Add prefix creation function

Changes to be committed:
	modified:   authentication/services.py
	modified:   biocompute/models.py
	modified:   config/settings.py
	modified:   docs/refactor.md
	modified:   prefix/apis.py
	modified:   prefix/models.py
	modified:   prefix/services.py
	modified:   tests/test_views/test_api_objects_drafts_create.py

Author: HadleyKing

authentication/services.py

@@ -190,7 +190,6 @@ def create_bcodb_user(email: str) -> User:
 
     return user
 
-
 def send_bcodb(data: str, request_info: dict):
     """
     """

biocompute/models.py

@@ -49,6 +49,7 @@ class Bco(models.Model):
     prefix = models.ForeignKey(Prefix, on_delete=models.CASCADE, to_field="prefix")
     owner = models.ForeignKey(
         User,
+        to_field="username",
         on_delete=models.CASCADE, 
         related_name="owned_bcos"
     )

config/settings.py

@@ -123,18 +123,13 @@
     },
 ]
 
-# Object-level permissions with django-guardian
-# Source: https://github.com/django-guardian/django-guardian#configuration
 AUTHENTICATION_BACKENDS = [
     "django.contrib.auth.backends.ModelBackend",
-    "guardian.backends.ObjectPermissionBackend",
 ]
 
 # --- APPLICATION --- #
 # Application definition
 
-# Token-based authentication.
-# Source: https://www.django-rest-framework.org/api-guide/authentication/#tokenau thentication
 INSTALLED_APPS = [
     "django.contrib.admin",
     "django.contrib.admindocs",
@@ -150,8 +145,6 @@
     'rest_framework_jwt.blacklist',
     "rest_framework_swagger",
     "reset_migrations",
-    "guardian",
-    # "api",
     "authentication",
     "biocompute",
     "prefix"

docs/refactor.md

@@ -27,6 +27,11 @@
 ### Refactor the BCO permission system
 - same situation as prefix
 
+## Permissions
+
+- BCO has `owner`, `auth_group` and `auth_user`
+- Prefix has `owner`, and `auth_group` 
+
 ## Items to look at later
 - `authentication.apis.RegisterUserNoVerificationAPI` has no swagger or tests
 - fix email and secrets
@@ -40,3 +45,11 @@
 - unwanted swagger endpoints
 - need tests for token
 - prefix api documentation and portal docs for prefix
+
+Prefix Perms:
+	add -> create new DRAFT
+	edit -> Change existing Draft
+	delete -> Delete Draft
+	publish -> Publish Draft
+	view -> View/download 
+   ONLY if private

prefix/apis.py

@@ -27,10 +27,15 @@
                 description="A description of what this prefix should represent.  For example, the prefix 'GLY' would be related to BCOs which were derived from GlyGen workflows.",
                 example="Test prefix description."
             ),
-            "authorized_groups": openapi.Schema(
-                type=openapi.TYPE_ARRAY,
-                description="Groups which can access the BCOs using this prefix. If it is none then anyone can access.",
-                items=openapi.Schema(type=openapi.TYPE_STRING, example="")
+            "certifying_key": openapi.Schema(
+                type=openapi.TYPE_STRING,
+                description="Hash of server and date-time of creation.",
+                example="12345678910"
+            ),
+            "public": openapi.Schema(
+                type=openapi.TYPE_BOOLEAN,
+                description="Flag to set permissions.",
+                example=True
             )
         },
     )

prefix/models.py

@@ -19,11 +19,6 @@ class Prefix(models.Model):
         on_delete=models.CASCADE,
         to_field="username"
     )
-    authorized_groups = models.ManyToManyField(
-        Group,
-        blank=True,
-        related_name='authorized_prefix'
-    )
     counter = models.IntegerField(
         default=0,
         help_text="Counter for object_id asignment"

prefix/services.py

@@ -4,6 +4,8 @@
 import re
 from urllib.parse import urlparse
 from django.conf import settings
+from django.contrib.auth.models import Permission
+from django.contrib.contenttypes.models import ContentType
 from django.utils import timezone
 from prefix.models import Prefix
 from django.db import transaction
@@ -20,6 +22,7 @@ class PrefixSerializer(serializers.Serializer):
     prefix = serializers.CharField(min_length=3, max_length=5)
     description = serializers.CharField()
     authorized_groups = serializers.ListField(child=serializers.CharField(allow_blank=True), required=False)
+    public = serializers.BooleanField(required=False)
 
     def validate(self, attrs):
         """Prefix Validator
@@ -41,65 +44,52 @@ def validate(self, attrs):
             if "create" in request.path_info:
                 pass
             else:
-                errors["prefix_name"] = f"That Prefix, {prefix_name}, was not found."
-
-
-
-        # remove blank 'authorized_groups' relic from legacy conversion
-        if attrs['authorized_groups'][0] == "":
-            attrs.pop("authorized_groups")
-
-        #check for groups
-        if 'authorized_groups' in attrs:
-            for group in attrs['authorized_groups']:
-                try:
-                    Group.objects.get(name=group)
-                except Group.DoesNotExist as err:
-                    errors['authorized_groups'] = f"Invalid group: {group}"
-
-        # If erros exist than raise and exception and return it, otherwise
-        # return validated data
-        if errors:
-            raise serializers.ValidationError(errors)
+               raise serializers.ValidationError({"prefix_name": f"That Prefix, {prefix_name}, was not found."})
 
         return attrs
 
     @transaction.atomic
     def create(self, validated_data):
         """Create function for Prefix
         """
-        authorized_group_names = validated_data.pop('authorized_groups', [])
+        public = validated_data.pop('public', [])
+        import pdb; pdb.set_trace()
         prefix_instance = Prefix.objects.create(**validated_data, created=timezone.now())
-        # Set ManyToMany relations
-        if authorized_group_names:
-            authorized_groups = Group.objects.filter(name__in=authorized_group_names)
-            prefix_instance.authorized_groups.set(authorized_groups)
+
         return prefix_instance
 
     @transaction.atomic
     def update(self, validated_data):
         """Update function for Prefix."""
         prefix_instance = Prefix.objects.get(prefix=validated_data['prefix'])
         if prefix_instance.owner != validated_data['owner']:
-            # import pdb; pdb.set_trace()
             return "denied"
         prefix_instance.description = validated_data.get('description', prefix_instance.description)
         prefix_instance.save()
 
-        if 'authorized_groups' in validated_data:
-            authorized_group_names = validated_data['authorized_groups']
-            # If the list is empty or contains only an empty string, clear the groups
-            if not authorized_group_names or authorized_group_names == [""]:
-                prefix_instance.authorized_groups.clear()
+        return prefix_instance
 
-            else:
-                # Filter groups that exist in the database
-                authorized_groups = Group.objects.filter(name__in=authorized_group_names)
-                
-                # Set the new groups, which automatically handles adding, keeping, or removing
-                prefix_instance.authorized_groups.set(authorized_groups)
+def create_permissions_for_prefix(instance=None, owner=User):
+    """Prefix Permission Creation
 
-        return prefix_instance
+    Creates permissions for a Prefix if it is not public. Owner is assigned
+     all permissions and then can add permissions to other users.
+    
+	'view' -> View/download Prefix drafts
+    'add' -> create new drafts for Prefix
+	'change' -> Change existing drafts for Prefix
+	'delete' -> Delete drafts for Prefix
+	'publish' -> Publish drafts for Prefix
+    """
+    try:
+        for perm in [ "view", "add", "change", "delete", "publish"]:
+            print(instance)
+            Permission.objects.create(
+                name="Can " + perm + " BCOs with prefix " + instance.prefix,
+                content_type=ContentType.objects.get(app_label="api", model="bco"),
+                codename=perm + "_" + instance.prefix,)
+    except:
+        return 0
 
 def prefix_counter_increment(prefix: Prefix) -> int:
     """Prefix Counter Increment 

tests/test_views/test_api_objects_drafts_create.py

@@ -42,10 +42,10 @@ def setUp(self):
                 "prefix": "BCO",
                 "authorized_users": ["hivelab"],
                 "contents": {
-                "object_id": "https://test.portal.biochemistry.gwu.edu/BCO_000001/DRAFT",
-                "spec_version": "https://w3id.org/ieee/ieee-2791-schema/2791object.json",
-                "etag": "11ee4c3b8a04ad16dcca19a6f478c0870d3fe668ed6454096ab7165deb1ab8ea"
-                }
+                    "object_id": "https://test.portal.biochemistry.gwu.edu/BCO_000001/DRAFT",
+                    "spec_version": "https://w3id.org/ieee/ieee-2791-schema/2791object.json",
+                    "etag": "11ee4c3b8a04ad16dcca19a6f478c0870d3fe668ed6454096ab7165deb1ab8ea"
+                    }
             },
             {
                 "object_id": "http://127.0.0.1:8000/TEST_000001",