Merge branch 'typo3V9' into 'master'

Typo3 v9

See merge request !123

ui/nG6/lib/class.tx_nG6_db.php

@@ -3695,60 +3695,7 @@ static function get_project_runs($project_id, $get_hidden=TRUE, $orderby='', $li
 				$GLOBALS['TYPO3_DB']->exec_UPDATEquery ('fe_users', 'fe_users.uid='.$userid, array('fe_users.usergroup' => $group));
 			}
 		}
-	}
-    
-    
-    /*
-     * DB integrity functions
-     *------------------------------------------------------------*/
-    
-    /**
-    * Check the integrity of 'fe_rights_levels' table.
-    */
-    static function check_db_rights_level(){
-	    $queryParts = Array(
-		    'SELECT' 	=> 'fe_rights_levels.right_level_id, fe_rights_levels.right_level_label ',
-		    'FROM' 		=> 'fe_rights_levels ',
-		    'WHERE' 	=> '',
-		    'GROUPBY' 	=> '',
-		    'ORDERBY' 	=> '',
-		    'LIMIT' 	=> '',
-	    );
-	    $res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
-	     
-	    $res_tab = array();
-	    while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
-		    $res_tab = array(
-			    'id' 	=>	$res_row['right_level_id'],
-			    'label'	=>	$res_row['right_level_label']
-		    );
-	    }
-	     
-	    // insert
-	    if( !in_array('member', array_values($res_tab)) ){
-		    $insert_rows = Array(
-			    'right_level_id' 	=> 0,
-			    'right_level_label' => 'member'
-		    );
-		    $GLOBALS['TYPO3_DB']->exec_INSERTquery('fe_rights_levels', $insert_rows);
-	    }
-	     
-	    if( !in_array('manager', array_values($res_tab)) ){
-		    $insert_rows = Array(
-		    	'right_level_id' 	=> 1,
-		        'right_level_label' => 'manager'
-		    );
-		    $GLOBALS['TYPO3_DB']->exec_INSERTquery('fe_rights_levels', $insert_rows);
-	    }
-	    
-	    if( !in_array('administrator', array_values($res_tab)) ){
-		    $insert_rows = Array(
-			    'right_level_id' 	=> 2,
-			    'right_level_label' => 'administrator'
-		    );
-		    $GLOBALS['TYPO3_DB']->exec_INSERTquery('fe_rights_levels', $insert_rows);
-	    }
-    }
+	}   
 }
 
 if (defined('TYPO3_MODE') && $TYPO3_CONF_VARS[TYPO3_MODE]['XCLASS']['ext/nG6/class.tx_nG6_db.php']) {

ui/nG6/lib/class.tx_nG6_utils.php

@@ -298,16 +298,9 @@ $template_mail.='<p>Yours sincerely</p>
 	 * @return hashed password
 	 */    
     static function hash_password($password){
-        $hashInstance = GeneralUtility::makeInstance(PasswordHashFactory::class)->getDefaultHashInstance('FE');
+        $hashInstance = TYPO3\CMS\Core\Utility\GeneralUtility::makeInstance(PasswordHashFactory::class)->getDefaultHashInstance('FE');
         $hashedPassword = $hashInstance->getHashedPassword($password);
-//         if (\TYPO3\CMS\Crypto\PasswordHashing\SaltedPasswordsUtility::isUsageEnabled('FE')) {
-//             $objSalt = \TYPO3\CMS\Core\Crypto\PasswordHashing\PasswordHashFactory::getSaltingInstance(NULL);
-//             if (is_object($objSalt)) {
-//                     $saltedPassword = $objSalt->getHashedPassword($password);
-//             }
-//     }
-
-			return $saltedPassword;
+        return $hashedPassword;
     }
      
     static function get_ssh_connection($user_login, $user_pwd){

ui/nG6/pi1/analyzes/AnalysisTemplate.tpl

@@ -138,7 +138,7 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 								</div>
 								<br />
 								<div class="alert alert-info" name="DownloadData_analysis">
-									<p style="text-align: center;">You can download your files easily with <a href="https://ng6.toulouse.inra.fr/index.php?id=59" target="_blank"><strong>Menu > Download</strong></a>. Please visit the <a href="https://ng6.toulouse.inra.fr/index.php?id=57" target="_blank"><strong>FAQ</strong></a> > "How to get my data?" section to know more.</p>
+									<p style="text-align: center;">You can download your files easily with <a href="https://ng6.toulouse.inra.fr/download" target="_blank"><strong>Menu > Download</strong></a>. Please visit the <a href="https://ng6.toulouse.inra.fr/faq" target="_blank"><strong>FAQ</strong></a> > "How to get my data?" section to know more.</p>
 								</div>
 								{foreach $dir|scandir as $file}
 								{assign var="link" value=(('fileadmin'|cat:'/'|cat:$analyse.directory)|cat:'/')|cat:$file}

ui/nG6/pi1/analyzes/FastQC.js

@@ -79,7 +79,7 @@ $(function () {
 			
 			//Build tbody
 			var tbody = "" ; 
-			var pattern_regexp = new RegExp( '<a[^>]+class="[^"]*imglink[^"]*"[^>]+href="(fileadmin\/data[_]*[a-z]*\/analyze\/[^"]+)' ) ;
+			var pattern_regexp = new RegExp( '<a[^>]+class="[^"]*imglink[^"]*"[^>]+href="(\/fileadmin\/data[_]*[a-z]*\/analyze\/[^"]+)' ) ;
 			for( var i = 0 ; i < samples.length ; i++ ) {
 				tbody += '<tr>' ; 
 				for( var j = 0 ; j < columns.length ; j++ ) {

ui/nG6/pi1/class.tx_nG6_pi1.php

@@ -84,8 +84,6 @@ class tx_nG6_pi1 extends \TYPO3\CMS\Frontend\Plugin\AbstractPlugin {
 			<link type="text/css" rel="stylesheet" media="screen" href="'.\TYPO3\CMS\Core\Utility\PathUtility::stripPathSitePrefix(ExtensionManagementUtility::extPath($this->extKey)).'res/css/jflow.min.css"/>
 			<link type="text/css" rel="stylesheet" media="screen" href="'.\TYPO3\CMS\Core\Utility\PathUtility::stripPathSitePrefix(ExtensionManagementUtility::extPath($this->extKey)).'res/css/tx_nG6.css"/>';			
 		
-		tx_nG6_db::check_db_rights_level();
-
 		// if asked to upgrade to version 1.2
 		if($this->piVars['upgrade']){
 			$content = '<div class="sub-content sc-top">'.tx_nG6_upgrade::upgrade($this->piVars['upgrade'], $this->conf["data"]).'</div>';
@@ -257,9 +255,9 @@ class tx_nG6_pi1 extends \TYPO3\CMS\Frontend\Plugin\AbstractPlugin {
 				
 				$txNG6Utils = new tx_nG6_utils;
 				//$smarty->register_object('tx_nG6_utils',$txNG6Utils);
-				$smarty->assign_by_ref('tx_nG6_utils', $txNG6Utils);
+				$smarty->assignByRef('tx_nG6_utils', $txNG6Utils);
 
-				$smarty->assign_by_ref('retention_policy', tx_nG6_utils::get_project_retention_policy($projects[key($projects)]['id']));
+				$smarty->assignByRef('retention_policy', tx_nG6_utils::get_project_retention_policy($projects[key($projects)]['id']));
 				$smarty->assign('space_purge_msg', tx_nG6_utils::get_project_purge_msg($projects[key($projects)]['id']));
 				
 			}	

ui/nG6/pi1/project_view.tpl

@@ -90,7 +90,7 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 			</table>
 			<br />
 				<div class="alert alert-info" name="Adding_user">
-					<p style="text-align: center;">Your role is defined on the <strong>Users tab</strong> below. If you are manager or owner, you can add a collaborator yourself. Please visit the <a href="https://ng6.toulouse.inra.fr/index.php?id=57" target="_blank"><strong>FAQ</strong></a> > "<strong>What about user management</strong>" & "<strong>How to add a user to my project</strong>" to know more.</p>
+					<p style="text-align: center;">Your role is defined on the <strong>Users tab</strong> below. If you are manager or owner, you can add a collaborator yourself. Please visit the <a href="https://ng6.toulouse.inra.fr/faq" target="_blank"><strong>FAQ</strong></a> > "<strong>What about user management</strong>" & "<strong>How to add a user to my project</strong>" to know more.</p>
 				</div>
 
 

ui/nG6/pi1/run_view.tpl

@@ -144,7 +144,7 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 					</div>
 					<br /> 
 					<div class="alert alert-info" name="DownloadData_run">
-						<p style="text-align: center;">You can download your files easily with <a href="https://ng6.toulouse.inra.fr/index.php?id=59" target="_blank"><strong>Menu > Download</strong></a>. Please visit the <a href="https://ng6.toulouse.inra.fr/index.php?id=57" target="_blank"><strong>FAQ</strong></a> > "<strong>How to get my data?</strong>" section to know more.</p>
+						<p style="text-align: center;">You can download your files easily with <a href="https://ng6.toulouse.inra.fr/download" target="_blank"><strong>Menu > Download</strong></a>. Please visit the <a href="https://ng6.toulouse.inra.fr/faq" target="_blank"><strong>FAQ</strong></a> > "<strong>How to get my data?</strong>" section to know more.</p>
 				</div>
 				{/if}
 				{assign var="nb_files" value=0}

ui/nG6/res/js/tx_nG6_pi1_analysis.js

@@ -198,6 +198,7 @@ $(function () {
     	// Build dataTable
     	if ($(this).children("tbody").children("tr").children("td:has(input:checkbox)").length > 0) {
 			$(this).DataTable({
+				"lengthMenu": [[10, 25, 50, -1], [10, 25, 50, "All"]],
 				"scrollX"		: "90%",
 				"sScrollXInner"	: "100%",
 	  			"order"		: [[1, 'desc']],
@@ -206,6 +207,7 @@ $(function () {
 		  	});
 	  	} else {
 		    $(this).DataTable({
+		    	"lengthMenu": [[10, 25, 50, -1], [10, 25, 50, "All"]],
 		    	"scrollX"		: "90%",
 				"sScrollXInner"	: "100%",
 	  			"order"		: [[1, 'desc']],

ui/nG6/res/js/tx_nG6_pi5.js

@@ -305,13 +305,13 @@ $(function () {
     		id    		: "download_url",
     		wfName 		: "DownloadURL",
     		run         : function(form_options, modal){
-    			form_options.parameters['url_base'] = location.href.replace(/index\.php.+/, "" ) + 'fileadmin';
+    			form_options.parameters['url_base'] = location.href.replace(/download/, "" ) + 'fileadmin';
     			// display modal box 
     			modal.$modal.modal();
 				modal.$modal.find('#wfform').wfform(form_options);
 				modal.$modal.find('#wfform').on('run.wfform', function(event, running_wf) {
 					_retrieve_url_list(modal, running_wf, 'output_urls.txt', function(filedata){
-						var link_prefix = location.href.replace(/index\.php.+/, "" ) + 'fileadmin' ;
+						var link_prefix = location.href.replace(/download/, "" ) + 'fileadmin' ;
 						var file_list = [];
     					$.each(filedata.trim().split('\n'), function(i, path){
     						file_list.push(link_prefix + path);

ui/nG6/res/smarty/libs/Smarty.class.php

@@ -738,8 +738,11 @@ class Smarty extends Smarty_Internal_Data {
     public function __call($name, $args)
     {
         static $camel_func;
-        if (!isset($camel_func))
-            $camel_func = create_function('$c', 'return "_" . strtolower($c[1]);');
+        if (!isset($camel_func)){
+            $camel_func = function ($matches) {
+                return "_" . strtolower($matches[1]);
+            };
+        }
         // see if this is a set/get for a property
         $first3 = strtolower(substr($name, 0, 3));
         if (in_array($first3, array('set', 'get')) && substr($name, 3, 1) !== '_') {