Merge branch 'master' into 'issue#151'

# Conflicts:
#   ui/nG6/class.tx_nG6_eid.php

src/ng6/analysis.py

@@ -743,7 +743,7 @@ class Analysis (Component):
                 raise Exception("Error while trying to rsync " + old_path + " to " + new_absolute_path + "\n" +
                                 "Command : " + str_cmd + "\n" + "Error code : " + str(retcode) + "\n")
         else:
-            print ("rsync could not be launched because the source and destination are the same, from " + old_path + " to " + new_absolute_path + "\n")
+            str_cmd = "Source and destination directories are the same : " + old_path + " , ignored.\n"
         
         new_retention = ng6conf.get_retention_date(space_id, self.date)
         
@@ -751,4 +751,4 @@ class Analysis (Component):
         t3mysql.update_fields('tx_nG6_analyze', str(self.id), ['directory','retention_date'], [str("/"+new_relative_path),new_retention] )
             
         return [retcode, str_cmd]
-    
\ No newline at end of file
+    

src/ng6/ng6workflow.py

@@ -446,6 +446,7 @@ class CasavaNG6Workflow(NG6Workflow):
 
         if self.is_casava:
             self.group_prefix = list((Utils.get_group_basenames(self.get_all_reads(), "read")).keys())
+            logging.getLogger("ng6").debug("CasavaNG6Workflow._preprocess enter" + str(self.group_prefix))
 
     def _process_casava_18(self, casava_directory, project_name, lane_number, input_files):
         logging.getLogger("ng6").debug("CasavaNG6Workflow._process_casava_18 enter")
@@ -643,10 +644,14 @@ class CasavaNG6Workflow(NG6Workflow):
         concatenatefastq = None
         filtered_read1_files = []
         filtered_read2_files = []
+        filtered_index_files = []
+        analysis_files = []
         saved_files = []
         logging.getLogger("ng6").debug("illumina_process entering")
         if self.is_casava :
             logging.getLogger("ng6").debug("illumina_process self.is_casava")
+            analysis_files = self.get_all_reads("read1") + self.get_all_reads("read2")
+            
             if len(self.log_files) > 0 :
                 add_log = self.add_component("BasicAnalysis", [self.log_files,"Log Files","Log files generated during primary analysis","-","-","-","gz", "","log.gz"])
             
@@ -657,39 +662,48 @@ class CasavaNG6Workflow(NG6Workflow):
                     demultiplex_stats = self.add_component("Demultiplex10XStats", [self.get_all_reads("read1"), self.undetermined_reads1, self.get_files_index("read1")])
                 else :
                     demultiplex_stats = self.add_component("DemultiplexStats", [self.get_all_reads("read1"), self.undetermined_reads1])                 
-
+            
+            #analysis files for fastq illumina and fastqc analysis
 
             if self.keep_reads != "all" :
                 logging.getLogger("ng6").debug("illumina_process self.keep_reads != all")
                 logging.getLogger("ng6").debug("illumina_process BEFORE FASTQILLUMINAFILTER self.get_all_reads() = " + ",".join(self.get_all_reads()))
                 logging.getLogger("ng6").debug("illumina_process self.group_prefix = " + ",".join(self.group_prefix))
                 # fastq illumina filter
-                fastqilluminafilter = self.add_component("FastqIlluminaFilter", [self.runobj,self.get_all_reads(), self.keep_reads, self.group_prefix])
-
+                
+                fastqilluminafilter = self.add_component("FastqIlluminaFilter", [self.runobj, self.get_all_reads(), self.keep_reads, self.group_prefix])
+                logging.getLogger("ng6").debug("illumina_process fastqilluminafilter = " + ",".join(filtered_read1_files))
                 
                 # list filtered files
                 if self.is_paired_end() :
                     # split read 1 and read 2 from filtered files list
-                    [filtered_read1_files, filtered_read2_files] = Utils.split_pair(fastqilluminafilter.fastq_files_filtered, (self.group_prefix is not None))
+                    if self.is_10Xcasava : 
+                        [filtered_read1_files, filtered_read2_files, filtered_index_files] = Utils.split_pair_and_index(fastqilluminafilter.fastq_files_filtered, (self.group_prefix is not None))
+                    else:
+                        [filtered_read1_files, filtered_read2_files] = Utils.split_pair(fastqilluminafilter.fastq_files_filtered, (self.group_prefix is not None))
                 else:
                     filtered_read1_files = fastqilluminafilter.fastq_files_filtered
                     filtered_read2_files = []
+                    filtered_index_files = []
                 filtered_read1_files = sorted(filtered_read1_files)
                 filtered_read2_files = sorted(filtered_read2_files)
+                filtered_index_files = sorted(filtered_index_files)
             else:
                 fastqilluminafilter = None
                 filtered_read1_files = self.get_all_reads("read1")
                 filtered_read2_files = self.get_all_reads("read2")
+                filtered_index_files = self.get_all_reads("index")
 
             # archive the files
             #TODO : if self.group_prefix == None, the create the output of fastqilluminafilter in the run.get_work_directory()
 
-            saved_files = filtered_read1_files + filtered_read2_files + self.get_all_reads("index")
+            saved_files = filtered_read1_files + filtered_read2_files + filtered_index_files            
             logging.getLogger("CasavaNG6Workflow").debug("illumina_process saved_files = " + ",".join(saved_files))
             reads_prefixes = None
             if self.group_prefix != None :
                 # concatenate fastq
                 reads_prefixes = list((Utils.get_group_basenames(saved_files, "read")).keys())
+                logging.getLogger("CasavaNG6Workflow").debug("illumina_process read_predixes = " + ",".join(reads_prefixes))
                 logging.getLogger("CasavaNG6Workflow").debug("illumina_process saved_files = " + ",".join(saved_files))
                 concatenatefastq = self.add_component("ConcatenateFilesGroups", [self.runobj,saved_files,reads_prefixes])
                 saved_files = concatenatefastq.concat_files
@@ -700,8 +714,11 @@ class CasavaNG6Workflow(NG6Workflow):
             fastqilluminafilter = None
             filtered_read1_files = self.get_all_reads("read1")
             filtered_read2_files = self.get_all_reads("read2")
+            filtered_index_files = self.get_all_reads("index")
             saved_files = self.get_all_reads()
 
+        # reads prefixes 
+        reads_prefixes =list((Utils.get_group_basenames(analysis_files, "read")).keys())
         # add raw
         addrawfiles = self.add_component("AddRawFiles", [self.runobj, saved_files, self.compression])
         contam = []
@@ -711,6 +728,9 @@ class CasavaNG6Workflow(NG6Workflow):
             contam.append(self.get_resource("yeast_bwa"))
         except : pass
 
+        logging.getLogger("CasavaNG6Workflow").debug("illumina_process files_analysis = " + ",".join(filtered_read1_files))
+        logging.getLogger("CasavaNG6Workflow").debug("illumina_process files_analysis = " + ",".join(filtered_read2_files))
+        logging.getLogger("CasavaNG6Workflow").debug("illumina_process files_analysis = " + ",".join(filtered_index_files))
         # contamination_search
         if contam :
             if self.contamination_databank:  contam.extend(self.contamination_databank)

src/ng6/run.py

@@ -494,7 +494,7 @@ class Run(object):
                 raise Exception("Error while trying to rsync " + old_path + " to " + new_absolute_path + "\n" +
                                 "Command : " + str_cmd + "\n" + "Error code : " + str(retcode) + "\n")
         else:
-            print ("rsync could not be launched because the source and destination are the same, from " + old_path + " to " + new_absolute_path + "\n")
+            str_cmd = "Source and destination directories are the same : " + old_path + " , ignored.\n"
         
         new_retention = ng6conf.get_retention_date(space_id, self.date)
         

