first step to make Parameter looks good

bin/jflow_server.py

@@ -154,7 +154,7 @@ class JFlowServer (object):
         wf_instances = self.wfmanager.get_available_workflows()
         for instance in wf_instances:
             parameters, parameters_per_groups, groups = [], {}, ["default"]
-            for param in instance.parameters:
+            for param in instance.get_parameters():
                 # if it's a multiple action change the action by the name
                 if param.action == jflow.parameter.MiltipleAction:
                     action = "MiltipleAction"

src/jflow/parameter.py

@@ -168,29 +168,29 @@ class MiltipleAppendAction(argparse.Action):
             final_values.append((param, final_hash[param]))
         items.append(final_values)
         setattr(namespace, self.dest, items)        
-        
-class Parameter(object):
-    """
-    """
+
+
+class AbstractParameter(object):
     
-    def __init__(self, name, help, flag, default=None, type=types.StringType, choices=None, 
-                 required=False, action="store", sub_parameters=[], group="default", display_name=None):
+    def __init__(self, name, help, default=None, type=types.StringType, choices=None, required=False,
+                 flag=None, action="store", sub_parameters=None, group="default", display_name=None):
 
         self.name = name
-        self.flag = flag
         self.help = help
         self.action = action
         self.nargs = None
-        self.sub_parameters = sub_parameters
+        if sub_parameters:
+            self.sub_parameters = sub_parameters
+        else: self.sub_parameters = []
         self.group = group
-        if display_name == None:
-            self.display_name = name
+        if flag == None:
+            self.flag = "--"+name.replace("_", "-")
+        else: self.flag = flag
+        if display_name == None: 
+            self.display_name = name.replace("_", " ").title()
         else: self.display_name = display_name
-        
         self.required = str(required).lower() in ("yes", "y", "true",  "t", "1")
         self.choices = choices
-        if self.choices:
-            self.choices = choices.split("|")
         
         if len(self.sub_parameters) > 0:
             self.nargs = "+"
@@ -239,7 +239,7 @@ class Parameter(object):
             self.default = {}
             for param in self.sub_parameters:
                 self.default[param.name] = param.default
-                
+    
     def export_to_argparse(self):
         if self.type == types.BooleanType and str(self.default).lower() in ("false",  "f", "0"):
             return {"help": self.help, "required": self.required, "dest": self.name, 
@@ -259,6 +259,98 @@ class Parameter(object):
     def get_type(self):
         return self.type.__name__
     
-    def __str__(self):
-        return self.name + ": " + str(self.flag) + " | " + self.help + " (default=" + \
-               str(self.default) + ", required=" + str(self.required) + ", flag=" + self.flag + ")"
+    
+class AbstractFile(object):
+    def __init__(self, file_format="any"):
+        self.file_format = file_format
+        self.parent_component_nameid = None
+
+
+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, flag=flag, group=group, display_name=display_name)
+        return dict.__init__(self, {})
+
+
+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, flag=flag, group=group, display_name=display_name)
+        return list.__init__(self, [])
+    
+
+class Parameter(str, AbstractParameter):
+    
+    def __new__(self, name, help, default="", type=types.StringType, choices=None, required=False,
+                flag=None, sub_parameters=None, group="default", display_name=None):
+        return str.__new__(self, default)
+    
+    def __init__(self, name, help, default="", type=types.StringType, choices=None, required=False,
+                 flag=None, sub_parameters=None, group="default", display_name=None):
+        AbstractParameter.__init__(self, name, help, flag=flag, type=type, choices=choices, required=required, 
+                                   action="store", sub_parameters=sub_parameters, group=group, display_name=display_name)
+        
+
+class InputFile(Parameter, AbstractFile):
+    
+    def __new__(self, name, help, file_format="any", default="", type=types.StringType, choices=None, 
+                required=False, flag=None, group="default", display_name=None):
+        return str.__new__(self, default)
+    
+    def __init__(self, name, help, file_format="any", default="", type=types.StringType, choices=None, 
+                required=False, flag=None, group="default", display_name=None):
+        AbstractFile.__init__(self, file_format)
+        Parameter.__init__(self, name, help, flag=flag, type=type, choices=choices, 
+                           required=required, group=group, display_name=display_name)
+    
+
+class OutputFile(Parameter, AbstractFile):
+    
+    def __new__(self, name, help, file_format="any", default="", type=types.StringType, choices=None, 
+                required=False, flag=None, group="default", display_name=None):
+        return str.__new__(self, default)
+    
+    def __init__(self, name, help, file_format="any", default="", type=types.StringType, choices=None, 
+                required=False, flag=None, group="default", display_name=None):
+        AbstractFile.__init__(self, file_format)
+        Parameter.__init__(self, name, help, flag=flag, type=type, choices=choices, 
+                           required=required, group=group, display_name=display_name)
+
+        
+class ParameterList(list, AbstractParameter):
+    
+    def __init__(self, name, help, default=[], type=types.StringType, choices=None, required=False,
+                 flag=None, sub_parameters=None, group="default", display_name=None):
+        AbstractParameter.__init__(self, name, help, flag=flag, 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])
+        elif default.__class__.__name__ == "list":
+            return list.__init__(self, default)
+        
+
+class InputFileList(ParameterList, AbstractFile):
+    
+    def __init__(self, name, help, file_format="any", default=[], type=types.StringType, choices=None, 
+                 required=False, flag=None, group="default", display_name=None):
+        AbstractFile.__init__(self, file_format)
+        ParameterList.__init__(self, name, help, flag=flag, type=type, choices=choices, 
+                               required=required, group=group, display_name=display_name)
+        if default.__class__.__name__ == "str":
+            return list.__init__(self, [default])
+        elif default.__class__.__name__ == "list":
+            return list.__init__(self, default)
+
+
+class OutputFileList(ParameterList, AbstractFile):
+    
+    def __init__(self, name, help, file_format="any", default=[], type=types.StringType, 
+                 choices=None, required=False, flag=None, group="default", display_name=None):
+        AbstractFile.__init__(self, file_format)
+        ParameterList.__init__(self, name, help, flag=flag, type=type, choices=choices, 
+                               required=required, group=group, display_name=display_name)
+        if default.__class__.__name__ == "str":
+            return list.__init__(self, [default])
+        elif default.__class__.__name__ == "list":
+            return list.__init__(self, default)

workflows/alignment/__init__.py

@@ -16,15 +16,37 @@
 #
 
 from jflow.workflow import Workflow
-
+from jflow.parameter import InputFileList, InputFile
 
 class Alignment (Workflow):
 
+    def get_name(self):
+        return "alignment"
+    
+    def get_description(self):
+        return "align reads against a reference genome"
+
+    def define_parameters(self, parameters_section=None):
+        self.add_input_file("read_1", "Which read1 files should be used", required=True, type="localfile", is_list=True)
+        self.add_input_file("read_2", "Which read2 files should be used (if single end, leave empty)", type="localfile", is_list=True)
+        self.add_input_file("reference_genome", "Which genome should the read being align on", required=True, type="localfile")
+        
+        self.add_multiple_parameter("test", "toto est dnas le gazon")
+        self.add_input_file("toto", "Whices should be used", required=True, is_list=True, add_to="test")
+        self.add_input_file("tot", "Whould be used", is_list=True, add_to="test")
+        
+    # prochaine etape:
+    #  - tester les types multiples
+    #  - Ajouter les types InputFile, InputFileList, OutputFile, OutputFileList
+    #  - trouver une methode pour ordonner les parameters (self.add_parameter ...)
+    
     def process(self):
-        """ 
-        Run the workflow
-        """
+        print ">>>>>>>>>>>>>>>>>>>> ", self.reference_genome
+        print ">>>>>>>>>>>>>>>>>>>> ", self.read_1
+        print ">>>>>>>>>>>>>>>>>>>> ", self.read_2
+        
         # index the reference genome
-        bwaindex = self.add_component("BWAIndex", [self.args["reference_genome"]])
+        #bwaindex = self.add_component("BWAIndex", [self.args["reference_genome"]])
         # align reads against indexed genome
-        bwa = self.add_component("BWA", [bwaindex.databank, self.args["read_1"], self.args["read_2"]])
\ No newline at end of file
+        #bwa = self.add_component("BWA", [bwaindex.databank, self.args["read_1"], self.args["read_2"]])
+        
\ No newline at end of file

workflows/alignment/workflow.properties

-#
-# 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/>.
-#
-
-[global]
-name = alignment
-description = align reads against a reference genome
-
-#
-# Parameter section
-# param.name: the parameter display name
-#      .flag: the command line flag to use the argument
-#      .help: a brief description of what the parameter does
-#      .default [None]: the value produced if the parameter is not provided
-#      .type [str]: the parameter type that should be tested, this can be:
-#          str|int|date|inputfile|urlfile|localfile|browsefile|bool|... all types 
-#          defined in the types.py package)
-#      .choices [None]: a container of the allowable values for the parameter
-#      .required [False]: whether or not the command-line option may be omitted
-#      .action [store]: the basic type of action to be taken (store|append)
-#	   .group [None]: gathers arguments into groups when displaying help messages / forms
-#	   .exclude [None]: will make sure that there is only one arguments provided
-#
-[parameters]
-read_1.name = Read 1
-read_1.flag = --read-1
-read_1.help = Which read1 files should be used
-read_1.required = True
-read_1.type = localfile
-read_1.action = append
-
-read_2.name = Read 2
-read_2.flag = --read-2
-read_2.help = Which read2 files should be used (if single end, leave empty)
-read_2.type = localfile
-read_2.action = append
-
-reference_genome.name = Reference genome
-reference_genome.flag = --reference-genome
-reference_genome.help = Which genome should the read being align on
-reference_genome.type = localfile
-reference_genome.required = True