Merge pull request #961 from sanger/develop

Prepare release 2.36.0

.github/workflows/add_prs_to_tech_debt_project.yml

@@ -0,0 +1,19 @@
+# Calls a reusable workflow in the .github repo,
+# which adds the PR that triggered this to the Technical Debt project board, if it is a depfu one.
+# Passes the 'PSD-AddToProject' GitHub App key and App Id as secrets to the reusable workflow.
+
+name: Add dependencies to technical debt project
+
+on:
+  # Triggered on creation of pull requests with any label,
+  # or when a label is added to an existing pull request.
+  pull_request:
+    types:
+      - labeled
+
+jobs:
+  call-workflow-add_to_technical_debt_project:
+    uses: sanger/.github/.github/workflows/add_to_tech_debt_project_reusable.yml@master
+    secrets:
+      app_id: ${{ secrets.ADD_TO_PROJECT_APP_ID_PSD }}
+      app_key: ${{ secrets.ADD_TO_PROJECT_APP_KEY_PSD }}

.github/workflows/assign_issue_number.yml

@@ -0,0 +1,12 @@
+name: Assign Issue Number
+
+on:
+  issues:
+    types: [opened]
+
+jobs:
+  call-add-to-project:
+    uses: sanger/.github/.github/workflows/generate_issue_number.yml@master
+    secrets:
+      app_id: ${{ secrets.ISSUE_GEN_APP_ID }}
+      app_key: ${{ secrets.ISSUE_GEN_APP_KEY }}

.github/workflows/automated_release.yml

@@ -114,6 +114,5 @@ jobs:
           account-type: org
           org-name: sanger
           keep-at-least: 5
-          skip-tags: latest
+          skip-tags: latest, *[!develop] # This will DELETE any images where the tag contains ANY characters in "develop", excluding '!'
           token: ${{ secrets.REMOVE_OLD_IMAGES }}
-

.github/workflows/ci.yml

@@ -132,4 +132,6 @@ jobs:
         run: |
           python -m pytest -x
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v3
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.release-version

@@ -1 +1 @@
-2.35.1
+2.36.0

Pipfile

@@ -20,17 +20,17 @@ colorlog = "~=6.8"
 eve = "~=2.1"
 flask-apscheduler = "~=1.13"
 flask-cors = "~=4.0"
-gunicorn = "~=21.2"
+gunicorn = "~=22.0"
 openpyxl = "~=3.1"
 pandas = "~=2.0"
 pika = "~=1.3"
 pymysql = "~=1.1"
 pyodbc = "~=5.1"
 python-dotenv = "~=1.0"
-requests = "~=2.31"
+requests = "~=2.32"
 slackclient = "~=2.9"
 sqlalchemy = "~=2.0"
-pymongo = "~=4.6.2"
+pymongo = "~=4.8.0"
 
 [requires]
 python_version = "3.8"

dependencies/down.sh

@@ -1,4 +1,4 @@
 #!/bin/bash
 
 cd "$(dirname "$0")"
-docker-compose down
+docker compose down

dependencies/up.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 cd "$(dirname "$0")"
-docker-compose up -d
+docker compose up -d
 
 # Initialise the MongoDB replica set after 5 seconds
 sleep 5

docker-compose.yml

@@ -1,4 +1,3 @@
-version: "3.8"
 services:
   lighthouse:
     build: .

lighthouse/helpers/plates.py

@@ -429,10 +429,11 @@ def convert_json_response_into_dict(barcode: str, json) -> dict:
 
 def get_from_ss_plates_samples_info(plate_barcode: str) -> requests.Response:
     ss_url: str = f"{app.config['SS_URL']}/api/v2/labware"
+    headers = _ss_headers()
 
     try:
         params = {"filter[barcode]": plate_barcode, "include": "purpose,receptacles.aliquots.sample"}
-        response = requests.get(f"{ss_url}", params=params)
+        response = requests.get(f"{ss_url}", params=params, headers=headers)
 
         LOGGER.debug(f"Response status code: {response.status_code}")
 
@@ -814,7 +815,9 @@ def plate_exists_in_ss_with_barcode(barcode: str) -> bool:
         params = {
             "filter[barcode]": barcode,
         }
-        response = requests.get(f"{ss_url}/api/v2/labware", params=params)
+        headers = _ss_headers()
+
+        response = requests.get(f"{ss_url}/api/v2/labware", params=params, headers=headers)
 
         LOGGER.debug(f"Response status code: {response.status_code}")
 

tests/helpers/test_plates_helpers.py

@@ -73,6 +73,8 @@
 
 # ---------- test helpers ----------
 
+SS_AUTH_HEADER_MATCHER = responses.matchers.header_matcher({"X-Sequencescape-Client-Id": "development"})
+
 
 @pytest.fixture
 def mock_event_helpers():
@@ -143,7 +145,7 @@ def test_get_from_ss_plates_samples_info_success(app, mocked_responses):
         )
         json = {"data": ["plate data"], "included": ["plate includes"]}
 
-        mocked_responses.add(responses.GET, ss_url, json=json, status=HTTPStatus.OK)
+        mocked_responses.add(responses.GET, ss_url, json=json, status=HTTPStatus.OK, match=[SS_AUTH_HEADER_MATCHER])
 
         response = get_from_ss_plates_samples_info(barcode)
         assert response.json() == json
@@ -163,7 +165,7 @@ def test_convert_json_response_into_dict():
     assert data == {"data": {"barcode": barcode, "positive_control": "A1", "negative_control": "B1"}, "error": None}
 
 
-def test_classify_samples_by_centre(app, samples, mocked_responses):
+def test_classify_samples_by_centre(samples):
     samples, _ = samples
     assert list(classify_samples_by_centre(samples).keys()) == ["centre_1", "centre_2"]
     assert len(classify_samples_by_centre(samples)["centre_1"]) == 11
@@ -177,7 +179,7 @@ def test_centre_prefixes_for_samples(samples):
     assert actual == ["centre_1", "centre_2"]
 
 
-def test_centre_prefix(app, centres, mocked_responses):
+def test_centre_prefix(app, centres):
     with app.app_context():
         assert get_centre_prefix("CENTRE_1") == "TC1"
         assert get_centre_prefix("centre_2") == "TC2"
@@ -1057,6 +1059,7 @@ def test_format_plate_destination(app, mocked_responses):
             f"{ss_url}?{urllib.parse.quote('filter[barcode]')}={plate_barcode}",
             json={"data": ["barcode exists!"]},
             status=HTTPStatus.OK,
+            match=[SS_AUTH_HEADER_MATCHER],
         )
         response = {
             "plate_barcode": "dest_123",
@@ -1095,12 +1098,14 @@ def test_plate_exists_in_ss_with_barcode(app, mocked_responses):
             f"{ss_url}?{urllib.parse.quote('filter[barcode]')}={first_plate_barcode}",
             json={"data": ["barcode exists!"]},
             status=HTTPStatus.OK,
+            match=[SS_AUTH_HEADER_MATCHER],
         )
         mocked_responses.add(
             responses.GET,
             f"{ss_url}?{urllib.parse.quote('filter[barcode]')}={second_plate_barcode}",
             json={"data": []},
             status=HTTPStatus.OK,
+            match=[SS_AUTH_HEADER_MATCHER],
         )
 
         assert plate_exists_in_ss_with_barcode(barcode=first_plate_barcode) is True