Merge branch 'issue#86' into 'master'

Merge branch Issue#86 into master

See merge request !31

src/ng6/utils.py

@@ -377,9 +377,10 @@ 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('/', '_'), id )
+                run_name = "Run_%s.%s" % ( re.sub( r"[^A-Za-z1-9]", "_", run['name']), id)
                 
                 raw_data_dir = os.path.join( output_folder, project_name, run_name, "RawData"  )
                 if source_dir not in src_directories :
@@ -392,6 +393,7 @@ 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 :
@@ -409,6 +411,7 @@ class Utils(object):
                 # 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)
                     dest_analysis_dir = os.path.join( output_folder, project_name, run_name, analysis_name )
                     if dest_analysis_dir not in dest_directories :
@@ -429,7 +432,6 @@ 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',

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
@@ -44,7 +46,6 @@ def create_symbolik_link (ids_dump_path, output_list, user_script, username, pas
         fh.close()
         prefixed_ids = ";".join(prefixed_ids)
         src_directories, dest_directories = Utils.get_directories_structure_and_content(ng6_username, data_folder, output_folder, prefixed_ids)
-        
         destinations = []
         with open(user_script, "w") as us: