Fix tests

tests/conftest.py

@@ -323,7 +323,7 @@ def data_repo_full(
 @pytest.fixture
 def mock_project_data_record():
     def _method(status):
-        config_values = config.Config()
+        config_values = config.Config(env_file_path=".test.env")
         if status == "open":
             mock_record = ngi_data.ProjectDataRecord(
                 "NGIS/2023/NGI123456.json",
@@ -441,3 +441,10 @@ def mocked_statusdb_conn_rows():
         },
     )
     return [row1, row2, row3]
+
+
+@pytest.fixture(autouse=True)
+def get_env_file_path():
+    """returns the test env file path"""
+
+    return ".test.env"

tests/test_daily_report.py

@@ -6,11 +6,11 @@
 from daily_read import daily_report, config, ngi_data, order_portal
 
 
-def test_write_report_to_out_dir(data_repo_full, mock_project_data_record, create_report_path):
+def test_write_report_to_out_dir(data_repo_full, mock_project_data_record, create_report_path, get_env_file_path):
     """Test existence of html report when provided with out_dir"""
     orderer = "[email protected]"
     order_id = "NGI123456"
-    config_values = config.Config()
+    config_values = config.Config(env_file_path=get_env_file_path)
     daily_rep = daily_report.DailyReport()
     with mock.patch("daily_read.statusdb.StatusDBSession"):
         data_master = ngi_data.ProjectDataMaster(config_values)

tests/test_ngi_data.py

@@ -9,9 +9,9 @@
 ####################################################### TESTS #########################################################
 
 
-def test_create_project_data_master(data_repo_full):
+def test_create_project_data_master(data_repo_full, get_env_file_path):
     """With existing git repo, test creation of a ProjectDataMaster class"""
-    config_values = config.Config()
+    config_values = config.Config(get_env_file_path)
     with mock.patch("daily_read.statusdb.StatusDBSession"):
         data_master = ngi_data.ProjectDataMaster(config_values)
 
@@ -21,9 +21,9 @@ def test_create_project_data_master(data_repo_full):
     assert data_master._data_fetched == False
 
 
-def test_create_project_data_master_no_commit(data_repo_no_commit):
+def test_create_project_data_master_no_commit(data_repo_no_commit, get_env_file_path):
     """With existing git repo but without commits, test creation of a ProjectDataMaster class"""
-    config_values = config.Config()
+    config_values = config.Config(get_env_file_path)
     with mock.patch("daily_read.statusdb.StatusDBSession"):
         data_master = ngi_data.ProjectDataMaster(config_values)
 
@@ -35,8 +35,8 @@ def test_create_project_data_master_no_commit(data_repo_no_commit):
     assert data_master.data_repo.commit().message == "Empty file as a first commit"
 
 
-def test_modified_or_new_no_commit(data_repo_no_commit):
-    config_values = config.Config()
+def test_modified_or_new_no_commit(data_repo_no_commit, get_env_file_path):
+    config_values = config.Config(get_env_file_path)
     with mock.patch("daily_read.statusdb.StatusDBSession"):
         data_master = ngi_data.ProjectDataMaster(config_values)
 
@@ -47,8 +47,8 @@ def test_modified_or_new_no_commit(data_repo_no_commit):
     assert len(set(file_names)) == 0
 
 
-def test_modified_or_new(data_repo_full):
-    config_values = config.Config()
+def test_modified_or_new(data_repo_full, get_env_file_path):
+    config_values = config.Config(get_env_file_path)
     with mock.patch("daily_read.statusdb.StatusDBSession"):
         data_master = ngi_data.ProjectDataMaster(config_values)
 
@@ -59,8 +59,8 @@ def test_modified_or_new(data_repo_full):
     assert len(set(file_names)) == 12
 
 
-def test_modified_or_new_untracked(data_repo_untracked):
-    config_values = config.Config()
+def test_modified_or_new_untracked(data_repo_untracked, get_env_file_path):
+    config_values = config.Config(get_env_file_path)
     with mock.patch("daily_read.statusdb.StatusDBSession"):
         data_master = ngi_data.ProjectDataMaster(config_values)
 
@@ -73,8 +73,8 @@ def test_modified_or_new_untracked(data_repo_untracked):
     assert "untracked_file" in file_names[0]
 
 
-def test_modified_or_new_staged(data_repo_new_staged):
-    config_values = config.Config()
+def test_modified_or_new_staged(data_repo_new_staged,get_env_file_path):
+    config_values = config.Config(get_env_file_path)
     with mock.patch("daily_read.statusdb.StatusDBSession"):
         data_master = ngi_data.ProjectDataMaster(config_values)
 
@@ -86,8 +86,8 @@ def test_modified_or_new_staged(data_repo_new_staged):
     assert any("staged_file" in s for s in file_names)
 
 
-def test_modified_or_new_modified_not_staged(data_repo_modified_not_staged):
-    config_values = config.Config()
+def test_modified_or_new_modified_not_staged(data_repo_modified_not_staged, get_env_file_path):
+    config_values = config.Config(get_env_file_path)
     with mock.patch("daily_read.statusdb.StatusDBSession"):
         data_master = ngi_data.ProjectDataMaster(config_values)
 
@@ -100,8 +100,8 @@ def test_modified_or_new_modified_not_staged(data_repo_modified_not_staged):
     assert "modified_file" in file_names[0]
 
 
-def test_modified_or_new_modified_staged(data_repo_modified_staged):
-    config_values = config.Config()
+def test_modified_or_new_modified_staged(data_repo_modified_staged, get_env_file_path):
+    config_values = config.Config(get_env_file_path)
     with mock.patch("daily_read.statusdb.StatusDBSession"):
         data_master = ngi_data.ProjectDataMaster(config_values)
 
@@ -114,8 +114,8 @@ def test_modified_or_new_modified_staged(data_repo_modified_staged):
     assert "modified_staged_file" in file_names[0]
 
 
-def test_modified_or_new_tracked(data_repo_tracked):
-    config_values = config.Config()
+def test_modified_or_new_tracked(data_repo_tracked, get_env_file_path):
+    config_values = config.Config(get_env_file_path)
     with mock.patch("daily_read.statusdb.StatusDBSession"):
         data_master = ngi_data.ProjectDataMaster(config_values)
 
@@ -127,19 +127,19 @@ def test_modified_or_new_tracked(data_repo_tracked):
     assert len(set(file_names)) == 0
 
 
-def test_get_unique_orderers(data_repo_full):
+def test_get_unique_orderers(data_repo_full, get_env_file_path):
     """Test getting unique orders in the project data from statusdb"""
-    config_values = config.Config()
+    config_values = config.Config(get_env_file_path)
     with mock.patch("daily_read.statusdb.StatusDBSession"):
         data_master = ngi_data.ProjectDataMaster(config_values)
         data_master.get_data()
         orderers = data_master.find_unique_orderers()
         assert orderers == set(["[email protected]"])
 
 
-def test_user_list(data_repo_full, tmp_path, mocked_statusdb_conn_rows):
+def test_user_list(data_repo_full, tmp_path, mocked_statusdb_conn_rows, get_env_file_path):
     """Test getting and reading users from the user list url"""
-    config_values = config.Config()
+    config_values = config.Config(get_env_file_path)
     temp_file = tmp_path / "test_file.txt"
     temp_file.write_text("[email protected]\n[email protected]")
     config_values.USERS_LIST_LOCATION = temp_file
@@ -154,9 +154,9 @@ def test_user_list(data_repo_full, tmp_path, mocked_statusdb_conn_rows):
         assert orderers == set(["[email protected]", "[email protected]"])
 
 
-def test_save_data_to_disk(data_repo_full, mocked_statusdb_conn_rows):
+def test_save_data_to_disk(data_repo_full, mocked_statusdb_conn_rows, get_env_file_path):
     """Test saving in git repo the data gotten from statusdb"""
-    config_values = config.Config()
+    config_values = config.Config(get_env_file_path)
     with mock.patch("daily_read.statusdb.StatusDBSession"):
         data_master = ngi_data.ProjectDataMaster(config_values)
         data_master.sources[0].statusdb_session.rows.return_value = mocked_statusdb_conn_rows
@@ -166,9 +166,9 @@ def test_save_data_to_disk(data_repo_full, mocked_statusdb_conn_rows):
         assert os.path.exists(os.path.join(config_values.DATA_LOCATION, "NGIS/2023/NGI123458.json"))
 
 
-def test_get_data_with_project(data_repo_full, mocked_statusdb_conn_rows):
+def test_get_data_with_project(data_repo_full, mocked_statusdb_conn_rows, get_env_file_path):
     """Test getting data for a specific order"""
-    config_values = config.Config()
+    config_values = config.Config(get_env_file_path)
     order_id = "NGI123457"
     with mock.patch("daily_read.statusdb.StatusDBSession"):
         data_master = ngi_data.ProjectDataMaster(config_values)
@@ -179,9 +179,9 @@ def test_get_data_with_project(data_repo_full, mocked_statusdb_conn_rows):
         assert data_master.data[order_id].internal_id_or_portal_id == "P123457"
 
 
-def test_get_data_with_project_unknown(data_repo_full, mocked_statusdb_conn_rows):
+def test_get_data_with_project_unknown(data_repo_full, mocked_statusdb_conn_rows, get_env_file_path):
     """Test error thrown when the order specified is not found in statusdb"""
-    config_values = config.Config()
+    config_values = config.Config(get_env_file_path)
     with mock.patch("daily_read.statusdb.StatusDBSession"):
         data_master = ngi_data.ProjectDataMaster(config_values)
         data_master.sources[0].statusdb_session.rows.return_value = mocked_statusdb_conn_rows
@@ -190,9 +190,9 @@ def test_get_data_with_project_unknown(data_repo_full, mocked_statusdb_conn_rows
 
 
 @mock.patch("daily_read.statusdb.StatusDBSession")
-def test_data_loc_not_abs(mock_status):
+def test_data_loc_not_abs(mock_status, get_env_file_path):
     """Test error thrown when given data location is not an absolute path"""
-    config_values = config.Config()
+    config_values = config.Config(get_env_file_path)
     config_values.DATA_LOCATION = "tests/test_data_location"
     with pytest.raises(
         ValueError, match=f"Data location is not an absolute path: {config_values.DATA_LOCATION}"
@@ -201,9 +201,9 @@ def test_data_loc_not_abs(mock_status):
 
 
 @mock.patch("daily_read.statusdb.StatusDBSession")
-def test_data_loc_not_dir(mock_status, tmp_path):
+def test_data_loc_not_dir(mock_status, tmp_path, get_env_file_path):
     """Test error thrown when data location is not a directory"""
-    config_values = config.Config()
+    config_values = config.Config(get_env_file_path)
     temp_file = tmp_path / "test_file.txt"
     temp_file.write_text("test")
     config_values.DATA_LOCATION = temp_file
@@ -213,11 +213,11 @@ def test_data_loc_not_dir(mock_status, tmp_path):
         ngi_data.ProjectDataMaster(config_values)
 
 
-def test_get_data_with_no_project_dates(data_repo_full, mocked_statusdb_conn_rows, caplog):
+def test_get_data_with_no_project_dates(data_repo_full, mocked_statusdb_conn_rows, caplog, get_env_file_path):
     """Test log output when no project dates are found in statusdb for a specific project"""
     from copy import deepcopy
 
-    config_values = config.Config()
+    config_values = config.Config(get_env_file_path)
     with mock.patch("daily_read.statusdb.StatusDBSession"):
         data_master = ngi_data.ProjectDataMaster(config_values)
         data_master.sources[0].statusdb_session.rows.return_value = mocked_statusdb_conn_rows
@@ -232,10 +232,10 @@ def test_get_data_with_no_project_dates(data_repo_full, mocked_statusdb_conn_row
             assert "No project dates found for NGI123459" in caplog.text
 
 
-def test_skip_order_with_no_year(data_repo_full, mocked_statusdb_conn_rows, caplog):
+def test_skip_order_with_no_year(data_repo_full, mocked_statusdb_conn_rows, caplog, get_env_file_path):
     """Test that orders with no order year (i.e. with no contract signed) are skipped"""
 
-    config_values = config.Config()
+    config_values = config.Config(get_env_file_path)
     with mock.patch("daily_read.statusdb.StatusDBSession"):
         data_master = ngi_data.ProjectDataMaster(config_values)
         data_master.sources[0].statusdb_session.rows.return_value = mocked_statusdb_conn_rows
@@ -247,20 +247,20 @@ def test_skip_order_with_no_year(data_repo_full, mocked_statusdb_conn_rows, capl
 
 
 @mock.patch("daily_read.statusdb.StatusDBSession")
-def test_no_source_specified(mock_status):
+def test_no_source_specified(mock_status, get_env_file_path):
     """Test error thrown when no sources are specified"""
 
-    config_values = config.Config()
+    config_values = config.Config(get_env_file_path)
     config_values.FETCH_FROM_NGIS = ""
     config_values.FETCH_FROM_SNPSEQ = ""
     config_values.FETCH_FROM_UGC = ""
     with pytest.raises(ValueError, match="There are no sources specified to fetch data from!") as err:
         ngi_data.ProjectDataMaster(config_values)
 
 
-def test_commit_staged_data(data_repo_full, mocked_statusdb_conn_rows):
+def test_commit_staged_data(data_repo_full, mocked_statusdb_conn_rows, get_env_file_path):
     """Test file is staged for commit and committed and then try adding it for staging again"""
-    config_values = config.Config()
+    config_values = config.Config(get_env_file_path)
     with mock.patch("daily_read.statusdb.StatusDBSession"):
         data_master = ngi_data.ProjectDataMaster(config_values)
         data_master.sources[0].statusdb_session.rows.return_value = mocked_statusdb_conn_rows

tests/test_order_portal.py

@@ -7,11 +7,11 @@
 from daily_read import order_portal, config, ngi_data
 
 
-def test_get_and_process_orders_open_upload_fail(data_repo_full, mock_project_data_record, caplog):
+def test_get_and_process_orders_open_upload_fail(data_repo_full, mock_project_data_record, caplog, get_env_file_path):
     """Test getting and processing an open order and upload to Order portal failing"""
     orderer = "[email protected]"
     order_id = "NGI123456"
-    config_values = config.Config()
+    config_values = config.Config(get_env_file_path)
     with mock.patch("daily_read.statusdb.StatusDBSession"):
         data_master = ngi_data.ProjectDataMaster(config_values)
 
@@ -32,11 +32,11 @@ def test_get_and_process_orders_open_upload_fail(data_repo_full, mock_project_da
         assert f"Report not uploaded for order with project id: {order_id}\nReason: 404" in caplog.text
 
 
-def test_get_and_process_orders_open_and_upload(data_repo_full, mock_project_data_record):
+def test_get_and_process_orders_open_and_upload(data_repo_full, mock_project_data_record, get_env_file_path):
     """Test getting and processing an open order and uploading its Project progress report and uploading the report to the Order portal"""
     orderer = "[email protected]"
     order_id = "NGI123456"
-    config_values = config.Config()
+    config_values = config.Config(get_env_file_path)
     with mock.patch("daily_read.statusdb.StatusDBSession"):
         data_master = ngi_data.ProjectDataMaster(config_values)
 
@@ -69,11 +69,11 @@ def test_get_and_process_orders_open_and_upload(data_repo_full, mock_project_dat
         )
 
 
-def test_get_and_process_orders_open_with_report_and_upload(data_repo_full, mock_project_data_record, caplog):
+def test_get_and_process_orders_open_with_report_and_upload(data_repo_full, mock_project_data_record, caplog, get_env_file_path):
     """Test getting, processing an open order with an existing Project progress report and uploading the report to the Order portal"""
     orderer = "[email protected]"
     order_id = "NGI123453"
-    config_values = config.Config()
+    config_values = config.Config(get_env_file_path)
     with mock.patch("daily_read.statusdb.StatusDBSession"):
         data_master = ngi_data.ProjectDataMaster(config_values)
 
@@ -109,11 +109,11 @@ def test_get_and_process_orders_open_with_report_and_upload(data_repo_full, mock
             assert f"Updated report for order with project id: {order_id}" in caplog.text
 
 
-def test_get_and_process_orders_open_to_aborted_with_report_and_upload(data_repo_full, mock_project_data_record):
+def test_get_and_process_orders_open_to_aborted_with_report_and_upload(data_repo_full, mock_project_data_record, get_env_file_path):
     """Test getting, processing an open order with an existing Project progress report and uploading the report to the Order portal"""
     orderer = "[email protected]"
     order_id = "NGI123461"
-    config_values = config.Config()
+    config_values = config.Config(get_env_file_path)
     with mock.patch("daily_read.statusdb.StatusDBSession"):
         data_master = ngi_data.ProjectDataMaster(config_values)
 
@@ -142,11 +142,11 @@ def test_get_and_process_orders_open_to_aborted_with_report_and_upload(data_repo
         )
 
 
-def test_get_and_process_orders_closed(data_repo_full, mock_project_data_record):
+def test_get_and_process_orders_closed(data_repo_full, mock_project_data_record, get_env_file_path):
     """Test getting and processing an order closed within the timeframe of Project progress report deletion"""
     orderer = "[email protected]"
     order_id = "NGI123455"
-    config_values = config.Config()
+    config_values = config.Config(get_env_file_path)
     with mock.patch("daily_read.statusdb.StatusDBSession"):
         data_master = ngi_data.ProjectDataMaster(config_values)
 
@@ -160,11 +160,11 @@ def test_get_and_process_orders_closed(data_repo_full, mock_project_data_record)
     assert modified_orders[orderer]["delete_report_for"]["All Raw data Delivered"][0] == data_master.data[order_id]
 
 
-def test_get_and_process_orders_mult_reports(data_repo_full, mock_project_data_record):
+def test_get_and_process_orders_mult_reports(data_repo_full, mock_project_data_record, get_env_file_path):
     """Test getting and processing orders with multiple Project progress reports"""
     orderer = "[email protected]"
     order_id = "NGI123454"
-    config_values = config.Config()
+    config_values = config.Config(get_env_file_path)
     with mock.patch("daily_read.statusdb.StatusDBSession"):
         data_master = ngi_data.ProjectDataMaster(config_values)
 
@@ -180,10 +180,10 @@ def test_get_and_process_orders_mult_reports(data_repo_full, mock_project_data_r
         op.process_orders(config_values.STATUS_PRIORITY_REV)
 
 
-def test_base_url_and_api_key_not_set(data_repo_full, mock_project_data_record):
+def test_base_url_and_api_key_not_set(data_repo_full, mock_project_data_record, get_env_file_path):
     """Test the conditions when environment variables ORDER_PORTAL_URL and ORDER_PORTAL_API_KEY are not set"""
     order_id = "NGI123456"
-    config_values = config.Config()
+    config_values = config.Config(get_env_file_path)
 
     order_portal_url = config_values.ORDER_PORTAL_URL
     api_key = config_values.ORDER_PORTAL_API_KEY

tests/test_statusdb.py

@@ -3,9 +3,9 @@
 from daily_read import config, statusdb
 
 
-def test_no_statusdb_conn(data_repo_full):
+def test_no_statusdb_conn(data_repo_full, get_env_file_path):
     """Test error thrown when statusdb conn fails"""
-    config_values = config.Config()
+    config_values = config.Config(get_env_file_path)
     # Escape special chars because match uses regex
     display_url_string = (
         rf"https:\/\/{config_values.STHLM_STATUSDB_USERNAME}:\*\*\*\*\*\*\*\*\*@{config_values.STHLM_STATUSDB_URL}"