Merge remote-tracking branch 'origin' into dev

src/jflow/config_reader.py

@@ -16,6 +16,7 @@
 #
 
 import os
+import re
 import sys
 import inspect
 import logging
@@ -29,7 +30,7 @@ class JFlowConfigReader(object):
     """
     
     CONFIG_FILE_PATH = "../../application.properties"
-    
+    USER_PATTERN = re.compile("###USER###")
     def __init__(self):
         """ 
         """
@@ -37,12 +38,18 @@ class JFlowConfigReader(object):
         self.reader.read(os.path.join(os.path.dirname(inspect.getfile(self.__class__)), self.CONFIG_FILE_PATH))
 
     def get_tmp_directory(self):
-        if not os.path.isdir(self.reader.get("storage", "tmp_directory").replace("###USER###",os.getenv("USER"))):
-            os.makedirs(self.reader.get("storage", "tmp_directory").replace("###USER###",os.getenv("USER")), 0o751)
-        return self.reader.get("storage", "tmp_directory").replace("###USER###",os.getenv("USER"))
-        
+        tmp_dir=self.reader.get("storage", "tmp_directory")
+        if self.USER_PATTERN.search(self.reader.get("storage", "tmp_directory")) is not None :
+            tmp_dir=tmp_dir.replace("###USER###",os.getenv("USER"))
+        if not os.path.isdir(tmp_dir):
+            os.makedirs(tmp_dir, 0o751)
+        return tmp_dir
+
     def get_work_directory(self):
-        return self.reader.get("storage", "work_directory").replace("###USER###",os.getenv("USER"))
+        if self.USER_PATTERN.search(self.reader.get("storage", "work_directory")) is None :
+            return self.reader.get("storage", "work_directory")
+        else:
+            return self.reader.get("storage", "work_directory").replace("###USER###",os.getenv("USER"))
     
     def get_exec(self, software):
         try:
@@ -59,9 +66,13 @@ class JFlowConfigReader(object):
           @return: the path to the log file
         """
         try:
-            return self.reader.get('storage', 'log_file').replace("###USER###",os.getenv("USER"))
+            if self.USER_PATTERN.search(self.reader.get("storage", "log_file")) is None :
+                return self.reader.get('storage', 'log_file')
+            else :
+                return self.reader.get('storage', 'log_file').replace("###USER###",os.getenv("USER"))
         except :
             raise NoOptionError("Failed when parsing the config file, no section logging found!")
+
         
     def get_makeflow_path(self):
         try:

src/jflow/workflow.py

@@ -383,24 +383,38 @@ class Workflow(threading.Thread):
                 all_nodes[ioparameter.name] = None
             elif issubclass(ioparameter.__class__, MultiParameter):
                 for subparam in ioparameter.sub_parameters:
-                    gr.add_node(subparam.name)
-                    all_nodes[subparam.name] = None
                     if issubclass(subparam.__class__, InputFile):
+                        all_nodes[subparam.name] = None
+                        gr.add_node(subparam.name)
                         gr.add_node_attribute(subparam.name, self.INPUTFILE_GRAPH_LABEL)
+                        gr.add_node_attribute(subparam.name, subparam.display_name)
                     elif issubclass(subparam.__class__, InputFileList):
+                        all_nodes[subparam.name] = None
+                        gr.add_node(subparam.name)
                         gr.add_node_attribute(subparam.name, self.INPUTFILES_GRAPH_LABEL)
+                        gr.add_node_attribute(subparam.name, subparam.display_name)
                     elif issubclass(subparam.__class__, InputDirectory):
+                        all_nodes[subparam.name] = None
+                        gr.add_node(subparam.name)
                         gr.add_node_attribute(subparam.name, self.INPUTDIRECTORY_GRAPH_LABEL)
-                    gr.add_node_attribute(subparam.name, subparam.display_name)
+                        gr.add_node_attribute(subparam.name, subparam.display_name)
             elif issubclass(ioparameter.__class__, MultiParameterList):
                 for subparam in ioparameter.sub_parameters:
-                    gr.add_node(subparam.name)
-                    all_nodes[subparam.name] = None                        
-                    if issubclass(subparam.__class__, InputDirectory):
-                        gr.add_node_attribute(subparam.name, self.INPUTDIRECTORY_GRAPH_LABEL)
-                    else:
+                    if issubclass(subparam.__class__, InputFile):
+                        all_nodes[subparam.name] = None
+                        gr.add_node(subparam.name)
+                        gr.add_node_attribute(subparam.name, self.INPUTFILE_GRAPH_LABEL)
+                        gr.add_node_attribute(subparam.name, subparam.display_name)
+                    elif issubclass(subparam.__class__, InputFileList):
+                        all_nodes[subparam.name] = None
+                        gr.add_node(subparam.name)
                         gr.add_node_attribute(subparam.name, self.INPUTFILES_GRAPH_LABEL)
-                    gr.add_node_attribute(subparam.name, subparam.display_name)
+                        gr.add_node_attribute(subparam.name, subparam.display_name)
+                    elif issubclass(subparam.__class__, InputDirectory):
+                        all_nodes[subparam.name] = None
+                        gr.add_node(subparam.name)
+                        gr.add_node_attribute(subparam.name, self.INPUTDIRECTORY_GRAPH_LABEL)
+                        gr.add_node_attribute(subparam.name, subparam.display_name)
         for cpt in self.components:
             gr.add_node(cpt.get_nameid())
             gr.add_node_attribute(cpt.get_nameid(), self.COMPONENT_GRAPH_LABEL)