Add DateParameter.

Fix bug on parameters.

src/jflow/component.py

@@ -102,7 +102,7 @@ class Component(object):
 
     def add_parameter(self, name, help, default=None, type=types.StringType, choices=None, 
                       required=False, flag=None, group="default", display_name=None, add_to=None):
-        new_param = Parameter(name, help, flag=flag, default=default, type=type, choices=choices, 
+        new_param = ParameterFactory.factory(name, help, flag=flag, default=default, type=type, choices=choices, 
                               required=required, group=group, display_name=display_name)
         # if this input should be added to a particular parameter
         if add_to:
@@ -131,7 +131,7 @@ class Component(object):
 
     def add_output_file(self, name, help, file_format="any", filename=None, group="default", display_name=None, add_to=None):
         filename = os.path.basename(filename)
-        new_param = OutputFile(name, help, default=os.path.join(self.output_directory, filename), 
+        new_param = OutputFile(name, help, default=os.path.join(self.output_directory, filename),
                                file_format=file_format, group=group, display_name=display_name)
         # if this input should be added to a particular parameter
         if add_to:

src/jflow/parameter.py

@@ -260,7 +260,7 @@ class AbstractParameter(object):
 
         # Set parameter type
         if type == "date":
-            self.type = types.MemberDescriptorType
+            self.type = date
         elif type == "multiple":
             self.type = "multiple"
         elif isinstance(type, types.FunctionType):
@@ -303,7 +303,7 @@ class AbstractIOFile(object):
 
 
 class MultiParameter(dict, AbstractParameter):
-    
+
     def __init__(self, name, help, required=False, flag=None, group="default", display_name=None):
         AbstractParameter.__init__(self, name, help, required=required, type="multiple", flag=flag, group=group, 
                                    display_name=display_name)
@@ -338,7 +338,7 @@ class MultiParameter(dict, AbstractParameter):
 
 
 class MultiParameterList(list, AbstractParameter):
-    
+
     def __init__(self, name, help, required=False, flag=None, group="default", display_name=None):
         AbstractParameter.__init__(self, name, help, required=required, type="multiple", flag=flag, 
                                    action="append", group=group, display_name=display_name)
@@ -347,9 +347,9 @@ class MultiParameterList(list, AbstractParameter):
     def add_sub_parameter(self, param):
         param_flag = param.flag[2:]
         if self.type == "multiple":
-            if param.required: req = [param_flag] 
+            if param.required: req = [param_flag]
             else: req = []
-            self.type = MultipleParameters({param_flag: param.type}, req, 
+            self.type = MultipleParameters({param_flag: param.type}, req,
                                            {param_flag: param.choices}, {}, {param_flag: param.default},
                                            {param_flag: param.action})
             if self.action == "append":
@@ -372,13 +372,31 @@ class MultiParameterList(list, AbstractParameter):
         self.sub_parameters.append(param)
 
 
+class ParameterFactory(object):
+    @staticmethod
+    def factory(*args, **kwargs):
+        if not kwargs.has_key( "type" ):
+            return StrParameter( *args, **kwargs )
+
+        if kwargs["type"] == "int" or kwargs["type"] is types.IntType:
+            return IntParameter( *args, **kwargs )
+        elif kwargs["type"] == "bool" or kwargs["type"] is types.BooleanType:
+            return BoolParameter( *args, **kwargs )
+        elif kwargs["type"] == "float" or kwargs["type"] is types.FloatType:
+            return FloatParameter( *args, **kwargs )
+        elif kwargs["type"] == "date" or kwargs["type"] == date:
+            return DateParameter( *args, **kwargs )
+        else:
+            return StrParameter( *args, **kwargs )
+
+
 def noneException(*args, **kwargs):
     raise Exception( "The parameter value is None." )
 
 
 class BoolParameter(int, AbstractParameter):
 
-    def __new__(self, name, help, default=None, type=types.BooleanType, choices=None, required=False,
+    def __new__(self, name, help, default=False, type=types.BooleanType, choices=None, required=False,
                 flag=None, sub_parameters=None, group="default", display_name=None):
         bool_default = False if default == None else bool(default)
         val = int.__new__(self, bool_default)
@@ -393,24 +411,24 @@ class BoolParameter(int, AbstractParameter):
 
     def __init__(self, name, help, default=None, type=types.BooleanType, choices=None, required=False,
                  flag=None, sub_parameters=None, group="default", display_name=None):
-        AbstractParameter.__init__(self, name, help, flag=flag, default=default, type=type, choices=choices, required=required, 
+        AbstractParameter.__init__(self, name, help, flag=flag, default=bool(default), type=type, choices=choices, required=required, 
                                    action="store", sub_parameters=sub_parameters, group=group, display_name=display_name)
 
+    def __str__(self):
+        if self.is_None:
+            noneException()
+        return str(bool(self))
+
     def __eq__(self, other):
         if other.__class__.__name__ == "NoneType":
             return self.is_None
         elif self.is_None:
             return False
         else:
-            return int(self) == int(other)
+            return int(self) == int(bool(other))
 
     def __ne__(self, other):
-        if other.__class__.__name__ == "NoneType":
-            return not self.is_None
-        elif self.is_None:
-            return True
-        else:
-            return int(self) != int(other)
+        return not (self == other)
 
     def __nonzero__(self):
         if self.is_None:
@@ -448,12 +466,7 @@ class IntParameter(int, AbstractParameter):
             return int(self) == int(other)
 
     def __ne__(self, other):
-        if other.__class__.__name__ == "NoneType":
-            return not self.is_None
-        elif self.is_None:
-            return True
-        else:
-            return int(self) != int(other)
+        return not (self == other)
 
     def __nonzero__(self):
         if self.is_None:
@@ -462,12 +475,12 @@ class IntParameter(int, AbstractParameter):
             return self != 0
 
 
-class FloatParameter(int, AbstractParameter):
+class FloatParameter(float, AbstractParameter):
 
     def __new__(self, name, help, default=None, type=types.FloatType, choices=None, required=False,
                 flag=None, sub_parameters=None, group="default", display_name=None):
         float_default = 0.0 if default == None else float(default)
-        val = int.__new__(self, float_default)
+        val = float.__new__(self, float_default)
         val.is_None = False
         if default == None:
             val.is_None = True
@@ -491,12 +504,7 @@ class FloatParameter(int, AbstractParameter):
             return float(self) == float(other)
 
     def __ne__(self, other):
-        if other.__class__.__name__ == "NoneType":
-            return not self.is_None
-        elif self.is_None:
-            return True
-        else:
-            return float(self) != float(other)
+        return not (self == other)
 
     def __nonzero__(self):
         if self.is_None:
@@ -534,12 +542,7 @@ class StrParameter(str, AbstractParameter):
             return str(self) == str(other)
 
     def __ne__(self, other):
-        if other.__class__.__name__ == "NoneType":
-            return not self.is_None
-        elif self.is_None:
-            return True
-        else:
-            return str(self) != str(other)
+        return not(self == other)
 
     def __nonzero__(self):
         if self.is_None:
@@ -548,20 +551,58 @@ class StrParameter(str, AbstractParameter):
             return (True if str(self) else False)
 
 
-class ParameterFactory(object):
-    @staticmethod
-    def factory(*args, **kwargs):
-        if not kwargs.has_key( "type" ):
-            return StrParameter( *args, **kwargs )
+class DateParameter(datetime.datetime, AbstractParameter):
 
-        if kwargs["type"] == "int" or kwargs["type"] is types.IntType:
-            return IntParameter( *args, **kwargs )
-        elif kwargs["type"] == "bool" or kwargs["type"] is types.BooleanType :
-            return BoolParameter( *args, **kwargs )
-        elif kwargs["type"] == "float" or kwargs["type"] is types.FloatType :
-            return FloatParameter( *args, **kwargs )
+    def __new__(self, name, help, default=None, type=date, choices=None, required=False,
+                flag=None, sub_parameters=None, group="default", display_name=None):
+        date_default = datetime.datetime.today()
+        if default != None and issubclass(default.__class__, datetime.datetime):
+            date_default = default
+        elif default != None:
+            date_default = date(default)
+
+        val = datetime.datetime.__new__(self, date_default.year, date_default.month, date_default.day)
+        if default != None:
+            val.is_None = False
         else:
-            return StrParameter( *args, **kwargs )
+            val.is_None = True
+            for attr in val.__dict__:
+                value = getattr(val, attr)
+                if callable(value) and attr not in ["__new__", "__init__", "__getattribute__", "__eq__", "__ne__", "__nonzero__"]:
+                    setattr(val, attr, noneException)
+        return val
+
+    def __init__(self, name, help, default=None, type=date, choices=None, required=False,
+                 flag=None, sub_parameters=None, group="default", display_name=None):
+        if default != None and not issubclass(default.__class__, datetime.datetime):
+            date_default = date(default)
+            default = datetime.datetime(date_default.year, date_default.month, date_default.day)
+        AbstractParameter.__init__(self, name, help, flag=flag, default=default, type=type, choices=choices, required=required, 
+                                   action="store", sub_parameters=sub_parameters, group=group, display_name=display_name)
+
+    def __eq__(self, other):
+        if other.__class__.__name__ == "NoneType":
+            return self.is_None
+        elif self.is_None:
+            return False
+        else:
+            return datetime.date(self.year, self.month, self.day) == other
+
+    def __ne__(self, other):
+        return not( self == other )
+
+    def __nonzero__(self):
+        if self.is_None:
+            return False
+        else:
+            return (True if datetime.date(self.year, self.month, self.day) else False)
+
+
+class AbstractInputFile(AbstractIOFile):
+    """
+     @summary : Parent of all InputFile(s) parameters.
+    """
+    pass
 
 
 class AbstractOutputFile(AbstractIOFile):
@@ -595,12 +636,12 @@ class InputFile(StrParameter, AbstractInputFile):
 
 class OutputFile(StrParameter, AbstractOutputFile):
 
-    def __new__(self, name, help, file_format="any", default="", choices=None, 
+    def __new__(self, name, help, file_format="any", default="", choices=None,
                 required=False, flag=None, group="default", display_name=None):
-        return StrParameter.__new__(self, name, help, flag=flag, default=default, type="localfile", choices=choices, 
+        return StrParameter.__new__(self, name, help, flag=flag, default=default, type="localfile", choices=choices,
                            required=required, group=group, display_name=display_name)
 
-    def __init__(self, name, help, file_format="any", default="", choices=None, 
+    def __init__(self, name, help, file_format="any", default="", choices=None,
                 required=False, flag=None, group="default", display_name=None):
         AbstractIOFile.__init__(self, file_format)
         StrParameter.__init__(self, name, help, flag=flag, default=default, type="localfile", choices=choices, 
@@ -612,7 +653,7 @@ class ParameterList(list, AbstractParameter):
     def __init__(self, name, help, default=None, type=types.StringType, choices=None, required=False,
                  flag=None, sub_parameters=None, group="default", display_name=None):
         if default == None: default = []
-        AbstractParameter.__init__(self, name, help, flag=flag, default=default, type=type, choices=choices, required=required, 
+        AbstractParameter.__init__(self, name, help, flag=flag, default=default, type=type, choices=choices, required=required,
                                    action="append", sub_parameters=sub_parameters, group=group, display_name=display_name)
         if default.__class__.__name__ == "str":
             return list.__init__(self, [default])

