Biocompute model (#284)

* Remove API app
Changes to be committed:
	deleted:    api/__init__.py
	deleted:    api/admin.py
	deleted:    api/apps.py
	deleted:    api/fixtures/bootstrap.json
	deleted:    api/fixtures/metafixtures
	deleted:    api/fixtures/metafixtures.json
	deleted:    api/keys.sh
	deleted:    api/migrations/0001_initial.py
	deleted:    api/migrations/0002_auto_20220124_2356.py
	deleted:    api/migrations/0003_rename_meta_table_prefix_table.py
	deleted:    api/migrations/0004_rename_group_info_groupinfo.py
	deleted:    api/migrations/0005_rename_prefixes_prefix.py
	deleted:    api/migrations/0006_delete_new_users.py
	deleted:    api/migrations/__init__.py
	deleted:    api/model/__init__.py
	deleted:    api/model/groups.py
	deleted:    api/model/prefix.py
	deleted:    api/models.py
	deleted:    api/permissions.py
	deleted:    api/rdb.sh
	deleted:    api/request_definitions/GET.schema
	deleted:    api/request_definitions/POST.schema
	deleted:    api/request_definitions/templates/DELETE_delete_object_by_id.schema
	deleted:    api/request_definitions/templates/GET_activate_account.schema
	deleted:    api/request_definitions/templates/GET_get_object_by_id.schema
	deleted:    api/request_definitions/templates/GET_retrieve_available_schema.schema
	deleted:    api/request_definitions/templates/POST_convert_existing_object_between_schemas.schema
	deleted:    api/request_definitions/templates/POST_convert_payload_to_schema.schema
	deleted:    api/request_definitions/templates/POST_new_account.schema
	deleted:    api/request_definitions/templates/POST_object_listing_by_token.schema
	deleted:    api/request_definitions/templates/POST_objects_draft.schema
	deleted:    api/request_definitions/templates/POST_objects_publish.schema
	deleted:    api/request_definitions/templates/POST_read_object.schema
	deleted:    api/request_definitions/templates/POST_validate_payload_against_schema.schema
	deleted:    api/scripts/__init__.py
	deleted:    api/scripts/method_specific/GET_draft_object_by_id.py
	deleted:    api/scripts/method_specific/GET_published_object_by_id.py
	deleted:    api/scripts/method_specific/GET_published_object_by_id_with_version.py
	deleted:    api/scripts/method_specific/GET_retrieve_available_schema.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_create.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_delete.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_modify.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_permissions.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_permissions_set.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_publish.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_read.py
	deleted:    api/scripts/method_specific/POST_api_objects_drafts_token.py
	deleted:    api/scripts/method_specific/POST_api_objects_publish.py
	deleted:    api/scripts/method_specific/POST_api_objects_published.py
	deleted:    api/scripts/method_specific/POST_api_objects_search.py
	deleted:    api/scripts/method_specific/POST_api_objects_token.py
	deleted:    api/scripts/method_specific/POST_validate_payload_against_schema.py
	deleted:    api/scripts/method_specific/__init__.py
	deleted:    api/scripts/utilities/DbUtils.py
	deleted:    api/scripts/utilities/FileUtils.py
	deleted:    api/scripts/utilities/JsonUtils.py
	deleted:    api/scripts/utilities/RequestUtils.py
	deleted:    api/scripts/utilities/ResponseUtils.py
	deleted:    api/scripts/utilities/SettingsUtils.py
	deleted:    api/scripts/utilities/UserUtils.py
	deleted:    api/scripts/utilities/__init__.py
	deleted:    api/serializers.py
	deleted:    api/signals.py
	deleted:    api/templates/api/account_activation_message.html
	deleted:    api/urls.py
	deleted:    api/validation_definitions/IEEE/2791object.json
	deleted:    api/validation_definitions/IEEE/description_domain.json
	deleted:    api/validation_definitions/IEEE/error_domain.json
	deleted:    api/validation_definitions/IEEE/execution_domain.json
	deleted:    api/validation_definitions/IEEE/io_domain.json
	deleted:    api/validation_definitions/IEEE/parametric_domain.json
	deleted:    api/validation_definitions/IEEE/provenance_domain.json
	deleted:    api/validation_definitions/IEEE/usability_domain.json
	deleted:    api/validation_definitions/IEEE_sub/IEEE2791-2020.schema
	deleted:    api/validation_definitions/IEEE_sub/domains/description_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/error_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/execution_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/io_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/parametric_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/provenance_domain.json
	deleted:    api/validation_definitions/IEEE_sub/domains/usability_domain.json
	deleted:    api/validation_definitions/uri_external
	deleted:    api/views.py
	new file:   config/settings.py
	modified:   config/urls.py

Changes not staged for commit:
	modified:   authentication/apis.py
	modified:   authentication/migrations/0001_initial.py
	deleted:    authentication/migrations/0002_newuser.py
	modified:   authentication/services.py
	modified:   docs/refactor.md
	modified:   search/selectors.py
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_database.py
	deleted:    tests/test_fixtures.py
	deleted:    tests/test_models
	modified:   tests/test_views/test_api_account_activate.py
	deleted:    tests/test_views/test_api_accounts_describe.py
	modified:   tests/test_views/test_api_auth_add.py
	modified:   tests/test_views/test_api_auth_reset_token.py
	deleted:    tests/test_views/test_api_groups_group_info.py
	deleted:    tests/test_views/test_api_groups_modify.py
	deleted:    tests/test_views/test_api_objects.py
	deleted:    tests/test_views/test_api_objects_drafts_create.py
	deleted:    tests/test_views/test_api_objects_drafts_modify.py
	deleted:    tests/test_views/test_api_objects_drafts_publish.py
	deleted:    tests/test_views/test_api_objects_search.py
	deleted:    tests/test_views/test_api_objects_validate.py
	deleted:    tests/test_views/test_api_prefixes_create.py
	deleted:    tests/test_views/test_api_prefixes_token.py
	deleted:    tests/test_views/test_get_object_id_draft.py
	deleted:    tests/test_views/test_get_objectid.py
	deleted:    tests/test_views/test_published_object_by_id.py
	modified:   token.json

* Framework for BioCompute model

Changes to be committed:
	new file:   biocompute/__init__.py
	new file:   biocompute/admin.py
	new file:   biocompute/apis.py
	new file:   biocompute/migrations/__init__.py
	new file:   biocompute/models.py
	new file:   biocompute/selectors.py
	new file:   biocompute/services.py
	new file:   biocompute/urls.py

* Added files for Prefix model

Changes to be committed:
	new file:   prefix/__init__.py
	new file:   prefix/admin.py
	new file:   prefix/apis.py
	new file:   prefix/apps.py
	new file:   prefix/migrations/__init__.py
	new file:   prefix/models.py
	new file:   prefix/selectors.py
	new file:   prefix/services.py
	new file:   prefix/urls.py

* Tests for authentication

Changes to be committed:
	modified:   .gitignore
	modified:   authentication/apis.py
	modified:   authentication/migrations/0001_initial.py
	deleted:    authentication/migrations/0002_newuser.py
	modified:   authentication/services.py
	new file:   biocompute/migrations/0001_initial.py
	modified:   docs/refactor.md
	new file:   prefix/migrations/0001_initial.py
	modified:   search/selectors.py
	new file:   test.json
	new file:   tests/fixtures/old_test_data.json
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_database.py
	deleted:    tests/test_fixtures.py
	deleted:    tests/test_models
	modified:   tests/test_views/test_api_account_activate.py
	renamed:    tests/test_views/test_api_accounts_describe.py -> tests/test_views/test_api_account_describe.py
	modified:   tests/test_views/test_api_auth_add.py
	modified:   tests/test_views/test_api_auth_reset_token.py
	deleted:    tests/test_views/test_api_groups_group_info.py
	deleted:    tests/test_views/test_api_groups_modify.py
	deleted:    tests/test_views/test_api_objects.py
	deleted:    tests/test_views/test_api_objects_drafts_create.py
	deleted:    tests/test_views/test_api_objects_drafts_modify.py
	deleted:    tests/test_views/test_api_objects_drafts_publish.py
	deleted:    tests/test_views/test_api_objects_search.py
	deleted:    tests/test_views/test_api_objects_validate.py
	deleted:    tests/test_views/test_api_prefixes_create.py
	deleted:    tests/test_views/test_api_prefixes_token.py
	deleted:    tests/test_views/test_get_object_id_draft.py
	deleted:    tests/test_views/test_get_objectid.py
	deleted:    tests/test_views/test_published_object_by_id.py
	modified:   token.json

* Move Swagger files and implement BCO draft create

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/models.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	new file:   config/services.py
	modified:   config/urls.py
	modified:   docs/refactor.md
	modified:   prefix/urls.py
	new file:   tests/fixtures/example_bco.py
	new file:   tests/test_views/test_api_objects_drafts_create.py

* Doc fix in Bco.models
Changes to be committed:
	modified:   biocompute/models.py

* Updated biocompute.model and prefix.model

Added the DraftsCreateApi and tests.
This included serializers for BCO creation
Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/services.py
	modified:   config/services.py
	modified:   prefix/models.py
	modified:   prefix/services.py
	modified:   test.json
	modified:   tests/fixtures/test_data.json
	new file:   tests/test_views/test_api_objects_drafts_create.py

Author: HadleyKing

biocompute/apis.py

@@ -6,17 +6,18 @@
 
 from drf_yasg import openapi
 from drf_yasg.utils import swagger_auto_schema
+from django.db import utils
 from rest_framework.views import APIView
 from rest_framework import status
 from rest_framework.permissions import IsAuthenticated
 from rest_framework.response import Response
 from tests.fixtures.example_bco import BCO_000001
-from config.services import legacy_api_converter
+from config.services import legacy_api_converter, response_constructor
 from biocompute.services import BcoDraftSerializer
 
 class DraftsCreateApi(APIView):
     """
-    Create BCO Draft
+    Create BCO Draft [Bulk Enabled]
 
     --------------------
 
@@ -63,49 +64,75 @@ class DraftsCreateApi(APIView):
     @swagger_auto_schema(
         request_body=request_body,
         responses={
-            200: "Creation of BCO draft is successful.",
-            300: "Some requests failed and some succeeded.",
-            400: "Bad request.",
+            200: "All requests were accepted.",
+            207: "Some requests failed and some succeeded. Each object submitted"
+                " will have it's own response object with it's own status"
+                " code and message.\n",
+            400: "All requests were rejected.",
             403: "Invalid token.",
         },
         tags=["BCO Management"],
     )
 
     def post(self, request) -> Response:
-        response_data = {}
+        response_data = []
         owner = request.user
         data = request.data
-        all_good = True
+        rejected_requests = False
+        accepted_requests = False
         if 'POST_api_objects_draft_create' in request.data:
             data = legacy_api_converter(request.data)
 
         for index, object in enumerate(data):
-            list_id = object.get("object_id", index)
+            response_id = object.get("object_id", index)
             bco = BcoDraftSerializer(data=object, context={'request': request})
 
             if bco.is_valid():
-                bco.create(bco.validated_data)
-                response_data[list_id] = "bco valid"
+                try:
+                    bco.create(bco.validated_data)
+                    response_data.append(response_constructor(
+                        identifier=bco['object_id'].value,
+                        status = "SUCCESS",
+                        code= 200,
+                        message= f"BCO {bco['object_id'].value} created",
+                    ))
+                    accepted_requests = True
+
+                except Exception as err:
+                    print(err)
+                    response_data.append(response_constructor(
+                        identifier=bco['object_id'].value,
+                        status = "SERVER ERROR",
+                        code= 500,
+                        message= f"BCO {bco['object_id'].value} failed",
+                    ))
 
             else:
-                response_data[list_id] = bco.errors
-                all_good = False
+                response_data.append(response_constructor(
+                    identifier=response_id,
+                    status = "REJECTED",
+                    code= 400,
+                    message= f"BCO {response_id} rejected",
+                    data=bco.errors
+                ))
+                rejected_requests = True
+
+            print(accepted_requests, rejected_requests )
 
-        if all_good is False:
+        if accepted_requests is False and rejected_requests == True:
+            return Response(
+                status=status.HTTP_400_BAD_REQUEST,
+                data=response_data
+            )
+        
+        if accepted_requests is True and rejected_requests is True:
             return Response(
                 status=status.HTTP_207_MULTI_STATUS,
                 data=response_data
             )
 
-        return Response(status=status.HTTP_200_OK, data=response_data)
-        
-        # def create(self, validated_data):
-        #     # Custom creation logic here, if needed
-        #     return Bco.objects.create(**validated_data)
-        
-        # def update(self, instance, validated_data):
-        #     # Custom update logic here, if needed
-        #     for attr, value in validated_data.items():
-        #         setattr(instance, attr, value)
-        #     instance.save()
-        #     return instance
+        if accepted_requests is True and rejected_requests is False:
+            return Response(
+                status=status.HTTP_200_OK,
+                data=response_data
+            )

biocompute/services.py

@@ -1,10 +1,14 @@
 #!/usr/bin/env python3
 # biocopmute/services.py
 
+import re
+from urllib.parse import urlparse
+from django.conf import settings
 from django.db import transaction
 from django.utils import timezone
 from biocompute.models import Bco
 from prefix.models import Prefix
+from prefix.services import prefix_counter_increment
 from django.contrib.auth.models import Group, User
 from rest_framework import serializers
 
@@ -13,6 +17,8 @@
 Service functions for working with BCOs
 """
 
+HOSTNAME = settings.PUBLIC_HOSTNAME
+
 class BcoDraftSerializer(serializers.Serializer):
     object_id = serializers.URLField(required=False)
     contents = serializers.JSONField()
@@ -21,6 +27,9 @@ class BcoDraftSerializer(serializers.Serializer):
     authorized_users = serializers.ListField(child=serializers.CharField(), required=False)
 
     def validate(self, attrs):
+        """BCO Draft Validator
+        """
+
         errors = {}
         request = self.context.get('request')
         attrs["owner"] = request.user
@@ -43,36 +52,38 @@ def validate(self, attrs):
 
         # Validate Prefix
         try:
-            attrs['prefix_instance'] = Prefix.objects.get(prefix=attrs['prefix'])
+            #set a name and instance for Prefix
+            attrs['prefix'] = Prefix.objects.get(prefix=attrs['prefix'])
+            attrs['prefix_name'] = attrs['prefix'].prefix
         except Prefix.DoesNotExist as err:
             errors['prefix'] = 'Invalid prefix.'
+            raise serializers.ValidationError(errors)
 
-        # Validate object_id match
-        if 'object_id' in attrs and attrs['object_id'] != attrs['contents'].get('object_id', ''):
-            errors["object_id"] = "object_id does not match object_id in contents."
-
-        # Validate that object_id is unique
-        object_id = attrs['contents'].get('object_id', '')
-        
-        if not Bco.objects.filter(object_id=object_id).exists():
-            pass
+        # Validate or create object_id
+        if 'object_id' in attrs:
+            id_errors = validate_bco_object_id(
+                attrs['object_id'],
+                attrs['prefix_name']
+            )
+            if id_errors != 0:
+                errors["object_id"] = id_errors
         else:
-            errors["object_id"] = f"That object_id, {attrs['object_id']}, already exists."
+            attrs['object_id'] = create_bco_id(attrs['prefix'])
 
+        # If erros exist than raise and exception and return it, otherwise
+        # return validated data
         if errors:
             raise serializers.ValidationError(errors)
 
         return attrs
 
     @transaction.atomic
     def create(self, validated_data):
-        # Remove the non-model field 'prefix' and use 'prefix_instance' instead
-        prefix_instance = validated_data.pop('prefix_instance', None)
-        validated_data.pop('prefix')
+        # Remove the non-model field 'prefix_name' and use 'prefix' instance instead
+        validated_data.pop('prefix_name')
         authorized_group_names = validated_data.pop('authorized_groups', [])
         authorized_usernames = validated_data.pop('authorized_users', [])
-
-        bco_instance = Bco.objects.create(**validated_data, prefix=prefix_instance, last_update=timezone.now())
+        bco_instance = Bco.objects.create(**validated_data, last_update=timezone.now())
 
         # Set ManyToMany relations
         if authorized_group_names:
@@ -84,3 +95,44 @@ def create(self, validated_data):
             bco_instance.authorized_users.set(authorized_users)
 
         return bco_instance
+
+
+def validate_bco_object_id(object_id: str, prefix_name: str):
+    """Validate BCO object ID
+
+    Function to validate a proposed BCO object_id. Will reject the ID if the 
+    following constraints are not met:
+      1. Correct hostname for this BCODB instance
+      2. Prefix submitted is not in the object_id
+      3. The object_id already exists
+    """
+    errors = []
+    
+    if HOSTNAME not in object_id:
+        errors.append("Object ID does not conform to the required format. "\
+            + f"The hostname {HOSTNAME} is not in {object_id}")
+    if prefix_name not in object_id:
+        errors.append(f"Object ID, {object_id}, does not contain the "\
+         + f"submitted prefix, {prefix_name}.")
+
+    if not Bco.objects.filter(object_id=object_id).exists():
+        pass
+    else:
+        errors.append(f"That object_id, {object_id}, already exists.")
+
+    if errors:
+        return errors
+    return 0
+
+def create_bco_id(prefix: Prefix) -> str:
+    """Create BCO object_id
+
+    Function to construct BCO object_id. Takes a Prefix model instance and 
+    returns a bco.object_id.
+    """
+
+    count = prefix_counter_increment(prefix)
+    bco_identifier = format(count, "06d")
+    bco_id = f"{HOSTNAME}/{prefix}_{bco_identifier}/DRAFT"
+    
+    return bco_id

config/services.py

@@ -13,4 +13,27 @@ def legacy_api_converter(data:dict) ->dict:
     """
 
     _, new_data = data.popitem()
-    return new_data
+    return new_data
+
+def response_constructor(
+        identifier: str,
+        status: str,
+        code: str,
+        message: str=None,
+        data: dict= None
+        )-> dict:
+    """Response Data Proccessing
+    """
+    response_object = {
+	    identifier: {
+            "request_status": status,
+            "status_code": code
+	    }
+    }
+    
+    if data is not None:
+        response_object[identifier]["data"] = data
+    if message is not None:
+        response_object[identifier]["message"] = message
+
+    return response_object

prefix/models.py

@@ -8,10 +8,26 @@ class Prefix(models.Model):
 
     prefix = models.CharField(primary_key=True, max_length=5)
     certifying_key = models.TextField(blank=True, null=True)
-    created = models.DateTimeField(default=timezone.now, blank=True, null=True)
+    created = models.DateTimeField(
+        default=timezone.now,
+        blank=True,
+        null=True
+    )
     description = models.TextField(blank=True, null=True)
-    owner = models.ForeignKey(User, on_delete=models.CASCADE, to_field="username")
-    authorized_groups = models.ManyToManyField(Group, blank=True, related_name='authorized_prefix')
+    owner = models.ForeignKey(
+        User,
+        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"
+    )
 
     def __str__(self):
         """String for representing the BCO model (in Admin site etc.)."""

prefix/services.py

@@ -0,0 +1,26 @@
+#!/usr/bin/env python3
+# prefix/services.py
+
+import re
+from urllib.parse import urlparse
+from django.conf import settings
+from django.utils import timezone
+from biocompute.models import Bco
+from prefix.models import Prefix
+from django.db.models import F
+
+"""Prefix Services
+
+Service functions for working with BCO Prefixes
+"""
+
+def prefix_counter_increment(prefix: Prefix) -> int:
+    """Prefix Counter Increment 
+    
+    Simple incrementing function.
+    Counter for BCO object_id asignment.
+    """
+    
+    Prefix.objects.update(counter=F("counter") + 1)
+    count = prefix.counter
+    return count

test.json

@@ -855,7 +855,8 @@
             "created": "2024-03-14T13:53:59Z",
             "description": "Default prefix for all BioCompute Objects",
             "owner": "AnonymousUser",
-            "authorized_groups": []
+            "authorized_groups": [],
+            "counter": 0
         }
     }
 ]

tests/fixtures/test_data.json

@@ -855,7 +855,8 @@
             "created": "2024-03-14T13:53:59Z",
             "description": "Default prefix for all BioCompute Objects",
             "owner": "AnonymousUser",
-            "authorized_groups": []
+            "authorized_groups": [],
+            "counter": 0
         }
     }
 ]