src/ng6/t3MySQLdb.py

@@ -202,7 +202,7 @@ class t3MySQLdb(object):
             right_level_id = qresult.rows[0][0]
             sql = "INSERT INTO tx_nG6_project (pid, tstamp, crdate, cruser_id, description, name, hidden, space_id) \
             VALUES ('%s','%s','%s','%s','%s','%s','%s','%s')" % (self.cfg_reader.get_pid(), crdate, crdate, admin_id,
-                                                            self.esc_q(pdescription), self.esc_q(name), hidden, space_id)
+                                                            self.esc_q(pdescription), self.esc_q(name), int(hidden), space_id)
             qresult = self.execute(sql, commit = True)
             project_id = qresult.lastrowid
             self.execute("INSERT INTO fe_rights (fe_user_id, project_id, right_id) VALUES ('%s','%s','%s')" % (admin_id,  project_id, right_level_id),
@@ -320,7 +320,7 @@ class t3MySQLdb(object):
         '%s', '%s', '%s', '%s', '%s', '%s', '%s', '%s', '%s', '%s', '%s', '%s', '%s')" % ( self.cfg_reader.get_pid(), crdate, crdate, cruser_id, self.esc_q(name),
                                                              calendar.timegm(date.timetuple()), directory, self.esc_q(species),
                                                              self.esc_q(data_nature), self.esc_q(type), nb_sequences,
-                                                             full_seq_size, self.esc_q(description), hidden, self.esc_q(sequencer),retention_date, "stored","0","0","0")
+                                                             full_seq_size, self.esc_q(description), int(hidden), self.esc_q(sequencer),retention_date, "stored","0","0","0")
         qresult = self.execute(sql, commit = True)
         run_id = qresult.lastrowid
 
@@ -471,7 +471,7 @@ class t3MySQLdb(object):
         if description:
             set_values.append(  "description='%s'" % self.esc_q(description))
         if hidden:
-            set_values.append(  "hidden=%s" % hidden )
+            set_values.append(  "hidden=%s" % int(hidden) )
         if sequencer:
             set_values.append(  "sequencer='%s'" % self.esc_q(sequencer))
         if storage_size:
@@ -673,7 +673,8 @@ class t3MySQLdb(object):
     #--------------------------------------------------------------------
     # Analyze functions
 
-    def add_analysis(self, aclass, name, description, cruser_login, date, directory, software, version, params, is_editable, retention_date, hidden=1, parent_uid=0):
+    def add_analysis(self, aclass, name, description, cruser_login, date, \
+    directory, software, version, params, is_editable, retention_date, hidden=1, parent_uid=0):
         """
         Update an Analyze
           @param aclass       : the class of the analysis
@@ -703,7 +704,7 @@ class t3MySQLdb(object):
         '%s', '%s', '%s', '%s', '%s', '%s' ,'%s', '%s', '%s', '%s', '%s', '%s', '%s')" % ( self.cfg_reader.get_pid(), crdate, crdate, cruser_id, aclass,
                                                           self.esc_q(name), self.esc_q(description), crdate,
                                                           directory, self.esc_q(software), self.esc_q(version),
-                                                          hidden, self.esc_q(params), analysis_is_editable, parent_uid, retention_date, "stored","0","0","0")
+                                                          int(hidden), self.esc_q(params), analysis_is_editable, parent_uid, retention_date, "stored","0","0","0")
         qresult = self.execute(sql, commit= True)
         analysis_id = qresult.lastrowid
 
@@ -1065,4 +1066,4 @@ class t3MySQLdb(object):
         qresult = self.execute(sql)
         return [ r[0] for r in qresult.rows ]
         
-        
\ No newline at end of file
+        

src/ng6/utils.py

@@ -290,7 +290,44 @@ class Utils(object):
             
         return [read_1_list, read_2_list]
 
