Merge pull request #123 from CSCfi/develop

Release 0.5.1

docs/conf.py

@@ -11,7 +11,7 @@
 author = "CSC Developers"
 
 # The full version, including alpha/beta/rc tags
-release = "0.5.0"
+release = "0.5.1"
 
 
 # -- General configuration ---------------------------------------------------

metadata_backend/__init__.py

@@ -1,5 +1,5 @@
 """Backend for submitting and validating XML Files containing ENA metadata."""
 
 __title__ = "metadata_backend"
-__version__ = VERSION = "0.5.0"
+__version__ = VERSION = "0.5.1"
 __author__ = "CSC Developers"

metadata_backend/api/handlers.py

@@ -16,7 +16,7 @@
 from ..helpers.parser import XMLToJSONParser
 from ..helpers.schema_loader import JSONSchemaLoader, SchemaNotFoundException, XMLSchemaLoader
 from ..helpers.validator import JSONValidator, XMLValidator
-from .operators import FolderOperator, Operator, XMLOperator
+from .operators import FolderOperator, Operator, XMLOperator, UserOperator
 
 
 class RESTApiHandler:
@@ -100,7 +100,7 @@ def get_page_param(param_name: str, default: int) -> int:
         link_headers = self._header_links(url, page_num, per_page, total_objects)
         LOG.debug(f"Pagination header links: {link_headers}")
         LOG.info(f"Querying for objects in {collection} " f"resulted in {total_objects} objects ")
-        return web.Response(body=result, status=200, headers=link_headers, content_type="application/json")
+        return web.Response(body=result, status=200, headers=link_headers, content_type="application/json",)
 
     async def _get_data(self, req: Request) -> Dict:
         """Get the data content from a request.
@@ -199,7 +199,7 @@ async def post_object(self, req: Request) -> Response:
         url = f"{req.scheme}://{req.host}{req.path}"
         location_headers = {"Location": f"{url}{accession_id}"}
         LOG.info(f"POST object with accesssion ID {accession_id} " f"in schema {collection} was successful.")
-        return web.Response(body=body, status=201, headers=location_headers, content_type="application/json")
+        return web.Response(body=body, status=201, headers=location_headers, content_type="application/json",)
 
     async def query_objects(self, req: Request) -> Response:
         """Query metadata objects from database.
@@ -223,8 +223,8 @@ async def delete_object(self, req: Request) -> Response:
 
         accession_id = req.match_info["accessionId"]
         db_client = req.app["db_client"]
-        await Operator(db_client).delete_metadata_object(collection, accession_id)
-        LOG.info(f"DELETE object with accesssion ID {accession_id} " f"in schema {collection} was successful.")
+        accession_id = await Operator(db_client).delete_metadata_object(collection, accession_id)
+        LOG.info(f"DELETE object with accession ID {accession_id} " f"in schema {collection} was successful.")
         return web.Response(status=204)
 
     async def put_object(self, req: Request) -> Response:
@@ -252,9 +252,9 @@ async def put_object(self, req: Request) -> Response:
             content = await self._get_data(req)
             JSONValidator(content, schema_type).validate
             operator = Operator(db_client)
-        await operator.replace_metadata_object(collection, accession_id, content)
+        accession_id = await operator.replace_metadata_object(collection, accession_id, content)
         body = json.dumps({"accessionId": accession_id})
-        LOG.info(f"PUT object with accesssion ID {accession_id} " f"in schema {collection} was successful.")
+        LOG.info(f"PUT object with accession ID {accession_id} " f"in schema {collection} was successful.")
         return web.Response(body=body, status=200, content_type="application/json")
 
     async def patch_object(self, req: Request) -> Response:
@@ -278,9 +278,9 @@ async def patch_object(self, req: Request) -> Response:
         else:
             content = await self._get_data(req)
             operator = Operator(db_client)
-        await operator.update_metadata_object(collection, accession_id, content)
+        accession_id = await operator.update_metadata_object(collection, accession_id, content)
         body = json.dumps({"accessionId": accession_id})
-        LOG.info(f"PATCH object with accesssion ID {accession_id} " f"in schema {collection} was successful.")
+        LOG.info(f"PATCH object with accession ID {accession_id} " f"in schema {collection} was successful.")
         return web.Response(body=body, status=200, content_type="application/json")
 
     async def get_folders(self, req: Request) -> Response:
@@ -304,6 +304,7 @@ async def post_folder(self, req: Request) -> Response:
         """
         db_client = req.app["db_client"]
         content = await self._get_data(req)
+        JSONValidator(content, "folders").validate
         operator = FolderOperator(db_client)
         folder = await operator.create_folder(content)
         body = json.dumps({"folderId": folder})
@@ -323,7 +324,7 @@ async def get_folder(self, req: Request) -> Response:
         db_client = req.app["db_client"]
         operator = FolderOperator(db_client)
         folder = await operator.read_folder(folder_id)
-        LOG.info(f"GET folder with folder ID {folder_id} was successful.")
+        LOG.info(f"GET folder with ID {folder_id} was successful.")
         return web.Response(body=json.dumps(folder), status=200, content_type="application/json")
 
     async def patch_folder(self, req: Request) -> Response:
@@ -340,8 +341,8 @@ async def patch_folder(self, req: Request) -> Response:
         patch_ops = await self._get_data(req)
         allowed_paths = ["/name", "/description", "/metadataObjects"]
         for op in patch_ops:
-            if not any([i in op["path"] for i in allowed_paths]):
-                reason = f"Request contains '{op['path']}' key that cannot be" " updated to folders."
+            if all(i not in op["path"] for i in allowed_paths):
+                reason = f"Request contains '{op['path']}' key that cannot be updated to folders."
                 LOG.error(reason)
                 raise web.HTTPBadRequest(reason=reason)
         patch = JsonPatch(patch_ops)
@@ -365,6 +366,57 @@ async def delete_folder(self, req: Request) -> Response:
         LOG.info(f"DELETE folder with ID {folder} was successful.")
         return web.Response(status=204)
 
+    async def get_user(self, req: Request) -> Response:
+        """Get one user by its user ID.
+
+        :param req: GET request
+        :returns: JSON response containing user object
+        """
+        user_id = req.match_info["userId"]
+        db_client = req.app["db_client"]
+        operator = UserOperator(db_client)
+        user = await operator.read_user(user_id)
+        LOG.info(f"GET user with ID {user_id} was successful.")
+        return web.Response(body=json.dumps(user), status=200, content_type="application/json")
+
+    async def patch_user(self, req: Request) -> Response:
+        """Update user object with a specific user ID.
+
+        :param req: PATCH request
+        :returns: JSON response containing user ID for updated user object
+        """
+        user_id = req.match_info["userId"]
+        db_client = req.app["db_client"]
+
+        # Check patch operations in request are valid
+        patch_ops = await self._get_data(req)
+        allowed_paths = ["/drafts", "/folders"]
+        for op in patch_ops:
+            if all(i not in op["path"] for i in allowed_paths):
+                reason = f"Request contains '{op['path']}' key that cannot be updated to user object."
+                LOG.error(reason)
+                raise web.HTTPBadRequest(reason=reason)
+        patch = JsonPatch(patch_ops)
+
+        operator = UserOperator(db_client)
+        user = await operator.update_user(user_id, patch)
+        body = json.dumps({"userId": user})
+        LOG.info(f"PATCH user with ID {user} was successful.")
+        return web.Response(body=body, status=200, content_type="application/json")
+
+    async def delete_user(self, req: Request) -> Response:
+        """Delete user from database.
+
+        :param req: DELETE request
+        :returns: HTTP No Content response
+        """
+        user_id = req.match_info["userId"]
+        db_client = req.app["db_client"]
+        operator = UserOperator(db_client)
+        user = await operator.delete_user(user_id)
+        LOG.info(f"DELETE user with ID {user} was successful.")
+        return web.Response(status=204)
+
 
 class SubmissionAPIHandler:
     """Handler for non-rest API methods."""

metadata_backend/api/middlewares.py

@@ -73,7 +73,10 @@ async def jwt_authentication(req: Request, handler: Callable) -> Response:
 
         # Include claims that are required to be present
         # in the payload of the token
-        claims_options = {"iss": {"essential": True, "values": ["haka_iss", "elixir_iss"]}, "exp": {"essential": True}}
+        claims_options = {
+            "iss": {"essential": True, "values": ["haka_iss", "elixir_iss"]},
+            "exp": {"essential": True},
+        }
 
         # Decode and validate token
         try: