Fix process reference problem

Author: samirelanduk

nextflow/command.py

@@ -1,6 +1,7 @@
 import os
 import re
 import time
+import weakref
 import subprocess
 from datetime import datetime
 from nextflow.io import get_file_text, get_process_ids_to_paths, get_file_creation_time
@@ -98,8 +99,7 @@ def _run(
         )
         log_start += diff
         if execution and poll: yield execution
-        process_finished = not submission.process or submission.process.poll() is not None
-        if execution and execution.return_code and process_finished:
+        if execution and execution.return_code and execution.finished:
             if not poll: yield execution
             break
 
@@ -142,7 +142,7 @@ def submit_execution(
     :param str dag: the filename to use for the DAG report.
     :param str trace: the filename to use for the trace report.
     :rtype: ``nextflow.models.ExecutionSubmission``"""
-    
+
     if not run_path and not io: run_path = os.path.abspath(".")
     if not run_path and io: run_path = io.abspath(".")
     if not output_path: output_path = run_path
@@ -153,14 +153,15 @@ def submit_execution(
     )
     start = datetime.now()
     if runner:
-        process = None
         runner(nextflow_command)
     else:
         process = subprocess.Popen(
             nextflow_command, universal_newlines=True, shell=True
         )
+        process._child_created = False  # disables warning machinery
+        weakref.finalize(process, lambda: None)
     submission = ExecutionSubmission(
-        pipeline_path, run_path, output_path, log_path, nextflow_command, timezone, process
+        pipeline_path, run_path, output_path, log_path, nextflow_command, timezone
     )
     if resume:
         wait_for_log_creation(submission.log_path, start, io)

nextflow/models.py

@@ -16,7 +16,6 @@ class ExecutionSubmission:
     log_path: str
     nextflow_command: str
     timezone: str
-    process: Any
 
 
 

tests/unit/test_command.py

@@ -47,8 +47,6 @@ def test_can_run_with_custom_values(self, mock_ex, mock_sleep, mock_submit):
     @patch("nextflow.command.get_execution")
     def test_can_run_and_poll(self, mock_ex, mock_sleep, mock_submit):
         submission = Mock()
-        submission.process.poll = MagicMock()
-        submission.process.poll.side_effect = [None, None, 1]
         mock_submit.return_value = submission
         mock_executions = [Mock(finished=False), Mock(finished=True)]
         mock_ex.side_effect = [[None, 20], [mock_executions[0], 40], [mock_executions[1], 20]]
@@ -98,7 +96,6 @@ def test_can_submit_with_default_values(self, mock_run, mock_nc, mock_abs):
         self.assertEqual(submission.log_path, "/run")
         self.assertEqual(submission.nextflow_command, mock_nc.return_value)
         self.assertEqual(submission.timezone, None)
-        self.assertEqual(submission.process, mock_run.return_value)
 
 
     @patch("nextflow.command.make_nextflow_command")
@@ -124,7 +121,6 @@ def test_can_submit_with_custom_values(self, mock_wait, mock_run, mock_nc):
         self.assertEqual(submission.log_path, "/log")
         self.assertEqual(submission.nextflow_command, mock_nc.return_value)
         self.assertEqual(submission.timezone, "UTC")
-        self.assertEqual(submission.process, mock_run.return_value)
 
 
     @patch("nextflow.command.make_nextflow_command")
@@ -144,7 +140,6 @@ def test_can_submit_with_custom_io(self, mock_run, mock_nc):
         self.assertEqual(submission.log_path, io.abspath.return_value)
         self.assertEqual(submission.nextflow_command, mock_nc.return_value)
         self.assertEqual(submission.timezone, None)
-        self.assertEqual(submission.process, mock_run.return_value)
 
 
     @patch("nextflow.command.make_nextflow_command")
@@ -159,7 +154,6 @@ def test_can_run_with_custom_runner(self, mock_nc):
         self.assertEqual(submission.log_path, os.path.abspath("."))
         self.assertEqual(submission.nextflow_command, mock_nc.return_value)
         self.assertEqual(submission.timezone, None)
-        self.assertEqual(submission.process, None)
 
 
 

tests/unit/test_submission.py

@@ -5,20 +5,17 @@
 class SubmissionreationTests(TestCase):
 
     def test_can_create_execution_submission(self):
-        process = Mock()
         submission = ExecutionSubmission(
             pipeline_path="/main.nf",
             run_path="/executions/123",
             output_path="/executions/123/out",
             log_path="/executions/123/out/nextflow.log",
             nextflow_command="nextflow run /main.nf",
             timezone="UTC",
-            process=process
         )
         self.assertEqual(submission.pipeline_path, "/main.nf")
         self.assertEqual(submission.run_path, "/executions/123")
         self.assertEqual(submission.output_path, "/executions/123/out")
         self.assertEqual(submission.log_path, "/executions/123/out/nextflow.log")
         self.assertEqual(submission.nextflow_command, "nextflow run /main.nf")
-        self.assertEqual(submission.timezone, "UTC")
-        self.assertEqual(submission.process, process)
+        self.assertEqual(submission.timezone, "UTC")