App Integration Secret Packages

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: #2

bayer/admin.py

@@ -3,7 +3,7 @@ from django.contrib import admin
 # Register your models here.
 from .models import (
     PESCompound,
-    PESStructure
+    PESStructure, NewsEntry
 )
 
 
@@ -15,5 +15,10 @@ class PESStructureAdmin(admin.ModelAdmin):
     pass
 
 
+class NewsEntryAdmin(admin.ModelAdmin):
+    pass
+
+
 admin.site.register(PESCompound, PESCompoundAdmin)
 admin.site.register(PESStructure, PESStructureAdmin)
+admin.site.register(NewsEntry, NewsEntryAdmin)

bayer/context_processors.py

@@ -0,0 +1,25 @@
+"""
+Context processors for enviPy application.
+
+Context processors automatically make variables available to all templates.
+"""
+
+
+from django.utils import timezone
+from .models import NewsEntry
+
+
+def news_entries_context(request):
+    """
+    Provides package data for the search modal which is included globally
+    in framework_modern.html.
+
+    Returns:
+        dict: Context dictionary with reviewed and unreviewed packages
+    """
+
+
+    qs = NewsEntry.objects.filter(publication_date__lte=timezone.now()).order_by('-publication_date')[:3]
+    return {
+        "news_entries": qs,
+    }

bayer/migrations/0005_newsentry.py

@@ -0,0 +1,29 @@
+# Generated by Django 6.0.3 on 2026-10-16 07:50
+
+import django.db.models.deletion
+import uuid
+from django.conf import settings
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('bayer', '0004_package_shareable'),
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='NewsEntry',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('uuid', models.UUIDField(default=uuid.uuid4, unique=True, verbose_name='UUID of this object')),
+                ('url', models.TextField(null=True, unique=True, verbose_name='URL')),
+                ('title', models.TextField(verbose_name='Title')),
+                ('publication_date', models.DateTimeField(verbose_name='Date')),
+                ('content', models.TextField(verbose_name='Content')),
+                ('author', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to=settings.AUTH_USER_MODEL)),
+            ],
+        ),
+    ]

bayer/migrations/0006_remove_newsentry_url.py

@@ -0,0 +1,17 @@
+# Generated by Django 6.0.3 on 2026-10-16 07:59
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('bayer', '0005_newsentry'),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name='newsentry',
+            name='url',
+        ),
+    ]

bayer/migrations/0007_alter_newsentry_publication_date.py

@@ -0,0 +1,19 @@
+# Generated by Django 6.0.3 on 2026-11-09 21:43
+
+import django.utils.timezone
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('bayer', '0006_remove_newsentry_url'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='newsentry',
+            name='publication_date',
+            field=models.DateTimeField(default=django.utils.timezone.now, verbose_name='Date'),
+        ),
+    ]

bayer/models.py

@@ -1,10 +1,12 @@
 from typing import List
+from uuid import uuid4
 import urllib.parse
 import nh3
 from django.conf import settings as s
 from django.db import models, transaction
 from django.db.models import QuerySet
 from django.urls import reverse
+from django.utils import timezone
 
 from epdb.models import (
     EnviPathModel,
@@ -27,7 +29,7 @@ class Package(EnviPathModel):
 
     class Classification(models.IntegerChoices):
         INTERNAL = 0, "Internal"
-        RESTRICTED = 10 , "Restricted"
+        RESTRICTED = 10, "Restricted"
         SECRET = 20, "Secret"
 
     classification_level = models.IntegerField(
@@ -109,7 +111,7 @@ class PESCompound(Compound):
     @staticmethod
     @transaction.atomic
     def create(
-        package: "Package", pes_data: dict, name: str = None, description: str = None, *args, **kwargs
+            package: "Package", pes_data: dict, name: str = None, description: str = None, *args, **kwargs
     ) -> "Compound":
 
         pes_url = pes_data["pes_url"]
@@ -161,7 +163,6 @@ class PESCompound(Compound):
                 normalized_structure=True,
             )
 
-
         cs = PESStructure.create(
             c,
             pes_url,
@@ -218,13 +219,13 @@ class PESStructure(CompoundStructure):
 
     @transaction.atomic
     def add_structure(
-        self,
-        smiles: str,
-        name: str = None,
-        description: str = None,
-        default_structure: bool = False,
-        *args,
-        **kwargs,
+            self,
+            smiles: str,
+            name: str = None,
+            description: str = None,
+            default_structure: bool = False,
+            *args,
+            **kwargs,
     ) -> "CompoundStructure":
         raise ValueError("Not supported!")
 
@@ -236,3 +237,23 @@ class PESStructure(CompoundStructure):
             "image": f"{reverse('depict_pes')}?pesLink={urllib.parse.quote(self.pes_link)}",
             "image_type": "png",
         }
+
+
+class NewsEntry(models.Model):
+    uuid = models.UUIDField(
+        null=False, blank=False, verbose_name="UUID of this object", unique=True, default=uuid4
+    )
+    title = models.TextField(verbose_name="Title")
+    publication_date = models.DateTimeField(verbose_name="Date", default=timezone.now)
+    content = models.TextField(verbose_name="Content")
+    author = models.ForeignKey("epdb.User", on_delete=models.SET_NULL, blank=True, null=True)
+
+    @property
+    def url(self):
+        return f"{s.SERVER_URL}/news/{self.uuid}"
+
+    def save(self, *args, **kwargs):
+        if not self.url:
+            self.url = self._url()
+
+        super().save(*args, **kwargs)

bayer/templates/modals/collections/new_pes_modal.html

@@ -36,8 +36,8 @@
       img.onerror = () => {
         this.pesVizHtml = `
           <div class='alert alert-error' role='alert'>
-            <h4 class='alert-heading'>Could not render PES!</h4>
-            <p>Could not render PES - Do you have access?</p>
+            <h4 class='alert-heading'>Failed to fetch this PES!</h4>
+            <p>Either the PES-ID is incorrect, or you're missing sufficient permissions to access this (potentially secret) item. In case you're missing permissions you can request the entitlement cs.u.enviPath_secret_data_user_group on go/idnow to gain access.</p>
           </div>`;
       };
     },

bayer/templates/objects/news_entry.html

@@ -0,0 +1,47 @@
+
+{% extends "framework_modern.html" %}
+
+{% block content %}
+  <div class="mx-auto max-w-4xl px-4 py-8">
+    {# Header / Title row #}
+    <div class="mb-6 flex items-center justify-between">
+      <h1 class="text-2xl font-bold">{{ news_entry.title }}</h1>
+    </div>
+
+    {# Meta info card #}
+    <div class="card bg-base-100 shadow mb-6">
+      <div class="card-body">
+        <div class="grid grid-cols-1 gap-4 sm:grid-cols-2">
+          <div>
+            <span class="text-sm font-semibold text-base-content/60">Published</span>
+            <p class="mt-1">{{ news_entry.publication_date|date:"N j, Y, P" }}</p>
+          </div>
+          <div>
+            <span class="text-sm font-semibold text-base-content/60">Author</span>
+            <p class="mt-1">
+              {% if news_entry.author %}
+                {{ news_entry.author.get_full_name|default:news_entry.author.username }}
+              {% else %}
+                <span class="text-base-content/40 italic">Unknown</span>
+              {% endif %}
+            </p>
+          </div>
+        </div>
+      </div>
+    </div>
+
+    {# Content card #}
+    <div class="card bg-base-100 shadow">
+      <div class="card-body prose max-w-none">
+        {{ news_entry.content|safe }}
+      </div>
+    </div>
+
+    {# Back link #}
+    <div class="mt-6">
+      <a href="javascript:history.back()" class="btn btn-ghost btn-sm">
+        ← Back
+      </a>
+    </div>
+  </div>
+{% endblock content %}

bayer/urls.py

@@ -16,4 +16,5 @@ urlpatterns = [
         v.create_pes_node,
         name="create pes node",
     ),
+    re_path(rf"^news/(?P<news_entry_uuid>{UUID})$", v.news_detail, name="news detail"),
 ]

bayer/views.py

@@ -4,12 +4,12 @@ import logging
 import requests
 from django.conf import settings as s
 from django.http import HttpResponse, HttpResponseBadRequest, HttpResponseNotAllowed
-from django.shortcuts import redirect
+from django.shortcuts import redirect, render
 
-from bayer.models import PESCompound
+from bayer.models import PESCompound, NewsEntry
 from epdb.logic import PackageManager
 from epdb.models import Pathway, Node, Group
-from epdb.views import _anonymous_or_real, error
+from epdb.views import _anonymous_or_real, get_base_context, error
 from utilities.decorators import package_permission_required
 
 Package = s.GET_PACKAGE_MODEL()
@@ -18,7 +18,13 @@ Package = s.GET_PACKAGE_MODEL()
 logger = logging.getLogger(__name__)
 
 
-def has_secret_group(user):
+def has_pes_allowance(user):
+    if user.principal_type == user.PrincipalType.APP:
+        return user.app_details.pes_allowance != user.app_details.PESAllowance.NONE
+
+    return True
+
+def has_secret_pes_allowance(user):
     """
     Determines if the specified user belongs to any secret group.
 
@@ -32,6 +38,9 @@ def has_secret_group(user):
         bool: True if the user belongs to at least one secret group,
         False otherwise.
     """
+    if user.principal_type == user.PrincipalType.APP:
+        return user.app_details.pes_allowance == user.app_details.PESAllowance.SECRET
+
     return Group.objects.filter(secret=True, user_member=user).exists()
 
 
@@ -196,6 +205,10 @@ def get_application_token(prod: bool) -> str:
 
 def fetch_pes(request, pes_url, user) -> dict:
 
+    if not has_pes_allowance(user):
+        logger.info(f"User {user.username} does not have permission to fetch PESs")
+        raise ValueError(f"User {user.username} does not have permission to fetch PESs")
+
     for k, v in s.PES_API_MAPPING.items():
         if pes_url.startswith(k):
 
@@ -215,7 +228,7 @@ def fetch_pes(request, pes_url, user) -> dict:
                 }
 
                 # Restrict request if user is not part of any secret group
-                if not has_secret_group(user):
+                if not has_secret_pes_allowance(user):
                     headers["app-classification-level-restriction"] = "restrict-pes-secret-structure-access"
 
 
@@ -257,3 +270,12 @@ def visualize_pes(request):
             if rep.get('type') == 'color':
                 image_data = base64.b64decode(rep.get('base64').replace("data:image/png;base64,", ""))
                 return HttpResponse(image_data, content_type="image/png")
+
+
+def news_detail(request, news_entry_uuid):
+    current_user = _anonymous_or_real(request)
+    context = get_base_context(request, current_user)
+
+    context["entry"] = NewsEntry.objects.get(uuid=news_entry_uuid)
+
+    return render(request, "objects/news_entry.html", context)

bb4g/__init__.py

@@ -29,6 +29,8 @@ class SamplingAlgorithm(enum.Enum):
 class BB4GConfig(EnviPyModel):
     sampling_algorithm: SamplingAlgorithm = SamplingAlgorithm.EXACT
     cutoff: int = -5
+    model: str = "rat"
+    mode: str | None = None
 
     class UI:
         title = "BB4G Configuration"
@@ -44,6 +46,18 @@ class BB4GConfig(EnviPyModel):
             order=2,
             placeholder="If unset defaults to -5"
         )
+        model = UIConfig(
+            widget=WidgetType.TEXT,
+            label="BB4G Model",
+            order=3,
+            placeholder="If unset defaults to rat"
+        )
+        mode = UIConfig(
+            widget=WidgetType.TEXT,
+            label="BB4G Mode",
+            order=4,
+            placeholder="If unset defaults to None"
+        )
 
