Add option to archive the workdir

beeflow/client/bee_client.py

@@ -242,7 +242,9 @@ def submit(wf_name: str = typer.Argument(..., help='the workflow name'),  # pyli
            workdir: pathlib.Path = typer.Argument(...,
            help='working directory for workflow containing input + output files',),
            no_start: bool = typer.Option(False, '--no-start', '-n',
-                                         help='do not start the workflow')):
+                                         help='do not start the workflow'),
+           archive_workdir: bool = typer.Option(False, '--archive-workdir', '-a',
+                                                help='archive a copy of the workdir')):
     """Submit a new workflow."""
     def is_parent(parent, path):
         """Return true if the path is a child of the other path."""
@@ -312,6 +314,51 @@ def is_parent(parent, path):
     if os.path.commonpath([os.path.realpath('/var/tmp'), workdir]) == os.path.realpath('/var/tmp'):
         error_exit("Workflow working directory cannot be in \"/var/tmp\"")
 
+    # TODO: this should be in a function somewhere
+    total_size = 0
+    size_limit_mb = 1000
+    total_size_limit = size_limit_mb * 1024 ** 2
+    n_files = 0
+    n_files_limit = 10_000
+    n_dirs = 0
+    n_dirs_limit = 1000
+    reason = ''
+    # check the workdir isn't too large/contains too many things
+    for dirpath, dirnames, filenames in os.walk(workdir):
+        n_files += len(filenames)
+        if n_files > n_files_limit:
+            reason = f'Directory contains more than {n_files_limit} files'
+            break
+        n_dirs += len(dirnames)
+        if n_dirs > n_dirs_limit:
+            reason = f'Directory contains more than {n_dirs_limit} subdirectories'
+            break
+        for fname in filenames:
+            fp = os.path.join(dirpath, fname)
+            # skip if it is symbolic link
+            if not os.path.islink(fp):
+                total_size += os.path.getsize(fp)
+                if total_size > total_size_limit:
+                    reason = f'Total file size of directory is greater than {size_limit_mb}MB'
+                    break
+        else:
+            continue
+        break
+
+    if len(reason) > 0 and archive_workdir:
+        archive_workdir = False
+        ans = input(f"""
+    ******************
+    **   WARNING    **
+    ******************
+    Are you sure you want to archive the workdir at:
+
+    {workdir}
+
+    {reason} [y/n]? """)
+        if ans.lower() in ("y", "yes"):
+            archive_workdir = True
+
     # TODO: Can all of this information be sent as a file?
     data = {
         'wf_name': wf_name.encode(),
@@ -320,6 +367,7 @@ def is_parent(parent, path):
         'workflow': jsonpickle.encode(workflow),
         'tasks': jsonpickle.encode(tasks, warn=True),
         'no_start': no_start,
+        'archive_workdir': archive_workdir,
     }
     files = {
         'workflow_archive': wf_tarball

beeflow/common/integration/utils.py

@@ -77,7 +77,8 @@ def run(self):
             bee_client.package(Path(self.path), Path(tarball_dir))
             print('Submitting and starting workflow')
             self.wf_id = bee_client.submit(self.name, self.tarball, self.main_cwl,
-                                           self.job_file, self.workdir, no_start=False)
+                                           self.job_file, self.workdir, no_start=False,
+                                           archive_workdir=False)
         except bee_client.ClientError as error:
             raise CIError(*error.args) from error
 

beeflow/remote/remote.py

@@ -82,7 +82,8 @@ def submit_new_wf_long(wf_name: str, tarball_name: str, main_cwl_file: str, job_
                           main_cwl_file,
                           job_file,
                           workdir_path,
-                          no_start=False)
+                          no_start=False,
+                          archive_workdir=False)
         output["result"] = "Submitted new workflow" + str(wf_name)
         return output
     except bee_client.ClientError as error:

beeflow/wf_manager/resources/wf_list.py

@@ -51,12 +51,12 @@ def extract_wf(wf_id, filename, workflow_archive):
 
 @shared_task(ignore_result=True)
 def init_workflow(wf_id, wf_name, wf_dir, wf_workdir, no_start, workflow=None,
-                  tasks=None):
+                  tasks=None, archive_workdir=False):
     """Initialize the workflow in a separate process."""
     db = connect_db(wfm_db, db_path)
     wf_utils.connect_neo4j_driver(db.info.get_port('bolt'))
     wf_utils.setup_workflow(wf_id, wf_name, wf_dir, wf_workdir, no_start,
-                            workflow, tasks)
+                            workflow, tasks, archive_workdir)
 
 
 db_path = wf_utils.get_db_path()
@@ -93,6 +93,7 @@ def post(self):
         reqparser.add_argument('tasks', type=str, required=True,
                                location='form')
         reqparser.add_argument('no_start', type=str, required=True, location='form')
+        reqparser.add_argument('archive_workdir', type=str, required=True, location='form')
         reqparser.add_argument('workflow_archive', type=FileStorage, required=False,
                                location='files')
         data = reqparser.parse_args()
@@ -102,6 +103,7 @@ def post(self):
         wf_workdir = data['workdir']
         # Note we have to check for the 'true' string value
         no_start = data['no_start'].lower() == 'true'
+        archive_workdir = data['archive_workdir'].lower() == 'true'
         workflow = jsonpickle.decode(data['workflow'])
         # May have to decode the list and task objects separately
         tasks = [jsonpickle.decode(task) if isinstance(task, str) else task
@@ -113,7 +115,8 @@ def post(self):
         db.workflows.init_workflow(wf_id, wf_name, wf_dir)
 
         init_workflow.delay(wf_id, wf_name, wf_dir, wf_workdir,
-                            no_start, workflow=workflow, tasks=tasks)
+                            no_start, workflow=workflow, tasks=tasks,
+                            archive_workdir=archive_workdir)
 
         return make_response(jsonify(msg='Workflow uploaded', status='ok',
                              wf_id=wf_id), 201)

beeflow/wf_manager/resources/wf_update.py

@@ -33,6 +33,16 @@ def archive_workflow(db, wf_id, final_state=None):
     os.makedirs(dags_dir, exist_ok=True)
     wf_utils.export_dag(wf_id, dags_dir, graphmls_dir, no_dag_dir=True, copy_dag_in_archive=False)
 
+    # Archive workdir
+    wfi = wf_utils.get_workflow_interface(wf_id)
+    _, tasks = wfi.get_workflow()
+    # metadata related to the workdir is redundantly stored on each task
+    archive_workdir = wfi.get_task_metadata(tasks[0])['archive_workdir']
+    if archive_workdir:
+        workdir = wfi.get_task_metadata(tasks[0])['workdir']
+        workdir_dir = workflow_dir + "/workdir"
+        shutil.copytree(workdir, workdir_dir, dirs_exist_ok=True)
+
     wf_state = f'Archived/{final_state}' if final_state is not None else 'Archived'
     db.workflows.update_workflow_state(wf_id, wf_state)
     wf_utils.update_wf_status(wf_id, wf_state)

beeflow/wf_manager/resources/wf_utils.py

@@ -266,7 +266,7 @@ def connect_neo4j_driver(bolt_port):
 
 
 def setup_workflow(wf_id, wf_name, wf_dir, wf_workdir, no_start, workflow=None,
-                   tasks=None):
+                   tasks=None, archive_workdir=False):
     """Initialize Workflow in Separate Process."""
     wfi = get_workflow_interface(wf_id)
     wfi.initialize_workflow(workflow)
@@ -279,6 +279,7 @@ def setup_workflow(wf_id, wf_name, wf_dir, wf_workdir, no_start, workflow=None,
         wfi.add_task(task, task_state)
         metadata = wfi.get_task_metadata(task)
         metadata['workdir'] = wf_workdir
+        metadata['archive_workdir'] = archive_workdir
         wfi.set_task_metadata(task, metadata)
         db.workflows.add_task(task.id, wf_id, task.name, task_state)