Fix serialisation bug with DateParameter.

application.properties

@@ -28,6 +28,8 @@ limit_submission = 100
 server_socket_host = 127.0.0.1
 # on which socket port should run the web server
 server_socket_port = 8080
+# date format
+date_format = %d/%m/%Y
 
 [email]
 # if you want an email to be sent at the end of the workflow execution

bin/jflow_server.py

@@ -22,6 +22,7 @@ import json
 import sys
 from functools import wraps
 import time
+import datetime
 import os
 import argparse
 import logging
@@ -76,6 +77,12 @@ def CORS():
     cherrypy.response.headers['Access-Control-Allow-Headers'] = 'Content-Type, Content-Range, Content-Disposition'
 cherrypy.tools.CORS = cherrypy.Tool('before_finalize', CORS)
 
+class JFlowJSONEncoder (json.JSONEncoder):
+    def default(self, obj):
+        if isinstance(obj, (datetime.date, datetime.datetime)):
+            return obj.strftime( JFlowConfigReader().get_date_format() )
+        else:
+            return json.JSONEncoder.default(self, obj)
 
 class JFlowServer (object):
 
@@ -94,7 +101,7 @@ class JFlowServer (object):
             value = func(*args, **kw)
             cherrypy.response.headers["Content-Type"] = "application/json"
             # if JSONP request
-            if kw.has_key("callback"): return kw["callback"] + "(" + json.dumps(value) + ")"
+            if kw.has_key("callback"): return kw["callback"] + "(" + json.dumps(value, cls=JFlowJSONEncoder) + ")"
             # else return the JSON
             else: return json.dumps(value)
         return wrapper
@@ -146,7 +153,7 @@ class JFlowServer (object):
                       "start_time": start_time,
                       "end_time": end_time,
                       "components": components}
-         
+
             return status
 
     @cherrypy.expose
@@ -173,9 +180,19 @@ class JFlowServer (object):
                               "name": param.name,
                               "display_name": param.display_name,
                               "group": param.group}
+                if hash_param["type"] == "date":
+                    hash_param["format"] = self.jflow_config_reader.get_date_format()
+                    if hash_param["format"] == '%d/%m/%Y':
+                        hash_param["format"] = 'dd/mm/yyyy'
+                    elif hash_param["format"] == '%d/%m/%y':
+                        hash_param["format"] = 'dd/mm/yy'
+                    elif hash_param["format"] == '%Y/%m/%d':
+                        hash_param["format"] = 'yyyy/mm/dd'
+                    elif hash_param["format"] == '%y/%m/%d':
+                        hash_param["format"] = 'yy/mm/dd'
                 # if it's a multiple type add sub parameters
                 if type(param.type) == jflow.parameter.MultipleParameters:
-                    hash_param["sub_parameters"] = [] 
+                    hash_param["sub_parameters"] = []
                     for sub_param in param.sub_parameters:
                         hash_param["sub_parameters"].append({"help": sub_param.help,
                               "required": sub_param.required,
@@ -186,6 +203,16 @@ class JFlowServer (object):
                               "name": param.name + JFlowServer.MULTIPLE_TYPE_SPLITER + sub_param.flag,
                               "display_name": sub_param.display_name,
                               "group": param.group})
+                        if hash_param["type"] == "date":
+                            hash_param["format"] = self.jflow_config_reader.get_date_format()
+                            if hash_param["format"] == '%d/%m/%Y':
+                                hash_param["format"] = 'dd/mm/yyyy'
+                            elif hash_param["format"] == '%d/%m/%y':
+                                hash_param["format"] = 'dd/mm/yy'
+                            elif hash_param["format"] == '%Y/%m/%d':
+                                hash_param["format"] = 'yyyy/mm/dd'
+                            elif hash_param["format"] == '%y/%m/%d':
+                                hash_param["format"] = 'yy/mm/dd'
                 parameters.append(hash_param)
                 if parameters_per_groups.has_key(param.group):
                     parameters_per_groups[param.group].append(hash_param)
@@ -202,27 +229,26 @@ class JFlowServer (object):
     @cherrypy.expose
     @jsonify
     def run_workflow(self, **kwargs):
-    	try:
-        	kwargs_modified = {}
-        	for key in kwargs.keys():
-        	    parts = key.split(JFlowServer.MULTIPLE_TYPE_SPLITER)
+        try:
+            kwargs_modified = {}
+            for key in kwargs.keys():
+                parts = key.split(JFlowServer.MULTIPLE_TYPE_SPLITER)
                 # if this is a classic Parameter
-        	    if len(parts) == 1:
-        	        kwargs_modified[key] = kwargs[key]
+                if len(parts) == 1:
+                    kwargs_modified[key] = kwargs[key]
                 # if this is a MultiParameter
-        	    elif len(parts) == 2:
-        	        if kwargs_modified.has_key(parts[0]):
-        	            kwargs_modified[parts[0]].append((parts[1], kwargs[key]))
-        	        else:
-        	            kwargs_modified[parts[0]] = [(parts[1], kwargs[key])]
+                elif len(parts) == 2:
+                    if kwargs_modified.has_key(parts[0]):
+                        kwargs_modified[parts[0]].append((parts[1], kwargs[key]))
+                    else:
+                        kwargs_modified[parts[0]] = [(parts[1], kwargs[key])]
                 # if this is a MultiParameterList
                 # TODO: du cote interface faire qq chose du genre: key.sub_key.1 ... donc si len == 3 
                 # l'objectif etant d'avoir une structure de type: [[(sub_key1: val), (sub_key2: val)], [(sub_key1: val2), (sub_key2: val2)]]
-                
-        	workflow = self.wfmanager.run_workflow(kwargs_modified["workflow_class"], kwargs_modified)
-        	return { "status" : 0, "content" : self.jsonify_workflow_status(workflow, True) }
-    	except Exception as err:
-    		return { "status" : 1, "content" : str(err) }
+            workflow = self.wfmanager.run_workflow(kwargs_modified["workflow_class"], kwargs_modified)
+            return { "status" : 0, "content" : self.jsonify_workflow_status(workflow, True) }
+        except Exception as err:
+            return { "status" : 1, "content" : str(err) }
 
     @cherrypy.expose
     @jsonify

src/jflow/config_reader.py

@@ -73,7 +73,14 @@ class JFlowConfigReader(object):
             sys.stderr.write("Error: 'makeflow' path connot be retrieved either in the PATH and in the application.properties file!\n")
             sys.exit(1)
         return exec_path
-    
+
+    def get_date_format(self):
+        try:
+            date_format = self.reader.get("global", "date_format")
+        except:
+            raise Error("Failed when parsing the config file, no parameter date_format!")
+        return date_format
+
     def get_batch(self):
         try:
             type = self.reader.get("global", "batch_system_type")

src/jflow/parameter.py

@@ -587,6 +587,14 @@ class DateParameter(datetime.datetime, AbstractParameter):
         else:
             return (True if datetime.date(self.year, self.month, self.day) else False)
 
+    def __reduce__(self):
+        return (DateParameter, (self.name, self.help, self.default, date, self.choices, self.required,
+                 self.flag, self.sub_parameters, self.group, self.display_name), None, None, None)
+
+    def __reduce_ex__(self, protocol):
+        return (DateParameter, (self.name, self.help, self.default, date, self.choices, self.required,
+                 self.flag, self.sub_parameters, self.group, self.display_name), None, None, None)
+
 
 class AbstractInputFile(AbstractIOFile):
     """
@@ -616,7 +624,7 @@ class AbstractInputFile(AbstractIOFile):
             return [file_path, True]
         except:
             return [input, False]
-        
+
     def check(self, ifile):
         try:
             eval(self.file_format)
@@ -673,7 +681,7 @@ class InputFile(StrParameter, AbstractInputFile):
         if is_local: new_path = input
         self.check(new_path)
         return new_path
-            
+
 
 class OutputFile(StrParameter, AbstractOutputFile):
 

src/jflow/workflow.py

@@ -100,7 +100,7 @@ class Workflow(threading.Thread):
             if type: self.engine_arguments += ' -T ' + type
             if options : self.engine_arguments += ' -B "' + options + '"'
         except: self.engine_arguments = None
-        
+
         self.id = id
         self.name = self.get_name()
         self.description = self.get_description()
@@ -669,14 +669,14 @@ class Workflow(threading.Thread):
             # if post processing has ne been done yet
             if self.step == 3:
                 self.post_process()
-                if self.status == self.STATUS_STARTED: self.status = self.STATUS_COMPLETED        
+                if self.status == self.STATUS_STARTED: self.status = self.STATUS_COMPLETED
                 self.end_time = time.time()
                 self._serialize()
                 self._send_email()
         except:
             logging.getLogger("wf." + str(self.id)).exception("RunWorflowException")
             raise
-    
+
     def _update_status_from_log(self):
         # first update the status from weaver folders
         # TODO update self.end_time

src/js/jflow-wfform.js

@@ -508,7 +508,7 @@ jQuery.validator.addMethod("exclude_required", function(value, element, options)
 			'  </select>',
 			// if param is a date 
 			'{{else param.type == "date"}}',
-			'  <div class="input-append date" data-date="${param.default}" data-date-format="dd/mm/yyyy">',
+			'  <div class="input-append date" data-date="${param.default}" data-date-format="${param.format}">',
 			'    <input id="${param.name}" name="${param.name}" class="${param.group} ${input_size} span2" type="text" value="${param.default}">',
 			'    <button class="btn" type="button"><i class="icon-calendar"></i></button>',
 			'  </div>',

workflows/types.py

@@ -17,12 +17,12 @@
 
 import argparse
 import datetime
+from jflow.config_reader import JFlowConfigReader
 
 
 def date(datestr):
     try:
-        return datetime.datetime.strptime(datestr, '%d/%m/%Y')
+        return datetime.datetime.strptime(datestr, JFlowConfigReader().get_date_format())
     except:
         raise argparse.ArgumentTypeError("'" + datestr + "' is an invalid date!")
-    
-        
\ No newline at end of file
+