adjusted migration

Initial bayer app

Show Pack Classification

Adjusted docker compose to bayer specifics

Adjusted Dockerfile for Bayer

Adding secret flags to group, add secret pools to packages

Adjusted View for Package creation

Prep configs, added Package Create Modal

wip

More on PES

wip

wip

epdb/legacy_api.py

@@ -1,17 +1,22 @@
+import hashlib
 from collections import defaultdict
 from typing import Any, Dict, List, Optional
 
+import jwt
+import requests
+
 import nh3
 from django.conf import settings as s
 from django.contrib.auth import get_user_model
 from django.http import HttpResponse, JsonResponse
 from django.shortcuts import redirect
 from ninja import Field, Form, Query, Router, Schema
+from ninja.errors import HttpError
+from ninja.security import HttpBearer
 from ninja.security import SessionAuth
 
 from utilities.chem import FormatConverter
 from utilities.misc import PackageExporter
-
 from .logic import (
     EPDBURLParser,
     GroupManager,
@@ -59,7 +64,46 @@ def _anonymous_or_real(request):
     return get_user_model().objects.get(username="anonymous")
 
 
-router = Router(auth=SessionAuth(csrf=False))
+def validate_token(token: str) -> dict:
+    TENANT_ID = s.MS_ENTRA_TENANT_ID
+    CLIENT_ID = s.MS_ENTRA_CLIENT_ID
+
+    # Fetch Microsoft's public keys
+    jwks_uri = f"https://login.microsoftonline.com/{TENANT_ID}/discovery/v2.0/keys"
+    jwks = requests.get(jwks_uri).json()
+
+    header = jwt.get_unverified_header(token)
+
+    public_key = jwt.algorithms.RSAAlgorithm.from_jwk(
+        next(k for k in jwks["keys"] if k["kid"] == header["kid"])
+    )
+
+    claims = jwt.decode(
+        token,
+        public_key,
+        algorithms=["RS256"],
+        audience=[CLIENT_ID, f"api://{CLIENT_ID}"],
+        issuer=f"https://sts.windows.net/{TENANT_ID}/",
+    )
+    return claims
+
+
+class MSBearerTokenAuth(HttpBearer):
+
+    def authenticate(self, request, token):
+        if token is None:
+            return None
+
+        claims = validate_token(token)
+
+        if not User.objects.filter(uuid=claims['oid']).exists():
+            return None
+
+        request.user = User.objects.get(uuid=claims['oid'])
+        return request.user
+
+
+router = Router(auth=MSBearerTokenAuth())
 
 
 class Error(Schema):
@@ -153,21 +197,6 @@ class SimpleModel(SimpleObject):
     identifier: str = "relative-reasoning"
 
 
-################
-# Login/Logout #
-################
-@router.post("/", response={200: SimpleUser, 403: Error}, auth=None)
-def login(request, loginusername: Form[str], loginpassword: Form[str]):
-    from django.contrib.auth import authenticate, login
-
-    email = User.objects.get(username=loginusername).email
-    user = authenticate(username=email, password=loginpassword)
-    if user:
-        login(request, user)
-        return user
-    else:
-        return 403, {"message": "Invalid username and/or password"}
-
 
 ########
 # User #
@@ -1929,13 +1958,16 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
         educts = []
         products = []
 
+        subclasses = CompoundStructure.__subclasses__()
+
         if e.edgeAsSmirks:
             for ed in e.edgeAsSmirks.split(">>")[0].split("\\."):
                 stand_ed = FormatConverter.standardize(ed, remove_stereo=True)
                 educts.append(
                     Node.objects.get(
                         pathway=pw,
-                        default_node_label=CompoundStructure.objects.get(
+                        default_node_label=CompoundStructure.objects.not_instance_of(*subclasses).
+                        get(
                             compound__package=p, smiles=stand_ed
                         ).compound.default_structure,
                     )
@@ -1946,7 +1978,8 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
                 products.append(
                     Node.objects.get(
                         pathway=pw,
-                        default_node_label=CompoundStructure.objects.get(
+                        default_node_label=CompoundStructure.objects.not_instance_of(*subclasses).
+                        get(
                             compound__package=p, smiles=stand_pr
                         ).compound.default_structure,
                     )