QA: Validation

docs/instructions.rst

@@ -9,23 +9,25 @@ Environment Setup
 The application requires some environmental arguments in order to run properly, these are illustrated in
 the table below.
 
-+-------------+-------------------------------+-------------------------------------+
-| ENV         | Default                       | Description                         |
-+-------------+-------------------------------+-------------------------------------+
-| `DB_HOST`   | `postgresql://localhost:5432` | The URL for the PostgreSQL server.  |
-+-------------+-------------------------------+-------------------------------------+
-| `DB_NAME`   | `rems`                        | Name of the database.               |
-+-------------+-------------------------------+-------------------------------------+
-| `DB_USER`   | `rems`                        | Database username.                  |
-+-------------+-------------------------------+-------------------------------------+
-| `DB_PASS`   | `rems`                        | Database password.                  |
-+-------------+-------------------------------+-------------------------------------+
-| `APP_HOST`  | `0.0.0.0`                     | Default Host for the Web Server.    |
-+-------------+-------------------------------+-------------------------------------+
-| `APP_PORT`  | `8080`                        | Default port for the Web Server.    |
-+-------------+-------------------------------+-------------------------------------+
-| `DEBUG`     | `True`                        | If set to `True`, logs all actions. |
-+-------------+-------------------------------+-------------------------------------+
++------------- +-------------------------------+-------------------------------------+
+| ENV          | Default                       | Description                         |
++------------- +-------------------------------+-------------------------------------+
+| `DB_HOST`    | `postgresql://localhost:5432` | The URL for the PostgreSQL server.  |
++------------- +-------------------------------+-------------------------------------+
+| `DB_NAME`    | `rems`                        | Name of the database.               |
++------------- +-------------------------------+-------------------------------------+
+| `DB_USER`    | `rems`                        | Database username.                  |
++------------- +-------------------------------+-------------------------------------+
+| `DB_PASS`    | `rems`                        | Database password.                  |
++------------- +-------------------------------+-------------------------------------+
+| `APP_HOST`   | `0.0.0.0`                     | Default Host for the Web Server.    |
++------------- +-------------------------------+-------------------------------------+
+| `APP_PORT`   | `8080`                        | Default port for the Web Server.    |
++------------- +-------------------------------+-------------------------------------+
+| `PUBLIC_KEY` | `None`                        | Mandatory api key.                  |
++------------- +-------------------------------+-------------------------------------+
+| `DEBUG`      | `True`                        | If set to `True`, logs all actions. |
++------------- +-------------------------------+-------------------------------------+
 
 Setting the necessary environment variables can be done  e.g. via the command line:
 
@@ -37,6 +39,7 @@ Setting the necessary environment variables can be done  e.g. via the command li
     $ export DB_PASS=rems
     $ export HOST=0.0.0.0
     $ export PORT=8080
+    $ export PUBLIC_KEY=secret_string
     $ export DEBUG=True
 
 .. _app-setup:

elixir_rems_proxy/app.py

@@ -5,23 +5,24 @@
 
 from aiohttp import web
 
+from .schemas import load_schema
+from .utils.validate import validate, api_key, check_user
 from .utils.db_pool import init_db_pool
 from .utils.process import process_post_request, process_get_request, process_patch_request, process_delete_request
 from .utils.logging import LOG
-# from .utils.validate import validate IMPLEMENT JSON SCHEMA VALIDATION
-
 
 routes = web.RouteTableDef()
 
 
 @routes.get('/', name='index')
 async def api_get(request):
     """Return name of service, doubles as a health check function."""
-    LOG.debug('INDEX Request received.')
+    LOG.debug('INFO Request received.')
     return web.Response(text='ELIXIR AAI API for REMS')
 
 
 @routes.post('/user')
+@validate(load_schema("post"))
 async def user_post(request):
     """POST request to the /user endpoint.
 
@@ -67,6 +68,7 @@ async def user_get(request):
 
 @routes.patch('/user/')
 @routes.patch('/user/{user}')
+@validate(load_schema("patch"))
 async def user_patch(request):
     """PATCH request to the /user endpoint.
 
@@ -99,9 +101,8 @@ async def user_delete(request):
 
     if 'user' in request.match_info:
         user_identifier = request.match_info['user']
-        processed_request = await process_delete_request(user_identifier, db_pool)
-        if processed_request:
-            return web.HTTPOk(text='User was deleted')
+        await process_delete_request(user_identifier, db_pool)
+        return web.HTTPOk(text='User was deleted')
     else:
         raise web.HTTPBadRequest(text='Username not provided')
 
@@ -121,7 +122,7 @@ async def close_db(app):
 def init_app():
     """Initialise the app."""
     LOG.info('Initialise the server.')
-    app = web.Application()
+    app = web.Application(middlewares=[api_key(), check_user()])
     app.router.add_routes(routes)
     app.on_startup.append(init_db)
     app.on_cleanup.append(close_db)

elixir_rems_proxy/schemas/__init__.py

@@ -0,0 +1,13 @@
+"""Load JSON Schemas."""
+
+import os
+import json
+
+
+def load_schema(name):
+    """Load JSON schemas."""
+    module_path = os.path.dirname(__file__)
+    path = os.path.join(module_path, f'{name}.json')
+    with open(os.path.abspath(path), 'r') as fp:
+        data = fp.read()
+    return json.loads(data)

elixir_rems_proxy/schemas/get.json

@@ -0,0 +1,42 @@
+{
+    "definitions": {},
+    "type": "object",
+    "required": [
+      "permissions"
+    ],
+    "properties": {
+      "permissions": {
+        "type": "array",
+        "items": {
+          "type": "object",
+          "required": [
+            "affiliation",
+            "source_signature",
+            "url_prefix",
+            "datasets"
+          ],
+          "properties": {
+            "affiliation": {
+              "type": "string",
+              "default": ""
+            },
+            "source_signature": {
+              "type": "string",
+              "default": ""
+            },
+            "url_prefix": {
+              "type": "string",
+              "default": ""
+            },
+            "datasets": {
+              "type": "array",
+              "items": {
+                "type": "string",
+                "default": ""
+              }
+            }
+          }
+        }
+      }
+    }
+  }

elixir_rems_proxy/schemas/patch.json

@@ -0,0 +1,63 @@
+{
+  "definitions": {},
+  "type": "object",
+  "required": [
+    "user_identifier",
+    "affiliation",
+    "datasets"
+  ],
+  "properties": {
+    "user_identifier": {
+      "type": "string",
+      "default": ""
+    },
+    "affiliation": {
+      "type": "string",
+      "default": ""
+    },
+    "datasets": {
+      "type": "array",
+      "items": {
+        "type": "object",
+        "required": [
+          "permissions"
+        ],
+        "properties": {
+          "permissions": {
+            "type": "array",
+            "items": {
+              "type": "object",
+              "required": [
+                "affiliation",
+                "source_signature",
+                "url_prefix",
+                "datasets"
+              ],
+              "properties": {
+                "affiliation": {
+                  "type": "string",
+                  "default": ""
+                },
+                "source_signature": {
+                  "type": "string",
+                  "default": ""
+                },
+                "url_prefix": {
+                  "type": "string",
+                  "default": ""
+                },
+                "datasets": {
+                  "type": "array",
+                  "items": {
+                    "type": "string",
+                    "default": ""
+                  }
+                }
+              }
+            }
+          }
+        }
+      }
+    }
+  }
+}

elixir_rems_proxy/schemas/post.json

@@ -0,0 +1,63 @@
+{
+  "definitions": {},
+  "type": "object",
+  "required": [
+    "user_identifier",
+    "affiliation",
+    "datasets"
+  ],
+  "properties": {
+    "user_identifier": {
+      "type": "string",
+      "default": ""
+    },
+    "affiliation": {
+      "type": "string",
+      "default": ""
+    },
+    "datasets": {
+      "type": "array",
+      "items": {
+        "type": "object",
+        "required": [
+          "permissions"
+        ],
+        "properties": {
+          "permissions": {
+            "type": "array",
+            "items": {
+              "type": "object",
+              "required": [
+                "affiliation",
+                "source_signature",
+                "url_prefix",
+                "datasets"
+              ],
+              "properties": {
+                "affiliation": {
+                  "type": "string",
+                  "default": ""
+                },
+                "source_signature": {
+                  "type": "string",
+                  "default": ""
+                },
+                "url_prefix": {
+                  "type": "string",
+                  "default": ""
+                },
+                "datasets": {
+                  "type": "array",
+                  "items": {
+                    "type": "string",
+                    "default": ""
+                  }
+                }
+              }
+            }
+          }
+        }
+      }
+    }
+  }
+}

elixir_rems_proxy/utils/db_actions.py

@@ -1,5 +1,7 @@
 """Database Queries."""
 
+from aiohttp import web
+
 from ..utils.logging import LOG
 
 
@@ -111,4 +113,4 @@ async def delete_user(user, connection):
         return True
     except Exception as e:
         LOG.debug(f'An error occurred while attempting to delete user -> {e}')
-        return None
+        raise web.HTTPInternalServerError(text='Database error when attempting to remove user')