make datetime consistent accross output

big_scape/cli/benchmark_cli.py

@@ -52,12 +52,12 @@ def benchmark(ctx, *args, **kwargs):
     ctx.obj.update(ctx.params)
     ctx.obj["mode"] = "Benchmark"
 
-    # workflow validations
-    validate_output_paths(ctx)
-
     # set start time and label
     set_start(ctx.obj)
 
+    # workflow validations
+    validate_output_paths(ctx)
+
     # initialize logger
     init_logger(ctx.obj)
     init_logger_file(ctx.obj)

big_scape/cli/cli_validations.py

@@ -22,7 +22,7 @@ def set_start(param_dict) -> None:
     """get start time and set label in a run parameter dict"""
 
     start_time: datetime = datetime.now()
-    timestamp = start_time.strftime("%d-%m-%Y_%H-%M-%S")
+    timestamp = start_time.strftime("%Y-%m-%d_%H-%M-%S")
     if param_dict["label"]:
         param_dict["label"] = f"{param_dict['label']}_{timestamp}"
     else:
@@ -116,7 +116,7 @@ def validate_output_dir(ctx, param, output_dir) -> Path:
 def validate_output_paths(ctx) -> None:
     """Sets the output paths to default output_dir if not provided"""
 
-    timestamp = time.strftime("%Y-%m-%d_%H-%M-%S", time.localtime())
+    timestamp = ctx.obj["label"]
 
     if "db_path" in ctx.obj and ctx.obj["db_path"] is None:
         db_path = ctx.obj["output_dir"] / Path(f"{ctx.obj['output_dir'].name}.db")

big_scape/cli/cluster_cli.py

@@ -138,16 +138,16 @@ def cluster(ctx, *args, **kwargs):
     ctx.obj["propagate"] = True  # compatibility with query wrt cc generation
     ctx.obj["mode"] = "Cluster"
 
+    # set start time and run label
+    set_start(ctx.obj)
+
     # workflow validations
     validate_binning_cluster_workflow(ctx)
     validate_pfam_path(ctx)
     validate_domain_include_list(ctx)
     validate_output_paths(ctx)
     validate_disk_only(ctx)
 
-    # set start time and run label
-    set_start(ctx.obj)
-
     # initialize logger
     init_logger(ctx.obj)
     init_logger_file(ctx.obj)

big_scape/cli/query_cli.py

@@ -99,16 +99,16 @@ def query(ctx, *args, **kwarg):
     ctx.obj["exclude_classes"] = None
     ctx.obj["include_classes"] = None
 
+    # set start time and label
+    set_start(ctx.obj)
+
     # workflow validations
     validate_pfam_path(ctx)
     validate_output_paths(ctx)
     validate_binning_query_workflow(ctx)
     validate_query_record(ctx)
     validate_disk_only(ctx)
 
-    # set start time and label
-    set_start(ctx.obj)
-
     # initialize logger
     init_logger(ctx.obj)
     init_logger_file(ctx.obj)