Fix #44 and add support for comments starting with '#'

PyOphidia/client.py

@@ -905,16 +905,23 @@ def wisvalid(self, workflow):
             return False
         w = None
 
-        # Remove comment blocks
-        checked_workflow = re.sub(re.compile(r"/\*.*?\*/|//.*?\n", re.DOTALL), "\n", workflow)
-
-        if isinstance(checked_workflow, str):
+        if isinstance(workflow, str):
             try:
+                # Remove comment blocks
+                checked_workflow = re.sub(r"(?m)^ *#.*\n?", "", workflow)
+                pattern = r"(\".*?\"|\'.*?\')|(/\*.*?\*/|//[^\r\n]*$)"
+                regex = re.compile(pattern, re.MULTILINE|re.DOTALL)
+                def _replacer(match):
+                    if match.group(2) is not None:
+                        return ""
+                    else:
+                        return match.group(1)
+                checked_workflow = regex.sub(_replacer, checked_workflow)
                 w = json.loads(checked_workflow)
             except ValueError:
                 return False, "Workflow is not a valid JSON"
-        elif isinstance(checked_workflow, dict):
-            w = checked_workflow
+        elif isinstance(workflow, dict):
+            w = workflow
         else:
             return False, "Workflow is not a valid dictionary"
         if "name" not in w or not w["name"]:

PyOphidia/experiment.py

@@ -460,6 +460,39 @@ def start_experiment(data):
         experiment = start_experiment(data)
         return experiment
 
+    def validate(self):
+        """
+        Check the workflow experiment definition validity
+
+        Returns
+        -------
+        True in case of valid workflow, False otherwise
+
+        Example
+        -------
+        e1 = Experiment(name="Experiment 1", author="sample author",
+                       abstract="sample abstract")
+        t1 = e1.newTask(operator="oph_reduce", arguments={'operation': 'avg'},
+                         dependencies={})
+        e1.validate()
+        """
+        try:
+            from client import Client
+        except ImportError:
+            from .client import Client
+
+        client = Client(
+            local_mode=True,
+        )
+
+        experiment_validity = client.wisvalid(
+            json.dumps(self.workflow_to_json())
+        )
+        if experiment_validity[1] == "experiment is valid":
+            return True
+        else:
+            return False
+
     def check(self, filename="sample.dot", visual=True):
         """
         Check the workflow experiment definition validity and display the
@@ -521,26 +554,7 @@ def _find_subgraphs(tasks):
                 cluster_counter += 1
             return subgraphs_list
 
-        def _check_experiment_validity():
-
-            try:
-                from client import Client
-            except ImportError:
-                from .client import Client
-
-            client = Client(
-                local_mode=True,
-            )
-
-            experiment_validity = client.wisvalid(
-                json.dumps(self.workflow_to_json())
-            )
-            if experiment_validity[1] == "experiment is valid":
-                return True
-            else:
-                return False
-
-        experiment_validity = _check_experiment_validity()
+        experiment_validity = self.validate()
         self.__param_check(
             [
                 {"name": "filename", "value": filename, "type": str},