class.tx_nG6_pi1.php 21.7 KB
Newer Older
Jerome Mariette's avatar
Jerome Mariette 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
<?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!
***************************************************************/
/**
 * Plugin 'nG6' for the 'nG6' extension.
 *
 * @author	PF bioinformatique de Toulouse <>
 */

require_once(PATH_tslib.'class.tslib_pibase.php');
31
32
require_once(t3lib_extMgm::extPath('nG6').'/lib/class.tx_nG6_db.php');
require_once(t3lib_extMgm::extPath('nG6').'/lib/class.tx_nG6_utils.php');
33
require_once(t3lib_extMgm::extPath('nG6').'/lib/class.tx_nG6_upgrade.php');
34
require_once(t3lib_extMgm::extPath('nG6').'/res/smarty/libs/Smarty.class.php'); 
Jerome Mariette's avatar
Jerome Mariette committed
35
36

class tx_nG6_pi1 extends tslib_pibase {
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
37
	
Jerome Mariette's avatar
Jerome Mariette committed
38
39
40
41
42
43
44
45
46
47
48
49
	var $prefixId = 'tx_nG6_pi1';		// Same as class name
	var $scriptRelPath = 'pi1/class.tx_nG6_pi1.php';	// Path to this script relative to the extension dir.
	var $extKey = 'nG6';	// The extension key.
	
	/**
	 * Main method of your PlugIn
	 *
	 * @param	string		$content: The content of the PlugIn
	 * @param	array		$conf: The PlugIn Configuration
	 * @return	The content that should be displayed on the website
	 */
	function main($content,$conf)	{
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
50
		
Jerome Mariette's avatar
Jerome Mariette committed
51
52
53
		if (strstr($this->cObj->currentRecord,'tt_content'))	{
			$conf['pidList'] = $this->cObj->data['pages'];
		}
Jerome Mariette's avatar
Jerome Mariette committed
54
55
		// Setting the TypoScript passed to this function in $this->conf
		$this->conf=$conf;
56
		
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
57
		$this->pi_setPiVarDefaults();
Jerome Mariette's avatar
Jerome Mariette committed
58
59
60
		// Configuring so caching is not expected. This value means that no cHash params are ever set. We do this, because it's a USER_INT object!
		$this->pi_USER_INT_obj=1;
		// Loading the LOCAL_LANG values
61
62
		$this->pi_loadLL();		
		
63
		// Add the ng6 plugins css
Jerome Mariette's avatar
Jerome Mariette committed
64
		$GLOBALS['TSFE']->additionalHeaderData[$this->prefixId] = '
Penom Nom's avatar
Penom Nom committed
65
66
67
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.min.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.dataTables.min.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/wysihtml5-0.3.0.min.js"></script>
Jerome Mariette's avatar
Jerome Mariette committed
68
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/bootstrap.min.js"></script>
philippe's avatar
philippe committed
69
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/bootstrap-editable.min.js"></script>			
Penom Nom's avatar
Penom Nom committed
70
71
72
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/bootstrap3-wysihtml5.all.min.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/dataTables.bootstrap.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/typeahead.bundle.js"></script>
Penom Nom's avatar
Penom Nom committed
73
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jflow.min.js"></script>
Jerome Mariette's avatar
Jerome Mariette committed
74
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/tx_nG6_pi1.js"></script>
75
76
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/tx_nG6_utils.js"></script>
			
Penom Nom's avatar
Penom Nom committed
77
78
79
80
81
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/bootstrap3-wysihtml5.min.css"/>
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/dataTables.bootstrap.css"/>
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/bootstrap-editable.css"/>	
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/typeaheadjs.css"/>	
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/font-awesome.css"/>
Penom Nom's avatar
Penom Nom committed
82
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/jflow.min.css"/>
Jerome Mariette's avatar
Jerome Mariette committed
83
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/tx_nG6.css"/>';			
Jerome Mariette's avatar
Jerome Mariette committed
84
		
85
86
		tx_nG6_db::check_db_rights_level();

Jerome Mariette's avatar
Jerome Mariette committed
87
		// if asked to upgrade to version 1.2
88
		if($this->piVars['upgrade']){
89
			$content = '<div class="sub-content sc-top">'.tx_nG6_upgrade::upgrade($this->piVars['upgrade'], $this->conf["data"]).'</div>';
Celine Noirot's avatar
Celine Noirot committed
90
91
92
93
94
		} 
		else if(! $this->pi_is_install_finalized()) {
			$content .= $this->pi_install_view();
		}
		else {
Jerome Mariette's avatar
Jerome Mariette committed
95
96
97
98
99
100
101
102
103
104
105
			switch((string)$this->conf['view'])	{
				// If the plugin is configured to display results by run
				case 'run':
					if ($this->piVars['analyze_id']) {
						$content .= $this->pi_analyze_view();
					} else {
						$content .= $this->pi_run_view();
					}
					break;
				// If the plugin is not configured, display by project is default
				default:
106
107
108
109
110
111
112
					if ($this->piVars['analyze_id']) {
						$content .= $this->pi_analyze_view();
					} elseif ($this->piVars['project_id'] && $this->piVars['run_id']) {
						$content .= $this->pi_run_view();
					} else {
						$content .= $this->pi_project_view();
					}
Jerome Mariette's avatar
Jerome Mariette committed
113
					break;
Jerome Mariette's avatar
Jerome Mariette committed
114
115
			}
		}
Jerome Mariette's avatar
Jerome Mariette committed
116
		return $this->pi_wrapInBaseClass($content);
Penom Nom's avatar
Penom Nom committed
117
		
Jerome Mariette's avatar
Jerome Mariette committed
118
	}
Jerome Mariette's avatar
Jerome Mariette committed
119

120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
	/**
	 * return a redirection view
	 * @return string
	 */
	function redirect_view(){
		$protocol = strpos(strtolower($_SERVER['SERVER_PROTOCOL']),'https')	=== FALSE ? 'http' : 'https';
		$host     = $_SERVER['HTTP_HOST'];
		$script   = $_SERVER['SCRIPT_NAME'];
		$currentUrl = $protocol . '://' . $host . $script ;
		return '<div class="sub-content"><br/><div class="alert alert-warning"><b>Access denied</b> - You are not authorized to access this page. You will be redirected in 3 seconds ' .
				'Click <a href="' . $currentUrl . '">here</a> if the redirection did not work'.
				'<meta http-equiv="refresh" content="3; URL=' . $currentUrl . '"></div></div>';
	}
	
	
Jerome Mariette's avatar
Jerome Mariette committed
135
	/**
Jerome Mariette's avatar
Jerome Mariette committed
136
	 * Return the project view
Jerome Mariette's avatar
Jerome Mariette committed
137
	 */
Jerome Mariette's avatar
Jerome Mariette committed
138
	function pi_project_view()	{		
Jerome Mariette's avatar
Jerome Mariette committed
139
		$projects = array();
Jerome Mariette's avatar
Jerome Mariette committed
140
141
142
		if (!$GLOBALS['TSFE']->loginUser) { $user_id = null; }
		else { $user_id = $GLOBALS['TSFE']->fe_user->user['uid']; }
		
143
		$single_project_display = false;
Jerome Mariette's avatar
Jerome Mariette committed
144
145
		// If a single element
		if ($this->piVars['project_id']) {
Jerome Mariette's avatar
Jerome Mariette committed
146
147
			if (tx_nG6_db::user_is_authorized($user_id, $this->piVars['project_id'], $this->piVars['run_id'])) {
				$projects = array('project_'.$this->piVars['project_id'] => tx_nG6_db::select_project($this->piVars['project_id']));
148
				$single_project_display = true ;
Jerome Mariette's avatar
Jerome Mariette committed
149
			}
Jerome Mariette's avatar
Jerome Mariette committed
150
		} else {
Jerome Mariette's avatar
Jerome Mariette committed
151
			$projects = tx_nG6_db::select_all_user_projects($user_id, 'tx_nG6_project.name');
Jerome Mariette's avatar
Jerome Mariette committed
152
		}
Jerome Mariette's avatar
Jerome Mariette committed
153
154
155
156
157
158
159
160
161
162
		
