class.tx_nG6_eid.php 29 KB
Newer Older
Penom Nom's avatar
Penom Nom committed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
<?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(PATH_t3lib.'class.t3lib_befunc.php');
require_once(PATH_t3lib.'stddb/tables.php');
require_once(t3lib_extMgm::extPath('cms','ext_tables.php'));
require_once(PATH_t3lib.'class.t3lib_db.php');
require_once(t3lib_extMgm::extPath('nG6').'/lib/class.tx_nG6_db.php');
require_once(t3lib_extMgm::extPath('nG6').'/lib/class.tx_nG6_utils.php');
require_once(t3lib_extMgm::extPath('nG6').'/lib/class.tx_nG6_process.php');

/**
 * Class 'tx_nG6_eid' for the 'nG6' extension.
 * This class is in charge of all communication between the client and the server using AJAX
 *
 * @author	PF bioinformatique de Toulouse <>
 */
class tx_nG6_eid {

    /**
     * The main function of the tx_nG6_eid, this function is the one called when using ajax
     */
    function main() {

    	// Connect to the databse
    	tslib_eidtools::connectDB();
    	$type = trim(t3lib_div::_GP('type'));
49
    	$user_id = trim(t3lib_div::_GP('user_id'));
Penom Nom's avatar
Penom Nom committed
50
51
52
53
54
    	
    	// If the type of data requested is project
    	if ($type == 'project') {
    		$project_id = trim(t3lib_div::_GP('id'));
	    	// Select all runs linked to the project
55
	    	$project_runs = tx_nG6_db::get_project_runs($user_id, $project_id, 'tx_nG6_run.date DESC');
Penom Nom's avatar
Penom Nom committed
56
57
58
59
60
61
	    	// for each run
	    	$html_tree = '';
			foreach($project_runs as $run_id => $run_values) {
				$html_tree .= '<li class="jstree-closed" name=\''.str_replace(array('###SPAN_NAME###', '###SPAN_DATE###'), array($run_values['name'], strftime('%d-%m-%y',$run_values['date'])), trim(t3lib_div::_GP('run_short_description'))).'\' id=\''.$run_id.'\'> <a href=\'#\'>'.str_replace(array('###SPAN_NAME###', '###SPAN_DATE###', '###SPAN_NB_SEQ###', '###SPAN_SPECIES###'), array($run_values['name'], strftime('%d-%m-%y',$run_values['date']), $run_values['nb_sequences'], $run_values['species']), trim(t3lib_div::_GP('run_description'))).'</a></li>';
			}
	    	// Then all project analysis
62
	    	$project_analysis = tx_nG6_db::get_project_analysis($user_id, $project_id, 'tx_nG6_analyze.name');
Penom Nom's avatar
Penom Nom committed
63
64
65
66
67
68
69
70
71
72
			foreach($project_analysis as $analyse_id => $analyse_values) {  
				$html_tree .= '<li name=\''.str_replace(array('###SPAN_NAME###'), array($analyse_values["name"]), trim(t3lib_div::_GP('analyse_description'))).'\' id=\''.$analyse_id.'\'> <a href=\'#\'>'.str_replace(array('###SPAN_NAME###'), array($analyse_values["name"]), trim(t3lib_div::_GP('analyse_description'))).'</a></li>';
			}
			// Return the html_tree
	    	print $html_tree;
	    	
	    // If the type of data requested is run
    	} else if ($type == 'run'){
			$run_id = trim(t3lib_div::_GP('id'));
			// Select all analysis linked to the run and the run information
73
			$run_analysis = tx_nG6_db::get_run_analysis($user_id, $run_id, 'tx_nG6_analyze.name');
Penom Nom's avatar
Penom Nom committed
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
			$run_info = tx_nG6_db::select_run($run_id);
	    	// for each analysis
	    	$html_tree = '';
			$html_tree .= '<li name=\'run_'.$run_id.'_'.trim(t3lib_div::_GP("raw_data_description")).'\'  id=\'data_'.$run_id.'\'> <a href=\'#\'>'.trim(t3lib_div::_GP("raw_data_description")).'</a></li>';
			foreach($run_analysis as $analyse_id => $analyse_values) {   
				$html_tree .= '<li name=\'run_'.$run_id.'_'.str_replace(array('###SPAN_NAME###'), array($analyse_values["name"]), trim(t3lib_div::_GP('analyse_description'))).'\' id=\''.$analyse_id.'\'> <a href=\'#\'>'.str_replace(array('###SPAN_NAME###'), array($analyse_values["name"]), trim(t3lib_div::_GP('analyse_description'))).'</a></li>';
			}
			// Return the html_tree
			print $html_tree;
	    	
