Merge branch 'master' into 'dev'

# Conflicts:
#   ui/nG6/pi6/class.tx_nG6_pi6.php

src/jflow/config_reader.py

@@ -112,7 +112,7 @@ class JFlowConfigReader(object):
           
     def get_socket_options(self):
         try:
-            return [self.reader.get("global", "server_socket_host"), int(self.reader.get("global", "server_socket_port")), self.reader.get("global", "server_socket_protocol")]
+            return [self.reader.get("global", "server_socket_host"), int(self.reader.get("global", "server_socket_port")), self.reader.get("global", "server_socket_protocol"), self.reader.get("global", "server_socket_proxied")]
         except:
             return ["127.0.0.1", 8080,"http"]
         

src/jflow/server.py

@@ -530,7 +530,7 @@ class JFlowServer (object):
         socket_opt = self.jflow_config_reader.get_socket_options()
         if not os.path.isdir(path):
             return {
-                    'url':socket_opt[2]+'://' + socket_opt[0] + ':' + str(socket_opt[1]) + '/' + path.replace(work_dir, web_path),
+                    'url':socket_opt[2]+'://' + str(socket_opt[3]) + '/' + path.replace(work_dir, web_path),
                     'size': get_octet_string_representation(os.path.getsize(os.path.abspath(path))),
                     'extension': os.path.splitext(path)[1]
                    }

src/ng6/analysis.py

@@ -752,14 +752,19 @@ class Analysis (Component):
             
         return [retcode, str_cmd]
     
-def get_web_filepath(self, file_name, base_filepath='fileadmin' ):
+    def get_web_filepath(self, file_name, base_filepath='fileadmin' ):
         """
           returns the full web filepath from a given filename 
           @param file_name     : the path to the file to link
           @param base_filepath : the first directory in the path (depends on the server's directory structure)
           @return              : the full web filepath
         """
-        return base_filepath + os.path.join(self.get_directory(), file_name)
+        curr_dir=self.directory
+        if self.id != None : 
+            t3mysql = t3MySQLdb()
+            curr_dir= t3mysql.select_analysis_directory(self.id)
 
+        return base_filepath + os.path.join(self.directory, file_name)
+        
         
         

src/ng6/exceptions.py

@@ -35,4 +35,17 @@ class UnsavedRunError(Exception):
 
     def __str__(self):
         return repr(self.message)
-    
\ No newline at end of file
+    
+    
+class UnsavedAnalysisError(Exception):
+    """
+    Exception to be raised when an operation is performed and the analysis has not been saved yet
+    """
+    def __init__(self, message=None):
+        if message is not None:
+            self.message = message
+        else:
+            self.message = "The analysis has to be saved before to call this method."
+
+    def __str__(self):
+        return repr(self.message)
\ No newline at end of file

ui/nG6/class.tx_nG6_eid.php

@@ -929,6 +929,8 @@ class tx_nG6_eid {
                 $purge_delay = trim(\TYPO3\CMS\Core\Utility\GeneralUtility::_GP('purge_delay'));
                 $purge_demand_filter_space = trim(\TYPO3\CMS\Core\Utility\GeneralUtility::_GP('purge_demand_filter_space'));
                 $purge_demand_filter_delay_exceeded = trim(\TYPO3\CMS\Core\Utility\GeneralUtility::_GP('purge_demand_filter_delay_exceeded'));
+                
+                
                 print json_encode(tx_nG6_db::get_purge_demand_list($purge_delay,$purge_demand_filter_space,$purge_demand_filter_delay_exceeded));
     	}  elseif ($type == 'refresh_purge_list') {
                 $max_retention_date = trim(\TYPO3\CMS\Core\Utility\GeneralUtility::_GP('max_retention_date'));
@@ -937,8 +939,6 @@ class tx_nG6_eid {
     		$without_laboratories_id = trim(\TYPO3\CMS\Core\Utility\GeneralUtility::_GP('without_lab'));
                 $with_laboratories_id = trim(\TYPO3\CMS\Core\Utility\GeneralUtility::_GP('with_lab'));
     		$create_users = trim(\TYPO3\CMS\Core\Utility\GeneralUtility::_GP('create_users'));
-    		//Change date format
-                //print ('test');
     		print json_encode(tx_nG6_db::filter_list_retention_data_info($filter_space,$max_retention_date,$create_users, $without_laboratories_id,$with_laboratories_id));
         } elseif ($type == 'delete_purge_data') {
                  //Delete data link to the list of purge demand

ui/nG6/lib/class.tx_nG6_db.php

@@ -194,6 +194,10 @@ class tx_nG6_db {
 			$conditions[] = "project_id in (" . $project_list_ids.")" ;
 		}
         $where = join(' AND ', $conditions);
+
+        $log_file_path = tx_nG6_utils::get_log_path();
+		error_log(date("d/m/Y, h:i:s")." IN filter_list_retention_data_info(), where=".$where." \n", 3, $log_file_path);
+        //error_log(" IN filter_list_retention_data_info(), where=".$where." \n", 3, $log_file_path);
         
         return (tx_nG6_db::select_list_retention_data_info($where));
 	}
@@ -214,6 +218,7 @@ class tx_nG6_db {
 	}
 	
 	static function select_list_retention_data_info($where) {
+		
 		$by_project=array();
 		$empty_res_structure = array(
 						'project_name'			=> "",
@@ -333,6 +338,10 @@ class tx_nG6_db {
 			}
 		}
 		
