class.tx_nG6_pi1.php 24 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').'/res/smarty/libs/Smarty.class.php'); 
Jerome Mariette's avatar
Jerome Mariette committed
34
35

class tx_nG6_pi1 extends tslib_pibase {
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
36
	
Jerome Mariette's avatar
Jerome Mariette committed
37
38
39
40
41
42
43
44
45
46
47
48
	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
49
		
Jerome Mariette's avatar
Jerome Mariette committed
50
51
52
		if (strstr($this->cObj->currentRecord,'tt_content'))	{
			$conf['pidList'] = $this->cObj->data['pages'];
		}
Jerome Mariette's avatar
Jerome Mariette committed
53
54
		// Setting the TypoScript passed to this function in $this->conf
		$this->conf=$conf;
55
56
		$this->internal['results_at_a_time'] = $conf["results_at_a_time"];
		
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
57
		$this->pi_setPiVarDefaults();
Jerome Mariette's avatar
Jerome Mariette committed
58
59
60
61
		// 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
		$this->pi_loadLL();
62

63
64
65
		// Add the ng6 plugins css
		$GLOBALS['TSFE']->additionalHeaderData[$this->prefixId] = '<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
66
		// If the user is authorized to access the specified project/run, display the page
67
		if (tx_nG6_db::user_is_authorized($GLOBALS['TSFE']->fe_user->user['usergroup'], $this->piVars['project_id'], $this->piVars['run_id'])) {
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
68
			switch((string)$this->conf['view'])	{
Jerome Mariette's avatar
Jerome Mariette committed
69
				// If the plugin is configured to display results by project
Jerome Mariette's avatar
Jerome Mariette committed
70
71
				case 'project':
					if ($this->piVars['analyze_id']) {
Jerome Mariette's avatar
Jerome Mariette committed
72
						return $this->pi_wrapInBaseClass($this->pi_analyze_view('analyze'));
Jerome Mariette's avatar
Jerome Mariette committed
73
					} elseif ($this->piVars['project_id'] && $this->piVars['run_id']) {
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
74
						return $this->pi_wrapInBaseClass($this->pi_run_view());
75
76
					}elseif ($this->piVars['project_id'] && $this->piVars['summary']) {
						return $this->pi_wrapInBaseClass($this->pi_project_summary());
Jerome Mariette's avatar
Jerome Mariette committed
77
					} else {
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
78
						return $this->pi_wrapInBaseClass($this->pi_project_view());
Jerome Mariette's avatar
Jerome Mariette committed
79
80
					}
					break;
Jerome Mariette's avatar
Jerome Mariette committed
81
				// If the plugin is configured to display results by run
Jerome Mariette's avatar
Jerome Mariette committed
82
83
				case 'run':
					if ($this->piVars['analyze_id']) {
Jerome Mariette's avatar
Jerome Mariette committed
84
						return $this->pi_wrapInBaseClass($this->pi_analyze_view('analyze'));
Jerome Mariette's avatar
Jerome Mariette committed
85
					} else {
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
86
						return $this->pi_wrapInBaseClass($this->pi_run_view());
Jerome Mariette's avatar
Jerome Mariette committed
87
					}
Jerome Mariette's avatar
Jerome Mariette committed
88
89
					break;
				// If the plugin is not configured, display by project is default
Jerome Mariette's avatar
Jerome Mariette committed
90
				default:
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
91
					return $this->pi_wrapInBaseClass($this->pi_project_view());
Jerome Mariette's avatar
Jerome Mariette committed
92
					break;
Jerome Mariette's avatar
Jerome Mariette committed
93
			}
Jerome Mariette's avatar
Jerome Mariette committed
94
		// If the user is not authorized
Jerome Mariette's avatar
Jerome Mariette committed
95
		} else {
Jerome Mariette's avatar
Jerome Mariette committed
96
			return $this->pi_wrapInBaseClass($this->pi_getLL('not_authorized','[not_authorized]'));
Jerome Mariette's avatar
Jerome Mariette committed
97
98
		}
	}
99
	
