Fix reset error: addresses issue #757

beeflow/client/bee_client.py

@@ -106,15 +106,25 @@ def _resource(tag=""):
     return _url() + str(tag)
 
 
+def get_wf_list():
+    """Get the list of all workflows."""
+    try:
+        conn = _wfm_conn()
+        resp = conn.get(_url(), timeout=60)
+    except requests.exceptions.ConnectionError:
+        error_exit('Could not reach WF Manager.')
+
+    if resp.status_code != requests.codes.okay:  # pylint: disable=no-member
+        error_exit('WF Manager did not return workflow list')
+
+    logging.info('List Jobs:  {resp.text}')
+    return jsonpickle.decode(resp.json()['workflow_list'])
+
+
 def check_short_id_collision():
     """Check short workflow IDs for colliions; increase short ID length if detected."""
     global short_id_len  #noqa: Not a constant
-    conn = _wfm_conn()
-    resp = conn.get(_url(), timeout=60)
-    if resp.status_code != requests.codes.okay:  # pylint: disable=no-member
-        error_exit(f"Checking for ID collision failed: {resp.status_code}")
-
-    workflow_list = jsonpickle.decode(resp.json()['workflow_list'])
+    workflow_list = get_wf_list()
     if workflow_list:
         while short_id_len < MAX_ID_LEN:
             id_list = [_short_id(job[1]) for job in workflow_list]
@@ -133,18 +143,7 @@ def check_short_id_collision():
 def match_short_id(wf_id):
     """Match user-provided short workflow ID to full workflow IDs."""
     matched_ids = []
-
-    try:
-        conn = _wfm_conn()
-        resp = conn.get(_url(), timeout=60)
-    except requests.exceptions.ConnectionError:
-        error_exit('Could not reach WF Manager.')
-
-    if resp.status_code != requests.codes.okay:  # pylint: disable=no-member
-        error_exit(f'Could not match ID: {wf_id}. Code {resp.status_code}')
-        # raise ApiError("GET /jobs".format(resp.status_code))
-
-    workflow_list = jsonpickle.decode(resp.json()['workflow_list'])
+    workflow_list = get_wf_list()
     if workflow_list:
         for job in workflow_list:
             if job[1].startswith(wf_id):
@@ -370,12 +369,12 @@ def package(wf_path: pathlib.Path = typer.Argument(...,
 
 @app.command()
 def remove(wf_id: str = typer.Argument(..., callback=match_short_id)):
-    """Remove a cancelled or archived workflow with a workflow ID."""
+    """Remove cancelled, paused, or archived workflow with a workflow ID."""
     long_wf_id = wf_id
 
     wf_status = get_wf_status(wf_id)
     print(f"Workflow Status is {wf_status}")
-    if wf_status in ('Cancelled', 'Archived'):
+    if wf_status in ('Cancelled', 'Archived', 'Paused'):
         verify = f"All stored information for workflow {_short_id(wf_id)} will be removed."
         verify += "\nContinue to remove? yes(y)/no(n): """
         response = input(verify)
@@ -421,17 +420,7 @@ def unpackage(package_path, dest_path):
 @app.command('list')
 def list_workflows():
     """List all workflows."""
-    try:
-        conn = _wfm_conn()
-        resp = conn.get(_url(), timeout=60)
-    except requests.exceptions.ConnectionError:
-        error_exit('Could not reach WF Manager.')
-
-    if resp.status_code != requests.codes.okay:  # pylint: disable=no-member
-        error_exit('WF Manager did not return workflow list')
-
-    logging.info('List Jobs:  {resp.text}')
-    workflow_list = jsonpickle.decode(resp.json()['workflow_list'])
+    workflow_list = get_wf_list()
     if workflow_list:
         typer.secho("Name\tID\tStatus", fg=typer.colors.GREEN)
 
@@ -521,10 +510,10 @@ def resume(wf_id: str = typer.Argument(..., callback=match_short_id)):
 
 @app.command()
 def cancel(wf_id: str = typer.Argument(..., callback=match_short_id)):
-    """Cancel a workflow."""
+    """Cancel a paused or running workflow."""
     long_wf_id = wf_id
     wf_status = get_wf_status(wf_id)
-    if wf_status == "Running":
+    if wf_status in ('Running', 'Paused'):
         try:
             conn = _wfm_conn()
             resp = conn.delete(_resource(long_wf_id), json={'option': 'cancel'}, timeout=60)

beeflow/client/core.py

@@ -14,16 +14,24 @@
 import socket
 import sys
 import shutil
+import datetime
 import time
 
 import daemon
 import typer
 
+from beeflow.client import bee_client
 from beeflow.common.config_driver import BeeConfig as bc
 from beeflow.common import cli_connection
 from beeflow.common import paths
 from beeflow.wf_manager.resources import wf_utils
 
