class.tx_nG6_pi1.php 35.9 KB
Newer Older
Celine Noirot's avatar
Celine Noirot committed
1

Jerome Mariette's avatar
Jerome Mariette committed
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
<?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
34
	
Jerome Mariette's avatar
Jerome Mariette committed
35
36
37
38
39
40
41
42
43
44
45
46
	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
47
		
Jerome Mariette's avatar
Jerome Mariette committed
48
49
50
		if (strstr($this->cObj->currentRecord,'tt_content'))	{
			$conf['pidList'] = $this->cObj->data['pages'];
		}
51
52
53
		$this->conf=$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
54
55
56
		$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
57
		
Jerome Mariette's avatar
Jerome Mariette committed
58
59
60
61
62
		$piFlexForm = $this->cObj->data['pi_flexform'];
		print_r($piFlexForm);
		
		
		
Jerome Mariette's avatar
Jerome Mariette committed
63
		if ($this->userIsAuthorized()) {
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
64
			switch((string)$this->conf['view'])	{
Jerome Mariette's avatar
Jerome Mariette committed
65
66
				case 'project':
					if ($this->piVars['analyze_id']) {
Jerome Mariette's avatar
Jerome Mariette committed
67
						return $this->pi_wrapInBaseClass($this->pi_analyze_view('analyze'));
Jerome Mariette's avatar
Jerome Mariette committed
68
					} elseif ($this->piVars['project_id'] && $this->piVars['run_id']) {
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
69
						return $this->pi_wrapInBaseClass($this->pi_run_view());
Jerome Mariette's avatar
Jerome Mariette committed
70
					} else {
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
71
						return $this->pi_wrapInBaseClass($this->pi_project_view());
Jerome Mariette's avatar
Jerome Mariette committed
72
73
74
75
					}
					break;
				case 'run':
					if ($this->piVars['analyze_id']) {
Jerome Mariette's avatar
Jerome Mariette committed
76
						return $this->pi_wrapInBaseClass($this->pi_analyze_view('analyze'));
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_run_view());
Jerome Mariette's avatar
Jerome Mariette committed
79
80
81
					}
				break;
				default:
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
82
					return $this->pi_wrapInBaseClass($this->pi_project_view());
Jerome Mariette's avatar
Jerome Mariette committed
83
84
85
86
87
88
89
90
91
92
93
94
				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
95
96
97
	function pi_project_view()	{

		if ($this->piVars['project_id'])	{ // If a single element should be displayed
Jerome Mariette's avatar
Jerome Mariette committed
98
99
100
101
102
103
104
105
106
107
			$queryParts = array(
				'SELECT' => '*',
				'FROM' => 'tx_nG6_project',
				'WHERE' => 'tx_nG6_project.uid = '.$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
108
			return $this->pi_project_single_view();
Jerome Mariette's avatar
Jerome Mariette committed
109
		} else {
110
111
112
113
114
115
116
117
118
119
		
			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
120
121
			// If the user is not logged on display demonstration project
			if (!$GLOBALS['TSFE']->loginUser) { 
Jerome Mariette's avatar
Jerome Mariette committed
122
				$where = 'fe_group=0';
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
123
			} else {
Jerome Mariette's avatar
Jerome Mariette committed
124
				$where = 'fe_group IN ('.$this->getCurrentUserGroups().')';	
Jerome Mariette's avatar
Jerome Mariette committed
125
			}
Jerome Mariette's avatar
Jerome Mariette committed
126
127
128
129
130
131
			$queryParts = array(
				'SELECT' => '*',
				'FROM' => 'tx_nG6_project',
				'WHERE' => $where,
				'GROUPBY' => '',
				'ORDERBY' => '',
132
				'LIMIT' => $limit
Jerome Mariette's avatar
Jerome Mariette committed
133
134
			);
			$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
135
136
			// If there is at least one result
			if ($GLOBALS['TYPO3_DB']->sql_num_rows($res) > 0) {
137
				//request total in DB
Jerome Mariette's avatar
Jerome Mariette committed
138
139
140
141
142
143
144
145
146
147
148
149
150
151
				$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
152
			} else { // If no results
Jerome Mariette's avatar
Jerome Mariette committed
153
				return $this->getFieldHeader('no_raw');
154
			}
Jerome Mariette's avatar
Jerome Mariette committed
155
156
157
158
159
		}
	}

