Pause running workflows when stopping beeflow with 'beeflow core stop'

beeflow/client/core.py

@@ -440,16 +440,26 @@ def status():
 @app.command()
 def stop(query='yes'):
     """Stop the current running beeflow daemon."""
-    if query == 'yes':
+    # Check workflow states; warn if there are active states, pause running workflows
+    workflow_list = bee_client.get_wf_list()
+    concern_states = {'Running', 'Initializing', 'Waiting'}
+    concern = {item for row in workflow_list for item in row}.intersection(concern_states)
+    # For the interactive case
+    if query == 'yes' and concern:
         ans = input("""
-              ** Please ensure all workflows are complete before stopping beeflow. **
-              ** Check the status of workflows by running 'beeflow list'.    **
+              **   There are running workflows.    **
+              ** Running workflows will be paused. **
 
               Are you sure you want to kill beeflow components? [y/n] """)
     else:
         ans = 'y'
     if ans.lower() != 'y':
         return
+    # Pause running or waiting workflows
+    workflow_list = bee_client.get_wf_list()
+    for _name, wf_id, state in workflow_list:
+        if state in {'Running', 'Waiting'}:
+            bee_client.pause(wf_id)
     resp = cli_connection.send(paths.beeflow_socket(), {'type': 'quit'})
     if resp is None:
         beeflow_log = paths.log_fname('beeflow')
@@ -459,7 +469,7 @@ def stop(query='yes'):
         sys.exit(1)
     # As long as it returned something, we should be good
     beeflow_log = paths.log_fname('beeflow')
-    if query == "no":
+    if query == "yes":
         print(f'Beeflow has stopped. Check the log at "{beeflow_log}".')