class.tx_nG6_eid.php 38.8 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
<?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');
Jerome Mariette's avatar
Jerome Mariette committed
32
require_once(t3lib_extMgm::extPath('nG6').'/res/smarty/libs/Smarty.class.php');
Penom Nom's avatar
Penom Nom committed
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49

/**
 * 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'));
50
    	$user_id = trim(t3lib_div::_GP('user_id'));
Penom Nom's avatar
Penom Nom committed
51

Penom Nom's avatar
Penom Nom committed
52
53
54
55
    	// 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
Penom Nom's avatar
Penom Nom committed
56
	    	$project_runs = tx_nG6_db::get_user_project_runs($user_id, $project_id, 'tx_nG6_run.date DESC');
Penom Nom's avatar
Penom Nom committed
57
58
59
60
61
62
	    	// 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
Penom Nom's avatar
Penom Nom committed
63
	    	$project_analysis = tx_nG6_db::get_user_project_analysis($user_id, $project_id, 'tx_nG6_analyze.name');
Penom Nom's avatar
Penom Nom committed
64
65
66
67
68
69
70
71
72
73
			foreach($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
Penom Nom's avatar
Penom Nom committed
74
			$run_analysis = tx_nG6_db::get_user_run_analysis($user_id, $run_id, 'tx_nG6_analyze.name');
Penom Nom's avatar
Penom Nom committed
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
			$run_info = tx_nG6_db::select_run($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'));
95
				$retcode = $this->create_symbolic_links($user_id, $user_login, $user_pwd, $ids, $data_folder, $user_directory);
Penom Nom's avatar
Penom Nom committed
96
97
98
99
100
101
102
103
104
105
				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'));
106
				$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
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
				$process = new Process("tcsh ".$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 => $value) {
Jerome Mariette's avatar
Jerome Mariette committed
135
		    		tx_nG6_db::hide_project($value);
Penom Nom's avatar
Penom Nom committed
136
137
138
	    		}
    		} else if ($hide_level == 'run') {
	    		foreach($tab_ids as $id => $value) {
139
		    		tx_nG6_db::hide_run($value, $user_id);
Penom Nom's avatar
Penom Nom committed
140
141
142
	    		}
    		} else if ($hide_level == 'analysis') {
	    		foreach($tab_ids as $id => $value) {
143
		    		tx_nG6_db::hide_analysis($value, $user_id);
Penom Nom's avatar
Penom Nom committed
144
145
146
147
148
149
150
151
152
153
154
155
156
	    		}
    		}

        // 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 => $value) {
Jerome Mariette's avatar
Jerome Mariette committed
157
		    		tx_nG6_db::unhide_project($value);
Penom Nom's avatar
Penom Nom committed
158
159
160
	    		}
    		} else if ($unhide_level == 'run') {
	    		foreach($tab_ids as $id => $value) {
Jerome Mariette's avatar
Jerome Mariette committed
161
		    		tx_nG6_db::unhide_run($value, true);
Penom Nom's avatar
Penom Nom committed
162
163
164
	    		}
    		} else if ($unhide_level == 'analysis') {
	    		foreach($tab_ids as $id => $value) {
Jerome Mariette's avatar
Jerome Mariette committed
165
		    		tx_nG6_db::unhide_analysis($value, true);
Penom Nom's avatar
Penom Nom committed
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
193
	    		}
    		}
    		
    	// 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) {
Jerome Mariette's avatar
Jerome Mariette committed
194
			    		$res = tx_nG6_db::delete_project($value, $user_login, $user_pwd, $data_folder);
Penom Nom's avatar
Penom Nom committed
195
196
197
198
			    		if ($res != 0) { break; }
		    		}
	    		} else if ($delete_level == 'run') {
		    		foreach($tab_ids as $id => $value) {
Jerome Mariette's avatar
Jerome Mariette committed
199
			    		$res = tx_nG6_db::delete_run($value, $user_login, $user_pwd, $data_folder);
Penom Nom's avatar
Penom Nom committed
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
			    		if ($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 => $value) {
Jerome Mariette's avatar
Jerome Mariette committed
218
	    		tx_nG6_db::publish_project($value);
Penom Nom's avatar
Penom Nom committed
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
    		}
    		
        // 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") {
Jerome Mariette's avatar
Jerome Mariette committed
240
    				$full_size += tx_nG6_db::get_run_size($value, $data_folder, true);
Penom Nom's avatar
Penom Nom committed
241
    			} else if ($view == "project") {
Jerome Mariette's avatar
Jerome Mariette committed
242
    				$full_size += tx_nG6_db::get_project_size($value, $data_folder, true);
Penom Nom's avatar
Penom Nom committed
243
244
245
246
247
248
    			}
    		}
    		print tx_nG6_utils::get_octet_string_representation($full_size);
    	
    	// If update a field
    	} else if ($type == 'update_db_field') {
249
    		
Penom Nom's avatar
Penom Nom committed
250
    		//Retrieve infomation
251
    		$table = trim(t3lib_div::_GP('table'));
252
    		$id     = trim(t3lib_div::_GP('pk'));
Penom Nom's avatar
Penom Nom committed
253
254
255
256
    		$field  = trim(t3lib_div::_GP('field'));
    		$value  = trim(t3lib_div::_GP('value'));
    	
    		//If change concernes a date
257
    		if( $field == "date" || $field == "crdate" ) {
Penom Nom's avatar
Penom Nom committed
258
    			//Change date format
259
260
    			$date = explode('-', $value);
    			$timestamp = mktime (0, 0, 1, $date[1], $date[2], $date[0]);
Penom Nom's avatar
Penom Nom committed
261
    			//Update the entity
262
    			tx_nG6_db::update_field($table, $id, $field, $timestamp);
Penom Nom's avatar
Penom Nom committed
263
    		}
264
    		else {
Penom Nom's avatar
Penom Nom committed
265
    			//Update the entity
266
    			tx_nG6_db::update_field($table, $id, $field, $value);
Penom Nom's avatar
Penom Nom committed
267
268
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
    		}
    		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
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
    		
    	} 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'));
444
445
    		$name_start = trim(t3lib_div::_GP('name_start'));
    		
Jerome Mariette's avatar
Jerome Mariette committed
446
    		// user search
447
    		if($col != 'title' && $col != 'location' && $col != 'organism'){
Jerome Mariette's avatar
Jerome Mariette committed
448
449
450
451
452
453
454
455
456
457
458
459
    			$res = tx_nG6_db::get_all_names_starting_with($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{
460
    			if ($col == "location" || $col == "organism") { $col = "tx_nG6_".$col; }
461
    			$res = tx_nG6_db::get_all_starts_with_in_group($name_start, $col);
Jerome Mariette's avatar
Jerome Mariette committed
462
463
464
465
466
    		}
    		$json_res = json_encode($res);
    		print $json_res;
    	
    	// add a new member on project
Jerome Mariette's avatar
Jerome Mariette committed
467
    	} else if ($type == 'add_user') {
Jerome Mariette's avatar
Jerome Mariette committed
468
469
470
471
472
    		
    		$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'));
473
474
475
    		$group_name	= trim(t3lib_div::_GP('title'));
    		$location	= trim(t3lib_div::_GP('location'));
    		$organism	= trim(t3lib_div::_GP('organism'));
476
477
478
479
480
481
482
483
    		$email = trim(t3lib_div::_GP('email'));
    		$first_name = trim(t3lib_div::_GP('first_name'));
    		$last_name = trim(t3lib_div::_GP('last_name'));
    		$password = trim(t3lib_div::_GP('password'));
			$cruser_id = trim(t3lib_div::_GP('creator'));
			$clearpassword = trim(t3lib_div::_GP('clearpassword'));
			$from_email = trim(t3lib_div::_GP('from_email'));
			$pid = trim(t3lib_div::_GP('pid'));
484
			$project_url = trim(t3lib_div::_GP('project_url'));
Jerome Mariette's avatar
Jerome Mariette committed
485
			$send_an_email = filter_var(trim(t3lib_div::_GP('send_an_email')), FILTER_VALIDATE_BOOLEAN);
486
			
