minor

Dockerfile

@@ -30,12 +30,13 @@ RUN mkdir -p -m 0700 /root/.ssh \
     && ssh-keyscan git.envipath.com >> /root/.ssh/known_hosts
 
 # We'll need access to private repos, let docker make use of host ssh agent and use it like:
-# docker build --ssh default -t envipath/envipy:1.0 .
+# docker build --ssh default -t envipath/envipy-bayer:1.0 .
 RUN --mount=type=ssh \
     uv sync --locked --extra ms-login --extra pepper-plugin
 
 # Now copy source and do a final sync to install the project itself
 # Ensure .dockerignore is reasonable
+COPY bb4g bb4g
 COPY biotransformer biotransformer
 COPY bayer bayer
 COPY bridge bridge

bayer/views.py

@@ -103,20 +103,15 @@ def create_pes_node(request, package_uuid, pathway_uuid):
 
 
 def fetch_pes(request, pes_url) -> dict:
-    proxies = {
-        "http": "http://10.185.190.100:8080",
-        "https": "http://10.185.190.100:8080",
-    }
-
     from epauth.views import get_access_token_from_request
     token = get_access_token_from_request(request)
 
-    if token or True:
+    if token:
         for k, v in s.PES_API_MAPPING.items():
             if pes_url.startswith(k):
                 pes_id = pes_url.split('/')[-1]
 
-                if pes_id == 'dummy' or True:
+                if pes_id == 'dummy':
                     import json
                     res_data = json.load(open(s.BASE_DIR / "fixtures/pes.json"))
                     res_data["pes_url"] = pes_url
@@ -125,7 +120,7 @@ def fetch_pes(request, pes_url) -> dict:
                     headers = {"Authorization": f"Bearer {token['access_token']}"}
                     params = {"pes_reg_entity_corporate_id": pes_id}
 
-                    res = requests.get(v, headers=headers, params=params, proxies=proxies)
+                    res = requests.get(v, headers=headers, params=params, proxies=s.PROXIES or None)
 
                     try:
                         res.raise_for_status()

bb4g/__init__.py

@@ -2,9 +2,11 @@ import json
 import math
 from datetime import datetime
 from typing import List
-
+import enum
 import requests
 from django.conf import settings as s
+from envipy_additional_information import EnviPyModel, UIConfig, WidgetType
+from envipy_additional_information import register
 
 from bridge.contracts import Classifier  # noqa: I001
 from bridge.dto import (
@@ -15,12 +17,36 @@ from bridge.dto import (
     TransformationProductPrediction,
 )  # noqa: I001
 
+class SamplingAlgorithm(enum.Enum):
+    EXACT = "exact"
+
+
+@register("bb4gconfig")
+class BB4GConfig(EnviPyModel):
+    sampling_algorithm: SamplingAlgorithm = SamplingAlgorithm.EXACT
+    cutoff: int = -5
+
+    class UI:
+        title = "BB4G Configuration"
+        sampling_algorithm = UIConfig(
+            widget=WidgetType.SELECT,
+            label="BB4G Sampling Algorithm",
+            order=1,
+            placeholder="If unset defaults to 'exact'"
+        )
+        cutoff = UIConfig(
+            widget=WidgetType.NUMBER,
+            label="BB4G Cutoff",
+            order=2,
+            placeholder="If unset defaults to -5"
+        )
+
 
 # Once stable these will be exposed by enviPy-plugins lib
 class BB4G(Classifier):
-    Config = None
+    Config = BB4GConfig
 
-    def __init__(self, config=None):
+    def __init__(self, config: BB4GConfig | None = None):
         super().__init__(config)
         self.url = f"{s.BB4G_URL}"
 
@@ -29,10 +55,6 @@ class BB4G(Classifier):
             "Authorization": f"Bearer {self.token}",
             "Content-Type": "application/json",
         }
-        self.proxies = {
-            "http": s.HTTP_PROXY,
-            "https": s.HTTPS_PROXY,
-        }
 
     def acquire_token(self):
         BB4G_TENANT_ID = s.BB4G_TENANT_ID
@@ -65,7 +87,7 @@ class BB4G(Classifier):
         started = False
         retries = 0
         while not started and retries < 5:
-            res = requests.post(f"{self.url}/start", headers=header, data={}, proxies=self.proxies)
+            res = requests.post(f"{self.url}/start", headers=header, data={}, proxies=s.PROXIES or None)
 
             if res.status_code == 200:
                 started = True
@@ -140,11 +162,11 @@ class BB4G(Classifier):
         for smi in smiles:
             data = {
                 "smiles": smi,
-                "sampling_alg": "exact",
+                "sampling_alg": self.config.sampling_algorithm.value,
-                "cutoff": -5,
+                "cutoff": self.config.cutoff,
             }
 
