#154: Fix issue with the API when served via WSGI

datagateway_api/src/api_start_utils.py

@@ -0,0 +1,160 @@
+import json
+import logging
+from pathlib import Path
+
+from apispec import APISpec
+from flask_cors import CORS
+from flask_restful import Api
+from flask_swagger_ui import get_swaggerui_blueprint
+
+from datagateway_api.common.backends import create_backend
+from datagateway_api.common.config import config
+from datagateway_api.src.resources.entities.entity_endpoint import (
+    get_count_endpoint,
+    get_endpoint,
+    get_find_one_endpoint,
+    get_id_endpoint,
+)
+from datagateway_api.src.resources.entities.entity_map import endpoints
+from datagateway_api.src.resources.non_entities.sessions_endpoints import (
+    session_endpoints,
+)
+from datagateway_api.src.resources.table_endpoints.table_endpoints import (
+    count_instrument_facility_cycles_endpoint,
+    count_instrument_investigation_endpoint,
+    instrument_facility_cycles_endpoint,
+    instrument_investigation_endpoint,
+)
+from datagateway_api.src.swagger.apispec_flask_restful import RestfulPlugin
+from datagateway_api.src.swagger.initialise_spec import initialise_spec
+
+log = logging.getLogger()
+
+
+class CustomErrorHandledApi(Api):
+    """
+    This class overrides `handle_error` function from the API class from `flask_restful`
+    to correctly return response codes and exception messages from uncaught exceptions
+    """
+
+    def handle_error(self, e):
+        return str(e), e.status_code
+
+
+def create_app_infrastructure(flask_app):
+    swaggerui_blueprint = get_swaggerui_blueprint(
+        "", "/openapi.json", config={"app_name": "DataGateway API OpenAPI Spec"},
+    )
+    flask_app.register_blueprint(swaggerui_blueprint, url_prefix="/")
+    spec = APISpec(
+        title="DataGateway API",
+        version="1.0",
+        openapi_version="3.0.3",
+        plugins=[RestfulPlugin()],
+        security=[{"session_id": []}],
+    )
+
+    CORS(flask_app)
+    flask_app.url_map.strict_slashes = False
+    api = CustomErrorHandledApi(flask_app)
+
+    initialise_spec(spec)
+
+    return (api, spec)
+
+
+def create_api_endpoints(flask_app, api, spec):
+    try:
+        backend_type = flask_app.config["TEST_BACKEND"]
+        config.set_backend_type(backend_type)
+    except KeyError:
+        backend_type = config.get_backend_type()
+
+    backend = create_backend(backend_type)
+
+    for entity_name in endpoints:
+        get_endpoint_resource = get_endpoint(
+            entity_name, endpoints[entity_name], backend,
+        )
+        api.add_resource(get_endpoint_resource, f"/{entity_name.lower()}")
+        spec.path(resource=get_endpoint_resource, api=api)
+
+        get_id_endpoint_resource = get_id_endpoint(
+            entity_name, endpoints[entity_name], backend,
+        )
+        api.add_resource(get_id_endpoint_resource, f"/{entity_name.lower()}/<int:id_>")
+        spec.path(resource=get_id_endpoint_resource, api=api)
+
+        get_count_endpoint_resource = get_count_endpoint(
+            entity_name, endpoints[entity_name], backend,
+        )
+        api.add_resource(get_count_endpoint_resource, f"/{entity_name.lower()}/count")
+        spec.path(resource=get_count_endpoint_resource, api=api)
+
+        get_find_one_endpoint_resource = get_find_one_endpoint(
+            entity_name, endpoints[entity_name], backend,
+        )
+        api.add_resource(
+            get_find_one_endpoint_resource, f"/{entity_name.lower()}/findone",
+        )
+        spec.path(resource=get_find_one_endpoint_resource, api=api)
+
+    # Session endpoint
+    session_endpoint_resource = session_endpoints(backend)
+    api.add_resource(session_endpoint_resource, "/sessions")
+    spec.path(resource=session_endpoint_resource, api=api)
+
+    # Table specific endpoints
+    instrument_facility_cycle_resource = instrument_facility_cycles_endpoint(backend)
+    api.add_resource(
+        instrument_facility_cycle_resource, "/instruments/<int:id_>/facilitycycles",
+    )
+    spec.path(resource=instrument_facility_cycle_resource, api=api)
+
+    count_instrument_facility_cycle_res = count_instrument_facility_cycles_endpoint(
+        backend,
+    )
+    api.add_resource(
+        count_instrument_facility_cycle_res,
+        "/instruments/<int:id_>/facilitycycles/count",
+    )
+    spec.path(resource=count_instrument_facility_cycle_res, api=api)
+
+    instrument_investigation_resource = instrument_investigation_endpoint(backend)
+    api.add_resource(
+        instrument_investigation_resource,
+        "/instruments/<int:instrument_id>/facilitycycles/<int:cycle_id>/investigations",
+    )
+    spec.path(resource=instrument_investigation_resource, api=api)
+
+    count_instrument_investigation_resource = count_instrument_investigation_endpoint(
+        backend,
+    )
+    api.add_resource(
+        count_instrument_investigation_resource,
+        "/instruments/<int:instrument_id>/facilitycycles/<int:cycle_id>/investigations"
+        "/count",
+    )
+    spec.path(resource=count_instrument_investigation_resource, api=api)
+
+
+def openapi_config(spec):
+    # Reorder paths (e.g. get, patch, post) so openapi.yaml only changes when there's a
+    # change to the Swagger docs, rather than changing on each startup
+    if config.is_generate_swagger():
+        log.debug("Reordering OpenAPI docs to alphabetical order")
+        for entity_data in spec._paths.values():
+            for endpoint_name in sorted(entity_data.keys()):
+                entity_data.move_to_end(endpoint_name)
+
+    openapi_spec_path = Path(__file__).parent / "swagger/openapi.yaml"
+    with open(openapi_spec_path, "w") as f:
+        f.write(spec.to_yaml())
+
+
+def create_openapi_endpoint(app, api_spec):
+    @app.route("/openapi.json")
+    def specs():
+        resp = app.make_response(json.dumps(api_spec.to_dict(), indent=2))
+        resp.mimetype = "application/json"
+        return resp

