From 654ff31dece02f09b9ac7de18a1c690a97cded09 Mon Sep 17 00:00:00 2001
From: sfmig <33267254+sfmig@users.noreply.github.com>
Date: Wed, 4 Oct 2023 19:31:14 +0100
Subject: [PATCH] add check for output directory to tests

---
 brainglobe_workflows/cellfinder/cellfinder_main.py | 2 +-
 tests/test_integration/test_cellfinder_workflow.py | 8 ++++++++
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/brainglobe_workflows/cellfinder/cellfinder_main.py b/brainglobe_workflows/cellfinder/cellfinder_main.py
index 2c4bf30e..acea6498 100644
--- a/brainglobe_workflows/cellfinder/cellfinder_main.py
+++ b/brainglobe_workflows/cellfinder/cellfinder_main.py
@@ -214,7 +214,7 @@ def setup_workflow(cellfinder_cache_dir=CELLFINDER_CACHE_DIR):
     timestamp = datetime.datetime.now()
     timestamp_formatted = timestamp.strftime("%Y%m%d_%H%M%S")
     output_path_timestamped = Path(
-        str(config.output_path) + timestamp_formatted
+        str(config.output_path_basename) + timestamp_formatted
     )
     output_path_timestamped.mkdir(parents=True, exist_ok=True)
     # add to config
diff --git a/tests/test_integration/test_cellfinder_workflow.py b/tests/test_integration/test_cellfinder_workflow.py
index 765939ca..a4128fd7 100644
--- a/tests/test_integration/test_cellfinder_workflow.py
+++ b/tests/test_integration/test_cellfinder_workflow.py
@@ -75,6 +75,10 @@ def test_run_with_env_var_config(config_from_env_var, caplog, logger_str):
         "provided GIN repository" in caplog.messages
     )
 
+    # check output directory and output file exist
+    assert Path(cfg.output_path).exists()
+    assert (Path(cfg.output_path) / cfg.detected_cells_filename).is_file()
+
 
 def test_run_with_default_config(cellfinder_cache_dir, caplog, logger_str):
     # check environment var is not defined
@@ -92,6 +96,10 @@ def test_run_with_default_config(cellfinder_cache_dir, caplog, logger_str):
         "provided GIN repository" in caplog.messages
     )
 
+    # check output directory and output file exist
+    assert Path(cfg.output_path).exists()
+    assert (Path(cfg.output_path) / cfg.detected_cells_filename).is_file()
+
 
 # test running on local data?
 # def test_run_with_default_config_local(