Jerome Mariette's avatar
Jerome Mariette committed
487
488
489
490
491
    		// if group not exists, create group
    		$group_id = tx_nG6_db::get_group_id($group_name);
    		if( !isset($group_id) ){
    			
    			$cruser_id = trim(t3lib_div::_GP('creator'));
492
    			tx_nG6_db::create_new_group($cruser_id, $group_name, $organism, $location);
Jerome Mariette's avatar
Jerome Mariette committed
493
494
495
496
    			$group_id = tx_nG6_db::get_group_id($group_name);
    			
    		}
    			
Jerome Mariette's avatar
Jerome Mariette committed
497
    		$user = tx_nG6_db::select_user_by_username($user_name);
Jerome Mariette's avatar
Jerome Mariette committed
498

Jerome Mariette's avatar
Jerome Mariette committed
499
    		// if user does not exists in DB
Jerome Mariette's avatar
Jerome Mariette committed
500
    		if(!isset($user)){
501
502
503
    		
    			$create_user_email = trim(t3lib_div::_GP('create_user_email'));
    			$create_user_title = trim(t3lib_div::_GP('create_user_title'));
Jerome Mariette's avatar
Jerome Mariette committed
504
    			
Jerome Mariette's avatar
Jerome Mariette committed
505
    			$res_code = tx_nG6_db::add_user($user_name, $first_name, $last_name, $email, $password, $cruser_id, $group_id, $pid);
Jerome Mariette's avatar
Jerome Mariette committed
506
    			
Jerome Mariette's avatar
Jerome Mariette committed
507
508
    			if ($res_code == 0) {
	    			// find the new user id
Jerome Mariette's avatar
Jerome Mariette committed
509
	    			$user = tx_nG6_db::select_user_by_username($user_name);
Jerome Mariette's avatar
Jerome Mariette committed
510
511
	    			
	    			// authorize new access
Jerome Mariette's avatar
Jerome Mariette committed
512
	    			tx_nG6_db::add_access_to_project($user["uid"], $project_id, $right_id);
Jerome Mariette's avatar
Jerome Mariette committed
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
	    			
	    			if ($send_an_email) {
		    			// send an email to the new user
		    			$message = str_replace("###USER_FIRST_NAME###", $first_name, $create_user_email);
		    			$message = str_replace("###USER_LAST_NAME###", $last_name, $message);
		    			$message = str_replace("###USER_LOGIN###", $user_name, $message);
		    			$message = str_replace("###USER_PASSWORD###", $clearpassword, $message);
		    			$message = str_replace("###PROJECT_LINK###", $project_url, $message);
		    			$msg_table = explode('\n', $message);
		    			$message = implode("\n", $msg_table);
		    			mail($email, $create_user_title, $message, "From: <".$from_email.">");
		    		}
	    			print '2'; // ok
	    		} else if ($res_code == 1) {
	    			print '4'; // username exists
	    		} else if ($res_code == 2) {
	    			print '5'; // email exists
Jerome Mariette's avatar
Jerome Mariette committed
530
	    		}
Jerome Mariette's avatar
Jerome Mariette committed
531
	    		
Jerome Mariette's avatar
Jerome Mariette committed
532
    		// user exists in DB
Jerome Mariette's avatar
Jerome Mariette committed
533
534
535
536
    		} else if ($user["username"] != $user_name || $user["email"] != $email || $user["first_name"] != $first_name || $user["last_name"] != $last_name) {
    			// there is difference between information provided and the user account
    			print '3';
    		} else {
Jerome Mariette's avatar
Jerome Mariette committed
537
    			// can user access to the project ? 
Jerome Mariette's avatar
Jerome Mariette committed
538
    			if(tx_nG6_db::get_user_right_on_project($user["uid"], $project_id) == -1){
Jerome Mariette's avatar
Jerome Mariette committed
539
540

    				// authorize new access
Jerome Mariette's avatar
Jerome Mariette committed
541
    				tx_nG6_db::add_access_to_project($user["uid"], $project_id, $right_id);
Jerome Mariette's avatar
Jerome Mariette committed
542
543
    				
	    			// send an email to the  user
Jerome Mariette's avatar
Jerome Mariette committed
544
	    			if ($email != "" && $send_an_email) {
Jerome Mariette's avatar
Jerome Mariette committed
545
	    			
546
547
		    			$add_user_email = trim(t3lib_div::_GP('add_user_email'));
		    			$add_user_title = trim(t3lib_div::_GP('add_user_title'));
Jerome Mariette's avatar
Jerome Mariette committed
548
549
550
551
552
	    				$project = tx_nG6_db::select_project($project_id);
		    			$message = str_replace("###USER_FIRST_NAME###", $first_name, $add_user_email);
		    			$message = str_replace("###USER_LAST_NAME###", $last_name, $message);
		    			$message = str_replace("###PROJECT_NAME###", $project["name"], $message);
		    			$message = str_replace("###PROJECT_DESCRIPTION###", $project["description"], $message);
553
		    			$message = str_replace("###PROJECT_LINK###", $project_url, $message);
Jerome Mariette's avatar
Jerome Mariette committed
554
555
556
		    			$msg_table = explode('\n', $message);
		    			$message = implode("\n", $msg_table);
		    			mail($email, $add_user_title, $message, "From: <".$from_email.">");
Jerome Mariette's avatar
Jerome Mariette committed
557
		    			
Jerome Mariette's avatar
Jerome Mariette committed
558
		    		}
Jerome Mariette's avatar
Jerome Mariette committed
559
    				print '0';
Jerome Mariette's avatar
Jerome Mariette committed
560
    				
Jerome Mariette's avatar
Jerome Mariette committed
561
562
563
564
565
    			} else {
    				print '1';	// already access to the project
    			}
    		}
	    	
Jerome Mariette's avatar
Jerome Mariette committed
566
567
568
569
570
571
572
573
574
575
576
577
    	} elseif($type == 'get_size_per_group'){

    		$usergroup = intVal(trim(t3lib_div::_GP('usergroup')));
    		$data_folder = trim(t3lib_div::_GP('data_folder'));
    		$get_analyzes = false;
    		if(trim(t3lib_div::_GP('get_analyzes')) == '1'){
    			$get_analyzes = true;
    		}
    		$get_cumulatives = false;
    		if(trim(t3lib_div::_GP('get_cumulatives')) == '1'){
    			$get_cumulatives = true;
    		}			
Jerome Mariette's avatar
Jerome Mariette committed
578
    		$size_tab = tx_nG6_db::get_size($usergroup, $data_folder, $get_analyzes, $get_cumulatives, 0);
Jerome Mariette's avatar
Jerome Mariette committed
579
580
581
    		$encode_size_tab = json_encode($size_tab);
    		print $encode_size_tab;

Jerome Mariette's avatar
Jerome Mariette committed
582
583
584
585
586
587
588
589
590
591
592
593
594
    	} elseif($type == 'runs_table') {
    		$smarty = new Smarty();
    		$smarty->setTemplateDir(t3lib_extMgm::extPath('nG6').'/pi1');
    		$smarty->setCompileDir(t3lib_extMgm::extPath('nG6').'/res/smarty/templates_c');
    		$smarty->setCacheDir(t3lib_extMgm::extPath('nG6').'/res/smarty/cache');
    		$smarty->setConfigDir(t3lib_extMgm::extPath('nG6').'/res/smarty/configs');
    		$smarty->security = true;
    		$smarty->security_settings['MODIFIER_FUNCS'] = array('count');
    		$project_id = intVal(trim(t3lib_div::_GP('project_id')));
    		$user_id = intVal(trim(t3lib_div::_GP('user_id')));
    		$login_user = intVal(trim(t3lib_div::_GP('login_user')));
    		$page_id = intVal(trim(t3lib_div::_GP('page_id')));
    		$project_runs = tx_nG6_db::get_project_runs($project_id);
595
    		$is_project_admin = tx_nG6_db::is_administrator($user_id, 'project', $project_id);
Jerome Mariette's avatar
Jerome Mariette committed
596
597
598
599
600
601
602
603
604
    		$is_at_least_admin_of_1_run = false;
    		foreach($project_runs as $run_id => $run_values) {
    			$is_admin = tx_nG6_db::is_administrator($user_id, 'run', $run_values['id']);
    			$project_runs[$run_id]['is_admin'] = $is_admin;
    			if ($is_admin) { $is_at_least_admin_of_1_run = true; }
    			$href = '<a href="index.php?id='.$page_id.'&tx_nG6_pi1[run_id]='.$run_values['id'].'&tx_nG6_pi1[project_id]='.$run_values['project_id'].'">'.$run_values['name'].'</a>';
    			$project_runs[$run_id]['href'] = $href;
    		}
    		$smarty->assign('runs', $project_runs);
605
    		$smarty->assign('is_project_admin', $is_project_admin);
Jerome Mariette's avatar
Jerome Mariette committed
606
607
608
    		$smarty->assign('is_at_least_admin_of_1_run', $is_at_least_admin_of_1_run);
    		$smarty->assign('login_user', $login_user);
    		print $smarty->fetch('run_table.tpl');
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
    		
    	} elseif($type == 'projects_table') {
    		$smarty = new Smarty();
    		$smarty->setTemplateDir(t3lib_extMgm::extPath('nG6').'/pi1');
    		$smarty->setCompileDir(t3lib_extMgm::extPath('nG6').'/res/smarty/templates_c');
    		$smarty->setCacheDir(t3lib_extMgm::extPath('nG6').'/res/smarty/cache');
    		$smarty->setConfigDir(t3lib_extMgm::extPath('nG6').'/res/smarty/configs');
    		$smarty->security = true;
    		$smarty->security_settings['MODIFIER_FUNCS'] = array('count');
    		$user_id = trim(t3lib_div::_GP('user_id'));
    		$login_user = intVal(trim(t3lib_div::_GP('login_user')));
    		$page_id = intVal(trim(t3lib_div::_GP('page_id')));
    		$projects = tx_nG6_db::select_all_user_projects($user_id, 'tx_nG6_project.name');
    		$is_at_least_admin_of_1_project = false;
    		foreach($projects as $project_id => $project_values) {
    			$is_admin = tx_nG6_db::is_project_administrator($user_id, $project_values['id']);
    			if ($is_admin) { $is_at_least_admin_of_1_project = true; }
    			$projects[$project_id]['is_admin'] = $is_admin;
    			$projects[$project_id]['is_manager'] = tx_nG6_db::is_project_manager($user_id, $project_values['id']);
    			$projects[$project_id]['is_member'] = tx_nG6_db::is_project_member($user_id, $project_values['id']);
    			$href = '<a href="index.php?id='.$page_id.'&tx_nG6_pi1[project_id]='.$project_values['id'].'">'.$project_values['name'].'</a>';
    			$projects[$project_id]['href'] = $href;
    		}
    		$smarty->assign('projects', $projects);
    		$smarty->assign('is_at_least_admin_of_1_project', $is_at_least_admin_of_1_project);
    		$smarty->assign('login_user', $login_user);
    		print $smarty->fetch('project_table.tpl');
636
637
638
639
640
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
666
667
668
669
670
    		
