[Feature] Sync Features from Client Repo (#425)

- New PackageImporter
- Fix persisting Molfile on Structure creation
- Add NonPersistent Prediction
- Pathway View Options
- Edit Node Fix

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#425

.env.prod.example

@@ -3,10 +3,20 @@ EP_DATA_DIR=
 ALLOWED_HOSTS=
 DEBUG=
 LOG_LEVEL=
+MODEL_BUILDING_ENABLED=
+APPLICABILITY_DOMAIN_ENABLED=
 ENVIFORMER_PRESENT=
-FLAG_CELERY_PRESENT=
+ENVIFORMER_DEVICE=
-SERVER_URL=
 PLUGINS_ENABLED=
+SERVER_URL=
+SERVER_PATH=
+ADMIN_APPROVAL_REQUIRED=
+REGISTRATION_MANDATORY=
+LOG_DIR=
+# Celery
+FLAG_CELERY_PRESENT=
+CELERY_BROKER_URL=
+CELERY_RESULT_BACKEND=
 # DB
 POSTGRES_SERVICE_NAME=
 POSTGRES_DB=
@@ -16,5 +26,30 @@ POSTGRES_PORT=
 # MAIL
 EMAIL_HOST_USER=
 EMAIL_HOST_PASSWORD=
-# MATOMO
+DEFAULT_FROM_EMAIL=
-MATOMO_SITE_ID
+SERVER_EMAIL=
+# SENTRY
+SENTRY_ENABLED=
+SENTRY_DSN=
+SENTRY_ENVIRONMENT=
+# MS ENTRA
+MS_ENTRA_ENABLED=
+MS_CLIENT_ID=
+MS_CLIENT_SECRET=
+MS_TENANT_ID=
+MS_REDIRECT_URI=
+MS_SCOPES=
+# Tenant
+TENANT=
+EPDB_PACKAGE_MODEL=
+# Captcha
+CAP_ENABLED=
+CAP_API_BASE=
+CAP_SITE_KEY=
+CAP_SECRET_KEY=
+# QUARKUS (JAVA)
+ENVIRULE_ENABLED=
+FINGERPRINT_URL=
+# Biotransformer
+BIOTRANSFORMER_ENABLED=
+BIOTRANSFORMER_URL=

Dockerfile

@@ -6,18 +6,23 @@ ENV PYTHONDONTWRITEBYTECODE=1 \
 
 WORKDIR /app
 
+
 RUN apt-get update && apt-get install -y --no-install-recommends \
     build-essential \
     libpq-dev \
     curl \
     openssh-client \
     git \
-    nodejs \
+    ca-certificates \
-    npm \
     && rm -rf /var/lib/apt/lists/*
 
-# Install pnpm
+# Install Node 22 + pnpm
-RUN npm install -g pnpm
+RUN curl -fsSL https://deb.nodesource.com/setup_22.x | bash - \
+    && apt-get update \
+    && apt-get install -y --no-install-recommends nodejs \
+    && corepack enable \
+    && corepack prepare pnpm@latest --activate \
+    && rm -rf /var/lib/apt/lists/*
 
 RUN curl -LsSf https://astral.sh/uv/install.sh | sh
 ENV PATH="/root/.local/bin:${PATH}"
@@ -32,15 +37,17 @@ RUN mkdir -p -m 0700 /root/.ssh \
 # 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 .
 RUN --mount=type=ssh \
-    uv sync --locked --extra ms-login --extra pepper-plugin
+    uv sync --locked --extra pepper-plugin
 
 # Now copy source and do a final sync to install the project itself
 # Ensure .dockerignore is reasonable
+COPY biotransformer biotransformer
 COPY bridge bridge
 COPY envipath envipath
 COPY epapi epapi
 COPY epauth epauth
 COPY epdb epdb
+COPY epiuclid epiuclid
 COPY fixtures fixtures
 COPY migration migration
 COPY pepper pepper
@@ -71,6 +78,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     libxrender1 \
     libxext6 \
     libfontconfig1 \
+    nano \
     && rm -rf /var/lib/apt/lists/*
 
 RUN useradd -ms /bin/bash django

bridge/contracts.py

@@ -254,7 +254,14 @@ 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

@@ -191,11 +191,21 @@ ADMIN_APPROVAL_REQUIRED = os.environ.get("ADMIN_APPROVAL_REQUIRED", "False") ==
 # SESAME_MAX_AGE = 300
 # # TODO set to "home"
 # LOGIN_REDIRECT_URL = "/"
+
+
+SERVER_HOST = os.environ.get("SERVER_URL", "http://localhost:8000")
+SERVER_PATH = os.environ.get("SERVER_PATH", "")
+
+SERVER_URL = SERVER_HOST
+if SERVER_PATH:
+    SERVER_URL = os.path.join(SERVER_HOST, SERVER_PATH)
+
+
 LOGIN_URL = "/login/"
+if SERVER_PATH:
+    LOGIN_URL = f"/{SERVER_PATH}/login/"
 
-SERVER_URL = os.environ.get("SERVER_URL", "http://localhost:8000")
+CSRF_TRUSTED_ORIGINS = [SERVER_HOST]
-
-CSRF_TRUSTED_ORIGINS = [SERVER_URL]
 
 AMBIT_URL = "http://localhost:9001"
 DEFAULT_VALUES = {"description": "no description"}
@@ -229,6 +239,8 @@ PAGINATION_MAX_PER_PAGE_SIZE = int(
 STATIC_ROOT = STATIC_DIR
 
 STATIC_URL = "/static/"
+if SERVER_PATH:
+    STATIC_URL = f"/{SERVER_PATH}/static/"
 
 # Where the sources are stored...
 STATICFILES_DIRS = (BASE_DIR / "static",)
@@ -331,10 +343,11 @@ DEFAULT_MODEL_THRESHOLD = 0.25
 
 # Loading Plugins
 PLUGINS_ENABLED = os.environ.get("PLUGINS_ENABLED", "False") == "True"
-BASE_PLUGINS = [
+BASE_PLUGINS = os.environ.get("BASE_PLUGINS", None)
-    "pepper.PEPPER",
+if BASE_PLUGINS:
-    "biotransformer.Biotransformer",
+    BASE_PLUGINS = BASE_PLUGINS.split(",")
-]
+else:
+    BASE_PLUGINS = []
 
 CLASSIFIER_PLUGINS = {}
 PROPERTY_PLUGINS = {}
@@ -387,7 +400,6 @@ LOGIN_EXEMPT_URLS = [
     "/o/userinfo/",
     "/password_reset/",
     "/reset/",
-    "/microsoft/",
     "/terms",
     "/privacy",
     "/cookie-policy",
@@ -396,8 +408,13 @@ LOGIN_EXEMPT_URLS = [
     "/careers",
     "/cite",
     "/legal",
+    "/entra/",
+    "/auth/",
 ]
 
+if SERVER_PATH:
+    LOGIN_EXEMPT_URLS = [f"/{SERVER_PATH}{x}" for x in LOGIN_EXEMPT_URLS]
+
 # MS AD/Entra
 MS_ENTRA_ENABLED = os.environ.get("MS_ENTRA_ENABLED", "False") == "True"
 if MS_ENTRA_ENABLED:
@@ -424,5 +441,4 @@ CAP_SECRET_KEY = os.environ.get("CAP_SECRET_KEY", None)
 BIOTRANSFORMER_ENABLED = os.environ.get("BIOTRANSFORMER_ENABLED", "False") == "True"
 FLAGS["BIOTRANSFORMER"] = BIOTRANSFORMER_ENABLED
 if BIOTRANSFORMER_ENABLED:
-    INSTALLED_APPS.append("biotransformer")
     BIOTRANSFORMER_URL = os.environ.get("BIOTRANSFORMER_URL", None)

envipath/urls.py

@@ -21,19 +21,27 @@ from django.urls import include, path
 
 from .api import api_v1, api_legacy
 
+PATH_PREFIX = s.SERVER_PATH
+if PATH_PREFIX and not PATH_PREFIX.endswith("/"):
+    PATH_PREFIX += "/"
+
+
 urlpatterns = [
-    path("", include("epdb.urls")),
+    path(f"{PATH_PREFIX}", include("epdb.urls")),
-    path("admin/", admin.site.urls),
+    path(f"{PATH_PREFIX}admin/", admin.site.urls),
-    path("api/v1/", api_v1.urls),
+    path(f"{PATH_PREFIX}api/v1/", api_v1.urls),
-    path("api/legacy/", api_legacy.urls),
+    path(f"{PATH_PREFIX}api/legacy/", api_legacy.urls),
-    path("o/", include("oauth2_provider.urls", namespace="oauth2_provider")),
+    path(f"{PATH_PREFIX}o/", include("oauth2_provider.urls", namespace="oauth2_provider")),
 ]
 
 if "migration" in s.INSTALLED_APPS:
-    urlpatterns.append(path("", include("migration.urls")))
+    urlpatterns.append(path(f"{PATH_PREFIX}", include("migration.urls")))
 
 if s.MS_ENTRA_ENABLED:
-    urlpatterns.append(path("", include("epauth.urls")))
+    urlpatterns.append(path(f"{PATH_PREFIX}", include("epauth.urls")))
+
+if s.TENANT != "public":
+    urlpatterns.append(path(f"{PATH_PREFIX}", include(f"{s.TENANT}.urls")))
 
 # Custom error handlers
 handler400 = "epdb.views.handler400"

epapi/tests/v1/test_api_permissions.py

@@ -117,25 +117,28 @@ class APIPermissionTestBase(TestCase):
 
         # Create test compounds in each package
         cls.reviewed_compound = Compound.create(
-            cls.reviewed_package, "C", "Reviewed Compound", "Test compound"
+            cls.reviewed_package, "C", name="Reviewed Compound", description="Test compound"
         )
         cls.owned_compound = Compound.create(
-            cls.unreviewed_package_owned, "CC", "Owned Compound", "Test compound"
+            cls.unreviewed_package_owned, "CC", name="Owned Compound", description="Test compound"
         )
         cls.read_compound = Compound.create(
-            cls.unreviewed_package_read, "CCC", "Read Compound", "Test compound"
+            cls.unreviewed_package_read, "CCC", name="Read Compound", description="Test compound"
         )
         cls.write_compound = Compound.create(
-            cls.unreviewed_package_write, "CCCC", "Write Compound", "Test compound"
+            cls.unreviewed_package_write, "CCCC", name="Write Compound", description="Test compound"
         )
         cls.all_compound = Compound.create(
-            cls.unreviewed_package_all, "CCCCC", "All Compound", "Test compound"
+            cls.unreviewed_package_all, "CCCCC", name="All Compound", description="Test compound"
         )
         cls.no_access_compound = Compound.create(
-            cls.unreviewed_package_no_access, "CCCCCC", "No Access Compound", "Test compound"
+            cls.unreviewed_package_no_access,
+            "CCCCCC",
+            name="No Access Compound",
+            description="Test compound",
         )
         cls.group_compound = Compound.create(
-            cls.group_package, "CCCCCCC", "Group Compound", "Test compound"
+            cls.group_package, "CCCCCCC", name="Group Compound", description="Test compound"
         )
 
 

epapi/tests/v1/test_contract_get_entities.py

@@ -294,8 +294,8 @@ class CompoundPaginationAPITest(BaseTestAPIGetPaginated, TestCase):
         return Compound.create(
             package,
             smiles,
-            f"Reviewed Compound {idx:03d}",
+            name=f"Reviewed Compound {idx:03d}",
-            "Compound for pagination tests",
+            description="Compound for pagination tests",
         )
 
     @classmethod
@@ -305,8 +305,8 @@ class CompoundPaginationAPITest(BaseTestAPIGetPaginated, TestCase):
         return Compound.create(
             package,
             smiles,
-            f"Draft Compound {idx:03d}",
+            name=f"Draft Compound {idx:03d}",
-            "Compound for pagination tests",
+            description="Compound for pagination tests",
         )
 
 

epapi/v1/endpoints/groups.py

@@ -0,0 +1,23 @@
+from django.conf import settings as s
+from ninja import Router
+from ninja_extra.pagination import paginate
+
+from epdb.logic import GroupManager
+
+from ..pagination import EnhancedPageNumberPagination
+from ..schemas import GroupOutSchema
+
+router = Router()
+
+
+@router.get("/groups/", response=EnhancedPageNumberPagination.Output[GroupOutSchema])
+@paginate(
+    EnhancedPageNumberPagination,
+    page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
+)
+def list_all_groups(request):
+    """
+    List all groups the user has access to.
+    """
+    user = request.user
+    return GroupManager.get_groups(user)

epapi/v1/endpoints/joblogs.py

@@ -0,0 +1,26 @@
+from django.conf import settings as s
+from ninja import Router
+from ninja_extra.pagination import paginate
+
+from epdb.models import JobLog
+from ..pagination import EnhancedPageNumberPagination
+from ..schemas import JobLogOutSchema
+
+router = Router()
+
+
+@router.get("/joblog/", response=EnhancedPageNumberPagination.Output[JobLogOutSchema])
+@paginate(
+    EnhancedPageNumberPagination,
+    page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
+)
+def list_all_joblogs(request):
+    """
+    List all JobLogs from reviewed packages.
+    """
+    current_user = request.user
+
+    if current_user.is_superuser:
+        return JobLog.objects.all().order_by("-created")
+    else:
+        return JobLog.objects.filter(user=current_user).order_by("-created")

epapi/v1/endpoints/settings.py

@@ -15,9 +15,9 @@ router = Router()
     EnhancedPageNumberPagination,
     page_size=s.API_PAGINATION_DEFAULT_PAGE_SIZE,
 )
-def list_all_pathways(request):
+def list_all_settings(request):
     """
-    List all pathways from reviewed packages.
+    List all settings the user has access to.
     """
     user = request.user
     return SettingManager.get_all_settings(user)

epapi/v1/router.py

@@ -1,6 +1,7 @@
 from ninja import Router
 from ninja.security import SessionAuth
 
+from envipath import settings as s
 from .auth import BearerTokenAuth
 from .endpoints import (
     packages,
@@ -13,8 +14,9 @@ from .endpoints import (
     structure,
     additional_information,
     settings,
+    groups,
+    joblogs,
 )
-from envipath import settings as s
 
 # Main router with authentication
 router = Router(
@@ -35,6 +37,8 @@ router.add_router("", models.router)
 router.add_router("", structure.router)
 router.add_router("", additional_information.router)
 router.add_router("", settings.router)
+router.add_router("", groups.router)
+router.add_router("", joblogs.router)
 
 if s.IUCLID_EXPORT_ENABLED:
     from epiuclid.api import router as iuclid_router

epapi/v1/schemas.py

@@ -1,7 +1,10 @@
-from ninja import FilterSchema, FilterLookup, Schema
+from datetime import datetime
 from typing import Annotated, Optional, List, Dict, Any
 from uuid import UUID
 
+from django.urls import reverse
+from ninja import Field, FilterSchema, FilterLookup, Schema
+
 
 # Filter schema for query parameters
 class ReviewStatusFilter(FilterSchema):
@@ -126,3 +129,30 @@ class SettingOutSchema(Schema):
     url: str = ""
     name: str
     description: str
+
+
+class GroupOutSchema(Schema):
+    uuid: UUID
+    url: str = ""
+    name: str
+    description: str
+
+
+class SimpleUserOutSchema(Schema):
+    uuid: UUID
+    url: str
+    name: str = Field(alias="username")
+
+
+class JobLogOutSchema(Schema):
+    user: SimpleUserOutSchema
+    id: UUID = Field(alias="task_id")
+    url: str
+    name: str = Field(alias="job_name")
+    created: datetime = Field(alias="created")
+    status: str = Field(alias="status")
+    done: Optional[datetime] = Field(None, alias="done_at")
+
+    @staticmethod
+    def resolve_url(obj):
+        return reverse("job detail", kwargs={"job_uuid": obj.task_id})

epauth/urls.py

@@ -3,6 +3,6 @@ from django.urls import path
 from . import views
 
 urlpatterns = [
-    path("microsoft/login/", views.microsoft_login, name="microsoft_login"),
+    path("entra/login/", views.entra_login, name="entra_login"),
-    path("microsoft/callback/", views.microsoft_callback, name="microsoft_callback"),
+    path("auth/redirect/", views.entra_callback, name="entra_callback"),
 ]

epauth/views.py

@@ -1,34 +1,49 @@
 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.shortcuts import redirect
-from django.contrib.auth import get_user_model
 
 from epdb.logic import UserManager
 
 
-def microsoft_login(request):
+def get_msal_app_with_cache(request):
+    """
+    Create MSAL app with session-based token cache.
+    """
+    cache = msal.SerializableTokenCache()
+
+    # Load cache from session if it exists
+    if request.session.get("msal_token_cache"):
+        cache.deserialize(request.session["msal_token_cache"])
+
     msal_app = msal.ConfidentialClientApplication(
         client_id=s.MS_ENTRA_CLIENT_ID,
         client_credential=s.MS_ENTRA_CLIENT_SECRET,
-        authority=s.MS_ENTRA_AUTHORITY
+        authority=s.MS_ENTRA_AUTHORITY,
+        token_cache=cache,
+    )
+
+    return msal_app, cache
+
+
+def entra_login(request):
+    msal_app = msal.ConfidentialClientApplication(
+        client_id=s.MS_ENTRA_CLIENT_ID,
+        client_credential=s.MS_ENTRA_CLIENT_SECRET,
+        authority=s.MS_ENTRA_AUTHORITY,
     )
 
     flow = msal_app.initiate_auth_code_flow(
-        scopes=s.MS_ENTRA_SCOPES,
+        scopes=s.MS_ENTRA_SCOPES, redirect_uri=s.MS_ENTRA_REDIRECT_URI
-        redirect_uri=s.MS_ENTRA_REDIRECT_URI
     )
 
     request.session["msal_auth_flow"] = flow
     return redirect(flow["auth_uri"])
 
 
-def microsoft_callback(request):
+def entra_callback(request):
-    msal_app = msal.ConfidentialClientApplication(
+    msal_app, cache = get_msal_app_with_cache(request)
-        client_id=s.MS_ENTRA_CLIENT_ID,
-        client_credential=s.MS_ENTRA_CLIENT_SECRET,
-        authority=s.MS_ENTRA_AUTHORITY
-    )
 
     flow = request.session.pop("msal_auth_flow", None)
     if not flow:
@@ -37,30 +52,84 @@ def microsoft_callback(request):
     # Acquire token using the flow and callback request
     result = msal_app.acquire_token_by_auth_code_flow(flow, request.GET)
 
-    if "access_token" in result:
+    # Save the token cache to session
-        # Optional: Fetch user info from Microsoft Graph
+    if cache.has_state_changed:
-        import requests
+        request.session["msal_token_cache"] = cache.serialize()
-        resp = requests.get(
-            "https://graph.microsoft.com/v1.0/me",
-            headers={"Authorization": f"Bearer {result['access_token']}"}
-        )
-        user_info = resp.json()
 
-        user_name = user_info["displayName"]
+    claims = result["id_token_claims"]
-        user_email = user_info["mail"]
-        user_oid = user_info["id"]
 
-        # Get implementing class
+    user_name = claims.get("name")
-        User = get_user_model()
+    user_email = claims.get("emailaddress", claims.get("email"))
+    user_oid = claims.get("oid")
 
-        if User.objects.filter(uuid=user_oid).exists():
+    if not all([user_name, user_email, user_oid]):
-            login(request, User.objects.get(uuid=user_oid))
+        raise ValueError("Missing required claims in ID token")
-        else:
-            u = UserManager.create_user(user_name, user_email, None, uuid=user_oid, is_active=True)
-            login(request, u)
 
-        # TODO Group Sync
+    # Get implementing class
+    User = get_user_model()
 
-        return redirect("/")
+    if User.objects.filter(uuid=user_oid).exists():
+        u = User.objects.get(uuid=user_oid)
 
-    return redirect("/")  # Handle errors
+        if u.username != user_name:
+            u.username = user_name
+            u.save()
+
+    else:
+        u = UserManager.create_user(user_name, user_email, None, uuid=user_oid, is_active=True)
+
+    login(request, u)
+
+    return redirect(s.SERVER_URL)  # Handle errors
+
+
+def get_access_token_from_request(request, scopes=None):
+    """
+    Get an access token from the request using MSAL token cache.
+    """
+
+    # Check if auth via Access Token
+    if request.headers.get("Authorization"):
+        return {"access_token": request.headers.get("Authorization").split(" ")[1]}
+
+    if scopes is None:
+        scopes = s.MS_ENTRA_SCOPES
+
+    # Get user from request (must be authenticated)
+    if not request.user.is_authenticated:
+        return None
+
+    # Create MSAL app with persistent cache
+    msal_app, cache = get_msal_app_with_cache(request)
+
+    # Try to get accounts from cache
+    accounts = msal_app.get_accounts()
+
+    if not accounts:
+        return None
+
+    # Find the account that matches the current user
+    user_account = None
+    for account in accounts:
+        if account.get("local_account_id") == str(request.user.uuid):
+            user_account = account
+            break
+
+    # If no matching account found, use the first available account
+    if not user_account and accounts:
+        user_account = accounts[0]
+
+    if not user_account:
+        return None
+
+    # Try to acquire token silently from cache
+    result = msal_app.acquire_token_silent(scopes=scopes, account=user_account)
+
+    # Save cache changes back to session
+    if cache.has_state_changed:
+        request.session["msal_token_cache"] = cache.serialize()
+
+    if result and "access_token" in result:
+        return result
+
+    return None

epdb/admin.py

@@ -1,5 +1,8 @@
+import logging
+
 from django.conf import settings as s
 from django.contrib import admin
+from django.contrib import messages
 
 from .models import (
     AdditionalInformation,
@@ -29,6 +32,8 @@ from .models import (
 
 Package = s.GET_PACKAGE_MODEL()
 
+logger = logging.getLogger(__name__)
+
 
 class AdditionalInformationAdmin(admin.ModelAdmin):
     pass
@@ -45,6 +50,113 @@ class UserAdmin(admin.ModelAdmin):
         "date_joined",
     ]
 
+    actions = ["send_welcome_mail", "send_affiliation_mail"]
+
+    @admin.action(description="Send welcome mail")
+    def send_welcome_mail(self, request, queryset):
+        from django.core.mail import EmailMultiAlternatives
+
+        tpl = """Hello {username},
+
+Your account has been successfully activated.
+
+To log in, please visit
+https://envipath.org/password_reset/
+and request a new password.
+
+If you have any questions or feedback, feel free to visit our community forum at
+https://community.envipath.org/.
+You do not need to register again for the forum - you can log in using your enviPath account by clicking "Log In" and then "Log in with enviPath."
+
+Best regards,
+
+The enviPath Team"""
+
+        users = []
+
+        for user in queryset:
+            if user.is_active:
+                logger.info(f"{user.username} already active - not sending mail again")
+                continue
+            try:
+                msg = EmailMultiAlternatives(
+                    "Your enviPath Account Is Now Active",
+                    tpl.format(username=user.username),
+                    "admin@envipath.org",
+                    [user.email],
+                    bcc=["admin@envipath.org"],
+                )
+
+                msg.send(fail_silently=False)
+
+                user.is_active = True
+                user.password = "ASDF"
+                user.save()
+
+                users.append(user)
+                logger.info(f"{user.username} -> {user.email} mail sent")
+            except Exception as e:
+                logger.info(f"Error sending mail to {user.username}: {e}")
+
+        self.message_user(
+            request, f"Sent welcome mail to {[u.email for u in users]}", messages.SUCCESS
+        )
+
+    @admin.action(description="Send affiliation mail")
+    def send_affiliation_mail(self, request, queryset):
+        from django.core.mail import EmailMultiAlternatives
+
+        tpl = """Dear {username},
+
+Thank you for your interest in enviPath!
+
+Please note that the public enviPath system is intended for non-commercial use only.
+We see that you registered using the email address {email}.
+If possible, we kindly ask you to register using an official email address that reflects your affiliation (e.g., a university, NGO, or research organization).
+
+If you would like us to update your account, simply reply to this email and let us know which address we should use.
+We will then change it in our system, and you will receive a password reset email at the new address.
+
+If you are registering with a company email address and are interested in commercial use, you are very welcome to book a meeting with us so we can discuss how we can best support you.
+To book a meeting, please visit https://envipath.com/book
+
+If changing to an affiliation email address is not possible, please contact us at registration@envipath.org
+
+Best regards,
+
+enviPath team"""
+
+        users = []
+
+        for user in queryset:
+            if user.is_active or user.contacted:
+                logger.info(
+                    f"{user.username} already active or already contacted - not sending mail again"
+                )
+                continue
+            try:
+                msg = EmailMultiAlternatives(
+                    "Regarding your enviPath registration",
+                    tpl.format(username=user.username, email=user.email),
+                    "admin@envipath.org",
+                    [user.email],
+                    bcc=["admin@envipath.org"],
+                )
+
+                msg.send(fail_silently=False)
+
+                user.contacted = True
+                user.save()
+
+                users.append(user)
+                logger.info(f"{user.username} -> {user.email} affiliation mail sent")
+            except Exception as e:
+                logger.info(f"Error sending mail to {user.username}: {e}")
+
+        self.message_user(
+            request, f"Sent affiliation mail to {[u.email for u in users]}", messages.SUCCESS
+        )
+
 
 class UserPackagePermissionAdmin(admin.ModelAdmin):
     pass

epdb/exceptions.py

@@ -0,0 +1,10 @@
+class InvalidSMILESException(Exception):
+    pass
+
+
+class InvalidMolfileException(Exception):
+    pass
+
+
+class PackageImportException(Exception):
+    pass

epdb/legacy_api.py

@@ -386,23 +386,50 @@ class PackageSchema(Schema):
 
     @staticmethod
     def resolve_readers(obj: Package):
-        users = User.objects.filter(
+        readers = []
-            id__in=UserPackagePermission.objects.filter(
-                package=obj, permission=UserPackagePermission.READ[0]
-            ).values_list("user", flat=True)
-        ).distinct()
 
-        return [{u.id: u.get_name()} for u in users]
+        user_ids = UserPackagePermission.objects.filter(package=obj).values_list("user", flat=True)
+
+        users = User.objects.filter(id__in=user_ids).distinct()
+
+        for u in users:
+            readers.append({"id": str(u.url), "identifier": "user", "name": u.get_name()})
+
+        group_ids = GroupPackagePermission.objects.filter(package=obj).values_list(
+            "group", flat=True
+        )
+
+        groups = Group.objects.filter(id__in=group_ids).distinct()
+
+        for g in groups:
+            readers.append({"id": str(g.url), "identifier": "group", "name": g.get_name()})
+
+        return readers
 
     @staticmethod
     def resolve_writers(obj: Package):
-        users = User.objects.filter(
+        writers = []
-            id__in=UserPackagePermission.objects.filter(
-                package=obj, permission=UserPackagePermission.WRITE[0]
-            ).values_list("user", flat=True)
-        ).distinct()
 
-        return [{u.id: u.get_name()} for u in users]
+        user_ids = UserPackagePermission.objects.filter(
+            package=obj,
+            permission__in=[UserPackagePermission.WRITE[0], UserPackagePermission.ALL[0]],
+        ).values_list("user", flat=True)
+
+        users = User.objects.filter(id__in=user_ids).distinct()
+
+        for u in users:
+            writers.append({"id": str(u.url), "identifier": "user", "name": u.get_name()})
+
+        group_ids = GroupPackagePermission.objects.filter(
+            package=obj, permission=[UserPackagePermission.WRITE[0], UserPackagePermission.ALL[0]]
+        ).values_list("group", flat=True)
+
+        groups = Group.objects.filter(id__in=group_ids).distinct()
+
+        for g in groups:
+            writers.append({"id": str(g.url), "identifier": "group", "name": g.get_name()})
+
+        return writers
 
     @staticmethod
     def resolve_review_comment(obj):
@@ -764,6 +791,7 @@ def get_package_compound_structure(request, package_uuid, compound_uuid, structu
 
 class CreateCompound(Schema):
     compoundSmiles: str
+    compoundMolFile: str | None = None
     compoundName: str | None = None
     compoundDescription: str | None = None
     inchi: str | None = None
@@ -777,9 +805,13 @@ def create_package_compound(
 ):
     try:
         p = get_package_for_write(request.user, package_uuid)
-        # inchi is not used atm
         c = Compound.create(
-            p, c.compoundSmiles, c.compoundName, c.compoundDescription, inchi=c.inchi
+            p,
+            c.compoundSmiles,
+            molfile=c.compoundMolFile,
+            name=c.compoundName,
+            description=c.compoundDescription,
+            inchi=c.inchi,
         )
         return redirect(c.url)
     except ValueError as e:
@@ -799,6 +831,27 @@ def delete_compound(request, package_uuid, compound_uuid):
         }
 
 
+class CreateCompoundStructure(Schema):
+    smiles: str
+    name: str | None = None
+    description: str | None = None
+    inchi: str | None = None
+    molfile: str | None = None
+
+
+@router.post("/package/{uuid:package_uuid}/compound/{uuid:compound_uuid}/structure")
+def create_package_compound_structure(
+    request, package_uuid, compound_uuid, structure: Form[CreateCompoundStructure]
+):
+    try:
+        p = get_package_for_write(request.user, package_uuid)
+        c = Compound.objects.get(package=p, uuid=compound_uuid)
+        cs = CompoundStructure.create(c, structure.smiles, structure.name, structure.description)
+        return redirect(cs.url)
+    except ValueError as e:
+        return 400, {"message": str(e)}
+
+
 @router.delete(
     "/package/{uuid:package_uuid}/compound/{uuid:compound_uuid}/structure/{uuid:structure_uuid}"
 )
@@ -1325,6 +1378,7 @@ class ScenarioSchema(Schema):
     aliases: List[str] = Field([], alias="aliases")
     collection: Dict["str", List[Dict[str, Any]]] = Field([], alias="collection")
     collectionID: Optional[str] = None
+    date: str = Field(None, alias="scenario_date")
     description: str = Field(None, alias="description")
     id: str = Field(None, alias="url")
     identifier: str = "scenario"
@@ -1468,28 +1522,56 @@ def create_package_additional_information(request, package_uuid):
         scen = request.POST.get("scenario")
         scenario = Scenario.objects.get(package=p, url=scen)
 
-        url_parser = EPDBURLParser(request.POST.get("attach_obj"))
+        if request.POST.get("adInfoTypes[]"):
-        attach_obj = url_parser.get_object()
+            url_parser = EPDBURLParser(request.POST.get("attach_obj"))
+            attach_obj = url_parser.get_object()
 
-        if not hasattr(attach_obj, "additional_information"):
+            if not hasattr(attach_obj, "additional_information"):
-            raise ValueError("Can't attach additional information to this object!")
+                raise ValueError("Can't attach additional information to this object!")
 
-        if not attach_obj.url.startswith(p.url):
+            if not attach_obj.url.startswith(p.url):
-            raise ValueError(
+                raise ValueError(
-                "Additional Information can only be set to objects stored in the same package!"
+                    "Additional Information can only be set to objects stored in the same package!"
-            )
+                )
 
-        types = request.POST.get("adInfoTypes[]", "").split(",")
+            types = request.POST.get("adInfoTypes[]", "").split(",")
 
-        for t in types:
+            for t in types:
-            ai = build_additional_information_from_request(request, t)
+                ai = build_additional_information_from_request(request, t)
 
-            AdditionalInformation.create(
+                AdditionalInformation.create(
-                p,
+                    p,
-                ai,
+                    ai,
-                scenario=scenario,
+                    scenario=scenario,
-                content_object=attach_obj,
+                    content_object=attach_obj,
-            )
+                )
+
+        elif request.POST.get("ais"):
+            import json
+
+            parsed_ais = json.loads(request.POST.get("ais"))
+
+            for ai_type, ais in parsed_ais.items():
+                for ai in ais:
+                    attach_obj = None
+                    if ai.get("related"):
+                        url_parser = EPDBURLParser(ai.get("related").get("url"))
+                        attach_obj = url_parser.get_object()
+
+                        if not hasattr(attach_obj, "additional_information"):
+                            raise ValueError("Can't attach additional information to this object!")
+
+                        if not attach_obj.url.startswith(p.url):
+                            raise ValueError(
+                                "Additional Information can only be set to objects stored in the same package!"
+                            )
+
+                    AdditionalInformation.create(
+                        p,
+                        AdditionalInformation.from_dict(ai_type, ai),
+                        scenario=scenario,
+                        content_object=attach_obj,
+                    )
 
         # TODO implement additional information endpoint ?
         return redirect(f"{scenario.url}")
@@ -1533,13 +1615,14 @@ class PathwayNode(Schema):
     dt50s: List[Dict[str, str]] = Field([], alias="dt50s")
     engineeredIntermediate: bool = Field(None, alias="engineered_intermediate")
     id: str = Field(None, alias="url")
-    idcomp: str = Field(None, alias="default_node_label.url")
+    idcomp: str = Field(None, alias="node_label_id")
-    idreact: str = Field(None, alias="default_node_label.url")
+    idreact: str = Field(None, alias="node_label_id")
     image: str = Field(None, alias="image")
     imageSize: int = Field(None, alias="image_size")
     name: str = Field(None, alias="name")
     proposed: List[Dict[str, str]] = Field([], alias="proposed_intermediate")
-    smiles: str = Field(None, alias="default_node_label.smiles")
+    smiles: str = Field(None, alias="smiles")
+    pseudo: bool = Field(False, alias="pseudo")
 
     @staticmethod
     def resolve_atom_count(obj: Node):
@@ -1552,24 +1635,10 @@ class PathwayNode(Schema):
         # TODO
         return []
 
-    @staticmethod
-    def resolve_engineered_intermediate(obj: Node):
-        # TODO
-        return False
-
-    @staticmethod
-    def resolve_image(obj: Node):
-        return f"{obj.default_node_label.url}?image=svg"
-
     @staticmethod
     def resolve_image_size(obj: Node):
         return 400
 
-    @staticmethod
-    def resolve_proposed_intermediate(obj: Node):
-        # TODO
-        return []
-
 
 class PathwaySchema(Schema):
     aliases: List[str] = Field([], alias="aliases")
@@ -1693,6 +1762,29 @@ def create_package_pathway(
         return 403, {"message": str(e)}
 
 
+@router.post("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}")
+def update_pathway(request, package_uuid, pathway_uuid):
+    try:
+        p = get_package_for_write(request.user, package_uuid)
+
+        if request.POST.get("scenario"):
+            pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
+            scen = Scenario.objects.get(package=p, url=request.POST.get("scenario"))
+
+            pw.scenarios.add(scen)
+            pw.save()
+
+            return redirect(f"{pw.url}")
+
+        else:
+            return 400, {"message": "No scenario specified!"}
+
+    except ValueError:
+        return 403, {
+            "message": f"Deleting Pathway with id {pathway_uuid} failed due to insufficient rights!"
+        }
+
+
 @router.delete("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}")
 def delete_pathway(request, package_uuid, pathway_uuid):
     try:
@@ -1798,6 +1890,7 @@ def get_package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
 
 class CreateNode(Schema):
     nodeAsSmiles: str
+    nodeAsMolFile: str | None = None
     nodeName: str | None = None
     nodeReason: str | None = None
     nodeDepth: str | None = None
@@ -1813,11 +1906,18 @@ def add_pathway_node(request, package_uuid, pathway_uuid, n: Form[CreateNode]):
         pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
 
         if n.nodeDepth is not None and n.nodeDepth.strip() != "":
-            node_depth = int(n.nodeDepth)
+            node_depth = int(float(n.nodeDepth))
         else:
             node_depth = -1
 
-        n = Node.create(pw, n.nodeAsSmiles, node_depth, n.nodeName, n.nodeReason)
+        n = Node.create(
+            pw,
+            n.nodeAsSmiles,
+            node_depth,
+            molfile=n.nodeAsMolFile,
+            name=n.nodeName,
+            description=n.nodeReason,
+        )
 
         return redirect(n.url)
     except ValueError:
@@ -1958,6 +2058,10 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
             for pr in e.products.split(","):
                 products.append(Node.objects.get(pathway=pw, url=pr.strip()))
 
+        multi_step = False
+        if e.multistep and e.multistep.strip() == "true":
+            multi_step = True
+
         new_e = Edge.create(
             pathway=pw,
             start_nodes=educts,
@@ -1965,11 +2069,15 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
             rule=None,
             name=None,
             description=e.edgeReason,
+            multi_step=multi_step,
         )
 
+        # Update depths as sideeffect of above operation
+        pw.update_depths()
+
         return redirect(new_e.url)
     except ValueError:
-        return 403, {"message": "Adding node failed!"}
+        return 403, {"message": "Adding Edge failed!"}
 
 
 @router.delete("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}/edge/{uuid:edge_uuid}")
@@ -2160,3 +2268,26 @@ def get_setting(request, setting_uuid):
         return 403, {
             "message": f"Getting Setting with id {setting_uuid} failed due to insufficient rights!"
         }
+
+
+########
+# Util #
+########
+class NonPersistent(Schema):
+    smiles: str
+    setting_url: str = Field(..., alias="settingUri")
+
+
+@router.post("/util", response={200: Any, 403: Error})
+def predict(request, np: Form[NonPersistent]):
+    try:
+        from epdb.logic import SPathway
+
+        setting = SettingManager.get_setting_by_url(request.user, np.setting_url)
+        spw = SPathway(prediction_setting=setting, root_nodes=[np.smiles])
+        spw.predict()
+        return spw.to_json()
+    except ValueError:
+        return 403, {
+            "message": f"Getting Setting with id {np.setting_url} failed due to insufficient rights!"
+        }

epdb/logic.py

@@ -264,8 +264,12 @@ class GroupManager(object):
         return bool(re.findall(GroupManager.group_pattern, url))
 
     @staticmethod
-    def create_group(current_user, name, description):
+    def create_group(current_user, name, description, *args, **kwargs):
         g = Group()
+
+        if "uuid" in kwargs:
+            g.uuid = kwargs["uuid"]
+
         # Clean for potential XSS
         g.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
         g.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
@@ -341,52 +345,17 @@ class PackageManager(object):
 
     @staticmethod
     def readable(user, package):
-        if (
+        return (
-            UserPackagePermission.objects.filter(package=package, user=user).exists()
+            PackageManager.has_package_permission(user, package, "read") | package.reviewed is True
-            or GroupPackagePermission.objects.filter(
+        )
-                package=package, group__in=GroupManager.get_groups(user)
-            )
-            or package.reviewed is True
-            or user.is_superuser
-        ):
-            return True
-
-        return False
 
     @staticmethod
     def writable(user, package):
-        if (
+        return PackageManager.has_package_permission(user, package, "write")
-            UserPackagePermission.objects.filter(
-                package=package, user=user, permission=Permission.WRITE[0]
-            ).exists()
-            or GroupPackagePermission.objects.filter(
-                package=package,
-                group__in=GroupManager.get_groups(user),
-                permission=Permission.WRITE[0],
-            ).exists()
-            or UserPackagePermission.objects.filter(
-                package=package, user=user, permission=Permission.ALL[0]
-            ).exists()
-            or user.is_superuser
-        ):
-            return True
-        return False
 
     @staticmethod
     def administrable(user, package):
-        if (
+        return PackageManager.has_package_permission(user, package, "all")
-            UserPackagePermission.objects.filter(
-                package=package, user=user, permission=Permission.ALL[0]
-            ).exists()
-            or GroupPackagePermission.objects.filter(
-                package=package,
-                group__in=GroupManager.get_groups(user),
-                permission=Permission.ALL[0],
-            ).exists()
-            or user.is_superuser
-        ):
-            return True
-        return False
 
     @staticmethod
     def has_package_permission(user: "User", package: Union[str, UUID, "Package"], permission: str):
@@ -470,7 +439,9 @@ class PackageManager(object):
             # remove package if user is owner and package is reviewed e.g. admin
             qs = qs.filter(reviewed=False)
 
-        return qs.distinct()
+        qs = qs.distinct()
+
+        return qs
 
     @staticmethod
     def get_all_writeable_packages(user):
@@ -514,7 +485,9 @@ class PackageManager(object):
 
         qs = qs.filter(reviewed=False)
 
-        return qs.distinct()
+        qs = qs.distinct()
+
+        return qs
 
     @staticmethod
     def get_packages():
@@ -716,6 +689,10 @@ class PackageManager(object):
                 struc.description = structure["description"]
                 struc.aliases = structure.get("aliases", [])
                 struc.smiles = structure["smiles"]
+
+                if structure.get("molfile"):
+                    struc.molfile = structure["molfile"]
+
                 struc.save()
 
                 for scen in structure["scenarios"]:
@@ -1018,52 +995,9 @@ class PackageManager(object):
 
         print("Fixing Node depths...")
         total_pws = Pathway.objects.filter(package=pack).count()
+
         for p, pw in enumerate(Pathway.objects.filter(package=pack)):
-            in_count = defaultdict(lambda: 0)
+            pw.update_depths()
-            out_count = defaultdict(lambda: 0)
-
-            for e in pw.edges:
-                # TODO check if this will remain
-                for react in e.start_nodes.all():
-                    out_count[str(react.uuid)] += 1
-
-                for prod in e.end_nodes.all():
-                    in_count[str(prod.uuid)] += 1
-
-            root_nodes = []
-            for n in pw.nodes:
-                num_parents = in_count[str(n.uuid)]
-                if num_parents == 0:
-                    # must be a root node or unconnected node
-                    if n.depth != 0:
-                        n.depth = 0
-                        n.save()
-
-                    # Only root node may have children
-                    if out_count[str(n.uuid)] > 0:
-                        root_nodes.append(n)
-
-            levels = [root_nodes]
-            seen = set()
-            # Do a bfs to determine depths starting with level 0 a.k.a. root nodes
-            for i, level_nodes in enumerate(levels):
-                new_level = []
-                for n in level_nodes:
-                    for e in n.out_edges.all():
-                        for prod in e.end_nodes.all():
-                            if str(prod.uuid) not in seen:
-                                old_depth = prod.depth
-                                if old_depth != i + 1:
-                                    prod.depth = i + 1
-                                    prod.save()
-
-                                new_level.append(prod)
-
-                    seen.add(str(n.uuid))
-
-                if new_level:
-                    levels.append(new_level)
-
             print(f"{p + 1}/{total_pws} fixed.", end="\r")
 
         return pack
@@ -1077,7 +1011,7 @@ class PackageManager(object):
         add_import_timestamp=True,
         trust_reviewed=False,
     ) -> Package:
-        importer = PackageImporter(data, preserve_uuids, add_import_timestamp, trust_reviewed)
+        importer = PackageImporter(data, preserve_uuids)
         imported_package = importer.do_import()
 
         up = UserPackagePermission()
@@ -1894,6 +1828,11 @@ class SPathway(object):
                 "to": to_indices,
             }
 
+            if edge.rule:
+                e["rule"] = edge.rule.simple_json()
+            if edge.probability:
+                e["probability"] = edge.probability
+
             edges.append(e)
 
         return {

epdb/management/commands/bootstrap.py

@@ -99,11 +99,15 @@ class Command(BaseCommand):
                 new_license.image_link = f"https://licensebuttons.net/l/{cc_string}/4.0/88x31.png"
                 new_license.save()
 
-    def import_package(self, data, owner):
+    def import_package(self, data, owner, all_envipath_user_group):
-        return PackageManager.import_legacy_package(
+        p = PackageManager.import_legacy_package(
             data, owner, keep_ids=True, add_import_timestamp=False, trust_reviewed=True
         )
 
