Updated config file to .secrets

also updated accounts/describe
Changes to be committed:
	modified:   .gitignore
	new file:   .secrets.example
	modified:   authentication/selectors.py
	modified:   biocompute/apis.py
	modified:   biocompute/models.py
	modified:   biocompute/selectors.py
	modified:   config/settings.py
	deleted:    server.conf
	deleted:    sever.conf.example

Author: HadleyKing

.gitignore

@@ -130,11 +130,8 @@ dmypy.json
 
 # --- USER-ADDED IGNORES --- #
 
-# The settings file.
-config/settings.py
-
 # The server configuration file.
-server.conf
+.secrets
 
 # The migrations folder.
 # bco_api/api/migrations/

.secrets.example

@@ -0,0 +1,14 @@
+[DJANGO_KEYS]
+SECRET_KEY=
+ANON_KEY=
+
+[SERVER]
+PRODUCTION=
+SERVER_VERSION=
+HOSTNAME=
+HUMAN_READABLE_HOSTNAME=
+PUBLIC_HOSTNAME=
+SERVER_URL=
+#DATABASE=
+DATABASE=
+EMAIL_BACKEND=

authentication/selectors.py

@@ -5,7 +5,8 @@
 from django.contrib.auth.models import User, Permission
 from authentication.models import Authentication, NewUser
 from rest_framework.authtoken.models import Token
-
+from prefix.selectors import get_user_prefixes
+from biocompute.selectors import get_authorized_bcos
 
 def get_anon()-> User:
     """Get AnonymosUser
@@ -73,27 +74,15 @@ def get_user_info(user: User) -> dict:
     other_info = {
         "permissions": {},
         "account_creation": "",
-        "account_expiration": "",
     }
-    user_perms = {"user": [], "groups": []}
-
-    for permission in user.user_permissions.all():
-        if permission.name not in user_perms["user"]:
-            user_perms["user"].append(permission.name)
-
-    for group in user.groups.all():
-        if group.name not in user_perms["groups"]:
-            user_perms["groups"].append(group.name)
-        for permission in Permission.objects.filter(group=group):
-            if permission.name not in user_perms["user"]:
-                user_perms["user"].append(permission.name)
+    user_perms = {"prefixes": get_user_prefixes(user), "BCOs": get_authorized_bcos(user)}
 
     other_info["permissions"] = user_perms
 
     other_info["account_creation"] = user.date_joined
 
     return {
-        "hostname": settings.ALLOWED_HOSTS[0],
+        "hostname": settings.HOSTNAME,
         "human_readable_hostname": settings.HUMAN_READABLE_HOSTNAME,
         "public_hostname": settings.PUBLIC_HOSTNAME,
         "token": token.key,

biocompute/apis.py

@@ -53,7 +53,7 @@
                 ),
                 "authorized_users": openapi.Schema(
                     type=openapi.TYPE_ARRAY,
-                    description="Users which can access the BCO draft.",
+                    description="Users that can access the BCO draft.",
                     items=openapi.Schema(type=openapi.TYPE_STRING, example="tester")
                 ),
                 "contents": openapi.Schema(

biocompute/models.py

@@ -30,7 +30,7 @@ class Bco(models.Model):
     owner = ForeignKey(User)
         String representing the django.contrib.auth.models.User that 'owns' the object
     authorized_users: ManyToManyField(User)
-        String representing the User that has access to the object
+        String representing the Users that have access to the object
     prefix: str
         Prefix for the BCO
     state:str

biocompute/selectors.py

@@ -10,6 +10,7 @@
 from datetime import datetime
 from django.conf import settings
 from django.contrib.auth. models import User
+from django.db.models import Q
 from prefix.selectors import (
     user_can_view_prefix,
     user_can_modify_prefix,
@@ -225,6 +226,27 @@ def retrieve_bco(bco_accession:str, user:User, bco_version:str=None) -> bool:
 
     return bco_instance
 
+def get_authorized_bcos(user: User):
+    """
+    Retrieve all BioCompute Objects (BCOs) that a specific user is authorized
+    to access, excluding those in 'DELETE' state.
+
+    Parameters:
+    - user (User): 
+        The Django User instance for whom to retrieve authorized BCOs.
+
+    Returns:
+    - QuerySet: 
+        A Django QuerySet containing the BCOs the user is authorized to access.
+    """
+
+    bcos = Bco.objects.filter(
+        Q(owner=user) | Q(authorized_users=user)
+    ).exclude(state='DELETE').values_list('object_id', flat=True).distinct()
+
+
+    return bcos
+
 def object_id_deconstructor(object_id=str) -> list:
     """
     Deconstructs a BioCompute Object (BCO) identifier into its constituent 

config/settings.py

@@ -9,80 +9,30 @@
 
 # --- SECURITY SETTINGS --- #
 # Load the server config file.
-server_config = configparser.ConfigParser()
-server_config.read(BASE_DIR + "/server.conf")
-
-# Quick-start development settings - unsuitable for production
-# See https://docs.djangoproject.com/en/3.0/howto/deployment/checklist/
-
-# Is this a production server?
-PRODUCTION = server_config["PRODUCTION"]["production"]
+secrets = configparser.ConfigParser()
+secrets.read(BASE_DIR + "/.secrets")
+PRODUCTION = secrets["SERVER"]["PRODUCTION"]
+DEBUG = PRODUCTION
 
 # Set the anonymous user's key.
-ANON_KEY = server_config["KEYS"]["anon"]
+ANON_KEY = secrets["DJANGO_KEYS"]["ANON_KEY"]
 
 # SECURITY WARNING: keep the secret key used in production secret!
-SECRET_KEY = "$vz@#@^q(od&$rf&*6^z!m5nh6qw2*cq*j6fha#^h9(r7$xqy4"
+SECRET_KEY = secrets["DJANGO_KEYS"]["SECRET_KEY"]
 
 # SECURITY WARNING: don't run with debug turned on in production!
-DEBUG = PRODUCTION
 
+# The publicly accessible hostname.
+HOSTNAME = secrets["SERVER"]["HOSTNAME"]
 # The human-readable hostname.
-HUMAN_READABLE_HOSTNAME = server_config["HRHOSTNAME"]["hrnames"]
-
-if server_config["GROUP_PREFIX"]["allow_all_creation"] == "True":
-    GROUP = True
-    PREFIX = True
-elif server_config["GROUP_PREFIX"]["allow_group_creation"] == "True":
-    GROUP = True
-elif server_config["GROUP_PREFIX"]["allow_prefix_creation"] == "True":
-    PREFIX = True
-
+HUMAN_READABLE_HOSTNAME = secrets["SERVER"]["HUMAN_READABLE_HOSTNAME"]
 # The publicly accessible hostname.
-if server_config["PRODUCTION"]["production"] == "True":
-    PUBLIC_HOSTNAME = server_config["PUBLICHOSTNAME"]["prod_name"]
-elif server_config["PRODUCTION"]["production"] == "False":
-    PUBLIC_HOSTNAME = server_config["PUBLICHOSTNAME"]["name"]
+PUBLIC_HOSTNAME = secrets["SERVER"]["PUBLIC_HOSTNAME"]
+# import pdb; pdb.set_trace()
 
