Merge branch 'feature/fix-code-linting-#184' into feature/test-multip…

…le-backends-#150

README.md

@@ -29,8 +29,9 @@ machine.
 ### pyenv (Python Version Management)
 To start, install [pyenv](https://github.com/pyenv/pyenv). There is a Windows version of
 this tool ([pyenv-win](https://github.com/pyenv-win/pyenv-win)), however this is
-currently untested on this repoThis is used to manage the various versions of Python
-that will be used to test/lint Python during development. Install by executing the following:
+currently untested on this repo. This is used to manage the various versions of Python
+that will be used to test/lint Python during development. Install by executing the
+following:
 
 ```bash
 curl https://pyenv.run | bash
@@ -125,7 +126,8 @@ used to lint/format/test the code in the included `noxfile.py`. To install Nox,
 as shown below. Nox is not listed as a Poetry dependency because this has the potential
 to cause issues if Nox was executed inside Poetry (see
 [here](https://medium.com/@cjolowicz/nox-is-a-part-of-your-global-developer-environment-like-poetry-pre-commit-pyenv-or-pipx-1cdeba9198bd)
-for more detailed reasoning):
+for more detailed reasoning). If you do choose to install these packages within a
+virtual environment, you do not need the `--user` option:
 
 ```bash
 pip install --user --upgrade nox
@@ -156,6 +158,21 @@ Currently, the following Nox sessions have been created:
   automated tests in `test/`, tests for the database and ICAT backends, and non-backend
   specific tests. More details [here](#running-tests).
 
+Each Nox session builds an environment using the repo's dependencies (defined using
+Poetry) using `install_with_constraints()`. This stores the dependencies in a
+`requirements.txt`-like format temporarily during this process, using the OS' default
+temporary location. This could result in permissions issues (this has been seen by a
+colleague on Windows), so adding the `--tmpdir [DIRECTORY PATH]` allows the user to
+define where this file should be stored. Due to Nox session being initiated in the
+command line, this argument needs to be a positional argument (denoted by the `--` in
+the Nox command). This argument is optional, but **must** be the final argument avoid
+interference with Nox's argument parsing. An example:
+
+```bash
+nox -s lint -- util datagateway_api --tmpdir /root
+```
+
+
 ### Pre Commit (Automated Checks during Git Commit)
 To make use of Git's ability to run custom hooks, [pre-commit](https://pre-commit.com/)
 is used. Like Nox, Pip is used to install this tool:
@@ -281,45 +298,68 @@ This is illustrated below.
 
 
 `````
-─── datagateway_api
-    ├── common
-    │   ├── database
-    │   │   ├── backend.py
-    │   │   ├── filters.py
-    │   │   ├── helpers.py
-    │   │   ├── models.py
-    │   │   └── session_manager.py
-    │   ├── icat
-    │   ├── backends.py
-    │   ├── constants.py
-    │   ├── exceptions.py
-    │   ├── filters.py
-    │   └── helpers.py
-    ├── src
-    │   ├── resources
-    │   │   ├── entities
-    │   │   │   ├── entity_endpoint.py
-    │   │   │   └── entity_map.py
-    │   │   └── non_entities
-    │   │       └── <non_entity>_endpoints.py
-    │   ├── swagger
-    │   │   ├── openapi.yaml
-    │   │   └── swagger_generator.py
-    │   └── main.py
-    ├── test
-    │   ├── resources
-    │   │   ├── entities
-    │   │   │   └──test_<entity>.py
-    │   │   └── non_entities
-    │   │       └── test_<non_entity>.py
-    │   └── test_base
-    │       ├── constants.py
-    │       └── rest_test.py
-    ├── util
-    │   └── icat_db_generator.py
-    ├── logs.log
-    └── config.json
+.
+├── .flake8
+├── .gitignore
+├── .pre-commit-config.yaml
+├── LICENSE
+├── README.md
+├── config.json.example
+├── datagateway_api
+│   ├── common
+│   │   ├── backend.py
+│   │   ├── backends.py
+│   │   ├── config.py
+│   │   ├── constants.py
+│   │   ├── database
+│   │   │   ├── backend.py
+│   │   │   ├── filters.py
+│   │   │   ├── helpers.py
+│   │   │   ├── models.py
+│   │   │   └── session_manager.py
+│   │   ├── date_handler.py
+│   │   ├── exceptions.py
+│   │   ├── filter_order_handler.py
+│   │   ├── filters.py
+│   │   ├── helpers.py
+│   │   ├── icat
+│   │   │   ├── backend.py
+│   │   │   ├── filters.py
+│   │   │   ├── helpers.py
+│   │   │   └── query.py
+│   │   └── logger_setup.py
+│   └── src
+│       ├── main.py
+│       ├── resources
+│       │   ├── entities
+│       │   │   ├── entity_endpoint.py
+│       │   │   └── entity_map.py
+│       │   ├── non_entities
+│       │   │   └── sessions_endpoints.py
+│       │   └── table_endpoints
+│       │       └── table_endpoints.py
+│       └── swagger
+│           ├── apispec_flask_restful.py
+│           ├── initialise_spec.py
+│           └── openapi.yaml
+├── noxfile.py
+├── poetry.lock
+├── postman_collection_icat.json
+├── pyproject.toml
+├── test
+│   ├── test_base.py
+│   ├── test_database_helpers.py
+│   ├── test_entityHelper.py
+│   └── test_helpers.py
+└── util
+    └── icat_db_generator.py
  `````
+
+The directory tree can be generated using the following command:
+
+ `git ls-tree -r --name-only HEAD | grep -v __init__.py | tree --fromfile`
+
+
 #### Main
 `main.py` is where the flask_restful api is set up. This is where each endpoint resource
 class is generated and mapped to an endpoint.

datagateway_api/src/resources/non_entities/sessions_endpoints.py

@@ -60,9 +60,9 @@ def post(self):
                           description: Session ID
                           example: xxxxxx-yyyyyyy-zzzzzz
               400:
-                description: Bad request. User credentials not provided in request body
+                description: Bad request - User credentials not provided in request body
               403:
-                 description: Forbidden. User credentials were invalid
+                 description: Forbidden - User credentials were invalid
             """
             if not (
                 request.data

datagateway_api/src/resources/table_endpoints/table_endpoints.py

@@ -31,7 +31,7 @@ def get(self, id_):
             parameters:
                 - in: path
                   required: true
-                  name: id
+                  name: id_
                   description: The id of the instrument to retrieve the facility cycles
                       of
                   schema:
@@ -98,7 +98,7 @@ def get(self, id_):
             parameters:
                 - in: path
                   required: true
-                  name: id
+                  name: id_
                   description: The id of the instrument to count the facility cycles of
                   schema:
                     type: integer

datagateway_api/src/swagger/initialise_spec.py

@@ -64,8 +64,8 @@ def initialise_spec(spec):
                                             {"type": "number"},
                                             {"type": "integer"},
                                             {"type": "boolean"},
-                                        ]
-                                    }
+                                        ],
+                                    },
                                 },
                             },
                             {
@@ -105,8 +105,8 @@ def initialise_spec(spec):
                                         "oneOf": [
                                             {"type": "number"},
                                             {"type": "integer"},
-                                        ]
-                                    }
+                                        ],
+                                    },
                                 },
                             },
                             {
@@ -117,8 +117,8 @@ def initialise_spec(spec):
                                         "oneOf": [
                                             {"type": "number"},
                                             {"type": "integer"},
-                                        ]
-                                    }
+                                        ],
+                                    },
                                 },
                             },
                             {

datagateway_api/src/swagger/openapi.yaml

@@ -87,9 +87,9 @@ components:
       schema:
         type: integer
     WHERE_FILTER:
-      description: Apply where filters to the query. The possible operators are like,
-        gte, lte, in and eq. Please modify the examples before executing a request
-        if you are having issues with the example values.
+      description: 'Apply where filters to the query. The possible operators are:
+        ne, like, lt, lte, gt, gte, in and eq. Please modify the examples before executing
+        a request if you are having issues with the example values.'
       examples:
         eq:
           value:
@@ -10817,9 +10817,9 @@ paths:
                 type: object
           description: Success - returns a session ID
         '400':
-          description: Bad request. User credentials not provided in request body
+          description: Bad request - User credentials not provided in request body
         '403':
-          description: Forbidden. User credentials were invalid
+          description: Forbidden - User credentials were invalid
       security: []
       summary: Login
       tags:

noxfile.py

@@ -7,8 +7,8 @@
 code_locations = "datagateway_api", "test", "util", "noxfile.py"
 
 
-def install_with_constraints(session, *args, **kwargs):
-    with tempfile.NamedTemporaryFile() as requirements:
+def install_with_constraints(session, req_dir=None, *args, **kwargs):
+    with tempfile.NamedTemporaryFile(dir=req_dir) as requirements:
         session.run(
             "poetry",
             "export",
@@ -20,18 +20,35 @@ def install_with_constraints(session, *args, **kwargs):
         session.install(f"--constraint={requirements.name}", *args, **kwargs)
 
 
+def get_tmp_dir(session):
+    tmp_dir = None
+
+    try:
+        if session.posargs[-2] == "--tmpdir":
+            tmp_dir = session.posargs.pop(-1)
+            session.posargs.remove("--tmpdir")
+    except IndexError:
+        session.log("Info: No --tmpdir option given")
+
+    return tmp_dir
+
+
 @nox.session(python="3.6", reuse_venv=True)
 def black(session):
+    tmp_dir = get_tmp_dir(session)
     args = session.posargs or code_locations
-    install_with_constraints(session, "black")
+
+    install_with_constraints(session, tmp_dir, "black")
     session.run("black", *args, external=True)
 
 
 @nox.session(python="3.6", reuse_venv=True)
 def lint(session):
+    tmp_dir = get_tmp_dir(session)
     args = session.posargs or code_locations
     install_with_constraints(
         session,
+        tmp_dir,
         "flake8",
         "flake8-bandit",
         "flake8-black",
@@ -49,8 +66,9 @@ def lint(session):
 
 @nox.session(python="3.6", reuse_venv=True)
 def safety(session):
-    install_with_constraints(session, "safety")
-    with tempfile.NamedTemporaryFile() as requirements:
+    tmp_dir = get_tmp_dir(session)
+    install_with_constraints(session, tmp_dir, "safety")
+    with tempfile.NamedTemporaryFile(dir=tmp_dir) as requirements:
         session.run(
             "poetry",
             "export",