added an option to not make the dags dir, set to false for archive

beeflow/client/bee_client.py

@@ -627,7 +627,9 @@ def reexecute(wf_name: str = typer.Argument(..., help='The workflow name'),
 @app.command()
 def dag(wf_id: str = typer.Argument(..., callback=match_short_id),
         output_dir: pathlib.Path = typer.Argument(...,
-        help='Path to the where the dag directory will be')):
+        help='Path to the where the dag output will be'),
+        no_dag_dir: bool = typer.Option(False, '--no-dag-dir',
+        help='do not make a subdirectory within ouput_dir for the dags')):
     """Export a DAG of the workflow to a GraphML file."""
     output_dir = output_dir.resolve()
 
@@ -639,7 +641,7 @@ def dag(wf_id: str = typer.Argument(..., callback=match_short_id),
 
     # output_dir must be a string
     output_dir = str(output_dir)
-    wf_utils.export_dag(wf_id, output_dir)
+    wf_utils.export_dag(wf_id, output_dir, no_dag_dir)
     typer.secho(f"DAG for workflow {_short_id(wf_id)} has been exported successfully.",
                 fg=typer.colors.GREEN)
 

beeflow/common/gdb/generate_graph.py

@@ -11,12 +11,16 @@
 graphmls_dir = os.path.join(bee_workdir, 'graphmls')
 
 
-def generate_viz(wf_id, output_dir):
+def generate_viz(wf_id, output_dir, no_dag_dir):
     """Generate a PNG of a workflow graph from a GraphML file."""
     short_id = wf_id[:6]
     graphml_path = graphmls_dir + "/" + short_id + ".graphml"
-    dags_dir = output_dir + "/" + short_id + "_dags"
-    os.makedirs(dags_dir, exist_ok=True)
+
+    if no_dag_dir:
+        dags_dir = output_dir
+    else:
+        dags_dir = output_dir + "/" + short_id + "_dags"
+        os.makedirs(dags_dir, exist_ok=True)
 
     output_path = dags_dir + "/" + short_id + ".png"
     if os.path.exists(output_path):

beeflow/wf_manager/resources/wf_update.py

@@ -37,7 +37,7 @@ def archive_workflow(db, wf_id, final_state=None):
     archive_path = f'../archives/{wf_id}.tgz'
     # We use tar directly since tarfile is apparently very slow
     workflows_dir = wf_utils.get_workflows_dir()
-    wf_utils.export_dag(wf_id, workflow_dir)
+    wf_utils.export_dag(wf_id, workflow_dir, no_dag_dir=True)
     subprocess.call(['tar', '-czf', archive_path, wf_id], cwd=workflows_dir)
     remove_wf_dir = bc.get('DEFAULT', 'delete_completed_workflow_dirs')
     if remove_wf_dir:

beeflow/wf_manager/resources/wf_utils.py

@@ -294,12 +294,12 @@ def setup_workflow(wf_id, wf_name, wf_dir, wf_workdir, no_start, workflow=None,
         start_workflow(wf_id)
 
 
-def export_dag(wf_id, output_dir):
+def export_dag(wf_id, output_dir, no_dag_dir):
     """Export the DAG of the workflow."""
     wfi = get_workflow_interface(wf_id)
     wfi.export_graphml()
     update_graphml(wf_id)
-    generate_viz(wf_id, output_dir)
+    generate_viz(wf_id, output_dir, no_dag_dir)
 
 
 def start_workflow(wf_id):