	/**
	 * Creates a list from a database query
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
160
	 * 
Jerome Mariette's avatar
Jerome Mariette committed
161
162
163
164
	 * @param	ressource	$res: A database result ressource
	 * @return	A HTML list if result items
	 */
	function pi_project_list_view($res)	{
165
		$nb_project = 0;
Jerome Mariette's avatar
Jerome Mariette committed
166
167
168
169
170
		$content = '<table'.$this->pi_classParam('listrow').'>
						<tr>
							<th>'.$this->getFieldHeader('project_name').'</th>
							<th>'.$this->getFieldHeader('description').'</th>
						</tr>';
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
		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
199
200
201
202
203
		}
	}

	/**
	 * Display a single item from the database
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
204
	 * 
Jerome Mariette's avatar
Jerome Mariette committed
205
206
	 * @return	HTML of a single database entry
	 */
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
207
	function pi_project_single_view()	{
Jerome Mariette's avatar
Jerome Mariette committed
208
209
210
		$content = '<div'.$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
211
212
		             </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
213
214
		return $content;
	}
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
215

Jerome Mariette's avatar
Jerome Mariette committed
216
217
218
219
220
	/**
	 * Shows a list of database entries
	 *
	 * @return	HTML list of table entries
	 */
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
221
222
    function pi_run_view() {
		if ($this->piVars['run_id'])    {       // If a single element should be displayed:
223
		
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
224
225
			$queryParts = array(
				'SELECT' => 'tx_nG6_run.uid AS run_id, tx_nG6_run.name AS name, tx_nG6_project.name AS project_name,' .
Jerome Mariette's avatar
Jerome Mariette committed
226
							'tx_nG6_run.date AS date, tx_nG6_run.species AS run_species, tx_nG6_run.data_nature AS run_data_nature,' .
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
227
228
							'tx_nG6_run.type AS run_type, tx_nG6_run.nb_sequences AS run_nb_sequences, tx_nG6_run.full_seq_size AS run_full_seq_size,' .
							'tx_nG6_run.description AS run_description, tx_nG6_run.sequencer AS run_sequencer,' .
229
230
							'tx_nG6_run.directory AS run_directory, tx_nG6_run.hidden AS run_hidden, tx_nG6_project.name AS project_name,' .
							'tx_nG6_project.fe_group AS project_fe_group',
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
231
232
233
234
235
236
				'FROM' => 'tx_nG6_run INNER JOIN (tx_nG6_project_run INNER JOIN tx_nG6_project ON tx_nG6_project_run.project_id=tx_nG6_project.uid)' .
						  'ON tx_nG6_run.uid=tx_nG6_project_run.run_id',
                'WHERE' => 'tx_nG6_run.uid='.$this->piVars['run_id'],
                'GROUPBY' => '',
                'ORDERBY' => '',
                'LIMIT' => ''
237
238
239
240
            );             
         
         $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
241
			return $this->pi_run_single_view();
242
243
244
245
246
247
248
249
250
251
		} 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
252
			// First off, build the rigth sql request
Jerome Mariette's avatar
Jerome Mariette committed
253
			if ($this->piVars['project_id']) {
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
254
255
				$where = 'tx_nG6_project_run.project_id='.$this->piVars['project_id'];

Jerome Mariette's avatar
Jerome Mariette committed
256
257
			} else {
				if (!$GLOBALS['TSFE']->loginUser) { // If the user is not logged on
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
258
					$where = 'project_id IN ('.$GLOBALS['TYPO3_DB']->SELECTquery('uid', 'tx_nG6_project', 'fe_group=0').')';
259
260
            } 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
261
            }
262
263
         }
         // Then execute it
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
264
265
			$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
266
							'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
267
							'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,' .
268
269
							'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
270
271
272
273
				'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' => '',
Celine Noirot's avatar
Celine Noirot committed
274
                'ORDERBY' => 'tx_nG6_run.date DESC, tx_nG6_run.name ASC',
275
                'LIMIT' => $limit
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
276
            );
277
278
279
         $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
280
281
282
283
284
285
286
287
288
289
290
			//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);
291
292
	         //generate HTML   
         	$run_list= $this->pi_run_list_view($res);
Jerome Mariette's avatar
Jerome Mariette committed
293
294
         	$nav_links = 	$this->pi_navigation_link_view('run_page', $this->piVars['run_page'], $total_count);
     		return $run_list ."\n". $nav_links;
295
296
297
         } else { // no results
             return $this->getFieldHeader('no_raw');
         }
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
298
299
300
       }
    }

Jerome Mariette's avatar
Jerome Mariette committed
301
302
303
304
305
306
	/**
	 * Creates a list from a database query
	 *
	 * @param	ressource	$res: A database result ressource
	 * @return	A HTML list if result items
	 */
307
	function pi_run_list_view($res)	{		
308
		$nb_run = 0;
Jerome Mariette's avatar
Jerome Mariette committed
309
310
311
312
313
		if ($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
314
315
316
317
318
319
320
321
322
323
							<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
324
325
						</tr>';
		while($this->internal['currentRow'] = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res))	{
326
327
328
329
			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>'.$this->getFieldContent('project_name').'</td>
Jerome Mariette's avatar
Jerome Mariette committed
330
					<td>'.$this->getFieldContent('date').'</td>
331
332
333
334
335
336
337
338
339
340
341
342
					<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());
				$user_allowed = false;
343
			   foreach($this->getSuperGroupsOf($this->internal['currentRow']['project_fe_group']) AS $valeur) {
344
345
346
347
					if (in_array($valeur, $user_groups)) {
						$user_allowed = true;
						$nb_run++;
					}
348
349
			   }
			   if ($user_allowed) {
350
351
352
					$content .= '<tr>
						<td '.$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').' >'.$this->getFieldContent('project_name').'</td>
Jerome Mariette's avatar
Jerome Mariette committed
353
						<td '.$this->pi_classParam('hidden').' >'.$this->getFieldContent('date').'</td>
354
355
356
357
358
359
360
361
						<td '.$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').' >'.$this->getFieldContent('run_sequencer').'</td>
						</tr>';
362
			   }
363
364
365
			}
		}
		if ($nb_run > 0) {
366
367
			$content .= "\n".'</table>' ; 		
			return $content;
368
369
		} else {
			return '';
Jerome Mariette's avatar
Jerome Mariette committed
370
371
372
373
374
		}
	}

	/**
	 * Display a single item from the database
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
375
376
	 * 
	 * @param	ressource	$res: A database result ressource
Jerome Mariette's avatar
Jerome Mariette committed
377
378
	 * @return	HTML of a single database entry
	 */
379
	function pi_run_single_view() {		
Jerome Mariette's avatar
Jerome Mariette committed
380
		$content = '<div'.$this->pi_classParam('singleView').'><h2>Run '.$this->internal['currentRow']['name'].' :</h2>';
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
381
		$content .= '<p><strong>'.$this->getFieldContent('run_description').'</strong></p> </div>
Jerome Mariette's avatar
Jerome Mariette committed
382
383
384
				<table'.$this->pi_classParam('listrow').'>
					<tr>
						<th align="left">'.$this->getFieldHeader('project_name').' :</th>
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
385
						<td align="left">'.$this->getFieldContent('project_name').'</td>
Jerome Mariette's avatar
Jerome Mariette committed
386
387
388
					</tr>	
					<tr>
						<th align="left">'.$this->getFieldHeader('date').' :</th>
Jerome Mariette's avatar
Jerome Mariette committed
389
						<td align="left">'.$this->getFieldContent('date').'</td>
Jerome Mariette's avatar
Jerome Mariette committed
390
391
392
					</tr>					
					<tr>
						<th align="left">'.$this->getFieldHeader('species').' :</th>
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
393
						<td align="left">'.$this->getFieldContent('run_species').'</td>
Jerome Mariette's avatar
Jerome Mariette committed
394
395
396
					</tr>
					<tr>
						<th align="left">'.$this->getFieldHeader('type').' :</th>
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
397
						<td align="left">'.$this->getFieldContent('run_type').'</td>
Jerome Mariette's avatar
Jerome Mariette committed
398
399
400
					</tr>
					<tr>
						<th align="left">'.$this->getFieldHeader('data_nature').' :</th>
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
401
						<td align="left">'.$this->getFieldContent('run_data_nature').'</td>
Jerome Mariette's avatar
Jerome Mariette committed
402
403
404
					</tr>
					<tr>
						<th align="left">'.$this->getFieldHeader('nb_sequences').' :</th>
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
405
						<td align="left">'.$this->getFieldContent('run_nb_sequences').'</td>
Jerome Mariette's avatar
Jerome Mariette committed
406
407
408
					</tr>
					<tr>
						<th align="left">'.$this->getFieldHeader('full_seq_size').' :</th>
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
409
						<td align="left">'.$this->getFieldContent('run_full_seq_size').'</td>
Jerome Mariette's avatar
Jerome Mariette committed
410
411
412
					</tr>						
					<tr>
						<th align="left">'.$this->getFieldHeader('sequencer').' :</th>
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
413
						<td align="left">'.$this->getFieldContent('run_sequencer').'</td>
Jerome Mariette's avatar
Jerome Mariette committed
414
415
416
					</tr>
					<tr>
						<th align="left">'.$this->getFieldHeader('downloads').' :</th>
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
417
						<td align="left">'.$this->get_downloads_list().'</td>
Jerome Mariette's avatar
Jerome Mariette committed
418
419
					</tr>
				</table>';
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
420
		$content .= $this->pi_analyze_view('run');
421
		
Jerome Mariette's avatar
Jerome Mariette committed
422
423
424
425
426
427
428
429
430
		return $content.$this->pi_getEditPanel();
	}
	
	/**
	 * Shows a list of database entries
	 *
	 * @param	string		$type: What kind of analyze is it : run or project
	 * 	 * @return	HTML list of table entries
	 */
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
431
	function pi_analyze_view($type)	{
432
		
Jerome Mariette's avatar
Jerome Mariette committed
433
434
435
436
437
438
439
440
441
442
443
		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
444
			return $this->pi_analyze_single_view();
Jerome Mariette's avatar
Jerome Mariette committed
445
		} else {
446
447
448
449
450
451
452
453
454
455
		