	    // If downloading data is requested
    	} else if ($type == 'download') {
    		$format = trim(t3lib_div::_GP('format'));
    		// If link in home directory
    		if ($format == 'home_link') {
				$ids = trim(t3lib_div::_GP('ids'));
				$data_folder = trim(t3lib_div::_GP('data_folder'));
				$user_login = trim(t3lib_div::_GP('user_login'));
				$user_pwd = trim(t3lib_div::_GP('user_pwd'));
				$user_directory = trim(t3lib_div::_GP('user_directory'));
94
				$retcode = $this->create_symbolic_links($user_id, $user_login, $user_pwd, $ids, $data_folder, $user_directory);
Penom Nom's avatar
Penom Nom committed
95
96
97
98
99
100
101
102
103
104
				print $retcode;
				
			// If a .tar.gz file
    		} else {
				$ids = trim(t3lib_div::_GP('ids'));
				$data_folder = trim(t3lib_div::_GP('data_folder'));
				$tmp_folder = trim(t3lib_div::_GP('tmp_folder'));
				$user_email = trim(t3lib_div::_GP('user_email'));
				$title_email = trim(t3lib_div::_GP('title_email'));
				$msg_email = trim(t3lib_div::_GP('msg_email'));
105
				$archive_info = $this->create_archive_script($user_id, $ids, $data_folder, $tmp_folder, "tar.gz", $user_email, $title_email, $msg_email); 
Penom Nom's avatar
Penom Nom committed
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
				$process = new Process("tcsh ".$archive_info[0]);
			    print "pid=".$process->getPid()."&archive_path=".$archive_info[1];
    		}
    		
    	// If asked to check a job status
    	} else if($type == 'check_status') {
    		$pid = trim(t3lib_div::_GP('pid'));
    		$archive_path = trim(t3lib_div::_GP('archive_path'));
    		$process = new Process();
    		$process->setPid($pid);
    		// If the job is done
    		if ($process->status()) {
    			print "pid=0&archive_path=".$archive_path;
    		// If the job is still runing
    		} else {
    			print "pid=".$process->getPid()."&archive_path=".$archive_path;
    		}
            
    	// If asked to hide a {project/run}
    	} else if ($type == 'hide') {
    		
    		$ids = trim(t3lib_div::_GP('ids'));
    		// {project/run}_id to array (1;2;3;...) -> [1;2;3;...]
    		$tab_ids = explode(";",$ids);
    		$hide_level = trim(t3lib_div::_GP('hide_level'));
    		
    		if ($hide_level == 'project') {
	    		foreach($tab_ids as $id => $value) {
134
		    		tx_nG6_db::hide_project($value, $user_id);
Penom Nom's avatar
Penom Nom committed
135
136
137
	    		}
    		} else if ($hide_level == 'run') {
	    		foreach($tab_ids as $id => $value) {
138
		    		tx_nG6_db::hide_run($value, $user_id);
Penom Nom's avatar
Penom Nom committed
139
140
141
	    		}
    		} else if ($hide_level == 'analysis') {
	    		foreach($tab_ids as $id => $value) {
142
		    		tx_nG6_db::hide_analysis($value, $user_id);
Penom Nom's avatar
Penom Nom committed
143
144
145
146
147
148
149
150
151
152
153
154
155
	    		}
    		}

        // If asked to unhide a {project/run}
    	} else if ($type == 'unhide') {
    		    		
    		$ids = trim(t3lib_div::_GP('ids'));
    		// {project/run}_id to array (1;2;3;...) -> [1;2;3;...]
    		$tab_ids = explode(";",$ids);
    		$unhide_level = trim(t3lib_div::_GP('unhide_level'));

    		if ($unhide_level == 'project') {
	    		foreach($tab_ids as $id => $value) {
156
		    		tx_nG6_db::unhide_project($value, $user_id);
Penom Nom's avatar
Penom Nom committed
157
158
159
	    		}
    		} else if ($unhide_level == 'run') {
	    		foreach($tab_ids as $id => $value) {
160
		    		tx_nG6_db::unhide_run($value, $user_id);
Penom Nom's avatar
Penom Nom committed
161
162
163
	    		}
    		} else if ($unhide_level == 'analysis') {
	    		foreach($tab_ids as $id => $value) {
164
		    		tx_nG6_db::unhide_analysis($value, $user_id);
Penom Nom's avatar
Penom Nom committed
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
	    		}
    		}
    		
    	// If asked to delete a {project/run/analyze}	
    	} else if ($type == 'delete') {

    		$ids = trim(t3lib_div::_GP('ids'));
    		// {project/run}_id to array (1;2;3;...) -> [1;2;3;...]
    		$tab_ids = explode(";",$ids);
    		$delete_level = trim(t3lib_div::_GP('del_level'));
    		$data_folder = trim(t3lib_div::_GP('data_folder'));
			$user_login = trim(t3lib_div::_GP('user_login'));
			$user_pwd = trim(t3lib_div::_GP('user_pwd'));

    		$res = 0;
    		// check login and password
    		if (isset($user_login) && isset($user_pwd) && $user_login != 'undefined' && $user_pwd != 'undefined') {
    			$res = 0;
		    	$connection = ssh2_connect('127.0.0.1', 22);
				if (!$connection) { $res = 3; }
				if (!ssh2_auth_password($connection, $user_login, $user_pwd)) { $res=2;}
    		} else {
    			$res = 3;
    		}
			
			if ($res == 0) {
	    		if ($delete_level == 'project') {
		    		foreach($tab_ids as $id => $value) {
193
			    		$res = tx_nG6_db::delete_project($user_id, $value, $user_login, $user_pwd, $data_folder);
Penom Nom's avatar
Penom Nom committed
194
195
196
197
			    		if ($res != 0) { break; }
		    		}
	    		} else if ($delete_level == 'run') {
		    		foreach($tab_ids as $id => $value) {
198
			    		$res = tx_nG6_db::delete_run($user_id, $value, $user_login, $user_pwd, $data_folder);
Penom Nom's avatar
Penom Nom committed
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
			    		if ($res != 0) { break; }
		    		}
	    		} else if ($delete_level == 'analysis') {
		    		foreach($tab_ids as $id => $value) {
			    		$res = tx_nG6_db::delete_analysis($value, $user_login, $user_pwd, $data_folder);
			    		if ($res != 0) { break; }
		    		}
	    		}
			}
    		print $res;

        // If asked to publish a project
    	} else if ($type == 'publish') {
    		    		
    		$ids = trim(t3lib_div::_GP('ids'));
    		// project_id to array (1;2;3;...) -> [1;2;3;...]
    		$tab_ids = explode(";",$ids);
    		foreach($tab_ids as $id => $value) {
217
	    		tx_nG6_db::publish_project($value, $user_id);
Penom Nom's avatar
Penom Nom committed
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
    		}
    		
        // If asked to unpublish a project
    	} else if ($type == 'unpublish') {
    		    		
    		$ids = trim(t3lib_div::_GP('ids'));
    		// project_id to array (1;2;3;...) -> [1;2;3;...]
    		$tab_ids = explode(";",$ids);
    		foreach($tab_ids as $id => $value) {
	    		tx_nG6_db::unpublish_project($value);
    		}
    		
        // If asked the size
    	} else if ($type == 'get_size') {
    		$ids = trim(t3lib_div::_GP('ids'));
    		$view = trim(t3lib_div::_GP('view'));
    		$data_folder = trim(t3lib_div::_GP('data_folder'));
    		$tab_ids = explode(",",$ids);
    		$full_size = 0;
    		foreach($tab_ids as $id => $value) {
    			if ($view == "run") {
239
    				$full_size += tx_nG6_db::get_run_size($value, $data_folder, $user_id);
Penom Nom's avatar
Penom Nom committed
240
    			} else if ($view == "project") {
241
    				$full_size += tx_nG6_db::get_project_size($value, $data_folder, $user_id);
Penom Nom's avatar
Penom Nom committed
242
243
244
245
246
247
248
249
    			}
    		}
    		print tx_nG6_utils::get_octet_string_representation($full_size);
    	
