Prefix registry (#318)

* Created test_objects_drafts_modify, hasn't passed test yet

* Created test_objects_drafts_modify, hasn't passed test yet

* Created test_objects_drafts_modify, hasn't passed test yet

* new tests

* Update modify_prefix permissions
Changes to be committed:
	modified:   authentication/selectors.py
	modified:   config/fixtures/local_data.json
	modified:   prefix/services.py

* Created and tested test_objects_drafts_modify API

* Fixes for Prefix creation

Changes to be committed:
	modified:   config/services.py
	modified:   prefix/apis.py
	modified:   tests/test_apis/test_api_prefix/test_prefixes_create.py

* Add UserSearch endpoint

Changes to be committed:
	modified:   prefix/apis.py
	modified:   prefix/selectors.py
	modified:   search/apis.py
	modified:   search/urls.py

* Fixes for deployment

 Changes to be committed:
	modified:   .secrets.example
	modified:   admin_only/bco_api.service
	modified:   biocompute/apis.py
	modified:   config/fixtures/test_portal.json
	modified:   config/settings.py
	modified:   tests/fixtures/test_data.json
	modified:   tests/test_apis/test_biocompute/test_objects_drafts_create.py

* test_objects_drafts_publish failed. Kicking back to Hadley for more investigation

* Update bco_api.conf

Changes to be committed:
	modified:   admin_only/bco_api.conf

---------

Co-authored-by: tianywan819 <[email protected]>
Co-authored-by: acoleman29 <[email protected]>

Author: 3 people

.secrets.example

@@ -4,11 +4,12 @@ ANON_KEY=
 
 [SERVER]
 PRODUCTION=
+DEBUG=True
+ALLOWED_HOSTS=
 SERVER_VERSION=
 HOSTNAME=
 HUMAN_READABLE_HOSTNAME=
 PUBLIC_HOSTNAME=
 SERVER_URL=
-#DATABASE=
 DATABASE=
 EMAIL_BACKEND=

admin_only/bco_api.conf

@@ -51,7 +51,7 @@ server {
         return 204;
         }
 
-        root /var/www/bcoeditor/portal/build/;
+        root root /var/www/bcoeditor/portal_userdb/client/build;
         try_files $uri /index.html;
         #try_files $uri $uri/ =404;
     }

admin_only/bco_api.service

@@ -1,10 +1,10 @@
 [Unit]
-Description=BCO Test API gunicorn daemon
+Description=BCODB API gunicorn daemon
 Requires=bco_api.socket
 After=network.target
 
 [Service]
 User=bco_api_user
 Group=nginx
-WorkingDirectory=/var/www/bcoeditor/bco_api/bco_api/
-ExecStart=/var/www/bcoeditor/bco_api/env/bin/gunicorn --access-logfile /var/log/gunicorn/api_stdout.log --log-level=debug --log-file /var/log/gunicorn/api_stderr.log --workers 3 --bind unix:/var/run/bco_api.sock bco_api.wsgi:application
+WorkingDirectory=/var/www/bcoeditor/bco_api/
+ExecStart=/var/www/bcoeditor/bco_api/env/bin/gunicorn --access-logfile /var/log/gunicorn/api_stdout.log --log-level=debug --log-file /var/log/gunicorn/api_stderr.log --workers 3 --bind unix:/var/run/bco_api.sock config.wsgi:application

authentication/selectors.py

@@ -2,10 +2,12 @@
 
 import jwt
 from django.conf import settings
-from django.contrib.auth.models import User, Permission
+from django.contrib.auth.models import User
+from django.db.models import Q
 from authentication.models import Authentication, NewUser
 from rest_framework.authtoken.models import Token
 from prefix.selectors import get_user_prefixes
+from prefix.models import Prefix
 from biocompute.selectors import get_authorized_bcos
 
 def get_anon()-> User:
@@ -70,22 +72,18 @@ def get_user_info(user: User) -> dict:
         A dict with the user information.
     """
 