-
+    @staticmethod
+    def split_pair_and_index ( file_list, is_casava=False ):
+        """
+        Return the list of read 1, the list of read 2 and the list of index read from a list
+          @param file_list : the list
+          @param is_casava : files names in file_list are in CASVAVA format 
+        """
+        read_1_list = []
+        read_2_list = []
+        read_index_list = []
+        logging.getLogger("Utils").debug("split_pair_and_index. Entering")
+        if is_casava:
+            logging.getLogger("Utils").debug("split_pair_and_index. is_casava")
+            for file in file_list:
+                logging.getLogger("Utils").debug("split_pair_and_index. file = " + file)
+                basename_without_ext = os.path.basename(file).split(".")[0]
+                file_name_fields = basename_without_ext.split(Utils.CASAVA_FILENAME_SEPARATOR)
+                read_tag = file_name_fields[Utils.CASAVA_FILENAME['read']-1]
+                if read_tag == "R1":
+                    read_1_list.append(file)
+                elif read_tag == "R2":
+                    read_2_list.append(file)
+                else:
+                    read_index_list.append(file)
+        else:
+            sorted_list = sorted( file_list )
+            logging.getLogger("Utils").debug("split_pair_and_index. file_list = " + ", ".join(file_list))
+            logging.getLogger("Utils").debug("split_pair_and_index. sorted_list = " + ", ".join(sorted_list))
+            for i in range(0,len(sorted_list),3):
+                logging.getLogger("Utils").debug("split_pair_and_index. sorted_list[i] = " + sorted_list[i])
+                logging.getLogger("Utils").debug("split_pair_and_index. sorted_list[i+1] = " + sorted_list[i+1])
+                logging.getLogger("Utils").debug("split_pair_and_index. sorted_list[i+1] = " + sorted_list[i+2])
+                read_1_list.append(sorted_list[i])
+                read_2_list.append(sorted_list[i+1])
+                read_index_list.append(sorted_list[i+2])
+            
+        return [read_1_list, read_2_list, read_index_list]
+    
     @staticmethod
     def get_group_basenames( file_list, group_by ):
         """
@@ -361,6 +398,17 @@ class Utils(object):
         return "".join(dec)
         """
     
+    
+    @staticmethod
+    def get_project_dirname(project_id, project_name):
+        return "Project_%s.%s" % ( re.sub( r"[\s\/]", "_", project_name), project_id )
+    @staticmethod
+    def get_run_dirname(run_id, run_name):
+        return "Run_%s.%s" % ( re.sub( r"[^A-Za-z0-9]", "_", run_name), run_id)
+    @staticmethod
+    def get_analyse_dirname(analyse_id, analyse_name):
+        return "Analyse_%s.%s"%( re.sub( r"[\s\/]", "_", analyse_name), analyse_id )
+    
     @staticmethod
     def get_directories_structure_and_content(ng6_username, data_folder, output_folder, prefixed_ids):
         from ng6.t3MySQLdb import t3MySQLdb
@@ -372,20 +420,21 @@ class Utils(object):
         try : user_id = t3mysql.get_user_id(ng6_username)
         except : pass
         
+        
         for prefixed_id in prefixed_ids.split(';') :
             vals = prefixed_id.split('_')
             prefix = vals[0]
             id = vals[1]
-            
             if prefix == "data" or prefix == "run" :
                 run = t3mysql.select_run_informations(id)
                 source_dir = data_folder +'/'+ run['directory']
-                project_name = "Project_%s.%s" % ( re.sub( r"[\s\/]", "_", run['project_name']), run['project_id'] )
+                project_name = Utils.get_project_dirname(run['project_id'],run['project_name'])
                 
                 #run_name = "Run_%s.%s" %( run['name'].replace(' ', '_').replace('/', '_'), id )
-                run_name = "Run_%s.%s" % ( re.sub( r"[^A-Za-z0-9]", "_", run['name']), id)
+                run_name = Utils.get_run_dirname(id,run['name'])
                 
                 raw_data_dir = os.path.join( output_folder, project_name, run_name, "RawData"  )
+                print (run, source_dir,project_name,run_name)
                 if source_dir not in src_directories :
                     src_directories.append(source_dir)
                 if raw_data_dir not in dest_directories :
@@ -394,7 +443,7 @@ class Utils(object):
                 if prefix == "run" :
                     for analyse_id, analyse_values in t3mysql.get_user_run_analysis(user_id, id, 'tx_nG6_analyze.name').items() :
                         analysis_dir = data_folder + '/' + analyse_values["directory"]
-                        analysis_name = "Analyse_%s.%s"%( re.sub( r"[\s\/]", "_", analyse_values['name']), analyse_id )
+                        analysis_name = Utils.get_analyse_dirname(analyse_id, analyse_values['name'] )
                         dest_analysis_dir = os.path.join( output_folder, project_name, run_name, analysis_name  )
                         
                         if analysis_dir not in src_directories :
@@ -409,19 +458,19 @@ class Utils(object):
                 if source_dir not in src_directories :
                     src_directories.append(source_dir)
                 
-                project_name = "Project_%s.%s" % ( re.sub( r"[\s\/]", "_", analyse["project_name"]), analyse["project_id"])
-                
+                project_name = Utils.get_project_dirname(analyse['project_id'],analyse['project_name'])
                 # it's a run analysis
-                if analyse["run_id"]:
-                    run_name = "Run_%s.%s" % ( re.sub( r"[\s\/]", "_", analyse["run_name"]), analyse["run_id"])
-                    
-                    analysis_name = "Analyse_%s.%s" % ( re.sub( r"[\s\/]", "_", analyse["name"]), id)
+                if analyse["run_id"]:                    
+                    run_name = Utils.get_run_dirname(analyse["run_id"], analyse["run_name"])
+
+                    analysis_name = Utils.get_analyse_dirname(id, analyse['name'] )
                     dest_analysis_dir = os.path.join( output_folder, project_name, run_name, analysis_name )
+                    
                     if dest_analysis_dir not in dest_directories :
                         dest_directories.append(dest_analysis_dir)
                 # it's a project analysis
                 else :
-                    analysis_name = "Project_analyses/%s.%s" % ( re.sub( r"[\s\/]", "_", analyse["name"]), id)
+                    analysis_name = "Project_"+ Utils.get_analyse_dirname(id, analyse['name'] ) 
                     dest_analysis_dir = os.path.join( output_folder, project_name, analysis_name )
                     if dest_analysis_dir not in dest_directories :
                         dest_directories.append(dest_analysis_dir)
@@ -439,6 +488,9 @@ class Utils(object):
     
     @staticmethod    
     def rsync_getcmd( source, destination):
+        if source == "" or not os.path.isdir(source) :
+             return [ 0, "Source directory '" + source + "' doesn't exist, ignored."]
+        
         if not source.endswith("/"):
             source+="/"
         cmd = ["rsync", "-avh", "--perms", "--times", "--remove-sent-files", source, destination]

ui/nG6/class.tx_nG6_eid.php

+
+
 <?php
 /***************************************************************
 *  Copyright notice

ui/nG6/felogin.html

@@ -50,8 +50,6 @@
 <div class="sub-content sc-top-bottom">
     
 	<div class="ng6-content-header-left">
-		<h2>###STATUS_HEADER###</h2>
-		<p>###STATUS_MESSAGE###</p>
 		<!-- ###LOGIN_FORM### -->
 		<form action="###ACTION_URI###" target="_top" method="post" onsubmit="###ON_SUBMIT###" class="form-horizontal">
 			<fieldset>
@@ -130,8 +128,6 @@
 <div class="sub-content sc-top-bottom">
 
 	<div class="ng6-content-header-left">
-		<h2>###STATUS_HEADER###</h2>
-		<p>###STATUS_MESSAGE###</p>
 		<!-- ###LOGIN_FORM### -->
 		<form action="###ACTION_URI###" target="_top" method="post" onsubmit="###ON_SUBMIT###" class="form-horizontal">
 			<fieldset>

ui/nG6/lib/class.tx_nG6_utils.php

@@ -286,6 +286,7 @@ please have a look at our storage fees (<a href="###URL_PRICE###">###URL_PRICE##
     	return($config_file_content);
     }
     
+    //Return a php array containing the section relative to the given space_id
     static function get_retention_policy_from_space_id($space_id = "default"){
     	$config_file_content = tx_nG6_utils::get_config_content();
 		
@@ -420,6 +421,8 @@ please have a look at our storage fees (<a href="###URL_PRICE###">###URL_PRICE##
 		