100
101
	/**
	 * Shows the summary and statistics for a project
Jerome Mariette's avatar
Jerome Mariette committed
102
	 * TODELETE
103
104
105
	 * @return	HTML list of table entries
	 */
	function pi_project_summary()	{
Jerome Mariette's avatar
Jerome Mariette committed
106
107
108
		$project_runs = tx_nG6_db::get_project_runs($GLOBALS['TSFE']->fe_user->user['usergroup'], $this->piVars['project_id']);
		$content = "Le projet ".$this->piVars['project_id']." contient ".count($project_runs)." runs.";
		return $content;
109
	}
110
	
Jerome Mariette's avatar
Jerome Mariette committed
111
112
113
114
115
	/**
	 * Shows a list of database entries
	 *
	 * @return	HTML list of table entries
	 */
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
116
117
	function pi_project_view()	{

Jerome Mariette's avatar
Jerome Mariette committed
118
119
120
121
		// If a single element should be displayed
		if ($this->piVars['project_id'])	{
			
			return $this->pi_project_single_view($this->piVars['project_id']);
122

Jerome Mariette's avatar
Jerome Mariette committed
123
		// If multiple projects
Jerome Mariette's avatar
Jerome Mariette committed
124
		} else {
Jerome Mariette's avatar
Jerome Mariette committed
125
126
127
			
			// If the user is on a specific page
			if (isset($this->piVars['project_page'])) {
128
129
				$current_page = intval($this->internal['results_at_a_time']) * (intval($this->piVars['project_page']) -1);
				$limit = "$current_page".",". $this->internal['results_at_a_time'] ;
Jerome Mariette's avatar
Jerome Mariette committed
130
131
132
133
134
135
			} else $limit = '0,'.$this->internal['results_at_a_time'] ; 
			
			// Select all user projects
			$projects = tx_nG6_db::select_all_user_projects($GLOBALS['TSFE']->fe_user->user['usergroup'], 'tx_nG6_project.name', $limit);
			$all_projects = tx_nG6_db::select_all_user_projects($GLOBALS['TSFE']->fe_user->user['usergroup']);
			
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
136
			// If there is at least one result
Jerome Mariette's avatar
Jerome Mariette committed
137
138
139
140
141
142
143
144
145
			if (count($projects) > 0) {

	         	$project_list = $this->pi_project_list_view($projects);
	         	$nav_links = $this->pi_navigation_link_view('project_page', $this->piVars['project_page'], count($all_projects));
         		return $project_list.$nav_links;
         		
         	// If there is no results to display		
			} else { 
				return $this->pi_getLL('no_raw','[no_raw]');
146
			}
Jerome Mariette's avatar
Jerome Mariette committed
147
148
149
150
151
		}
	}

	/**
	 * Creates a list from a database query
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
152
	 * 
Jerome Mariette's avatar
Jerome Mariette committed
153
154
155
	 * @param	ressource	$res: A database result ressource
	 * @return	A HTML list if result items
	 */
Jerome Mariette's avatar
Jerome Mariette committed
156
157
158
	function pi_project_list_view($projects)	{

		// First add the table header
Jerome Mariette's avatar
Jerome Mariette committed
159
		$content = '<table'.$this->pi_classParam('listrow').'>
Jerome Mariette's avatar
Jerome Mariette committed
160
161
162
					<tr>
					<th>'.$this->pi_getLL('project_name','[project_name]').'</th>
					<th>'.$this->pi_getLL('description','[description]').'</th>
163
					</tr>';
Jerome Mariette's avatar
Jerome Mariette committed
164
165
166
167
168
169
170
171
172
173
174
						
		// Then the row for each project	
		foreach($projects as $project_id => $project_values) {
			// If it's not a hidden project
			$hidden = $this->pi_classParam('hidden');
			if ($project_values['hidden'] == 0) { $hidden = ''; }
				$content .= '<tr>
							 <td '.$hidden.' >'.$this->pi_list_linkSingle($project_values['name'],$project_values['id'],1, array('project_id'=>$project_values['id'])).'</td>
							 <td '.$hidden.' >'.$project_values['description'].'</td>
							 </tr>';

Jerome Mariette's avatar
Jerome Mariette committed
175
		}
Jerome Mariette's avatar
Jerome Mariette committed
176
177
		// Return the whole table
		return $content .= '</table>';
Jerome Mariette's avatar
Jerome Mariette committed
178
179
180
	}