		// If there is no project the user can access
		if (count($projects) > 0) {
			$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');		
Jerome Mariette's avatar
Jerome Mariette committed
163
			// Add some information to the table
Jerome Mariette's avatar
Jerome Mariette committed
164
165
166
167
168
169
170
171
172
173
174
			$project_ids = "";
			foreach($projects as $project_id => $project_values) {
				// project admin ?
				$projects[$project_id]['is_admin'] = tx_nG6_db::is_project_administrator($GLOBALS['TSFE']->fe_user->user['uid'], $project_values['id']);
				// project manager ?
				$projects[$project_id]['is_manager'] = tx_nG6_db::is_project_manager($GLOBALS['TSFE']->fe_user->user['uid'], $project_values['id']);
				// project member ?
				$projects[$project_id]['is_member'] = tx_nG6_db::is_project_member($GLOBALS['TSFE']->fe_user->user['uid'], $project_values['id']);
				
				$project_ids .= $project_values['id'].",";
				$projects[$project_id]['href'] = $this->pi_list_linkSingle($project_values['name'],$project_values['id'],1, array('project_id'=>$project_values['id']));
Jerome Mariette's avatar
Jerome Mariette committed
175
			}
Jerome Mariette's avatar
Jerome Mariette committed
176
177
178
			$smarty->assign('projects', $projects);
			$smarty->assign('login_user', $GLOBALS['TSFE']->loginUser);
			$smarty->assign('user_id', $GLOBALS['TSFE']->fe_user->user['uid']);
Jerome Mariette's avatar
Jerome Mariette committed
179
			$smarty->assign('user_login', $GLOBALS['TSFE']->fe_user->user['username']);
Jerome Mariette's avatar
Jerome Mariette committed
180
181
182
183
184
			$smarty->assign('data_folder', $this->conf["data"]);
			$smarty->assign('from_email', $this->conf["FromEmail"]);
			$smarty->assign('server_name', $this->conf["server_name"]);
			$smarty->assign('project_ids', substr($project_ids,0,-1));
			$smarty->assign('pid', $this->conf['userpidList']);
Jerome Mariette's avatar
Jerome Mariette committed
185
			$smarty->assign('server_url', $this->conf['server_url']);
186
			$smarty->assign('single_project_display', $single_project_display);
187
			$smarty->assign('is_ng6_admin', tx_nG6_db::is_ng6_administrator($user_id) ? true : false);
188
			
Jerome Mariette's avatar
Jerome Mariette committed
189
			// If it's a single project, add runs and analysis information
190
			if ($single_project_display) {
191
192
193
194
195
				
				//comments on the project
				$comments = tx_nG6_db::get_all_project_comments($projects[key($projects)]['id']);
				$smarty->assign('comments', $comments);
				
Jerome Mariette's avatar
Jerome Mariette committed
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
				// Get all users on project
				$project_users = tx_nG6_db::get_all_users_on_project($projects[key($projects)]['id']);
				$smarty->assign('project_users', $project_users);
	
				// Add some information to the table
				$project_runs = tx_nG6_db::get_project_runs($projects[key($projects)]['id']);
				foreach($project_runs as $run_id => $run_values) {
					$project_runs[$run_id]['is_admin'] = tx_nG6_db::is_administrator($GLOBALS['TSFE']->fe_user->user['uid'], 'run', $run_values['id']);
					$project_runs[$run_id]['href'] = $this->pi_list_linkSingle($run_values['name'],$run_values['id'],1, array('run_id'=>$run_values['id'], 'project_id'=>$run_values['project_id']));
				}
				$smarty->assign('project_runs', $project_runs);
				$project_analysis = tx_nG6_db::get_project_analysis($projects[key($projects)]['id']);
				
				// Add some information to the table
				foreach($project_analysis as $analysis_id => $analysis_values) {
					$project_analysis[$analysis_id]['is_admin'] = tx_nG6_db::is_administrator($GLOBALS['TSFE']->fe_user->user['uid'], 'analyze', $analysis_values['id']);
					$project_analysis[$analysis_id]['href'] = $this->pi_list_linkSingle($analysis_values['name'],$analysis_values['id'],1, array('analyze_id'=>$analysis_values['id'], 'project_id'=>$this->piVars['project_id']));
				}
214
				$smarty->assign('h_analysis', tx_nG6_utils::trace_hierarchy($project_analysis));
Jerome Mariette's avatar
Jerome Mariette committed
215
216
217
218
				$smarty->assign('project_analysis', $project_analysis);
			}	
			return $smarty->fetch('project_view.tpl');
		} else {
219
			return $this->redirect_view();
Jerome Mariette's avatar
Jerome Mariette committed
220
		}
Jerome Mariette's avatar
Jerome Mariette committed
221
	}
222
	
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
223

Jerome Mariette's avatar
Jerome Mariette committed
224
	/**
Jerome Mariette's avatar
Jerome Mariette committed
225
	 * Return the run view
Jerome Mariette's avatar
Jerome Mariette committed
226
	 */
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
227
    function pi_run_view() {
228

Jerome Mariette's avatar
Jerome Mariette committed
229
		$runs = array();
Jerome Mariette's avatar
Jerome Mariette committed
230
231
232
		if (!$GLOBALS['TSFE']->loginUser) { $user_id = null; }
		else { $user_id = $GLOBALS['TSFE']->fe_user->user['uid']; }
		
233
		$single_run_display = false;
Jerome Mariette's avatar
Jerome Mariette committed
234
235
		// If a single element
		if ($this->piVars['run_id']) {
Jerome Mariette's avatar
Jerome Mariette committed
236
237
			if (tx_nG6_db::user_is_authorized($user_id, $this->piVars['project_id'], $this->piVars['run_id'])) {
				$runs = array('run_'.$this->piVars['run_id'] => tx_nG6_db::select_run($this->piVars['run_id']));
238
				$single_run_display = true;
Jerome Mariette's avatar
Jerome Mariette committed
239
			}
Jerome Mariette's avatar
Jerome Mariette committed
240
		} else {
Jerome Mariette's avatar
Jerome Mariette committed
241
			$runs = tx_nG6_db::select_all_user_runs($user_id);
Jerome Mariette's avatar
Jerome Mariette committed
242
		}
243
		
Jerome Mariette's avatar
Jerome Mariette committed
244
245
246
247
248
249
250
251
252
		if (count($runs) > 0) {
			$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');
	
Jerome Mariette's avatar
Jerome Mariette committed
253
			// Add some information to the table
Jerome Mariette's avatar
Jerome Mariette committed
254
255
256
257
258
259
260
261
			$run_ids = "";
			foreach($runs as $run_id => $run_values) {
				if (tx_nG6_db::is_administrator($user_id, 'run', $run_values['id']) ) {
					$runs[$run_id]['is_admin'] = true;
				} else {
					$runs[$run_id]['is_admin'] = false;
				}
				$run_ids .= $run_values['id'].",";
Jerome Mariette's avatar
Jerome Mariette committed
262
				if ($this->piVars['project_id']) {
Jerome Mariette's avatar
Jerome Mariette committed
263
					$runs[$run_id]['href'] = $this->pi_list_linkSingle($run_values['name'],$run_values['id'],1, array('run_id'=>$run_values['id'], 'project_id'=>$run_values['project_id']));	
Jerome Mariette's avatar
Jerome Mariette committed
264
				} else {
Jerome Mariette's avatar
Jerome Mariette committed
265
					$runs[$run_id]['href'] = $this->pi_list_linkSingle($run_values['name'],$run_values['id'],1, array('run_id'=>$run_values['id']));
Jerome Mariette's avatar
Jerome Mariette committed
266
267
				}
			}
Jerome Mariette's avatar
Jerome Mariette committed
268
269
			$smarty->assign('runs', $runs);
			$smarty->assign('login_user', $GLOBALS['TSFE']->loginUser);
Jerome Mariette's avatar
Jerome Mariette committed
270
			$smarty->assign('user_login', $GLOBALS['TSFE']->fe_user->user['username']);
Jerome Mariette's avatar
Jerome Mariette committed
271
272
273
			$smarty->assign('user_id', $GLOBALS['TSFE']->fe_user->user['uid']);
			$smarty->assign('data_folder', $this->conf["data"]);
			$smarty->assign('server_name', $this->conf["server_name"]);
Jerome Mariette's avatar
Jerome Mariette committed
274
			$smarty->assign('server_url', $this->conf['server_url']);
Jerome Mariette's avatar
Jerome Mariette committed
275
			$smarty->assign('run_ids', substr($run_ids,0,-1));
276
			$smarty->assign('single_run_display', $single_run_display);
Jerome Mariette's avatar
Jerome Mariette committed
277
278
			
			// If it's a single run, add analysis information
279
			if ($single_run_display) {
280
281
282
283
284
				
				//comments on the run
				$comments = tx_nG6_db::get_all_run_comments($runs[key($runs)]['id']);
				$smarty->assign('comments', $comments);
				
Jerome Mariette's avatar
Jerome Mariette committed
285
286
287
288
289
290
291
292
293
294
				$run_analysis = tx_nG6_db::get_run_analysis($runs[key($runs)]['id']);
				// Add some information to the table
				foreach($run_analysis as $analysis_id => $analysis_values) {
					$run_analysis[$analysis_id]['is_admin'] = tx_nG6_db::is_administrator($GLOBALS['TSFE']->fe_user->user['uid'], 'analyze', $analysis_values['id']);
					if ($this->piVars['project_id']) {
						$run_analysis[$analysis_id]['href'] = $this->pi_list_linkSingle($analysis_values['name'],$analysis_values['id'],1, array('analyze_id'=>$analysis_values['id'], 'project_id'=>$this->piVars['project_id'], 'run_id'=>$this->piVars['run_id']));
					} else {
						$run_analysis[$analysis_id]['href'] = $this->pi_list_linkSingle($analysis_values['name'],$analysis_values['id'],1, array('analyze_id'=>$analysis_values['id'], 'run_id'=>$this->piVars['run_id']));
					}
				}
295
				$smarty->assign('h_analysis', tx_nG6_utils::trace_hierarchy($run_analysis));
Jerome Mariette's avatar
Jerome Mariette committed
296
297
298
299
				$smarty->assign('run_analysis', $run_analysis);
			}		
			return $smarty->fetch('run_view.tpl');
		} else {
300
			return $this->redirect_view();
Jerome Mariette's avatar
Jerome Mariette committed
301
		}
302
303
	}
	
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
304

Jerome Mariette's avatar
Jerome Mariette committed
305
	/**
Jerome Mariette's avatar
Jerome Mariette committed
306
	 * Return the analysis view
Jerome Mariette's avatar
Jerome Mariette committed
307
	 */
Jerome Mariette's avatar
Jerome Mariette committed
308
	function pi_analyze_view() {
309
310
311
312
313
314
		if (!$GLOBALS['TSFE']->loginUser) { $user_id = null; }
		else { $user_id = $GLOBALS['TSFE']->fe_user->user['uid']; }
		
		// is project admin
		$is_project_admin = tx_nG6_db::is_project_administrator($GLOBALS['TSFE']->fe_user->user['uid'], $this->piVars['project_id']);
		
315
		// First select the analyse
Jerome Mariette's avatar
Jerome Mariette committed
316
		$analyse = tx_nG6_db::select_analyse($this->piVars['analyze_id']);
Jerome Mariette's avatar
Jerome Mariette committed
317
		
318
319
320
321
322
323
324
325
326
327
		// Handle old fashion
		if (file_exists($this->conf['data'].$analyse['directory'].'/index.html' )) {
			// Add the analyse description
			$content = '<div id="img_dialog" title=""></div>';
			$content .= '<input type="hidden" id="analyse_name" value="'.$analyse['name'].'" />';
			$content .= '<div'.$this->pi_classParam('singleView').'>';
			$content .= '<h2>Analyse '.$analyse['name'].' : <span>'.$analyse['description'].'</span></h2></div>';
			$fp = fopen((string)$this->conf['data'].$analyse['directory'].'/index.html',"r");
			while (!feof($fp)) {
				$content .= fgets($fp, 4096);
Jerome Mariette's avatar
Jerome Mariette committed
328
			}
329
			return $content;
330
		// Else meaning using smarty
Jerome Mariette's avatar
Jerome Mariette committed
331
		} else {
332
333
334
335
336
337
338
339
340
			
			$smarty = new Smarty();
			$smarty->setTemplateDir(t3lib_extMgm::extPath('nG6').'/pi1/analyzes');
			$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');

341
			$smarty->assign('is_project_admin', $is_project_admin);
342
			$smarty->assign('analyse', $analyse);
343
			$analysis_size = tx_nG6_db::get_analysis_size($this->piVars['analyze_id']);
344
			$smarty->assign('analyse_size', tx_nG6_utils::get_octet_string_representation($analysis_size));
Jerome Mariette's avatar
Jerome Mariette committed
345
			$smarty->assign('data_folder', $this->conf["data"]);
Penom Nom's avatar
Penom Nom committed
346
			$smarty->assign('analyze_id', $this->piVars['analyze_id']);
Penom Nom's avatar
Penom Nom committed
347
			$smarty->assign('server_url', $this->conf['server_url']);
348
			$smarty->assign('user_login', $GLOBALS['TSFE']->fe_user->user['username']);
349
			$smarty->assign('user_id', $GLOBALS['TSFE']->fe_user->user['uid']);
350
351
			
			// Then select analyse results
Jerome Mariette's avatar
Jerome Mariette committed
352
			$results = tx_nG6_db::select_analyse_results($this->piVars['analyze_id']);		
353
354
			$smarty->assign('analyse_results', $results);
			
355
356
357
358
			//comments on the analysis
			$comments = tx_nG6_db::get_all_analyze_comments($this->piVars['analyze_id']);
			$smarty->assign('comments', $comments);
			
359
360
361
362
363
364
365
			// Select the run file description	
			if ($analyse['run_id'] != 'None') {
				$descriptions = tx_nG6_db::select_mid_descriptions($analyse['run_id']);
			} else {
				$descriptions = array();
			}
			$smarty->assign('descriptions', $descriptions);
366
			$smarty->assign('data_folder', $this->conf['data']);		
367
			// Try to process the analyse template
368
369
			try {
				if (file_exists(t3lib_extMgm::extPath($this->extKey).'pi1/analyzes/'.$analyse['class'].'.js')) {
370
					$GLOBALS['TSFE']->additionalHeaderData[$this->prefixId] .= '
Jerome Mariette's avatar
Jerome Mariette committed
371
						<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'pi1/analyzes/'.$analyse['class'].'.js"></script>';
372
				}
Jerome Mariette's avatar
Jerome Mariette committed
373
374
				$GLOBALS['TSFE']->additionalHeaderData[$this->prefixId] .= '
					<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/tx_nG6_pi1_analysis.js"></script>
Penom Nom's avatar
Penom Nom committed
375
					<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.venny.min.js"></script>
Jerome Mariette's avatar
Jerome Mariette committed
376
377
378
					<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.highcharts.js"></script>
					<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.highcharts.exporting.js"></script>
					<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.highcharts.more.js"></script>
379
					<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.highcharts.exportcsv.js"></script>
Jerome Mariette's avatar
Jerome Mariette committed
380
381
382
383
					<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jsphylosvg-min.js"></script>
					<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/raphael-min.js"></script>
					<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/unitip.js"></script>
					<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.jstree.min.js"></script>
Penom Nom's avatar
Penom Nom committed
384
					<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/d3-3.4.4.min.js"></script>
Jerome Mariette's avatar
Jerome Mariette committed
385
					<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/unitip.css"/>';
386
387
				return $smarty->fetch($analyse['class'].'.tpl'); 
			} catch (Exception $e) { 
Jerome Mariette's avatar
Jerome Mariette committed
388
				return 'No template found for class ' . $analyse['class'];
389
			}
Jerome Mariette's avatar
Jerome Mariette committed
390
391
		}
	}
Celine Noirot's avatar
Celine Noirot committed
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
	/**
	 * Return the install view
	 */
	function pi_install_view() {
		$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');
		$smarty->assign('server_name', $this->conf["server_name"]);
		$smarty->assign('server_url', $this->conf['server_url']);
		$smarty->assign('pid', $this->conf['userpidList']);
		return $smarty->fetch('install_view.tpl');
	}
	/**
	 * Does installation need is finalized ( admin_install user exist in db )
	 *
	 * @param	integer		Alternative page ID for the link. (By default this function links to the SAME page!)
	 * @return	boolean		If true, intallation allready finalysed
	 */
	function pi_is_install_finalized()	{
		$res = tx_nG6_db::select_user_by_username("admin_install");
Jerome Mariette's avatar
Jerome Mariette committed
416
		if ($res == null) {
Celine Noirot's avatar
Celine Noirot committed
417
			return true;
Jerome Mariette's avatar
Jerome Mariette committed
418
		} else {
Celine Noirot's avatar
Celine Noirot committed
419
420
421
			return false;
		}
	}
Jerome Mariette's avatar
Jerome Mariette committed
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
	
	/**
	 * Overloading of the tslib_pibase->pi_list_linkSingle function so piVars[showUid] is not set.
	 * Uses pi_linkTP for the linking
	 *
	 * @param	string		The content string to wrap in <a> tags
	 * @param	integer		UID of the record for which to display details (basically this will become the value of [showUid]
	 * @param	boolean		See pi_linkTP_keepPIvars
	 * @param	array		Array of values to override in the current piVars. Same as $overrulePIvars in pi_linkTP_keepPIvars
	 * @param	boolean		If true, only the URL is returned, not a full link
	 * @param	integer		Alternative page ID for the link. (By default this function links to the SAME page!)
	 * @return	string		The input string wrapped in <a> tags
	 * @see pi_linkTP(), pi_linkTP_keepPIvars()
	 */
	function pi_list_linkSingle($str,$uid,$cache=FALSE,$mergeArr=array(),$urlOnly=FALSE,$altPageId=0)	{
		if ($this->prefixId)	{
			if ($cache)	{
				$overrulePIvars=(array)$mergeArr;
				$str = $this->pi_linkTP($str,Array($this->prefixId=>$overrulePIvars),$cache,$altPageId);
			} else {
				$overrulePIvars=(array)$mergeArr;
				$str = $this->pi_linkTP_keepPIvars($str,$overrulePIvars,$cache,0,$altPageId);
			}

				// If urlOnly flag, return only URL as it has recently be generated.
			if ($urlOnly)	{
				$str = $this->cObj->lastTypoLinkUrl;
			}
		}
		return $str;
	}
453
	
Jerome Mariette's avatar
Jerome Mariette committed
454
455
456
457
458
459
}

if (defined('TYPO3_MODE') && $TYPO3_CONF_VARS[TYPO3_MODE]['XCLASS']['ext/nG6/pi1/class.tx_nG6_pi1.php'])	{
	include_once($TYPO3_CONF_VARS[TYPO3_MODE]['XCLASS']['ext/nG6/pi1/class.tx_nG6_pi1.php']);
}

Penom Nom's avatar
Penom Nom committed
460
?>