-# Source: https://dzone.com/articles/how-to-fix-django-cors-error
 
-# Check for open (public) access to the API.
-if server_config["REQUESTS_FROM"]["public"].strip() == "false":
-
-    # Process the requester groups.
-
-    # configparser automatically strips white space off the
-    # ends of arguments.
-    requesters = [
-        server_config["REQUESTS_FROM"][i].strip()
-        for i in server_config["REQUESTS_FROM"]
-    ]
-    requesters.remove("false")
-    requesters = [i.split(",") for i in requesters]
-
-    # Flatten the list.
-    # Source: https://stackabuse.com/python-how-to-flatten-list-of-lists/
-    flattened = [item.strip() for sublist in requesters for item in sublist]
-
-    if server_config["PRODUCTION"]["production"] == "True":
-        ALLOWED_HOSTS = [
-            i.strip() for i in server_config["HOSTNAMES"]["prod_names"].split(",")
-        ]
-    elif server_config["PRODUCTION"]["production"] == "False":
-        ALLOWED_HOSTS = [
-            i.strip() for i in server_config["HOSTNAMES"]["names"].split(",")
-        ]
-
-    CORS_ORIGIN_ALLOW_ALL = False
-    CORS_ORIGIN_WHITELIST = tuple(flattened)
-
-elif server_config["REQUESTS_FROM"]["public"].strip() == "true":
-    if server_config["PRODUCTION"]["production"] == "True":
-        ALLOWED_HOSTS = [server_config["HOSTNAMES"]["prod_names"].split(",")[0], "*"]
-        CORS_ORIGIN_ALLOW_ALL = True
-    elif server_config["PRODUCTION"]["production"] == "False":
-        ALLOWED_HOSTS = [server_config["HOSTNAMES"]["names"].split(",")[0], "*"]
-        CORS_ORIGIN_ALLOW_ALL = True
+CORS_ORIGIN_ALLOW_ALL = True
+CORS_ORIGIN_WHITELIST = ["*"]
 
 # Use the REST framework
 REST_FRAMEWORK = {
@@ -94,8 +44,6 @@
     ],
     "DEFAULT_PERMISSION_CLASSES": ["rest_framework.permissions.IsAuthenticated"],
     "DEFAULT_SCHEMA_CLASS": "rest_framework.schemas.coreapi.AutoSchema",
-    
-
 }
 
 JWT_AUTH = {
@@ -197,7 +145,7 @@
 DATABASES = {
     "default": {
         "ENGINE": "django.db.backends.sqlite3",
-        "NAME": server_config["DATABASES"]["path"],
+        "NAME": secrets["SERVER"]["DATABASE"],
     }
 }
 
@@ -219,8 +167,8 @@
 # https://docs.djangoproject.com/en/3.0/howto/static-files/
 
 STATIC_URL = "/api/static/"
-# STATICFILES_DIRS = [os.path.join(BASE_DIR, 'static')]
-STATIC_ROOT = "/var/www/bcoeditor/bco_api/bco_api/static/"
+STATICFILES_DIRS = [os.path.join(BASE_DIR, 'static')]
+# STATIC_ROOT = "/var/www/bcoeditor/bco_api/bco_api/static/"
 
 # ----- CUSTOM VARIABLES AND METHODS ----- #
 # Load request and validation templates (definitions).
@@ -229,26 +177,9 @@
 # First, the request definitions.
 
 # Make the object naming accessible as a dictionary.
-OBJECT_NAMING = {}
-
-if server_config["PRODUCTION"]["production"] == "True":
-
-    for i in server_config["OBJECT_NAMING"]:
-        if i.split("_")[0] == "prod":
-
-            # Strip out the production flag.
-            STRIPPED = "_".join(i.split("_")[1:])
-
-            OBJECT_NAMING[STRIPPED] = server_config["OBJECT_NAMING"][i]
-
-elif server_config["PRODUCTION"]["production"] == "False":
-
-    for i in server_config["OBJECT_NAMING"]:
-        if i.split("_")[0] != "prod":
-            OBJECT_NAMING[i] = server_config["OBJECT_NAMING"][i]
 
 # emailing notifications
-EMAIL_BACKEND = "django.core.mail.backends.console.EmailBackend"
+EMAIL_BACKEND = secrets["SERVER"]["EMAIL_BACKEND"]
 EMAIL_HOST = "localhost"
 EMAIL_PORT = 25
 DEFAULT_AUTO_FIELD = "django.db.models.AutoField"