Merge branch 'dot_files' into wfcommons_test

Author: rafaelfsilva

wfcommons/common/workflow.py

@@ -172,10 +172,11 @@ def write_json(self, json_file_path: Optional[pathlib.Path] = None) -> None:
             specification_tasks.append(task_spec)
 
             # add machines to the workflow json object
-            for machine in task.machines:
-                if machine.name not in machines_list:
-                    machines_list.append(machine.name)
-                    workflow_machines.append(machine.as_dict())
+            if task.machines:
+                for machine in task.machines:
+                    if machine.name not in machines_list:
+                        machines_list.append(machine.name)
+                        workflow_machines.append(machine.as_dict())
 
             # add files to the workflow json object (input and output)
             for file in task.input_files:
@@ -228,7 +229,7 @@ def read_dot(self, dot_file_path: Optional[pathlib.Path] = None) -> None:
         tasks_map = {}
         for node in graph.nodes(data=True):
             task_id = f"{node[1]['label']}_ID{node[0]}"
-            task = Task(name=task_id, id=task_id, runtime=0, task_id=node[0])
+            task = Task(name=node[1]['label'], task_id=task_id, runtime=0)
             self.add_task(task)
             tasks_map[node[0]] = task_id
 

wfcommons/wfgen/abstract_recipe.py

@@ -203,7 +203,7 @@ def _generate_task_files(self, task: Task) -> List[File]:
 
         # generate output files
         output_files_list = self._generate_files(task.task_id, task_recipe['output'], FileLink.OUTPUT)
-        task.output_files = self.tasks_files[task.task_id]
+        task.output_files = output_files_list
 
         # obtain input files from parents
         input_files = []