 
 # Once stable these will be exposed by enviPy-plugins lib
@@ -167,6 +181,8 @@ class BB4G(Classifier):
                 "smiles": smi,
                 "sampling_alg": self.config.sampling_algorithm.value,
                 "cutoff": self.config.cutoff,
+                "model": self.config.model,
+                "mode": self.config.mode,
             }
 
             retries = 0

envipath/settings.py

@@ -114,6 +114,7 @@ TEMPLATES = [
                 "django.contrib.auth.context_processors.auth",
                 "django.contrib.messages.context_processors.messages",
                 "epdb.context_processors.package_context",
+                "bayer.context_processors.news_entries_context"
             ],
         },
     },

epauth/views.py

@@ -102,7 +102,7 @@ def entra_callback(request):
 
     else:
         auth_log.info(f"Registering {user_name} with OID {user_oid}")
-        u = UserManager.create_user(user_name, user_email, None, uuid=user_oid, is_active=True)
+        u = UserManager.create_user(user_name, user_email, None, uuid=user_oid, is_active=True, add_to_group=False)
         registered = True
 
     auth_log.info(f"User {user_name} {'(admin) ' if u.is_superuser else ''}with OID {user_oid} successfully logged in as {u.username} from {get_remote_address(request)}")

epdb/admin.py

@@ -6,6 +6,7 @@ from django.contrib import messages
 
 from .models import (
     AdditionalInformation,
+    AppDetails,
     ClassifierPluginModel,
     Compound,
     CompoundStructure,
@@ -40,6 +41,10 @@ class AdditionalInformationAdmin(admin.ModelAdmin):
     pass
 
 
+class AppDetailsAdmin(admin.ModelAdmin):
+    pass
+
+
 class UserAdmin(admin.ModelAdmin):
     list_display = [
         "username",
@@ -282,3 +287,4 @@ admin.site.register(Setting, SettingAdmin)
 admin.site.register(Scenario, ScenarioAdmin)
 admin.site.register(ExternalDatabase, ExternalDatabaseAdmin)
 admin.site.register(ExternalIdentifier, ExternalIdentifierAdmin)
+admin.site.register(AppDetails, AppDetailsAdmin)

epdb/legacy_api.py

@@ -5,6 +5,7 @@ from typing import Any, Dict, List, Optional
 import jwt
 import nh3
 import requests
+from django.db import transaction
 from django.conf import settings as s
 from django.contrib.auth import get_user_model
 from django.core.cache import cache
@@ -43,7 +44,7 @@ from .models import (
     Scenario,
     SimpleAmbitRule,
     User,
-    UserPackagePermission,
+    UserPackagePermission, AppDetails,
 )
 from .views import delete_with_log, get_remote_address
 
@@ -122,7 +123,6 @@ def validate_token(token: str) -> dict:
 class MSBearerTokenAuth(HttpBearer):
 
     def authenticate(self, request, token):
-
         auth_log.info(f"Authentication request by {get_remote_address(request)}")
 
         if token is None:
@@ -130,6 +130,11 @@ class MSBearerTokenAuth(HttpBearer):
 
         claims = validate_token(token)
 
+        if claims.get("roles") is None or claims.get("roles") == [] or "envipath_registered_user" not in claims.get(
+                "roles"):
+            auth_log.error(f"API authentication attempt by {get_remote_address(request)} failed due to missing role")
+            return None
+
         if not User.objects.filter(uuid=claims['oid']).exists():
             auth_log.info(f"Authentication request by {get_remote_address(request)} failed!")
             return None
@@ -564,7 +569,7 @@ class UpdatePackage(Schema):
     write: str | None = None
 
 
-@router.post("/package/{uuid:package_uuid}", response={200: PackageSchema | Any, 400: Error})
+@router.post("/package/{uuid:package_uuid}", response={200: PackageSchema | Any, 400: Error, 403: Error})
 def update_package(request, package_uuid, pack: Form[UpdatePackage]):
     try:
         p = get_package_for_write(request.user, package_uuid)
@@ -590,6 +595,9 @@ def update_package(request, package_uuid, pack: Form[UpdatePackage]):
                 grantee = GroupManager.get_group_lp(pack.ppsURI)
             else:
                 grantee = UserManager.get_user_lp(pack.ppsURI)
+                if grantee.principal_type == request.user.PrincipalType.APP:
+                    if not request.user.is_superuser:
+                        return 403, {"message": "You are not allowed to grant permissions to an app!"}
 
             PackageManager.grant_read(request.user, p, grantee)
             return HttpResponse(status=200)
@@ -598,6 +606,9 @@ def update_package(request, package_uuid, pack: Form[UpdatePackage]):
                 grantee = GroupManager.get_group_lp(pack.ppsURI)
             else:
                 grantee = UserManager.get_user_lp(pack.ppsURI)
+                if grantee.principal_type == request.user.PrincipalType.APP:
+                    if not request.user.is_superuser:
+                        return 403, {"message": "You are not allowed to grant permissions to an app!"}
 
             PackageManager.grant_write(request.user, p, grantee)
             return HttpResponse(status=200)
@@ -2148,6 +2159,7 @@ class CreateEdge(Schema):
     products: str | None = None  # Node URIs comma sep
     multistep: str | None = None
     edgeReason: str | None = None
+    probability: float | None = None
 
 
 @router.post(
@@ -2215,6 +2227,10 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
             multi_step=multi_step,
         )
 
+        if e.probability:
+            new_e.kv["probability"] = e.probability
+            new_e.save()
+
         # Update depths as sideeffect of above operation
         pw.update_depths()
 
@@ -2473,3 +2489,79 @@ def export(request, q: Query[PackageExportInSchema]):
         return 403, {
             "message": f"Exporting Package with id {q.package_uuid} failed due to insufficient rights!"
         }
+
+
+class RegisterApplicationInSchema(Schema):
+    oid: str
+    client_id: str
+    name: str
+    secret: bool = False
+    data_pool_uuid: str | None = None
+    pes: str | None
+
+
+@router.post("/integration", response={200: Any, 403: Error})
+@transaction.atomic
+def register_app(request, app: Form[RegisterApplicationInSchema]):
+    try:
+        user = request.user
+        if user.is_superuser:
+            user_name = f"APP_{app.oid}"
+            user_email = f"{app.oid}@bayer.com"
+            u = UserManager.create_user(user_name, user_email, None, uuid=app.oid, is_active=True, add_to_group=False)
+
+            # Adjust objects
+            u.principal_type = User.PrincipalType.APP
+
+            if app.pes:
+                pes_choice = next(
+                    choice for choice in AppDetails.PESAllowance
+                    if choice.label.lower() == app.pes.lower()
+                )
+
+                if pes_choice is None:
+                    pes_choice = AppDetails.PESAllowance.NONE
+            else:
+                pes_choice = AppDetails.PESAllowance.NONE
+
+            if app.data_pool_uuid is not None:
+                if not Group.objects.filter(uuid=app.data_pool_uuid, secret=True).exists():
+                    return 400, {"message": f"Group with id {app.data_pool_uuid} does not exist!"}
+
+                data_pool = Group.objects.get(uuid=app.data_pool_uuid, secret=True)
+            else:
+                data_pool = None
+
+            app_details = AppDetails.objects.create(
+                owner=user,
+                client_id=app.client_id,
+                display_name=app.name,
+                secret_allowed=app.secret,
+                data_pool=data_pool,
+                pes_allowance=pes_choice,
+            )
+            u.app_details = app_details
+
+            u.save()
+
+            # Add the integration to the "All enviPath Users" Group
+            all_envipath_users = Group.objects.get(name="All enviPath Users")
+            if not all_envipath_users.user_member.contains(u):
+                all_envipath_users.user_member.add(u)
+
+            if app.secret:
+                if app.data_pool_uuid is None or app.data_pool_uuid.strip() == "":
+                    return 400, {"message": "Secret is only allowed if data pool is specified!"}
+
+                default_package = u.default_package
+                default_package.data_pool = Group.objects.get(uuid=app.data_pool_uuid, secret=True)
+                default_package.classification_level = default_package.Classification.SECRET
+                default_package.save()
+
+            return 200, {"message": "Application registered successfully"}
+        else:
+            raise ValueError("Only superusers can register apps")
+    except ValueError as e:
+        return 403, {
+            "message": f"Registering application failed due to {e}"
+        }

epdb/logic.py

@@ -220,11 +220,14 @@ class UserManager(object):
             u.save()
 
         if add_to_group:
-            g = Group.objects.get(public=True, name="enviPath Users")
-            g.user_member.add(u)
-            g.save()
-            u.default_group = g
-            u.save()
+            if Group.objects.filter(public=True, name="enviPath Users").exists():
+                g = Group.objects.get(public=True, name="enviPath Users")
+                g.user_member.add(u)
+                g.save()
+                u.default_group = g
+                u.save()
+            else:
+                logger.info(f"add_to_group was set to True but no public group named 'enviPath Users' exists.")
 
         return u
 
@@ -373,9 +376,12 @@ class PackageManager(object):
         groups = GroupManager.get_groups(user)
 
         # EDIT START
-
         if package.classification_level == Package.Classification.SECRET:
-            if package.data_pool not in groups:
+            if user.principal_type == user.PrincipalType.APP:
+                if not user.app_details.secret_allowed or package.data_pool != user.app_details.data_pool:
+                    return False
+
+            elif package.data_pool not in groups:
                 return False
 
         # EDIT END
@@ -437,6 +443,10 @@ class PackageManager(object):
     @staticmethod
     def check_package_classification(user, pack: Package):
         if pack.classification_level == Package.Classification.SECRET:
+            if user.principal_type == user.PrincipalType.APP:
+                if pack.data_pool == user.app_details.data_pool:
+                    return pack
+
             if pack.data_pool.user_member.filter(id=user.id).exists():
                 return pack
 
@@ -581,6 +591,9 @@ class PackageManager(object):
         if caller_perm != Permission.ALL[0] and not caller.is_superuser:
             raise ValueError("Only owner are allowed to modify permissions")
 
+        if isinstance(grantee, Group) and package.classification_level == package.Classification.SECRET:
+            raise ValueError("Cannot grant permissions to a Group on a secret package")
+
         data = {
             "package": package,
         }

epdb/migrations/0031_user_principal_type_appdetails_user_app_details.py

@@ -0,0 +1,34 @@
+# Generated by Django 6.0.3 on 2026-10-07 08:08
+
+import django.db.models.deletion
+from django.conf import settings
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('epdb', '0030_auto_20260814_0741'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='user',
+            name='principal_type',
+            field=models.IntegerField(choices=[(0, 'Internal'), (10, 'Restricted')], default=0),
+        ),
+        migrations.CreateModel(
+            name='AppDetails',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('client_id', models.TextField(verbose_name='Client ID')),
+                ('display_name', models.TextField(verbose_name='Display Name')),
+                ('owner', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)),
+            ],
+        ),
+        migrations.AddField(
+            model_name='user',
+            name='app_details',
+            field=models.OneToOneField(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='epdb.appdetails'),
+        ),
+    ]

epdb/migrations/0032_alter_user_principal_type.py

@@ -0,0 +1,18 @@
+# Generated by Django 6.0.3 on 2026-10-07 08:56
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('epdb', '0031_user_principal_type_appdetails_user_app_details'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='user',
+            name='principal_type',
+            field=models.IntegerField(choices=[(0, 'User'), (10, 'App')], default=0),
+        ),
+    ]

epdb/migrations/0033_remove_user_app_details.py

@@ -0,0 +1,17 @@
+# Generated by Django 6.0.3 on 2026-10-07 08:57
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('epdb', '0032_alter_user_principal_type'),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name='user',
+            name='app_details',
+        ),
+    ]

epdb/migrations/0034_user_app_details.py

@@ -0,0 +1,19 @@
+# Generated by Django 6.0.3 on 2026-10-07 10:14
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('epdb', '0033_remove_user_app_details'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='user',
+            name='app_details',
+            field=models.OneToOneField(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='epdb.appdetails'),
+        ),
+    ]

epdb/migrations/0035_appdetails_data_pool_appdetails_secret_allowed.py

@@ -0,0 +1,24 @@
+# Generated by Django 6.0.3 on 2026-10-07 10:26
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('epdb', '0034_user_app_details'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='appdetails',
+            name='data_pool',
+            field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.group'),
+        ),
+        migrations.AddField(
+            model_name='appdetails',
+            name='secret_allowed',
+            field=models.BooleanField(default=False),
+        ),
+    ]

epdb/migrations/0036_appdetails_pes_allowance.py

@@ -0,0 +1,18 @@
+# Generated by Django 6.0.3 on 2026-10-07 10:27
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('epdb', '0035_appdetails_data_pool_appdetails_secret_allowed'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='appdetails',
+            name='pes_allowance',
+            field=models.IntegerField(choices=[(0, 'None'), (10, 'Non Secret'), (20, 'Secret')], default=0),
+        ),
+    ]

epdb/models.py

@@ -84,6 +84,17 @@ class User(AbstractUser):
     USERNAME_FIELD = "email"
     REQUIRED_FIELDS = ["username"]
 
