From efba643ad0886e57185341c2cd1df85bb3f3059d Mon Sep 17 00:00:00 2001
From: Catarina Loureiro <catarina.salesesantosloureiro@wur.nl>
Date: Thu, 5 Dec 2024 11:04:19 +0100
Subject: [PATCH] make datetime consistent accross output

---
 big_scape/cli/benchmark_cli.py   | 6 +++---
 big_scape/cli/cli_validations.py | 4 ++--
 big_scape/cli/cluster_cli.py     | 6 +++---
 big_scape/cli/query_cli.py       | 6 +++---
 4 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/big_scape/cli/benchmark_cli.py b/big_scape/cli/benchmark_cli.py
index 14403cc5..7eac876d 100644
--- a/big_scape/cli/benchmark_cli.py
+++ b/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)
diff --git a/big_scape/cli/cli_validations.py b/big_scape/cli/cli_validations.py
index fd0bd365..958fde92 100644
--- a/big_scape/cli/cli_validations.py
+++ b/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")
diff --git a/big_scape/cli/cluster_cli.py b/big_scape/cli/cluster_cli.py
index 96153d69..4418186d 100644
--- a/big_scape/cli/cluster_cli.py
+++ b/big_scape/cli/cluster_cli.py
@@ -138,6 +138,9 @@ 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)
@@ -145,9 +148,6 @@ def cluster(ctx, *args, **kwargs):
     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)
diff --git a/big_scape/cli/query_cli.py b/big_scape/cli/query_cli.py
index ed571d3f..5609f187 100644
--- a/big_scape/cli/query_cli.py
+++ b/big_scape/cli/query_cli.py
@@ -99,6 +99,9 @@ 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)
@@ -106,9 +109,6 @@ def query(ctx, *args, **kwarg):
     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)