);	
75
76
77
78
79
			$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
			return ($res);
	}
	
	function select_count_in_view($view,$where) {
Celine Noirot's avatar
Celine Noirot committed
80
		#select count All runs per project
81
82
83
84
85
86
87
88
89
		$queryParts = array(
					'SELECT' 	=> 'project_id , count(*) AS count',
					'FROM' 		=> $view ,
					'WHERE' 	=> $where,
					'GROUPBY' 	=> 'project_id',
					'ORDERBY' 	=> '',
					'LIMIT' 	=> ''
			);
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
Celine Noirot's avatar
Celine Noirot committed
90
                return ($res);
Gerald Salin's avatar
Gerald Salin committed
91

92
93
	}

Celine Noirot's avatar
Celine Noirot committed
94
95
	function get_project_list_by_group_filter($create_user_id, $without_group_id, $with_group_id){
		$where=Array();
96
97
		$list_project_id_filter_by_group="";
		$list_project_id_laboratories="";
Celine Noirot's avatar
Celine Noirot committed
98
99
		### Search for project without group_id implied
                if($without_group_id !=""){
100
101
102
103
			#select all project_id with group OR/AND without group
			$queryParts=array(
				'SELECT' => 'project_id',
				'FROM' => 'tx_nG6_view_project_user',
Celine Noirot's avatar
Celine Noirot committed
104
				'WHERE' => 'user_group IN ( '.$without_group_id .')',
105
106
107
108
109
110
111
				'GROUPBY' 	=> '',
				'ORDERBY' 	=> '',
				'LIMIT' 	=> ''
			);
		
			$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
			while($res_row= $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
112
				if( $list_project_id_filter_by_group != ""){
113
					$list_project_id_filter_by_group .= ",".$res_row['project_id'];
114
115
				}else{
					$list_project_id_filter_by_group = $res_row['project_id'];
116
117
				}
			}
Celine Noirot's avatar
Celine Noirot committed
118
			$where[] = "uid NOT IN (".$list_project_id_filter_by_group.")";
119
		}
Celine Noirot's avatar
Celine Noirot committed
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
                ### Search for project with group_id implied
                if($with_group_id !=""){
			#select all project_id with group OR/AND without group
			$queryParts=array(
				'SELECT' => 'project_id',
				'FROM' => 'tx_nG6_view_project_user',
				'WHERE' => 'user_group IN ( '.$with_group_id .')',
				'GROUPBY' 	=> '',
				'ORDERBY' 	=> '',
				'LIMIT' 	=> ''
			);
		
			$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
			while($res_row= $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
				if( $list_project_id_filter_by_group != ""){
					$list_project_id_filter_by_group .= ",".$res_row['project_id'];
				}else{
					$list_project_id_filter_by_group = $res_row['project_id'];
				}
139
			}
Celine Noirot's avatar
Celine Noirot committed
140
141
142
143
144
			$where[] = "uid IN (".$list_project_id_filter_by_group.")";
		}
		### add create user filter
		if($create_user_id != ""){
				$where[] = "cruser_id IN (".$create_user_id.")";
145
146
147
		}
		$queryParts=array(
			'SELECT' => 'uid AS project_id',
148
			'FROM' => 'tx_nG6_project',
Celine Noirot's avatar
Celine Noirot committed
149
			'WHERE' => join (' AND ', $where),
150
151
152
153
154
155
156
			'GROUPBY' 	=> '',
			'ORDERBY' 	=> '',
			'LIMIT' 	=> ''
		);
		
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
		while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
157
158
			if ($list_project_id_laboratories != "") {
				$list_project_id_laboratories .=",".$res_row['project_id'];
159
			}else{
160
				$list_project_id_laboratories=$res_row['project_id'];
161
162
163
164
165
166
				
			}
		}
    	return ($list_project_id_laboratories);
		
	}
167
	
168
169
170
        ################################
        # OBSOLETE / PURGE management
        ################################
171
	//Get list of obsolete run/analyses per project
Celine Noirot's avatar
Celine Noirot committed
172
	function filter_list_retention_data_info($filter_size, $max_retention_date, $create_user_id, $without_user_group_id,$with_user_group_id) {
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
		$conditions=Array();
                //filter by date
                if ( $max_retention_date != "" ) {
                        //from user filter value
                        $conditions[] =  ' DATEDIFF( FROM_UNIXTIME( retention_date ) , STR_TO_DATE( "'.$max_retention_date.'", "%d/%m/%Y" ) ) <0';
                } else {
                        //from now
                        $conditions[] =  ' DATEDIFF( FROM_UNIXTIME( retention_date ) , now( ) ) <0';
                }
                $conditions[] = 'purge_demand_id IS NULL';

                $conditions[] = 'state IN ( \'stored\', \'extended\')';                
		
                if ($filter_size != "") {
			$conditions[] = "storage_size > $filter_size";
188
		}
189

190
		$project_list_ids = "";
Celine Noirot's avatar
Celine Noirot committed
191
192
193
		if ($create_user_id != "" or $without_user_group_id != "" or $with_user_group_id != "") {
                        #retrieve list of project id created by a user and with or without a list of group_id
			$project_list_ids = tx_nG6_db::get_project_list_by_group_filter($create_user_id,$without_user_group_id, $with_user_group_id);
194
			$conditions[] = "project_id in (" . $project_list_ids.")" ;
195
		}
196
                $where = join(' AND ', $conditions);
197
198
199
		return (tx_nG6_db::select_list_retention_data_info($where));
	}
	
200
201
202
203
204
205
206
207
208
	function select_a_project_retention_data_info($project_id=null, $all=FALSE) {
		$condition=Array();
		if ($all === FALSE) {
			$condition[]='DATEDIFF( FROM_UNIXTIME( retention_date ) , now( ) ) <0';
		}
		if (null != $project_id) {
			$condition[]="project_id = " . $project_id ;
		}
		$where = join( ' AND ', $condition);
209
210
211
212
213
		return(tx_nG6_db::select_list_retention_data_info($where));
	}
	
	function select_list_retention_data_info($where) {
		$by_project=array();
214
215
216
217
218
219
220
221
222
223
224
225
226
227
		$empty_res_structure = array(
						'project_name'			=> "",
						'state'					=> array("purged"  => array ('nb_run' => 0, 'size_run' => 0, 'run_ids'=> array(),
                                                "nb_analyze"=> 0, "size_analyze"=> 0, 'analysis_ids'=> array()),
                                                "extended"  => array ('nb_run' => 0, 'size_run' => 0, 'run_ids'=> array(),
                                                "nb_analyze"=> 0, "size_analyze"=> 0, 'analysis_ids'=> array()),
                                                "stored"  => array (	'nb_run' => 0, 'size_run' => 0, 'run_ids'=> array(),
							                                                "nb_analyze"=> 0, "size_analyze"=> 0, 'analysis_ids'=> array()
						                                                 )
                                                ),
						'total_purgeable_size'	=> 0,
						'nb_runs'				=>0,
						'nb_analyses'			=>0);
		//select obsolete runs
228
229
		$res = tx_nG6_db::select_all_in_view( "tx_nG6_view_project_run" , $where);
		while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
230
			$current_project_id = $res_row['project_id'];			
231
			if (!isset ($by_project[$res_row['project_id']])) {
232
233
				$by_project[$current_project_id]= $empty_res_structure;
				$by_project[$current_project_id]['project_name']= $res_row['project_name'];
Gerald Salin's avatar
Gerald Salin committed
234
			}
235
236
237
238
239
240
241
242
243
			if ($res_row['run_id'] != "") {
             $by_project[$res_row['project_id']]['state'][$res_row['state']]['nb_run']+=1;
             $key = 'storage_size';
				 if($res_row['state'] == "purged"){
				 	$key = "purged_size";
             }
             $by_project[$current_project_id]['state'][$res_row['state']]['size_run']+=$res_row[$key];
             $by_project[$current_project_id]['state'][$res_row['state']]['run_ids'][]=$res_row['run_id'];
				 $by_project[$current_project_id]['total_purgeable_size'] += $res_row['storage_size'];
244
			}
Gerald Salin's avatar
Gerald Salin committed
245
		}
246
		//select obsolete analyses of a run
247
		$res = tx_nG6_db::select_all_in_view("tx_nG6_view_project_run_analyze",$where,'10');
248
		while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
249
			$current_project_id = $res_row['project_id'];
250
			if (!isset ($by_project[$res_row['project_id']])) {
251
252
				$by_project[$current_project_id]= $empty_res_structure;
				$by_project[$current_project_id]['project_name']= $res_row['project_name'];
253
			}
254
255
256
257
258
259
260
261
262
			if ($res_row['analyze_id'] != ""){
        	  $by_project[$current_project_id]['state'][$res_row['state']]['nb_analyze'] += 1;
           $key = 'storage_size';
           if($res_row['state'] == "purged"){
           	$key = "purged_size";
           }
           $by_project[$current_project_id]['state'][$res_row['state']]['size_analyze'] += $res_row[$key];
           $by_project[$current_project_id]['state'][$res_row['state']]['analysis_ids'][]=$res_row['analyze_id'];
           $by_project[$current_project_id]['total_purgeable_size'] += $res_row['storage_size'];
263
264
			}
		}			
Gerald Salin's avatar
Gerald Salin committed
265
		
266
		//select obsolete analyses of a project
267
268
		$res = tx_nG6_db::select_all_in_view("tx_nG6_view_project_analyze", $where);
		while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
269
			$current_project_id = $res_row['project_id'];
270
			if (!isset ($by_project[$res_row['project_id']])) {
271
272
				$by_project[$current_project_id]= $empty_res_structure;
				$by_project[$current_project_id]['project_name']= $res_row['project_name'];
Gerald Salin's avatar
Gerald Salin committed
273
			}
Celine Noirot's avatar
Celine Noirot committed
274
275
			
			if ($res_row['analyze_id'] != ""){
276
				$by_project[$current_project_id]['state'][$res_row['state']]['nb_analyze'] += 1;
277
                $key = 'storage_size';
noirot's avatar
noirot committed
278
                if($res_row['state'] == "purged"){
279
280
                	$key = "purged_size";
                }
281
282
283
                $by_project[$current_project_id]['state'][$res_row['state']]['size_analyze'] += $res_row[$key];
				$by_project[$current_project_id]['state'][$res_row['state']]['analysis_ids'][]=$res_row['analyze_id'];
				$by_project[$current_project_id]['total_purgeable_size'] += $res_row['storage_size'];
284
                               
Gerald Salin's avatar
Gerald Salin committed
285
286
			}
		}
287
288
289
290
291
		
		$res = tx_nG6_db::select_count_in_view("tx_nG6_view_project_run","");
		while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
			if (isset ($by_project[$res_row['project_id']])) {
				$by_project[$res_row['project_id']]["nb_runs"]=$res_row['count'];
292
293
			}
		}
294
295
296
297
298
		
		$res = tx_nG6_db::select_count_in_view("tx_nG6_view_project_run_analyze","");
		while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
			if (isset ($by_project[$res_row['project_id']])) {
				$by_project[$res_row['project_id']]["nb_analyses"]=$res_row['count'];
299
300
301
			}
		}

302
303
304
305
306
307
308
309
		$res = tx_nG6_db::select_count_in_view("tx_nG6_view_project_analyze","");
		while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
			if (isset ($by_project[$res_row['project_id']])) {
				if (!isset ($by_project[$res_row['project_id']]["nb_analyses"])) {
					$by_project[$res_row['project_id']]["nb_analyses"]=$res_row['count'];
				}else{
					$by_project[$res_row['project_id']]["nb_analyses"]+=$res_row['count'];
				}
Gerald Salin's avatar
Gerald Salin committed
310
311
			}
		}
312
313
314
315
316
317
318
319
		
		#retrieve user per project
		$res = tx_nG6_db::select_all_in_view("tx_nG6_view_project_user", "");
		while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
			if(isset($by_project[$res_row['project_id']])){
				if (!isset ($by_project[$res_row['project_id']]["users"])) {
					$by_project[$res_row['project_id']]["users"]=array();
				}
320
				array_push($by_project[$res_row['project_id']]["users"],array ('user_id' => $res_row['user_id'], 'user_name' => $res_row['user_name'], 'email' =>$res_row['email'], 'groups' =>$res_row['user_group'], 'right_level_label' =>$res_row['right_level_label'], 'user_group_title' => $res_row['user_group_title']));
321
322
323
324
325
			}
		}
		
		return($by_project);
	}
Gerald Salin's avatar
Gerald Salin committed
326

327
328
329
330
331
332
333
    /**
     * Add purge initial purge demand in db
     *
     * @param	int	$project_id	project id link to the purge demand
     * @param	int	$total_purgeable_size	size of files to purge
     * @return	New purge id
     */
334
335
    function add_purge_demand($cruser_id, $project_id, $total_purgeable_size, $all_runs_ids, $all_analyses_ids,$user_ids){
      $date= time();
336
337
    	$purge_data = array(
			'cruser_id'			=>	$cruser_id,
338
339
340
         'project_id'      => $project_id,
         'analyze_ids'     => implode(',',$all_analyses_ids),
         'run_ids'         => implode(',',$all_runs_ids),
341
			'mail_sent_date'	=>	$date,
342
         'purge_size'      => $total_purgeable_size,
343
344
345
346
347
348
349
			'demand_state'	=>	"sent",
			'tstamp'			=> 	$date,
			'crdate'			=> 	$date
        );
    
    	$GLOBALS['TYPO3_DB']->exec_INSERTquery('tx_nG6_purge_demand', $purge_data);
        $purge_demand_id = $GLOBALS['TYPO3_DB']->sql_insert_id();
Celine Noirot's avatar
Celine Noirot committed
350
351
        tx_nG6_db::update_field('tx_nG6_run', $all_runs_ids, array('mail_sent_date','purge_demand_id'),array($date,$purge_demand_id));
        tx_nG6_db::update_field('tx_nG6_analyze',$all_analyses_ids,array('mail_sent_date','purge_demand_id'),array($date,$purge_demand_id));
352
        
353
        foreach($user_ids as $a_id){
354
355
                $purge_data_user = array(
                        'tstamp'			=> 	$date,
356
357
								'crdate'			=> 	$date,
                        'cruser_id'          =>	$cruser_id,
358
                        'purge_demand_id'    =>  $purge_demand_id,
359
                        'fe_users_id'        =>  $a_id
360
361
362
363
364
                );
                $GLOBALS['TYPO3_DB']->exec_INSERTquery('tx_nG6_purge_demand_fe_users', $purge_data_user);
        }
    	return $purge_demand_id;
    }
Celine Noirot's avatar
Celine Noirot committed
365
    
366
    function get_purge_demand_from_id($values_str){
Celine Noirot's avatar
Celine Noirot committed
367
368
        #select all demand id not processed
        $queryParts=array(
369
370
                'SELECT' => ' uid as demand_id,project_id,purge_size,mail_sent_date,processed_date,demand_state,analyze_ids,run_ids',
                'FROM' => 'tx_nG6_purge_demand',
371
                'WHERE' => 'uid IN ('.$values_str.')',
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
                'GROUPBY' 	=> '',
                'ORDERBY' 	=> '',
                'LIMIT' 	=> ''
        );
        
        $res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
        $result=array();
        while($res_row= $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
                $result[]=array(
                "demand_id"=>$res_row["demand_id"],
                "project_id"=>$res_row["project_id"],
                "purge_size"=>$res_row["purge_size"],
                "mail_sent_date"=>$res_row["mail_sent_date"],
                "processed_date"=>$res_row["processed_date"],
                "demand_state"=>$res_row["demand_state"],
                "analyze_ids"=>$res_row["analyze_ids"],
                "run_ids"=>$res_row["run_ids"]
                );
        }
        return($result);
    }  
Celine Noirot's avatar
Celine Noirot committed
393
394
    
    
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
    function get_purge_demand_list($delay_in_days){
        #select all demand id not processed
        $queryParts=array(
                'SELECT' => 'tx_nG6_purge_demand.uid AS demand_id, `tx_nG6_purge_demand`.project_id AS project_id, tx_nG6_project.name as project_name, 
                `tx_nG6_purge_demand`.purge_size AS purge_size, `tx_nG6_purge_demand`.mail_sent_date, `tx_nG6_purge_demand`.demand_state, 
                `fe_users`.username, `fe_groups`.title AS user_group_title, 
                DATEDIFF( FROM_UNIXTIME( `tx_nG6_purge_demand`.mail_sent_date ) , now( ) ) >'.$delay_in_days.' AS delay_excedeed',
                'FROM' => '`tx_nG6_purge_demand`
INNER JOIN tx_nG6_project ON tx_nG6_project.uid = tx_nG6_purge_demand.project_id
INNER JOIN `tx_nG6_purge_demand_fe_users` ON `tx_nG6_purge_demand_fe_users`.`purge_demand_id` = tx_nG6_purge_demand.uid
INNER JOIN fe_users ON fe_users.uid = `tx_nG6_purge_demand_fe_users`.`fe_users_id`
INNER JOIN fe_groups ON fe_groups.uid = fe_users.usergroup',
                'WHERE' => '`tx_nG6_purge_demand`.processed_date IS NULL',
                'GROUPBY' 	=> '',
                'ORDERBY' 	=> '',
                'LIMIT' 	=> ''
        );
        $results=array();
        $res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
        while($res_row= $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
                
                if ( array_key_exists($res_row["demand_id"] , $results)){
                        $results[$res_row["demand_id"]]["users"][]=array("username"=>$res_row["username"], "user_group_title"=>$res_row["user_group_title"]);
                } else {
                        $results[$res_row["demand_id"]]=array("project_id"=>$res_row["project_id"],
                                "purge_size"=>$res_row["purge_size"],
Celine Noirot's avatar
Celine Noirot committed
421
                                "mail_sent_date"=>date("d/m/Y",$res_row["mail_sent_date"]),
422
423
424
425
426
427
428
                                "project_name"=>$res_row["project_name"],
                                "demand_state"=>$res_row["demand_state"],
                                "delay_excedeed"=>$res_row["delay_excedeed"],
                                "users"=>array(array("username"=>$res_row["username"], "user_group_title"=>$res_row["user_group_title"]))
                                );
                }
        }
429
        return ($results);
430
431
    }
	
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
        function extend_retention_date($demand_ids, $date, $type_extend){
                                //TODO extend thanks to the type
                //extend
                $all_demands=tx_nG6_db::get_purge_demand_from_id( join(', ', $demand_ids));
                $all_runs=array();
                $all_analyses=array();
                
                foreach($all_demands as $res){
                        if ($res["state"] != "deleted")
                        {
                                if ($type_extend == 'extend_all_project') {
                                        //extend all project
                                        $curr_project_id=$res["project_id"];
                                        $all_project_filter = " project_id =".$curr_project_id. " AND DATEDIFF( FROM_UNIXTIME( retention_date ), FROM_UNIXTIME(" .$date. ") ) <0
                                        AND state in ('extended','stored') ";
                                        // get all info of a project even non obsolete run analyse (by TRUE parameter)
                                        $res_project_analyze = tx_nG6_db::select_all_in_view("tx_nG6_view_project_analyze", $all_project_filter);
                                        $res_project_run = tx_nG6_db::select_all_in_view("tx_nG6_view_project_run", $all_project_filter);
                                        $res_project_run_analyze = tx_nG6_db::select_all_in_view("tx_nG6_view_project_run_analyze", $all_project_filter);
                                        while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res_project_analyze)) {
                                                $all_analyses[] = $res_row["analyze_id"];
                                                }
                                        while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res_project_run_analyze)) {
                                                $all_analyses[] = $res_row["analyze_id"];
                                                }
                                        while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res_project_run)) {
                                                $all_runs[] = $res_row["run_id"];
                                                }
                                } else {
                                        $all_analyses=array_merge($all_analyses,explode(',',$res["analyze_ids"]));
                                        $all_runs=array_merge($all_runs,explode(',',$res["run_ids"]));
                                }
                                                                                                        
                        }
                }
                tx_nG6_db::update_field('tx_nG6_run', $all_runs, 
                        array("retention_date","data_state", "mail_sent_date","purge_demand_id"),
                        array($date,"extended","","NULL"),
                        array("purge_demand_id"));
                tx_nG6_db::update_field('tx_nG6_analyze',$all_analyses,
                        array("retention_date","data_state", "mail_sent_date","purge_demand_id"),
                        array($date,"extended","","NULL"),
                        array("purge_demand_id"));
                tx_nG6_db::update_field('tx_nG6_purge_demand',$demand_ids,
                        array("processed_date","demand_state"),
                        array($date,"extended"));
                return("Done extend");
                
        }	
        
        function delete_purge_demand($demand_ids,$user_login, $user_pwd, $data_folder){
                $date= time();
                $all_demands=tx_nG6_db::get_purge_demand_from_id($demand_ids);
                $directories=array();
                $res = 0 ;
                foreach($all_demands as $demand){
                        if ($demand["state"] != "deleted"){      
                                foreach(explode(',',$demand["analyze_ids"]) as $a_id){
                                       $res = tx_nG6_db::purge_analysis($a_id, $user_login, $user_pwd, $data_folder);
                                       if ($res != 0) {
                                              break;  
                                        }
                                }
                                if ($res == 0) {
                                        foreach(explode(',',$demand["run_ids"]) as $r_id){
                                                $res = tx_nG6_db::purge_run($r_id, $user_login, $user_pwd, $data_folder);
                                                if ($res != 0) {
                                                      break;  
                                                }
                                        }
                                }
                                else {
                                        break;
                                }
                        }
                }
                # finally set purge demand as purged
                if ($res == 0){
                        tx_nG6_db::update_field('tx_nG6_purge_demand',explode(',',$demand_ids),
                        array("processed_date","demand_state"),
                        array($date,"purged"));
                }
                return $res;
        }	
516
517
518
    /**
     * Select all project for the current user
     *
519
     * @param	string	$by	by can group, organism, location
520
521
     * @param	string	$role	role can be create_user, manager
     * @return	table with all projects
522
523
524
     */
    function select_projects_repartition($role, $by='title') {
    	if ($role == "create_user") {
525
    		$queryParts = array(
526
    				'SELECT' 	=> 'tx_nG6_project.uid as pid, fe_groups.title as title, fe_groups.uid as group_id , fe_groups.tx_nG6_organism as organism, fe_groups.tx_nG6_location as location',
527
528
529
530
531
532
533
    				'FROM' 		=> 'tx_nG6_project '
    				.' INNER JOIN fe_users ON tx_nG6_project.cruser_id=fe_users.uid '
    				.' INNER JOIN fe_groups ON fe_groups.uid=fe_users.usergroup ',
    				'WHERE' 	=> "",
    				'GROUPBY' 	=> '',
    				'ORDERBY' 	=> '',
    				'LIMIT' 	=> ''
534
535
536
537
    		);
    		//$where = "tx_nG6_project.cruser_id="
    	} else if ($role == "manager") {
	    	$queryParts = array(
538
    				'SELECT' 	=> 'tx_nG6_project.uid as pid, fe_groups.title as title, fe_groups.uid as group_id , fe_groups.tx_nG6_organism as organism, fe_groups.tx_nG6_location as location',
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
	    			'FROM' 		=> 'tx_nG6_project '
	    			.' INNER JOIN fe_rights ON tx_nG6_project.uid=fe_rights.project_id '
	    			.' INNER JOIN fe_users ON fe_rights.fe_user_id=fe_users.uid '
	    			.' INNER JOIN fe_groups ON fe_groups.uid=fe_users.usergroup ',
	    			'WHERE' 	=> "fe_rights.right_id=1",
	    			'GROUPBY' 	=> '',
	    			'ORDERBY' 	=> '',
	    			'LIMIT' 	=> ''
	    	);
    	}
    	$by_title = array() ;
    	$by_organism = array();
    	$by_location = array();
    	$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
    	while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
554
555
556
    		if (!isset ($by_title[$res_row['title']])) {
    			$by_title[$res_row['title']] = array(
    					'count'			=> 1,
557
    					'group_id'	=> $res_row['group_id'],
558
559
    					'organism'		=> $res_row['organism'],
    					'location'		=> $res_row['location']);
560
561
562
563
    		} else {
    			$by_title[$res_row['title']]['count'] += 1;
    		}
    		
564
565
566
567
568
    		if (!isset ($by_organism[$res_row['organism']])) {
    			$by_organism[$res_row['organism']] = array(
    					'count'			=> 1);
    		} else {
    			$by_organism[$res_row['organism']]['count'] += 1;
569
570
    		}
    		
571
572
573
574
575
576
    		if (!isset ($by_location[$res_row['location']])) {
    			$by_location[$res_row['location']] = array(
    					'count'			=> 1);
    		} else {
    			$by_location[$res_row['location']]['count'] += 1;
    		}
577
578
579
580
581
582
583
584
585
    	}
    	if ($by=='title') {
    		return ($by_title);
    	} else if ($by=='organism') {
    		return ($by_organism);
    	} else if ($by=='location') {
    		return ($by_location);
    	}
    }
Jerome Mariette's avatar
Jerome Mariette committed
586

587
    function select_projects_evolution($values, $by, $role, $cumulate) {
Celine Noirot's avatar
Celine Noirot committed
588
589
590
591
592
593
        if ($by == "organism" || $by == "location") {
                $by = "tx_nG6_".$by;
        }

        $from = "" ;
        $where = "fe_groups.".$by." IN ('".implode("', '", $values)."')" ;
Penom Nom's avatar
Penom Nom committed
594
595
596
597
598
599
600
601
602
    	if ($role == "create_user") {
    		$from = 'tx_nG6_project '
	    			.' INNER JOIN fe_users ON tx_nG6_project.cruser_id=fe_users.uid '
	    			.' INNER JOIN fe_groups ON fe_groups.uid=fe_users.usergroup ' ;
    	} else if ($role == "manager") {
    		$from = 'tx_nG6_project '
    				.' INNER JOIN fe_rights ON tx_nG6_project.uid=fe_rights.project_id '
    				.' INNER JOIN fe_users ON fe_rights.fe_user_id=fe_users.uid '
    				.' INNER JOIN fe_groups ON fe_groups.uid=fe_users.usergroup ';
Jerome Mariette's avatar
Jerome Mariette committed
603
    		$where .= " AND fe_rights.right_id=1" ;
Penom Nom's avatar
Penom Nom committed
604
605
    	}
    	$queryParts = array(
Jerome Mariette's avatar
Jerome Mariette committed
606
    			'SELECT' 	=> 'tx_nG6_project.crdate, count(tx_nG6_project.crdate) nb',
Penom Nom's avatar
Penom Nom committed
607
608
    			'FROM' 		=> $from,
    			'WHERE' 	=> $where,
Jerome Mariette's avatar
Jerome Mariette committed
609
610
    			'GROUPBY' 	=> 'tx_nG6_project.crdate',
    			'ORDERBY' 	=> 'tx_nG6_project.crdate',
Penom Nom's avatar
Penom Nom committed
611
612
613
614
615
    			'LIMIT' 	=> ''
    	);
    	$results = array();
    	$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
    	while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
616
617
618
619
620
    		if ($cumulate && count($results) > 0) {
    			$results[] = array($res_row["crdate"], $res_row["nb"] + $results[count($results)-1][1]);
    		} else {
    			$results[] = array($res_row["crdate"], $res_row["nb"]);
    		}
Penom Nom's avatar
Penom Nom committed
621
622
623
624
    	}
    	return $results;
    }

625
    function select_projects_distribution($values, $by, $role) {
Celine Noirot's avatar
Celine Noirot committed
626
627
628
629
630
        $from = "" ;
        $where = "" ;
        if ($by == "organism" || $by == "location") {
                $by = "tx_nG6_".$by;
        }
631
632
633
634
635
636
637
638
639
640
    	if ($role == "create_user") {
    		$from = 'tx_nG6_project '
	    			.' INNER JOIN fe_users ON tx_nG6_project.cruser_id=fe_users.uid '
	    			.' INNER JOIN fe_groups ON fe_groups.uid=fe_users.usergroup ' ;
    	} else if ($role == "manager") {
    		$from = 'tx_nG6_project '
    				.' INNER JOIN fe_rights ON tx_nG6_project.uid=fe_rights.project_id '
    				.' INNER JOIN fe_users ON fe_rights.fe_user_id=fe_users.uid '
    				.' INNER JOIN fe_groups ON fe_groups.uid=fe_users.usergroup ';
    		$where = "fe_rights.right_id=1" ;
641
    	}
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
    	$queryParts = array(
    			'SELECT' 	=> 'fe_groups.'.$by.', count(fe_groups.'.$by.') nb',
    			'FROM' 		=> $from,
    			'WHERE' 	=> $where,
    			'GROUPBY' 	=> 'fe_groups.'.$by,
    			'ORDERBY' 	=> '',
    			'LIMIT' 	=> ''
    	);
    	$results = array();
    	$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
    	$others = 0 ;
    	while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
    		if( in_array($res_row[$by], $values) ) {
    			$results[] = array($res_row[$by], $res_row["nb"]);
    		} else {
    			$others += $res_row["nb"] ;
    		}
    	}
    	if ($others != 0) { 
    		$results[] = array("OTHERS", $others);
    	}
    	return $results;
    }
    
666
667
668
    function select_storage_distribution($values, $by, $role, $get_analyzes, $octet) {
    	if ($by == "organism" || $by == "location") {
    		$by = "tx_nG6_".$by;
Jerome Mariette's avatar
Jerome Mariette committed
669
670
671
672
673
    	}
    	$storage_unit = "full_seq_size";
    	if ($octet) {
    		$storage_unit = "storage_size";
    	}
674
675
676
    	$from = "" ;
    	$where = "" ;
    	if ($role == "create_user") {
Jerome Mariette's avatar
Jerome Mariette committed
677
678
    		$from = 'tx_nG6_project '
    		.' INNER JOIN tx_nG6_project_run ON tx_nG6_project_run.project_id= tx_nG6_project.uid'
679
680
681
682
    		.' INNER JOIN tx_nG6_run ON tx_nG6_project_run.run_id= tx_nG6_run.uid'
    		.' INNER JOIN fe_users ON tx_nG6_project.cruser_id=fe_users.uid '
    		.' INNER JOIN fe_groups ON fe_groups.uid=fe_users.usergroup ' ;
    	} else if ($role == "manager") {
Jerome Mariette's avatar
Jerome Mariette committed
683
    		$from = 'tx_nG6_project '
684
    		.' INNER JOIN tx_nG6_project_run ON tx_nG6_project_run.project_id= tx_nG6_project.uid'
Jerome Mariette's avatar
Jerome Mariette committed
685
    		.' INNER JOIN tx_nG6_run ON tx_nG6_project_run.run_id= tx_nG6_run.uid'
686
687
688
689
690
691
692
693
694
695
696
697
    		.' INNER JOIN fe_rights ON tx_nG6_project.uid=fe_rights.project_id '
    		.' INNER JOIN fe_users ON fe_rights.fe_user_id=fe_users.uid '
    		.' INNER JOIN fe_groups ON fe_groups.uid=fe_users.usergroup ';
    		$where = "fe_rights.right_id=1" ;
    	}
    	$queryParts = array(
    			'SELECT' 	=> 'tx_nG6_run.uid, tx_nG6_run.'.$storage_unit.', fe_groups.'.$by,
    			'FROM' 		=> $from,
    			'WHERE' 	=> $where,
    			'GROUPBY' 	=> '',
    			'ORDERBY' 	=> '',
    			'LIMIT' 	=> ''
Jerome Mariette's avatar
Jerome Mariette committed
698
    	);
699
700
701
702
703
    	
    	$results = array();
    	$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
    	$others = 0 ;
    	while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
Jerome Mariette's avatar
Jerome Mariette committed
704
			
705
706
707
708
709
710
    		$analyses_size = 0;
    		if ($get_analyzes && $octet) {
    			$run_analysis = tx_nG6_db::get_run_analysis($res_row["uid"]);
    			foreach($run_analysis as $analyse_id => $analyze_values) {
    				$analyses_size += intval($analyze_values["storage_size"]);
    			}
Jerome Mariette's avatar
Jerome Mariette committed
711
712
713
    		}
    		if( in_array($res_row[$by], $values) ) {
    			
714
    			if( array_key_exists( $res_row[$by], $results) ) {
Jerome Mariette's avatar
Jerome Mariette committed
715
716
717
    				$results[$res_row[$by]] += $res_row[$storage_unit] + $analyses_size;
    			} else {
    				$results[$res_row[$by]] = $res_row[$storage_unit] + $analyses_size;
718
719
720
721
722
723
724
    			}
    		} else {
    			$others += $res_row[$storage_unit] + $analyses_size;
    		}
    	}
    	if ($others != 0) {
    		$results["OTHERS"] = $others;
Jerome Mariette's avatar
Jerome Mariette committed
725
726
    	}
    	$final_results = array();
727
728
729
730
    	foreach($results as $group_key => $group_values) {
    		$final_results[] = array( $group_key, $group_values );
    	}
    	return $final_results;
731
732
    }
    
733
	function select_storage_evolution($values, $by, $role, $get_analyzes, $octet, $cumulate) {
734
735
736
737
738
        if ($by == "organism" || $by == "location") {
                $by = "tx_nG6_".$by;
        }
        $storage_unit = "full_seq_size";
        if ($octet) {
739
        	$storage_unit = "storage_size";
740
741
742
        }
        $from = "" ;
        $where = "fe_groups.".$by." IN ('".implode("', '", $values)."')" ;
743
       
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
        if ($role == "create_user") {
                $from = 'tx_nG6_project '
                .' INNER JOIN tx_nG6_project_run ON tx_nG6_project_run.project_id= tx_nG6_project.uid'
                .' INNER JOIN tx_nG6_run ON tx_nG6_project_run.run_id= tx_nG6_run.uid'
                .' INNER JOIN fe_users ON tx_nG6_project.cruser_id=fe_users.uid '
                .' INNER JOIN fe_groups ON fe_groups.uid=fe_users.usergroup ' ;
        } else if ($role == "manager") {
                $from = 'tx_nG6_project '
                .' INNER JOIN tx_nG6_project_run ON tx_nG6_project_run.project_id= tx_nG6_project.uid'
                .' INNER JOIN tx_nG6_run ON tx_nG6_project_run.run_id= tx_nG6_run.uid'
                .' INNER JOIN fe_rights ON tx_nG6_project.uid=fe_rights.project_id '
                .' INNER JOIN fe_users ON fe_rights.fe_user_id=fe_users.uid '
                .' INNER JOIN fe_groups ON fe_groups.uid=fe_users.usergroup ';
                $where .= " AND fe_rights.right_id=1" ;
        }
        $queryParts = array(
                        'SELECT'        => 'tx_nG6_run.uid, tx_nG6_run.crdate, tx_nG6_run.'.$storage_unit.', tx_nG6_run.purged_size, fe_groups.'.$by,
                        'FROM'          => $from,
                        'WHERE'         => $where,
                        'GROUPBY'       => '',
                        'ORDERBY'       => 'tx_nG6_run.crdate',
                        'LIMIT'         => ''
        );
Jerome Mariette's avatar
Jerome Mariette committed
767

768
769
770
771
772
773
774
775
776
777
778
779
780
781
        $results = array();
        $res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
        while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
                $analyses_size = 0;
                $analyses_size_purged = 0;
                if ($get_analyzes && $octet) {
                        $run_analysis = tx_nG6_db::get_run_analysis($res_row["uid"]);
                        foreach($run_analysis as $analyse_id => $analyze_values) {
                                $analyses_size += intval($analyze_values["storage_size"]);
                                $analyses_size_purged += intval($analyze_values["purged_size"]) + intval($analyze_values["storage_size"]);
                        }
                }

                if( array_key_exists( $res_row["crdate"], $results) ) {
782
783
                        $results[$res_row["crdate"]][0] += $res_row[$storage_unit] + $analyses_size;
                        $results[$res_row["crdate"]][1] += $res_row["purged_size"] + $analyses_size_purged;
784
785
786
787
                } else {
                        $results[$res_row["crdate"]] = array($res_row[$storage_unit] + $analyses_size, $res_row["purged_size"] + $analyses_size_purged);
                }
        }
788
        
789
790
791
792
793
794
795
796
797
798
        $final_results = array();
        foreach($results as $group_key => $group_values) {
                if ($cumulate && count($final_results) > 0) {
                        $final_results[] = array( $group_key, $group_values[0] + $final_results[count($final_results)-1][1],$group_values[0] + $group_values[1] + $final_results[count($final_results)-1][2]);
                } else {
                        $final_results[] = array( $group_key, $group_values[0], $group_values[0] + $group_values[1] );
                }

        }
        return $final_results;
Jerome Mariette's avatar
Jerome Mariette committed
799
    }
800

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
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
	/**
	 * Add a comment to the comment table
	 * @param unknown $table_name
	 * @param unknown $id_label
	 * @param unknown $element_id
	 * @param unknown $cruser_id
	 * @param unknown $new_comment
	 */
    function add_comment($table_name, $id_label, $id, $cruser_id, $new_comment){
    	$new_comment = htmlentities($new_comment, ENT_QUOTES | ENT_COMPAT | ENT_HTML5);
    	$comment_data = array(
    	 		'cruser_id'			=>	$cruser_id,
    	 		'comment'			=>	$new_comment,
    	 		'tstamp'			=> 	time(),
    	 		'crdate'			=> 	time()
    	);
    	$GLOBALS['TYPO3_DB']->exec_INSERTquery('tx_nG6_comment', $comment_data);
    	$comment_id =  $GLOBALS['TYPO3_DB']->sql_insert_id();
    	
    	$comment_link_data = array(
    	 		'cruser_id'		=>	$cruser_id,
    	 		$id_label		=>	$id,
    			'comment_id'	=> 	$comment_id,
    	 		'tstamp'		=> 	time(),
    	 		'crdate'		=> 	time()
    	);
    	
    	$GLOBALS['TYPO3_DB']->exec_INSERTquery($table_name, $comment_link_data);
    	return $GLOBALS['TYPO3_DB']->sql_insert_id();
    }

    /**
     * Retrieve all comments from a given project, run or analysis
     * @param unknown $table_name
     * @param unknown $id_label
     * @param unknown $uid
     * @return multitype:multitype:unknown
     */
    function get_all_comments($table_name, $id_label, $id){
    	$comments = array();
    	$temp = array();
    	$queryParts = array(
    			'SELECT' 	=> 'tx_nG6_comment.uid AS comment_id, '.
    			'tx_nG6_comment.comment AS comment, '.
    			'tx_nG6_comment.cruser_id AS cruser_id, '.
    			'tx_nG6_comment.crdate AS comment_crdate ',
    			'FROM' 		=> $table_name .' INNER JOIN tx_nG6_comment ON '. $table_name . '.comment_id=tx_nG6_comment.uid',
    			'WHERE' 	=> $table_name . '.' . $id_label . '=' . $id,
    			'ORDERBY' 	=> 'comment_id',
    	);
    	 
    	$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
    	while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
    		$comment_id = $row['comment_id'];
    		if (!isset ($temp['comment_'.$comment_id])) {
    			$temp['comment_'.$comment_id] = '';
    			$user_info = tx_nG6_db::get_user_informations($row['cruser_id']);
    			$comments[] = array(
    					'id'			=> $comment_id,
    					'comment'		=> html_entity_decode($row['comment'], ENT_QUOTES | ENT_COMPAT | ENT_HTML5),
    					'date'			=> date( 'd.M.Y-H:i' ,$row['comment_crdate']),
    					'cruser_info'	=> $user_info,
    			);
    		}
    	}
    	return $comments;
    }
    
    /**
     * Delete a given commentary from the database
     * @param unknown $table_name
     * @param unknown $id_label
     * @param unknown $id
     * @param unknown $comment_id
     */
    function delete_comment($table_name, $id_label, $id, $comment_id){
    	
    	$res = 0 ;
    	//from association table
880
    	$where = $table_name.'.'.$id_label.'='.$id.' AND '.$table_name.'.comment_id='.$comment_id ;
881
882
    	$res = $GLOBALS['TYPO3_DB']-> exec_DELETEquery ($table_name, $where);
    	
883
884
885
886
887
    	//from comment table
    	$where = 'tx_nG6_comment.uid='.$comment_id ;
    	$res = $GLOBALS['TYPO3_DB']-> exec_DELETEquery ('tx_nG6_comment', $where);
    	if ($res != 1) {
    		$res = 1 ;
888
889
890
891
892
893
894
895
896
897
898
899
900
901
    	}
    	return $res ;
    }
    
    /**
     * Update an existing comment
     * @param unknown $comment_id
     * @param unknown $new_comment
     */
    function update_comment($comment_id, $new_comment){
    	return $GLOBALS['TYPO3_DB']-> exec_UPDATEquery ('tx_nG6_comment', 'uid='.$comment_id, array('comment' => $new_comment));
    }
    
    
902
903
904
905
	/*
	 * Project functions
	 *------------------------------------------------------------*/

906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
    /**
     * Add a comment to the project described by project_id
     * @param unknown $project_id
     * @param unknown $cruser_id
     * @param unknown $new_comment
     */
    function add_project_comment($project_id, $cruser_id, $new_comment){
    	return tx_nG6_db::add_comment('tx_nG6_project_comment', 'project_id', $project_id, $cruser_id, $new_comment);
    }
    
    /**
     * Retrieve all comments from a given project
     * @param unknown $project_id
     */
    function get_all_project_comments($project_id){
    	return tx_nG6_db::get_all_comments('tx_nG6_project_comment', 'project_id', $project_id);
    }
    
    /**
     * Delete a given project comment
     * @param unknown $project_id
     * @param unknown $comment_id
     */
    function delete_project_comment($project_id, $comment_id){
    	return tx_nG6_db::delete_comment('tx_nG6_project_comment', 'project_id', $project_id, $comment_id);
    }
    
933
934
	/**
	 * Select all project for the current user
935
	 * 
936
	 * @param	string	$user_id	the user id
937
938
	 * @return	table with all projects
	 */
939
	function select_all_user_projects($user_id, $orderby='', $limit='') {		
940
		$projects = array();
Jerome Mariette's avatar
Jerome Mariette committed
941
		
942
		// If the user is not logged on display demonstration project
Jerome Mariette's avatar
Jerome Mariette committed
943
944
945
		if ($user_id == null) { $where = 'tx_nG6_project.public=0'; } 
		else { $where = 'fe_rights.fe_user_id='.$user_id; }
		
946
		//First, get the analyzis project-scale
947
		$queryParts = array(
948
949
950
			'SELECT' => 'tx_nG6_project.uid AS project_id, '.
						'tx_nG6_project.name AS project_name, '.
						'tx_nG6_project.description AS project_description, '.
951
						'tx_nG6_project.public AS project_public, '.
Jerome Mariette's avatar
Jerome Mariette committed
952
						'tx_nG6_project.crdate AS project_crdate, '.
953
954
						'tx_nG6_project.hidden AS project_hidden ',
			'FROM' => 'tx_nG6_project INNER JOIN fe_rights ON fe_rights.project_id=tx_nG6_project.uid',
955
956
			'WHERE' => $where,
			'GROUPBY' => '',
Jerome Mariette's avatar
Jerome Mariette committed
957
958
			'ORDERBY' => $orderby,
			'LIMIT' => $limit
959
		);
960
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);		
961
962
		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
			$project_id = $row['project_id'];
Jerome Mariette's avatar
Jerome Mariette committed
963
			if (!isset ($projects['project_'.$project_id])) {		
964
				$projects['project_'.$project_id] = array(
965
					'id'			=> $project_id,				
966
					'name'			=> $row['project_name'],
Jerome Mariette's avatar
Jerome Mariette committed
967
					'hidden'		=> $row['project_hidden'],
Jerome Mariette's avatar
Jerome Mariette committed
968
					'date'			=> $row['project_crdate'],
969
					'public'		=> $row['project_public'],
970
971
					'description'	=> $row['project_description']);
			}
972
						
973
		}		
974
975
976
		return $projects;
	}

Penom Nom's avatar
Penom Nom committed
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
	/**
	* Select all project for the current user
	*
	* @param	string	$user_id	the user id
	* @return	table with all projects
	*/
	function get_user_projects($user_id, $orderby='', $limit='') {
		$projects = array();
	
		// If the user is not logged on display demonstration project
		if ($user_id == null) {
			$where = 'tx_nG6_project.public=0';
		}
		else { 
				$where = 'fe_rights.fe_user_id='.$user_id.' AND ((fe_rights.right_id<>2 AND tx_nG6_project.hidden=0) '
				.'OR fe_rights.right_id=2)' ;
		}
	
		//First, get the analyzis project-scale
		$queryParts = array(
				'SELECT' => 'tx_nG6_project.uid AS project_id, '.
							'tx_nG6_project.name AS project_name, '.
							'tx_nG6_project.description AS project_description, '.
							'tx_nG6_project.public AS project_public, '.
							'tx_nG6_project.crdate AS project_crdate, '.
							'tx_nG6_project.hidden AS project_hidden ',
				'FROM' => 'tx_nG6_project INNER JOIN fe_rights ON fe_rights.project_id=tx_nG6_project.uid',
				'WHERE' => $where,
				'GROUPBY' => '',
				'ORDERBY' => $orderby,
				'LIMIT' => $limit
		);
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
			$project_id = $row['project_id'];
			if (!isset ($projects['project_'.$project_id])) {
				$projects['project_'.$project_id] = array(
						'id'			=> $project_id,				
						'name'			=> $row['project_name'],
						'hidden'		=> $row['project_hidden'],
						'date'			=> $row['project_crdate'],
						'public'		=> $row['project_public'],
						'description'	=> $row['project_description']);
			}
	
		}
		return $projects;
	}

1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
	/**
	 * 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
1042
1043
1044
1045
		$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
1046
					 'date'			=> $vals['crdate'],
Jerome Mariette's avatar
Jerome Mariette committed
1047
1048
					 'public'		=> $vals['public'],
					 'description'	=> $vals['description']);
1049
1050
1051
1052
1053
1054
1055
1056
	}

	/**
	 * Select all runs linked to the specified project
	 *
	 * @param	string	$project_id	the project id
	 * @return	hash table with all runs information
	 */
1057
function get_project_runs($project_id, $orderby='', $limit='') {
1058
    	
1059
		// First select all runs from the database
1060
		$queryParts = Array( 
1061
1062
1063
1064
			'SELECT' => 'tx_nG6_run.uid AS run_id,'.
					 	'tx_nG6_run.directory AS run_directory,'.
					 	'tx_nG6_run.species AS run_species,'.
						'tx_nG6_run.description AS run_description, '.
Jerome Mariette's avatar
Jerome Mariette committed
1065
1066
1067
						'tx_nG6_run.data_nature AS run_data_nature, '.
						'tx_nG6_run.sequencer AS run_sequencer, '.
						'tx_nG6_run.type AS run_type, '.
1068
						'tx_nG6_run.name AS run_name, '.
Jerome Mariette's avatar
Jerome Mariette committed
1069
1070
						'tx_nG6_run.nb_sequences AS run_nb_sequences, '.
						'tx_nG6_run.full_seq_size AS run_full_seq_size, '.
1071
1072
						'tx_nG6_run.date AS run_date, '.
						'tx_nG6_run.hidden AS run_hidden, '.
1073
1074
1075
1076
1077
						'tx_nG6_run.data_state AS run_data_state, '.
						'tx_nG6_run.retention_date AS run_retention_date, '.
						'tx_nG6_run.purged_date AS run_purged_date, '.
						'tx_nG6_run.purged_size AS run_purged_size, '.
						'tx_nG6_run.mail_sent_date AS run_mail_sent_date, '.
1078
1079
						'tx_nG6_project.uid AS project_id, '.
						'tx_nG6_project.name AS project_name ',
Jerome Mariette's avatar
Jerome Mariette committed
1080
			'FROM' => 'tx_nG6_project '.
1081
1082
  						'INNER JOIN tx_nG6_project_run ON  tx_nG6_project.uid=tx_nG6_project_run.project_id '.
  						'INNER JOIN tx_nG6_run ON tx_nG6_project_run.run_id=tx_nG6_run.uid ',
Jerome Mariette's avatar
Jerome Mariette committed
1083
			'WHERE' => 'tx_nG6_project.uid='.$project_id,
1084
			'GROUPBY' => '',
Jerome Mariette's avatar
Jerome Mariette committed
1085
1086
			'ORDERBY' => $orderby,
			'LIMIT' 	=> $limit
Penom Nom's avatar
Penom Nom committed
1087
1088
1089
		);

	
1090
1091
1092
1093
		// 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
1094
1095
			$run_id = $row['run_id'];				
			if (!isset($results['run_'.$run_id])) {				
1096
				$results['run_'.$run_id] = array( 
Jerome Mariette's avatar
Jerome Mariette committed
1097
					'id'			=> $run_id,
1098
					'directory'		=> $row['run_directory'], 
1099
					'name' 			=> $row['run_name'],
Jerome Mariette's avatar
Jerome Mariette committed
1100
1101
					'project_name' 	=> $row['project_name'],
					'hidden'		=> $row['run_hidden'],
1102
					'species' 		=> $row['run_species'],
Jerome Mariette's avatar
Jerome Mariette committed
1103
1104
1105
					'nb_sequences' 	=> $row['run_nb_sequences'],
					'full_seq_size' => $row['run_full_seq_size'],
					'project_id' 	=> $row['project_id'],
1106
					'date'			=> $row['run_date'],
Jerome Mariette's avatar
Jerome Mariette committed
1107
1108
1109
					'data_nature'	=> $row['run_data_nature'],
					'sequencer'		=> $row['run_sequencer'],
					'type'			=> $row['run_type'],
1110
1111
1112
1113
1114
1115
					'description' 	=> $row['run_description'],
					'data_state' 	=> $row['run_data_state'],
					'retention_date' 	=> $row['run_retention_date'],
					'purged_date' 	=> $row['run_purged_date'],
					'purged_size' 	=> $row['run_purged_size'],
					'mail_sent_date' 	=> $row['run_mail_sent_date'],
1116
				);
1117
			}						
1118
1119
1120
		}
		return $results;
    }
Penom Nom's avatar
Penom Nom committed
1121
1122
1123
1124
1125
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
    /**
     * Select all runs linked to the specified project for the user
     *
     * @param	string	$user_id	the user id
     * @param	string	$project_id	the project id
     * @return	hash table with all runs information
     */
     function get_user_project_runs($user_id, $project_id, $orderby='', $limit='') {
    	// If the user is not logged on display demonstration project
	    if ($user_id == null) {
	    	$where = 'tx_nG6_project.uid='.$project_id.' AND tx_nG6_project.public=0 AND tx_nG6_run.hidden=0';
	    }
	    else {
	    	$where = 'fe_users.uid='.$user_id.' AND '.'tx_nG6_project.uid='.$project_id.
	    		' AND ((fe_rights.right_id<>2 AND tx_nG6_run.hidden=0) OR fe_rights.right_id=2)' ;
	    }
    	
	    // First select all runs from the database
	    $queryParts = Array(
		    'SELECT' => 'tx_nG6_run.uid AS run_id,'.
			    'tx_nG6_run.directory AS run_directory,'.
			    'tx_nG6_run.species AS run_species,'.
			    'tx_nG6_run.description AS run_description, '.
			    'tx_nG6_run.data_nature AS run_data_nature, '.
			    'tx_nG6_run.sequencer AS run_sequencer, '.
			    'tx_nG6_run.type AS run_type, '.
			    'tx_nG6_run.name AS run_name, '.
			    'tx_nG6_run.nb_sequences AS run_nb_sequences, '.
			    'tx_nG6_run.full_seq_size AS run_full_seq_size, '.
			    'tx_nG6_run.date AS run_date, '.
			    'tx_nG6_run.hidden AS run_hidden, '.
1152
1153
1154
1155
1156
			    'tx_nG6_run.data_state AS run_data_state, '.
				'tx_nG6_run.retention_date AS run_retention_date, '.
				'tx_nG6_run.purged_date AS run_purged_date, '.
				'tx_nG6_run.purged_size AS run_purged_size, '.
				'tx_nG6_run.mail_sent_date AS run_mail_sent_date, '.
Penom Nom's avatar
Penom Nom committed
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
			    'tx_nG6_project.uid AS project_id, '.
			    'tx_nG6_project.name AS project_name ',
		    'FROM' => 'tx_nG6_run '.
			    'INNER JOIN tx_nG6_project_run ON tx_nG6_run.uid=tx_nG6_project_run.run_id '.
			    'INNER JOIN tx_nG6_project ON tx_nG6_project_run.project_id=tx_nG6_project.uid '.
			    'INNER JOIN fe_rights ON tx_nG6_project.uid=fe_rights.project_id '.
			    'INNER JOIN fe_users ON fe_rights.fe_user_id=fe_users.uid ',
		    'WHERE' => $where,
		    'GROUPBY' => '',
		    'ORDERBY' => $orderby,
		    'LIMIT' 	=> $limit
	    );
    
	    // Then create the result hash table
	    $results = array();
	    $res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
	    while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
	    	$run_id = $row['run_id'];
	    	if (!isset($results['run_'.$run_id])) {
			    $results['run_'.$run_id] = array(
			    'id'			=> $run_id,
			    'directory'		=> $row['run_directory'],
			    'name' 			=> $row['run_name'],
1180
			    'project_name' 	=> $row['project_name'],
Penom Nom's avatar
Penom Nom committed
1181
			    'hidden'		=> $row['run_hidden'],
1182
1183
1184
1185
1186
1187
			    'data_state' 	=> $row['run_data_state'],
				'retention_date' 	=> $row['run_retention_date'],
				'purged_date' 	=> $row['run_purged_date'],
				'purged_size' 	=> $row['run_purged_size'],
				'mail_sent_date' 	=> $row['run_mail_sent_date'],
			    'species' 		=> $row['run_species'],
Penom Nom's avatar
Penom Nom committed
1188
			    'nb_sequences' 	=> $row['run_nb_sequences'],
1189
1190
1191
1192
1193
1194
			    'full_seq_size' => $row['run_full_seq_size'],
			    'project_id' 	=> $row['project_id'],
			    'date'			=> $row['run_date'],
			    'data_nature'	=> $row['run_data_nature'],
			    'sequencer'		=> $row['run_sequencer'],
			    'type'			=> $row['run_type'],
Penom Nom's avatar
Penom Nom committed
1195
1196
1197
1198
1199
1200
1201
			    'description' 	=> $row['run_description']
			    				);
		    }
	    }
	    return $results;
    }

1202
1203
1204
1205
1206
1207
	/**
	 * Select all analysis linked to the specified project
	 *
	 * @param	string	$project_id	the project id
	 * @return	hash table with all analysis information
	 */
Jerome Mariette's avatar
Jerome Mariette committed
1208
    function get_project_analysis($project_id, $orderby='', $limit='') {
1209
1210
    	
    	// First select all analysis from the database    	
1211
    	$queryParts = array( 
1212
1213
			'SELECT' => 'tx_nG6_analyze.uid AS analyze_id,'. 
						'tx_nG6_analyze.directory AS analyze_directory,'. 
1214
						'tx_nG6_analyze.name AS analyze_name, '.
1215
						'tx_nG6_analyze.class AS analyze_class, '.
1216
						'tx_nG6_analyze.date AS analyze_date, '.
Jerome Mariette's avatar
Jerome Mariette committed
1217
1218
						'tx_nG6_analyze.software AS analyze_software, '.
						'tx_nG6_analyze.version AS analyze_version, '.
1219
1220
1221
1222
1223
						'tx_nG6_analyze.data_state AS analyze_data_state, '.
						'tx_nG6_analyze.retention_date AS analyze_retention_date, '.
						'tx_nG6_analyze.purged_date AS analyze_purged_date, '.
						'tx_nG6_analyze.purged_size AS analyze_purged_size, '.
						'tx_nG6_analyze.mail_sent_date AS analyze_mail_sent_date, '.
1224
						'tx_nG6_analyze.params AS analyze_params, '.
1225
						'tx_nG6_analyze.description AS analyze_description, '.
1226
    					'tx_nG6_analyze.is_editable AS analyze_is_editable, '.
Jerome Mariette's avatar
Jerome Mariette committed
1227
						'tx_nG6_analyze.parent_uid AS analyze_parent_uid, '.
1228
						'tx_nG6_analyze.hidden AS analyze_hidden ',
Jerome Mariette's avatar
Jerome Mariette committed
1229
			'FROM' => 'tx_nG6_project '.
1230
1231
						'INNER JOIN tx_nG6_project_analyze ON tx_nG6_project.uid = tx_nG6_project_analyze.project_id '.
						'INNER JOIN tx_nG6_analyze ON tx_nG6_analyze.uid=tx_nG6_project_analyze.analyze_id ',
Jerome Mariette's avatar
Jerome Mariette committed
1232
			'WHERE' => 'tx_nG6_project.uid='.$project_id,
1233
			'GROUPBY' => '',
Jerome Mariette's avatar
Jerome Mariette committed
1234
1235
			'ORDERBY' => $orderby,
			'LIMIT' => $limit
1236
1237
1238
1239
1240
1241
		);
		// 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 = $row['analyze_id'];
Jerome Mariette's avatar
Jerome Mariette committed
1242
			if (!isset ($results['analyse_'.$analyze_id])) {				
1243
1244
				$results['analyse_'.$analyze_id] = array( 
					'directory'		=> $row['analyze_directory'], 
1245
					'name' 			=> $row['analyze_name'],
1246
					'class'			=> $row['analyze_class'],
Jerome Mariette's avatar
Jerome Mariette committed
1247
1248
					'id' 			=> $row['analyze_id'],
					'hidden' 		=> $row['analyze_hidden'],
1249
					'params' 		=> $row['analyze_params'],
Jerome Mariette's avatar
Jerome Mariette committed
1250
1251
					'software' 		=> $row['analyze_software'],
					'version' 		=> $row['analyze_version'],
1252
1253
1254
1255
1256
					'data_state' 		=> $row['analyze_data_state'],
					'retention_date' 		=> $row['analyze_retention_date'],
					'purged_date' 		=> $row['analyze_purged_date'],
					'purged_size' 		=> $row['analyze_purged_size'],
					'mail_sent_date' 		=> $row['analyze_mail_sent_date'],
1257
					'date'			=> $row['analyze_date'],
Jerome Mariette's avatar
Jerome Mariette committed
1258
					'description' 	=> $row['analyze_description'],
1259
					'is_editable' 	=> $row['analyze_is_editable'],
Jerome Mariette's avatar
Jerome Mariette committed
1260
					'parent_id'		=> $row['analyze_parent_uid']	
1261
				);
1262
			}						
1263
1264
1265
1266
		}
		return $results;
    }

Penom Nom's avatar
Penom Nom committed
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
    /**
    * Select all analysis linked to the specified project for the user
    *
    * @param	string	$user_id	the user id
    * @param	string	$project_id	the project id
    * @return	hash table with all analysis information
    */
    function get_user_project_analysis($user_id, $project_id, $orderby='', $limit='') {
    	// If the user is not logged on display demonstration project
    	if ($user_id == null) {
    		$where = 'tx_nG6_project.uid='.$project_id.' AND tx_nG6_project.public=0 AND tx_nG6_run.hidden=0';
    	}
    	else {
    		$where = 'fe_users.uid='.$user_id.' AND tx_nG6_project.uid='.$project_id.
    					' AND ((fe_rights.right_id<>2 AND tx_nG6_analyze.hidden=0) OR fe_rights.right_id=2)' ;
    	}
    	
    	// First select all analysis from the database
    	$queryParts = array(
    			'SELECT' => 'tx_nG6_analyze.uid AS analyze_id,'. 
    						'tx_nG6_analyze.directory AS analyze_directory,'. 
    						'tx_nG6_analyze.name AS analyze_name, '.
    						'tx_nG6_analyze.class AS analyze_class, '.
    						'tx_nG6_analyze.date AS analyze_date, '.
    						'tx_nG6_analyze.software AS analyze_software, '.
    						'tx_nG6_analyze.version AS analyze_version, '.
1293
1294
1295
1296
1297
    						'tx_nG6_analyze.data_state AS analyze_data_state, '.
							'tx_nG6_analyze.retention_date AS analyze_retention_date, '.
							'tx_nG6_analyze.purged_date AS analyze_purged_date, '.
							'tx_nG6_analyze.purged_size AS analyze_purged_size, '.
							'tx_nG6_analyze.mail_sent_date AS analyze_mail_sent_date, '.
Penom Nom's avatar
Penom Nom committed
1298
1299
    						'tx_nG6_analyze.params AS analyze_params, '.
    						'tx_nG6_analyze.description AS analyze_description, '.
1300
    						'tx_nG6_analyze.is_editable AS analyze_is_editable, '.
Penom Nom's avatar
Penom Nom committed
1301
1302
1303
1304
1305
1306
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
1324
1325
1326
1327
1328
    						'tx_nG6_analyze.parent_uid AS analyze_parent_uid, '.
    						'tx_nG6_analyze.hidden AS analyze_hidden ',
    			'FROM' => 'tx_nG6_analyze '.
    						'INNER JOIN tx_nG6_project_analyze ON tx_nG6_analyze.uid = tx_nG6_project_analyze.analyze_id '.
    						'INNER JOIN tx_nG6_project ON tx_nG6_project_analyze.project_id=tx_nG6_project.uid '.
							'INNER JOIN fe_rights ON tx_nG6_project.uid=fe_rights.project_id '.
					  		'INNER JOIN fe_users ON fe_rights.fe_user_id=fe_users.uid ',
    			'WHERE' => $where,
    			'GROUPBY' => '',
    			'ORDERBY' => $orderby,
    			'LIMIT' => $limit
    	);
    	// Then create the result hash table
    	$results = array();
    	$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
    	while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
    		$analyze_id = $row['analyze_id'];
    		if (!isset ($results['analyse_'.$analyze_id])) {
    			$results['analyse_'.$analyze_id] = array(
    					'directory'		=> $row['analyze_directory'], 
    					'name' 			=> $row['analyze_name'],
    					'class'			=> $row['analyze_class'],
    					'id' 			=> $row['analyze_id'],
    					'hidden' 		=> $row['analyze_hidden'],
    					'params' 		=> $row['analyze_params'],
    					'software' 		=> $row['analyze_software'],
    					'version' 		=> $row['analyze_version'],
    					'date'			=> $row['analyze_date'],
1329
1330
1331
1332
1333
    					'data_state' 		=> $row['analyze_data_state'],
						'retention_date' 		=> $row['analyze_retention_date'],
						'purged_date' 		=> $row['analyze_purged_date'],
						'purged_size' 		=> $row['analyze_purged_size'],
						'mail_sent_date' 		=> $row['analyze_mail_sent_date'],
Penom Nom's avatar
Penom Nom committed
1334
    					'description' 	=> $row['analyze_description'],
1335
    					'is_editable' 	=> $row['analyze_is_editable'],
Penom Nom's avatar
Penom Nom committed
1336
1337
1338
1339
1340
1341
1342
    					'parent_id'		=> $row['analyze_parent_uid']	
    			);
    		}
    	}
    	return $results;
    }

1343
1344
1345
1346
1347
    /**
     * Hide a project and sublevels (runs & analyzes) datas from database project
     * 
     * @param	string	$p_id	the project id to hide
     */