-            resp = requests.post(f"{self.url}/compute", headers=header, data=json.dumps(data), proxies=self.proxies)
+            resp = requests.post(f"{self.url}/compute", headers=header, data=json.dumps(data), proxies=s.PROXIES or None)
 
             resp.raise_for_status()
 

bridge/contracts.py

@@ -254,7 +254,15 @@ class Classifier(Plugin):
     def parse_config(cls, data: dict | None = None) -> EnviPyModel | None:
         if cls.Config is None:
             return None
-        return cls.Config(**(data or {}))
+
+        # remove empty strings a.k.a unset params to not overwrite defaults
+        cpy = {}
+        if data is not None:
+            for k, v in data.items():
+                if v != "":
+                    cpy[k] = v
+
+        return cls.Config(**cpy)
 
     @classmethod
     def create(cls, data: dict | None = None):

envipath/settings.py

@@ -143,6 +143,12 @@ if os.environ.get("USE_TEMPLATE_DB", False) == "True":
         "TEMPLATE": os.environ["TEMPLATE_DB"],
     }
 
+CACHES = {
+    "default": {
+        "BACKEND": "django.core.cache.backends.locmem.LocMemCache",
+        "LOCATION": "unique-snowflake",
+    }
+}
 
 # Password validation
 # https://docs.djangoproject.com/en/4.2/ref/settings/#auth-password-validators
@@ -474,3 +480,14 @@ if DATA_POOL_MAPPING:
 else:
     DATA_POOL_MAPPING = {}
 
+PROXIES = {}
+if os.environ.get("HTTP_PROXY"):
+    PROXIES["http"] = os.environ.get("HTTP_PROXY")
+    PROXIES["https"] = os.environ.get("HTTPS_PROXY")
+
+# BB4g
+BB4G_URL = os.environ.get("BB4G_URL")
+BB4G_TENANT_ID = os.environ.get("BB4G_TENANT_ID")
+BB4G_CLIENT_ID = os.environ.get("BB4G_CLIENT_ID")
+BB4G_CLIENT_SECRET = os.environ.get("BB4G_CLIENT_SECRET")
+BB4G_SCOPE = os.environ.get("BB4G_SCOPE")

epauth/urls.py

@@ -5,4 +5,5 @@ from . import views
 urlpatterns = [
     path("entra/login/", views.entra_login, name="entra_login"),
     path("auth/redirect/", views.entra_callback, name="entra_callback"),
+    path("auth/token/", views.get_token, name="get_token"),
 ]

epauth/views.py

@@ -2,9 +2,11 @@ import msal
 from django.conf import settings as s
 from django.contrib.auth import get_user_model
 from django.contrib.auth import login
+from django.http import HttpResponse
 from django.shortcuts import redirect
 
-from epdb.logic import UserManager
+from epdb.logic import UserManager, GroupManager
+from epdb.models import Group
 
 
 def get_msal_app_with_cache(request):
@@ -81,10 +83,12 @@ def entra_callback(request):
     login(request, u)
 
     # EDIT START
+
     # Ensure groups exists in eP
     for id, name in s.ENTRA_SECRET_GROUPS.items():
         if not Group.objects.filter(uuid=id).exists():
-            g = GroupManager.create_group(User.objects.get(username="admin"), name, f"Synced Entra Group {name} ", uuid=id)
+            g = GroupManager.create_group(User.objects.get(username="admin"), name, f"Synced Entra Group {name} ",
+                                          uuid=id)
         else:
             g = Group.objects.get(uuid=id)
         # Ensure its secret
@@ -93,7 +97,8 @@ def entra_callback(request):
 
     for id, name in s.ENTRA_GROUPS.items():
         if not Group.objects.filter(uuid=id).exists():
-            g = GroupManager.create_group(User.objects.get(username="admin"), name, f"Synced Entra Group {name} ", uuid=id)
+            g = GroupManager.create_group(User.objects.get(username="admin"), name, f"Synced Entra Group {name} ",
+                                          uuid=id)
         else:
             g = Group.objects.get(uuid=id)
 
@@ -152,3 +157,9 @@ def get_access_token_from_request(request, scopes=None):
         return result
 
     return None
+
+
+def get_token(request):
+    token = get_access_token_from_request(request)
+    msg = f"{token}"
+    return HttpResponse(msg, content_type='text/plain')

epdb/legacy_api.py

@@ -1,19 +1,17 @@
-import hashlib
 from collections import defaultdict
 from typing import Any, Dict, List, Optional
 
 import jwt
-import requests
-
 import nh3
+import requests
 from django.conf import settings as s
 from django.contrib.auth import get_user_model
+from django.core.cache import cache
 from django.http import HttpResponse, JsonResponse
 from django.shortcuts import redirect
+from jwt import InvalidIssuerError
 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
@@ -51,6 +49,26 @@ from .models import (
 Package = s.GET_PACKAGE_MODEL()
 