src/jflow/workflow.py

@@ -238,13 +238,13 @@ class Workflow(threading.Thread):
             return [file_path, True]
         except:
             return [input, False]
-    
+
     def _set_parameters(self, args):
         parameters = self.get_parameters()
         for param in parameters:
             try: args[param.name] = args[param.name].encode('ascii','ignore')
             except: pass
-            if param.__class__ ==  StrParameter or param.__class__ == IntParameter or param.__class__ == FloatParameter or param.__class__ == BoolParameter:
+            if param.__class__ ==  StrParameter or param.__class__ == IntParameter or param.__class__ == FloatParameter or param.__class__ == BoolParameter or param.__class__ == DateParameter:
                 if args[param.name]: default = args[param.name]
                 else: default = param.default
                 new_param = ParameterFactory.factory(param.name, param.help, default=default, type=param.type, choices=param.choices, 
@@ -259,7 +259,7 @@ class Workflow(threading.Thread):
                     except: is_local = False
                     if not is_uri and not is_local and param.type.__name__ == "inputfile" or param.type.__name__ == "browsefile":
                         default = os.path.join(self.jflow_config_reader.get_tmp_directory(), (args[param.name]))
-                else: 
+                else:
                     default = param.default
                 new_param = InputFile(param.name, param.help, file_format=param.file_format, default=default, type=param.type, 
                                       choices=param.choices, required=param.required, flag=param.flag, 
@@ -274,15 +274,15 @@ class Workflow(threading.Thread):
                     # handle url inputs
                     for path in path2test:
                         new_url, is_uri = self._download_urlfile(path)
-                        if is_uri: 
+                        if is_uri:
                             default_vals.append(new_url)
                             path2test.remove(path)
                     # handle localfile
-                    for path in path2test:    
+                    for path in path2test:
                         if os.path.isfile(path):
                             default_vals.append(path)
                             path2test.remove(path)
-                    # handle upload inputs 
+                    # handle upload inputs
                     if param.type.__name__ == "inputfile" or param.type.__name__ == "browsefile":
                         for path in path2test:
                             default_vals.append(os.path.join(self.jflow_config_reader.get_tmp_directory(), (path)))
@@ -316,7 +316,7 @@ class Workflow(threading.Thread):
                             final_sub_args[sub_param.name] = sub_param.default
                     final_vals.append(final_sub_args)
                 self.__setattr__(param.name, final_vals)
-    
+
     def get_execution_graph(self):
         graph = Graph()
         for cpt in self.components:
@@ -326,7 +326,7 @@ class Workflow(threading.Thread):
                      or issubclass( ioparameter.__class__, InputFileList) or issubclass( ioparameter.__class__, OutputFileList) ):
                     graph.add_edge({ioparameter.component_nameid, ioparameter.parent_component_nameid})
         return graph
-    
+
     def set_stderr(self):
         if hasattr(self, "stderr") and self.stderr is not None:
             os.rename( self.stderr, os.path.join(self.directory, str(time.time()) + "wf_stderr.old") )
@@ -339,12 +339,12 @@ class Workflow(threading.Thread):
         file_handler.setFormatter(formatter)
         logger.addHandler(file_handler)
         self.stderr = stderr
-    
+
     @staticmethod
     def config_parser(arg_lines):
         for arg in arg_lines:
             yield arg
-    
+
     def get_errors(self):
         error = {
                  "title"     : "",