    	// If update a field
    	} else if ($type == 'update_db_field') {
    	
    		//Retrieve infomation
250
    		$table = trim(t3lib_div::_GP('table'));
Penom Nom's avatar
Penom Nom committed
251
252
253
254
255
    		$id     = trim(t3lib_div::_GP('id'));
    		$field  = trim(t3lib_div::_GP('field'));
    		$value  = trim(t3lib_div::_GP('value'));
    	
    		//If change concernes a date
Jerome Mariette's avatar
Jerome Mariette committed
256
    		if( $field == "date" || $field == "crdate" )
Penom Nom's avatar
Penom Nom committed
257
258
259
260
261
262
    		{
    			//Change date format
    			$date = explode('-', $value) ;
    			$timestamp = mktime (0, 0, 1, $date[1], $date[0], $date[2]) ;
    	
    			//Update the entity
263
    			tx_nG6_db::update_field($table, $id, $field, $timestamp);
Penom Nom's avatar
Penom Nom committed
264
265
266
267
    		}
    		else
    		{
    			//Update the entity
268
    			tx_nG6_db::update_field($table, $id, $field, $value);
Penom Nom's avatar
Penom Nom committed
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
    		}
    		print $value;
    	
    	// If asked the krona page
    	} else if ($type == 'get_krona') {
    		
    		$data_folder = trim(t3lib_div::_GP('data_folder'));
    		$file_name = trim(t3lib_div::_GP('file_name'));
    		$sequence_name = trim(t3lib_div::_GP('sequence_name'));
    		
    		$doc = new DomDocument();
    		$data_root = $doc->createElement('data');
    		$doc->appendChild($data_root);
    		$attr_data_root = $doc->createAttribute("xml:id");
    		$data_root->appendChild($attr_data_root);
    		
    		$t_data_root = $doc->createTextNode('data_root');
    		$attr_data_root->appendChild($t_data_root);
    		$data_root->setIdAttribute("xml:id", true);
    		
    		$magnitude = $doc->createElement('magnitude');
    		$magnitude->setAttribute("attribute", "g");
    		$magnitude = $data_root->appendChild($magnitude);
    		$magnitudet = $doc->createTextNode('');
    		$magnitudet = $magnitude->appendChild($magnitudet); 
    		
    		$color = $doc->createElement('color');
    		$color = $data_root->appendChild($color);    		
    		$colort = $doc->createTextNode('');
    		$colort = $color->appendChild($colort); 
    		
    		$attributes = $doc->createElement('attributes');
    		$attributes->setAttribute("g", $sequence_name);
    		$attributes = $data_root->appendChild($attributes);  
    		$attributest = $doc->createTextNode('');
    		$attributest = $attributes->appendChild($attributest); 
    		
    		$datasets = $doc->createElement('datasets');
    		$datasets->setAttribute("names", $file_name);
    		$datasets = $data_root->appendChild($datasets); 
    		$datasetst = $doc->createTextNode('');
    		$datasetst = $datasets->appendChild($datasetst); 

			$file_path = trim(t3lib_div::_GP('file_path'));
			$file_path = $data_folder."/".$file_path;
			
			// If the file exists
			$total = 0;
			if (file_exists($file_path)) {
				$lines = file($file_path);
				// Loop through our array
				foreach ($lines as $line_num => $line) {
					if ($line != "") {
						$mparts = explode("\t", trim($line));
						if ($mparts[0] != "taxlevel" and $mparts[0] != "0") {
							// If this guy doesnt exist yet
							$id_searched = str_replace(".", "_", "node_".$mparts[1]);
							if (is_null($doc->getElementById($id_searched))) {
    	        				$parentl = implode("_", array_slice(explode(".", $mparts[1]), 0, -1));
        	        			// If no parent yet, this is the root
        	        			if (is_null($doc->getElementById("node_".$parentl))) {
        	        				$current_node = $doc->createElement('node');
        	        				$current_node->setAttribute("name", $mparts[2]);
        	        				$current_node->setAttribute("g", $mparts[4]);
        	        				$id = $doc->getElementById("data_root");
        	        				$id->appendChild($current_node);
        	        				$attr_current_node = $doc->createAttribute("xml:id");
									$current_node->appendChild($attr_current_node);	        	        				
        	        				$t_current_node = $doc->createTextNode("node_".str_replace(".", "_", $mparts[1]));
									$attr_current_node->appendChild($t_current_node);
									$current_node->setIdAttribute("xml:id", true);
						    		$current_nodet = $doc->createTextNode('');
						    		$current_nodet = $current_node->appendChild($current_nodet);
        	        			} else {
        	        				$current_node = $doc->createElement('node');
        	        				$current_node->setAttribute("name", $mparts[2]);
        	        				$current_node->setAttribute("g", $mparts[4]);
        	        				$id = $doc->getElementById("node_".$parentl);
        	        				$id->appendChild($current_node);
        	        				$attr_current_node = $doc->createAttribute("xml:id");
									$current_node->appendChild($attr_current_node);	        	        				
        	        				$t_current_node = $doc->createTextNode("node_".str_replace(".", "_", $mparts[1]));
									$attr_current_node->appendChild($t_current_node);
									$current_node->setIdAttribute("xml:id", true);
						    		$current_nodet = $doc->createTextNode('');
						    		$current_nodet = $current_node->appendChild($current_nodet); 
        	        			}
    	        			}
						}
						if ($mparts[0] == "1") {
							$total += (int)$mparts[4];
						}
					}
				}
			}    			
			
    		$color->setAttribute("attribute", "g");
    		$color->setAttribute("valueStart", "0");
    		$color->setAttribute("valueEnd", (string)$total);
    		$color->setAttribute("hueStart", "120");
    		$color->setAttribute("hueEnd", "360");
			
			$xml_string = $doc->saveXML();
			$xml_parts = explode("\n", $xml_string);
    		$val = '<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">';
    		$val .= '<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="fr" lang="fr">';
    		$val .= '<head>';
    		$val .= '</head>';
    		$val .= '<body>';
    		$val .= '<div id="options" style="position:absolute;left:0;top:0"></div>';
    		$val .= '<div id="details" style="position:absolute;top:1%;right:2%;text-align:right;"></div>';
    		$val .= '<canvas id="canvas" width="100%" height="100%">This browser does not support HTML5</canvas><div>';
    		$val .= '<img id="hiddenImage" src="http://krona.sourceforge.net/img/hidden.png" visibility="hide"/>';
    		$val .= '<script name="tree" src="'.t3lib_extMgm::siteRelPath('nG6').'res/js/krona-1.1.js"></script>';
    		$val .= $xml_parts[1];
    		$val .= '</div>';
    		$val .= '</body>';
    		$val .= '</html>';
    		print $val;
Jerome Mariette's avatar
Jerome Mariette committed
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
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
516
517
518
519
520
521
522
    		
    	} else if ($type == 'delete_users') {
    		
    		$ids = trim(t3lib_div::_GP('ids'));
    		// users_id to array (1;2;3;...) -> [1;2;3;...]
    		$tab_ids = explode(";",$ids);
			$project_id = trim(t3lib_div::_GP('project_id'));
			
			// try to delete users in project ...
			if($project_id != "") {				
				$none_access = "";
				foreach($tab_ids as $id => $del_user_id) {
					tx_nG6_db::delete_access_to_project($del_user_id, $project_id);
					
					// find if user can't access to any project
					$users_access = tx_nG6_db::count_number_of_project_access($del_user_id);
					if($users_access == '0'){
						$none_access .= $del_user_id.";";
					}
				}
				
				if($none_access == ""){		// everybody has at least one access to a project
					$others_access = '0';	
				}else{						// list separate by coma of users who can't access to any project
					$others_access = substr($none_access, 0, -1);
				}
				
				print $others_access;
				
			// delete users of DB...
			}else{
				
				foreach($tab_ids as $k_id => $v_id){
					// delete group
					$gid = tx_nG6_db::get_user_usergroup($v_id);
					// delete user
					tx_nG6_db::delete_user($v_id);
					if(tx_nG6_db::count_users_in_group($gid) == 0){
						tx_nG6_db::delete_group($gid);
					}
				}
				
			}
			
		// to change users' right on project
    	} else if ($type == 'change_right') {
    		
			$project_id = trim(t3lib_div::_GP('project_id'));
			$c_user_id = trim(t3lib_div::_GP('c_user_id'));
			$right_id = trim(t3lib_div::_GP('right_id'));

			tx_nG6_db::change_access_to_project($c_user_id, $project_id, $right_id);
			
		// jquery autocomplete
    	} else if ($type == 'autocomplete') {
    		
    		$col = trim(t3lib_div::_GP('gender'));
    		$project_id = trim(t3lib_div::_GP('project_id'));

    		// user search
    		if($col != 'group'){
    			
    			$name_start = trim(t3lib_div::_GP('name_start'));
    			$res = tx_nG6_db::get_all_names_starting_with($name_start, $col);
    			
	    		foreach($res as $res_id => $res_val){
	    			// find right on project
	    			$res[$res_id]['right_id'] = tx_nG6_db::get_user_right_on_project($res_val['uid'], $project_id);
	    			
	    			// find creator username 
	    			$cruser_infos = tx_nG6_db::get_user_informations($res[$res_id]['cruser_id']);
	    			$res[$res_id]['cruser_username'] = $cruser_infos['username'];
	    		}
	    		
	    	// group search
    		}else{
    			$group_name_start = trim(t3lib_div::_GP('group_name'));
    			$res = tx_nG6_db::get_all_group_starting_with($group_name_start);
    		}
    		
    		$json_res = json_encode($res);
    		print $json_res;
    	
    	// add a new member on project
    	} else if ($type == 'new_user') {
    		
    		$part 		= trim(t3lib_div::_GP('part'));
    		$user_name	= trim(t3lib_div::_GP('username'));
    		$project_id = trim(t3lib_div::_GP('project_id'));
    		$right_id	= trim(t3lib_div::_GP('right'));
    		$group_name	= trim(t3lib_div::_GP('group'));
    		
    		// if group not exists, create group
    		$group_id = tx_nG6_db::get_group_id($group_name);
    		if( !isset($group_id) ){
    			
    			$cruser_id = trim(t3lib_div::_GP('creator'));
    			tx_nG6_db::create_new_group($cruser_id, $group_name);
    			$group_id = tx_nG6_db::get_group_id($group_name);
    			
    		}
    			
    		$c_user_id = tx_nG6_db::get_user_id_by_username($user_name);

    		// if user not exists in DB
    		if(!isset($c_user_id)){
    			
    			$first_name = trim(t3lib_div::_GP('first_name'));
    			$last_name = trim(t3lib_div::_GP('last_name'));
    			$email = trim(t3lib_div::_GP('email'));
    			$password = trim(t3lib_div::_GP('password'));
    			$cruser_id = trim(t3lib_div::_GP('creator'));

    			tx_nG6_db::create_new_user($user_name, $first_name, $last_name, $email, $password, $cruser_id, $group_id);
    			
    			// find the new user id
    			$new_id = tx_nG6_db::get_user_id_by_username($user_name);
    			
    			// authorize new access
    			tx_nG6_db::add_access_to_project($new_id, $project_id, $right_id);
    			print '2';
    			
    		// user exists in DB
    		}else{
    			// can user access to the project ? 
    			if(tx_nG6_db::get_user_right_on_project($c_user_id, $project_id) == -1){

    				// authorize new access
    				tx_nG6_db::add_access_to_project($c_user_id, $project_id, $right_id);
    				print '0';
    			} else {
    				print '1';	// already access to the project
    			}
    		}
	    	
Penom Nom's avatar
Penom Nom committed
523
524
525
526
527
528
    	}
    }

	/**
	 * Creates an archiving script to archive data from ids
	 *
529
	 * @param	string	$user_id		the user id 
Penom Nom's avatar
Penom Nom committed
530
531
532
533
534
535
536
537
538
	 * @param	array	$ids			list of ids to download 
	 * @param	string	$data_folder	the data folder where are stored the data
	 * @param	string	$tmp_folder		the output directory
	 * @param	string	$format			the archiving format (tar.gz)
	 * @param	string	$user_email		the user email
	 * @param	string	$title_email		the email title to send
	 * @param	string	$msg_email		the email message to send
	 * @return	array (the path to the script, the url path to the final archive)
	 */
539
	private function create_archive_script($user_id, $ids, $data_folder, $tmp_folder, $format, $user_email, $title_email, $msg_email) {
Penom Nom's avatar
Penom Nom committed
540
541
542
543
544
		// First get the archive name where will be stored the data
		$random_key = tx_nG6_utils::create_random_key(10);
		$archive_path = $tmp_folder."/ng6_".$random_key;
		while( file_exists($archive_path) )
			$archive_path = $tmp_folder."/ng6_".$random_key;
Penom Nom's avatar
Penom Nom committed
545
		
Penom Nom's avatar
Penom Nom committed
546
		// Then get the directories structure
547
		$directories = $this->get_directories_structure_and_content($user_id, $ids, $data_folder, $archive_path);
Penom Nom's avatar
Penom Nom committed
548
		$archive_script_path = $tmp_folder."/ng6_".$random_key.".sh";
Penom Nom's avatar
Penom Nom committed
549
		
Penom Nom's avatar
Penom Nom committed
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
		// And write down the script in charge to create the archive
		$fp = fopen($archive_script_path, 'w');
		foreach($directories[0] as $index => $src_directory) {
			if (!file_exists( $directories[1][$index])) {
				fwrite($fp, "mkdir -p ".$directories[1][$index]."\n");
			}
			// For each files in the source directory
			foreach(scandir($src_directory) as $file) {
				if (is_file($src_directory."/".$file) and $file != "analyse.xml" and $file != "index.html" and $file != "run.cfg") {
					fwrite($fp, "cp ".$src_directory."/".$file." ".$directories[1][$index]."\n");
				}
			}
		}
		fwrite($fp, "cd ".$tmp_folder."\n");
		fwrite($fp, "tar -czf ng6_".$random_key.".tar.gz ng6_".$random_key."\n");
		fwrite($fp, "rm -rf ".$archive_path."\n");
		fwrite($fp, 'echo "'.str_replace(array('SPAN_ARCHIVE_NAME'), array("ng6_".$random_key.".tar.gz"), $msg_email).'" | mail -s "'.$title_email.'" '.$user_email."\n");
		fclose($fp);
		return array($archive_script_path, "ng6_".$random_key.".tar.gz");
    }

	/**
	 * Creates symbolic links between ids from data_folder into user_directory
	 *
574
	 * @param	string	$user_id		the user id 
Penom Nom's avatar
Penom Nom committed
575
576
577
578
579
580
581
	 * @param	string	$user_login		the user login to make ssh
	 * @param	string	$user_pwd		the user pwd to make ssh
	 * @param	array	$ids			list of ids to download 
	 * @param	string	$data_folder	the data folder where are stored the data
	 * @param	string	$user_directory	the output directory
	 * @return	0=>everything ok, 1=>user rigth problem, 2=>wrong authentification, 3=>connection error
	 */
582
	private function create_symbolic_links($user_id, $user_login, $user_pwd, $ids, $data_folder, $user_directory) {
Penom Nom's avatar
Penom Nom committed
583
584
585
586
		// First try to connect the specified user using ssh
		$connection = ssh2_connect('127.0.0.1', 22);
		if (!$connection) return 3;
		if (!ssh2_auth_password($connection, $user_login, $user_pwd)) return 2;
Penom Nom's avatar
Penom Nom committed
587
		
Penom Nom's avatar
Penom Nom committed
588
		// Then get the directories structure
589
		$directories = $this->get_directories_structure_and_content($user_id, $ids, $data_folder, $user_directory);
Penom Nom's avatar
Penom Nom committed
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
		// And process the directories structure
		$creation = true;
		foreach($directories[0] as $index => $src_directory) {
			if (!file_exists("ssh2.sftp://".$connection.$directories[1][$index])) {
				if (!mkdir("ssh2.sftp://".$connection.$directories[1][$index], 0755, true)) {
					$creation = false;
					break;
				}
				// For each files in the source directory
				foreach(scandir($src_directory) as $file) {
					if (is_file($src_directory."/".$file) and $file != "analyse.xml" and $file != "index.html" and $file != "run.cfg") {
						if (!ssh2_exec($connection, 'ln -s '.$src_directory.'/'.$file.' '.$directories[1][$index].'/'.$file)) {
							$creation = false;
							break;
						}
					}
				}
			}
		}
		if (!$creation) return 1;
		return 0;
    }

	/**
	 * Returns a table with the right directories structure considering ids
	 *
616
	 * @param	string	$user_id	the user id
Penom Nom's avatar
Penom Nom committed
617
618
619
620
621
	 * @param	array	$ids			List of ids to download 
	 * @param	string	$data_folder	The data folder where are stored the data
	 * @param	string	$output_folder	The output directory
	 * @return	array	[0] => source_directories, [1] => dest_directories
	 */
622
	private function get_directories_structure_and_content($user_id, $ids, $data_folder, $output_folder) {
Penom Nom's avatar
Penom Nom committed
623
624
625
626

		$src_directories = array();
		$dest_directories = array();
		$vals = preg_split("/;/", $ids);
Penom Nom's avatar
Penom Nom committed
627
		
Penom Nom's avatar
Penom Nom committed
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
		// Characters to be replaced in the names of the run, the analyses ...
		$char_to_replace = array(' ','/');
		
		// For each project/run/analysis
		foreach($vals as $val) {
			if ($val != "undefined" && $val != "") {
				$id = preg_split("/_/", $val);
				if ($id[0] == "data") {
					$run = tx_nG6_db::select_run($id[1]);
					if (!in_array($data_folder.$run["directory"], $src_directories)) {
						$src_directories[] = $data_folder.$run["directory"];
						$ddest = $output_folder."/Project_".str_replace($char_to_replace, '_', $run["project_name"]);
						$ddest .= '.'.$run["project_id"]."/Run_".str_replace($char_to_replace, '_', $run["name"]).".".$id[1]."/RawData";
						$dest_directories[] = $ddest;
					}
				} else if ($id[0] == "run") {
					$run = tx_nG6_db::select_run($id[1]);
					if (!in_array($data_folder.$run["directory"], $src_directories)) {
						$src_directories[] = $data_folder.$run["directory"];
						$ddest = $output_folder."/Project_".str_replace($char_to_replace, '_', $run["project_name"]);
						$ddest .= '.'.$run["project_id"]."/Run_".str_replace($char_to_replace, '_', $run["name"]).".".$id[1]."/RawData";
						$dest_directories[] = $ddest;
					}
651
					foreach(tx_nG6_db::get_run_analysis($user_id, $id[1], 'tx_nG6_analyze.name') as $analyse_id => $analyse_values) {
Penom Nom's avatar
Penom Nom committed
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
						$aid = preg_split("/_/", $analyse_id);
						if (!in_array($data_folder.$analyse_values["directory"], $src_directories)) {
							$src_directories[] = $data_folder.$analyse_values["directory"];
							$ddest = $output_folder."/Project_".str_replace($char_to_replace, '_', $run["project_name"]);
							$ddest .= '.'.$run["project_id"]."/Run_".str_replace($char_to_replace, '_', $run["name"]);
							$ddest .= ".".$id[1]."/Analyse_".str_replace($char_to_replace, '_', $analyse_values["name"]).".".$aid[1];
							$dest_directories[] = $ddest;
						}
					}
				} else if ($id[0] == "analyse") {
					$analyse = tx_nG6_db::select_analyse($id[1]);
					if (!in_array($data_folder.$analyse["directory"], $src_directories)) {
						$src_directories[] = $data_folder.$analyse["directory"];
						// If it's a project analyse
						if ($analyse["run_id"] == 'None') {
							$ddest = $output_folder."/Project_".str_replace($char_to_replace, '_', $analyse["project_name"]);
							$ddest .= ".".$analyse["project_id"]."/Project_analyses/".str_replace($char_to_replace, '_', $analyse["name"]).".".$id[1];
							$dest_directories[] = $ddest;
						} else {
							$ddest = $output_folder."/Project_".str_replace($char_to_replace, '_', $analyse["project_name"]);
							$ddest .= ".".$analyse["project_id"]."/Run_".str_replace($char_to_replace, '_', $analyse["run_name"]);
							$ddest .= ".".$analyse["run_id"]."/Analyse_".str_replace($char_to_replace, '_', $analyse["name"]).".".$id[1];
							$dest_directories[] = $ddest;
						}
					}
				}
			}
		}
		return array($src_directories, $dest_directories);
    }
    
}

if (defined('TYPO3_MODE') && $TYPO3_CONF_VARS[TYPO3_MODE]['XCLASS']['ext/nG6/class.tx_nG6_eid.php']) {
    include_once($TYPO3_CONF_VARS[TYPO3_MODE]['XCLASS']['ext/nG6/class.tx_nG6_eid.php']);
}

// Instanciation
$SOBE = t3lib_div::makeInstance('tx_nG6_eid');
$SOBE->main();

693
?>