Fix for issue#86

src/ng6/utils.py

@@ -377,9 +377,9 @@ class Utils(object):
             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'] )
-                run_name = "Run_%s.%s" %( run['name'].replace(' ', '_').replace('/', '_'), id )
+                
+                run_name = "Run_%s.%s" %( run['name'].replace(' ', '_').replace('/', '_').replace('\\','_').replace('(','_').replace(')','_'), id )
                 
                 raw_data_dir = os.path.join( output_folder, project_name, run_name, "RawData"  )
                 if source_dir not in src_directories :
@@ -392,6 +392,7 @@ class Utils(object):
                         analysis_dir = data_folder + '/' + analyse_values["directory"]
                         analysis_name = "Analyse_%s.%s"%( re.sub( r"[\s\/]", "_", analyse_values['name']), analyse_id )
                         dest_analysis_dir = os.path.join( output_folder, project_name, run_name, analysis_name  )
+                        
                         if analysis_dir not in src_directories :
                             src_directories.append(analysis_dir)
                         if dest_analysis_dir not in dest_directories :
@@ -429,7 +430,6 @@ class Utils(object):
             if os.path.isdir(e) :
                 sources.append(e)
                 destinations.append(dest_directories[i])
-        
         return sources, destinations 
         
         

ui/nG6/res/js/tx_nG6_pi5.js

@@ -83,6 +83,7 @@ $(function () {
 	};	
 	
 	var _retrieve_data = function(workflow_id, callback, error_callback){
+		console.log("IN _retrieve_data, workflow_id=" + workflow_id);
     	$.ajax({
             url : $("#server_url").val() + '/get_workflow_outputs?workflow_id=' + workflow_id,
             dataType : 'jsonp',
@@ -159,15 +160,20 @@ $(function () {
 			button = this;
 			button.disabled = true;
 			
+			console.log("IN _retrieve_url_list, before _retrieve_data, step 1");
 			_get_workflow_status(running_wf.id , 
 				// successcb
 				function(statusdata){
 					if (statusdata.status == "completed"){
+						console.log("IN _retrieve_url_list, before _retrieve_data, running_wf.id=" + running_wf.id);
 						_retrieve_data(running_wf.id, function(data){
 							$(button).hide();
 			            	$.each(data, function(i, component) {
 	    			    		$.each(component, function(filename, file) {
 	    			    			if (filename == ufilename){
+	    			    				console.log("IN _retrieve_url_list, before _display_file_content, step 2");
+	    			    				console.log("IN _retrieve_url_list, file.url="+file.url);
+	    			    				console.log("IN _retrieve_url_list, process_data="+process_data);
 	    			    				_display_file_content(file.url, modal.$body, process_data);
 	    			    			}
 	    			    		});
@@ -286,6 +292,7 @@ $(function () {
     			modal.$modal.modal();
 				modal.$modal.find('#wfform').wfform(form_options);
 				modal.$modal.find('#wfform').on('run.wfform', function(event, running_wf) {
+					console.log("IN download_options, before _retrieve_url_list");
 					_retrieve_url_list(modal, running_wf, 'output_list.txt');
 				});
     		},

workflows/download_symlink/components/createsymlink.py

@@ -17,6 +17,7 @@
 
 import os
 import pickle
+import logging
 
 from jflow.component import Component
 from ng6.utils import Utils
@@ -27,6 +28,7 @@ def create_symbolik_link (ids_dump_path, output_list, user_script, username, pas
     import os
     import pickle
     import subprocess
+    import logging
     
     from ng6.config_reader import NG6ConfigReader 
     from ng6.utils import Utils, SSH
@@ -43,8 +45,10 @@ def create_symbolik_link (ids_dump_path, output_list, user_script, username, pas
         prefixed_ids = pickle.load(fh)
         fh.close()
         prefixed_ids = ";".join(prefixed_ids)
+        logging.getLogger("createsymlink").debug("Before Utils.get_directories_structure_and_content()")
         src_directories, dest_directories = Utils.get_directories_structure_and_content(ng6_username, data_folder, output_folder, prefixed_ids)
-        
+        logging.getLogger("createsymlink").debug("src_directories = " + ",".join(src_directories))
+        logging.getLogger("createsymlink").debug("dest_directories = " + ",".join(dest_directories))
         destinations = []
         with open(user_script, "w") as us: