class.tx_nG6_pi1.php 34.9 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
31
32
<?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');

class tx_nG6_pi1 extends tslib_pibase {
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
33
	
Jerome Mariette's avatar
Jerome Mariette committed
34
35
36
37
38
39
40
41
42
43
44
45
	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
46
		
Jerome Mariette's avatar
Jerome Mariette committed
47
48
49
		if (strstr($this->cObj->currentRecord,'tt_content'))	{
			$conf['pidList'] = $this->cObj->data['pages'];
		}
50
51
52
		$this->conf=$conf;		// Setting the TypoScript passed to this function in $this->conf		
		$this->internal['results_at_a_time'] = $conf["results_at_a_time"];
		
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
53
54
55
		$this->pi_setPiVarDefaults();
		$this->pi_USER_INT_obj=1;	// 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_loadLL();		// Loading the LOCAL_LANG values
56
		
Jerome Mariette's avatar
Jerome Mariette committed
57
		if ($this->userIsAuthorized()) {
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
58
			switch((string)$this->conf['view'])	{
Jerome Mariette's avatar
Jerome Mariette committed
59
60
				case 'project':
					if ($this->piVars['analyze_id']) {
Jerome Mariette's avatar
Jerome Mariette committed
61
						return $this->pi_wrapInBaseClass($this->pi_analyze_view('analyze'));
Jerome Mariette's avatar
Jerome Mariette committed
62
					} elseif ($this->piVars['project_id'] && $this->piVars['run_id']) {
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
63
						return $this->pi_wrapInBaseClass($this->pi_run_view());
Jerome Mariette's avatar
Jerome Mariette committed
64
					} else {
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
65
						return $this->pi_wrapInBaseClass($this->pi_project_view());
Jerome Mariette's avatar
Jerome Mariette committed
66
67
68
69
					}
					break;
				case 'run':
					if ($this->piVars['analyze_id']) {
Jerome Mariette's avatar
Jerome Mariette committed
70
						return $this->pi_wrapInBaseClass($this->pi_analyze_view('analyze'));
Jerome Mariette's avatar
Jerome Mariette committed
71
					} else {
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
72
						return $this->pi_wrapInBaseClass($this->pi_run_view());
Jerome Mariette's avatar
Jerome Mariette committed
73
74
75
					}
				break;
				default:
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
76
					return $this->pi_wrapInBaseClass($this->pi_project_view());
Jerome Mariette's avatar
Jerome Mariette committed
77
78
79
80
81
82
83
84
85
86
87
88
				break;
			}
		} else {
			return $this->pi_wrapInBaseClass($this->getFieldHeader('not_authorized'));
		}
	}
		
	/**
	 * Shows a list of database entries
	 *
	 * @return	HTML list of table entries
	 */
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
89
90
91
	function pi_project_view()	{

		if ($this->piVars['project_id'])	{ // If a single element should be displayed
Jerome Mariette's avatar
Jerome Mariette committed
92
93
94
95
96
97
98
99
100
101
			$queryParts = array(
				'SELECT' => '*',
				'FROM' => 'tx_nG6_project',
				'WHERE' => 'tx_nG6_project.uid = '.$this->piVars['project_id'],
				'GROUPBY' => '',
				'ORDERBY' => '',
				'LIMIT' => ''
			);
			$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
			$this->internal['currentRow'] = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res);
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
102
			return $this->pi_project_single_view();
Jerome Mariette's avatar
Jerome Mariette committed
103
		} else {
104
105
106
107
108
109
110
111
112
113
		
			if (isset($this->piVars['project_page']))	//project position 
			{
				$current_page = intval($this->internal['results_at_a_time']) * (intval($this->piVars['project_page']) -1);
				$limit = "$current_page".",". $this->internal['results_at_a_time'] ;
			}
			else
				$limit = '0,'.$this->internal['results_at_a_time'] ; 		
		
		
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
114
115
			// If the user is not logged on display demonstration project
			if (!$GLOBALS['TSFE']->loginUser) { 
Jerome Mariette's avatar
Jerome Mariette committed
116
				$where = 'fe_group=0';
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
117
			} else {
Jerome Mariette's avatar
Jerome Mariette committed
118
				$where = 'fe_group IN ('.$this->getCurrentUserGroups().')';	
Jerome Mariette's avatar
Jerome Mariette committed
119
			}
Jerome Mariette's avatar
Jerome Mariette committed
120
121
122
123
124
125
			$queryParts = array(
				'SELECT' => '*',
				'FROM' => 'tx_nG6_project',
				'WHERE' => $where,
				'GROUPBY' => '',
				'ORDERBY' => '',
126
				'LIMIT' => $limit
Jerome Mariette's avatar
Jerome Mariette committed
127
128
			);
			$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
129
130
			// If there is at least one result
			if ($GLOBALS['TYPO3_DB']->sql_num_rows($res) > 0) {
131
				//request total in DB
Jerome Mariette's avatar
Jerome Mariette committed
132
133
134
135
136
137
138
139
140
141
142
143
144
145
				$queryPartsc = array(
					'SELECT' => $queryParts['SELECT'],
					'FROM' => $queryParts['FROM'],
					'WHERE' => $queryParts['WHERE'],
					'GROUPBY' => '',
					'ORDERBY' => '',
					'LIMIT' => ''
				);
				$resc = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryPartsc);
	         	$total_count = $GLOBALS['TYPO3_DB']->sql_num_rows($resc);
		         //generate HTML   
	         	$project_list= $this->pi_project_list_view($res);
	         	$nav_links = 	$this->pi_navigation_link_view('project_page', $this->piVars['project_page'], $total_count);
         		return $project_list ."\n". $nav_links;			
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
146
			} else { // If no results
Jerome Mariette's avatar
Jerome Mariette committed
147
				return $this->getFieldHeader('no_raw');
148
			}
Jerome Mariette's avatar
Jerome Mariette committed
149
150
151
152
153
		}
	}

	/**
	 * Creates a list from a database query
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
154
	 * 
Jerome Mariette's avatar
Jerome Mariette committed
155
156
157
158
	 * @param	ressource	$res: A database result ressource
	 * @return	A HTML list if result items
	 */
	function pi_project_list_view($res)	{
159
		$nb_project = 0;
Jerome Mariette's avatar
Jerome Mariette committed
160
161
162
163
164
		$content = '<table'.$this->pi_classParam('listrow').'>
						<tr>
							<th>'.$this->getFieldHeader('project_name').'</th>
							<th>'.$this->getFieldHeader('description').'</th>
						</tr>';
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
		while($this->internal['currentRow'] = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res))	{
			if ($this->internal['currentRow']['hidden'] == 0) { // If it's not a hidden project
				$content .= '<tr>
					<td>'.$this->getFieldContent('name', array('project_id'=>$this->internal['currentRow']['uid'])).'</td>
					<td>'.$this->getFieldContent('description').'</td>
					</tr>';
				$nb_project++;
			} else {
				$user_groups = t3lib_div::intExplode(',',$this->getCurrentUserGroups());
				$user_allowed = false;
			    foreach($this->getSuperGroupsOf($this->internal['currentRow']['fe_group']) AS $valeur) {
					if (in_array($valeur, $user_groups)) {
						$user_allowed = true;
						$nb_project++;
					}
			    }
			    if ($user_allowed) {
					$content .= '<tr>
						<td '.$this->pi_classParam('hidden').' >'.$this->getFieldContent('name', array('project_id'=>$this->internal['currentRow']['uid'])).'</td>
						<td '.$this->pi_classParam('hidden').' >'.$this->getFieldContent('description').'</td>
						</tr>';
			    }
			}
		}
		if ($nb_project > 0) {
			return $content .= '</table>';
		} else {
			return $this->getFieldHeader('no_raw');
Jerome Mariette's avatar
Jerome Mariette committed
193
194
195
196
197
		}
	}

	/**
	 * Display a single item from the database
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
198
	 * 
Jerome Mariette's avatar
Jerome Mariette committed
199
200
	 * @return	HTML of a single database entry
	 */
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
201
	function pi_project_single_view()	{
Jerome Mariette's avatar
Jerome Mariette committed
202
203
204
		$content = '<div'.$this->pi_classParam('singleView').'>
			         <h2>Projet '.$this->internal['currentRow']['name'].' :</h2>
				     <p><strong>'.$this->getFieldContent('description').'</strong></p>
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
205
206
		             </div>'.$this->pi_getEditPanel().$this->pi_run_view($content, $this->conf, $this->internal['currentRow']['uid']);
		$content .= $this->pi_analyze_view('project');
Jerome Mariette's avatar
Jerome Mariette committed
207
208
		return $content;
	}
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
209

Jerome Mariette's avatar
Jerome Mariette committed
210
211
212
213
214
	/**
	 * Shows a list of database entries
	 *
	 * @return	HTML list of table entries
	 */
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
215
216
    function pi_run_view() {
		if ($this->piVars['run_id'])    {       // If a single element should be displayed:
217
		
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
218
219
			$queryParts = array(
				'SELECT' => 'tx_nG6_run.uid AS run_id, tx_nG6_run.name AS name, tx_nG6_project.name AS project_name,' .
Jerome Mariette's avatar
Jerome Mariette committed
220
							'tx_nG6_run.date AS date, tx_nG6_run.species AS run_species, tx_nG6_run.data_nature AS run_data_nature,' .
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
221
222
							'tx_nG6_run.type AS run_type, tx_nG6_run.nb_sequences AS run_nb_sequences, tx_nG6_run.full_seq_size AS run_full_seq_size,' .
							'tx_nG6_run.description AS run_description, tx_nG6_run.sequencer AS run_sequencer,' .
223
224
							'tx_nG6_run.directory AS run_directory, tx_nG6_run.hidden AS run_hidden, tx_nG6_project.name AS project_name,' .
							'tx_nG6_project.fe_group AS project_fe_group',
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
225
226
227
228
229
230
				'FROM' => 'tx_nG6_run INNER JOIN (tx_nG6_project_run INNER JOIN tx_nG6_project ON tx_nG6_project_run.project_id=tx_nG6_project.uid)' .
						  'ON tx_nG6_run.uid=tx_nG6_project_run.run_id',
                'WHERE' => 'tx_nG6_run.uid='.$this->piVars['run_id'],
                'GROUPBY' => '',
                'ORDERBY' => '',
                'LIMIT' => ''
231
232
233
234
            );             
         
         $res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
         $this->internal['currentRow'] = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res);
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
235
			return $this->pi_run_single_view();
236
237
238
239
240
241
242
243
244
245
		} else {        
		
			if (isset($this->piVars['run_page']))	//run position 
			{
				$current_page = intval($this->internal['results_at_a_time']) * (intval($this->piVars['run_page']) -1);
				$limit = "$current_page".",". $this->internal['results_at_a_time'] ;
			}
			else
				$limit = '0,'.$this->internal['results_at_a_time'] ; 
		   
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
246
			// First off, build the rigth sql request
Jerome Mariette's avatar
Jerome Mariette committed
247
			if ($this->piVars['project_id']) {
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
248
249
				$where = 'tx_nG6_project_run.project_id='.$this->piVars['project_id'];

Jerome Mariette's avatar
Jerome Mariette committed
250
251
			} else {
				if (!$GLOBALS['TSFE']->loginUser) { // If the user is not logged on
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
252
					$where = 'project_id IN ('.$GLOBALS['TYPO3_DB']->SELECTquery('uid', 'tx_nG6_project', 'fe_group=0').')';
253
254
            } else {
            	$where = 'project_id IN ('.$GLOBALS['TYPO3_DB']->SELECTquery('uid', 'tx_nG6_project', 'fe_group IN('.$this->getCurrentUserGroups().')').')';
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
255
            }
256
257
         }
         // Then execute it
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
258
259
			$queryParts = array(
				'SELECT' => 'tx_nG6_run.uid AS run_id, tx_nG6_run.name AS name, tx_nG6_project.name AS project_name,' .
Jerome Mariette's avatar
Jerome Mariette committed
260
							'tx_nG6_run.date AS date, tx_nG6_run.species AS run_species, tx_nG6_run.data_nature AS run_data_nature,' .
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
261
							'tx_nG6_run.type AS run_type, tx_nG6_run.nb_sequences AS run_nb_sequences, tx_nG6_run.full_seq_size AS run_full_seq_size,' .
262
263
							'tx_nG6_run.description AS run_description, tx_nG6_run.sequencer AS run_sequencer, tx_nG6_run.hidden AS run_hidden,' .
							'tx_nG6_project.name AS project_name, tx_nG6_project.fe_group AS project_fe_group',
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
264
265
266
267
				'FROM' => 'tx_nG6_run INNER JOIN (tx_nG6_project_run INNER JOIN tx_nG6_project ON tx_nG6_project_run.project_id=tx_nG6_project.uid)' .
						  'ON tx_nG6_run.uid=tx_nG6_project_run.run_id',
                'WHERE' => $where,
                'GROUPBY' => '',
Jerome Mariette's avatar
Jerome Mariette committed
268
                'ORDERBY' => 'tx_nG6_run.date DESC',
269
                'LIMIT' => $limit
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
270
            );
271
272
273
         $res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);			
         
         if ($GLOBALS['TYPO3_DB']->sql_num_rows($res) > 0) { // There is some results to display
Jerome Mariette's avatar
Jerome Mariette committed
274
275
276
277
278
279
280
281
282
283
284
			//request total in DB
			$queryPartsc = array(
				'SELECT' => $queryParts['SELECT'],
				'FROM' => $queryParts['FROM'],
				'WHERE' => $queryParts['WHERE'],
                'GROUPBY' => '',
                'ORDERBY' => '',
                'LIMIT' => ''
            );
			$resc = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryPartsc);
         	$total_count = $GLOBALS['TYPO3_DB']->sql_num_rows($resc);
285
286
	         //generate HTML   
         	$run_list= $this->pi_run_list_view($res);
Jerome Mariette's avatar
Jerome Mariette committed
287
288
         	$nav_links = 	$this->pi_navigation_link_view('run_page', $this->piVars['run_page'], $total_count);
     		return $run_list ."\n". $nav_links;
289
290
291
         } else { // no results
             return $this->getFieldHeader('no_raw');
         }
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
292
293
294
       }
    }

Jerome Mariette's avatar
Jerome Mariette committed
295
296
297
298
299
300
	/**
	 * Creates a list from a database query
	 *
	 * @param	ressource	$res: A database result ressource
	 * @return	A HTML list if result items
	 */
301
	function pi_run_list_view($res)	{		
302
		$nb_run = 0;
Jerome Mariette's avatar
Jerome Mariette committed
303
304
305
306
307
		if ($this->piVars['project_id']) {
			$content = '<br /> <h3> '.$this->getFieldHeader('runs_done').'</h3> <br />';
		}
		$content .= '<table'.$this->pi_classParam('listrow').'>
						<tr>
Jerome Mariette's avatar
w3C ok    
Jerome Mariette committed
308
309
310
311
312
313
314
315
316
317
							<th>'.$this->getFieldHeader('run_name').'</th>
							<th>'.$this->getFieldHeader('project_name').'</th>
							<th>'.$this->getFieldHeader('date').'</th>
							<th>'.$this->getFieldHeader('species').'</th>
							<th>'.$this->getFieldHeader('data_nature').'</th>
							<th>'.$this->getFieldHeader('type').'</th>
							<th>'.$this->getFieldHeader('nb_sequences').'</th>
							<th>'.$this->getFieldHeader('full_seq_size').'</th>
							<th>'.$this->getFieldHeader('description').'</th>
							<th>'.$this->getFieldHeader('sequencer').'</th>
Jerome Mariette's avatar
Jerome Mariette committed
318
319
						</tr>';
		while($this->internal['currentRow'] = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res))	{
320
321
322
323
			if ($this->internal['currentRow']['run_hidden'] == 0) { // If it's not a hidden run
				$content .= '<tr>
					<td>'.$this->getFieldContent('name', array('run_id'=>$this->internal['currentRow']['run_id'], 'project_id'=>$this->piVars['project_id'])).'</td>
					<td>'.$this->getFieldContent('project_name').'</td>
Jerome Mariette's avatar
Jerome Mariette committed
324
					<td>'.$this->getFieldContent('date').'</td>
325
326
327
328
329
330
331
332
333
334
335
336
					<td>'.$this->getFieldContent('run_species').'</td>
					<td>'.$this->getFieldContent('run_data_nature').'</td>
					<td>'.$this->getFieldContent('run_type').'</td>
					<td>'.$this->getFieldContent('run_nb_sequences').'</td>
					<td>'.$this->getFieldContent('run_full_seq_size').'</td>
					<td>'.$this->getFieldContent('run_description').'</td>
					<td>'.$this->getFieldContent('run_sequencer').'</td>
					</tr>';
				$nb_run++;
			} else {
				$user_groups = t3lib_div::intExplode(',',$this->getCurrentUserGroups());
				$user_allowed = false;
337
			   foreach($this->getSuperGroupsOf($this->internal['currentRow']['project_fe_group']) AS $valeur) {
338
339
340
341
					if (in_array($valeur, $user_groups)) {
						$user_allowed = true;
						$nb_run++;
					}
342
343
			   }
			   if ($user_allowed) {
344
345
346
					$content .= '<tr>
						<td '.$this->pi_classParam('hidden').' >'.$this->getFieldContent('name', array('run_id'=>$this->internal['currentRow']['run_id'], 'project_id'=>$this->piVars['project_id'])).'</td>
						<td '.$this->pi_classParam('hidden').' >'.$this->getFieldContent('project_name').'</td>
Jerome Mariette's avatar
Jerome Mariette committed
347
						<td '.$this->pi_classParam('hidden').' >'.$this->getFieldContent('date').'</td>
348
349
350
351
352
353
354
355
						<td '.$this->pi_classParam('hidden').' >'.$this->getFieldContent('run_species').'</td>
						<td '.$this->pi_classParam('hidden').' >'.$this->getFieldContent('run_data_nature').'</td>
						<td '.$this->pi_classParam('hidden').' >'.$this->getFieldContent('run_type').'</td>
						<td '.$this->pi_classParam('hidden').' >'.$this->getFieldContent('run_nb_sequences').'</td>
						<td '.$this->pi_classParam('hidden').' >'.$this->getFieldContent('run_full_seq_size').'</td>
						<td '.$this->pi_classParam('hidden').' >'.$this->getFieldContent('run_description').'</td>
						<td '.$this->pi_classParam('hidden').' >'.$this->getFieldContent('run_sequencer').'</td>
						</tr>';
356
			   }
357
358
359
			}
		}
		if ($nb_run > 0) {
360
361
			$content .= "\n".'</table>' ; 		
			return $content;
362
363
		} else {
			return '';
Jerome Mariette's avatar
Jerome Mariette committed
364
365
366
367
368
		}
	}

	/**
	 * Display a single item from the database
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
369
370
	 * 
	 * @param	ressource	$res: A database result ressource
Jerome Mariette's avatar
Jerome Mariette committed
371
372
	 * @return	HTML of a single database entry
	 */
373
	function pi_run_single_view() {		
Jerome Mariette's avatar
Jerome Mariette committed
374
		$content = '<div'.$this->pi_classParam('singleView').'><h2>Run '.$this->internal['currentRow']['name'].' :</h2>';
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
375
		$content .= '<p><strong>'.$this->getFieldContent('run_description').'</strong></p> </div>
Jerome Mariette's avatar
Jerome Mariette committed
376
377
378
				<table'.$this->pi_classParam('listrow').'>
					<tr>
						<th align="left">'.$this->getFieldHeader('project_name').' :</th>
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
379
						<td align="left">'.$this->getFieldContent('project_name').'</td>
Jerome Mariette's avatar
Jerome Mariette committed
380
381
382
					</tr>	
					<tr>
						<th align="left">'.$this->getFieldHeader('date').' :</th>
Jerome Mariette's avatar
Jerome Mariette committed
383
						<td align="left">'.$this->getFieldContent('date').'</td>
Jerome Mariette's avatar
Jerome Mariette committed
384
385
386
					</tr>					
					<tr>
						<th align="left">'.$this->getFieldHeader('species').' :</th>
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
387
						<td align="left">'.$this->getFieldContent('run_species').'</td>
Jerome Mariette's avatar
Jerome Mariette committed
388
389
390
					</tr>
					<tr>
						<th align="left">'.$this->getFieldHeader('type').' :</th>
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
391
						<td align="left">'.$this->getFieldContent('run_type').'</td>
Jerome Mariette's avatar
Jerome Mariette committed
392
393
394
					</tr>
					<tr>
						<th align="left">'.$this->getFieldHeader('data_nature').' :</th>
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
395
						<td align="left">'.$this->getFieldContent('run_data_nature').'</td>
Jerome Mariette's avatar
Jerome Mariette committed
396
397
398
					</tr>
					<tr>
						<th align="left">'.$this->getFieldHeader('nb_sequences').' :</th>
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
399
						<td align="left">'.$this->getFieldContent('run_nb_sequences').'</td>
Jerome Mariette's avatar
Jerome Mariette committed
400
401
402
					</tr>
					<tr>
						<th align="left">'.$this->getFieldHeader('full_seq_size').' :</th>
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
403
						<td align="left">'.$this->getFieldContent('run_full_seq_size').'</td>
Jerome Mariette's avatar
Jerome Mariette committed
404
405
406
					</tr>						
					<tr>
						<th align="left">'.$this->getFieldHeader('sequencer').' :</th>
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
407
						<td align="left">'.$this->getFieldContent('run_sequencer').'</td>
Jerome Mariette's avatar
Jerome Mariette committed
408
409
410
					</tr>
					<tr>
						<th align="left">'.$this->getFieldHeader('downloads').' :</th>
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
411
						<td align="left">'.$this->get_downloads_list().'</td>
Jerome Mariette's avatar
Jerome Mariette committed
412
413
					</tr>
				</table>';
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
414
		$content .= $this->pi_analyze_view('run');
415
		
Jerome Mariette's avatar
Jerome Mariette committed
416
417
418
419
420
421
422
423
424
		return $content.$this->pi_getEditPanel();
	}
	
	/**
	 * Shows a list of database entries
	 *
	 * @param	string		$type: What kind of analyze is it : run or project
	 * 	 * @return	HTML list of table entries
	 */
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
425
	function pi_analyze_view($type)	{
426
		
Jerome Mariette's avatar
Jerome Mariette committed
427
428
429
430
431
432
433
434
435
436
437
		if ($type == 'analyze')	{	// If a single element should be displayed:
			$queryParts = array(
				'SELECT' => '*',
				'FROM' => 'tx_nG6_analyze',
				'WHERE' => 'tx_nG6_analyze.uid = '.$this->piVars['analyze_id'],
				'GROUPBY' => '',
				'ORDERBY' => '',
				'LIMIT' => ''
			);
			$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
			$this->internal['currentRow'] = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res);
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
438
			return $this->pi_analyze_single_view();
Jerome Mariette's avatar
Jerome Mariette committed
439
		} else {
440
441
442
443
444
445
446
447
448
449
		
			if (isset($this->piVars['analyze_page']))	//run position 
			{
				$current_page = intval($this->internal['results_at_a_time']) * (intval($this->piVars['analyze_page']) -1);
				$limit = "$current_page".",". $this->internal['results_at_a_time'] ;
			}
			else
				$limit = '0,'.$this->internal['results_at_a_time'] ; 	
				
		
Jerome Mariette's avatar
Jerome Mariette committed
450
451
452
			if ($type == 'run') {
				// Selects Analyzis done on this run
				$queryParts = array(
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
453
					'SELECT' => 'tx_nG6_analyze.uid AS uid, tx_nG6_analyze.name AS name, tx_nG6_analyze.description AS description,' .
454
455
456
457
458
459
460
								'tx_nG6_analyze.software AS software, tx_nG6_analyze.version AS version, tx_nG6_analyze.hidden AS hidden,' .
								'tx_nG6_project.fe_group AS project_fe_group',
					'FROM' => 'tx_nG6_analyze INNER JOIN (tx_nG6_run_analyze INNER JOIN ( tx_nG6_run INNER JOIN ( tx_nG6_project_run INNER JOIN tx_nG6_project ' .
							  'ON tx_nG6_project_run.project_id=tx_nG6_project.uid ) ' .
							  'ON tx_nG6_run.uid=tx_nG6_project_run.run_id ) ' .
							  'ON tx_nG6_run.uid=tx_nG6_run_analyze.run_id ) ' .
							  'ON tx_nG6_analyze.uid=tx_nG6_run_analyze.analyze_id ',
Jerome Mariette's avatar
Jerome Mariette committed
461
462
					'WHERE' => 'tx_nG6_run_analyze.run_id = '.$this->piVars['run_id'],
					'GROUPBY' => '',
Jerome Mariette's avatar
Jerome Mariette committed
463
					'ORDERBY' => 'tx_nG6_analyze.name',
464
					'LIMIT' => $limit
Jerome Mariette's avatar
Jerome Mariette committed
465
466
467
468
				);
			} elseif ($type == 'project') {
				// Selects Analyzis done on this project
				$queryParts = array(
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
469
					'SELECT' => 'tx_nG6_analyze.uid AS uid, tx_nG6_analyze.name AS name, tx_nG6_analyze.description AS description,' .
470
471
472
473
								'tx_nG6_analyze.software AS software, tx_nG6_analyze.version AS version, tx_nG6_analyze.hidden AS hidden,' .
								'tx_nG6_project.fe_group AS project_fe_group',
					'FROM' => 'tx_nG6_analyze INNER JOIN ( tx_nG6_project_analyze INNER JOIN tx_nG6_project ON tx_nG6_project.uid=tx_nG6_project_analyze.project_id ) ' .
							  'ON tx_nG6_analyze.uid=tx_nG6_project_analyze.analyze_id',
Jerome Mariette's avatar
Jerome Mariette committed
474
475
					'WHERE' => 'tx_nG6_project_analyze.project_id = '.$this->piVars['project_id'],
					'GROUPBY' => '',
Jerome Mariette's avatar
Jerome Mariette committed
476
					'ORDERBY' => 'tx_nG6_analyze.name',
477
					'LIMIT' => $limit
Jerome Mariette's avatar
Jerome Mariette committed
478
				);
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
479
			}	
480
			$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);		
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
481
			$content='';
482
			if ($GLOBALS['TYPO3_DB']->sql_num_rows($res) > 0) {	
Jerome Mariette's avatar
Jerome Mariette committed
483
484
485
486
487
488
489
490
491
492
493
494
				//request total in DB
				$queryPartsc = array(
					'SELECT' => $queryParts['SELECT'],
					'FROM' => $queryParts['FROM'],
					'WHERE' => $queryParts['WHERE'],
	                'GROUPBY' => '',
	                'ORDERBY' => '',
	                'LIMIT' => ''
	            );
				$resc = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryPartsc);
	         	$total_count = $GLOBALS['TYPO3_DB']->sql_num_rows($resc);
		         //generate HTML   
495
496
497
				$analyze_list=$this->pi_analyze_list_view($res , $total_count);
				$nav_links = $this->pi_navigation_link_view('analyze_page', $this->piVars['analyze_page'], $total_count);
				$content.= $analyze_list ."\n".$nav_links;
Jerome Mariette's avatar
Jerome Mariette committed
498
			}
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
499
			return $content;
Jerome Mariette's avatar
Jerome Mariette committed
500
501
502
503
504
505
506
507
508
509
		}
	}

	/**
	 * Creates a list from a database query
	 *
	 * @param	ressource	$res: A database result ressource
	 * @return	A HTML list if result items
	 */
	function pi_analyze_list_view($res)	{
510
		$nb_analyse = 0;
Jerome Mariette's avatar
Jerome Mariette committed
511
512
513
		$content.='<br /> <h3> '.$this->getFieldHeader('analyzes_done').'</h3> <br />
				<table'.$this->pi_classParam('listrow').'>
					<tr>
Jerome Mariette's avatar
w3C ok    
Jerome Mariette committed
514
515
516
517
						<th>'.$this->getFieldHeader('name').'</th>
						<th>'.$this->getFieldHeader('description').'</th>
						<th>'.$this->getFieldHeader('software').'</th>
						<th>'.$this->getFieldHeader('version').'</th>
Jerome Mariette's avatar
Jerome Mariette committed
518
519
					</tr>';
		while($this->internal['currentRow'] = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res))	{
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
			if ($this->internal['currentRow']['hidden'] == 0) { // If it's not a hidden project
				$content .= '<tr>
					<td>'.$this->getFieldContent('name', array('analyze_id'=>$this->internal['currentRow']['uid'], 'run_id'=>$this->piVars['run_id'], 'project_id'=>$this->piVars['project_id'])).'</td>
					<td>'.$this->getFieldContent('description').'</td>
					<td>'.$this->getFieldContent('software').'</td>
					<td>'.$this->getFieldContent('version').'</td>
					</tr>';
				$nb_analyse++;
			} else {
				$user_groups = t3lib_div::intExplode(',',$this->getCurrentUserGroups());
				$user_allowed = false;
			    foreach($this->getSuperGroupsOf($this->internal['currentRow']['project_fe_group']) AS $valeur) {
					if (in_array($valeur, $user_groups)) {
						$user_allowed = true;
						$nb_analyse++;
					}
			    }
			    if ($user_allowed) {
					$content .= '<tr>
						<td '.$this->pi_classParam('hidden').' >'.$this->getFieldContent('name', array('analyze_id'=>$this->internal['currentRow']['uid'], 'run_id'=>$this->piVars['run_id'], 'project_id'=>$this->piVars['project_id'])).'</td>
						<td '.$this->pi_classParam('hidden').' >'.$this->getFieldContent('description').'</td>
						<td '.$this->pi_classParam('hidden').' >'.$this->getFieldContent('software').'</td>
						<td '.$this->pi_classParam('hidden').' >'.$this->getFieldContent('version').'</td>
						</tr>';
			    }
			}
Jerome Mariette's avatar
Jerome Mariette committed
546
		}
547
548
549
		if ($nb_analyse > 0) {			
			$content .= "\n".'</table>' ;						
			return $content ;
550
551
552
		} else {
			return '';
		}		
Jerome Mariette's avatar
Jerome Mariette committed
553
554
	}

Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
555

Jerome Mariette's avatar
Jerome Mariette committed
556
557
558
559
560
	/**
	 * Display a single item from the database
	 *
	 * @return	HTML of a single database entry
	 */
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
561
	function pi_analyze_single_view() {
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590

		// add the jquery libs + the tree plugins and its css
		$GLOBALS['TSFE']->additionalHeaderData[$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($this->extKey).'res/js/jquery.url.packed.js"></script>
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($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"/>';

		// Sets the page content
		$content = '<script type="text/javascript" class="source">
						$(function () { 
						    $("#img_dialog").dialog({
							    autoOpen: false,
						        width: 850,
						        bgiframe: true,
						        resizable: false,
						        position: "center",
							    modal: true,
						        overlay: {
						            backgroundColor: "#000",
						            opacity: 0.5
						        }
						    });
591
592
593
594
595
596
597
598
599
600
                            $(".tx-nG6-pi1-imglink").click(function() {
                               	jQuery.url.setUrl($(this).attr("href"));
                               	$("#img_dialog").dialog("option", "title", "nG6 - '.$this->internal['currentRow']['name'].'");
                               	if (jQuery.url.param("file")) {
                                       	$("#img_dialog").html(\'<img src="\'+jQuery.url.param("file")+\'"/>\').dialog("open");
                               	} else {
                                       	$("#img_dialog").html(\'<img src="\'+$(this).attr("href")+\'"/>\').dialog("open");
                               	}
                               	return false;
                            });
601
602
603
604
605
606
607
						});
					</script>  ';


		$content .= '<div id="img_dialog" title=""></div>';

		$content .= '<div'.$this->pi_classParam('singleView').'><h2>Analyse '.$this->internal['currentRow']['name'].' : <span>'.$this->getFieldContent('description').'</span></h2></div>';
Jerome Mariette's avatar
Jerome Mariette committed
608
		if (file_exists($this->conf['data'].$this->internal['currentRow']['directory'].'/index.html' )) {
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
609
			$fp = fopen((string)$this->conf['data'].$this->internal['currentRow']['directory'].'/index.html',"r"); //lecture du fichier
Jerome Mariette's avatar
Jerome Mariette committed
610
611
612
613
			while (!feof($fp)) { //on parcourt toutes les lignes
				$content .= fgets($fp, 4096); // lecture du contenu de la ligne
			}
		}
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
614
		else {
Jerome Mariette's avatar
Jerome Mariette committed
615
			$content .= $this->getFieldHeader('not_synchro');
Jerome Mariette's avatar
Jerome Mariette committed
616
617
618
619
620
621
622
623
624
625
626
627
628
		}
		return $content;
	}
	
	/**
	 * Returns the content of a given field
	 *
	 * @param	string		$fN: name of table field
	 * @return	Value of the field
	 */
	function getFieldContent($fN, $mergeArr=array())	{
		switch($fN) {
			case 'uid':
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
629
				return $this->pi_list_linkSingle($this->internal['currentRow'][$fN],$this->internal['currentRow']['uid'],1, $mergeArr);	
Jerome Mariette's avatar
Jerome Mariette committed
630
631
			break;
			case 'name':
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
632
				return $this->pi_list_linkSingle($this->internal['currentRow'][$fN],$this->internal['currentRow']['uid'],1, $mergeArr);	
Jerome Mariette's avatar
Jerome Mariette committed
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
			break;
			case 'date':
					// %A %e. %B %Y
				return strftime('%d-%m-%y',$this->internal['currentRow']['date']);
			break;			
			default:
				return $this->internal['currentRow'][$fN];
			break;
		}
	}
	/**
	 * Returns the label for a fieldname from local language array
	 *
	 * @param	[type]		$fN: ...
	 * @return	[type]		...
	 */
	function getFieldHeader($fN)	{
		switch($fN) {
			
			default:
				return $this->pi_getLL('listFieldHeader_'.$fN,'['.$fN.']');
			break;
		}
	}
	
	/**
	 * Returns a sorting link for a column header
	 *
	 * @param	string		$fN: Fieldname
	 * @return	The fieldlabel wrapped in link that contains sorting vars
	 */
	function getFieldHeader_sortLink($fN)	{
		return $this->pi_linkTP_keepPIvars($this->getFieldHeader($fN),array('sort'=>$fN.':'.($this->internal['descFlag']?0:1)));
	}
	
	/**
	 * 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;
	}
	
	/**
	 * Display a list of downloadable file
	 *
	 * @return	HTML of a list of downlabale links
	 */
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
704
705
	function get_downloads_list() {
		$directory = (string)$this->conf['data'].$this->internal['currentRow']['run_directory'];
Jerome Mariette's avatar
Jerome Mariette committed
706
707
708
709
710
711
		try {
			if (!is_dir($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>';
			while($entry = @readdir($my_directory)) {
				if(!is_dir($directory.'/'.$entry)&& $entry != '.' && $entry != '..' && !$this->endsWith($entry, ".cfg")) {
Jerome Mariette's avatar
Jerome Mariette committed
712
					$link = 'fileadmin/'.$this->internal['currentRow']['run_directory'].'/'.$entry;
Jerome Mariette's avatar
Jerome Mariette committed
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
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
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
					$download .= '<li><a href="'.$link.'" target="_blank">'.$entry.'</a></li>';
				}
			}
			$download .= '</ul>';		
			closedir($my_directory);
			return $download;
		}
		catch (Exception $e) {
			return $this->getFieldHeader('not_synchro');
		}
	}
	
	// return true if $str ends with $sub
	function endsWith( $str, $sub ) {
		return ( substr( $str, strlen( $str ) - strlen( $sub ) ) == $sub );
	}
	
	function getCurrentUserGroups() {
		$tab_groups = array();
		$this->getSubGroups($GLOBALS['TSFE']->fe_user->user['usergroup'], '', $tab_groups);
		$groups = '';
		foreach($tab_groups as $valeur) { $groups .= $valeur.','; }
		return substr($groups, 0, -1);	
	}

	/**
	 * Fetches subgroups of groups. Function is called recursively for each subgroup.
	 * Function was previously copied from t3lib_userAuthGroup->fetchGroups and has been slightly modified.
	 *
	 * @param	string		Commalist of fe_groups uid numbers
	 * @param	string		List of already processed fe_groups-uids so the function will not fall into a eternal recursion.
	 * @return	array
	 * @access private
	 */
	function getSubGroups($grList, $idList='', &$groups)	{

			// Fetching records of the groups in $grList (which are not blocked by lockedToDomain either):
		$lockToDomain_SQL = ' AND (lockToDomain=\'\' OR lockToDomain IS NULL OR lockToDomain=\''.$this->authInfo['HTTP_HOST'].'\')';
		if (!$this->authInfo['showHiddenRecords'])	$hiddenP = 'AND hidden=0 ';
		$res = $GLOBALS['TYPO3_DB']->exec_SELECTquery('uid,subgroup', 'fe_groups', 'deleted=0 '.$hiddenP.' AND uid IN ('.$grList.')'.$lockToDomain_SQL);

		$groupRows = array();	// Internal group record storage

			// The groups array is filled
		while ($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res))	{
			if(!in_array($row['uid'], $groups))	{ $groups[] = $row['uid']; }
			$groupRows[$row['uid']] = $row;
		}

			// Traversing records in the correct order
		$include_staticArr = t3lib_div::intExplode(',', $grList);
		foreach($include_staticArr as $uid)	{	// traversing list

				// Get row:
			$row=$groupRows[$uid];
			if (is_array($row) && !t3lib_div::inList($idList,$uid))	{	// Must be an array and $uid should not be in the idList, because then it is somewhere previously in the grouplist

					// Include sub groups
				if (trim($row['subgroup']))	{
					$theList = implode(',',t3lib_div::intExplode(',',$row['subgroup']));	// Make integer list
					$this->getSubGroups($theList, $idList.','.$uid, $groups);		// Call recursively, pass along list of already processed groups so they are not recursed again.
				}
			}
		}
	}
	
	function userIsAuthorized () {
		if ($this->piVars['project_id']) {
			$queryParts = array(
				'SELECT' => 'fe_group',
				'FROM' => 'tx_nG6_project',
				'WHERE' => 'uid='.$this->piVars['project_id'],
				'GROUPBY' => '',
				'ORDERBY' => '',
				'LIMIT' => ''
			);
			$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
			$val = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res);
			$authorized_group = $val['fe_group'];
		} elseif ($this->piVars['run_id']) {
			$queryParts = array(
				'SELECT' => 'project_id',
				'FROM' => 'tx_nG6_project_run',
				'WHERE' => 'run_id='.$this->piVars['run_id'],
				'GROUPBY' => '',
				'ORDERBY' => '',
				'LIMIT' => ''
			);
			$res1 = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
			$val = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res1);
			$queryParts = array(
				'SELECT' => 'fe_group',
				'FROM' => 'tx_nG6_project',
				'WHERE' => 'uid='.$val['project_id'],
				'GROUPBY' => '',
				'ORDERBY' => '',
				'LIMIT' => ''
			);
			$res2 = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
			$val = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res2);
			$authorized_group = $val['fe_group'];
		} else {
			return true;
		}
		if (!$GLOBALS['TSFE']->loginUser) { // If the user is not logged on
			return $authorized_group == 0;
		} else {
			return in_array($authorized_group, split(",", $this->getCurrentUserGroups()));
		}
	}
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
	
	function getSuperGroupsOf ($group) {
		// First get the super group of the given group
		$queryParts = array(
			'SELECT' => 'uid, subgroup',
			'FROM' => 'fe_groups',
			'WHERE' => '',
			'GROUPBY' => '',
			'ORDERBY' => '',
			'LIMIT' => ''
		);
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
		$reslist = array();
		$i = 0;
		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res))	{
			if (in_array($group, t3lib_div::intExplode(',',$row['subgroup']))) {
				$reslist[$i] = $row['uid'];
				$i++;
			}
		}
		return $reslist;
	}
	
846
847
848
849
850
851
852
853
854
855
856
857
858
859
	/**
	 * Display links for navigation in run lists or analyse lists. Called only if $end>1
	 *
	 * @param	$name		name of the variable set in GET: run_page or analyze_page
	 * @param	$start	current page number
	 * @param	$maxline	current total number of rows
	 *
	 * @return	HTML navigation links
	 */
	function pi_navigation_link_view($name, $start, $total_count) 
	{  
		$start = intval($start);		
		
		//max page number
Jerome Mariette's avatar
Jerome Mariette committed
860
		$end = $total_count/$this->internal['results_at_a_time'] ;
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
		$end = ceil($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;
		
		if( $end == '1' )	{			//do nothing
			return '' ;
		}		
		elseif($start == '1')	{		//don't display << nor <
			$go_back = '';
		}
		elseif($start == $end)	{	//don't display > nor >>
			$go_ahead = '';		
		}
		else 		{	//display both
		}		
		$content = '<div align="right">'.$go_back .' '. $current_pos .' '. $go_ahead .'</div>' ;
		return $content;
	}	
889
890
	
	
Jerome Mariette's avatar
Jerome Mariette committed
891
892
893
894
895
896
897
898
899
900
		
}



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']);
}

?>