Dockerfile

@@ -85,6 +85,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     libxext6 \
     libfontconfig1 \
     nano \
+    openjdk-21-jre-headless \
     && rm -rf /var/lib/apt/lists/*
 
 RUN useradd -ms /bin/bash django

bayer/views.py

@@ -8,7 +8,7 @@ from django.shortcuts import redirect
 
 from bayer.models import PESCompound
 from epdb.logic import PackageManager
-from epdb.models import Pathway, Node
+from epdb.models import Pathway, Node, Group
 from epdb.views import _anonymous_or_real, error
 from utilities.decorators import package_permission_required
 
@@ -18,6 +18,23 @@ Package = s.GET_PACKAGE_MODEL()
 logger = logging.getLogger(__name__)
 
 
+def has_secret_group(user):
+    """
+    Determines if the specified user belongs to any secret group.
+
+    This function checks whether the given user is a member of any group
+    that is marked as secret.
+
+    Args:
+        user: The user for whom the check is performed.
+
+    Returns:
+        bool: True if the user belongs to at least one secret group,
+        False otherwise.
+    """
+    return Group.objects.filter(secret=True, user_member=user).exists()
+
+
 @package_permission_required()
 def create_pes(request, package_uuid):
     current_user = _anonymous_or_real(request)
@@ -38,7 +55,7 @@ def create_pes(request, package_uuid):
 
         if pes_link:
             try:
-                pes_data = fetch_pes(request, pes_link)
+                pes_data = fetch_pes(request, pes_link, current_user)
             except ValueError as e:
                 return error(
                     request,
@@ -98,7 +115,7 @@ def create_pes_node(request, package_uuid, pathway_uuid):
 
         if pes_link:
             try:
-                pes_data = fetch_pes(request, pes_link)
+                pes_data = fetch_pes(request, pes_link, current_user)
             except ValueError as e:
                 return error(
                     request,
@@ -157,53 +174,82 @@ def create_pes_node(request, package_uuid, pathway_uuid):
         return HttpResponseNotAllowed(["POST"])
 
 
-def fetch_pes(request, pes_url) -> dict:
-    from epauth.views import get_access_token_from_request
-    token = get_access_token_from_request(request)
+def get_application_token(prod: bool) -> str:
+    scope = f"{s.PROD_PES_SCOPE if prod else s.NON_PROD_PES_SCOPE}/.default"
 
-    if token is None:
-        token = pes_url.split('/')[-1] == 'dummy'
+    url = f"https://login.microsoftonline.com/{s.MS_TENANT_ID}/oauth2/v2.0/token"
+    data = {
+        "grant_type": "client_credentials",
+        "client_id": s.MS_ENTRA_CLIENT_ID,
+        "client_secret": s.MS_ENTRA_CLIENT_SECRET,
+        "scope": scope,
+    }
 
-    if token:
-        for k, v in s.PES_API_MAPPING.items():
-            if pes_url.startswith(k):
-                pes_id = pes_url.split('/')[-1]
+    try:
+        response = requests.post(url, data=data)
+        response.raise_for_status()
+        return response.json()["access_token"]
+    except requests.exceptions.HTTPError as e:
+        logger.error(f"Could not fetch application token: {e}")
+        raise ValueError(f"Could not fetch application token!")
 
-                if pes_id == 'dummy':
-                    import json
-                    res_data = json.load(open(s.BASE_DIR / "fixtures/pes.json"))
+
+def fetch_pes(request, pes_url, user) -> dict:
+
+    for k, v in s.PES_API_MAPPING.items():
+        if pes_url.startswith(k):
+
+            prod = "cropkey-np" not in pes_url
+
+            pes_id = pes_url.split('/')[-1]
+
+            if pes_id == 'dummy':
+                import json
+                res_data = json.load(open(s.BASE_DIR / "fixtures/pes.json"))
+                res_data["pes_url"] = pes_url
+                return res_data
+            else:
+                headers = {
+                    "accept": "*/*",
+                    "authorization": "Bearer " + get_application_token(prod),
+                }
+
+                # Restrict request if user is not part of any secret group
+                if not has_secret_group(user):
+                    headers["app-classification-level-restriction"] = "restrict-pes-secret-structure-access"
+
+
+                params = {"pes_reg_entity_corporate_id": pes_id}
+
+                res = requests.get(v, headers=headers, params=params, proxies=s.PROXIES or None)
+
+                try:
+                    res.raise_for_status()
+                    pes_data = res.json()
+
+                    # Handle missing response
+                    if "detail" in pes_data and "The following PES Reg Entities Corporate Ids could not be found" in pes_data["detail"]:
+                        raise ValueError(f"PES with id {pes_id} not found")
+
+                    # Ensure we have a entity
+                    if len(pes_data) == 0:
+                        raise ValueError(f"PES with id {pes_id} not found")
+
+                    res_data = pes_data[0]
                     res_data["pes_url"] = pes_url
                     return res_data
-                else:
-                    headers = {"Authorization": f"Bearer {token['access_token']}"}
-                    params = {"pes_reg_entity_corporate_id": pes_id}
 
-                    res = requests.get(v, headers=headers, params=params, proxies=s.PROXIES or None)
+                except requests.exceptions.HTTPError as e:
+                    raise ValueError(f"Error fetching PES with id {pes_id}: {e}")
 
-                    try:
-                        res.raise_for_status()
-                        pes_data = res.json()
-
-                        if len(pes_data) == 0:
-                            raise ValueError(f"PES with id {pes_id} not found")
-
-                        res_data = pes_data[0]
-                        res_data["pes_url"] = pes_url
-                        return res_data
-
-                    except requests.exceptions.HTTPError as e:
-                        raise ValueError(f"Error fetching PES with id {pes_id}: {e}")
-        else:
-            raise ValueError(f"Unknown URL {pes_url}")
-    else:
-        raise ValueError("Could not fetch access token from request.")
+    raise ValueError(f"Unknown URL {pes_url}")
 
 
 def visualize_pes(request):
     pes_link = request.GET.get('pesLink')
 
     if pes_link:
-        pes_data = fetch_pes(request, pes_link)
+        pes_data = fetch_pes(request, pes_link, request.user)
 
         representations = pes_data.get('representations')
 

epauth/views.py

@@ -9,7 +9,7 @@ from django.shortcuts import redirect
 
 from epdb.logic import UserManager, GroupManager
 from epdb.models import Group
-from epdb.views import get_remote_address
+from epdb.views import get_remote_address, error
 
 auth_log = logging.getLogger("auth")
 
@@ -72,6 +72,15 @@ def entra_callback(request):
 
     claims = result["id_token_claims"]
 
+    if claims.get("roles") is None or claims.get("roles") == [] or "envipath_registered_user" not in claims.get("roles"):
+        auth_log.error(f"Login attempt by {get_remote_address(request)} failed due to missing role")
+        return error(
+            request,
+            "Login Failed",
+            "The user is not authenticated. A reason for this might be a missing assignment to the respective enviPath group.",
+            403,
+        )
+
     user_name = claims.get("name")
     # preferred_username is a fallback for 2nd CWID
     user_email = claims.get("emailaddress", claims.get("email", claims.get("preferred_username")))

epdb/legacy_api.py

@@ -889,7 +889,7 @@ def create_package_compound(
             from bayer.models import PESCompound
 
             try:
-                pes_data = fetch_pes(request, c.pesLink)
+                pes_data = fetch_pes(request, c.pesLink, request.user)
             except ValueError as e:
                 return 400, {"message": f"Could not fetch PES data for {c.pesLink}"}
 
@@ -2014,7 +2014,7 @@ def add_pathway_node(request, package_uuid, pathway_uuid, n: Form[CreateNode]):
             from bayer.models import PESCompound
 
             try:
-                pes_data = fetch_pes(request, n.pesLink)
+                pes_data = fetch_pes(request, n.pesLink, request.user)
             except ValueError as e:
                 return 400, {"message": f"Could not fetch PES data for {n.pesLink}"}