Handle no ###USER### to replace. Bug on docker/

src/jflow/config_reader.py

@@ -29,7 +29,7 @@ class JFlowConfigReader(object):
     """
     
     CONFIG_FILE_PATH = "../../application.properties"
-    
+    USER_PATTERN = re.compile("###USER###")
     def __init__(self):
         """ 
         """
@@ -37,12 +37,18 @@ 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 +65,13 @@ 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:
@@ -118,6 +128,12 @@ class JFlowConfigReader(object):
             return self.reader.get("components", component_class+".batch_options")
         except:
             return ""
+
+    def get_component_modules(self, component_class):
+        try:
+            return self.reader.get("components", component_class+".modules").split(",")
+        except:
+            return []
     
     def get_workflow_group(self, workflow_class):
         try: