Merge branch 'master' into feature/configurable-backend-#125

common/backends.py

@@ -10,6 +10,7 @@
 import uuid
 import sys
 from common.exceptions import AuthenticationError
+import datetime
 
 
 class Backend(ABC):
@@ -218,7 +219,8 @@ class DatabaseBackend(Backend):
     def login(self, credentials):
         if credentials["username"] == "user" and credentials["password"] == "password":
             session_id = str(uuid.uuid1())
-            insert_row_into_table(SESSION, SESSION(ID=session_id))
+            insert_row_into_table(SESSION, SESSION(ID=session_id, USERNAME="simple/root",
+                                                   EXPIREDATETIME=datetime.datetime.now() + datetime.timedelta(days=1)))
             return session_id
         else:
             raise AuthenticationError("Username and password are incorrect")

common/helpers.py

@@ -47,6 +47,7 @@ def queries_records(method):
     Decorator for endpoint resources that search for a record in a table
     :param method: The method for the endpoint
     :return: Will return a 404, "No such record" if a MissingRecordError is caught
+    :return: Will return a 400, "Error message" if other expected errors are caught
     """
 
     @wraps(method)

dev-requirements.in

@@ -1,2 +1 @@
-Faker == 2.0.2
-pyyaml == 5.1.2
+Faker == 2.0.2

dev-requirements.txt

@@ -2,10 +2,9 @@
 # This file is autogenerated by pip-compile
 # To update, run:
 #
-#    pip-compile '.\dev-requirements.in'
+#    pip-compile dev-requirements.in
 #
 faker==2.0.2
 python-dateutil==2.8.0    # via faker
-pyyaml==5.1.2
 six==1.12.0               # via faker, python-dateutil
 text-unidecode==1.3       # via faker

requirements.in

@@ -2,3 +2,6 @@ flask_restful == 0.3.7
 sqlalchemy == 1.3.8
 pymysql == 0.9.3
 flask-cors == 3.0.8
+apispec == 3.3.0
+flask-swagger-ui == 3.25.0
+pyyaml == 5.1.2

requirements.txt

@@ -2,18 +2,21 @@
 # This file is autogenerated by pip-compile
 # To update, run:
 #
-#    pip-compile '.\requirements.in'
+#    pip-compile requirements.in
 #
 aniso8601==8.0.0          # via flask-restful
+apispec==3.3.0
 click==7.0                # via flask
 flask-cors==3.0.8
-flask==1.1.1              # via flask-cors, flask-restful
+flask-swagger-ui==3.25.0
+flask==1.1.1              # via flask-cors, flask-restful, flask-swagger-ui
 flask_restful==0.3.7
 itsdangerous==1.1.0       # via flask
 jinja2==2.10.1            # via flask
 markupsafe==1.1.1         # via jinja2
 pymysql==0.9.3
 pytz==2019.2              # via flask-restful
+pyyaml==5.1.2
 six==1.12.0               # via flask-cors, flask-restful
 sqlalchemy==1.3.8
 werkzeug==0.16.0          # via flask

src/main.py

@@ -1,6 +1,7 @@
 from flask import Flask
 from flask_cors import CORS
 from flask_restful import Api
+from flask_swagger_ui import get_swaggerui_blueprint
 
 from common.config import config
 from common.logger_setup import setup_logger
@@ -11,10 +12,16 @@
 from src.resources.table_endpoints.table_endpoints import UsersInvestigations, UsersInvestigationsCount, \
     InstrumentsFacilityCycles, InstrumentsFacilityCyclesCount, InstrumentsFacilityCyclesInvestigations, \
     InstrumentsFacilityCyclesInvestigationsCount
-from src.swagger.swagger_generator import swagger_gen
 from common.exceptions import ApiError
+from apispec import APISpec
+from pathlib import Path
+import json
+from src.swagger.apispec_flask_restful import RestfulPlugin
+from src.swagger.initialise_spec import initialise_spec
 
-swagger_gen.write_swagger_spec()
+
+spec = APISpec(title="DataGateway API", version="1.0", openapi_version="3.0.3",
+               plugins=[RestfulPlugin()], security=[{"session_id": []}])
 
 app = Flask(__name__)
 cors = CORS(app)
@@ -27,33 +34,77 @@ def handle_error(e):
     return str(e), e.status_code
 
 
+swaggerui_blueprint = get_swaggerui_blueprint(
+    "",
+    "/openapi.json",
+    config={
+        'app_name': "DataGateway API OpenAPI Spec"
+    },
+)
+
+app.register_blueprint(swaggerui_blueprint, url_prefix="/")
+
 setup_logger()
 
+initialise_spec(spec)
+
 for entity_name in endpoints:
-    api.add_resource(get_endpoint(
-        entity_name, endpoints[entity_name]), f"/{entity_name.lower()}")
-    api.add_resource(get_id_endpoint(
-        entity_name, endpoints[entity_name]), f"/{entity_name.lower()}/<int:id>")
-    api.add_resource(get_count_endpoint(
-        entity_name, endpoints[entity_name]), f"/{entity_name.lower()}/count")
-    api.add_resource(get_find_one_endpoint(
-        entity_name, endpoints[entity_name]), f"/{entity_name.lower()}/findone")
+    get_endpoint_resource = get_endpoint(entity_name, endpoints[entity_name])
+    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])
+    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])
+    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])
+    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
 api.add_resource(Sessions, "/sessions")
+spec.path(resource=Sessions, api=api)
 
 # Table specific endpoints
 api.add_resource(UsersInvestigations, "/users/<int:id>/investigations")
+spec.path(resource=UsersInvestigations, api=api)
 api.add_resource(UsersInvestigationsCount,
                  "/users/<int:id>/investigations/count")
+spec.path(resource=UsersInvestigationsCount, api=api)
 api.add_resource(InstrumentsFacilityCycles,
                  "/instruments/<int:id>/facilitycycles")
+spec.path(resource=InstrumentsFacilityCycles, api=api)
 api.add_resource(InstrumentsFacilityCyclesCount,
                  "/instruments/<int:id>/facilitycycles/count")
+spec.path(resource=InstrumentsFacilityCyclesCount, api=api)
 api.add_resource(InstrumentsFacilityCyclesInvestigations,
                  "/instruments/<int:instrument_id>/facilitycycles/<int:cycle_id>/investigations")
+spec.path(resource=InstrumentsFacilityCyclesInvestigations, api=api)
 api.add_resource(InstrumentsFacilityCyclesInvestigationsCount,
                  "/instruments/<int:instrument_id>/facilitycycles/<int:cycle_id>/investigations/count")
+spec.path(resource=InstrumentsFacilityCyclesInvestigationsCount, api=api)
+
+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
 
 
 if __name__ == "__main__":