     }
     
+    
+    
 
     
 }

ui/nG6/res/js/tx_nG6_pi1.js

+
 /***************************************************************
 *  Copyright notice
 *
@@ -1590,7 +1591,7 @@ function deletePRAHandler() {
 	    		    	url: val_url,
 	    		    	success: function(val, status, xhr) {
 	    		    		// return code : 0 = ok, 1 = right error, 2 = authentication error, 3 = connexion error		    				   
-	    		    		if (val == "0") {
+	    		    		if (val == '0') {
 	    	        			// Uncheck all checkboxes
 	    	        			$(':checked').each(function(i){
 	    	    		    		$(this).attr('checked',false);
@@ -1599,11 +1600,11 @@ function deletePRAHandler() {
 	    		    			location.reload();
 	    		    		} else {
 	    		    			$("#modal-label-tmpl").html("Error");
-	    		    			if (val == "1") {
+	    		    			if (val == '1') {
 	    		    				$("#modal-body-tmpl").html("<div class='tx-nG6-pi1-error'>You don't have write permission on the specified directory.</div>");
-	    		    			} else if (val == "2") {
+	    		    			} else if (val == '2') {
 	    		    				$("#modal-body-tmpl").html("<div class='tx-nG6-pi1-error'>An error occurred during login. Most likely you didn't enter the username or password correctly. Be certain that you enter them precisely as they are, including upper/lower case.</div>");
-	    		    			} else if (val == "3") {
+	    		    			} else if (val == '3') {
 	    		    				$("#modal-body-tmpl").html("<div class='tx-nG6-pi1-error'>An error occurred during server connection. Please contact the site administrator.</div>");
 	    		    			}
 	    		    			$("#modal-foot-tmpl").html('<button class="btn btn-default" data-dismiss="modal" aria-hidden="true"><i class="glyphicon glyphicon-remove"></i> Close</button>');
@@ -2237,8 +2238,68 @@ function setChangeSpaceForm(){
 	
 	//When clicking 'migrate'
     $("#run_workflow").click(function(){
-    	$('#change_space_id_form').wfform('run');
+    		
+    		var params = simpleQueryParams(location.href),
+    		project_id = params["tx_nG6_pi1[project_id]"];    		
+    	
+    		//We show a modal to check if the given SSH user + password is ok
+			var switch_space_auth_html = [
+                '<div class="tx-nG6-pi1-login">',
+                '	This functionality is only available if you have an account on the ' + $("#server_name").val() + ' server. <br /> <br /> ',
+                '	<form class="form-horizontal" id="tx-nG6-pi1-login-form" >',
+                '		<div class="input-group" style="margin-left:50px">',
+    		 	'			<span class="input-group-addon"><i class="glyphicon glyphicon-user"></i></span>',
+    		 	'			<input class="form-control" style="width:200px" type="text" id="user_login_val" name="user_login_val" placeholder="Username"/>',
+    		 	'		</div><br/>',
+		 		'		<div class="input-group" style="margin-left:50px">',
+			 	'			<span class="input-group-addon"><i class="glyphicon glyphicon-wrench"></i></span>',
+			 	'			<input class="form-control" style="width:200px" type="password" id="user_pwd_val" name="user_pwd_val" placeholder="Password"/>',
+			 	'		</div>',
+			 	'	</form>',
+			 	'</div>'
+			].join('');
+			$("#modal-label-tmpl").html("Migrate");
+    		$("#modal-body-tmpl").html(switch_space_auth_html);
+    		$("#modal-foot-tmpl").html('<button class="btn btn-default" data-dismiss="modal" aria-hidden="true"><i class="glyphicon glyphicon-remove"></i> Close</button>' +
+    								   '<button id="modal-btn-migrate" class="btn btn-primary"><i class="glyphicon glyphicon-trash"></i> Migrate</button>');
+    		$("#ng6modal").modal();
+    		
+    		$("#modal-btn-migrate").click(function(){
+    			var params = simpleQueryParams(location.href),
+        		project_id = params["tx_nG6_pi1[project_id]"]; 
+    			
+    			//We call the ajax check "check_ssh_user"
+    	    	var val_url = "index.php?eID=tx_nG6&type=check_ssh_user";
+    			   val_url += "&user_login=" + $("#user_login_val").val() + "&user_pwd=" + $("#user_pwd_val").val() + "&project_id=" + project_id;
+    	    		
+    	    		$.ajax({
+    			    	url: val_url,
+    			    	success: function(val, status, xhr) {
+    			    		// return codes : 0 = ok, 2 = authentication error, 3 = connexion error, 4 = the user doesn't have the rights		    				   
+    			    		// For no reason I understand, the string returned is "\n\n<ret_code>", so we parse it to int.
+    			    		val = parseInt(val);
+    			    		if (val == 0) {
+    			    			$("#ng6modal").modal('hide');
+    			    			//Run switch_space_id workflow
+    		    	        	$('#change_space_id_form').wfform('run');
+
+    			    		} else {
+    			    			$("#modal-label-tmpl").html("Error");
+    			    			if (val == 2) {
+    			    				$("#modal-body-tmpl").html("<div class='tx-nG6-pi1-error'>An error occurred during login. Most likely you didn't enter the username or password correctly. Be certain that you enter them precisely as they are, including upper/lower case.</div>");
+    			    			} else if (val == 3) {
+    			    				$("#modal-body-tmpl").html("<div class='tx-nG6-pi1-error'>An error occurred during server connection. Please contact the site administrator.</div>");
+    			    			} else if(val == 4){
+    			    				$("#modal-body-tmpl").html("<div class='tx-nG6-pi1-error'>The user you entered doesn't have the rights to perform this action.</div>");
+    			    			}
+    			    			$("#modal-foot-tmpl").html('<button class="btn btn-default" data-dismiss="modal" aria-hidden="true"><i class="glyphicon glyphicon-remove"></i> Close</button>');
+    			        		$("#ng6modal").modal();
+    			    		}
+    				   }
+    			   });
+    		});
     });
+
     
     //The status label has to be display just for a few seconds each time we hit "Migrate" or "Refresh" 
 	$("#change_space_id_status").hide();

ui/nG6/res/smarty/libs/plugins/modifier.get_description.php

@@ -109,6 +109,8 @@ function get_casava_1_8_desc($string, $desc) {
     			$best_description = $description." (R1)";
     		} elseif (preg_match("/_R2/i", $string)) {
     			$best_description = $description." (R2)";
+    		} elseif (preg_match("/_I1/i", $string)) {
+    			$best_description = $description." (I1)";
     		}
     	}
     }

ui/nG6/template/css/style.css

@@ -68,20 +68,22 @@ a img { border: 0; }
 }
 
 .ng6-content-header-left {
-	box-shadow: -4px 0 5px -5px grey, 5px 0 5px -6px grey;
+    box-shadow: -4px 0 5px -5px grey, 5px 0 5px -6px grey;
     margin: 0;
+    margin-left: 10px;
+    margin-right: 20px;
     padding: 10px;
-    width: 375px;
+    width: 400px;
     height: 275px;
     text-align: justify;
     float: left;
     background-color: #FaFaFa;
 }
 .ng6-content-header-right {
-	box-shadow: -4px 0 5px -5px grey, 5px 0 5px -6px grey;
+    box-shadow: -4px 0 5px -5px grey, 5px 0 5px -6px grey;
     margin: 0;
     padding: 10px;
-    width: 625px;
+    width: 710px;
     text-align: justify;
     float: left;
     background-color: #FaFaFa;
@@ -143,7 +145,7 @@ a img { border: 0; }
 	padding: 0;
 	margin-left: auto;
     margin-right: auto;
-    width: 1300px;
+    width: 1000px;
     color: #BBBABA;
     display: block;
     line-height: 1.5em;

workflows/illumina_10X/__init__.py

@@ -37,4 +37,4 @@ class Illumina10XQualityCheck (CasavaNG6Workflow):
 
 
     def process(self):
-        fastqilluminafilter, filtered_read1_files, filtered_read2_files, concat_files = self.illumina_process()
\ No newline at end of file
+        fastqilluminafilter, filtered_read1_files, filtered_read2_files, concat_files, concatenatefastq = self.illumina_process()
\ No newline at end of file

workflows/switch_space_id/components/move_project.py

@@ -29,53 +29,54 @@ def migrate_project (project_id, new_space_id, output):
     from ng6.analysis import Analysis
     from ng6.project import Project
     from ng6.run import Run
-
-    with open( output,'w') as fh :
-        ng6conf = NG6ConfigReader()
-        base_path = ng6conf.get_save_directory()
-        
-        project = Project.get_from_id(project_id)
-        
-        logging.getLogger("migrate_project").debug("Migrating project '" + str(project.name) + "' (" + str(project.id) + ") to " + str(new_space_id) + "\n")
-        fh.write("Migrating project '" + str(project.name) + "' (" + str(project.id) + ") to " + str(new_space_id) + "\n")
+    
+    def log_to_output_files (log_text, log_file):
+        fh = open(log_file, "a")        
+        fh.write(log_text)
+        fh.close()
+        logging.getLogger("move_project.py").debug(log_text)
+        print( "os.path.exists("+log_file+")=" + str(os.path.exists(log_file)))
+    
+    ng6conf = NG6ConfigReader()
+    base_path = ng6conf.get_save_directory()
         
-        old_space_id = project.space_id
-        logging.getLogger("migrate_project").debug("old_space_id = " + old_space_id + ", new_space_id = " + new_space_id + "\n")
-        fh.write("old_space_id = " + old_space_id + ", new_space_id = " + new_space_id + "\n")
+    project = Project.get_from_id(project_id)
+    old_space_id = project.space_id        
+       
+    str_log="MIGRATE PROJECT: '" + str(project.name) + "' (" + str(project.id) + ") from " + old_space_id + " to " + str(new_space_id) + "\n"
+    log_to_output_files(str_log, output)
+       
+    runs = project.get_runs()
+    for run in runs :
+        str_log="\t -  ##RUN '" + run.name + "' (" + str(run.id) + ") - " + run.directory + "\n"
+        log_to_output_files(str_log, output)
         
-        str_cmds = []
-        runs = project.get_runs()
-        for run in runs :
-            fh.write("Migrating run '" + run.name + "' (" + str(run.id) + ")" + " to " + str(new_space_id) + "\n")
-            logging.getLogger("migrate_project").debug("Migrating run '" + run.name + "' (" + str(run.id) + ")" + " to " + str(new_space_id) + "\n")
-            str_cmds.append(run.change_space(new_space_id) )
-            fh.write("Migrating successful! \n")
-            logging.getLogger("migrate_project").debug("Migrating successful! \n")
-            
-            run_analyzes = run.get_analysis()
-            for analysis in run_analyzes :
-                fh.write("Migrating analysis '" + analysis.name + "' (" + str(analysis.id) + ")" + " to " + str(new_space_id) + "\n")
-                logging.getLogger("migrate_project").debug("Migrating analysis '" + analysis.name + "' (" + str(analysis.id) + ")" + " to " + str(new_space_id) + "\n")
-                str_cmds.append(analysis.change_space(new_space_id) )
-                fh.write("Migrating successful! \n")
-                logging.getLogger("migrate_project").debug("Migrating successful! \n")
+        (ret_code, ret_command) = run.change_space(new_space_id) 
+        str_log = "\t   RET CODE: " + str(ret_code) + " CMD : " +  ret_command + "\n"
+        log_to_output_files(str_log, output)
+       
+        run_analyzes = run.get_analysis()
+        for analysis in run_analyzes :
+            str_log = "\t\t - ###ANALYSE " + analysis.name+ "' (" + str(analysis.id) + ") - " + analysis.directory + "\n"
+            log_to_output_files(str_log, output)
             
-        analyzes = project.get_analysis()
-        for analysis in analyzes :
-            fh.write("Migrating analysis '" + analysis.name + "' (" + str(analysis.id) + ")" + " to " + str(new_space_id) + "\n")
-            logging.getLogger("migrate_project").debug("Migrating analysis '" + analysis.name + "' (" + str(analysis.id) + ")" + " to " + str(new_space_id) + "\n")
-            str_cmds.append(analysis.change_space(new_space_id) )
-            fh.write("Migrating successful! \n")
-            logging.getLogger("migrate_project").debug("Migrating successful! \n")
-        
-        for command in str_cmds:
-            fh.write("Command launched : "+ str(command[1]) + "\n" )
-            logging.getLogger("migrate_project").debug("Command launched : "+ str(command[1]) + "\n" )
-            fh.write("Returned code : "+ str(command[0]) + "\n" )
-            logging.getLogger("migrate_project").debug("Returned code : "+ str(command[0]) +