Misc fixes and refactorings

gxformat2/converter.py

@@ -520,10 +520,10 @@ def __init__(self):
 
     def step_id(self, label_or_id):
         if label_or_id in self.labels:
-            id = self.labels[label_or_id]
+            id_ = self.labels[label_or_id]
         else:
-            id = label_or_id
-        return int(id)
+            id_ = label_or_id
+        return int(id_)
 
     def step_output(self, value):
         value_parts = str(value).split("/")

gxformat2/export.py

@@ -14,33 +14,31 @@
 
 
 def _copy_common_properties(from_native_step, to_format2_step):
-    annotation = from_native_step.get("annotation", "")
+    annotation = from_native_step.get("annotation")
     if annotation:
         to_format2_step["doc"] = annotation
-    position = from_native_step.get("position", None)
-    if position:
-        to_format2_step["position"] = position
-    when_exp = from_native_step.get("when", None)
-    if when_exp is not None:
-        to_format2_step["when"] = when_exp
+    for prop in ("position", "when"):
+        value = from_native_step.get(prop)
+        if value:
+            to_format2_step[prop] = value
 
 
-def from_galaxy_native(format2_dict, tool_interface=None, json_wrapper=False):
+def from_galaxy_native(native_workflow_dict, tool_interface=None, json_wrapper=False):
     """Convert native .ga workflow definition to a format2 workflow.
 
     This is highly experimental and currently broken.
     """
     data = OrderedDict()
     data['class'] = 'GalaxyWorkflow'
-    _copy_common_properties(format2_dict, data)
-    if "name" in format2_dict:
-        data["label"] = format2_dict.pop("name")
+    _copy_common_properties(native_workflow_dict, data)
+    if "name" in native_workflow_dict:
+        data["label"] = native_workflow_dict.pop("name")
     for top_level_key in ['tags', 'uuid', 'report']:
-        value = format2_dict.get(top_level_key)
+        value = native_workflow_dict.get(top_level_key)
         if value:
             data[top_level_key] = value
 
-    native_steps = format2_dict.get("steps")
+    native_steps = native_workflow_dict.get("steps")
 
     label_map = {}
     all_labeled = True
@@ -79,19 +77,17 @@ def from_galaxy_native(format2_dict, tool_interface=None, json_wrapper=False):
                 inputs[step_id] = input_dict["type"]
             else:
                 inputs[step_id] = input_dict
-            continue
 
-        if module_type == "pause":
+        elif module_type == "pause":
             step_dict = OrderedDict()
             optional_props = ['label']
             _copy_common_properties(step, step_dict)
             _copy_properties(step, step_dict, optional_props=optional_props)
             _convert_input_connections(step, step_dict, label_map)
             step_dict["type"] = "pause"
             steps.append(step_dict)
-            continue
 
-        if module_type == 'subworkflow':
+        elif module_type == 'subworkflow':
             step_dict = OrderedDict()
             optional_props = ['label']
             _copy_common_properties(step, step_dict)
@@ -102,25 +98,25 @@ def from_galaxy_native(format2_dict, tool_interface=None, json_wrapper=False):
             subworkflow = from_galaxy_native(subworkflow_native_dict, tool_interface=tool_interface, json_wrapper=False)
             step_dict["run"] = subworkflow
             steps.append(step_dict)
-            continue
 
-        if module_type != 'tool':
-            raise NotImplementedError("Unhandled module type %s" % module_type)
+        elif module_type == 'tool':
+            step_dict = OrderedDict()
+            optional_props = ['label', 'tool_shed_repository']
+            required_props = ['tool_id', 'tool_version']
+            _copy_properties(step, step_dict, optional_props, required_props)
+            _copy_common_properties(step, step_dict)
 
-        step_dict = OrderedDict()
-        optional_props = ['label', 'tool_shed_repository']
-        required_props = ['tool_id', 'tool_version']
-        _copy_properties(step, step_dict, optional_props, required_props)
-        _copy_common_properties(step, step_dict)
+            tool_state = _tool_state(step)
+            tool_state.pop("__page__", None)
+            tool_state.pop("__rerun_remap_job_id__", None)
+            step_dict['tool_state'] = tool_state
 
-        tool_state = _tool_state(step)
-        tool_state.pop("__page__", None)
-        tool_state.pop("__rerun_remap_job_id__", None)
-        step_dict['tool_state'] = tool_state
+            _convert_input_connections(step, step_dict, label_map)
+            _convert_post_job_actions(step, step_dict)
+            steps.append(step_dict)
 
-        _convert_input_connections(step, step_dict, label_map)
-        _convert_post_job_actions(step, step_dict)
-        steps.append(step_dict)
+        else:
+            raise NotImplementedError(f"Unhandled module type {module_type}")
 
     data['inputs'] = inputs
     data['outputs'] = outputs
@@ -147,12 +143,12 @@ def _tool_state(step):
     return tool_state
 
 
-def _copy_properties(from_native_step, to_format2_step, optional_props=[], required_props=[]):
-    for prop in optional_props:
+def _copy_properties(from_native_step, to_format2_step, optional_props=None, required_props=None):
+    for prop in optional_props or []:
         value = from_native_step.get(prop)
         if value:
             to_format2_step[prop] = value
-    for prop in required_props:
+    for prop in required_props or []:
         value = from_native_step.get(prop)
         to_format2_step[prop] = value