-    token = Token.objects.get(user=user.pk)
-    other_info = {
-        "permissions": {},
-        "account_creation": "",
-    }
-    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.HOSTNAME,
         "human_readable_hostname": settings.HUMAN_READABLE_HOSTNAME,
         "public_hostname": settings.PUBLIC_HOSTNAME,
-        "token": token.key,
+        "token": Token.objects.get(user=user.pk).key,
         "username": user.username,
-        "other_info": other_info,
+        "permissions": {
+            "owned_prefixes": Prefix.objects.filter(
+                Q(owner=user)
+            ).values_list('prefix', flat=True).distinct(),
+            "permissions": get_user_prefixes(user),
+            "BCOs": get_authorized_bcos(user)
+        },
+        "account_creation": user.date_joined
     }

biocompute/apis.py

@@ -101,11 +101,12 @@ def post(self, request) -> Response:
         data = request.data
         rejected_requests = False
         accepted_requests = False
-        if 'POST_api_objects_draft_create' in request.data:
+        if 'POST_api_objects_drafts_create' in request.data:
             data = legacy_api_converter(request.data)
 
         for index, object in enumerate(data):
-            response_id = object.get("object_id", index)
+            response_id = object["contents"].get("object_id", index)
+            # response_id = object.get("object_id", index)
             bco_prefix = object.get("prefix", index)
             prefix_permitted = user_can_draft_prefix(owner, bco_prefix)
 
@@ -346,7 +347,7 @@ def post(self, request) -> Response:
             data = legacy_api_converter(request.data)
 
         for index, object in enumerate(data):
-            response_id = object["contents"].get("object_id", index)
+            response_id = object.get("object_id", index)
             modify_permitted = user_can_modify_bco(response_id, requester)
 
             if modify_permitted is None:
@@ -556,6 +557,8 @@ def post(self, request) -> Response:
             data = legacy_api_converter(request.data)
 
         for index, object in enumerate(data):
+            import pdb; pdb.set_trace()
+            # response_id = object["contents"].get("object_id", index)
             response_id = object.get("object_id", index)
             bco_instance = user_can_publish_bco(object, requester)
 

config/fixtures/local_data.json

@@ -846,39 +846,39 @@
     },
     {
         "model": "authtoken.token",
-        "pk": "1ef53d4042d14299918a4e1f21d2be128a2a7427",
+        "pk": "0bd55c955fcbfc269f6dc8f61ea107674cafdecb",
         "fields": {
             "user": 5,
             "created": "2024-03-14T15:21:04.318Z"
         }
     },
     {
         "model": "authtoken.token",
-        "pk": "49020e6fb85eb19a15bbdfb5cf6a1a28aaa8c1ce",
+        "pk": "bd97d8cbec1fc7234e11e80957496aefc20c6395",
         "fields": {
             "user": 7,
             "created": "2024-04-03T10:53:08.951Z"
         }
     },
     {
         "model": "authtoken.token",
-        "pk": "705531f3b2fbf80bb5a5b9d0cf4ee663676b4579",
+        "pk": "c400a6076a2dfe7e9906ab86c6ad4574d1d60e03",
         "fields": {
             "user": 4,
             "created": "2024-03-14T15:21:14.996Z"
         }
     },
     {
         "model": "authtoken.token",
-        "pk": "b8e588c4bdfb366420007827054042e8e594ec51",
+        "pk": "627626823549f787c3ec763ff687169206626149",
         "fields": {
             "user": 1,
             "created": "2024-03-14T13:53:45.793Z"
         }
     },
     {
         "model": "authtoken.token",
-        "pk": "ba1a932a6af59930293e087c1633fa60927b6690",
+        "pk": "3f5504d88a5085d0452b19350fb6f82ae7097dd0",
         "fields": {
             "user": 6,
             "created": "2024-03-14T15:21:09.348Z"
@@ -4393,5 +4393,17 @@
             "counter": 7,
             "public": true
         }
+    },
+    {
+        "model": "prefix.prefix",
+        "pk": "HIVE",
+        "fields": {
+            "certifying_key": "lazc=!pr35pau5b2x-x70y3_t++d5^s4cgk=mjo5o3^9zvrzki",
+            "created": "2024-03-14T13:53:59Z",
+            "description": "Test HIVE prefix",
+            "owner": "hivelab",
+            "counter": 0,
+            "public": true
+        }
     }
 ]