datagateway_api/src/main.py

@@ -1,178 +1,27 @@
-import json
 import logging
-from pathlib import Path
 
-from apispec import APISpec
 from flask import Flask
-from flask_cors import CORS
-from flask_restful import Api
-from flask_swagger_ui import get_swaggerui_blueprint
 
-from datagateway_api.common.backends import create_backend
 from datagateway_api.common.config import config
 from datagateway_api.common.logger_setup import setup_logger
-from datagateway_api.src.resources.entities.entity_endpoint import (
-    get_count_endpoint,
-    get_endpoint,
-    get_find_one_endpoint,
-    get_id_endpoint,
+from datagateway_api.src.api_start_utils import (
+    create_api_endpoints,
+    create_app_infrastructure,
+    create_openapi_endpoint,
+    openapi_config,
 )
-from datagateway_api.src.resources.entities.entity_map import endpoints
-from datagateway_api.src.resources.non_entities.sessions_endpoints import (
-    session_endpoints,
-)
-from datagateway_api.src.resources.table_endpoints.table_endpoints import (
-    count_instrument_facility_cycles_endpoint,
-    count_instrument_investigation_endpoint,
-    instrument_facility_cycles_endpoint,
-    instrument_investigation_endpoint,
-)
-from datagateway_api.src.swagger.apispec_flask_restful import RestfulPlugin
-from datagateway_api.src.swagger.initialise_spec import initialise_spec
 
 setup_logger()
 log = logging.getLogger()
 log.info("Logging now setup")
 
 app = Flask(__name__)
-
-
-class CustomErrorHandledApi(Api):
-    """
-    This class overrides `handle_error` function from the API class from `flask_restful`
-    to correctly return response codes and exception messages from uncaught exceptions
-    """
-
-    def handle_error(self, e):
-        return str(e), e.status_code
-
-
-def create_app_infrastructure(flask_app):
-    swaggerui_blueprint = get_swaggerui_blueprint(
-        "", "/openapi.json", config={"app_name": "DataGateway API OpenAPI Spec"},
-    )
-    flask_app.register_blueprint(swaggerui_blueprint, url_prefix="/")
-    spec = APISpec(
-        title="DataGateway API",
-        version="1.0",
-        openapi_version="3.0.3",
-        plugins=[RestfulPlugin()],
-        security=[{"session_id": []}],
-    )
-
-    CORS(flask_app)
-    flask_app.url_map.strict_slashes = False
-    api = CustomErrorHandledApi(flask_app)
-
-    initialise_spec(spec)
-
-    return (api, spec)
-
-
-def handle_error(e):
-    return str(e), e.status_code
-
-
-def create_api_endpoints(flask_app, api, spec):
-    try:
-        backend_type = flask_app.config["TEST_BACKEND"]
-        config.set_backend_type(backend_type)
-    except KeyError:
-        backend_type = config.get_backend_type()
-
-    backend = create_backend(backend_type)
-
-    for entity_name in endpoints:
-        get_endpoint_resource = get_endpoint(
-            entity_name, endpoints[entity_name], backend,
-        )
-        api.add_resource(get_endpoint_resource, f"/{entity_name.lower()}")
-        spec.path(resource=get_endpoint_resource, api=api)
-
-        get_id_endpoint_resource = get_id_endpoint(
-            entity_name, endpoints[entity_name], backend,
-        )
-        api.add_resource(get_id_endpoint_resource, f"/{entity_name.lower()}/<int:id_>")
-        spec.path(resource=get_id_endpoint_resource, api=api)
-
-        get_count_endpoint_resource = get_count_endpoint(
-            entity_name, endpoints[entity_name], backend,
-        )
-        api.add_resource(get_count_endpoint_resource, f"/{entity_name.lower()}/count")
-        spec.path(resource=get_count_endpoint_resource, api=api)
-
-        get_find_one_endpoint_resource = get_find_one_endpoint(
-            entity_name, endpoints[entity_name], backend,
-        )
-        api.add_resource(
-            get_find_one_endpoint_resource, f"/{entity_name.lower()}/findone",
-        )
-        spec.path(resource=get_find_one_endpoint_resource, api=api)
-
-    # Session endpoint
-    session_endpoint_resource = session_endpoints(backend)
-    api.add_resource(session_endpoint_resource, "/sessions")
-    spec.path(resource=session_endpoint_resource, api=api)
-
-    # Table specific endpoints
-    instrument_facility_cycle_resource = instrument_facility_cycles_endpoint(backend)
-    api.add_resource(
-        instrument_facility_cycle_resource, "/instruments/<int:id_>/facilitycycles",
-    )
-    spec.path(resource=instrument_facility_cycle_resource, api=api)
-
-    count_instrument_facility_cycle_res = count_instrument_facility_cycles_endpoint(
-        backend,
-    )
-    api.add_resource(
-        count_instrument_facility_cycle_res,
-        "/instruments/<int:id_>/facilitycycles/count",
-    )
-    spec.path(resource=count_instrument_facility_cycle_res, api=api)
-
-    instrument_investigation_resource = instrument_investigation_endpoint(backend)
-    api.add_resource(
-        instrument_investigation_resource,
-        "/instruments/<int:instrument_id>/facilitycycles/<int:cycle_id>/investigations",
-    )
-    spec.path(resource=instrument_investigation_resource, api=api)
-
-    count_instrument_investigation_resource = count_instrument_investigation_endpoint(
-        backend,
-    )
-    api.add_resource(
-        count_instrument_investigation_resource,
-        "/instruments/<int:instrument_id>/facilitycycles/<int:cycle_id>/investigations"
-        "/count",
-    )
-    spec.path(resource=count_instrument_investigation_resource, api=api)
-
-
-def openapi_config(spec):
-    # Reorder paths (e.g. get, patch, post) so openapi.yaml only changes when there's a
-    # change to the Swagger docs, rather than changing on each startup
-    if config.is_generate_swagger():
-        log.debug("Reordering OpenAPI docs to alphabetical order")
-        for entity_data in spec._paths.values():
-            for endpoint_name in sorted(entity_data.keys()):
-                entity_data.move_to_end(endpoint_name)
-
-    openapi_spec_path = Path(__file__).parent / "swagger/openapi.yaml"
-    with open(openapi_spec_path, "w") as f:
-        f.write(spec.to_yaml())
-
-
-@app.route("/openapi.json")
-def specs():
-    resp = app.make_response(json.dumps(spec.to_dict(), indent=2))
-    resp.mimetype = "application/json"
-    return resp
-
+api, spec = create_app_infrastructure(app)
+create_api_endpoints(app, api, spec)
+openapi_config(spec)
+create_openapi_endpoint(app, spec)
 
 if __name__ == "__main__":
-    api, spec = create_app_infrastructure(app)
-    create_api_endpoints(app, api, spec)
-    openapi_config(spec)
     app.run(
         host=config.get_host(), port=config.get_port(), debug=config.is_debug_mode(),
     )

test/conftest.py

@@ -8,7 +8,10 @@
     insert_row_into_table,
 )
 from datagateway_api.common.database.models import SESSION
-from datagateway_api.src.main import create_api_endpoints, create_app_infrastructure
+from datagateway_api.src.api_start_utils import (
+    create_api_endpoints,
+    create_app_infrastructure,
+)
 
 
 @pytest.fixture()
@@ -33,6 +36,10 @@ def flask_test_app():
 
 @pytest.fixture(scope="package")
 def flask_test_app_db():
+    """
+    This is in the common conftest file because this test app is also used in
+    non-backend specific tests
+    """
     db_app = Flask(__name__)
     db_app.config["TESTING"] = True
     db_app.config["TEST_BACKEND"] = "db"

test/icat/conftest.py

@@ -8,7 +8,10 @@
 import pytest
 
 from datagateway_api.common.config import config
-from datagateway_api.src.main import create_api_endpoints, create_app_infrastructure
+from datagateway_api.src.api_start_utils import (
+    create_api_endpoints,
+    create_app_infrastructure,
+)
 from test.icat.test_query import prepare_icat_data_for_assertion