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src/jflow/workflow.py

@@ -183,6 +183,35 @@ class Workflow(threading.Thread):
             self.params_order.append(name)
             self.__setattr__(name, new_param)
     
+    def add_exclusion_rule(self, *args2exclude):
+        # first of all, are this parameter exist
+        params2exclude = []
+        for arg2exclude in args2exclude:
+            try:
+                params2exclude.append(self.__getattribute__(arg2exclude))
+            except: pass
+        # everything is ok, let's go
+        if len(params2exclude) == len(args2exclude):
+            new_group = "exclude-"+uuid.uuid4().hex[:5]
+            for paramsexclude in params2exclude:
+                paramsexclude.group = new_group
+        # it might be a mutliple param rule
+        else:
+            for attribute_value in self.__dict__.values():
+                if issubclass(attribute_value.__class__, MultiParameter) or issubclass(attribute_value.__class__, MultiParameterList):
+                    params2exclude = []
+                    for sub_param in attribute_value.sub_parameters:
+                        if sub_param.name in args2exclude:
+                            params2exclude.append(sub_param)
+                    if len(params2exclude) == len(args2exclude):
+                        new_group = "exclude-"+uuid.uuid4().hex[:5]
+                        flags2exclude = []
+                        for paramsexclude in params2exclude:
+                            paramsexclude.group = new_group
+                            flags2exclude.append(paramsexclude.flag)
+                        attribute_value.type.excludes[new_group] = flags2exclude
+                        break
+    
     def _set_parameters(self, args):
         parameters = self.get_parameters()
         for param in parameters:

workflows/alignment/__init__.py

@@ -31,24 +31,23 @@ class Alignment (Workflow):
         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_multiple_parameter("test", "toto est dnas le gazon", required=True)
         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, type="localfile", add_to="test")
-        #self.exclude_parameters("read_1", "read_2")
+        self.add_input_file("tot_2", "Whould be used", type="int", add_to="test")
         
+        self.add_exclusion_rule("read_1", "read_2")
+        self.add_exclusion_rule("toto", "tot_2")
         
     # prochaine etape:
-    #  - tester les types multiples
-    #  - Ajouter les types InputFile, InputFileList, OutputFile, OutputFileList
-    #  - trouver une methode pour ordonner les parameters (self.add_parameter ...)
+    #  - prendre en compte les execludes
     
     def process(self):
-        print ">>>>>>>>>>>>>>>>>>>> ", self.reference_genome
-        print ">>>>>>>>>>>>>>>>>>>> ", self.read_1
-        print ">>>>>>>>>>>>>>>>>>>> ", self.read_2
-        print ">>>>>>>>>>>>>>>>>>>> ", self.test
+        pass
+        #print self.read_1
+        #print self.read_2
+        #print self.reference_genome
+        #print self.test
         
-        print "gg ", self.test.help
         
         # index the reference genome
         #bwaindex = self.add_component("BWAIndex", [self.args["reference_genome"]])