+    class PrincipalType(models.IntegerChoices):
+        USER = 0, "User"
+        APP = 10 , "App"
+
+    principal_type = models.IntegerField(
+        choices=PrincipalType,
+        default=PrincipalType.USER,
+    )
+
+    app_details = models.OneToOneField("epdb.AppDetails", on_delete=models.CASCADE, null=True, blank=True)
+
     def get_name(self):
         return self.username
 
@@ -103,6 +114,25 @@ class User(AbstractUser):
         return self.default_setting
 
 
+class AppDetails(models.Model):
+    owner = models.ForeignKey(User, on_delete=models.CASCADE)
+    client_id = models.TextField(blank=False, null=False, verbose_name="Client ID")
+    display_name = models.TextField(blank=False, null=False, verbose_name="Display Name")
+
+    secret_allowed = models.BooleanField(default=False)
+    data_pool = models.ForeignKey("epdb.Group", null=True, blank=True, on_delete=models.SET_NULL)
+
+    class PESAllowance(models.IntegerChoices):
+        NONE = 0, "None"
+        NON_SECRET = 10 , "Non Secret"
+        SECRET = 20, "Secret"
+
+    pes_allowance = models.IntegerField(
+        choices=PESAllowance,
+        default=PESAllowance.NONE,
+    )
+
+
 class APIToken(TimeStampedModel):
     """
     API authentication token for users.
@@ -2041,7 +2071,10 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
     def empty_due_to_threshold(self):
         return self.kv.get("empty_due_to_threshold", False)
 
-    def d3_json(self):
+    def merged_d3_json(self):
+        return self.d3_json(merged=True)
+
+    def d3_json(self, merged=False):
         # Ideally it would be something like this but
         # to reduce crossing in edges do a DFS
         # nodes = [n.d3_json() for n in self.nodes]
@@ -2049,15 +2082,68 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
         nodes = []
         processed = set()
 
+        structure_to_combined_nodes = dict()
+        node_to_combined_node = dict()
         queue = list()
-        for n in self.root_nodes:
-            queue.append(n)
 
-        # Add unconnected nodes
-        for n in self.nodes.order_by("url"):
-            if len(n.out_edges.all()) == 0:
-                if n not in queue:
-                    queue.append(n)
+        class CombinedNode(object):
+
+            def __init__(self, representative: "Node"):
+                self.representative = representative
+                self.nodes = set([self.representative])
+
+            def ids(self):
+                return [n.id for n in self.nodes]
+
+            def d3_json(self):
+                d3_json = self.representative.d3_json()
+                compound = self.representative.default_node_label.compound
+                d3_json["name"] = compound.get_name()
+                d3_json["smiles"] = compound.default_structure.smiles
+                d3_json["node_label_id"] = compound.default_structure.url
+                d3_json["image"] = f"{compound.default_structure.url}?image=svg",
+                d3_json["image_svg"] = IndigoUtils.mol_to_svg(
+                    compound.default_structure.molfile
+                    if compound.default_structure.molfile is not None
+                       and compound.default_structure.molfile.strip()
+                    else compound.default_structure.smiles,
+                    width=40,
+                    height=40,
+                ),
+
+                return d3_json
+
+            def __repr__(self):
+                return f"CombinedNode({self.nodes})"
+
+        if merged:
+            for n in self.nodes:
+                def_struct = n.default_node_label.compound.default_structure
+                if def_struct in structure_to_combined_nodes:
+                    structure_to_combined_nodes[def_struct].nodes.add(n)
+                else:
+                    cn = CombinedNode(n)
+                    structure_to_combined_nodes[def_struct] = cn
+
+            # for n in self.nodes.order_by("url"):
+            #     if len(n.out_edges.all()) == 0:
+            #         if n not in queue:
+            #             queue.append(n)
+
+            for cn in structure_to_combined_nodes.values():
+                for n in cn.nodes:
+                    node_to_combined_node[n] = cn
+
+            queue = list(structure_to_combined_nodes.values())
+        else:
+            for n in self.nodes:
+                queue.append(n)
+
+            # Add unconnected nodes
+            for n in self.nodes.order_by("url"):
+                if len(n.out_edges.all()) == 0:
+                    if n not in queue:
+                        queue.append(n)
 
         for i in queue:
             processed.add(i)
@@ -2067,25 +2153,56 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
             processed.add(current)
             nodes.append(current.d3_json())
 
-            for e in self.edges.filter(start_nodes=current).order_by("url").distinct():
+            if merged:
+                q = Q(start_nodes__in=current.ids())
+            else:
+                q = Q(start_nodes=current)
+
+            for e in self.edges.filter(q).order_by("url").distinct():
                 for prod in e.end_nodes.all().order_by("url"):
-                    if prod not in queue and prod not in processed:
-                        queue.append(prod)
+
+                    if merged:
+                        def_struct = n.default_node_label.compound.default_structure
+                        if def_struct in structure_to_combined_nodes:
+                            structure_to_combined_nodes[def_struct].nodes.add(n)
+                        else:
+                            cn = CombinedNode(n)
+                            structure_to_combined_nodes[def_struct] = cn
+                            if cn not in queue and cn not in processed:
+                                queue.append(cn)
+                    else:
+                        if prod not in queue and prod not in processed:
+                            queue.append(prod)
 
         # We shouldn't lose or make up nodes...
-        if len(nodes) != len(self.nodes):
-            logger.debug(
-                f"{self.get_name()}: Num Nodes {len(nodes)} vs. DB Nodes {len(self.nodes)}"
-            )
+        if not merged:
+            if len(nodes) != len(self.nodes):
+                logger.debug(
+                    f"{self.get_name()}: Num Nodes {len(nodes)} vs. DB Nodes {len(self.nodes)}"
+                )
 
         links = [e.d3_json() for e in self.edges]
 
         # D3 links Nodes based on indices in nodes array
+        combined_node_depth_to_idx = dict()
         node_url_to_idx = dict()
         for i, n in enumerate(nodes):
             n["id"] = i
             node_url_to_idx[n["url"]] = i
 
+        # Add potential missing mappings
+        if merged:
+            cn_idx_mapping = dict()
+            for n in nodes:
+                for cn in processed:
+                    for sub_n in cn.nodes:
+                        if n["url"] == sub_n.url:
+                            cn_idx_mapping[cn] = n["id"]
+
+            for n in processed:
+                for sub_n in n.nodes:
+                    node_url_to_idx[sub_n.url] = cn_idx_mapping[n]
+
         adjusted_links = []
         for link in links:
             # Check if we'll need pseudo nodes
@@ -2456,6 +2573,20 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             else:
                 return self.default_node_label.name
 
+    def get_description(self, include_suffix=True):
+        default_desc = False
+
+        if self.description == "no description":
+            default_desc = True
+
+        if not default_desc:
+            return self.description
+        else:
+            if include_suffix:
+                return f"{self.default_node_label.description} (taken from underlying structure)"
+            else:
+                return self.default_node_label.description
+
     def d3_json(self):
         app_domain_data = self.get_app_domain_assessment_data()
 
@@ -2773,6 +2904,20 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             else:
                 return self.edge_label.name
 
+    def get_description(self, include_suffix=True):
+        default_desc = False
+
+        if self.description == "no description":
+            default_desc = True
+
+        if not default_desc:
+            return self.description
+        else:
+            if include_suffix:
+                return f"{self.edge_label.description} (taken from underlying reaction)"
+            else:
+                return self.edge_label.description
+
 
 class EPModel(PolymorphicModel, EnviPathModel, AdditionalInformationMixin):
     package = models.ForeignKey(

epdb/views.py

@@ -1292,14 +1292,21 @@ def package(request, package_uuid):
                 "user_id", flat=True
             )
         )
-        users = users.filter(is_active=True)
+        users = users.filter(is_active=True).exclude(username="anonymous")
+
+        if not current_user.is_superuser:
+            users = users.exclude(principal_type=User.PrincipalType.APP)
 
         group_perms = GroupPackagePermission.objects.filter(package=current_package)
-        groups = Group.objects.exclude(
-            id__in=GroupPackagePermission.objects.filter(package=current_package).values_list(
-                "group_id", flat=True
+
+        if current_package.classification_level == current_package.Classification.SECRET:
+            groups = Group.objects.none()
+        else:
+            groups = Group.objects.exclude(
+                id__in=GroupPackagePermission.objects.filter(package=current_package).values_list(
+                    "group_id", flat=True
+                )
             )
-        )
 
         context["users"] = users
         context["groups"] = groups
@@ -1324,6 +1331,12 @@ def package(request, package_uuid):
 
                 return redirect(s.SERVER_URL + "/package")
             elif hidden == "publish-package":
+                if current_package.classification_level == current_package.Classification.SECRET:
+                    return error(
+                        request,
+                        "Cannot publish a secret package",
+                        "You cannot publish a secret package.",
+                    )
                 for g in Group.objects.filter(public=True):
                     PackageManager.grant_read(current_user, current_package, g)
                 return redirect(current_package.url)
@@ -1376,6 +1389,9 @@ def package(request, package_uuid):
         elif any([grantee_url, read, write, owner]):
             if "user" in grantee_url:
                 grantee = UserManager.get_user_lp(grantee_url)
+                if grantee.principal_type == current_user.PrincipalType.APP:
+                    if not request.user.is_superuser:
+                        return error(request, "You are not allowed to grant permissions to an app!")
             else:
                 grantee = GroupManager.get_group_lp(grantee_url)
 
@@ -2297,6 +2313,7 @@ def package_pathway(request, package_uuid, pathway_uuid):
 
         context["pathway"] = current_pathway
         context["current_object"] = current_pathway
+        context["merged"] = request.GET.get("merged", False) == "true"
 
         context["breadcrumbs"] = [
             {"Home": s.SERVER_URL},
@@ -3314,6 +3331,11 @@ def jobs(request):
                 "This Package was generated automatically for the batch prediction task.",
             )
 
+            if current_user.default_package.classification_level == current_user.default_package.Classification.SECRET:
+                target_package.classification_level = current_user.default_package.Classification.SECRET
+                target_package.data_pool = current_user.default_package.data_pool
+                target_package.save()
+
             from .tasks import batch_predict, dispatch
 
             res = dispatch(

pyproject.toml

@@ -15,7 +15,6 @@ dependencies = [
     "django-polymorphic>=4.1.0",
     "enviformer",
     "envipy-additional-information",
-    "envipy-ambit>=0.1.0",
     "envipy-plugins",
     "epam-indigo>=1.30.1",
     "gunicorn>=23.0.0",

templates/index/index.html

@@ -185,19 +185,18 @@
                   <div
                     class="mt-4 rounded-lg border border-base-300 bg-base-50 px-4 py-2.5 text-sm text-base-content/70"
                   >
-                    Prediction will be stored in
+                    Prediction will be stored in Package
                     <strong class="text-base-content"
-                      >{{ meta.current_package.name|safe }}</strong
+                    ><a class="link" href="{{ meta.current_package.url }}">{{ meta.current_package.name|safe }}</a></strong
                     >
                     {% if meta.user.default_setting %}
                       using setting
                       <strong class="text-base-content"
-                        >{{ meta.user.default_setting.name|safe }}</strong
+                      ><a class="link" href="{{ meta.user.default_setting.url}}">{{ meta.user.default_setting.name|safe }}</a></strong
                       >
                     {% endif %}
-                    <br />
                     To use a different setting click
-                    <a class="label link" href="/predict">here</a>
+                    <a class="link" href="/predict">here</a>
                   </div>
                 {% endif %}
               </div>
@@ -222,23 +221,22 @@
                 >
                   Predict!
                 </button>
-                {% if meta.current_package %}
+                  {% if meta.current_package %}
                   <div
                     class="mt-4 rounded-lg border border-base-300 bg-base-50 px-4 py-2.5 text-sm text-base-content/70"
                   >
-                    Prediction will be stored in
+                    Prediction will be stored in Package
                     <strong class="text-base-content"
-                      >{{ meta.current_package.name|safe }}</strong
+                    ><a class="link" href="{{ meta.current_package.url }}">{{ meta.current_package.name|safe }}</a></strong
                     >
                     {% if meta.user.default_setting %}
                       using setting
                       <strong class="text-base-content"
-                        >{{ meta.user.default_setting.name|safe }}</strong
+                      ><a class="link" href="{{ meta.user.default_setting.url}}">{{ meta.user.default_setting.name|safe }}</a></strong
                       >
                     {% endif %}
-                    <br />
                     To use a different setting click
-                    <a class="label link" href="/predict">here</a>
+                    <a class="link" href="/predict">here</a>
                   </div>
                 {% endif %}
               </div>
@@ -262,17 +260,43 @@
     </div>
 
     <!-- Community News Section -->
-    <section class="bg-base-200 z-10 mx-8 py-16">
+    <section class="bg-base-200 z-10 mx-8 py-6">
       <div class="mx-auto max-w-7xl px-4">
-        <h2 class="h2 mb-8 text-left font-bold">Community Updates</h2>
+        <h2 class="h2 mb-8 text-left font-bold">News</h2>
 
-        <div id="community-news-container" class="flex justify-center gap-4">
-          <!-- News cards will be populated here -->
-          <div id="loading" class="flex w-full justify-center">
-            <span class="loading loading-spinner loading-lg"></span>
-          </div>
+        <div id="services-container" class="flex justify-center gap-4">
+          {% for ne in news_entries %}
+            <div class="card-body flex flex-col h-full justify-between p-5 w-96"> <!-- Fixed width applied via w-96 -->
+              <div>
+                <div class="flex items-center gap-2 mb-2">
+                  <div class="bg-primary/10 text-primary rounded-lg p-1.5">
+                    <svg xmlns="http://www.w3.org/2000/svg" class="h-4 w-4" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round">
+                      <path d="M3 9l9-7 9 7v11a2 2 0 0 1-2 2H5a2 2 0 0 1-2-2z"></path>
+                      <polyline points="9 22 9 12 15 12 15 22"></polyline>
+                    </svg>
+                  </div>
+                  <h3 class="card-title text-base font-semibold tracking-tight">
+                    {{ ne.title }} - {{ ne.publication_date|date }}
+                  </h3>
+                </div>
+                <p class="text-sm text-base-content/60 leading-snug line-clamp-4">
+                  {{ ne.content }}
+                </p>
+              </div>
+
+              <a href="{{ ne.url }}" class="btn btn-primary btn-sm w-full group-hover:btn-active mt-1">
+                Read Full
+                <svg xmlns="http://www.w3.org/2000/svg" class="h-3.5 w-3.5" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round">
+                  <path d="M18 13v6a2 2 0 0 1-2 2H5a2 2 0 0 1-2-2V8a2 2 0 0 1 2-2h6"></path>
+                  <polyline points="15 3 21 3 21 9"></polyline>
+                  <line x1="10" y1="14" x2="21" y2="3"></line>
+                </svg>
+              </a>
+            </div>
+          {% endfor %}
         </div>
 
+
         <div class="mt-6 text-right">
           <a
             href="https://community.envipath.org/c/announcements/10"
@@ -282,9 +306,6 @@
             Read More Announcements
           </a>
         </div>
-
-        <!-- Discourse API integration -->
-        <script src="{% static 'js/discourse-api.js' %}"></script>
       </div>
     </section>
 

templates/modals/objects/edit_user_modal.html

@@ -31,6 +31,7 @@
         {% csrf_token %}
 
         <div class="form-control mb-3">
+          {% if 1 == 0 %}
           <label class="label" for="default-package">
             <span class="label-text">Default Package</span>
           </label>
@@ -50,7 +51,7 @@
             {% endfor %}
           </select>
         </div>
-
+        {% endif %}
         <div class="form-control mb-3">
           <label class="label" for="default-group">
             <span class="label-text">Default Group</span>

templates/objects/edge.html

@@ -57,7 +57,7 @@
     <div class="collapse-arrow bg-base-200 collapse">
       <input type="checkbox" checked />
       <div class="collapse-title text-xl font-medium">Description</div>
-      <div class="collapse-content">{{ edge.description }}</div>
+      <div class="collapse-content">{{ edge.get_description }}</div>
     </div>
 
     {% if edge.aliases %}

templates/objects/node.html

@@ -60,7 +60,7 @@
       <div class="collapse-arrow bg-base-200 collapse">
         <input type="checkbox" checked />
         <div class="collapse-title text-xl font-medium">Description</div>
-        <div class="collapse-content">{{ node.description }}</div>
+        <div class="collapse-content">{{ node.get_description }}</div>
       </div>
     {% endif %}
     {% epdb_slot_templates "epdb.objects.node.viz" as viz_templates %}

templates/objects/pathway.html

@@ -227,6 +227,29 @@
                       Reaction Names
                     </a>
                   </li>
+                  <li>
+                    <a href="{% if merged %}{{ current_object.url }}{% else %}{{ current_object.url }}?merged=true{% endif %}" id="merged-toggle-button" class="cursor-pointer">
+                      <svg
+                        id="merged-icon"
+                        xmlns="http://www.w3.org/2000/svg"
+                        width="16"
+                        height="16"
+                        viewBox="0 0 24 24"
+                        fill="none"
+                        stroke="currentColor"
+                        stroke-width="2"
+                        stroke-linecap="round"
+                        stroke-linejoin="round"
+                        class="lucide lucide-eye"
+                      >
+                        <path
+                          d="M2 12s3-7 10-7 10 7 10 7-3 7-10 7-10-7-10-7Z"
+                        />
+                        <circle cx="12" cy="12" r="3" />
+                      </svg>
+                      Merged View
+                    </a>
+                  </li>
                   {% if pathway.setting.model.app_domain %}
                     <li>
                       <a id="app-domain-toggle-button" class="cursor-pointer">
@@ -544,8 +567,11 @@
       </div>
     {% endif %}
   </div>
+  {% if merged %}
+  {{ pathway.merged_d3_json|json_script:"pathway" }}
+  {% else %}
   {{ pathway.d3_json|json_script:"pathway" }}
-
+  {% endif %}
   <script>
     // Global switch for compound names view
     var compoundNamesViewEnabled = false;
@@ -557,6 +583,8 @@
     var timeseriesViewEnabled = false;
     // Predicted Property View
     var predictedPropertyViewEnabled = false;
+    // Merged View
+    var mergedViewEnabled = new URLSearchParams(window.location.search).get("merged") !== null;
 
     function goFullscreen(id) {
       var element = document.getElementById(id);
@@ -702,6 +730,23 @@
         });
       }
 
+      const mergedViewBtn = document.getElementById(
+        "merged-toggle-button",
+      );
+      if (mergedViewBtn) {
+          const icon = document.getElementById("merged-icon");
+          if (mergedViewEnabled) {
+            // Change to eye-off icon
+            icon.innerHTML =
+              '<path d="M9.88 9.88a3 3 0 1 0 4.24 4.24"/><path d="M10.73 5.08A10.43 10.43 0 0 1 12 5c7 0 10 7 10 7a13.16 13.16 0 0 1-1.67 2.68"/><path d="M6.61 6.61A13.526 13.526 0 0 0 2 12s3 7 10 7a9.74 9.74 0 0 0 5.39-1.61"/><line x1="2" x2="22" y1="2" y2="22"/>';
+          } else {
+            // Change back to eye icon
+            icon.innerHTML =
+              '<path d="M2 12s3-7 10-7 10 7 10 7-3 7-10 7-10-7-10-7Z"/><circle cx="12" cy="12" r="3"/>';
+        }
+      };
+
+
       // Timeseries toggle
       const timeseriesBtn = document.getElementById("timeseries-toggle-button");
       if (timeseriesBtn) {

templates/predict_pathway.html

@@ -2,11 +2,23 @@
 {% load static %}
 {% block content %}
   <div class="mx-auto w-full p-8">
-    <h1 class="h1 mb-4 text-3xl font-bold">
+    <h1 class="h1 mb-4 flex items-center gap-2 text-3xl font-bold">
       Predict a Pathway
 
-      <span class="text-base-content/50 text-xs"
-        >in <strong>{{ meta.current_package.name|safe }}</strong>
+      <span class="inline-flex items-center gap-1 text-base-content/50 text-xs"
+        >in <strong>{{ meta.current_package.name|safe }}</strong>{% if meta.url_contains_package %}
+      {% if meta.current_package.get_classification_level_display == "Restricted" %}
+        <img src="{% static 'images/restricted_mid.png' %}" width="100">
+      {% elif meta.current_package.get_classification_level_display == "Secret" %}
+        <img src="{% static 'images/secret_mid.png' %}" width="60">
+      {% endif %}
+    {% else %}
+      {% if meta.user.default_package.get_classification_level_display == "Restricted" %}
+        <img src="{% static 'images/restricted_mid.png' %}" width="100">
+      {% elif meta.user.default_package.get_classification_level_display == "Secret" %}
+        <img src="{% static 'images/secret_mid.png' %}" width="60">
+      {% endif %}
+    {% endif %}
       </span>
     </h1>
 

utilities/misc.py

@@ -214,6 +214,7 @@ class EdgeExportSchema(RefEdgeExportSchema):
     start_nodes: List[RefNodeExportSchema]
     end_nodes: List[RefNodeExportSchema]
     scenarios: List[RefScenarioExportSchema]
+    kv: Optional[dict]
 
 
 class PathwayExportSchema(RefPathwayExportSchema):
@@ -623,6 +624,7 @@ class PackageImporter:
                 new_e.description = e.description
                 new_e.aliases = e.aliases
                 new_e.edge_label = self._cache[e.edge_label.uuid]
+                new_e.kv = e.kv
                 new_e.save()
 
                 for sn in e.start_nodes:

uv.lock

@@ -802,7 +802,6 @@ dependencies = [
     { name = "django-polymorphic" },
     { name = "enviformer" },
     { name = "envipy-additional-information" },
-    { name = "envipy-ambit" },
     { name = "envipy-plugins" },
     { name = "epam-indigo" },
     { name = "gunicorn" },
@@ -859,7 +858,6 @@ requires-dist = [
     { name = "emcee", marker = "extra == 'pepper-plugin'", specifier = ">=3.1.6" },
     { name = "enviformer", git = "ssh://git@git.envipath.com/enviPath/enviformer.git?rev=main" },
     { name = "envipy-additional-information", git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git?branch=develop" },
-    { name = "envipy-ambit", git = "ssh://git@git.envipath.com/enviPath/enviPy-ambit.git" },
     { name = "envipy-plugins", git = "ssh://git@git.envipath.com/enviPath/enviPy-plugins.git?rev=v0.1.0" },
     { name = "epam-indigo", specifier = ">=1.30.1" },
     { name = "gunicorn", specifier = ">=23.0.0" },
@@ -899,14 +897,6 @@ dependencies = [
     { name = "pydantic" },
 ]
 
-[[package]]
-name = "envipy-ambit"
-version = "0.1.0"
-source = { git = "ssh://git@git.envipath.com/enviPath/enviPy-ambit.git#0c424ba153105a54f758569a784d5871989338d8" }
-dependencies = [
-    { name = "jpype1" },
-]
-
 [[package]]
 name = "envipy-plugins"
 version = "0.1.0"
@@ -1190,30 +1180,6 @@ wheels = [
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 ]
 
-[[package]]
-name = "jpype1"
-version = "1.6.0"
-source = { registry = "https://pypi.org/simple" }
-dependencies = [
-    { name = "packaging" },
-]
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-wheels = [
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-    { url = "https://files.pythonhosted.org/packages/6b/5d/51bde8695cc3eabcc465779f6dc23b149194bbcdcb8d221a9572422053f4/jpype1-1.6.0-cp312-cp312-manylinux2014_aarch64.manylinux_2_17_aarch64.whl", hash = "sha256:cf646459023a0dd71b3cc3aeeb977225a93f94c97839bb4e6146977b166c7caf", size = 468341, upload-time = "2025-07-07T13:50:40.739Z" },
-    { url = "https://files.pythonhosted.org/packages/7a/a1/50cdc2bf9e51c0828faabec6fad50d61aada5a57d0bc435f4db0c16eb2ca/jpype1-1.6.0-cp312-cp312-manylinux2014_i686.manylinux_2_17_i686.whl", hash = "sha256:7a98b34bc68a117881382dffa9b02d5e1d0d94325f85d7f564c33cc9e9d2916b", size = 511724, upload-time = "2025-07-07T13:50:42.479Z" },
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-
 [[package]]
 name = "jsonref"
 version = "1.1.0"