+		$log_file_path = tx_nG6_utils::get_log_path();
+		error_log(date("d/m/Y, h:i:s")." IN filter_list_retention_data_info(), return=".print_r($by_project,TRUE)." \n", 3, $log_file_path);
+		//error_log(" IN filter_list_retention_data_info(), return=".print_r($by_project,TRUE)." \n", 3, $log_file_path);
+		
 		return($by_project);
 	}
 
@@ -3055,9 +3064,10 @@ static function get_project_runs($project_id, $get_hidden=TRUE, $orderby='', $li
      * @param string $user_col		the fe_users column to use
      * @return array
      */
-    static function get_all_names_starting_with($name_start, $user_col) {
+    static function get_all_names_starting_with ($name_start, $user_col) {
     	$queryParts = Array(
-    		'SELECT' => 'fe_users.uid, fe_users.username, fe_users.last_name, fe_users.first_name, fe_users.password, fe_users.email, fe_users.cruser_id, fe_groups.title, fe_groups.tx_nG6_organism, fe_groups.tx_nG6_location',
+    		// 'SELECT' => 'fe_users.uid, fe_users.username, fe_users.last_name, fe_users.first_name, fe_users.password, fe_users.email, fe_users.cruser_id, fe_groups.title, fe_groups.tx_nG6_organism, fe_groups.tx_nG6_location',
+			'SELECT' => 'fe_users.uid, fe_users.username, fe_users.last_name, fe_users.first_name, fe_users.email, fe_users.cruser_id, fe_groups.title, fe_groups.tx_nG6_organism, fe_groups.tx_nG6_location',
 			'FROM' => 'fe_users INNER JOIN fe_groups ON fe_users.usergroup=fe_groups.uid',
 			'WHERE' => 'fe_users.'.$user_col.' LIKE "'.$name_start.'%"',
 			'GROUPBY' => '',
@@ -3072,7 +3082,7 @@ static function get_project_runs($project_id, $get_hidden=TRUE, $orderby='', $li
     			'username' 		=>	$res_row['username'],
     			'first_name' 	=>	$res_row['first_name'],
     			'last_name' 	=>	$res_row['last_name'],
-    			'password' 		=>	$res_row['password'],
+    			// 'password' 		=>	$res_row['password'],
     			'email' 		=>	$res_row['email'],
     			'title' 		=>	$res_row['title'],
     			'cruser_id' 	=>	$res_row['cruser_id'],

ui/nG6/lib/class.tx_nG6_utils.php

@@ -466,6 +466,29 @@ $template_mail.='<p>Yours sincerely</p>
     	return($path_to_save_dir);
     }
     
+    
+    static function get_log_path(){
+    	$config_file_content = tx_nG6_utils::get_config_content();
+        $array_config_content = explode(PHP_EOL, $config_file_content);
+    	$pattern_to_find = "log_file = ";
+    	$log_file_path_found = FALSE;
+    	
+    	//We want to return the log file path
+    	foreach($array_config_content as $line_id => $line_content){
+    		//if we found the right line
+    		if(strpos ( $line_content , $pattern_to_find) === 0){
+    			$log_file_path_found = TRUE;
+    		}
+    		    		
+    		if($log_file_path_found){
+    			$log_file_path = str_replace($pattern_to_find,'',$line_content);
+    			return($log_file_path);
+    		}
+    	}
+    	return('0');
+    }
+    
+    
     static function convert_epoch_timestamp_to_nice_date( $epoch_date ){
 		//return(gmdate('D, d M Y', $epoch_date));
 		return(gmdate('l jS \of F Y', $epoch_date));

workflows/ont_qc/components/demultiplexont.py

@@ -109,13 +109,13 @@ class Demultiplex_ONT (Analysis):
         str_input = ""
         str_output = ""
         for fastq in self.fastq_files:
-            str_input = str_input + " $" + str(iter)
-            iter = iter + 1
-        str_output = " $"+ str(iter)
+            str_input += ' ${' + str(iter) + '}'
+            iter += 1
+        str_output = ' ${'+ str(iter) + '}'
             
         # Create cmd
         self.add_shell_execution(self.get_exec_path("seqkit") +" stats --all " + str_input + ">" + str_output,
-            cmd_format='{EXE} {IN} {OUT}' ,
+            cmd_format='{EXE} {IN} {OUT}',
             map=False,
             inputs = [self.fastq_files],
             outputs = os.path.join(self.output_directory, "DemultiplexONT.output"))