 
+def get_cached_jwks(tenant_id: str, force=False) -> Dict:
+    """Get JWKS using Django cache"""
+    cache_key = f"jwks_{tenant_id}"
+
+    jwks = cache.get(cache_key)
+
+    if jwks is None or force:
+        # Cache miss, fetch new keys
+        jwks_uri = f"https://login.microsoftonline.com/{tenant_id}/discovery/v2.0/keys"
+        response = requests.get(jwks_uri)
+        response.raise_for_status()
+
+        jwks = response.json()
+
+        # Cache for 1 hour (3600 seconds)
+        cache.set(cache_key, jwks, 3600)
+
+    return jwks
+
+
 def get_package_for_write(user, package_uuid):
     p = PackageManager.get_package_by_id(user, package_uuid)
     if not PackageManager.writable(user, p):
@@ -68,9 +86,7 @@ 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 = get_cached_jwks(TENANT_ID)
-    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)
 
@@ -78,13 +94,21 @@ def validate_token(token: str) -> dict:
         next(k for k in jwks["keys"] if k["kid"] == header["kid"])
     )
 
+    # Handle V1 and V2 tokens
+    try:
         claims = jwt.decode(
             token,
             public_key,
             algorithms=["RS256"],
             audience=[CLIENT_ID, f"api://{CLIENT_ID}"],
-        issuer=f"https://sts.windows.net/{TENANT_ID}/",
+            issuer=[
+                f"https://sts.windows.net/{TENANT_ID}/",
+                f"https://login.microsoftonline.com/{TENANT_ID}/v2.0"
+            ]
         )
+    except Exception as e:
+        raise ValueError(f"Token verification failed! - {e}")
+
     return claims
 
 

epdb/views.py

@@ -937,12 +937,14 @@ def package_models(request, package_uuid):
                 "requires_rule_packages": True,
                 "requires_data_packages": True,
             },
-            "EnviFormer": {
+        }
+
+        if s.ENVIFORMER_PRESENT:
+            context["model_types"]["EnviFormer"] = {
                 "type": "enviformer",
                 "requires_rule_packages": False,
                 "requires_data_packages": True,
             },
-        }
 
         if s.FLAGS.get("PLUGINS", False):
             for k, v in s.CLASSIFIER_PLUGINS.items():

templates/collections/compounds_paginated.html

@@ -5,7 +5,7 @@
 
 {% block action_button %}
   <div class="flex items-center gap-2">
-    {% if meta.can_edit %}
+    {% if meta.can_edit or not meta.url_contains_package %}
       <button
         type="button"
         class="btn btn-primary btn-sm"

templates/collections/models_paginated.html

@@ -3,7 +3,8 @@
 {% block page_title %}Models{% endblock %}
 
 {% block action_button %}
-  {% if meta.can_edit and meta.enabled_features.MODEL_BUILDING %}
+  {% if meta.can_edit or not meta.url_contains_package %}
+    {% if meta.enabled_features.MODEL_BUILDING %}
       <button
         type="button"
         class="btn btn-primary btn-sm"
@@ -12,6 +13,7 @@
         New Model
       </button>
     {% endif %}
+  {% endif %}
 {% endblock action_button %}
 
 {% block action_modals %}

templates/collections/packages_paginated.html

@@ -3,7 +3,6 @@
 {% block page_title %}Packages{% endblock %}
 
 {% block action_button %}
-  {% if meta.can_edit %}
     <div class="flex items-center gap-2">
       <button
         type="button"
@@ -71,7 +70,6 @@
         </ul>
       </div>
     </div>
-  {% endif %}
 {% endblock action_button %}
 
 {% block action_modals %}

templates/collections/pathways_paginated.html

@@ -3,7 +3,7 @@
 {% block page_title %}Pathways{% endblock %}
 
 {% block action_button %}
-  {% if meta.can_edit %}
+  {% if meta.can_edit or not meta.url_contains_package %}
     <div class="flex items-center gap-2">
       <a
         class="btn btn-primary btn-sm"

templates/collections/reactions_paginated.html

@@ -3,7 +3,7 @@
 {% block page_title %}Reactions{% endblock %}
 
 {% block action_button %}
-  {% if meta.can_edit %}
+  {% if meta.can_edit or not meta.url_contains_package %}
     <button
       type="button"
       class="btn btn-primary btn-sm"

templates/collections/rules_paginated.html

@@ -3,7 +3,7 @@
 {% block page_title %}Rules{% endblock %}
 
 {% block action_button %}
-  {% if meta.can_edit %}
+  {% if meta.can_edit or not meta.url_contains_package %}
     <button
       type="button"
       class="btn btn-primary btn-sm"

templates/collections/scenarios_paginated.html

@@ -11,7 +11,7 @@
 {% endblock action_modals %}
 
 {% block action_button %}
-  {% if meta.can_edit %}
+  {% if meta.can_edit or not meta.url_contains_package  %}
     <button
       type="button"
       class="btn btn-primary btn-sm"

templates/collections/structures_paginated.html

@@ -3,7 +3,7 @@
 {% block page_title %}{{ page_title|default:"Structures" }}{% endblock %}
 
 {% block action_button %}
-  {% if meta.can_edit %}
+  {% if meta.can_edit or not meta.url_contains_package %}
     <button
       type="button"
       class="btn btn-primary btn-sm"