	/**
Jerome Mariette's avatar
Jerome Mariette committed
181
	 * Display a single project
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
182
	 * 
Jerome Mariette's avatar
Jerome Mariette committed
183
184
	 * @param	string	$project_id	the project id
	 * @return	HTML of a single project entry
Jerome Mariette's avatar
Jerome Mariette committed
185
	 */
Jerome Mariette's avatar
Jerome Mariette committed
186
187
188
189
190
191
	function pi_project_single_view($project_id)	{
		
		// First select the project values 
		$project = tx_nG6_db::select_project($project_id);
		
		// Add the project description
Jerome Mariette's avatar
Jerome Mariette committed
192
		$content = '<div'.$this->pi_classParam('singleView').'>
Jerome Mariette's avatar
Jerome Mariette committed
193
194
195
196
197
198
			        <h2>Projet '.$project['name'].' :</h2>
				    <p><strong>'.$project['description'].'</strong></p></div>';
		// The project runs view
		$content .= '<br /> <h3> '.$this->pi_getLL('runs_done','[runs_done]').'</h3> <br />';
		$content .= $this->pi_run_view();
		// And the analyses performed on the project
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
199
		$content .= $this->pi_analyze_view('project');
Jerome Mariette's avatar
Jerome Mariette committed
200
		return $content;
Jerome Mariette's avatar
Jerome Mariette committed
201
		
Jerome Mariette's avatar
Jerome Mariette committed
202
	}
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
203

Jerome Mariette's avatar
Jerome Mariette committed
204
205
206
207
208
	/**
	 * Shows a list of database entries
	 *
	 * @return	HTML list of table entries
	 */
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
209
    function pi_run_view() {
Jerome Mariette's avatar
Jerome Mariette committed
210
211
212
    	
    	// If a single element should be displayed
		if ($this->piVars['run_id'])    {       
213
		
Jerome Mariette's avatar
Jerome Mariette committed
214
			return $this->pi_run_single_view($this->piVars['run_id']);
215
		
Jerome Mariette's avatar
Jerome Mariette committed
216
217
218
219
220
		// If multiple runs
		} else {        
			
			// If the user is on a specific page
			if (isset($this->piVars['run_page'])) {
221
222
				$current_page = intval($this->internal['results_at_a_time']) * (intval($this->piVars['run_page']) -1);
				$limit = "$current_page".",". $this->internal['results_at_a_time'] ;
Jerome Mariette's avatar
Jerome Mariette committed
223
			} else $limit = '0,'.$this->internal['results_at_a_time'] ; 
224
		   
Jerome Mariette's avatar
Jerome Mariette committed
225
			// Select all runs from this project
Jerome Mariette's avatar
Jerome Mariette committed
226
			if ($this->piVars['project_id']) {
Jerome Mariette's avatar
Jerome Mariette committed
227
228
229
				$runs = tx_nG6_db::get_project_runs($GLOBALS['TSFE']->fe_user->user['usergroup'], $this->piVars['project_id'], 'tx_nG6_run.date DESC, tx_nG6_run.name ASC', $limit);
				$all_runs = tx_nG6_db::get_project_runs($GLOBALS['TSFE']->fe_user->user['usergroup'], $this->piVars['project_id']);
			// If no project defined, select all runs owned by the user
Jerome Mariette's avatar
Jerome Mariette committed
230
			} else {
Jerome Mariette's avatar
Jerome Mariette committed
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
            	$runs = tx_nG6_db::select_all_user_runs($GLOBALS['TSFE']->fe_user->user['usergroup'], 'tx_nG6_run.date DESC, tx_nG6_run.name ASC', $limit);
            	$all_runs = tx_nG6_db::select_all_user_runs($GLOBALS['TSFE']->fe_user->user['usergroup']);
         	}
	
         	// If there is some results to display
			if (count($runs) > 0) {

				$run_list = $this->pi_run_list_view($runs);
				$nav_links = $this->pi_navigation_link_view('run_page', $this->piVars['run_page'], count($all_runs));
				return $run_list ."\n". $nav_links;
 			
 			// If there is no results
 			} else { 
 				return $this->pi_getLL('no_raw','[no_raw]');
 			}
 			
		}
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
248
249
    }

Jerome Mariette's avatar
Jerome Mariette committed
250
251
252
253
254
255
	/**
	 * Creates a list from a database query
	 *
	 * @param	ressource	$res: A database result ressource
	 * @return	A HTML list if result items
	 */
Jerome Mariette's avatar
Jerome Mariette committed
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
	function pi_run_list_view($runs) {
		
		// First add the table header
		$content = '<table'.$this->pi_classParam('listrow').'>
					<tr>
					<th>'.$this->pi_getLL('run_name','[run_name]').'</th>
					<th>'.$this->pi_getLL('project_name','[project_name]').'</th>
					<th>'.$this->pi_getLL('date','[date]').'</th>
					<th>'.$this->pi_getLL('species','[species]').'</th>
					<th>'.$this->pi_getLL('data_nature','[data_nature]').'</th>
					<th>'.$this->pi_getLL('type','[type]').'</th>
					<th>'.$this->pi_getLL('nb_sequences','[nb_sequences]').'</th>
					<th>'.$this->pi_getLL('full_seq_size','[full_seq_size]').'</th>
					<th>'.$this->pi_getLL('description','[description]').'</th>
					<th>'.$this->pi_getLL('sequencer','[sequencer]').'</th>
271
					</tr>';
Jerome Mariette's avatar
Jerome Mariette committed
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
					
		// Then the row for each run
		foreach($runs as $run_id => $run_values) {
			
			// If the run is hidden
			$hidden = $this->pi_classParam('hidden');
			if ($run_values['hidden'] == 0) { $hidden = ''; }

			// Add the row information
			$content .= '<tr>
						 <td '.$hidden.' >'.$this->pi_list_linkSingle($run_values['name'],$run_id,1, array('run_id'=>$run_values['id'], 'project_id'=>$run_values['project_id'])).'</td>
						 <td '.$hidden.' >'.$run_values['project_name'].'</td>
						 <td '.$hidden.' >'.strftime('%d-%m-%y',$run_values['date']).'</td>
						 <td '.$hidden.' >'.$run_values['species'].'</td>
						 <td '.$hidden.' >'.$run_values['data_nature'].'</td>
						 <td '.$hidden.' >'.$run_values['type'].'</td>
						 <td '.$hidden.' >'.number_format($run_values['nb_sequences'], 0, ',', ' ').'</td>
						 <td '.$hidden.' >'.number_format($run_values['full_seq_size'], 0, ',', ' ').'</td>
						 <td '.$hidden.' >'.$run_values['description'].'</td>
						 <td '.$hidden.' >'.$run_values['sequencer'].'</td>
						 </tr>';
Jerome Mariette's avatar
Jerome Mariette committed
293
		}
Jerome Mariette's avatar
Jerome Mariette committed
294
295
296
		
		// Return the html table
		return $content .= '</table>' ;
Jerome Mariette's avatar
Jerome Mariette committed
297
298
299
300
	}

	/**
	 * Display a single item from the database
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
301
302
	 * 
	 * @param	ressource	$res: A database result ressource
Jerome Mariette's avatar
Jerome Mariette committed
303
304
	 * @return	HTML of a single database entry
	 */
Jerome Mariette's avatar
Jerome Mariette committed
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
	function pi_run_single_view($run_id) {	
		
		// First select the run
		$run = tx_nG6_db::select_run($run_id);
		
		// Add the run description to the page content
		$content = '<div'.$this->pi_classParam('singleView').'>';
		$content .= '<h2>Run '.$run['name'].' :</h2>';
		$content .= '<p><strong>'.$run['description'].'</strong></p> </div>
					 <table'.$this->pi_classParam('listrow').'>
					 <tr>
						<th align="left">'.$this->pi_getLL('project_name','[project_name]').' :</th>
						<td align="left">'.$run['project_name'].'</td>
					 </tr>	
					 <tr>
						<th align="left">'.$this->pi_getLL('date','[date]').' :</th>
						<td align="left">'.strftime('%d-%m-%y',$run['date']).'</td>
					 </tr>					
					 <tr>
						<th align="left">'.$this->pi_getLL('species','[species]').' :</th>
						<td align="left">'.$run['species'].'</td>
					 </tr>
					 <tr>
						<th align="left">'.$this->pi_getLL('type','[type]').' :</th>
						<td align="left">'.$run['type'].'</td>
					 </tr>
					 <tr>
						<th align="left">'.$this->pi_getLL('data_nature','[data_nature]').' :</th>
						<td align="left">'.$run['data_nature'].'</td>
					 </tr>
					 <tr>
						<th align="left">'.$this->pi_getLL('nb_sequences','[nb_sequences]').' :</th>
						<td align="left">'.number_format($run['nb_sequences'], 0, ',', ' ').'</td>
					 </tr>
					 <tr>
						<th align="left">'.$this->pi_getLL('full_seq_size','[full_seq_size]').' :</th>
						<td align="left">'.number_format($run['full_seq_size'], 0, ',', ' ').'</td>
					 </tr>						
					 <tr>
						<th align="left">'.$this->pi_getLL('sequencer','[sequencer]').' :</th>
						<td align="left">'.$run['sequencer'].'</td>
					 </tr>
					 <tr>
						<th align="left">'.$this->pi_getLL('downloads','[downloads]').' :</th>
						<td align="left">'.$this->get_downloads_list($run['directory']).'</td>
					 </tr>
					 </table>';
					 
		// Add the run analysis
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
354
		$content .= $this->pi_analyze_view('run');
355
		
Jerome Mariette's avatar
Jerome Mariette committed
356
357
		// Return the run HTML page
		return $content;
Jerome Mariette's avatar
Jerome Mariette committed
358
359
	}
	
Jerome Mariette's avatar
Jerome Mariette committed
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
388
	/**
	 * Display a list of downloadable file
	 *
	 * @return	HTML of a list of downlabale links
	 */
	function get_downloads_list($run_directory) {
		$directory = (string)$this->conf['data'].$run_directory;
		
		// Try to look at all files in the specified directory
		try {
			if (!is_dir($directory)) { throw new Exception('Error when attempting to open the data folder !'); }
			$my_directory = opendir($directory) or die('Error when attempting to open the data folder !');
			$download = '<p '.$this->pi_classParam('downloads').'><ul>';
			// For every files
			while($entry = @readdir($my_directory)) {
				if(!is_dir($directory.'/'.$entry)&& $entry != '.' && $entry != '..' && !tx_nG6_utils::ends_with($entry, ".cfg")) {
					$link = 'fileadmin/'.$run_directory.'/'.$entry;
					$download .= '<li><a href="'.$link.'" target="_blank">'.$entry.'</a></li>';
				}
			}
			$download .= '</ul>';		
			closedir($my_directory);
			return $download;
		}
		catch (Exception $e) {
			return $this->pi_getLL('not_synchro','[not_synchro]');
		}
	}	
	
Jerome Mariette's avatar
Jerome Mariette committed
389
390
391
392
393
394
	/**
	 * Shows a list of database entries
	 *
	 * @param	string		$type: What kind of analyze is it : run or project
	 * 	 * @return	HTML list of table entries
	 */
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
395
	function pi_analyze_view($type)	{
396
		
Jerome Mariette's avatar
Jerome Mariette committed
397
398
399
400
		// If a single element should be displayed:
		if ($type == 'analyze')	{
			
			return $this->pi_analyze_single_view($this->piVars['analyze_id']);
401
		
Jerome Mariette's avatar
Jerome Mariette committed
402
403
404
405
406
		// If multiple analyses
		} else {
			
			// If the user is on a specific page
			if (isset($this->piVars['analyze_page'])) {
407
408
				$current_page = intval($this->internal['results_at_a_time']) * (intval($this->piVars['analyze_page']) -1);
				$limit = "$current_page".",". $this->internal['results_at_a_time'] ;
Jerome Mariette's avatar
Jerome Mariette committed
409
410
411
			} else $limit = '0,'.$this->internal['results_at_a_time'] ; 
			