			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
456
457
458
			if ($type == 'run') {
				// Selects Analyzis done on this run
				$queryParts = array(
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
459
					'SELECT' => 'tx_nG6_analyze.uid AS uid, tx_nG6_analyze.name AS name, tx_nG6_analyze.description AS description,' .
460
461
462
463
464
465
466
								'tx_nG6_analyze.software AS software, tx_nG6_analyze.version AS version, tx_nG6_analyze.hidden AS hidden,' .
								'tx_nG6_project.fe_group AS project_fe_group',
					'FROM' => 'tx_nG6_analyze INNER JOIN (tx_nG6_run_analyze INNER JOIN ( tx_nG6_run INNER JOIN ( tx_nG6_project_run INNER JOIN tx_nG6_project ' .
							  'ON tx_nG6_project_run.project_id=tx_nG6_project.uid ) ' .
							  'ON tx_nG6_run.uid=tx_nG6_project_run.run_id ) ' .
							  'ON tx_nG6_run.uid=tx_nG6_run_analyze.run_id ) ' .
							  'ON tx_nG6_analyze.uid=tx_nG6_run_analyze.analyze_id ',
Jerome Mariette's avatar
Jerome Mariette committed
467
468
					'WHERE' => 'tx_nG6_run_analyze.run_id = '.$this->piVars['run_id'],
					'GROUPBY' => '',
Jerome Mariette's avatar
Jerome Mariette committed
469
					'ORDERBY' => 'tx_nG6_analyze.name',
470
					'LIMIT' => $limit
Jerome Mariette's avatar
Jerome Mariette committed
471
472
473
474
				);
			} elseif ($type == 'project') {
				// Selects Analyzis done on this project
				$queryParts = array(
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
475
					'SELECT' => 'tx_nG6_analyze.uid AS uid, tx_nG6_analyze.name AS name, tx_nG6_analyze.description AS description,' .
476
477
478
479
								'tx_nG6_analyze.software AS software, tx_nG6_analyze.version AS version, tx_nG6_analyze.hidden AS hidden,' .
								'tx_nG6_project.fe_group AS project_fe_group',
					'FROM' => 'tx_nG6_analyze INNER JOIN ( tx_nG6_project_analyze INNER JOIN tx_nG6_project ON tx_nG6_project.uid=tx_nG6_project_analyze.project_id ) ' .
							  'ON tx_nG6_analyze.uid=tx_nG6_project_analyze.analyze_id',
Jerome Mariette's avatar
Jerome Mariette committed
480
481
					'WHERE' => 'tx_nG6_project_analyze.project_id = '.$this->piVars['project_id'],
					'GROUPBY' => '',
Jerome Mariette's avatar
Jerome Mariette committed
482
					'ORDERBY' => 'tx_nG6_analyze.name',
483
					'LIMIT' => $limit
Jerome Mariette's avatar
Jerome Mariette committed
484
				);
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
485
			}	
486
			$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);		
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
487
			$content='';
488
			if ($GLOBALS['TYPO3_DB']->sql_num_rows($res) > 0) {	
Jerome Mariette's avatar
Jerome Mariette committed
489
490
491
492
493
494
495
496
497
498
499
500
				//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   
501
502
503
				$analyze_list=$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
504
			}
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
505
			return $content;
Jerome Mariette's avatar
Jerome Mariette committed
506
507
508
509
510
511
512
513
514
515
		}
	}

	/**
	 * 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)	{
516
		$nb_analyse = 0;
Jerome Mariette's avatar
Jerome Mariette committed
517
518
519
		$content.='<br /> <h3> '.$this->getFieldHeader('analyzes_done').'</h3> <br />
				<table'.$this->pi_classParam('listrow').'>
					<tr>
Jerome Mariette's avatar
w3C ok    
Jerome Mariette committed
520
521
522
523
						<th>'.$this->getFieldHeader('name').'</th>
						<th>'.$this->getFieldHeader('description').'</th>
						<th>'.$this->getFieldHeader('software').'</th>
						<th>'.$this->getFieldHeader('version').'</th>
Jerome Mariette's avatar
Jerome Mariette committed
524
525
					</tr>';
		while($this->internal['currentRow'] = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res))	{
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
			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
552
		}
553
554
555
		if ($nb_analyse > 0) {			
			$content .= "\n".'</table>' ;						
			return $content ;
556
557
558
		} else {
			return '';
		}		
Jerome Mariette's avatar
Jerome Mariette committed
559
560
	}

Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
561

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

		// 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,
590
						        position: "top",
591
592
593
594
595
596
							    modal: true,
						        overlay: {
						            backgroundColor: "#000",
						            opacity: 0.5
						        }
						    });
597
598
599
600
601
602
603
604
605
606
                            $(".tx-nG6-pi1-imglink").click(function() {
                               	jQuery.url.setUrl($(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;
                            });
607
608
609
610
611
612
613
						});
					</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
614
		if (file_exists($this->conf['data'].$this->internal['currentRow']['directory'].'/index.html' )) {
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
615
			$fp = fopen((string)$this->conf['data'].$this->internal['currentRow']['directory'].'/index.html',"r"); //lecture du fichier
Jerome Mariette's avatar
Jerome Mariette committed
616
617
618
			while (!feof($fp)) { //on parcourt toutes les lignes
				$content .= fgets($fp, 4096); // lecture du contenu de la ligne
			}
Jerome Mariette's avatar
Jerome Mariette committed
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
		} else if (file_exists($this->conf['data'].$this->internal['currentRow']['directory'].'/analyse.xml' )) {
			$xml = new DomDocument;
			$xml->load($this->conf['data'].$this->internal['currentRow']['directory'].'/analyse.xml');
			
			// Find out the analyse class
            $class = $xml->documentElement;
            $class_value = "";
			foreach ($class->childNodes AS $item) {
                if ($item->nodeName == "class") { $class_value = $item->nodeValue; } 
			}
			// If no class value : xml incorrect
			if ($class_value == "") { 
				$content .= $this->getFieldHeader('uncorrect_xml');
			} else {
				$xslt = new XSLTProcessor();
				$xsl = new DOMDocument();
				$xsl->load( 'typo3conf/ext/nG6/res/xsl/'.$this->LLkey.'.'.$class_value.'.xsl', LIBXML_NOCDATA);
				$xslt->importStylesheet( $xsl );
				$content .= $xslt->transformToXML( $xml ); 
			}
		} else {
Jerome Mariette's avatar
Jerome Mariette committed
640
			$content .= $this->getFieldHeader('not_synchro');
Jerome Mariette's avatar
Jerome Mariette committed
641
642
643
644
645
646
647
648
649
650
651
652
653
		}
		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
654
				return $this->pi_list_linkSingle($this->internal['currentRow'][$fN],$this->internal['currentRow']['uid'],1, $mergeArr);	
Jerome Mariette's avatar
Jerome Mariette committed
655
656
			break;
			case 'name':
Jerome Mariette's avatar
sql ok    
Jerome Mariette committed
657
				return $this->pi_list_linkSingle($this->internal['currentRow'][$fN],$this->internal['currentRow']['uid'],1, $mergeArr);	
Jerome Mariette's avatar
Jerome Mariette committed
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
			break;
			case 'date':
					// %A %e. %B %Y
				return strftime('%d-%m-%y',$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
729
730
	function get_downloads_list() {
		$directory = (string)$this->conf['data'].$this->internal['currentRow']['run_directory'];
Jerome Mariette's avatar
Jerome Mariette committed
731
732
733
734
735
736
		try {
			if (!is_dir($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
737
					$link = 'fileadmin/'.$this->internal['currentRow']['run_directory'].'/'.$entry;
Jerome Mariette's avatar
Jerome Mariette committed
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
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
					$download .= '<li><a href="'.$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 $authorized_group == 0;
		} else {
845
			return in_array($authorized_group, preg_split("/,/", $this->getCurrentUserGroups()));
Jerome Mariette's avatar
Jerome Mariette committed
846
847
		}
	}
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
	
	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;
	}
	
871
872
873
874
875
876
877
878
879
880
881
882
883
884
	/**
	 * 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
885
		$end = $total_count/$this->internal['results_at_a_time'] ;
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
		$end = ceil($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;
	}	
914
915
	
	
Jerome Mariette's avatar
Jerome Mariette committed
916
917
918
919
920
921
922
923
924
925
		
}



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']);
}

?>