    	} elseif($type == 'analyses_table') {    		
    		$smarty = new Smarty();
    		$smarty->setTemplateDir(t3lib_extMgm::extPath('nG6').'/pi1');
    		$smarty->setCompileDir(t3lib_extMgm::extPath('nG6').'/res/smarty/templates_c');
    		$smarty->setCacheDir(t3lib_extMgm::extPath('nG6').'/res/smarty/cache');
    		$smarty->setConfigDir(t3lib_extMgm::extPath('nG6').'/res/smarty/configs');
    		$smarty->security = true;
    		$smarty->security_settings['MODIFIER_FUNCS'] = array('count');
    		$user_id = trim(t3lib_div::_GP('user_id'));
    		$login_user = intVal(trim(t3lib_div::_GP('login_user')));
    		$page_id = intVal(trim(t3lib_div::_GP('page_id')));
    		$project_id = intVal(trim(t3lib_div::_GP('project_id')));
    		$run_id = intVal(trim(t3lib_div::_GP('run_id')));
    		if ($run_id != "") {
    			$analysis = tx_nG6_db::get_run_analysis($run_id);
    		} else {
    			$analysis = tx_nG6_db::get_project_analysis($project_id);
    		}
			// Add some information to the table
			foreach($analysis as $analysis_id => $analysis_values) {
				if (tx_nG6_db::is_administrator($user_id, 'analyze', $analysis_values['id'])) { $is_admin = true; }
				$analysis[$analysis_id]['is_admin'] = tx_nG6_db::is_administrator($user_id, 'analyze', $analysis_values['id']);
				if ($run_id != "") {
					$href = '<a href="index.php?id='.$page_id.'&tx_nG6_pi1[project_id]='.$project_id.'&tx_nG6_pi1[run_id]='.$run_id.'&tx_nG6_pi1[analyze_id]='.$analysis_values['id'].'">'.$analysis_values['name'].'</a>';
				} else {
					$href = '<a href="index.php?id='.$page_id.'&tx_nG6_pi1[project_id]='.$project_id.'&tx_nG6_pi1[analyze_id]='.$analysis_values['id'].'">'.$analysis_values['name'].'</a>';
				}
				$analysis[$analysis_id]['href'] = $href;
			}
			$smarty->assign('display_analysis_result', $is_admin);
			$smarty->assign('is_admin', $is_admin);
    		$smarty->assign('h_analysis', tx_nG6_utils::trace_hierarchy($analysis));
    		$smarty->assign('login_user', $login_user);
    		print $smarty->fetch('analysis_table.tpl');
Celine Noirot's avatar
Celine Noirot committed
671
672
673
    	} elseif($type == 'install') {
    		$res = tx_nG6_db::select_user_by_username("admin_install");
    		if ($res != null){
Jerome Mariette's avatar
Jerome Mariette committed
674
    			$res2 = tx_nG6_db::finalize_installation($res["uid"],
Celine Noirot's avatar
Celine Noirot committed
675
676
677
678
679
680
681
682
683
    					trim(t3lib_div::_GP('username')),
    					trim(t3lib_div::_GP('first_name')),
    					trim(t3lib_div::_GP('last_name')),
    					trim(t3lib_div::_GP('email')),
    					trim(t3lib_div::_GP('password')),
    					trim(t3lib_div::_GP('pid')),
    					trim(t3lib_div::_GP('project_name')),
    					trim(t3lib_div::_GP('description'))
    			);
Jerome Mariette's avatar
Jerome Mariette committed
684
685
686
687
688
689
    			// if there is a result, then log the user
    			if ($res2) {
    				$GLOBALS['TSFE'] = t3lib_div::makeInstance('tslib_fe', $GLOBALS['TYPO3_CONF_VARS'], t3lib_div::_GP('id'), '');
    				$GLOBALS['TSFE']->initFEuser();
    				$GLOBALS['TSFE']->fe_user->createUserSession(array('uid' =>$res["uid"]));
    			}
Celine Noirot's avatar
Celine Noirot committed
690
    		}
Celine Noirot's avatar
Celine Noirot committed
691
    		print $res;
692
693
694
695
    	} elseif($type == 'project_repartition') {
    		$role = trim(t3lib_div::_GP('role'));    		
    		$by = trim(t3lib_div::_GP('by'));
    		print json_encode(tx_nG6_db::select_projects_repartition($role, $by));
Celine Noirot's avatar
Celine Noirot committed
696
    	}    		
Penom Nom's avatar
Penom Nom committed
697
698
699
700
701
    }

	/**
	 * Creates an archiving script to archive data from ids
	 *
702
	 * @param	string	$user_id		the user id 
Penom Nom's avatar
Penom Nom committed
703
704
705
706
707
708
709
710
711
	 * @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	$msg_email		the email message to send
	 * @return	array (the path to the script, the url path to the final archive)
	 */
712
	private function create_archive_script($user_id, $ids, $data_folder, $tmp_folder, $format, $user_email, $title_email, $msg_email) {
Penom Nom's avatar
Penom Nom committed
713
714
715
716
717
		// 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
718
		
Penom Nom's avatar
Penom Nom committed
719
		// Then get the directories structure
720
		$directories = $this->get_directories_structure_and_content($user_id, $ids, $data_folder, $archive_path);
Penom Nom's avatar
Penom Nom committed
721
		$archive_script_path = $tmp_folder."/ng6_".$random_key.".sh";
Penom Nom's avatar
Penom Nom committed
722
		
Penom Nom's avatar
Penom Nom committed
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
		// 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
	 *
747
	 * @param	string	$user_id		the user id 
Penom Nom's avatar
Penom Nom committed
748
749
750
751
752
753
754
	 * @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	$user_directory	the output directory
	 * @return	0=>everything ok, 1=>user rigth problem, 2=>wrong authentification, 3=>connection error
	 */
755
	private function create_symbolic_links($user_id, $user_login, $user_pwd, $ids, $data_folder, $user_directory) {
Penom Nom's avatar
Penom Nom committed
756
757
758
759
		// 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
760
		
Penom Nom's avatar
Penom Nom committed
761
		// Then get the directories structure
762
		$directories = $this->get_directories_structure_and_content($user_id, $ids, $data_folder, $user_directory);
Penom Nom's avatar
Penom Nom committed
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
		// 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
	 *
Penom Nom's avatar
Penom Nom committed
789
	 * @param	string	$user_id		The user id
Penom Nom's avatar
Penom Nom committed
790
791
792
793
794
	 * @param	array	$ids			List of ids to download 
	 * @param	string	$data_folder	The data folder where are stored the data
	 * @param	string	$output_folder	The output directory
	 * @return	array	[0] => source_directories, [1] => dest_directories
	 */
795
	private function get_directories_structure_and_content($user_id, $ids, $data_folder, $output_folder) {
Penom Nom's avatar
Penom Nom committed
796
797
798
799

		$src_directories = array();
		$dest_directories = array();
		$vals = preg_split("/;/", $ids);
Penom Nom's avatar
Penom Nom committed
800
		
Penom Nom's avatar
Penom Nom committed
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
		// 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[] = $ddest;
					}
Penom Nom's avatar
Penom Nom committed
824
					foreach(tx_nG6_db::get_user_run_analysis($user_id, $id[1], 'tx_nG6_analyze.name') as $analyse_id => $analyse_values) {
Penom Nom's avatar
Penom Nom committed
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
						$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);
Jerome Mariette's avatar
Jerome Mariette committed
854
    }    
Penom Nom's avatar
Penom Nom committed
855
856
857
858
859
860
861
862
863
864
}

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();

865
?>