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

.gitignore

@@ -143,3 +143,4 @@ server.conf
 static/
 # JetBrains IDEs
 .idea/
+backups

authentication/apis.py

@@ -11,7 +11,6 @@
 from rest_framework.permissions import IsAuthenticated
 from rest_framework.response import Response
 from rest_framework.views import APIView
-from api.scripts.utilities.UserUtils import UserUtils
 from authentication.models import Authentication, NewUser
 from authentication.selectors import (
     check_user_email,
@@ -534,7 +533,7 @@ def post(self, request):
             Token.objects.create(user=request.user)            
             return Response(
                 status=status.HTTP_200_OK,
-                data=UserUtils().get_user_info(username=request.user)
+                data=get_user_info(user=request.user)
             )
 
         except Exception as error:

authentication/migrations/0001_initial.py

@@ -1,8 +1,9 @@
-# Generated by Django 3.2.10 on 2023-03-27 20:46
+# Generated by Django 3.2.13 on 2024-03-14 13:52
 
 from django.conf import settings
 from django.db import migrations, models
 import django.db.models.deletion
+import django.utils.timezone
 
 
 class Migration(migrations.Migration):
@@ -14,6 +15,17 @@ class Migration(migrations.Migration):
     ]
 
     operations = [
+        migrations.CreateModel(
+            name='NewUser',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('email', models.EmailField(max_length=254)),
+                ('temp_identifier', models.TextField(max_length=100)),
+                ('token', models.TextField(blank=True, null=True)),
+                ('hostname', models.TextField(blank=True, null=True)),
+                ('created', models.DateTimeField(default=django.utils.timezone.now)),
+            ],
+        ),
         migrations.CreateModel(
             name='Authentication',
             fields=[

authentication/services.py

@@ -9,6 +9,7 @@
 from django.contrib.auth.models import User, Group
 from django.core.mail import send_mail
 from rest_framework import exceptions, status, serializers
+from rest_framework.authtoken.models import Token
 from rest_framework.response import Response
 from rest_framework_jwt.authentication import BaseAuthentication
 from rest_framework_jwt.settings import api_settings
@@ -173,6 +174,7 @@ def send_new_user_email(user_info: dict) -> 0:
     print("Email signal sent")
     return 0
 
+@transaction.atomic
 def create_bcodb_user(email: str) -> User:
     """Create BCODB user
     """
@@ -183,10 +185,9 @@ def create_bcodb_user(email: str) -> User:
     )
     user.set_unusable_password()
     user.full_clean()
+    Token.objects.create(user=user)
     user.save()
-    user.groups.add(Group.objects.get(name="bco_drafter"))
-    user.groups.add(Group.objects.get(name="bco_publisher"))
-
+
     return user
 
 

biocompute/migrations/0001_initial.py

@@ -0,0 +1,33 @@
+# Generated by Django 3.2.13 on 2024-03-14 13:52
+
+from django.conf import settings
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    initial = True
+
+    dependencies = [
+        ('auth', '0012_alter_user_first_name_max_length'),
+        ('prefix', '0001_initial'),
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='Bco',
+            fields=[
+                ('object_id', models.TextField(primary_key=True, serialize=False)),
+                ('contents', models.JSONField()),
+                ('state', models.CharField(choices=[('REFERENCED', 'referenced'), ('PUBLISHED', 'published'), ('DRAFT', 'draft'), ('DELETE', 'delete')], default='DRAFT', max_length=20)),
+                ('last_update', models.DateTimeField()),
+                ('access_count', models.IntegerField(default=0)),
+                ('authorized_groups', models.ManyToManyField(blank=True, to='auth.Group')),
+                ('authorized_users', models.ManyToManyField(blank=True, related_name='authorized_bcos', to=settings.AUTH_USER_MODEL)),
+                ('owner', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='owned_bcos', to=settings.AUTH_USER_MODEL)),
+                ('prefix', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='prefix.prefix')),
+            ],
+        ),
+    ]

docs/refactor.md

@@ -6,4 +6,12 @@
 ## Items to look at later
 - `authentication.apis.RegisterUserNoVerificationAPI` has no swagger or tests
 - fix email and secrets
+<<<<<<< Local Changes
+- install a `test_template` for Swagger responses
+- provide example values that are usable for testing APIs.
+- certifying key for prefix as a JWT? 
+- owner = models.ForeignKey(
+        User,
+        on_delete=models.CASCADE, 
 
+- need tests for token

prefix/migrations/0001_initial.py

@@ -0,0 +1,30 @@
+# Generated by Django 3.2.13 on 2024-03-14 13:14
+
+from django.conf import settings
+from django.db import migrations, models
+import django.db.models.deletion
+import django.utils.timezone
+
+
+class Migration(migrations.Migration):
+
+    initial = True
+
+    dependencies = [
+        ('auth', '0012_alter_user_first_name_max_length'),
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='Prefix',
+            fields=[
+                ('prefix', models.CharField(max_length=5, primary_key=True, serialize=False)),
+                ('certifying_key', models.TextField(blank=True, null=True)),
+                ('created', models.DateTimeField(blank=True, default=django.utils.timezone.now, null=True)),
+                ('description', models.TextField(blank=True, null=True)),
+                ('authorized_groups', models.ManyToManyField(blank=True, related_name='authorized_prefix', to='auth.Group')),
+                ('owner', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, to_field='username')),
+            ],
+        ),
+    ]

search/selectors.py

@@ -4,13 +4,10 @@
 Set of selector functions to handle searching the BCODB
 """
 
-from api.models import BCO
+from biocompute.models import Bco
 from django.db.models import QuerySet
 from django.db.models.query import QuerySet
 from django.contrib.auth.models import User
-from guardian.shortcuts import get_objects_for_user
-from itertools import chain
-from api.scripts.utilities.UserUtils import UserUtils
 
 return_values = [
           "contents",