workflows/test/__init__.py

+#
+# Copyright (C) 2012 INRA
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+# 
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+from jflow.workflow import Workflow
+from jflow.parameter import InputFileList, InputFile
+
+class Test (Workflow):
+    
+    def get_description(self):
+        return "use for test jflow core modifications"
+
+    def define_parameters(self, parameters_section=None):
+        self.add_multiple_parameter_list("multi1", "Multiple.")
+        self.add_parameter("test_A1", "Multiple float null.", add_to="multi1", type="float")
+        self.add_parameter("test_A2", "Multiple float default 1.", add_to="multi1", type="float", default=1)
+        self.add_parameter("test_A3", "Multiple int default 2.", add_to="multi1", type=int, default=2)
+        self.add_parameter("test_A4", "Multiple int null.", add_to="multi1", type=int)
+        self.add_parameter("test_A5", "Multiple date default str '20/08/2014'.", add_to="multi1", type="date", default="20/08/2014")
+        self.add_parameter("test_A6", "date default null.", add_to="multi1", type="date")
+        self.add_parameter("test_A7", "Multiple string default str 'None'.", add_to="multi1", default="None")
+        self.add_parameter("test_A8", "Multiple string null.", add_to="multi1")
+        self.add_parameter("test_A9", "Multiple bool default True.", add_to="multi1", type="bool", default=True)
+        self.add_parameter("test_A10", "Multiple bool default 3.", add_to="multi1", type="bool", default=3)
+        self.add_parameter("test_A11", "Multiple bool default null.", add_to="multi1", type="bool")
+        self.add_input_file("test_A12", "Multiple InputFile default null.", add_to="multi1")
+        self.add_input_file("test_A13", "Multiple InputFile default application.properties.", add_to="multi1", default="application.properties")
+        self.add_parameter("test_B1", "float null.", type="float")
+        self.add_parameter("test_B2", "float default 1.", type="float", default=1)
+        self.add_parameter("test_B3", "int default 2.", type=int, default=2)
+        self.add_parameter("test_B4", "int null.", type=int)
+        self.add_parameter("test_B5", "date default str 20/08/2014.", type="date", default="20/08/2014")
+        self.add_parameter("test_B6", "date default null.", type="date")
+        self.add_parameter("test_B7", "string default str None.", default="None")
+        self.add_parameter("test_B8", "string null.")
+        self.add_parameter("test_B9", "bool default True.", type="bool", default=True)
+        self.add_parameter("test_B10", "bool default false.", type="bool", default=False)
+        self.add_parameter("test_B11", "bool default null.", type="bool")
+        self.add_input_file("test_B12", "Multiple InputFile default null.")
+        self.add_input_file("test_B13", "Multiple InputFile default application.properties.", default="application.properties")
+        self.add_multiple_parameter_list("multi2", "Multiple required.", required=True)
+        self.add_parameter("valid", "Multiple required.", add_to="multi2", default="ok")
+        self.add_parameter("test_C1", "Multiple float null.", add_to="multi2", type="float")
+        self.add_parameter("test_C2", "Multiple float default 1.", add_to="multi2", type="float", default=1)
+        self.add_parameter("test_C3", "Multiple int default 2.", add_to="multi2", type=int, default=2)
+        self.add_parameter("test_C4", "Multiple int null.", add_to="multi2", type=int)
+        self.add_parameter("test_C5", "Multiple date default str '20/08/2014'.", add_to="multi2", type="date", default="20/08/2014")
+        self.add_parameter("test_C6", "date default null.", add_to="multi2", type="date")
+        self.add_parameter("test_C7", "Multiple string default str 'None'.", add_to="multi2", default="None")
+        self.add_parameter("test_C8", "Multiple string null.", add_to="multi2")
+        self.add_parameter("test_C9", "Multiple bool default True.", add_to="multi2", type="bool", default=True)
+        self.add_parameter("test_C10", "Multiple bool default 3.", add_to="multi2", type="bool", default=3)
+        self.add_parameter("test_C11", "Multiple bool default null.", add_to="multi2", type="bool")
+        self.add_input_file("test_C12", "Multiple InputFile default null.", add_to="multi2")
+        self.add_input_file("test_C13", "Multiple InputFile default application.properties.", add_to="multi2", default="application.properties")##### Pb localfile and urlfile
+
+    def process(self):
+        print "###################### Workflow ############################"
+        for attr in self.params_order:
+            value = getattr(self, attr)
+            print attr
+            print value
+            print "class   : " + value.__class__.__name__
+            print "is None : " + str(value is None)
+            print "== None : " + str(value == None)
+            print ""
+        test_parameters = self.add_component("TestComponentParameters", [
+                                                                         self.test_B1,
+                                                                         self.test_B2,
+                                                                         self.test_B3,
+                                                                         self.test_B4,
+                                                                         self.test_B5,
+                                                                         self.test_B6,
+                                                                         self.test_B7,
+                                                                         self.test_B8,
+                                                                         self.test_B9,
+                                                                         self.test_B10,
+                                                                         self.test_B11,
+                                                                         self.test_B12,
+                                                                         self.test_B13,
+                                                                         self.multi2[0]["test_C1"],
+                                                                         self.multi2[0]["test_C2"],
+                                                                         self.multi2[0]["test_C3"],
+                                                                         self.multi2[0]["test_C4"],
+                                                                         self.multi2[0]["test_C5"],
+                                                                         self.multi2[0]["test_C6"],
+                                                                         self.multi2[0]["test_C7"],
+                                                                         self.multi2[0]["test_C8"],