Merge pull request #392 from sanger/dpl-058-versioned-api

DPL-058-01: Versioned API

.release-version

@@ -1 +1 @@
-1.24.0
+1.25.0

README.md

@@ -293,14 +293,11 @@ you start these dependencies here, there's no need to also attempt to do so in
 the Lighthouse repository. They are the same resources in both and the second
 one to be started will show exceptions about ports already being allocated:
 
-    docker-compose -f dependencies/docker-compose.yml up -d
+    ./dependencies/up.sh
 
-The `-d` is optional and runs the containers in the background. If you want to
-observe the logs in real time or just prefer to keep the process going in
-another terminal, exclude the option. If you've already used the option and
-want to shut the databases back down, you can do so with:
+When you want to shut the databases back down, you can do so with:
 
-    docker-compose -f dependencies/docker-compose.yml down
+    ./dependencies/down.sh
 
 To build and run the container for Crawler, run from the root of the repository:
 

crawler/__init__.py

@@ -22,20 +22,25 @@ def create_app(config_object: str = None) -> Flask:
     # setup logging
     logging.config.dictConfig(app.config["LOGGING"])
 
-    if app.config.get("ENABLE_CHERRYPICKER_ENDPOINTS", False):
-        from crawler.blueprints import cherrypicker_test_data
-
-        app.register_blueprint(cherrypicker_test_data.bp)
-
     if app.config.get("SCHEDULER_RUN", False):
         scheduler.init_app(app)
         scheduler.start()
 
+    setup_routes(app)
+
     @app.get("/health")
-    def health_check():
+    def _():
+        """Checks the health of Crawler by checking that there is a scheduled job to run Crawler periodically"""
         if scheduler.get_job(SCHEDULER_JOB_ID_RUN_CRAWLER):
             return "Crawler is working", HTTPStatus.OK
 
         return "Crawler is not working correctly", HTTPStatus.INTERNAL_SERVER_ERROR
 
     return app
+
+
+def setup_routes(app):
+    if app.config.get("ENABLE_CHERRYPICKER_ENDPOINTS", False):
+        from crawler.routes.v1 import routes as v1_routes
+
+        app.register_blueprint(v1_routes.bp, url_prefix="/v1")

crawler/blueprints/cherrypicker_test_data.py → crawler/routes/common/cherrypicker_test_data.py

@@ -1,7 +1,7 @@
 import logging
 from datetime import datetime, timezone
 
-from flask import Blueprint, request
+from flask import request
 
 from crawler.constants import FIELD_STATUS_COMPLETED, FLASK_ERROR_MISSING_PARAMETERS, FLASK_ERROR_UNEXPECTED
 from crawler.helpers.responses import bad_request, internal_server_error, ok
@@ -10,11 +10,8 @@
 
 logger = logging.getLogger(__name__)
 
-bp = Blueprint("cherrypicker", __name__)
 
-
-@bp.post("/cherrypick-test-data")
-def generate_test_data_endpoint() -> FlaskResponse:
+def generate_test_data_v1() -> FlaskResponse:
     """Generates cherrypicker test data for a number of plates with defined
     numbers of positives per plate.
 

crawler/routes/v1/routes.py

@@ -0,0 +1,11 @@
+from flask import Blueprint
+
+from crawler.routes.common.cherrypicker_test_data import generate_test_data_v1
+from crawler.types import FlaskResponse
+
+bp = Blueprint("v1_routes", __name__)
+
+
+@bp.post("/cherrypick-test-data")
+def generate_test_data_endpoint() -> FlaskResponse:
+    return generate_test_data_v1()

dependencies/down.sh

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

dependencies/up.sh

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

tests/blueprints/test_cherrypicker_data_blueprint.py → tests/routes/v1/test_cptd_endpoints.py

@@ -8,7 +8,8 @@
 from crawler.helpers.general_helpers import is_found_in_list
 from crawler.jobs.cherrypicker_test_data import CherrypickerDataError
 
-barcode_metadata = [
+ENDPOINT = "/v1/cherrypick-test-data"
+BARCODE_METADATA = [
     ["Plate-1", "positive samples: 30"],
     ["Plate-2", "positive samples: 50"],
 ]
@@ -18,7 +19,7 @@
 
 @pytest.fixture
 def logger_messages():
-    with patch("crawler.blueprints.cherrypicker_test_data.logger") as logger:
+    with patch("crawler.routes.common.cherrypicker_test_data.logger") as logger:
         infos = []
         logger.info.side_effect = lambda msg: infos.append(msg)
 
@@ -30,13 +31,13 @@ def logger_messages():
 
 @pytest.fixture
 def process_mock():
-    with patch("crawler.blueprints.cherrypicker_test_data.process") as process:
+    with patch("crawler.routes.common.cherrypicker_test_data.process") as process:
         yield process
 
 
 @pytest.mark.parametrize("json", [{}, {"run_id": None}])
 def test_generate_endpoint_invalid_json(json, client, logger_messages):
-    response = client.post("/cherrypick-test-data", json=json)
+    response = client.post(ENDPOINT, json=json)
     assert response.status_code == HTTPStatus.BAD_REQUEST
     assert "run_id" not in response.json
     assert "plates" not in response.json
@@ -47,12 +48,12 @@ def test_generate_endpoint_invalid_json(json, client, logger_messages):
 
 
 def test_generate_endpoint_success(client, logger_messages, process_mock):
-    process_mock.return_value = barcode_metadata
+    process_mock.return_value = BARCODE_METADATA
     test_run_id = "0123456789abcdef01234567"
-    response = client.post("/cherrypick-test-data", json={"run_id": test_run_id})
+    response = client.post(ENDPOINT, json={"run_id": test_run_id})
     assert response.status_code == HTTPStatus.OK
     assert response.json["run_id"] == test_run_id
-    assert response.json["plates"] == barcode_metadata
+    assert response.json["plates"] == BARCODE_METADATA
     assert response.json["status"] == FIELD_STATUS_COMPLETED
     assert "timestamp" in response.json
     assert "errors" not in response.json
@@ -63,7 +64,7 @@ def test_generate_endpoint_handles_CherrypickerDataError_exception(client, logge
     test_error_message = "Test Error!"
     test_error = CherrypickerDataError(test_error_message)
     process_mock.side_effect = test_error
-    response = client.post("/cherrypick-test-data", json={"run_id": "test_id"})
+    response = client.post(ENDPOINT, json={"run_id": "test_id"})
     assert response.status_code == HTTPStatus.INTERNAL_SERVER_ERROR
     assert "run_id" not in response.json
     assert "plates" not in response.json
@@ -76,7 +77,7 @@ def test_generate_endpoint_handles_CherrypickerDataError_exception(client, logge
 def test_generate_endpoint_handles_generic_exception(client, logger_messages, process_mock):
     test_error = ConnectionError()
     process_mock.side_effect = test_error
-    response = client.post("/cherrypick-test-data", json={"run_id": "test_id"})
+    response = client.post(ENDPOINT, json={"run_id": "test_id"})
     assert response.status_code == HTTPStatus.INTERNAL_SERVER_ERROR
     assert "run_id" not in response.json
     assert "plates" not in response.json