template API test

tests/resources/templates/dose_response.json

@@ -0,0 +1 @@
+{"newtemplate":"create_new","PROTOCOL_TOP_CATEGORY":"TOX","pageNo":0,"user_role":["role_lab"],"templates":"c5dd3ac9-9340-44b0-9be8-6724c5e34c99","METHOD":"Dose response ","EXPERIMENT":"Generic dose response template","conditions":[{"conditon_name":"concentration","condition_unit":"ug/ml","condition_type":"c_concentration "},{"conditon_name":"time","condition_unit":"h","condition_type":"c_time "},{"conditon_name":"Replicate","condition_type":"c_replicate_tech "},{"conditon_name":"Experiment","condition_type":"c_replicate_bio "}],"PROTOCOL_CATEGORY_CODE":"ENM_0000068_SECTION","raw_data":true,"RESULTS":"raw data ( absorbance) \ncell viability  (%)","raw_data_report":[{"raw_conditions":["concentration","time","Experiment","Replicate"],"raw_endpoint":"Absorbance","raw_unit":"A.U.","raw_type":"value_num"}],"question3":[{"results_conditions":["concentration","time","Experiment"],"result_name":"Cell viability","result_unit":"%","result_type":"value_num"}],"METADATA_PARAMETERS":[{"param_name":"Serum concentration in culture medium"},{"param_name":"Detailed cell type/line specification","param_group":"CELL LINE DETAILS","param_type":"value_text "},{"param_name":"Cell line short-name","param_group":"CELL LINE DETAILS","param_type":"value_text "},{"param_name":"Supplier","param_group":"CELL LINE DETAILS","param_type":"value_text "},{"param_name":"Passage no","param_group":"CELL LINE DETAILS","param_type":"value_num"},{"param_name":"Plate details as applic.","param_group":"CULTURE CONDITIONS","param_type":"value_text "},{"param_name":"Make / type","param_group":"CULTURE CONDITIONS","param_type":"value_text "},{"param_name":"Number of cells per well","param_group":"CULTURE CONDITIONS","param_type":"value_num"},{"param_name":"Total volume per well","param_group":"CULTURE CONDITIONS","param_type":"value_num"},{"param_name":"Medium (Supplier/Lot No.)","param_group":"MEDIUM","param_type":"value_text "},{"param_name":"Serum (inc. supplier/Lot No.)","param_group":"CULTURE CONDITIONS","param_type":"value_text "},{"param_name":"Serum concentration in treatment medium","param_group":"CULTURE CONDITIONS","param_type":"value_num"},{"param_name":"Was serum heat inactivated? If app.","param_group":"CULTURE CONDITIONS","param_type":"value_text "},{"param_name":"Submerged, ALI, or semi-ALI","param_group":"CULTURE CONDITIONS","param_type":"value_text "},{"param_name":"Exposure method","param_group":"ENVIRONMENT","param_type":"value_text "}],"METADATA_SAMPLE_INFO":[{"param_sample_name":"ID","param_sample_group":"ID"},{"param_sample_name":"Name","param_sample_group":"NAME"},{"param_sample_name":"CAS No","param_sample_group":"CASRN"},{"param_sample_name":"Nanomaterial Supplier","param_sample_group":"SUPPLIER"},{"param_sample_name":"Material State","param_sample_group":"OTHER_METADATA"},{"param_sample_name":"Batch","param_sample_group":"BATCH"},{"param_sample_name":"Vial","param_sample_group":"BATCH"}],"METADATA_SAMPLE_PREP":[{"param_sampleprep_name":"Date of preparation (YYYY-MM-DD)","param_sampleprep_group":"OTHER_METADATA","param_type":"value_text "},{"param_sampleprep_name":"Endotoxin confirmed as absent?","param_sampleprep_group":"OTHER_METADATA","param_type":"value_text "},{"param_sampleprep_name":"Effective concentration range used lowest-to-highest, inc units","param_sampleprep_group":"OTHER_METADATA","param_type":"value_text "},{"param_sampleprep_name":"Specify standard dispersion protocol used","param_sampleprep_group":"DISPERSION","param_type":"value_text "},{"param_sampleprep_name":"Dispersion agent","param_sampleprep_group":"DISPERSION","param_type":"value_text "},{"param_sampleprep_name":" Additives used? If yes, specify which & conc. used:","param_sampleprep_group":"DISPERSION","param_type":"value_text "},{"param_sampleprep_name":"Dispersed in cell culture medium","param_sampleprep_group":"DISPERSION","param_type":"value_text "},{"param_sampleprep_name":"Aids used to disperse","param_sampleprep_group":"DISPERSION","param_type":"value_text "},{"param_sampleprep_name":"Sonication-Bath","param_sampleprep_group":"DISPERSION","param_type":"value_text "},{"param_sampleprep_name":"Sonication-tip","param_sampleprep_group":"DISPERSION","param_type":"value_text "},{"param_sampleprep_name":"Vortexing","param_sampleprep_group":"DISPERSION","param_type":"value_text "},{"param_sampleprep_name":"Stirring","param_sampleprep_group":"DISPERSION","param_type":"value_text "},{"param_sampleprep_name":"Specify time-duration","param_sampleprep_group":"DISPERSION","param_type":"value_text "},{"param_sampleprep_name":"Energy (for sonication)","param_sampleprep_group":"DISPERSION","param_type":"value_text "}],"template_author":"xqa"}

tests/test_api_template.py

@@ -4,15 +4,49 @@
 from pathlib import Path
 import json
 import warnings
-
-
+import pytest
+from importlib import resources
+import yaml
+import os.path 
 TEST_JSON_PATH = Path(__file__).parent / "resources/templates/dose_response.json"
 
 client = TestClient(app)
 #warnings.warn("test")
-#print("test")
 
-def test_template():
+
+@pytest.fixture(scope="module")
+def config_dict():
+    print("\nModule-level setup: Loading config or other resources")
+    with resources.path('rcapi.config', 'config.yaml') as config_path:
+        with open(config_path, 'r') as config_file:
+            CONFIG_DICT = yaml.safe_load(config_file)
+            assert "upload_dir" in CONFIG_DICT,CONFIG_DICT
+    return CONFIG_DICT
+
+@pytest.fixture
+def clean_template_dir(config_dict):
+    print("\nSetting up resources before the test")
+    TEMPLATE_DIR = os.path.join(config_dict["upload_dir"],"TEMPLATES")
+    print(TEMPLATE_DIR)
+    remove_files_in_folder(TEMPLATE_DIR)
+    # Perform setup operations here, if any
+    yield  # This is where the test runs
+    print("\nCleaning up resources after the test")
+    remove_files_in_folder(TEMPLATE_DIR)
+    # Perform cleanup operations here, if any
+
+def remove_files_in_folder(folder_path):
+    folder_path = Path(folder_path)
+    file_list = folder_path.glob('*')
+    for file_path in file_list:
+        try:
+            if file_path.is_file():
+                file_path.unlink()
+                print(f"Removed file: {file_path}")
+        except Exception as e:
+            print(f"Error removing file {file_path}: {e}")
+
+def test_template(clean_template_dir):
     response = client.get("/template")
     assert response.status_code == 200
     assert response.json() == {"template" : []}
@@ -24,7 +58,7 @@ def get_task_result(response_post):
     assert result_uuid is not None, task_json
     return result_uuid
 
-def test_upload_and_retrieve_json():
+def test_upload_and_retrieve_json(clean_template_dir):
     # Step 1: Upload JSON
     json_content = {}
     with open(TEST_JSON_PATH, "rb") as file: