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Merge pull request #33 from aanil/fix_git
Update Readme: first draft, log error instead of raising exception on failed upload, cleanup tests a bit
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -7,7 +7,7 @@ | |
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| from datetime import date, timedelta | ||
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| from daily_read import ngi_data, config | ||
| from daily_read import ngi_data, config, order_portal | ||
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| dummy_order_open = { | ||
| "orderer": "[email protected]", | ||
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@@ -376,30 +376,26 @@ def create_report_path(tmp_path): | |
| return create_report_path | ||
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| def mocked_requests_get(*args, **kwargs): | ||
| class MockResponse: | ||
| def __init__(self, json_data, status_code): | ||
| self.json_data = json_data | ||
| self.status_code = status_code | ||
| @pytest.fixture(autouse=True) | ||
| def mocked_requests_get(monkeypatch): | ||
| """order_portal.OrderPortal._get() mocked to return {'items': [order list]}.""" | ||
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| class MockResponse: | ||
| def json(self): | ||
| return self.json_data | ||
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| if args[0] == "api/v1/orders": | ||
| return MockResponse( | ||
| { | ||
| return { | ||
| "items": [ | ||
| order_portal_resp_order_processing, | ||
| order_portal_resp_order_closed, | ||
| order_portal_resp_order_processing_mult_reports, | ||
| order_portal_resp_order_processing_single_report, | ||
| order_portal_resp_order_processing_to_aborted, | ||
| ] | ||
| }, | ||
| 200, | ||
| ) | ||
| } | ||
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| def mock_get(*args, **kwargs): | ||
| return MockResponse() | ||
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| return MockResponse(None, 404) | ||
| monkeypatch.setattr(order_portal.OrderPortal, "_get", mock_get) | ||
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| @pytest.fixture | ||
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@@ -414,10 +410,7 @@ def mocked_statusdb_conn_rows(): | |
| "order_year": "2023", | ||
| "project_id": "P123457", | ||
| "project_name": "D.Dummysson_23_03", | ||
| "proj_dates": { | ||
| "2023-06-15": ["Samples Received"], | ||
| "2023-06-28": ["Reception Control finished", "Library QC finished"], | ||
| }, | ||
| "proj_dates": dummy_order_open["project_dates"], | ||
| "status": "Ongoing", | ||
| }, | ||
| ) | ||
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@@ -430,12 +423,7 @@ def mocked_statusdb_conn_rows(): | |
| "order_year": "2023", | ||
| "project_id": "P123458", | ||
| "project_name": "T.Dummysson_23_04", | ||
| "proj_dates": { | ||
| "2023-06-15": ["Samples Received"], | ||
| "2023-06-28": ["Reception Control finished", "Library QC finished"], | ||
| "2023-07-28": ["All Samples Sequenced"], | ||
| "2023-07-29": ["All Raw data Delivered"], | ||
| }, | ||
| "proj_dates": dummy_order_closed["project_dates"], | ||
| "status": "Closed", | ||
| }, | ||
| ) | ||
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||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,12 +1,37 @@ | ||
| import base64 | ||
| import logging | ||
| import pytest | ||
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| from conftest import mocked_requests_get | ||
| from unittest import mock | ||
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| from daily_read import order_portal, config, ngi_data | ||
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| def test_get_and_process_orders_open_upload_fail(data_repo_full, mock_project_data_record, caplog): | ||
| """Test getting and processing an open order and upload to Order portal failing""" | ||
| orderer = "[email protected]" | ||
| order_id = "NGI123456" | ||
| config_values = config.Config() | ||
| with mock.patch("daily_read.statusdb.StatusDBSession"): | ||
| data_master = ngi_data.ProjectDataMaster(config_values) | ||
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| data_master.data = {order_id: mock_project_data_record("open")} | ||
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| op = order_portal.OrderPortal(config_values, data_master) | ||
| op.get_orders(orderer=orderer) | ||
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| assert op.all_orders[0]["identifier"] == order_id | ||
| modified_orders = op.process_orders(config_values.STATUS_PRIORITY_REV) | ||
| assert modified_orders[orderer]["projects"]["Library QC finished"][0] == data_master.data[order_id] | ||
| with mock.patch("daily_read.order_portal.requests.post") as mock_post: | ||
| mock_post.return_value.status_code = 404 | ||
| uploaded = op.upload_report_to_order_portal( | ||
| "<html>test data</html>", modified_orders[orderer]["projects"]["Library QC finished"][0], "published" | ||
| ) | ||
| assert not uploaded | ||
| assert f"Report not uploaded for order with project id: {order_id}\nReason: 404" in caplog.text | ||
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| def test_get_and_process_orders_open_and_upload(data_repo_full, mock_project_data_record): | ||
| """Test getting and processing an open order and uploading its Project progress report and uploading the report to the Order portal""" | ||
| orderer = "[email protected]" | ||
|
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@@ -18,8 +43,7 @@ def test_get_and_process_orders_open_and_upload(data_repo_full, mock_project_dat | |
| data_master.data = {order_id: mock_project_data_record("open")} | ||
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| op = order_portal.OrderPortal(config_values, data_master) | ||
| with mock.patch("daily_read.order_portal.OrderPortal._get", side_effect=mocked_requests_get): | ||
| op.get_orders(orderer=orderer) | ||
| op.get_orders(orderer=orderer) | ||
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| assert op.all_orders[0]["identifier"] == order_id | ||
| modified_orders = op.process_orders(config_values.STATUS_PRIORITY_REV) | ||
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@@ -45,7 +69,7 @@ def test_get_and_process_orders_open_and_upload(data_repo_full, mock_project_dat | |
| ) | ||
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| def test_get_and_process_orders_open_with_report_and_upload(data_repo_full, mock_project_data_record): | ||
| def test_get_and_process_orders_open_with_report_and_upload(data_repo_full, mock_project_data_record, caplog): | ||
| """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" | ||
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@@ -56,31 +80,33 @@ def test_get_and_process_orders_open_with_report_and_upload(data_repo_full, mock | |
| data_master.data = {order_id: mock_project_data_record("open_with_report")} | ||
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| op = order_portal.OrderPortal(config_values, data_master) | ||
| with mock.patch("daily_read.order_portal.OrderPortal._get", side_effect=mocked_requests_get): | ||
| op.get_orders(orderer=orderer) | ||
| op.get_orders(orderer=orderer) | ||
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| assert op.all_orders[3]["identifier"] == order_id | ||
| modified_orders = op.process_orders(config_values.STATUS_PRIORITY_REV) | ||
| assert modified_orders[orderer]["projects"]["Library QC finished"][0] == data_master.data[order_id] | ||
| with mock.patch("daily_read.order_portal.requests.post") as mock_post: | ||
| mock_post.return_value.status_code = 200 | ||
| op.upload_report_to_order_portal( | ||
| "<html>test data</html>", modified_orders[orderer]["projects"]["Library QC finished"][0], "published" | ||
| ) | ||
| url = f"{config_values.ORDER_PORTAL_URL}/api/v1/report/{op.all_orders[3]['reports'][0]['iuid']}" | ||
| indata = dict( | ||
| order=order_id, | ||
| name="Project Progress", | ||
| status="published", | ||
| file=dict( | ||
| data=base64.b64encode("<html>test data</html>".encode()).decode("utf-8"), | ||
| filename="project_progress.html", | ||
| content_type="text/html", | ||
| ), | ||
| ) | ||
| mock_post.assert_called_once_with( | ||
| url, headers={"X-OrderPortal-API-key": config_values.ORDER_PORTAL_API_KEY}, json=indata | ||
| ) | ||
| with caplog.at_level(logging.INFO): | ||
| uploaded = op.upload_report_to_order_portal( | ||
| "<html>test data</html>", modified_orders[orderer]["projects"]["Library QC finished"][0], "published" | ||
| ) | ||
| url = f"{config_values.ORDER_PORTAL_URL}/api/v1/report/{op.all_orders[3]['reports'][0]['iuid']}" | ||
| indata = dict( | ||
| order=order_id, | ||
| name="Project Progress", | ||
| status="published", | ||
| file=dict( | ||
| data=base64.b64encode("<html>test data</html>".encode()).decode("utf-8"), | ||
| filename="project_progress.html", | ||
| content_type="text/html", | ||
| ), | ||
| ) | ||
| assert uploaded | ||
| mock_post.assert_called_once_with( | ||
| url, headers={"X-OrderPortal-API-key": config_values.ORDER_PORTAL_API_KEY}, json=indata | ||
| ) | ||
| assert f"Updated report for order with project id: {order_id}" in caplog.text | ||
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| def test_get_and_process_orders_open_to_aborted_with_report_and_upload(data_repo_full, mock_project_data_record): | ||
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@@ -94,8 +120,7 @@ def test_get_and_process_orders_open_to_aborted_with_report_and_upload(data_repo | |
| data_master.data = {order_id: mock_project_data_record("open_to_aborted_with_report")} | ||
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| op = order_portal.OrderPortal(config_values, data_master) | ||
| with mock.patch("daily_read.order_portal.OrderPortal._get", side_effect=mocked_requests_get): | ||
| op.get_orders(orderer=orderer) | ||
| op.get_orders(orderer=orderer) | ||
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| assert op.all_orders[4]["identifier"] == order_id | ||
| modified_orders = op.process_orders(config_values.STATUS_PRIORITY_REV) | ||
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@@ -128,8 +153,7 @@ def test_get_and_process_orders_closed(data_repo_full, mock_project_data_record) | |
| data_master.data = {order_id: mock_project_data_record("closed")} | ||
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| op = order_portal.OrderPortal(config_values, data_master) | ||
| with mock.patch("daily_read.order_portal.OrderPortal._get", side_effect=mocked_requests_get): | ||
| op.get_orders(orderer=orderer) | ||
| op.get_orders(orderer=orderer) | ||
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| assert op.all_orders[1]["identifier"] == order_id | ||
| modified_orders = op.process_orders(config_values.STATUS_PRIORITY_REV) | ||
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@@ -147,8 +171,7 @@ def test_get_and_process_orders_mult_reports(data_repo_full, mock_project_data_r | |
| data_master.data = {order_id: mock_project_data_record("open")} | ||
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| op = order_portal.OrderPortal(config_values, data_master) | ||
| with mock.patch("daily_read.order_portal.OrderPortal._get", side_effect=mocked_requests_get): | ||
| op.get_orders(orderer=orderer) | ||
| op.get_orders(orderer=orderer) | ||
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| assert op.all_orders[2]["identifier"] == order_id | ||
| with pytest.raises( | ||
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