			// If we want run analyses
Jerome Mariette's avatar
Jerome Mariette committed
412
413
			if ($type == 'run') {
				// Selects Analyzis done on this run
Jerome Mariette's avatar
Jerome Mariette committed
414
415
416
417
418
419
420
421
				$analyses = tx_nG6_db::get_run_analysis($GLOBALS['TSFE']->fe_user->user['usergroup'], $this->piVars['run_id'], 'tx_nG6_analyze.name', $limit);
				$all_analyses = tx_nG6_db::get_run_analysis($GLOBALS['TSFE']->fe_user->user['usergroup'], $this->piVars['run_id']);
			} else {
				$analyses = tx_nG6_db::get_project_analysis($GLOBALS['TSFE']->fe_user->user['usergroup'], $this->piVars['project_id'], 'tx_nG6_analyze.name', $limit);
				$all_analyses = tx_nG6_db::get_project_analysis($GLOBALS['TSFE']->fe_user->user['usergroup'], $this->piVars['project_id']);
			}

			// Define an empty content
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
422
			$content='';
Jerome Mariette's avatar
Jerome Mariette committed
423
424
425
426
427
428
			
			// If there is some analyse
			if (count($analyses) > 0) {	
				$analyze_list = $this->pi_analyze_list_view($analyses);
				$nav_links = $this->pi_navigation_link_view('analyze_page', $this->piVars['analyze_page'], count($all_analyses));
				$content.= $analyze_list.$nav_links;
Jerome Mariette's avatar
Jerome Mariette committed
429
			}
Jerome Mariette's avatar
Jerome Mariette committed
430
431
			
			// Return the final HTML
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
432
			return $content;
Jerome Mariette's avatar
Jerome Mariette committed
433
434
435
436
437
438
439
440
441
		}
	}

	/**
	 * Creates a list from a database query
	 *
	 * @param	ressource	$res: A database result ressource
	 * @return	A HTML list if result items
	 */
Jerome Mariette's avatar
Jerome Mariette committed
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
	function pi_analyze_list_view($analyses) {
		
		// First add the table header to the HTML
		$content = '<br /> <h3> '.$this->pi_getLL('analyzes_done','[analyzes_done]').'</h3> <br />
				   <table'.$this->pi_classParam('listrow').'>
				   <tr>
						<th>'.$this->pi_getLL('name','[name]').'</th>
						<th>'.$this->pi_getLL('description','[description]').'</th>
						<th>'.$this->pi_getLL('software','[software]').'</th>
						<th>'.$this->pi_getLL('version','[version]').'</th>
				   </tr>';
				   
		// Then the row for each analyse
		foreach($analyses as $analyse_id => $analyse_values) {

			// If it's not a hidden analyse
			$hidden = $this->pi_classParam('hidden');
			if ($analyse_values['hidden'] == 0) { $hidden = ''; }

			$content .= '<tr>
						 <td '.$hidden.' >'.$this->pi_list_linkSingle($analyse_values['name'],$analyse_values['id'],1, array('analyze_id'=>$analyse_values['id'], 'project_id'=>$this->piVars['project_id'], 'run_id'=>$this->piVars['run_id'])).'</td>
						 <td '.$hidden.' >'.$analyse_values['description'].'</td>
						 <td '.$hidden.' >'.$analyse_values['software'].'</td>
						 <td '.$hidden.' >'.$analyse_values['version'].'</td>
						 </tr>';

Jerome Mariette's avatar
Jerome Mariette committed
468
		}
Jerome Mariette's avatar
Jerome Mariette committed
469
		return $content.'</table>' ;	
Jerome Mariette's avatar
Jerome Mariette committed
470
471
	}

Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
472

Jerome Mariette's avatar
Jerome Mariette committed
473
474
475
476
477
	/**
	 * Display a single item from the database
	 *
	 * @return	HTML of a single database entry
	 */
Jerome Mariette's avatar
Jerome Mariette committed
478
479
480
	function pi_analyze_single_view($analyse_id) {
		
		// Add the jquery libs
481
482
483
484
485
486
487
488
		$GLOBALS['TSFE']->additionalHeaderData[$this->prefixId] = '
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.ui.core.min.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.ui.dialog.min.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.ui.draggable.min.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.ui.resizable.min.js"></script> 
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.bgiframe.min.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.url.packed.js"></script>
489
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/tx_nG6_pi1.js"></script>
490
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/tx_nG6.css"/>
491
492
493
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/jquery.ui.core.css"/>
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/jquery.ui.theme.css"/>
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/jquery.ui.dialog.css"/>';
494
495
496

		// First select the analyse
		$analyse = tx_nG6_db::select_analyse($analyse_id);
Jerome Mariette's avatar
Jerome Mariette committed
497
		
498
499
500
501
502
503
504
505
506
507
		// 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
508
			}
Jerome Mariette's avatar
Jerome Mariette committed
509
			
510
		// Else meaning using smarty
Jerome Mariette's avatar
Jerome Mariette committed
511
		} else {
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
			
			$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');

			$smarty->assign('analyse', $analyse);
			
			// Then select analyse results
			$results = tx_nG6_db::select_analyse_results($analyse_id);		
			$smarty->assign('analyse_results', $results);
			
			// 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);
			$smarty->assign('data_folder', $this->conf['data']);
Jerome Mariette's avatar
fix bug    
Jerome Mariette committed
535
			if (isset($this->LOCAL_LANG[$this->LLkey])) {
536
537
538
539
540
541
542
				$smarty->assign('llang', $this->LOCAL_LANG[$this->LLkey]);
			} else {
				$smarty->assign('llang', $this->LOCAL_LANG['default']);
			}			
			// Try to process the analyse template
			try { $content = $smarty->fetch($analyse['class'].'.tpl'); } 
			catch (Exception $e) { $content = str_replace(array('###ANALYSE_CLASS###'), array($analyse['class']), $this->pi_getLL('no_template_found','[no_template_found:###ANALYSE_CLASS###]')); }
Jerome Mariette's avatar
Jerome Mariette committed
543
		}
Jerome Mariette's avatar
Jerome Mariette committed
544
		
545
		// Return the analyse display
Jerome Mariette's avatar
Jerome Mariette committed
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
		return $content;
	}
	
	/**
	 * 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;
	}
	
580
581
582
	/**
	 * Display links for navigation in run lists or analyse lists. Called only if $end>1
	 *
Jerome Mariette's avatar
Jerome Mariette committed
583
	 * @param	$name	name of the variable set in GET: run_page or analyze_page
584
	 * @param	$start	current page number
Jerome Mariette's avatar
Jerome Mariette committed
585
	 * @param	$total_count	current total number of rows
586
587
588
589
590
591
592
593
	 *
	 * @return	HTML navigation links
	 */
	function pi_navigation_link_view($name, $start, $total_count) 
	{  
		$start = intval($start);		
		
		//max page number
Jerome Mariette's avatar
Jerome Mariette committed
594
		$end = $total_count/$this->internal['results_at_a_time'] ;
595
596
597
598
599
600
601
602
603
604
605
606
607
608
		$end = ceil($end) ;
		//repair URL mistakes caused by the nasty user  		
		if ($start > $end)
			$start = $end;
		if (($start < 1) or (! $start))
			$start = 1; 
					
		$start=(string)$start ; $end=(string)$end ;
		//create navigation links
		
		$go_back = $this->pi_linkTP_keepPIvars ('<<', array ($name => 1))	.' '.		$this->pi_linkTP_keepPIvars ('<', array ($name => $start-1));
		$go_ahead= $this->pi_linkTP_keepPIvars ('>', array ($name => $start+1)).' '.$this->pi_linkTP_keepPIvars ('>>', array ($name => $end)); 
		$current_pos = 'page '.$start. '/'.$end;
		
Jerome Mariette's avatar
Jerome Mariette committed
609
610
611
612
613
614
615
		//do nothing
		if( $end == '1' ) { return '' ;
		//don't display << nor <
		} elseif($start == '1')	{ $go_back = '';
		//don't display > nor >>
		} elseif($start == $end) { $go_ahead = '';
		//display both		
616
617
618
619
		}		
		$content = '<div align="right">'.$go_back .' '. $current_pos .' '. $go_ahead .'</div>' ;
		return $content;
	}	
Jerome Mariette's avatar
Jerome Mariette committed
620
621
622
623
624
625
626
627
		
}

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']);
}

?>