+from beeflow.common.db import wfm_db
+from beeflow.common.db.bdb import connect_db
+from beeflow.wf_manager.common import dep_manager
+
+db_path = wf_utils.get_db_path()
+
 
 class ComponentManager:
     """Component manager class."""
@@ -431,12 +439,15 @@ def status():
 
 
 @app.command()
-def stop():
+def stop(query='yes'):
     """Stop the current running beeflow daemon."""
-    stop_msg = ("\n** Please ensure all workflows are complete before stopping beeflow. **"
-                + "\n** Check the status of workflows by running 'beeflow list'.    **"
-                + "\nAre you sure you want to kill beeflow components? [y/n] ")
-    ans = input(stop_msg)
+    if query == 'yes':
+        stop_msg = ("\n** Please ensure all workflows are complete before stopping beeflow. **"
+                    + "\n** Check the status of workflows by running 'beeflow list'.    **"
+                    + "\nAre you sure you want to kill beeflow components? [y/n] ")
+        ans = input(stop_msg)
+    else:
+        ans = 'y'
     if ans.lower() != 'y':
         return
     resp = cli_connection.send(paths.beeflow_socket(), {'type': 'quit'})
@@ -448,74 +459,112 @@ def stop():
         sys.exit(1)
     # As long as it returned something, we should be good
     beeflow_log = paths.log_fname('beeflow')
-    print(f'Beeflow has stopped. Check the log at "{beeflow_log}".')
+    if query == "no":
+        print(f'Beeflow has stopped. Check the log at "{beeflow_log}".')
+
+
+def kill_active_workflows(active_states, workflow_list):
+    """Kill workflows with active states."""
+    db = connect_db(wfm_db, db_path)
+    success = True
+    for name, wf_id, state in workflow_list:
+        if state in active_states:
+            pid = db.workflows.get_gdb_pid(wf_id)
+            if pid > 0:
+                dep_manager.kill_gdb(pid)
+            else:
+                # Failure most likely caused by an Initializing workflow.
+                print(f"No process for {name}, {wf_id}, {state}.")
+                success = False
+    return success
+
+
+def archive_dir(dir_to_archive):
+    """Archive directories for archive flag in reset."""
+    archive_dirs = ['logs', 'container_archive', 'archives', 'workflows']
+    date_str = f"{datetime.datetime.now().strftime('%Y-%m-%d_%H%M%S')}"
+    backup_dir = f"{dir_to_archive}.{date_str}"
+    for a_dir in archive_dirs:
+        try:
+            shutil.copytree(f"{dir_to_archive}/{a_dir}",
+                            f"{backup_dir}/{a_dir}")
+        except FileNotFoundError:
+            pass
+    print("Archive flag enabled.",
+          "Existing logs, containers, and workflows backed up in:\n"
+          f"{backup_dir}")
+
+
+def handle_rm_error(err, dir_to_check, wf_list):
+    """Handle IO error caused by either initializing workflows or nfs files."""
+    # Check if only nfs mounts are causing the problem and ignore
+    dir_list = os.listdir(dir_to_check)
+    nfs_list = [x for x in dir_list if x.startswith('.nfs')]
+    if dir_list and (dir_list != nfs_list):
+        print(f"Unable to remove {dir_to_check} \n {err.strerror}")
+        # Often initializing workflows cause a problem
+        if any('Initializing' in sublist for sublist in wf_list):
+            warn('Initializing workflows may have prevented removal.\n')
+            print(f"Try removing {dir_to_check} manually, to complete reset.")
 
 
 @app.command()
 def reset(archive: bool = typer.Option(False, '--archive', '-a',
                                        help='Archive bee_workdir  before removal')):
-    """Delete the bee_workdir directory."""
-    # Check to see if the user is absolutely sure. Warning Message.
+    """Stop all components and delete the bee_workdir directory."""
+    # Check workflow states; warn if there are active states.
+    workflow_list = bee_client.get_wf_list()
+    active_states = {'Running', 'Paused', 'Initializing', 'Waiting'}
+    if {item for row in workflow_list for item in row}.intersection(active_states):
+        caution = """
+        **************************************************************
+          Caution: There are active workflows! They will be removed!
+          Try 'beeflow list' to view them.
+        **************************************************************
+        """
     absolutely_sure = ""
+    dir_to_delete = os.path.expanduser(wf_utils.get_bee_workdir())
+    warn(f"\n    A reset will remove this directory: {dir_to_delete}\n")
+    if archive:
+        print("    Archive flag is set: logs, workflows and containers will be backed up.")
+    print("""
+    A reset will:
+        Shutdown beeflow and all BEE components.
+        Delete the bee_workdir directory which results in:
+            Removing the archive of all workflows.
+            Removing the archive of workflow containers
+                (unless container_archive is configured elsewhere).
+            Reset all databases associated with the beeflow app.
+            Removing all beeflow logs.
+    Beeflow configuration files from bee_cfg will not be deleted.
+    """)
+    warn(f"{caution}\nAre you sure you want to reset?")
     while absolutely_sure != "y" or absolutely_sure != "n":
-        # Get the user's bee_workdir directory
-        directory_to_delete = os.path.expanduser(wf_utils.get_bee_workdir())
-        print(f"A reset will remove this directory: {directory_to_delete}")
-
-        absolutely_sure = input(
-            """
-Are you sure you want to reset?
-
-Please ensure all workflows are complete before running a reset
-Check the status of workflows by running 'beeflow list'
-
-A reset will shutdown beeflow and its components.
-
-A reset will delete the bee_workdir directory which results in:
-Removing the archive of workflows executed.
-Removing the archive of workflow containers.
-Reset all databases associated with the beeflow app.
-Removing all beeflow logs.
-
-Beeflow configuration files from bee_cfg will remain.
-
-Respond with yes(y)/no(n):  """)
+        absolutely_sure = input("Respond with yes(y)/no(n): ")
         if absolutely_sure in ("n", "no"):
             # Exit out if the user didn't really mean to do a reset
             sys.exit()
-        if absolutely_sure in ("y", "yes"):
+        elif absolutely_sure in ("y", "yes"):
+            # First stop all active workflow processes
+            workflow_list = bee_client.get_wf_list()
+            kill_active_workflows(active_states, workflow_list)
             # Stop all of the beeflow processes
-            resp = cli_connection.send(paths.beeflow_socket(), {'type': 'quit'})
-            if resp is not None:
-                print("Beeflow has been shutdown.")
-                print("Waiting for components to cleanly stop.")
-                # This wait is essential. It takes a minute to shut down.
-                time.sleep(5)
-
-            if os.path.exists(directory_to_delete):
-                # Save the bee_workdir directory if the archive option was set
-                if archive:
-                    if os.path.exists(directory_to_delete + "/logs"):
-                        shutil.copytree(directory_to_delete + "/logs",
-                                        directory_to_delete + ".backup/logs")
-                    if os.path.exists(directory_to_delete + "/container_archive"):
-                        shutil.copytree(directory_to_delete + "/container_archive",
-                                        directory_to_delete + ".backup/container_archive")
-                    if os.path.exists(directory_to_delete + "/archives"):
-                        shutil.copytree(directory_to_delete + "/archives",
-                                        directory_to_delete + ".backup/archives")
-                    if os.path.exists(directory_to_delete + "/workflows"):
-                        shutil.copytree(directory_to_delete + "/workflows",
-                                        directory_to_delete + ".backup/workflows")
-                    print("Archive flag enabled,")
-                    print("Existing logs, containers, and workflows backed up in:")
-                    print(f"{directory_to_delete}.backup")
-                shutil.rmtree(directory_to_delete)
-                print(f"{directory_to_delete} has been removed.")
-                sys.exit()
+            stop("quiet")
+            print("Beeflow is shutting down.")
+            print("Waiting for components to cleanly stop.")
+            # This wait is essential. It takes a minute to shut down.
+            time.sleep(5)
+
+            # Save the bee_workdir directory if the archive option was set
+            if archive:
+                archive_dir(dir_to_delete)
+            try:
+                shutil.rmtree(dir_to_delete)
+            except OSError as err:
+                handle_rm_error(err, dir_to_delete, workflow_list)
             else:
-                print(f"{directory_to_delete} does not exist. Exiting.")
-                sys.exit()
+                print(f"{dir_to_delete} has been removed.")
+            sys.exit()
         print("Please respond with either the letter (y) or (n).")