+        PackageManager.grant_read(owner, p, all_envipath_user_group)
+
+        return p
+
     def create_default_setting(self, owner, packages):
         s = SettingManager.create_setting(
             owner,
@@ -198,7 +202,7 @@ class Command(BaseCommand):
                     s.BASE_DIR / "fixtures" / "packages" / "2025-07-18" / p, encoding="utf-8"
                 ).read()
             )
-            imported_package = self.import_package(package_data, admin)
+            imported_package = self.import_package(package_data, admin, g)
             mapping[p.replace(".json", "")] = imported_package
 
         setting = self.create_default_setting(admin, [mapping["EAWAG-BBD"]])

epdb/migrations/0023_alter_compoundstructure_options_and_more.py

@@ -0,0 +1,49 @@
+# Generated by Django 6.0.3 on 2026-04-21 11:43
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0022_alter_classifierpluginmodel_data_packages_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterModelOptions(
+            name="compoundstructure",
+            options={},
+        ),
+        migrations.AlterModelOptions(
+            name="epmodel",
+            options={},
+        ),
+        migrations.AlterModelOptions(
+            name="parallelrule",
+            options={},
+        ),
+        migrations.AlterModelOptions(
+            name="rule",
+            options={},
+        ),
+        migrations.AlterModelOptions(
+            name="sequentialrule",
+            options={},
+        ),
+        migrations.AlterModelOptions(
+            name="simpleambitrule",
+            options={},
+        ),
+        migrations.AlterModelOptions(
+            name="simplerdkitrule",
+            options={},
+        ),
+        migrations.AlterModelOptions(
+            name="simplerule",
+            options={},
+        ),
+        migrations.AddField(
+            model_name="compoundstructure",
+            name="molfile",
+            field=models.TextField(blank=True, null=True, verbose_name="Molfile"),
+        ),
+    ]

epdb/migrations/0024_user_contacted.py

@@ -0,0 +1,17 @@
+# Generated by Django 6.0.3 on 2026-04-21 19:56
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0023_alter_compoundstructure_options_and_more"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="user",
+            name="contacted",
+            field=models.BooleanField(blank=True, null=True),
+        ),
+    ]

epdb/migrations/0025_auto_20260511_2025.py

@@ -0,0 +1,56 @@
+# Generated by Django 6.0.3 on 2026-05-11 20:25
+
+from django.db import migrations
+from envipy_additional_information import HalfLife, HalfLifeModel, HalfLifeWS
+
+MAPPING = {
+    "": HalfLifeModel.OTHER,
+    "HS-SFO": HalfLifeModel.HS_SFO,
+    "FOMC": HalfLifeModel.FOMC,
+    "FOTC": HalfLifeModel.DFOP,
+    "FMOC": HalfLifeModel.FOMC,
+    "DFOP": HalfLifeModel.DFOP,
+    "SFO + SFO": HalfLifeModel.SFO_SFO,
+    "FOMC-SFO": HalfLifeModel.FOMC_SFO,
+    "first order kinetics": HalfLifeModel.SFO,
+    "SFO²": HalfLifeModel.SFO,
+    "HS": HalfLifeModel.HS,
+    "top down": HalfLifeModel.OTHER,
+    "SFO": HalfLifeModel.SFO,
+    "First Order": HalfLifeModel.SFO,
+    "SFO/SFO": HalfLifeModel.SFO_SFO,
+    "FOMC + SFO": HalfLifeModel.FOMC_SFO,
+    "true": HalfLifeModel.SFO,
+    "SFO-SFO": HalfLifeModel.SFO_SFO,
+    "DFOP-SFO": HalfLifeModel.DFOP_SFO,
+}
+
+
+def forward_func(apps, schema_editor):
+    AdditionalInformation = apps.get_model("epdb", "AdditionalInformation")
+
+    hls = AdditionalInformation.objects.filter(type="HalfLife")
+
+    for hl in hls:
+        data = hl.data
+        data["model"] = MAPPING[data["model"]].value
+        hl.data = HalfLife(**data).model_dump(mode="json")
+        hl.save()
+
+    hlws = AdditionalInformation.objects.filter(type="HalfLifeWS")
+
+    for hl in hlws:
+        data = hl.data
+        data["model"] = MAPPING[data["model"]].value
+        hl.data = HalfLifeWS(**data).model_dump(mode="json")
+        hl.save()
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0024_user_contacted"),
+    ]
+
+    operations = [
+        migrations.RunPython(forward_func, reverse_code=migrations.RunPython.noop),
+    ]

epdb/migrations/0026_auto_20260602_1718.py

@@ -0,0 +1,48 @@
+# Generated by Django 6.0.3 on 2026-06-02 17:18
+
+from django.db import migrations
+from envipy_additional_information import DOI
+
+
+def forward_func(apps, schema_editor):
+    AdditionalInformation = apps.get_model("epdb", "AdditionalInformation")
+
+    refs = AdditionalInformation.objects.filter(type="Reference")
+
+    remaining = []
+
+    for ref in refs:
+        r = ref.data["reference"]
+        try:
+            # PubMed IDs are plain ints, try parsing
+            _ = int(r)
+            # Nothing to do
+        except ValueError:
+            DOMAINS = [
+                "http://dx.doi.org/",
+                "https://dx.doi.org/",
+                "http://doi.org/",
+                "https://doi.org/",
+            ]
+            for d in DOMAINS:
+                r = r.replace(d, "")
+
+            if r.startswith("10."):
+                ref.type = DOI.__name__
+                ref.data = {"doi": r}
+                ref.save()
+            else:
+                remaining.append(ref)
+
+    if len(remaining) > 0:
+        raise ValueError(f"Could not parse {len(remaining)} references")
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0025_auto_20260511_2025"),
+    ]
+
+    operations = [
+        migrations.RunPython(forward_func, reverse_code=migrations.RunPython.noop),
+    ]

epdb/migrations/0027_alter_compound_aliases_and_more.py

@@ -0,0 +1,150 @@
+# Generated by Django 6.0.3 on 2026-07-01 20:59
+
+import django.contrib.postgres.fields
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("epdb", "0026_auto_20260602_1718"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="compound",
+            name="aliases",
+            field=django.contrib.postgres.fields.ArrayField(
+                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="compound",
+            name="default_structure",
+            field=models.ForeignKey(
+                null=True,
+                on_delete=django.db.models.deletion.SET_NULL,
+                related_name="compound_default_structure",
+                to="epdb.compoundstructure",
+                verbose_name="Default Structure",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="compound",
+            name="scenarios",
+            field=models.ManyToManyField(
+                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="compoundstructure",
+            name="aliases",
+            field=django.contrib.postgres.fields.ArrayField(
+                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="compoundstructure",
+            name="scenarios",
+            field=models.ManyToManyField(
+                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="edge",
+            name="aliases",
+            field=django.contrib.postgres.fields.ArrayField(
+                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="edge",
+            name="edge_label",
+            field=models.ForeignKey(
+                null=True,
+                on_delete=django.db.models.deletion.CASCADE,
+                to="epdb.reaction",
+                verbose_name="Edge label",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="edge",
+            name="scenarios",
+            field=models.ManyToManyField(
+                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="node",
+            name="aliases",
+            field=django.contrib.postgres.fields.ArrayField(
+                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="node",
+            name="scenarios",
+            field=models.ManyToManyField(
+                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="pathway",
+            name="aliases",
+            field=django.contrib.postgres.fields.ArrayField(
+                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="pathway",
+            name="scenarios",
+            field=models.ManyToManyField(
+                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="reaction",
+            name="aliases",
+            field=django.contrib.postgres.fields.ArrayField(
+                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="reaction",
+            name="medline_references",
+            field=django.contrib.postgres.fields.ArrayField(
+                base_field=models.TextField(),
+                blank=True,
+                null=True,
+                verbose_name="Medline References",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="reaction",
+            name="rules",
+            field=models.ManyToManyField(
+                blank=True, related_name="reaction_rule", to="epdb.rule", verbose_name="Rule"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="reaction",
+            name="scenarios",
+            field=models.ManyToManyField(
+                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="rule",
+            name="aliases",
+            field=django.contrib.postgres.fields.ArrayField(
+                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="rule",
+            name="scenarios",
+            field=models.ManyToManyField(
+                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
+            ),
+        ),
+    ]

epdb/models.py

@@ -31,6 +31,10 @@ from sklearn.model_selection import ShuffleSplit
 
 from bridge.contracts import Property
 from bridge.dto import RunResult, PropertyPrediction
+from epdb.exceptions import (
+    InvalidMolfileException,
+    InvalidSMILESException,
+)
 from utilities.chem import FormatConverter, IndigoUtils, PredictionResult, ProductSet
 from utilities.ml import (
     ApplicabilityDomainPCA,
@@ -75,6 +79,7 @@ class User(AbstractUser):
         blank=False,
     )
     is_reviewer = models.BooleanField(default=False)
+    contacted = models.BooleanField(null=True, blank=True)
 
     USERNAME_FIELD = "email"
     REQUIRED_FIELDS = ["username"]
@@ -630,7 +635,7 @@ class EnviPathModel(TimeStampedModel):
 
 class AliasMixin(models.Model):
     aliases = ArrayField(
-        models.TextField(blank=False, null=False), verbose_name="Aliases", default=list
+        models.TextField(blank=False, null=False), verbose_name="Aliases", default=list, blank=True
     )
 
     @transaction.atomic
@@ -653,7 +658,9 @@ class AliasMixin(models.Model):
 
 
 class ScenarioMixin(models.Model):
-    scenarios = models.ManyToManyField("epdb.Scenario", verbose_name="Attached Scenarios")
+    scenarios = models.ManyToManyField(
+        "epdb.Scenario", verbose_name="Attached Scenarios", blank=True
+    )
 
     @transaction.atomic
     def set_scenarios(self, scenarios: List["Scenario"]):
@@ -779,12 +786,19 @@ class Compound(
         "CompoundStructure",
         verbose_name="Default Structure",
         related_name="compound_default_structure",
-        on_delete=models.CASCADE,
+        on_delete=models.SET_NULL,
         null=True,
     )
 
     external_identifiers = GenericRelation("ExternalIdentifier")
 
+    def get_structure_by_smiles(self, smiles: str) -> "CompoundStructure":
+        for struct in self.structures.all():
+            if struct.smiles == smiles:
+                return struct
+
+        raise ValueError(f"No structure with SMILES {smiles} found for {self.get_name()}")
+
     @property
     def structures(self) -> QuerySet:
         return CompoundStructure.objects.filter(compound=self)
@@ -853,16 +867,32 @@ class Compound(
     @staticmethod
     @transaction.atomic
     def create(
-        package: "Package", smiles: str, name: str = None, description: str = None, *args, **kwargs
+        package: "Package",
+        smiles: str,
+        molfile: str | None = None,
+        name: str | None = None,
+        description: str | None = None,
+        *args,
+        **kwargs,
     ) -> "Compound":
+        # Molfile has precendence over SMILES
+        if molfile is not None and molfile.strip() != "":
+            mol = FormatConverter.from_molfile(molfile)
+
+            if mol is None:
+                raise InvalidMolfileException("Given molfile is invalid")
+            else:
+                # Overwrite SMILES from molfile
+                smiles = FormatConverter.to_smiles(mol)
+
         if smiles is None or smiles.strip() == "":
-            raise ValueError("SMILES is required")
+            raise InvalidSMILESException("SMILES is required")
 
         smiles = smiles.strip()
 
         parsed = FormatConverter.from_smiles(smiles)
         if parsed is None:
-            raise ValueError("Given SMILES is invalid")
+            raise InvalidSMILESException("Given SMILES is invalid")
 
         standardized_smiles = FormatConverter.standardize(smiles, remove_stereo=True)
 
@@ -874,11 +904,16 @@ class Compound(
         if CompoundStructure.objects.filter(
             smiles=standardized_smiles, compound__package=package
         ).exists():
-            # TODO should we add a structure?
+            found_c = CompoundStructure.objects.get(
-            return CompoundStructure.objects.get(
                 smiles=standardized_smiles, compound__package=package
             ).compound
 
+            # As a direct match wasn't found add a new structure
+            # TODO return newly created structure
+            _ = found_c.add_structure(smiles, molfile=molfile, name=name, description=description)
+
+            return found_c
+
         # Generate Compound
         c = Compound()
         c.package = package
@@ -910,7 +945,12 @@ class Compound(
             )
 
         cs = CompoundStructure.create(
-            c, smiles, name=name, description=description, normalized_structure=is_standardized
+            c,
+            smiles,
+            molfile=molfile,
+            name=name,
+            description=description,
+            normalized_structure=is_standardized,
         )
 
         c.default_structure = cs
@@ -923,11 +963,22 @@ class Compound(
         self,
         smiles: str,
         name: str = None,
+        molfile: str = None,
         description: str = None,
         default_structure: bool = False,
         *args,
         **kwargs,
     ) -> "CompoundStructure":
+        # Molfile has precendence over SMILES
+        if molfile is not None and molfile.strip() != "":
+            mol = FormatConverter.from_molfile(molfile)
+
+            if mol is None:
+                raise InvalidMolfileException("Given molfile is invalid")
+            else:
+                # Overwrite SMILES from molfile
+                smiles = FormatConverter.to_smiles(mol)
+
         if smiles is None or smiles == "":
             raise ValueError("SMILES is required")
 
@@ -947,16 +998,28 @@ class Compound(
             )
 
         if is_standardized:
-            CompoundStructure.objects.get(smiles__in=smiles, compound__package=self.package)
+            CompoundStructure.objects.get(smiles=smiles, compound__package=self.package)
 
         # Check if we find a direct match for a given SMILES and/or its standardized SMILES
-        if CompoundStructure.objects.filter(
+        if CompoundStructure.objects.filter(smiles=smiles, compound__package=self.package).exists():
-            smiles__in=smiles, compound__package=self.package
+            found_cs = CompoundStructure.objects.get(smiles=smiles, compound__package=self.package)
-        ).exists():
+
-            return CompoundStructure.objects.get(smiles__in=smiles, compound__package=self.package)
+            if found_cs.molfile is None and (molfile is not None and molfile.strip() != ""):
+                logger.info(
+                    f"Setting molfile for found CompoundStructure(uuid={found_cs.uuid}) as it was empty"
+                )
+                found_cs.molfile = molfile
+                found_cs.save()
+
+            return found_cs
 
         cs = CompoundStructure.create(
-            self, smiles, name=name, description=description, normalized_structure=is_standardized
+            self,
+            smiles,
+            name=name,
+            molfile=molfile,
+            description=description,
+            normalized_structure=is_standardized,
         )
 
         if default_structure:
@@ -1112,6 +1175,7 @@ class CompoundStructure(
     canonical_smiles = models.TextField(blank=False, null=False, verbose_name="Canonical SMILES")
     inchikey = models.TextField(max_length=27, blank=False, null=False, verbose_name="InChIKey")
     normalized_structure = models.BooleanField(null=False, blank=False, default=False)
+    molfile = models.TextField(blank=True, null=True, verbose_name="Molfile")
 
     external_identifiers = GenericRelation("ExternalIdentifier")
 
@@ -1136,10 +1200,35 @@ class CompoundStructure(
     @staticmethod
     @transaction.atomic
     def create(
-        compound: Compound, smiles: str, name: str = None, description: str = None, *args, **kwargs
+        compound: Compound,
+        smiles: str,
+        molfile: str = None,
+        name: str = None,
+        description: str = None,
+        *args,
+        **kwargs,
     ):
+        # Molfile has precendence over SMILES
+        if molfile is not None and molfile.strip() != "":
+            mol = FormatConverter.from_molfile(molfile)
+
+            if mol is None:
+                raise InvalidMolfileException("Given molfile is invalid")
+            else:
+                # Overwrite SMILES from molfile
+                smiles = FormatConverter.to_smiles(mol)
+
         if CompoundStructure.objects.filter(compound=compound, smiles=smiles).exists():
-            return CompoundStructure.objects.get(compound=compound, smiles=smiles)
+            found_cs = CompoundStructure.objects.get(smiles=smiles, compound=compound)
+
+            if found_cs.molfile is None and (molfile is not None and molfile.strip() != ""):
+                logger.info(
+                    f"Setting molfile for found CompoundStructure(uuid={found_cs.uuid}) as it was empty"
+                )
+                found_cs.molfile = molfile
+                found_cs.save()
+
+            return found_cs
 
         if compound.pk is None:
             raise ValueError("Unpersisted Compound! Persist compound first!")
@@ -1152,8 +1241,12 @@ class CompoundStructure(
         if description is not None:
             cs.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
-        cs.smiles = smiles
         cs.compound = compound
+        cs.smiles = smiles
+
+        # Check if molfile is present and valid
+        if molfile is not None and molfile.strip() != "":
+            cs.molfile = molfile
 
         if "normalized_structure" in kwargs:
             cs.normalized_structure = kwargs["normalized_structure"]
@@ -1172,6 +1265,8 @@ class CompoundStructure(
 
     @property
     def as_svg(self, width: int = 800, height: int = 400):
+        if self.molfile is not None and self.molfile.strip() != "":
+            return IndigoUtils.mol_to_svg(self.molfile, width=width, height=height)
         return IndigoUtils.mol_to_svg(self.smiles, width=width, height=height)
 
     @property
@@ -1208,6 +1303,9 @@ class CompoundStructure(
 
         return dict(hls)
 
+    def d3_json(self):
+        return {}
+
 
 class EnzymeLink(EnviPathModel, KEGGIdentifierMixin):
     rule = models.ForeignKey("Rule", on_delete=models.CASCADE, db_index=True)
@@ -1605,10 +1703,15 @@ class Reaction(
     products = models.ManyToManyField(
         "epdb.CompoundStructure", verbose_name="Products", related_name="reaction_products"
     )
-    rules = models.ManyToManyField("epdb.Rule", verbose_name="Rule", related_name="reaction_rule")
+    rules = models.ManyToManyField(
+        "epdb.Rule", verbose_name="Rule", related_name="reaction_rule", blank=True
+    )
     multi_step = models.BooleanField(verbose_name="Multistep Reaction")
     medline_references = ArrayField(
-        models.TextField(blank=False, null=False), null=True, verbose_name="Medline References"
+        models.TextField(blank=False, null=False),
+        null=True,
+        verbose_name="Medline References",
+        blank=True,
     )
 
     external_identifiers = GenericRelation("ExternalIdentifier")
@@ -1625,7 +1728,7 @@ class Reaction(
         educts: Union[List[str], List[CompoundStructure]] = None,
         products: Union[List[str], List[CompoundStructure]] = None,
         rules: Union[Rule | List[Rule]] = None,
-        multi_step: bool = True,
+        multi_step: bool = False,
     ):
         _educts = []
         _products = []
@@ -1690,7 +1793,7 @@ class Reaction(
         if name is not None and name.strip() != "":
             r.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
 
-        if description is not None and name.strip() != "":
+        if description is not None and description.strip() != "":
             r.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
         r.multi_step = multi_step
@@ -1768,7 +1871,7 @@ class Reaction(
         return new_reaction
 
     def smirks(self):
-        return f"{'.'.join([cs.smiles for cs in self.educts.all()])}>>{'.'.join([cs.smiles for cs in self.products.all()])}"
+        return f"{'.'.join([cs.smiles for cs in self.educts.all().order_by('-pk')])}>>{'.'.join([cs.smiles for cs in self.products.all().order_by('-pk')])}"
 
     @property
     def as_svg(self):
@@ -1881,6 +1984,9 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                 if n not in queue:
                     queue.append(n)
 
+        for i in queue:
+            processed.add(i)
+
         while len(queue):
             current = queue.pop()
             processed.add(current)
@@ -1921,6 +2027,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                 # add links start -> pseudo
                 new_link = {
                     "name": link["name"],
+                    "plain_name": link["plain_name"],
                     "id": link["id"],
                     "url": link["url"],
                     "image": link["image"],
@@ -1930,6 +2037,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                     "source": node_url_to_idx[link["start_node_urls"][0]],
                     "target": pseudo_idx,
                     "app_domain": link.get("app_domain", None),
+                    "to_pseudo": True,
                 }
                 adjusted_links.append(new_link)
 
@@ -1937,6 +2045,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                 for target in link["end_node_urls"]:
                     new_link = {
                         "name": link["name"],
+                        "plain_name": link["plain_name"],
                         "id": link["id"],
                         "url": link["url"],
                         "image": link["image"],
@@ -1947,6 +2056,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                         "target": node_url_to_idx[target],
                         "app_domain": link.get("app_domain", None),
                         "multi_step": link["multi_step"],
+                        "from_pseudo": True,
                     }
                     adjusted_links.append(new_link)
 
@@ -2156,11 +2266,12 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
     def add_node(
         self,
         smiles: str,
-        name: Optional[str] = None,
+        molfile: str | None = None,
-        description: Optional[str] = None,
+        name: str | None = None,
-        depth: Optional[int] = 0,
+        description: str | None = None,
+        depth: int = -1,
     ):
-        return Node.create(self, smiles, depth, name=name, description=description)
+        return Node.create(self, smiles, depth, molfile=molfile, name=name, description=description)
 
     @transaction.atomic
     def add_edge(
@@ -2173,6 +2284,68 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
     ):
         return Edge.create(self, start_nodes, end_nodes, rule, name=name, description=description)
 
+    def update_depths(self):
+        # Collect number of in and out links per node
+        in_count = defaultdict(lambda: 0)
+        out_count = defaultdict(lambda: 0)
+
+        for e in self.edges:
+            for react in e.start_nodes.all():
+                out_count[str(react.uuid)] += 1
+
+            for prod in e.end_nodes.all():
+                in_count[str(prod.uuid)] += 1
+
+        depth_map = {}
+        depth_map[0] = list()
+        processed = set()
+
+        data_driven_root_nodes = (
+            self.node_set.all()
+            .annotate(prod_cnt=Count("edge_products"), educt_cnt=Count("edge_educts"))
+            .filter(prod_cnt=0, educt_cnt__gt=0)
+            .distinct()
+        )
+
+        # Eval QuerySet
+        root_nodes_by_depth = list(self.root_nodes)
+
+        data_driven_root_nodes.update(depth=0)
+        root_nodes = [n for n in data_driven_root_nodes]
+
+        for n in root_nodes_by_depth:
+            if n not in root_nodes:
+                if len(n.edge_products.all()) == 0:
+                    root_nodes.append(n)
+
+        for n in root_nodes:
+            depth_map[0].append(n)
+
+        # At most depth len(nodes) is possible
+        for i in range(self.nodes.count()):
+            level_nodes = depth_map.get(i, [])
+
+            if len(level_nodes) == 0:
+                break
+
+            unique_next_level = set()
+            for n in level_nodes:
+                processed.add(n)
+                for e in self.edges:
+                    if n in e.start_nodes.all():
+                        for p in e.end_nodes.all():
+                            if p not in processed:
+                                unique_next_level.add(p)
+
+            if len(unique_next_level) > 0:
+                depth_map[i + 1] = list(unique_next_level)
+
+        for depth, nodes in depth_map.items():
+            for n in nodes:
+                if n.depth != depth and depth != 0:
+                    n.depth = depth
+                    n.save()
+
 
 class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin):
     pathway = models.ForeignKey(
@@ -2194,17 +2367,19 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
     def _url(self):
         return "{}/node/{}".format(self.pathway.url, self.uuid)
 
-    def get_name(self):
+    def get_name(self, include_suffix=True):
         non_generic_name = True
 
-        if self.name == "no name":
+        if self.name is None or self.name == "no name":
             non_generic_name = False
 
-        return (
+        if non_generic_name:
-            self.name
+            return self.name
-            if non_generic_name
+        else:
-            else f"{self.default_node_label.name} (taken from underlying structure)"
+            if include_suffix:
-        )
+                return f"{self.default_node_label.name} (taken from underlying structure)"
+            else:
+                return self.default_node_label.name
 
     def d3_json(self):
         app_domain_data = self.get_app_domain_assessment_data()
@@ -2214,16 +2389,27 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             if isinstance(ai.get(), PropertyPrediction):
                 predicted_properties[ai.get().__class__.__name__].append(ai.data)
 
-        return {
+        # If we have Subclasses of a CompoundStructure we can overwrite keys (e.g. images)
+        # by overwriting keys
+        structure_data = self.default_node_label.d3_json()
+
+        res = {
             "depth": self.depth,
             "stereo_removed": self.stereo_removed,
             "url": self.url,
             "node_label_id": self.default_node_label.url,
             "image": f"{self.url}?image=svg",
             "image_svg": IndigoUtils.mol_to_svg(
-                self.default_node_label.smiles, width=40, height=40
+                self.default_node_label.molfile
+                if self.default_node_label.molfile is not None
+                and self.default_node_label.molfile.strip()
+                else self.default_node_label.smiles,
+                width=40,
+                height=40,
             ),
+            "image_type": "svg",
             "name": self.get_name(),
+            "plain_name": self.get_name(include_suffix=False),
             "smiles": self.default_node_label.smiles,
             "scenarios": [{"name": s.get_name(), "url": s.url} for s in self.scenarios.all()],
             "app_domain": {
@@ -2235,48 +2421,71 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             "predicted_properties": predicted_properties,
             "is_engineered_intermediate": self.kv.get("is_engineered_intermediate", False),
             "timeseries": self.get_timeseries_data(),
+            **structure_data,
         }
 
+        return res
+
     @staticmethod
     @transaction.atomic
     def create(
         pathway: "Pathway",
         smiles: str,
         depth: int,
-        name: Optional[str] = None,
+        molfile: str | None = None,
-        description: Optional[str] = None,
+        name: str | None = None,
+        description: str | None = None,
     ):
+        # Molfile has precendence over SMILES
+        if molfile is not None and molfile.strip() != "":
+            mol = FormatConverter.from_molfile(molfile)
+
+            if mol is None:
+                raise InvalidMolfileException("Given molfile is invalid")
+            else:
+                # Overwrite SMILES from molfile
+                smiles = FormatConverter.to_smiles(mol)
+
         stereo_removed = False
         if pathway.predicted and FormatConverter.has_stereo(smiles):
             smiles = FormatConverter.standardize(smiles, remove_stereo=True)
             stereo_removed = True
 
-        c = Compound.create(pathway.package, smiles, name=name, description=description)
+        c = Compound.create(
+            pathway.package, smiles, molfile=molfile, name=name, description=description
+        )
 
-        if Node.objects.filter(pathway=pathway, default_node_label=c.default_structure).exists():
+        structure = c.get_structure_by_smiles(smiles)
-            return Node.objects.get(pathway=pathway, default_node_label=c.default_structure)
+
+        if Node.objects.filter(pathway=pathway, default_node_label=structure).exists():
+            return Node.objects.get(pathway=pathway, default_node_label=structure)
 
         n = Node()
         n.stereo_removed = stereo_removed
         n.pathway = pathway
         n.depth = depth
 
-        n.default_node_label = c.default_structure
+        n.default_node_label = structure
         n.save()
 
-        n.node_labels.add(c.default_structure)
+        n.node_labels.add(structure)
         n.save()
 
         return n
 
     @property
     def as_svg(self):
+        if (
+            self.default_node_label.molfile is not None
+            and self.default_node_label.molfile.strip() != ""
+        ):
+            return IndigoUtils.mol_to_svg(self.default_node_label.molfile)
         return IndigoUtils.mol_to_svg(self.default_node_label.smiles)
 
     def get_timeseries_data(self):
         for ai in self.additional_information.all():
-            if ai.__class__.__name__ == "OECD301FTimeSeries":
+            if ai.type == "OECD301FTimeSeries":
-                return ai.model_dump(mode="json")
+                return ai.get().model_dump(mode="json")
 
         return None
 
@@ -2307,13 +2516,35 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
 
         return res
 
+    def is_proposed_intermediate(self):
+        collected = defaultdict(dict)
+        for ai in self.additional_information.filter(
+            type__in=["ProposedIntermediate", "TransformationProductImportance", "Confidence"],
+            scenario__isnull=False,
+        ):
+            collected[str(ai.scenario.uuid)]["scenarioId"] = ai.scenario.url
+            collected[str(ai.scenario.uuid)]["scenarioName"] = ai.scenario.name
+
+            if ai.type == "ProposedIntermediate":
+                collected[str(ai.scenario.uuid)]["proposed"] = True
+
+            if ai.type == "Confidence":
+                collected[str(ai.scenario.uuid)]["Confidence"] = ai.get().level
+
+            if ai.type == "TransformationProductImportance":
+                collected[str(ai.scenario.uuid)]["Transformation product importance"] = (
+                    ai.get().importance.value
+                )
+
+        return list(collected.values())
+
 
 class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin):
     pathway = models.ForeignKey(
         "epdb.Pathway", verbose_name="belongs to", on_delete=models.CASCADE, db_index=True
     )
     edge_label = models.ForeignKey(
-        "epdb.Reaction", verbose_name="Edge label", null=True, on_delete=models.SET_NULL
+        "epdb.Reaction", verbose_name="Edge label", null=True, on_delete=models.CASCADE
     )
     start_nodes = models.ManyToManyField(
         "epdb.Node", verbose_name="Start Nodes", related_name="edge_educts"
@@ -2328,6 +2559,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
     def d3_json(self):
         edge_json = {
             "name": self.get_name(),
+            "plain_name": self.get_name(include_suffix=False),
             "id": self.url,
             "url": self.url,
             "image": self.url + "?image=svg",
@@ -2392,6 +2624,8 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
         rule: Optional[Rule] = None,
         name: Optional[str] = None,
         description: Optional[str] = None,
+        *args,
+        **kwargs,
     ):
         e = Edge()
         e.pathway = pathway
@@ -2421,7 +2655,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             educts=[n.default_node_label for n in e.start_nodes.all()],
             products=[n.default_node_label for n in e.end_nodes.all()],
             rules=rule,
-            multi_step=False,
+            multi_step=kwargs.get("multi_step", False),
         )
 
         e.edge_label = r
@@ -2440,17 +2674,19 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
 
         return res
 
-    def get_name(self):
+    def get_name(self, include_suffix=True):
         non_generic_name = True
 
         if self.name == "no name":
             non_generic_name = False
 
-        return (
+        if non_generic_name:
-            self.name
+            return self.name
-            if non_generic_name
+        else:
-            else f"{self.edge_label.name} (taken from underlying reaction)"
+            if include_suffix:
-        )
+                return f"{self.edge_label.name} (taken from underlying reaction)"
+            else:
+                return self.edge_label.name
 
 
 class EPModel(PolymorphicModel, EnviPathModel, AdditionalInformationMixin):
@@ -4429,18 +4665,22 @@ class AdditionalInformation(models.Model):
 
         return f"{self.scenario.url}/additional-information/{self.uuid}"
 
-    def get(self) -> "EnviPyModel":
+    @staticmethod
+    def from_dict(ai_type: str, ai_data: Dict[str, Any]):
         from envipy_additional_information import registry
 
         MAPPING = {c.__name__: c for c in registry.list_models().values()}
         try:
-            inst = MAPPING[self.type](**self.data)
+            inst = MAPPING[ai_type](**ai_data)
         except Exception as e:
-            print(f"Error loading {self.type}: {e}")
+            print(f"Error loading {ai_type}: {e}")
             raise e
 
-        inst.__dict__["uuid"] = str(self.uuid)
+        return inst
 
+    def get(self) -> "EnviPyModel":
+        inst = AdditionalInformation.from_dict(self.type, self.data)
+        inst.__dict__["uuid"] = str(self.uuid)
         return inst
 
     def __str__(self) -> str:

epdb/views.py

@@ -19,6 +19,7 @@ from sentry_sdk import capture_exception
 
 from utilities.chem import FormatConverter, IndigoUtils
 from utilities.decorators import package_permission_required
+from .exceptions import InvalidMolfileException, InvalidSMILESException
 
 from .logic import (
     EPDBURLParser,
@@ -556,7 +557,7 @@ def packages(request):
 
         # Context for paginated template
         context["entity_type"] = "package"
-        context["api_endpoint"] = "/api/v1/packages/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/packages/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "packages"
 
@@ -614,7 +615,7 @@ def compounds(request):
 
         # Context for paginated template
         context["entity_type"] = "compound"
-        context["api_endpoint"] = "/api/v1/compounds/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/compounds/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_mode"] = "tabbed"
         context["list_title"] = "compounds"
@@ -643,7 +644,7 @@ def rules(request):
 
         # Context for paginated template
         context["entity_type"] = "rule"
-        context["api_endpoint"] = "/api/v1/rules/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/rules/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "rules"
 
@@ -671,7 +672,7 @@ def reactions(request):
 
         # Context for paginated template
         context["entity_type"] = "reaction"
-        context["api_endpoint"] = "/api/v1/reactions/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/reactions/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "reactions"
 
@@ -699,7 +700,7 @@ def pathways(request):
 
         # Context for paginated template
         context["entity_type"] = "pathway"
-        context["api_endpoint"] = "/api/v1/pathways/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/pathways/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "pathways"
 
@@ -729,7 +730,7 @@ def scenarios(request):
 
         # Context for paginated template
         context["entity_type"] = "scenario"
-        context["api_endpoint"] = "/api/v1/scenarios/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/scenarios/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "scenarios"
 
@@ -754,6 +755,11 @@ def models(request):
             {"Model": s.SERVER_URL + "/model"},
         ]
 
+        context["entity_type"] = "model"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/models/"
+        context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
+        context["list_title"] = "models"
+
         # Keep model_types for potential modal/action use
         context["model_types"] = {
             "ML Relative Reasoning": {
@@ -766,12 +772,14 @@ def models(request):
                 "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():
@@ -779,6 +787,9 @@ def models(request):
                     "type": k,
                     "requires_rule_packages": v.requires_rule_packages(),
                     "requires_data_packages": v.requires_data_packages(),
+                    "additional_parameters": v.Config.__name__.lower()
+                    if v.Config.__name__ != ""
+                    else None,
                 }
             for k, v in s.PROPERTY_PLUGINS.items():
                 context["model_types"][v.display()] = {
@@ -787,12 +798,6 @@ def models(request):
                     "requires_data_packages": v.requires_data_packages(),
                 }
 
-        # Context for paginated template
-        context["entity_type"] = "model"
-        context["api_endpoint"] = "/api/v1/models/"
-        context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
-        context["list_title"] = "models"
-
         return render(request, "collections/models_paginated.html", context)
 
     elif request.method == "POST":
@@ -871,7 +876,7 @@ def package_models(request, package_uuid):
         context["object_type"] = "model"
         context["breadcrumbs"] = breadcrumbs(current_package, "model")
         context["entity_type"] = "model"
-        context["api_endpoint"] = f"/api/v1/package/{current_package.uuid}/model/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/package/{current_package.uuid}/model/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "models"
 
@@ -906,12 +911,13 @@ 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():
@@ -1087,6 +1093,11 @@ def package_model(request, package_uuid, model_uuid):
                             }
                         )
 
+                        # Sort data by prob desc
+                        res["pred"] = sorted(
+                            res["pred"], key=lambda x: x["probability"], reverse=True
+                        )
+
                 return JsonResponse(res, safe=False)
 
             elif half_life:
@@ -1190,9 +1201,7 @@ def package(request, package_uuid):
     if request.method == "GET":
         if request.GET.get("export", False) == "true":
             filename = f"{current_package.get_name().replace(' ', '_')}_{current_package.uuid}.json"
-            pack_json = PackageManager.export_package(
+            pack_json = PackageManager.export_package(current_package)
-                current_package, include_models=False, include_external_identifiers=False
-            )
             response = JsonResponse(pack_json, content_type="application/json")
             response["Content-Disposition"] = f'attachment; filename="{filename}"'
 
@@ -1341,7 +1350,7 @@ def package_compounds(request, package_uuid):
         context["object_type"] = "compound"
         context["breadcrumbs"] = breadcrumbs(current_package, "compound")
         context["entity_type"] = "compound"
-        context["api_endpoint"] = f"/api/v1/package/{current_package.uuid}/compound/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/package/{current_package.uuid}/compound/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_mode"] = "tabbed"
         context["list_title"] = "compounds"
@@ -1375,12 +1384,18 @@ def package_compounds(request, package_uuid):
     elif request.method == "POST":
         compound_name = request.POST.get("compound-name")
         compound_smiles = request.POST.get("compound-smiles")
+        compound_molfile = request.POST.get("compound-molfile")
         compound_description = request.POST.get("compound-description")
+
         try:
             c = Compound.create(
-                current_package, compound_smiles, compound_name, compound_description
+                current_package,
+                compound_smiles,
+                molfile=compound_molfile,
+                name=compound_name,
+                description=compound_description,
             )
-        except ValueError as e:
+        except (InvalidSMILESException, InvalidMolfileException) as e:
             raise BadRequest(str(e))
 
         return redirect(c.url)
@@ -1494,7 +1509,7 @@ def package_compound_structures(request, package_uuid, compound_uuid):
         context["entity_type"] = "structure"
         context["page_title"] = f"{current_compound.get_name()} - Structures"
         context["api_endpoint"] = (
-            f"/api/v1/package/{current_package.uuid}/compound/{current_compound.uuid}/structure/"
+            f"{s.SERVER_PATH}/api/v1/package/{current_package.uuid}/compound/{current_compound.uuid}/structure/"
         )
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["compound"] = current_compound
@@ -1506,11 +1521,15 @@ def package_compound_structures(request, package_uuid, compound_uuid):
     elif request.method == "POST":
         structure_name = request.POST.get("structure-name")
         structure_smiles = request.POST.get("structure-smiles")
+        structure_molfile = request.POST.get("structure-molfile")
         structure_description = request.POST.get("structure-description")
 
         try:
             cs = current_compound.add_structure(
-                structure_smiles, structure_name, structure_description
+                structure_smiles,
+                molfile=structure_molfile,
+                name=structure_name,
+                description=structure_description,
             )
         except ValueError:
             return error(
@@ -1657,7 +1676,7 @@ def package_rules(request, package_uuid):
         context["object_type"] = "rule"
         context["breadcrumbs"] = breadcrumbs(current_package, "rule")
         context["entity_type"] = "rule"
-        context["api_endpoint"] = f"/api/v1/package/{current_package.uuid}/rule/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/package/{current_package.uuid}/rule/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "rules"
 
@@ -1865,7 +1884,7 @@ def package_reactions(request, package_uuid):
         context["object_type"] = "reaction"
         context["breadcrumbs"] = breadcrumbs(current_package, "reaction")
         context["entity_type"] = "reaction"
-        context["api_endpoint"] = f"/api/v1/package/{current_package.uuid}/reaction/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/package/{current_package.uuid}/reaction/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "reactions"
 
@@ -2015,7 +2034,7 @@ def package_pathways(request, package_uuid):
         context["object_type"] = "pathway"
         context["breadcrumbs"] = breadcrumbs(current_package, "pathway")
         context["entity_type"] = "pathway"
-        context["api_endpoint"] = f"/api/v1/package/{current_package.uuid}/pathway/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/package/{current_package.uuid}/pathway/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "pathways"
 
@@ -2081,12 +2100,14 @@ def package_pathways(request, package_uuid):
         else:
             prediction_setting = current_user.prediction_settings()
 
+        is_predict_mode = pw_mode in {"predict", "incremental"}
+
         pw = Pathway.create(
             current_package,
-            stand_smiles,
+            stand_smiles if is_predict_mode else smiles,
             name=name,
             description=description,
-            predicted=pw_mode in {"predict", "incremental"},
+            predicted=is_predict_mode,
         )
 
         # set mode
@@ -2328,7 +2349,16 @@ def package_pathway_nodes(request, package_uuid, pathway_uuid):
         node_description = request.POST.get("node-description")
 
         node_smiles = request.POST.get("node-smiles").strip()
-        current_pathway.add_node(node_smiles, name=node_name, description=node_description)
+        node_molfile = request.POST.get("node-molfile").strip()
+
+        try:
+            current_pathway.add_node(
+                node_smiles, molfile=node_molfile, name=node_name, description=node_description
+            )
+        except InvalidSMILESException:
+            return error(
+                request, "Node creation failed!", f"Given SMILES ({node_smiles}) is invalid"
+            )
 
         return redirect(current_pathway.url)
 
@@ -2436,7 +2466,26 @@ def package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
 
             return JsonResponse({"success": current_node.url})
 
-        return HttpResponseBadRequest()
+        new_node_name = request.POST.get("node-name")
+        new_node_description = request.POST.get("node-description")
+
+        if any([new_node_name, new_node_description]):
+            if new_node_name is not None and new_node_name.strip() != "":
+                new_node_name = nh3.clean(new_node_name.strip(), tags=s.ALLOWED_HTML_TAGS).strip()
+                current_node.name = new_node_name
+
+            if new_node_description is not None and new_node_description.strip() != "":
+                new_node_description = nh3.clean(
+                    new_node_description.strip(), tags=s.ALLOWED_HTML_TAGS
+                ).strip()
+                current_node.description = new_node_description
+
+            current_node.save()
+
+            return redirect(current_node.url)
+
+        return error(request, "Node update failed!", "No changes were made to the node")
+
     else:
         return HttpResponseNotAllowed(["GET", "POST"])
 
@@ -2506,6 +2555,9 @@ def package_pathway_edges(request, package_uuid, pathway_uuid):
             substrate_nodes, product_nodes, name=edge_name, description=edge_description
         )
 
+        # Update depths as sideeffect of above operation
+        current_pathway.update_depths()
+
         return redirect(current_pathway.url)
 
     else:
@@ -2591,7 +2643,7 @@ def package_scenarios(request, package_uuid):
         context["object_type"] = "scenario"
         context["breadcrumbs"] = breadcrumbs(current_package, "scenario")
         context["entity_type"] = "scenario"
-        context["api_endpoint"] = f"/api/v1/package/{current_package.uuid}/scenario/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/package/{current_package.uuid}/scenario/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "scenarios"
 
@@ -2846,9 +2898,15 @@ def groups(request):
             {"Group": s.SERVER_URL + "/group"},
         ]
 
-        context["objects"] = Group.objects.all()
+        # Context for paginated template
+        context["entity_type"] = "group"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/groups/"
+        context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
+        context["list_title"] = "groups"
+        context["list_mode"] = "combined"
+
+        return render(request, "collections/groups_paginated.html", context)
 
-        return render(request, "collections/objects_list.html", context)
     elif request.method == "POST":
         group_name = request.POST.get("group-name")
         group_description = request.POST.get("group-description", s.DEFAULT_VALUES["description"])
@@ -2940,7 +2998,7 @@ def settings(request):
 
         # Context for paginated template
         context["entity_type"] = "setting"
-        context["api_endpoint"] = "/api/v1/settings/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/settings/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "settings"
         context["list_mode"] = "combined"
@@ -3071,12 +3129,21 @@ def jobs(request):
             {"Home": s.SERVER_URL},
             {"Jobs": s.SERVER_URL + "/jobs"},
         ]
-        if current_user.is_superuser:
+        # if current_user.is_superuser:
-            context["jobs"] = JobLog.objects.all().order_by("-created")
+        #     context["jobs"] = JobLog.objects.all().order_by("-created")
-        else:
+        # else:
-            context["jobs"] = JobLog.objects.filter(user=current_user).order_by("-created")
+        #     context["jobs"] = JobLog.objects.filter(user=current_user).order_by("-created")
 
-        return render(request, "collections/joblog.html", context)
+        # Context for paginated template
+        context["entity_type"] = "joblog"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/joblog/"
+        context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
+        context["list_title"] = "joblog"
+        context["list_mode"] = "combined"
+
+        return render(request, "collections/joblog_paginated.html", context)
+
+        # return render(request, "collections/joblog.html", context)
 
     elif request.method == "POST":
         job_name = request.POST.get("job-name")

migration/views.py

@@ -65,6 +65,25 @@ def run_both_engines(SMILES, SMIRKS):
 
 
 def migration(request):
+    accepted_diffs = [
+        "bt0055-3469.1",
+        "bt0056-2685",
+        "bt0193-4263",
+        "bt0231-1871.1",
+        "bt0242-3803",
+        "bt0254-4224.1",
+        "bt0254-4224.2",
+        "bt0291-1129",
+        "bt0337-3543",
+        "bt0391-4285",
+        "bt0402-3576",
+        "bt0404-3928",
+        "bt0416-4269",
+        "bt0432-4254",
+        "bt0337-4117",
+        "bt0322-3393",
+    ]
+
     if request.method == "GET":
         context = get_base_context(request)
 
@@ -109,11 +128,11 @@ def migration(request):
                         ),
                         "id": str(r.uuid),
                         "url": r.url,
-                        "status": res,
+                        "status": res or r.name in accepted_diffs,
                     }
                 )
 
-                if res:
+                if res or r.name in accepted_diffs:
                     success += 1
                 else:
                     error += 1
@@ -135,7 +154,16 @@ def migration(request):
 
         for r in migration_status["results"]:
             r["detail_url"] = r["detail_url"].replace("http://localhost:8000", s.SERVER_URL)
+            if r["name"] in accepted_diffs:
+                r["status"] = True
 
+        migration_status["results"] = sorted(
+            migration_status["results"], key=lambda x: (x["status"], x["name"])
+        )
+
+        num_success = sum([int(x["status"]) for x in migration_status["results"]])
+        migration_status["success"] = num_success
+        migration_status["error"] = migration_status["total"] - num_success
         context.update(**migration_status)
 
         return render(request, "migration.html", context)

package.json

@@ -21,5 +21,11 @@
     "django",
     "tailwindcss",
     "daisyui"
-  ]
+  ],
+  "pnpm": {
+    "onlyBuiltDependencies": [
+      "@parcel/watcher",
+      "@tailwindcss/oxide"
+    ]
+  }
 }

pepper/__init__.py

@@ -46,7 +46,7 @@ class PepperPrediction(PropertyPrediction):
 
         import matplotlib.patches as mpatches
         import numpy as np
-        from matplotlib import pyplot as plt
+        from matplotlib.figure import Figure
         from scipy import stats
 
         """
@@ -101,7 +101,8 @@ class PepperPrediction(PropertyPrediction):
         mask_red = x > vp
 
         # Plot
-        fig, ax = plt.subplots(figsize=(9, 5.5))
+        fig = Figure(figsize=(9, 5.5))
+        ax = fig.subplots()
         ax.plot(x, y, color="#1f4e79", lw=2, label="Lognormal PDF")
 
         if np.any(mask_green):
@@ -146,13 +147,12 @@ class PepperPrediction(PropertyPrediction):
         ]
         ax.legend(handles=patches, frameon=True)
 
-        plt.tight_layout()
+        fig.tight_layout()
 
         # --- Export to SVG string ---
         buf = io.StringIO()
         fig.savefig(buf, format="svg", bbox_inches="tight")
         svg = buf.getvalue()
-        plt.close(fig)
         buf.close()
 
         return svg

pepper/impl/pepper.py

@@ -187,8 +187,9 @@ class Pepper:
         groups = [group for group in dataset.group_by("structure_id")]
 
         # Unless explicitly set compute everything serial
-        if os.environ.get("N_PEPPER_THREADS", 1) > 1:
+        n_threads = int(os.environ.get("N_PEPPER_THREADS", 1))
-            results = Parallel(n_jobs=os.environ["N_PEPPER_THREADS"])(
+        if n_threads > 1:
+            results = Parallel(n_jobs=n_threads)(
                 delayed(compute_bayes_per_group)(group[1])
                 for group in dataset.group_by("structure_id")
             )

pnpm-workspace.yaml

@@ -1,3 +1,5 @@
+allowBuilds:
+  '@parcel/watcher': true
 onlyBuiltDependencies:
   - '@parcel/watcher'
   - '@tailwindcss/oxide'

static/css/input.css

@@ -34,3 +34,12 @@
 }
 
 @import "./daisyui-theme.css";
+
+select.select[multiple] {
+  display: block;
+  white-space: normal;
+}
+
+p a {
+  @apply underline;
+}

static/js/alpine/components/widgets.js

@@ -59,6 +59,9 @@ document.addEventListener("alpine:init", () => {
     get isEditMode() {
       return this.mode === "edit";
     },
+    get isRequired() {
+      return (this.schema.required || []).indexOf(this.fieldName) > -1
+    }
   });
 
   // Text widget
@@ -293,6 +296,34 @@ document.addEventListener("alpine:init", () => {
     }),
   );
 
+    // PubMed link widget
+  Alpine.data(
+    "doiWidget",
+    (fieldName, data, schema, uiSchema, mode, debugErrors, context = null) => ({
+      ...baseWidget(
+        fieldName,
+        data,
+        schema,
+        uiSchema,
+        mode,
+        debugErrors,
+        context,
+      ),
+
+      get value() {
+        return this.data[this.fieldName] || "";
+      },
+      set value(v) {
+        this.data[this.fieldName] = v;
+      },
+      get doiUrl() {
+        return this.value
+          ? `https://dx.doi.org/${this.value}`
+          : null;
+      },
+    }),
+  );
+
   // Compound link widget
   Alpine.data(
     "compoundWidget",

static/js/alpine/pagination.js

@@ -5,6 +5,126 @@
  */
 
 document.addEventListener('alpine:init', () => {
+
+  const basePagination = (
+    items,
+    currentPage,
+    totalPages,
+    totalItems,
+    perPage,
+    isReviewed,
+    instanceId
+  ) => ({
+    items,
+    currentPage,
+    totalPages,
+    totalItems,
+    perPage,
+    isReviewed,
+    instanceId,
+
+    get paginatedItems() {
+      return this.items;
+    },
+
+    get showingStart() {
+      if (this.totalItems === 0) return 0;
+      return (this.currentPage - 1) * this.perPage + 1;
+    },
+
+    get showingEnd() {
+      if (this.totalItems === 0) return 0;
+      return Math.min((this.currentPage - 1) * this.perPage + this.items.length, this.totalItems);
+    },
+
+    nextPage() {
+      if (this.currentPage < this.totalPages) {
+        this.fetchPage(this.currentPage + 1);
+      }
+    },
+
+    prevPage() {
+      if (this.currentPage > 1) {
+        this.fetchPage(this.currentPage - 1);
+      }
+    },
+
+    goToPage(page) {
+      if (page >= 1 && page <= this.totalPages) {
+        this.fetchPage(page);
+      }
+    },
+
+    get pageNumbers() {
+      const pages = [];
+      const total = this.totalPages;
+      const current = this.currentPage;
+
+      if (total === 0) {
+        return pages;
+      }
+
+      if (total <= 7) {
+        for (let i = 1; i <= total; i++) {
+          pages.push({ page: i, isEllipsis: false, key: `${this.instanceId}-page-${i}` });
+        }
+      } else {
+        pages.push({ page: 1, isEllipsis: false, key: `${this.instanceId}-page-1` });
+
+        let rangeStart;
+        let rangeEnd;
+
+        if (current <= 4) {
+          rangeStart = 2;
+          rangeEnd = 5;
+        } else if (current >= total - 3) {
+          rangeStart = total - 4;
+          rangeEnd = total - 1;
+        } else {
+          rangeStart = current - 1;
+          rangeEnd = current + 1;
+        }
+
+        if (rangeStart > 2) {
+          pages.push({ page: '...', isEllipsis: true, key: `${this.instanceId}-ellipsis-start` });
+        }
+
+        for (let i = rangeStart; i <= rangeEnd; i++) {
+          pages.push({ page: i, isEllipsis: false, key: `${this.instanceId}-page-${i}` });
+        }
+
+        if (rangeEnd < total - 1) {
+          pages.push({ page: '...', isEllipsis: true, key: `${this.instanceId}-ellipsis-end` });
+        }
+
+        pages.push({ page: total, isEllipsis: false, key: `${this.instanceId}-page-${total}` });
+      }
+
+      return pages;
+    }
+  });
+
+  Alpine.data('paginatedList',
+    (items, options = {}) => ({
+      ...basePagination(items,1, 0, 0, options.perPage || 50, options.isReviewed || false, options.instanceId || Math.random().toString(36).substring(2, 9),),
+
+      init() {
+        this.fetchPage(1);
+      },
+
+      async fetchPage(page) {
+        this.totalItems = this.items.length;
+        this.totalPages = Math.ceil(this.items.length / this.perPage);
+        this.currentPage = page
+
+        const start = page * this.perPage - this.perPage;
+        const end = page * this.perPage;
+        return this.items.slice(start, end);
+      }
+
+    })
+  );
+
   Alpine.data('remotePaginatedList', (options = {}) => ({
     items: [],
     currentPage: 1,

static/js/pw.js

@@ -1,5 +1,37 @@
 console.log("loaded pw.js")
 
+function findPaths(source_idx, links) {
+    const resultLinks = new Set();
+    const visited = new Set();
+    // Helper function for depth-first search
+    function dfs(current) {
+
+        if (visited.has(current)) {
+            return;
+        }
+
+        if (links.filter(link => link.target.id === current).length === 0) {
+            return;
+        }
+
+        visited.add(current);
+        links.forEach(link => {
+            if (
+                link.target.id === current &&
+                !visited.has(link.source.id) &&
+                link.source.id !== link.target.id // Avoid self-loops
+            ) {
+                resultLinks.add(link); // Add link to result
+                dfs(link.source.id);
+            }
+        });
+        visited.delete(current);
+    }
+    // Start DFS
+    dfs(source_idx);
+    return Array.from(resultLinks);
+}
+
 function predictFromNode(url) {
     fetch("", {
         method: "POST",
@@ -23,6 +55,7 @@ function predictFromNode(url) {
 // elem = 'vizdiv'
 function draw(pathway, elem) {
 
+    const initialzoom = 2.5
     const nodeRadius = 20;
     const linkDistance = 100;
     const chargeStrength = -200;
@@ -34,6 +67,9 @@ function draw(pathway, elem) {
         const horizontalSpacing = 75; // horizontal space between nodes
         const depthMap = new Map();
 
+        // Avoid leaving unconnected Nodes leaving the viewport
+        nodes.forEach(node => {if (node.depth < 0)  node.depth = 0;});
+
         // Sort nodes by depth first to minimize crossings
         const sortedNodes = [...nodes].sort((a, b) => a.depth - b.depth);
 
@@ -63,7 +99,7 @@ function draw(pathway, elem) {
                 node.fx = width / 2 + depthMap.get(node.depth) * horizontalSpacing - ((nodesInLevel - 1) * horizontalSpacing) / 2;
             }
 
-            node.fy = node.depth * levelSpacing + 50;
+            node.fy = (node.depth + initialzoom + 0.5) * levelSpacing + 50;
             depthMap.set(node.depth, depthMap.get(node.depth) + 1);
         });
     }
@@ -101,12 +137,31 @@ function draw(pathway, elem) {
         // Update pseudo node positions first
         updatePseudoNodePositions();
 
-        link.attr("x1", d => d.source.x)
+        link.attr("d", d => {
-            .attr("y1", d => d.source.y)
+            // Check if it's a self-loop (source equals target)
-            .attr("x2", d => d.target.x)
+            if (d.source.id === d.target.id) {
-            .attr("y2", d => d.target.y);
+                // Create a bezier curve for self-loops
+                const x = d.source.x;
+                const y = d.source.y;
+                const loopRadius = nodeRadius * 2; // Adjust size of the loop
+
+                // Create a circular path to the left of the node
+                return `M ${x},${y - nodeRadius}
+                        C ${x - loopRadius},${y - nodeRadius - loopRadius}
+                          ${x - loopRadius},${y + nodeRadius + loopRadius}
+                          ${x},${y + nodeRadius}`;
+            } else {
+                // Regular straight line for normal edges
+                return `M ${d.source.x},${d.source.y} L ${d.target.x},${d.target.y}`;
+            }
+        });
 
         node.attr("transform", d => `translate(${d.x},${d.y})`);
+
+        linkText
+         .attr("x", d => (d.source.x + d.target.x) / 2)
+         .attr("y", d => (d.source.y + d.target.y) / 2);
+
     }
 
     function dragstarted(event, d) {
@@ -209,7 +264,7 @@ function draw(pathway, elem) {
     }
 
     // Wait before showing popup (ms)
-    var popupWaitBeforeShow = 1000;
+    var popupWaitBeforeShow = 750;
 
     // Custom popover element
     let popoverTimeout = null;
@@ -441,7 +496,7 @@ function draw(pathway, elem) {
         if (n.stereo_removed) {
             popupContent += "<span class='alert alert-warning alert-soft'>Removed stereochemistry for prediction</span>";
         }
-        popupContent += "<a href='" + n.url + "'>" + n.name + "</a><br>";
+        popupContent += "<a href='" + n.url + "'>" + n.plain_name + "</a><br>";
         popupContent += "Depth " + n.depth + "<br>"
 
         if (appDomainViewEnabled) {
@@ -463,7 +518,7 @@ function draw(pathway, elem) {
                     // TODO needs to be generic once we store it as AddInf
                     for (var s of n.predicted_properties["PepperPrediction"]) {
                         if (s["mean"] != null) {
-                            tempContent += "<b>DT50 predicted via Pepper:</b> " + s["mean"].toFixed(2) + "<br>"
+                            tempContent += "<b>DT50 predicted via Pepper:</b> " + s["mean"].toFixed(2) + " days<br>"
                         }
                     }
                 }
@@ -481,6 +536,21 @@ function draw(pathway, elem) {
             popupContent += '<b>Half-lives and related scenarios:</b><br>'
             for (var s of n.scenarios) {
                 popupContent += "<a href='" + s.url + "'>" + s.name + "</a><br>";
+                for (var prop in n.proposed) {
+                    if (n.proposed[prop].scenarioId === s.url) {
+                        if("proposed" in n.proposed[prop]){
+                            popupContent += "This compound is a proposed intermediate" + "<br>";
+                        }
+                        if("Confidence" in n.proposed[prop]){
+                            popupContent += "Confidence: " + n.proposed[prop]["Confidence"] + "<br>";
+                        }
+                        if("Transformation product importance" in n.proposed[prop]){
+                            popupContent += "Transformation product importance: " + n.proposed[prop]["Transformation product importance"] + "<br>";
+                        }
+                    }
+                }
+                popupContent += "<br>";
+
             }
         }
 
@@ -493,7 +563,7 @@ function draw(pathway, elem) {
     }
 
     function edge_popup(e) {
-        popupContent = "<a href='" + e.url + "'>" + e.name + "</a><br><br>";
+        popupContent = "<a href='" + e.url + "'>" + e.plain_name + "</a><br><br>";
 
         if (e.reaction.rules) {
             for (var rule of e.reaction.rules) {
@@ -544,7 +614,7 @@ function draw(pathway, elem) {
 
     // Add background rectangle FIRST to enable pan/zoom on empty space
     // This must be inserted before zoomable group so it's behind everything
-    svg.insert("rect", "#zoomable")
+    const rect = svg.insert("rect", "#zoomable")
         .attr("x", 0)
         .attr("y", 0)
         .attr("width", width)
@@ -553,6 +623,30 @@ function draw(pathway, elem) {
         .attr("pointer-events", "all")
         .style("cursor", "grab");
 
+    // Click on empty SVG space (not on a node or link)
+    rect.on("click", function(event) {
+        // Only treat it as a background click if the direct target is the rect itself
+        // (clicks on nodes/links bubble up but originate from different elements)
+        const target = event.target;
+        const isNode = target.closest && (
+            target.closest("circle") !== null ||
+            target.closest("image") !== null ||
+            target.closest(".node") !== null
+        );
+        const isLink = target.closest && (
+            target.closest("path.link") !== null ||
+            target.closest("path.link_no_arrow") !== null
+        );
+        if (!isNode && !isLink) {
+            // console.log("Clicked outside a node or link");
+            // Clear all highlights
+            d3.selectAll("circle").classed("highlighted", false);
+            d3.selectAll("path").classed("highlighted", false);
+            d3.selectAll("path").classed("inedge", false);
+            d3.selectAll("path").classed("outedge", false);
+        }
+    });
+
     // Zoom Funktion aktivieren
     const zoom = d3.zoom()
         .scaleExtent([0.5, 5])
@@ -563,6 +657,8 @@ function draw(pathway, elem) {
     // Apply zoom to the SVG element - this enables wheel zoom
     svg.call(zoom);
 
+    svg.call(zoom.scaleBy, initialzoom);
+
     // Also apply zoom to container to catch events that might not reach SVG
     // This ensures drag-to-pan works even when clicking on empty space
     container.call(zoom);
@@ -581,11 +677,11 @@ function draw(pathway, elem) {
         for (idx in parents) {
             p = nodes[parents[idx]]
             // console.log(p.depth)
-            if (p.depth >= n.depth) {
+            // if (p.depth >= n.depth) {
-                // keep the .5 steps for pseudo nodes
+            //     // keep the .5 steps for pseudo nodes
-                n.depth = n.pseudo ? p.depth + 1 : Math.floor(p.depth + 1);
+            //     n.depth = n.pseudo ? p.depth + 1 : Math.floor(p.depth + 1);
-                // console.log("Adjusting", orig_depth, Math.floor(p.depth + 1));
+            //     // console.log("Adjusting", orig_depth, Math.floor(p.depth + 1));
-            }
+            // }
         }
     });
 
@@ -597,15 +693,83 @@ function draw(pathway, elem) {
         .force("center", d3.forceCenter(width / 2, height / 4))
         .on("tick", ticked);
 
-    // Kanten zeichnen
+    // Draw Edges
-    const link = zoomable.append("g")
+    const linkGroup = zoomable.append("g")
-        .selectAll("line")
+      .selectAll("g")
-        .data(links)
+      .data(links)
-        .enter().append("line")
+      .enter()
-        // Check if target is pseudo and draw marker only if not pseudo
+      .append("g")
-        .attr("class", d => d.target.pseudo ? "link_no_arrow" : "link")
+      .attr("class", "link-group");
-        .attr("marker-end", d => d.target.pseudo ? '' : d.multi_step ? 'url(#doublearrow)' : 'url(#arrow)')
 
+    const link = linkGroup
+      .append("path")
+      .attr("class", d => d.target.pseudo ? "link_no_arrow" : "link")
+      .attr("marker-end", d => d.target.pseudo ? "" : "url(#arrow)")
+      .attr("fill", "none")
+
+      // Check if target is pseudo and draw marker only if not pseudo
+      .attr("class", d => d.target.pseudo ? "link_no_arrow" : "link")
+      .attr("marker-end", d => {
+        if (d.target.pseudo) return '';
+        if (d.source.id === d.target.id) return 'url(#curve-arrow)'; // Use curve arrow for self-loops
+          return d.multi_step ? 'url(#doublearrow)' : 'url(#arrow)';
+        }
+      )
+      .attr("fill", "none")
+      .on("click", function(event, d) {
+          const wasHighlighted = d3.select(this).classed("highlighted");
+          d3.selectAll("path").classed("highlighted", false);
+          if (!wasHighlighted) {
+            const toHighlight = [];
+            toHighlight.push(d.el);
+
+            if (d.source.pseudo || d.target.pseudo) {
+              if (d.target.pseudo) {
+                d3.selectAll("path").each(e => {
+                  if (e !== undefined && e.source.id === d.target.id) {
+                    toHighlight.push(e.el);
+                  }
+                });
+              } else {
+                d3.selectAll("path").each(e => {
+                  if (e !== undefined && (e.target.id === d.source.id || e.source.id === d.source.id)) {
+                    toHighlight.push(e.el);
+                  }
+                });
+              }
+            }
+
+            for (const e of toHighlight) {
+              d3.select(e).classed("highlighted", true);
+            }
+          }
+        });
+
+    function reaction_name(d) {
+        const to_pseudo = d?.to_pseudo || false;
+
+        if (to_pseudo) {
+            return "";
+        }
+
+        var suffix = "";
+        if ("reaction_probability" in d && d["reaction_probability"] !== null) {
+            suffix = " (p= " + d["reaction_probability"].toFixed(2) + ")"
+        }
+        return d.plain_name + suffix;
+    }
+
+    const linkText = linkGroup
+      .append("text")
+      .attr("class", "link-label")
+      .attr("text-anchor", "middle")
+      .attr("dy", -6)
+      .style("font-size", "4px")
+      .style("pointer-events", "none")
+      .style("display", "none")
+      .text(d => reaction_name(d))
+      .attr("x", d => (d.source.x + d.target.x) / 2)
+      .attr("y", d => (d.source.y + d.target.y) / 2);
 
     // add element to links array
     link.each(function (d) {
@@ -614,7 +778,7 @@ function draw(pathway, elem) {
 
     pop_add(link, "Reaction", edge_popup);
 
-    // Knoten zeichnen
+    // Draw Nodes
     const node = zoomable.append("g")
         .selectAll("g")
         .data(nodes)
@@ -622,10 +786,41 @@ function draw(pathway, elem) {
         .call(d3.drag()
             .on("start", dragstarted)
             .on("drag", dragged)
-            .on("end", dragended))
+            .on("end", dragended)
+        )
         .on("click", function (event, d) {
+          const wasHighlighted = d3.select(this).select("circle").classed("highlighted");
+          d3.selectAll('circle.highlighted').classed('highlighted', false);
+          d3.selectAll("path").classed("inedge", false);
+          d3.selectAll("path").classed("outedge", false);
+
+          if (!wasHighlighted) {
             d3.select(this).select("circle").classed("highlighted", !d3.select(this).select("circle").classed("highlighted"));
-        })
+            const inEdges = findPaths(d.id, links);
+            const outEdges = []
+            // Colorize out edges green
+            for (const l of links) {
+              if (l.source.id === d.id) {
+                outEdges.push(l);
+                if (l.target.pseudo) {
+                  for (const l2 of links) {
+                    if (l.target.id === l2.source.id) {
+                      outEdges.push(l2);
+                    }
+                  }
+                }
+              }
+            }
+
+            for (const e of inEdges) {
+              d3.select(e.el).classed("inedge", true);
+            }
+
+            for (const e of outEdges) {
+              d3.select(e.el).classed("outedge", true);
+            }
+          }
+        });
 
     // Kreise für die Knoten hinzufügen
     node.append("circle")
@@ -637,44 +832,56 @@ function draw(pathway, elem) {
     node.filter(d => !d.pseudo).each(function (d, i) {
         const g = d3.select(this);
 
-        // Parse the SVG string
+        if (d.image_type === "svg") {
-        const parser = new DOMParser();
+            // Parse the SVG string
-        const svgDoc = parser.parseFromString(d.image_svg, "image/svg+xml");
+            const parser = new DOMParser();
-        const svgElem = svgDoc.documentElement;
+            const svgDoc = parser.parseFromString(d.image_svg, "image/svg+xml");
+            const svgElem = svgDoc.documentElement;
 
-        // Create a unique prefix per node
+            // Create a unique prefix per node
-        const prefix = `node-${i}-`;
+            const prefix = `node-${i}-`;
 
-        // Rename all IDs and fix <use> references
+            // Rename all IDs and fix <use> references
-        svgElem.querySelectorAll('[id]').forEach(el => {
+            svgElem.querySelectorAll("[id]").forEach(el => {
-            const oldId = el.id;
+                const oldId = el.id;
-            const newId = prefix + oldId;
+                const newId = prefix + oldId;
-            el.id = newId;
+                el.id = newId;
 
-            const XLINK_NS = "http://www.w3.org/1999/xlink";
+                const XLINK_NS = "http://www.w3.org/1999/xlink";
-            // Update <use> elements that reference this old ID
+                // Update <use> elements that reference this old ID
-            const uses = Array.from(svgElem.querySelectorAll('use')).filter(
+                const uses = Array.from(svgElem.querySelectorAll("use")).filter(
-                u => u.getAttributeNS(XLINK_NS, 'href') === `#${oldId}`
+                    u => u.getAttributeNS(XLINK_NS, "href") === `#${oldId}`
-            );
+                );
 
-            uses.forEach(u => {
+                uses.forEach(u => {
-                u.setAttributeNS(XLINK_NS, 'href', `#${newId}`);
+                    u.setAttributeNS(XLINK_NS, "href", `#${newId}`);
+                });
             });
-        });
 
-        g.node().appendChild(svgElem);
+            g.node().appendChild(svgElem);
 
-        const vb = svgElem.viewBox.baseVal;
+            const vb = svgElem.viewBox.baseVal;
-        const svgWidth = vb.width || 40;
+            const svgWidth = vb.width || 40;
-        const svgHeight = vb.height || 40;
+            const svgHeight = vb.height || 40;
 
-        const scale = (nodeRadius * 2) / Math.max(svgWidth, svgHeight);
+            const scale = (nodeRadius * 2) / Math.max(svgWidth, svgHeight);
+
+            g.select("svg")
+                .attr("width", svgWidth * scale)
+                .attr("height", svgHeight * scale)
+                .attr("x", -svgWidth * scale / 2)
+                .attr("y", -svgHeight * scale / 2);
+        } else {
+            // We have a image type different than svg
+            // include it via img url
+            g.append("svg:image")
+                .attr("xlink:href", d.image)
+                .attr("width", 40)
+                .attr("height", 40)
+                .attr("x", -20)
+                .attr("y", -20);
+        }
 
-        g.select("svg")
-            .attr("width", svgWidth * scale)
-            .attr("height", svgHeight * scale)
-            .attr("x", -svgWidth * scale / 2)
-            .attr("y", -svgHeight * scale / 2);
     });
 
     // add element to nodes array
@@ -687,14 +894,14 @@ function draw(pathway, elem) {
 
 function serializeSVG(svgElement) {
 
-    svgElement.querySelectorAll("line.link").forEach(line => {
+    svgElement.querySelectorAll("path.link").forEach(line => {
         const style = getComputedStyle(line);
         line.setAttribute("stroke", style.stroke);
         line.setAttribute("stroke-width", style.strokeWidth);
         line.setAttribute("fill", style.fill);
     });
 
-    svgElement.querySelectorAll("line.link_no_arrow").forEach(line => {
+    svgElement.querySelectorAll("path.link_no_arrow").forEach(line => {
         const style = getComputedStyle(line);
         line.setAttribute("stroke", style.stroke);
         line.setAttribute("stroke-width", style.strokeWidth);

templates/actions/collections/group.html

@@ -1,8 +0,0 @@
-<li>
-  <a
-    role="button"
-    onclick="document.getElementById('new_group_modal').showModal(); return false;"
-  >
-    <span class="glyphicon glyphicon-plus"></span> New Group</a
-  >
-</li>

templates/actions/objects/pathway.html

@@ -1,3 +1,5 @@
+{% load envipytags %}
+
 {% if meta.can_edit %}
   <li>
     <a
@@ -15,7 +17,12 @@
       <i class="glyphicon glyphicon-plus"></i> Add Reaction</a
     >
   </li>
-  <li role="separator" class="divider"></li>
+  {% epdb_slot_templates "epdb.actions.objects.pathway.add" as action_button_templates %}
+
+  {% for tpl in action_button_templates %}
+    {% include tpl %}
+  {% endfor %}
+  <li role="separator" class="divider h-px"></li>
 {% endif %}
 <li>
   <a
@@ -67,7 +74,7 @@
       Rules</a
     >
   </li>
-  <li role="separator" class="divider"></li>
+  <li role="separator" class="divider h-px"></li>
   <li>
     <a
       class="button"
@@ -92,11 +99,16 @@
       <i class="glyphicon glyphicon-plus"></i> Set Aliases</a
     >
   </li>
-  <li role="separator" class="divider"></li>
+  <li role="separator" class="divider h-px"></li>
   <li>
     <a
       class="button"
-      onclick="document.getElementById('delete_pathway_node_modal').showModal(); return false;"
+      onclick="
+      const modal = document.getElementById('delete_pathway_node_modal');
+      modal.showModal();
+      window.dispatchEvent(new Event('modal-opened'));
+      return false;
+      "
     >
       <i class="glyphicon glyphicon-trash"></i> Delete Compound</a
     >
@@ -104,7 +116,12 @@
   <li>
     <a
       class="button"
-      onclick="document.getElementById('delete_pathway_edge_modal').showModal(); return false;"
+      onclick="
+      const modal = document.getElementById('delete_pathway_edge_modal');
+      modal.showModal();
+      window.dispatchEvent(new Event('modal-opened'));
+      return false;
+      "
     >
       <i class="glyphicon glyphicon-trash"></i> Delete Reaction</a
     >

templates/collections/_joblog_paginated_list_partial.html

@@ -0,0 +1,102 @@
+{# Partial for paginated list content - expects to be inside a remotePaginatedList Alpine.js context #}
+{# Variables: empty_text (string), show_review_badge (bool), always_show_badge (bool) #}
+{% load envipytags %}
+{# Loading state #}
+<div
+  x-show="isLoading"
+  class="mx-auto flex h-32 w-32 items-center justify-center"
+>
+  {% include "components/loading-spinner.html" %}
+</div>
+
+{# Error state #}
+<div
+  x-show="!isLoading && error"
+  class="alert alert-error/50 text-sm"
+  x-text="error"
+></div>
+
+{# Content #}
+<template x-if="!isLoading && !error">
+  <div>
+    {# Empty state #}
+    <div
+      x-show="totalItems === 0"
+      class="text-base-content/70 py-8 text-center"
+    >
+      <p>No {{ empty_text|default:"items" }} found.</p>
+    </div>
+
+    {# Items list #}
+    <ul class="menu bg-base-100 rounded-box w-full" x-show="totalItems > 0">
+      <table class="table-zebra table">
+        <thead>
+          <tr>
+            <th>User</th>
+
+            <th>ID</th>
+            <th>Name</th>
+            <th>Status</th>
+            <th>Queued At</th>
+            <th>Done At</th>
+          </tr>
+        </thead>
+        <tbody>
+          <template x-for="obj in paginatedItems" :key="obj.url">
+            <tr>
+              <td>
+                <a :href="obj.user.url"><span x-text="obj.user.name"></span></a>
+              </td>
+
+              <td>
+                <a :href="obj.url"><span x-text="obj.id"></span></a>
+              </td>
+              <td><span x-text="obj.name"></span></td>
+              <td><span x-text="obj.status"></span></td>
+              <td><span x-text="obj.created"></span></td>
+              <td><span x-text="obj.done"></span></td>
+            </tr>
+          </template>
+        </tbody>
+      </table>
+    </ul>
+
+    {# Pagination controls #}
+    <div
+      x-show="totalPages > 1"
+      class="mt-4 flex items-center justify-between px-2"
+    >
+      <span class="text-base-content/70 text-sm">
+        Showing <span x-text="showingStart"></span>-<span
+          x-text="showingEnd"
+        ></span>
+        of <span x-text="totalItems"></span>
+      </span>
+      <div class="join">
+        <button
+          class="join-item btn btn-sm"
+          :disabled="currentPage === 1"
+          @click="prevPage()"
+        >
+          «
+        </button>
+        <template x-for="item in pageNumbers" :key="item.key">
+          <button
+            class="join-item btn btn-sm"
+            :class="{ 'btn-active': item.page === currentPage }"
+            :disabled="item.isEllipsis"
+            @click="!item.isEllipsis && goToPage(item.page)"
+            x-text="item.page"
+          ></button>
+        </template>
+        <button
+          class="join-item btn btn-sm"
+          :disabled="currentPage === totalPages"
+          @click="nextPage()"
+        >
+          »
+        </button>
+      </div>
+    </div>
+  </div>
+</template>

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/groups_paginated.html

@@ -0,0 +1,21 @@
+{% extends "collections/paginated_base.html" %}
+
+{% block page_title %}Groups{% endblock %}
+
+{% block action_button %}
+  <button
+    type="button"
+    class="btn btn-primary btn-sm"
+    onclick="document.getElementById('new_group_modal').showModal(); return false;"
+  >
+    New Group
+  </button>
+{% endblock action_button %}
+
+{% block action_modals %}
+  {% include "modals/collections/new_group_modal.html" %}
+{% endblock action_modals %}
+
+{% block description %}
+  <p>Users can team up in groups to share packages.</p>
+{% endblock description %}

templates/collections/joblog_paginated.html

@@ -0,0 +1,13 @@
+{% extends "collections/paginated_base.html" %}
+
+{% block page_title %}Jobs{% endblock %}
+
+{% block action_button %}
+{% endblock action_button %}
+
+{% block action_modals %}
+{% endblock action_modals %}
+
+{% block description %}
+  <p>List of Jobs submitted.</p>
+{% endblock description %}

templates/collections/models_paginated.html

@@ -3,14 +3,16 @@
 {% 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 %}
-    <button
+    {% if meta.enabled_features.MODEL_BUILDING %}
-      type="button"
+      <button
-      class="btn btn-primary btn-sm"
+        type="button"
-      onclick="document.getElementById('new_model_modal').showModal(); return false;"
+        class="btn btn-primary btn-sm"
-    >
+        onclick="document.getElementById('new_model_modal').showModal(); return false;"
-      New Model
+      >
-    </button>
+        New Model
+      </button>
+    {% endif %}
   {% endif %}
 {% endblock action_button %}
 

templates/collections/packages_paginated.html

@@ -3,75 +3,73 @@
 {% block page_title %}Packages{% endblock %}
 
 {% block action_button %}
-  {% if meta.can_edit %}
+  <div class="flex items-center gap-2">
-    <div class="flex items-center gap-2">
+    <button
-      <button
+      type="button"
-        type="button"
+      class="btn btn-primary btn-sm"
-        class="btn btn-primary btn-sm"
+      id="new-package-button"
-        id="new-package-button"
+      onclick="document.getElementById('new_package_modal').showModal(); return false;"
-        onclick="document.getElementById('new_package_modal').showModal(); return false;"
+    >
+      <svg
+        xmlns="http://www.w3.org/2000/svg"
+        width="24"
+        height="24"
+        viewBox="0 0 24 24"
+        fill="none"
+        stroke="currentColor"
+        stroke-width="2"
+        stroke-linecap="round"
+        stroke-linejoin="round"
+        class="lucide lucide-folder-plus-icon lucide-folder-plus"
       >
+        <path d="M12 10v6" />
+        <path d="M9 13h6" />
+        <path
+          d="M20 20a2 2 0 0 0 2-2V8a2 2 0 0 0-2-2h-7.9a2 2 0 0 1-1.69-.9L9.6 3.9A2 2 0 0 0 7.93 3H4a2 2 0 0 0-2 2v13a2 2 0 0 0 2 2Z"
+        />
+      </svg>
+    </button>
+    <div class="dropdown dropdown-end">
+      <div tabindex="0" role="button" class="btn btn-sm">
+        Import
         <svg
           xmlns="http://www.w3.org/2000/svg"
-          width="24"
+          width="16"
-          height="24"
+          height="16"
           viewBox="0 0 24 24"
           fill="none"
           stroke="currentColor"
           stroke-width="2"
           stroke-linecap="round"
           stroke-linejoin="round"
-          class="lucide lucide-folder-plus-icon lucide-folder-plus"
+          class="lucide lucide-chevron-down ml-1"
         >
-          <path d="M12 10v6" />
+          <path d="m6 9 6 6 6-6" />
-          <path d="M9 13h6" />
-          <path
-            d="M20 20a2 2 0 0 0 2-2V8a2 2 0 0 0-2-2h-7.9a2 2 0 0 1-1.69-.9L9.6 3.9A2 2 0 0 0 7.93 3H4a2 2 0 0 0-2 2v13a2 2 0 0 0 2 2Z"
-          />
         </svg>
-      </button>
-      <div class="dropdown dropdown-end">
-        <div tabindex="0" role="button" class="btn btn-sm">
-          Import
-          <svg
-            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-chevron-down ml-1"
-          >
-            <path d="m6 9 6 6 6-6" />
-          </svg>
-        </div>
-        <ul
-          tabindex="-1"
-          class="dropdown-content menu bg-base-100 rounded-box z-50 w-56 p-2"
-        >
-          <li>
-            <a
-              role="button"
-              onclick="document.getElementById('import_package_modal').showModal(); return false;"
-            >
-              Import Package from JSON
-            </a>
-          </li>
-          <li>
-            <a
-              role="button"
-              onclick="document.getElementById('import_legacy_package_modal').showModal(); return false;"
-            >
-              Import Package from legacy JSON
-            </a>
-          </li>
-        </ul>
       </div>
+      <ul
+        tabindex="-1"
+        class="dropdown-content menu bg-base-100 rounded-box z-50 w-56 p-2"
+      >
+        <li>
+          <a
+            role="button"
+            onclick="document.getElementById('import_package_modal').showModal(); return false;"
+          >
+            Import Package from JSON
+          </a>
+        </li>
+        <li>
+          <a
+            role="button"
+            onclick="document.getElementById('import_legacy_package_modal').showModal(); return false;"
+          >
+            Import Package from legacy JSON
+          </a>
+        </li>
+      </ul>
     </div>
-  {% endif %}
+  </div>
 {% endblock action_button %}
 
 {% block action_modals %}

templates/collections/paginated_base.html

@@ -37,7 +37,11 @@
             perPage: {{ per_page|default:50 }}
           })"
       >
-        {% include "collections/_paginated_list_partial.html" with empty_text=list_title|default:"items" show_review_badge=True %}
+        {% if entity_type == 'joblog' %}
+          {% include "collections/_joblog_paginated_list_partial.html" with empty_text=list_title|default:"items" show_review_badge=True %}
+        {% else %}
+          {% include "collections/_paginated_list_partial.html" with empty_text=list_title|default:"items" show_review_badge=True %}
+        {% endif %}
       </div>
     {% else %}
       {# ===== TABBED MODE: Reviewed/Unreviewed tabs (default) ===== #}

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"

templates/components/schema_form.html

@@ -123,6 +123,17 @@
             </div>
           </template>
 
+          <!-- DOI link widget -->
+          <template
+            x-if="getWidget(fieldName, schema.properties[fieldName]) === 'doi-link'"
+          >
+            <div
+              x-data="doiWidget(fieldName, data, schema, uiSchema, mode, debugErrors, context)"
+            >
+              {% include "components/widgets/doi_link_widget.html" %}
+            </div>
+          </template>
+
           <!-- Compound link widget -->
           <template
             x-if="getWidget(fieldName, schema.properties[fieldName]) === 'compound-link'"

templates/components/widgets/doi_link_widget.html

@@ -0,0 +1,69 @@
+{# DOI link widget - pure HTML template #}
+<div class="form-control">
+  <div class="flex flex-col gap-2 sm:flex-row sm:items-baseline">
+    <!-- Label -->
+    <label class="label sm:w-48 sm:shrink-0">
+      <span
+        class="label-text"
+        :class="{
+              'text-error': $store.validationErrors.hasError(fieldName, context),
+              'text-sm text-base-content/60': isViewMode
+            }"
+        x-text="label"
+      ></span>
+    </label>
+
+    <!-- Input column -->
+    <div class="flex-1">
+      <!-- Help text -->
+      <template x-if="helpText">
+        <div class="label">
+          <span
+            class="label-text-alt text-base-content/60"
+            x-text="helpText"
+          ></span>
+        </div>
+      </template>
+
+      <!-- View mode: display as link -->
+      <template x-if="isViewMode">
+        <div class="mt-1">
+          <template x-if="value && doiUrl">
+            <a
+              :href="doiUrl"
+              class="link link-primary"
+              target="_blank"
+              x-text="value"
+            ></a>
+          </template>
+          <template x-if="!value">
+            <span class="text-base-content/50">—</span>
+          </template>
+        </div>
+      </template>
+
+      <!-- Edit mode -->
+      <template x-if="isEditMode">
+        <input
+          type="text"
+          class="input input-bordered w-full"
+          :class="{ 'input-error': $store.validationErrors.hasError(fieldName, context) }"
+          placeholder="DOI e.g. 10.1016/j.jhazmat.2016.08.036"
+          x-model="value"
+        />
+      </template>
+
+      <!-- Errors -->
+      <template x-if="$store.validationErrors.hasError(fieldName, context)">
+        <div class="label">
+          <template
+            x-for="errMsg in $store.validationErrors.getErrors(fieldName, context)"
+            :key="errMsg"
+          >
+            <span class="label-text-alt text-error" x-text="errMsg"></span>
+          </template>
+        </div>
+      </template>
+    </div>
+  </div>
+</div>

templates/components/widgets/select_widget.html

@@ -44,6 +44,7 @@
           :class="{ 'select-error': $store.validationErrors.hasError(fieldName, context) }"
           x-model="value"
           :multiple="multiple"
+          :required="isRequired"
         >
           <option value="" :selected="!value">Select...</option>
 

templates/modals/collections/new_model_modal.html

@@ -65,11 +65,11 @@
     },
 
     get showMlrr() {
-      return this.selectedType === 'mlrr';
+      return this.selectedType === 'ml-relative-reasoning';
     },
 
     get showRbrr() {
-      return this.selectedType === 'rbrr';
+      return this.selectedType === 'rule-based-relative-reasoning';
     },
 
     get showEnviformer() {

templates/modals/collections/new_prediction_setting_modal.html

@@ -203,11 +203,11 @@
               id="model-based-prediction-setting-threshold"
               name="model-based-prediction-setting-threshold"
               class="input input-bordered w-full"
-              placeholder="0.25"
+              value="0.25"
               type="number"
               min="0"
               max="1"
-              step="0.05"
+              step="any"
             />
           </div>
 

templates/modals/objects/delete_pathway_edge_modal.html

@@ -4,6 +4,22 @@
   id="delete_pathway_edge_modal"
   class="modal"
   x-data="modalForm({ state: { selectedEdge: '', imageUrl: '' } })"
+  @modal-opened.window="
+   const links = d3.selectAll('path.highlighted');
+   if (!links.empty()) {
+        const el = links.node();
+        const selectElement = document.getElementById('delete_pathway_edge_edges');
+        console.log(el);
+        console.log(el.__data__);
+        for (let option of selectElement.options) {
+            if (option.value === el.__data__.url) {
+                option.selected = true;
+                break;
+            }
+        }
+        selectElement.dispatchEvent(new Event('change'));
+   }
+  "
   @close="reset()"
 >
   <div class="modal-box">

templates/modals/objects/delete_pathway_node_modal.html

@@ -4,6 +4,19 @@
   id="delete_pathway_node_modal"
   class="modal"
   x-data="modalForm({ state: { selectedNode: '', imageUrl: '' } })"
+  @modal-opened.window="
+   const el = d3.select('circle.highlighted').node();
+   if (el !== null) {
+    const selectElement = document.getElementById('delete_pathway_node_nodes');
+    for (let option of selectElement.options) {
+        if (option.value === el.__data__.url) {
+            option.selected = true;
+            break;
+        }
+    }
+    selectElement.dispatchEvent(new Event('change'));
+   }
+  "
   @close="reset()"
 >
   <div class="modal-box">

templates/objects/compound.html

@@ -1,4 +1,5 @@
 {% extends "framework_modern.html" %}
+{% load envipytags %}
 
 {% block content %}
 
@@ -82,6 +83,12 @@
       <div class="collapse-content">{{ compound.description }}</div>
     </div>
 
+    <!-- Extension Slot for Viz -->
+    {% epdb_slot_templates "epdb.objects.compound.viz" as viz_templates %}
+    {% for tpl in viz_templates %}
+      {% include tpl %}
+    {% endfor %}
+
     <!-- Image Representation -->
     <div class="collapse-arrow bg-base-200 collapse">
       <input type="checkbox" checked />

templates/objects/compound_structure.html

@@ -1,4 +1,5 @@
 {% extends "framework_modern.html" %}
+{% load envipytags %}
 
 {% block content %}
 
@@ -50,6 +51,12 @@
       </div>
     </div>
 
+    <!-- Extension Slot for Viz -->
+    {% epdb_slot_templates "epdb.objects.compound_structure.viz" as viz_templates %}
+    {% for tpl in viz_templates %}
+      {% include tpl %}
+    {% endfor %}
+
     <!-- Image Representation -->
     <div class="collapse-arrow bg-base-200 collapse">
       <input type="checkbox" checked />

templates/objects/edge.html

@@ -92,7 +92,7 @@
         <div class="flex flex-wrap items-center justify-center gap-4">
           {% for educt in edge.start_nodes.all %}
             <a href="{{ educt.url }}" class="btn btn-outline btn-sm"
-              >{{ educt.name }}</a
+              >{{ educt.get_name }}</a
             >
           {% endfor %}
           <svg
@@ -112,7 +112,7 @@
           </svg>
           {% for product in edge.end_nodes.all %}
             <a href="{{ product.url }}" class="btn btn-outline btn-sm"
-              >{{ product.name }}</a
+              >{{ product.get_name }}</a
             >
           {% endfor %}
         </div>

templates/objects/group.html

@@ -56,7 +56,9 @@
         <ul class="menu bg-base-200 rounded-box">
           {% for um in group.user_member.all %}
             <li>
-              <a href="{{ um.url }}" class="hover:bg-base-300"
+              <a
+                href="{% if user.is_superuser %}{{ um.url }}{% else %}{{ "#" }}{% endif %}"
+                class="hover:bg-base-300"
                 >{{ um.username }}
                 {% if not um.is_active %}<i>(inactive)</i>{% endif %}</a
               >

templates/objects/node.html

@@ -1,4 +1,5 @@
 {% extends "framework_modern.html" %}
+{% load envipytags %}
 
 {% block content %}
 
@@ -54,6 +55,20 @@
       </div>
     </div>
 
+    <!-- Description -->
+    {% if node.description and node.description != "no description" %}
+      <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>
+    {% endif %}
+    {% epdb_slot_templates "epdb.objects.node.viz" as viz_templates %}
+
+    {% for tpl in viz_templates %}
+      {% include tpl %}
+    {% endfor %}
+
     <!-- Image Representation -->
     <div class="collapse-arrow bg-base-200 collapse">
       <input type="checkbox" checked />

templates/objects/pathway.html

@@ -1,5 +1,7 @@
 {% extends "framework_modern.html" %}
 {% load static %}
+{% load envipytags %}
+
 {% block content %}
   <script src="https://d3js.org/d3.v7.min.js"></script>
   <style>
@@ -19,12 +21,13 @@
     .link {
       stroke: #999;
       stroke-opacity: 0.6;
-      /* marker-end: url(#arrow); */
+      stroke-width: 1.5px;
     }
 
     .link_no_arrow {
       stroke: #999;
       stroke-opacity: 0.6;
+      stroke-width: 1.5px;
     }
 
     .node image {
@@ -70,12 +73,25 @@
       stroke: red;
       stroke-width: 3px;
     }
+
+    .inedge {
+      stroke: red;
+      stroke-width: 3px;
+    }
+    .outedge {
+      stroke: green;
+      stroke-width: 3px;
+    }
   </style>
   <script src="{% static 'js/pw.js' %}"></script>
 
   {% block action_modals %}
     {% include "modals/objects/add_pathway_node_modal.html" %}
     {% include "modals/objects/add_pathway_edge_modal.html" %}
+    {% epdb_slot_templates "epdb.modals.objects.pathway.add" as add_templates %}
+    {% for tpl in add_templates %}
+      {% include tpl %}
+    {% endfor %}
     {% include "modals/objects/download_pathway_csv_modal.html" %}
     {% include "modals/objects/download_pathway_image_modal.html" %}
     {% include "modals/objects/identify_missing_rules_modal.html" %}
@@ -100,7 +116,7 @@
     </div>
 
     <!-- Graphical Representation -->
-    <div class="collapse-arrow bg-base-200 collapse">
+    <div class="collapse-arrow bg-base-200 collapse overflow-y-auto">
       <input type="checkbox" checked />
       <div class="collapse-title text-xl font-medium">
         Graphical Representation
@@ -134,7 +150,7 @@
                 </div>
                 <ul
                   tabindex="0"
-                  class="dropdown-content menu bg-base-100 rounded-box z-50 w-52 p-2"
+                  class="dropdown-content menu bg-base-100 rounded-box z-50 w-96 p-2"
                 >
                   {% include "actions/objects/pathway.html" %}
                 </ul>
@@ -162,6 +178,52 @@
                   tabindex="0"
                   class="dropdown-content menu bg-base-100 rounded-box z-50 w-60 p-2"
                 >
+                  <li>
+                    <a id="compound-names-toggle-button" class="cursor-pointer">
+                      <svg
+                        id="compound-names-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>
+                      Compound Names
+                    </a>
+                  </li>
+                  <li>
+                    <a id="reaction-names-toggle-button" class="cursor-pointer">
+                      <svg
+                        id="reaction-names-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>
+                      Reaction Names
+                    </a>
+                  </li>
                   {% if pathway.setting.model.app_domain %}
                     <li>
                       <a id="app-domain-toggle-button" class="cursor-pointer">
@@ -361,6 +423,18 @@
               >
                 <path d="M 0 0 L 10 5 L 0 10 z" fill="#999" />
               </marker>
+              <marker
+                id="curve-arrow"
+                viewBox="0 0 10 10"
+                refX="10"
+                refY="5"
+                markerWidth="6"
+                markerHeight="6"
+                orient="auto"
+                markerUnits="strokeWidth"
+              >
+                <path d="M 0 0 L 10 5 L 0 10 z" fill="#999" />
+              </marker>
               <marker
                 id="doublearrow"
                 viewBox="0 0 20 30"
@@ -468,6 +542,10 @@
   {{ pathway.d3_json|json_script:"pathway" }}
 
   <script>
+    // Global switch for compound names view
+    var compoundNamesViewEnabled = false;
+    // Gloabl switch for reaction names view
+    var reactionNamesViewEnabled = false;
     // Global switch for app domain view
     var appDomainViewEnabled = false;
     // Global switch for timeseries view
@@ -503,6 +581,58 @@
         descContent.innerHTML = newDesc;
       }
 
+      const compoundNamesBtn = document.getElementById(
+        "compound-names-toggle-button",
+      );
+      if (compoundNamesBtn) {
+        compoundNamesBtn.addEventListener("click", function () {
+          compoundNamesViewEnabled = !compoundNamesViewEnabled;
+          const icon = document.getElementById("compound-names-icon");
+          if (compoundNamesViewEnabled) {
+            // 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"/>';
+            nodes.forEach((x) => {
+              if (x.name) {
+                d3.select(x.el)
+                  .append("text")
+                  .text((d) => d.plain_name)
+                  .attr("text-anchor", "middle")
+                  .attr("y", -20)
+                  .style("font-size", "4px");
+              }
+            });
+          } 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"/>';
+            nodes.forEach((x) => {
+              d3.select(x.el).select("text").remove();
+            });
+          }
+        });
+      }
+      const reactionNamesBtn = document.getElementById(
+        "reaction-names-toggle-button",
+      );
+      if (reactionNamesBtn) {
+        reactionNamesBtn.addEventListener("click", function () {
+          reactionNamesViewEnabled = !reactionNamesViewEnabled;
+          const icon = document.getElementById("reaction-names-icon");
+          if (reactionNamesViewEnabled) {
+            // 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"/>';
+            d3.selectAll(".link-label").style("display", null);
+          } 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"/>';
+            d3.selectAll(".link-label").style("display", "none");
+          }
+        });
+      }
+
       // App domain toggle
       const appDomainBtn = document.getElementById("app-domain-toggle-button");
       if (appDomainBtn) {

templates/predict_pathway.html

@@ -105,7 +105,7 @@
         ></iframe>
       </div>
 
-      <label class="select mb-8 w-full">
+      <label class="select mb-8 w-full" id="prediction-setting-label">
         <span class="label">Predictor</span>
         <select id="prediction-setting" name="prediction-setting">
           <option disabled>Select a Setting</option>
@@ -148,6 +148,21 @@
   </div>
   {# prettier-ignore-start #}
   <script>
+    // Hide predictor selection and update button text if mode is "build"
+    function radioChange(event) {
+      if (event.target.value === "build") {
+        document.getElementById("prediction-setting-label").hidden = true;
+        document.getElementById("predict-submit-button").innerText = "Build";
+      } else {
+        document.getElementById("prediction-setting-label").hidden = false;
+        document.getElementById("predict-submit-button").innerText = "Predict";
+      }
+    }
+    const radioButtons = document.querySelectorAll('input[name="predict"]');
+    radioButtons.forEach(radio => {
+      radio.addEventListener('change', radioChange);
+    });
+
     // Helper function to safely get Ketcher instance from iframe
     function getKetcherInstance(iframeId) {
       const ketcherFrame = document.getElementById(iframeId);
@@ -197,7 +212,13 @@
         e.preventDefault();
         const button = this;
         button.disabled = true;
-        button.textContent = "Predicting...";
+
+        // Set text depending on mode
+        if (document.getElementById("predict-submit-button").innerText === "Build") {
+          button.textContent = "Building...";
+        } else {
+          button.textContent = "Predicting...";
+        }
 
         // Get SMILES from either input or Ketcher
         const smilesInput = document.getElementById("predict-smiles");

templates/static/login_base.html

@@ -110,8 +110,6 @@
           <div
             class="text-base-content/50 flex items-center justify-center space-x-6 text-sm"
           >
-            <a href="/legal" class="link link-hover">Legal</a>
-            <span class="text-base-content/30">•</span>
             <a href="/terms" class="link link-hover">Terms of Use</a>
             <span class="text-base-content/30">•</span>
             <a href="/privacy" class="link link-hover">Privacy Policy</a>

tests/test_compound_model.py

@@ -1,5 +1,7 @@
 from django.conf import settings as s
 from django.test import TestCase, override_settings
+
+from epdb.exceptions import InvalidSMILESException, InvalidMolfileException
 from epdb.logic import PackageManager
 from epdb.models import Compound, User, CompoundStructure
 
@@ -17,6 +19,10 @@ class CompoundTest(TestCase):
         cls.user = User.objects.get(username="anonymous")
         cls.package = PackageManager.create_package(cls.user, "Anon Test Package", "No Desc")
 
+        # A valid V2000 molfile for 4-Nitrobenzoic acid (O=C(O)C1=CC=C([N+](=O)[O-])C=C1)
+        cls.VALID_MOLFILE = """\n  Mrv2211 01012500002D\n\n 12 12  0  0  0  0            999 V2000\n    1.4289   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.0000   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.7145   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    0.7145   -2.8875    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0\n    0.0000   -3.3000    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0\n    1.4289   -3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  2  0  0  0  0\n  2  3  1  0  0  0  0\n  3  4  2  0  0  0  0\n  4  5  1  0  0  0  0\n  5  6  2  0  0  0  0\n  6  1  1  0  0  0  0\n  2  7  1  0  0  0  0\n  7  8  2  0  0  0  0\n  7  9  1  0  0  0  0\n  5 10  1  0  0  0  0\n 10 11  1  0  0  0  0\n 10 12  2  0  0  0  0\nM  CHG  2  10   1  11  -1\nM  END\n"""
+        cls.INVALID_MOLFILE = "this is not a valid molfile"
+
     def test_smoke(self):
         c = Compound.create(
             self.package,
@@ -33,13 +39,13 @@ class CompoundTest(TestCase):
         self.assertEqual(c.description, "No Desc")
 
     def test_missing_smiles(self):
-        with self.assertRaises(ValueError):
+        with self.assertRaises(InvalidSMILESException):
             _ = Compound.create(self.package, smiles=None, name="Afoxolaner", description="No Desc")
 
-        with self.assertRaises(ValueError):
+        with self.assertRaises(InvalidSMILESException):
             _ = Compound.create(self.package, smiles="", name="Afoxolaner", description="No Desc")
 
-        with self.assertRaises(ValueError):
+        with self.assertRaises(InvalidSMILESException):
             _ = Compound.create(self.package, smiles="  ", name="Afoxolaner", description="No Desc")
 
     def test_smiles_are_trimmed(self):
@@ -96,7 +102,7 @@ class CompoundTest(TestCase):
         self.assertEqual(len(self.package.compounds), 1)
 
     def test_wrong_smiles(self):
-        with self.assertRaises(ValueError):
+        with self.assertRaises(InvalidSMILESException):
             _ = Compound.create(
                 self.package,
                 smiles="C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F",
@@ -188,3 +194,153 @@ class CompoundTest(TestCase):
 
         c1.set_default_structure(c2)
         self.assertNotEqual(default_structure, c2)
+
+    def test_create_structure_from_molfile(self):
+        c = Compound.create(
+            self.package,
+            smiles="PLACEHOLDER",
+            molfile=self.VALID_MOLFILE,
+            name="Molfile Compound",
+            description="Created from molfile",
+        )
+
+        cs = CompoundStructure.create(
+            compound=c,
+            smiles="PLACEHOLDER",
+            molfile=self.VALID_MOLFILE,
+            name="Molfile Structure",
+            description="Structure from molfile",
+        )
+
+        # The SMILES must have been derived from the molfile, not the placeholder
+        self.assertNotEqual(cs.smiles, "PLACEHOLDER")
+        self.assertIsNotNone(cs.smiles)
+        self.assertTrue(len(cs.smiles) > 0)
+
+    def test_create_structure_from_molfile_stores_molfile(self):
+        c = Compound.create(
+            self.package,
+            smiles="c1c(C(=O)O)ccc([N+]([O-])=O)c1",
+            name="Molfile Store Test",
+            description="No Desc",
+        )
+
+        cs = c.default_structure
+
+        # O=C(O)C1=CC=C([N+](=O)[O-])C=C1 will be overwritten with
+        # c1c(C(=O)O)ccc([N+]([O-])=O)c1 and molfile will be set
+        # on the existing structure
+        _ = CompoundStructure.create(
+            compound=c,
+            smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1",
+            molfile=self.VALID_MOLFILE,
+            name="Structure with Molfile",
+            description="No Desc",
+        )
+
+        # Fetch fresh from DB to confirm persistence
+        cs_db = CompoundStructure.objects.get(pk=cs.pk)
+        self.assertIsNotNone(cs_db.molfile)
+        self.assertNotEqual(cs_db.molfile.strip(), "")
+
+    def test_create_structure_from_invalid_molfile_raises(self):
+        c = Compound.create(
+            self.package,
+            smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1",
+            name="Invalid Molfile Test",
+            description="No Desc",
+        )
+
+        with self.assertRaises(InvalidMolfileException):
+            CompoundStructure.create(
+                compound=c,
+                smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1",
+                molfile=self.INVALID_MOLFILE,
+                name="Bad Structure",
+                description="No Desc",
+            )
+
+    def test_molfile_takes_precedence_over_smiles(self):
+        """When both molfile and smiles are supplied, molfile must win."""
+        c = Compound.create(
+            self.package,
+            smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1",
+            name="Precedence Test",
+            description="No Desc",
+        )
+
+        cs = CompoundStructure.create(
+            compound=c,
+            smiles="C",  # intentionally wrong / different SMILES
+            molfile=self.VALID_MOLFILE,
+            name="Molfile Wins",
+            description="No Desc",
+        )
+
+        # SMILES should be derived from molfile, not the supplied "C"
+        self.assertNotEqual(cs.smiles, "C")
+
+    def test_empty_molfile_falls_back_to_smiles(self):
+        """An empty or whitespace-only molfile should be ignored and SMILES used instead."""
+        c = Compound.create(
+            self.package,
+            smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1",
+            name="Empty Molfile Test",
+            description="No Desc",
+        )
+
+        cs = CompoundStructure.create(
+            compound=c,
+            smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1",
+            molfile="   ",  # whitespace only – should be ignored
+            name="Fallback to SMILES",
+            description="No Desc",
+        )
+
+        self.assertEqual(cs.smiles, "O=C(O)C1=CC=C([N+](=O)[O-])C=C1")
+
+    def test_none_molfile_falls_back_to_smiles(self):
+        """None as molfile should be ignored and SMILES used instead."""
+        c = Compound.create(
+            self.package,
+            smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1",
+            name="None Molfile Test",
+            description="No Desc",
+        )
+
+        cs = CompoundStructure.create(
+            compound=c,
+            smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1",
+            molfile=None,
+            name="Fallback None Molfile",
+            description="No Desc",
+        )
+
+        self.assertEqual(cs.smiles, "O=C(O)C1=CC=C([N+](=O)[O-])C=C1")
+
+    def test_molfile_deduplication(self):
+        """Creating a structure twice from the same molfile should return the existing object."""
+        c = Compound.create(
+            self.package,
+            smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1",
+            name="Molfile Dedup Test",
+            description="No Desc",
+        )
+
+        cs1 = CompoundStructure.create(
+            compound=c,
+            smiles="PLACEHOLDER",
+            molfile=self.VALID_MOLFILE,
+            name="Molfile Structure",
+            description="No Desc",
+        )
+
+        cs2 = CompoundStructure.create(
+            compound=c,
+            smiles="PLACEHOLDER",
+            molfile=self.VALID_MOLFILE,
+            name="Molfile Structure",
+            description="No Desc",
+        )
+
+        self.assertEqual(cs1.pk, cs2.pk)

tests/test_reaction_model.py

@@ -1,6 +1,7 @@
 from django.conf import settings as s
 from django.test import TestCase, override_settings
 
+from epdb.exceptions import InvalidSMILESException
 from epdb.logic import PackageManager
 from epdb.models import Compound, User, Reaction, Rule
 
@@ -163,7 +164,7 @@ class ReactionTest(TestCase):
         self.assertEqual(len(self.package.reactions), 1)
 
     def test_wrong_smiles(self):
-        with self.assertRaises(ValueError):
+        with self.assertRaises(InvalidSMILESException):
             _ = Reaction.create(
                 package=self.package,
                 name="Eawag BBD reaction r0001",

tests/views/test_compound_views.py

@@ -11,6 +11,9 @@ from epdb.models import Compound, Scenario, ExternalDatabase
 class CompoundViewTest(TestCase):
     fixtures = ["test_fixtures_incl_model.jsonl.gz"]
 
+    # A valid V2000 molfile for 4-Nitrobenzoic acid (O=C(O)C1=CC=C([N+](=O)[O-])C=C1)
+    VALID_MOLFILE = """\n  Mrv2211 01012500002D\n\n 12 12  0  0  0  0            999 V2000\n    1.4289   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.0000   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.7145   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    0.7145   -2.8875    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0\n    0.0000   -3.3000    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0\n    1.4289   -3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  2  0  0  0  0\n  2  3  1  0  0  0  0\n  3  4  2  0  0  0  0\n  4  5  1  0  0  0  0\n  5  6  2  0  0  0  0\n  6  1  1  0  0  0  0\n  2  7  1  0  0  0  0\n  7  8  2  0  0  0  0\n  7  9  1  0  0  0  0\n  5 10  1  0  0  0  0\n 10 11  1  0  0  0  0\n 10 12  2  0  0  0  0\nM  CHG  2  10   1  11  -1\nM  END\n"""
+
     @classmethod
     def setUpClass(cls):
         super(CompoundViewTest, cls).setUpClass()
@@ -396,3 +399,108 @@ class CompoundViewTest(TestCase):
 
         c = Compound.objects.get(url=compound_url)
         self.assertEqual(len(c.aliases), 0)
+
+    def test_create_compound_via_molfile(self):
+        """POSTing a valid molfile without a SMILES should create a compound successfully."""
+        response = self.client.post(
+            reverse("compounds"),
+            {
+                "compound-name": "4-Nitrobenzoic acid",
+                "compound-description": "Created from molfile",
+                "compound-molfile": self.VALID_MOLFILE,
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        compound_url = response.url
+
+        c = Compound.objects.get(url=compound_url)
+
+        self.assertEqual(c.name, "4-Nitrobenzoic acid")
+        self.assertEqual(c.description, "Created from molfile")
+        # SMILES should have been extracted from molfile, so it must be non-empty
+        self.assertIsNotNone(c.default_structure.smiles)
+        self.assertNotEqual(c.default_structure.smiles.strip(), "")
+
+    def test_create_compound_molfile_takes_precedence_over_smiles(self):
+        """When both molfile and SMILES are submitted, the molfile should win."""
+        response = self.client.post(
+            reverse("compounds"),
+            {
+                "compound-name": "4-Nitrobenzoic acid",
+                "compound-description": "Molfile precedence test",
+                "compound-smiles": "C",  # intentionally wrong/different
+                "compound-molfile": self.VALID_MOLFILE,
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        compound_url = response.url
+
+        c = Compound.objects.get(url=compound_url)
+
+        # The resulting SMILES must NOT be the dummy "C" supplied via compound-smiles
+        self.assertNotEqual(c.default_structure.smiles, "C")
+
+    def test_create_compound_via_invalid_molfile_returns_error(self):
+        """POSTing an invalid molfile should not create a compound and should return an error response."""
+        initial_count = self.user1_default_package.compounds.count()
+
+        response = self.client.post(
+            reverse("compounds"),
+            {
+                "compound-name": "Bad Molfile Compound",
+                "compound-description": "Should fail",
+                "compound-molfile": "this is not a molfile at all",
+            },
+        )
+
+        # The view should signal an error (non-2xx or a redirect to an error page, not 302 to a new compound)
+        self.assertNotEqual(response.status_code, 302)
+        # No new compound should have been created
+        self.assertEqual(self.user1_default_package.compounds.count(), initial_count)
+
+    def test_create_compound_via_empty_molfile_falls_back_to_smiles(self):
+        """Submitting an empty molfile with a valid SMILES should fall back to SMILES."""
+        response = self.client.post(
+            reverse("compounds"),
+            {
+                "compound-name": "Fallback SMILES Compound",
+                "compound-description": "Empty molfile fallback",
+                "compound-smiles": "C(CCl)Cl",
+                "compound-molfile": "   ",  # whitespace only
+            },
+        )
+
+        self.assertEqual(response.status_code, 302)
+        compound_url = response.url
+
+        c = Compound.objects.get(url=compound_url)
+        self.assertEqual(c.default_structure.smiles, "C(CCl)Cl")
+
+    def test_create_compound_via_molfile_deduplication(self):
+        """Submitting the same molfile twice should return the existing compound."""
+        response1 = self.client.post(
+            reverse("compounds"),
+            {
+                "compound-name": "4-Nitrobenzoic acid",
+                "compound-description": "Molfile dedup test",
+                "compound-molfile": self.VALID_MOLFILE,
+            },
+        )
+
+        self.assertEqual(response1.status_code, 302)
+        compound_url_1 = response1.url
+
+        response2 = self.client.post(
+            reverse("compounds"),
+            {
+                "compound-name": "4-Nitrobenzoic acid",
+                "compound-description": "Molfile dedup test",
+                "compound-molfile": self.VALID_MOLFILE,
+            },
+        )
+
+        self.assertEqual(response2.status_code, 302)
+        self.assertEqual(response2.url, compound_url_1)
+        self.assertEqual(self.user1_default_package.compounds.count(), 1)

tests/views/test_model_views.py

@@ -46,6 +46,14 @@ class ModelViewTest(TestCase):
         )
 
         expected = [
+            {
+                "products": [["CCN(CC)C(=O)C1=CC(C=O)=CC=C1"]],
+                "probability": 0.75,
+                "btrule": {
+                    "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/2f2e0c39-e109-4836-959f-2bda2524f022",
+                    "name": "bt0001-3568",
+                },
+            },
             {
                 "products": [["O=C(O)C1=CC(CO)=CC=C1", "CCNCC"]],
                 "probability": 0.25,
@@ -62,14 +70,6 @@ class ModelViewTest(TestCase):
                     "name": "bt0243-4301",
                 },
             },
-            {
-                "products": [["CCN(CC)C(=O)C1=CC(C=O)=CC=C1"]],
-                "probability": 0.75,
-                "btrule": {
-                    "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/2f2e0c39-e109-4836-959f-2bda2524f022",
-                    "name": "bt0001-3568",
-                },
-            },
         ]
 
         actual = response.json()["pred"]

tests/views/test_package_views.py

@@ -72,8 +72,10 @@ class PackageViewTest(TestCase):
 
     def test_import_package(self):
         file = SimpleUploadedFile(
-            "Fixture_Package.json",
+            "EAWAG-BBD_32de3cf4-e3e6-4168-956e-32fa5ddb0ce1.json",
-            open(s.FIXTURE_DIRS[0] / "Fixture_Package.json", "rb").read(),
+            open(
+                s.FIXTURE_DIRS[0] / "EAWAG-BBD_32de3cf4-e3e6-4168-956e-32fa5ddb0ce1.json", "rb"
+            ).read(),
             content_type="application/json",
         )
 
@@ -86,10 +88,11 @@ class PackageViewTest(TestCase):
 
         p = Package.objects.get(url=package_url)
 
-        self.assertEqual(p.pathways.count(), 22)
+        self.assertEqual(p.pathways.count(), 219)
-        self.assertEqual(p.rules.count(), 45)
+        self.assertEqual(p.rules.count(), 498)
-        self.assertEqual(p.compounds.count(), 223)
+        self.assertEqual(p.compounds.count(), 1399)
-        self.assertEqual(p.reactions.count(), 212)
+        self.assertEqual(p.reactions.count(), 1480)
+        self.assertEqual(p.scenarios.count(), 1914)
 
         upp = UserPackagePermission.objects.get(package=p, user=self.user1)
         self.assertEqual(upp.permission, Permission.ALL[0])

utilities/chem.py

@@ -88,6 +88,10 @@ class FormatConverter(object):
     def from_smiles(smiles):
         return Chem.MolFromSmiles(smiles)
 
+    @staticmethod
+    def from_molfile(molfile: str):
+        return Chem.MolFromMolBlock(molfile)
+
     @staticmethod
     def to_smiles(mol, canonical=False):
         return Chem.MolToSmiles(mol, canonical=canonical)
@@ -171,12 +175,17 @@ class FormatConverter(object):
             try:
                 Chem.Kekulize(mol)
             except Exception:
-                mc = Chem.Mol(mol.ToBinary())
+                mol = Chem.Mol(mol.ToBinary())
 
-        if not mc.GetNumConformers():
+        if not mol.GetNumConformers():
-            Chem.rdDepictor.Compute2DCoords(mc)
+            Chem.rdDepictor.Compute2DCoords(mol)
 
-        pass
+        drawer = rdMolDraw2D.MolDraw2DCairo(*mol_size)
+        opts = drawer.drawOptions()
+        opts.clearBackground = False
+        drawer.DrawMolecule(mol)
+        drawer.FinishDrawing()
+        return drawer.GetDrawingText()
 
     @staticmethod
     def normalize(smiles):

utilities/legacy.py

@@ -64,7 +64,7 @@
 
 import logging
 
-from envipy_additional_information import HalfLife, HalfLifeWS
+from envipy_additional_information import HalfLife, HalfLifeWS, HalfLifeModel
 from envipy_additional_information.information import Interval
 from envipy_additional_information.parsers import (
     AcidityParser,
@@ -125,6 +125,7 @@ from envipy_additional_information.parsers import (
     LiquidMatrixSourceParser,
     OxygenUptakeRateParser,
     InitiatingOrganismParser,
+    PFASConfidenceParser,
 )
 
 logger = logging.getLogger(__name__)
@@ -141,7 +142,7 @@ def get_parameter(request, paramname):
     res = request.POST.get(paramname)
     if res is not None and res.strip() != "":
         return res
-    return ValueError("Not all parameters are set!")
+    raise ValueError("Not all parameters are set!")
 
 
 def get_parameter_or_empty_string(request, paramname):
@@ -473,17 +474,12 @@ def build_additional_information_from_request(request, type_):
 
             comment = get_parameter_or_empty_string(request, "comment")
             source = get_parameter_or_empty_string(request, "source")
-            first_order = get_parameter_or_empty_string(request, "firstOrder")
+            # first_order = get_parameter_or_empty_string(request, "firstOrder")
             model = get_parameter_or_empty_string(request, "model")
             fit = get_parameter_or_empty_string(request, "fit")
 
-            if first_order != "":
+            if model:
-                if model != "":
+                model = HalfLifeModel(model.upper())
-                    raise ValueError("not both, model and firstOrder can be set!")
-                if first_order == "true":
-                    model = "SFO"
-                else:
-                    logger.info("firstOrder is set to false which is not meaningful")
 
             return HalfLife(model=model, fit=fit, comment=comment, dt50=i, source=source)
 
@@ -508,6 +504,10 @@ def build_additional_information_from_request(request, type_):
             comment_ws = get_parameter_or_empty_string(request, "comment_ws")
             source_ws = get_parameter_or_empty_string(request, "source_ws")
             model_ws = get_parameter_or_empty_string(request, "model_ws")
+
+            if model_ws:
+                model_ws = HalfLifeModel(model_ws.upper())
+
             fit_ws = get_parameter_or_empty_string(request, "fit_ws")
 
             dt50_total = IntervalParser.from_string(hl_ws_total)
@@ -674,7 +674,8 @@ def build_additional_information_from_request(request, type_):
         elif type_ == "studywst":
             # study_wst_cond = get_parameter(request, "studywstcond")
             raise ValueError("studywstcond is not yet implemented")
-
+        elif type_ == "pfasconfidence":
+            return PFASConfidenceParser.from_string(get_parameter(request, "level"))
         else:
             raise ValueError(f"No corresponding AdditionalInformation for {type_} found!")
 

uv.lock

@@ -17,7 +17,7 @@ wheels = [
 
 [[package]]
 name = "aiohttp"
-version = "3.13.3"
+version = "3.13.5"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "aiohappyeyeballs" },
@@ -28,76 +28,76 @@ dependencies = [
     { name = "propcache" },
     { name = "yarl" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/50/42/32cf8e7704ceb4481406eb87161349abb46a57fee3f008ba9cb610968646/aiohttp-3.13.3.tar.gz", hash = "sha256:a949eee43d3782f2daae4f4a2819b2cb9b0c5d3b7f7a927067cc84dafdbb9f88", size = 7844556, upload-time = "2026-01-03T17:33:05.204Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/77/9a/152096d4808df8e4268befa55fba462f440f14beab85e8ad9bf990516918/aiohttp-3.13.5.tar.gz", hash = "sha256:9d98cc980ecc96be6eb4c1994ce35d28d8b1f5e5208a23b421187d1209dbb7d1", size = 7858271, upload-time = "2026-03-31T22:01:03.343Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/a0/be/4fc11f202955a69e0db803a12a062b8379c970c7c84f4882b6da17337cc1/aiohttp-3.13.3-cp312-cp312-macosx_10_13_universal2.whl", hash = "sha256:b903a4dfee7d347e2d87697d0713be59e0b87925be030c9178c5faa58ea58d5c", size = 739732, upload-time = "2026-01-03T17:30:14.23Z" },
+    { url = "https://files.pythonhosted.org/packages/be/6f/353954c29e7dcce7cf00280a02c75f30e133c00793c7a2ed3776d7b2f426/aiohttp-3.13.5-cp312-cp312-macosx_10_13_universal2.whl", hash = "sha256:023ecba036ddd840b0b19bf195bfae970083fd7024ce1ac22e9bba90464620e9", size = 748876, upload-time = "2026-03-31T21:57:36.319Z" },
-    { url = "https://files.pythonhosted.org/packages/97/2c/621d5b851f94fa0bb7430d6089b3aa970a9d9b75196bc93bb624b0db237a/aiohttp-3.13.3-cp312-cp312-macosx_10_13_x86_64.whl", hash = "sha256:a45530014d7a1e09f4a55f4f43097ba0fd155089372e105e4bff4ca76cb1b168", size = 494293, upload-time = "2026-01-03T17:30:15.96Z" },
+    { url = "https://files.pythonhosted.org/packages/f5/1b/428a7c64687b3b2e9cd293186695affc0e1e54a445d0361743b231f11066/aiohttp-3.13.5-cp312-cp312-macosx_10_13_x86_64.whl", hash = "sha256:15c933ad7920b7d9a20de151efcd05a6e38302cbf0e10c9b2acb9a42210a2416", size = 499557, upload-time = "2026-03-31T21:57:38.236Z" },
-    { url = "https://files.pythonhosted.org/packages/5d/43/4be01406b78e1be8320bb8316dc9c42dbab553d281c40364e0f862d5661c/aiohttp-3.13.3-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:27234ef6d85c914f9efeb77ff616dbf4ad2380be0cda40b4db086ffc7ddd1b7d", size = 493533, upload-time = "2026-01-03T17:30:17.431Z" },
+    { url = "https://files.pythonhosted.org/packages/29/47/7be41556bfbb6917069d6a6634bb7dd5e163ba445b783a90d40f5ac7e3a7/aiohttp-3.13.5-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:ab2899f9fa2f9f741896ebb6fa07c4c883bfa5c7f2ddd8cf2aafa86fa981b2d2", size = 500258, upload-time = "2026-03-31T21:57:39.923Z" },
-    { url = "https://files.pythonhosted.org/packages/8d/a8/5a35dc56a06a2c90d4742cbf35294396907027f80eea696637945a106f25/aiohttp-3.13.3-cp312-cp312-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:d32764c6c9aafb7fb55366a224756387cd50bfa720f32b88e0e6fa45b27dcf29", size = 1737839, upload-time = "2026-01-03T17:30:19.422Z" },
+    { url = "https://files.pythonhosted.org/packages/67/84/c9ecc5828cb0b3695856c07c0a6817a99d51e2473400f705275a2b3d9239/aiohttp-3.13.5-cp312-cp312-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:a60eaa2d440cd4707696b52e40ed3e2b0f73f65be07fd0ef23b6b539c9c0b0b4", size = 1749199, upload-time = "2026-03-31T21:57:41.938Z" },
-    { url = "https://files.pythonhosted.org/packages/bf/62/4b9eeb331da56530bf2e198a297e5303e1c1ebdceeb00fe9b568a65c5a0c/aiohttp-3.13.3-cp312-cp312-manylinux2014_armv7l.manylinux_2_17_armv7l.manylinux_2_31_armv7l.whl", hash = "sha256:b1a6102b4d3ebc07dad44fbf07b45bb600300f15b552ddf1851b5390202ea2e3", size = 1703932, upload-time = "2026-01-03T17:30:21.756Z" },
+    { url = "https://files.pythonhosted.org/packages/f0/d3/3c6d610e66b495657622edb6ae7c7fd31b2e9086b4ec50b47897ad6042a9/aiohttp-3.13.5-cp312-cp312-manylinux2014_armv7l.manylinux_2_17_armv7l.manylinux_2_31_armv7l.whl", hash = "sha256:55b3bdd3292283295774ab585160c4004f4f2f203946997f49aac032c84649e9", size = 1721013, upload-time = "2026-03-31T21:57:43.904Z" },
-    { url = "https://files.pythonhosted.org/packages/7c/f6/af16887b5d419e6a367095994c0b1332d154f647e7dc2bd50e61876e8e3d/aiohttp-3.13.3-cp312-cp312-manylinux2014_ppc64le.manylinux_2_17_ppc64le.manylinux_2_28_ppc64le.whl", hash = "sha256:c014c7ea7fb775dd015b2d3137378b7be0249a448a1612268b5a90c2d81de04d", size = 1771906, upload-time = "2026-01-03T17:30:23.932Z" },
+    { url = "https://files.pythonhosted.org/packages/49/a0/24409c12217456df0bae7babe3b014e460b0b38a8e60753d6cb339f6556d/aiohttp-3.13.5-cp312-cp312-manylinux2014_ppc64le.manylinux_2_17_ppc64le.manylinux_2_28_ppc64le.whl", hash = "sha256:c2b2355dc094e5f7d45a7bb262fe7207aa0460b37a0d87027dcf21b5d890e7d5", size = 1781501, upload-time = "2026-03-31T21:57:46.285Z" },
-    { url = "https://files.pythonhosted.org/packages/ce/83/397c634b1bcc24292fa1e0c7822800f9f6569e32934bdeef09dae7992dfb/aiohttp-3.13.3-cp312-cp312-manylinux2014_s390x.manylinux_2_17_s390x.manylinux_2_28_s390x.whl", hash = "sha256:2b8d8ddba8f95ba17582226f80e2de99c7a7948e66490ef8d947e272a93e9463", size = 1871020, upload-time = "2026-01-03T17:30:26Z" },
+    { url = "https://files.pythonhosted.org/packages/98/9d/b65ec649adc5bccc008b0957a9a9c691070aeac4e41cea18559fef49958b/aiohttp-3.13.5-cp312-cp312-manylinux2014_s390x.manylinux_2_17_s390x.manylinux_2_28_s390x.whl", hash = "sha256:b38765950832f7d728297689ad78f5f2cf79ff82487131c4d26fe6ceecdc5f8e", size = 1878981, upload-time = "2026-03-31T21:57:48.734Z" },
-    { url = "https://files.pythonhosted.org/packages/86/f6/a62cbbf13f0ac80a70f71b1672feba90fdb21fd7abd8dbf25c0105fb6fa3/aiohttp-3.13.3-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:9ae8dd55c8e6c4257eae3a20fd2c8f41edaea5992ed67156642493b8daf3cecc", size = 1755181, upload-time = "2026-01-03T17:30:27.554Z" },
+    { url = "https://files.pythonhosted.org/packages/57/d8/8d44036d7eb7b6a8ec4c5494ea0c8c8b94fbc0ed3991c1a7adf230df03bf/aiohttp-3.13.5-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:b18f31b80d5a33661e08c89e202edabf1986e9b49c42b4504371daeaa11b47c1", size = 1767934, upload-time = "2026-03-31T21:57:51.171Z" },
-    { url = "https://files.pythonhosted.org/packages/0a/87/20a35ad487efdd3fba93d5843efdfaa62d2f1479eaafa7453398a44faf13/aiohttp-3.13.3-cp312-cp312-manylinux_2_31_riscv64.manylinux_2_39_riscv64.whl", hash = "sha256:01ad2529d4b5035578f5081606a465f3b814c542882804e2e8cda61adf5c71bf", size = 1561794, upload-time = "2026-01-03T17:30:29.254Z" },
+    { url = "https://files.pythonhosted.org/packages/31/04/d3f8211f273356f158e3464e9e45484d3fb8c4ce5eb2f6fe9405c3273983/aiohttp-3.13.5-cp312-cp312-manylinux_2_31_riscv64.manylinux_2_39_riscv64.whl", hash = "sha256:33add2463dde55c4f2d9635c6ab33ce154e5ecf322bd26d09af95c5f81cfa286", size = 1566671, upload-time = "2026-03-31T21:57:53.326Z" },
-    { url = "https://files.pythonhosted.org/packages/de/95/8fd69a66682012f6716e1bc09ef8a1a2a91922c5725cb904689f112309c4/aiohttp-3.13.3-cp312-cp312-musllinux_1_2_aarch64.whl", hash = "sha256:bb4f7475e359992b580559e008c598091c45b5088f28614e855e42d39c2f1033", size = 1697900, upload-time = "2026-01-03T17:30:31.033Z" },
+    { url = "https://files.pythonhosted.org/packages/41/db/073e4ebe00b78e2dfcacff734291651729a62953b48933d765dc513bf798/aiohttp-3.13.5-cp312-cp312-musllinux_1_2_aarch64.whl", hash = "sha256:327cc432fdf1356fb4fbc6fe833ad4e9f6aacb71a8acaa5f1855e4b25910e4a9", size = 1705219, upload-time = "2026-03-31T21:57:55.385Z" },
-    { url = "https://files.pythonhosted.org/packages/e5/66/7b94b3b5ba70e955ff597672dad1691333080e37f50280178967aff68657/aiohttp-3.13.3-cp312-cp312-musllinux_1_2_armv7l.whl", hash = "sha256:c19b90316ad3b24c69cd78d5c9b4f3aa4497643685901185b65166293d36a00f", size = 1728239, upload-time = "2026-01-03T17:30:32.703Z" },
+    { url = "https://files.pythonhosted.org/packages/48/45/7dfba71a2f9fd97b15c95c06819de7eb38113d2cdb6319669195a7d64270/aiohttp-3.13.5-cp312-cp312-musllinux_1_2_armv7l.whl", hash = "sha256:7c35b0bf0b48a70b4cb4fc5d7bed9b932532728e124874355de1a0af8ec4bc88", size = 1743049, upload-time = "2026-03-31T21:57:57.341Z" },
-    { url = "https://files.pythonhosted.org/packages/47/71/6f72f77f9f7d74719692ab65a2a0252584bf8d5f301e2ecb4c0da734530a/aiohttp-3.13.3-cp312-cp312-musllinux_1_2_ppc64le.whl", hash = "sha256:96d604498a7c782cb15a51c406acaea70d8c027ee6b90c569baa6e7b93073679", size = 1740527, upload-time = "2026-01-03T17:30:34.695Z" },
+    { url = "https://files.pythonhosted.org/packages/18/71/901db0061e0f717d226386a7f471bb59b19566f2cae5f0d93874b017271f/aiohttp-3.13.5-cp312-cp312-musllinux_1_2_ppc64le.whl", hash = "sha256:df23d57718f24badef8656c49743e11a89fd6f5358fa8a7b96e728fda2abf7d3", size = 1749557, upload-time = "2026-03-31T21:57:59.626Z" },
-    { url = "https://files.pythonhosted.org/packages/fa/b4/75ec16cbbd5c01bdaf4a05b19e103e78d7ce1ef7c80867eb0ace42ff4488/aiohttp-3.13.3-cp312-cp312-musllinux_1_2_riscv64.whl", hash = "sha256:084911a532763e9d3dd95adf78a78f4096cd5f58cdc18e6fdbc1b58417a45423", size = 1554489, upload-time = "2026-01-03T17:30:36.864Z" },
+    { url = "https://files.pythonhosted.org/packages/08/d5/41eebd16066e59cd43728fe74bce953d7402f2b4ddfdfef2c0e9f17ca274/aiohttp-3.13.5-cp312-cp312-musllinux_1_2_riscv64.whl", hash = "sha256:02e048037a6501a5ec1f6fc9736135aec6eb8a004ce48838cb951c515f32c80b", size = 1558931, upload-time = "2026-03-31T21:58:01.972Z" },
-    { url = "https://files.pythonhosted.org/packages/52/8f/bc518c0eea29f8406dcf7ed1f96c9b48e3bc3995a96159b3fc11f9e08321/aiohttp-3.13.3-cp312-cp312-musllinux_1_2_s390x.whl", hash = "sha256:7a4a94eb787e606d0a09404b9c38c113d3b099d508021faa615d70a0131907ce", size = 1767852, upload-time = "2026-01-03T17:30:39.433Z" },
+    { url = "https://files.pythonhosted.org/packages/30/e6/4a799798bf05740e66c3a1161079bda7a3dd8e22ca392481d7a7f9af82a6/aiohttp-3.13.5-cp312-cp312-musllinux_1_2_s390x.whl", hash = "sha256:31cebae8b26f8a615d2b546fee45d5ffb76852ae6450e2a03f42c9102260d6fe", size = 1774125, upload-time = "2026-03-31T21:58:04.007Z" },
-    { url = "https://files.pythonhosted.org/packages/9d/f2/a07a75173124f31f11ea6f863dc44e6f09afe2bca45dd4e64979490deab1/aiohttp-3.13.3-cp312-cp312-musllinux_1_2_x86_64.whl", hash = "sha256:87797e645d9d8e222e04160ee32aa06bc5c163e8499f24db719e7852ec23093a", size = 1722379, upload-time = "2026-01-03T17:30:41.081Z" },
+    { url = "https://files.pythonhosted.org/packages/84/63/7749337c90f92bc2cb18f9560d67aa6258c7060d1397d21529b8004fcf6f/aiohttp-3.13.5-cp312-cp312-musllinux_1_2_x86_64.whl", hash = "sha256:888e78eb5ca55a615d285c3c09a7a91b42e9dd6fc699b166ebd5dee87c9ccf14", size = 1732427, upload-time = "2026-03-31T21:58:06.337Z" },
-    { url = "https://files.pythonhosted.org/packages/3c/4a/1a3fee7c21350cac78e5c5cef711bac1b94feca07399f3d406972e2d8fcd/aiohttp-3.13.3-cp312-cp312-win32.whl", hash = "sha256:b04be762396457bef43f3597c991e192ee7da460a4953d7e647ee4b1c28e7046", size = 428253, upload-time = "2026-01-03T17:30:42.644Z" },
+    { url = "https://files.pythonhosted.org/packages/98/de/cf2f44ff98d307e72fb97d5f5bbae3bfcb442f0ea9790c0bf5c5c2331404/aiohttp-3.13.5-cp312-cp312-win32.whl", hash = "sha256:8bd3ec6376e68a41f9f95f5ed170e2fcf22d4eb27a1f8cb361d0508f6e0557f3", size = 433534, upload-time = "2026-03-31T21:58:08.712Z" },
-    { url = "https://files.pythonhosted.org/packages/d9/b7/76175c7cb4eb73d91ad63c34e29fc4f77c9386bba4a65b53ba8e05ee3c39/aiohttp-3.13.3-cp312-cp312-win_amd64.whl", hash = "sha256:e3531d63d3bdfa7e3ac5e9b27b2dd7ec9df3206a98e0b3445fa906f233264c57", size = 455407, upload-time = "2026-01-03T17:30:44.195Z" },
+    { url = "https://files.pythonhosted.org/packages/aa/ca/eadf6f9c8fa5e31d40993e3db153fb5ed0b11008ad5d9de98a95045bed84/aiohttp-3.13.5-cp312-cp312-win_amd64.whl", hash = "sha256:110e448e02c729bcebb18c60b9214a87ba33bac4a9fa5e9a5f139938b56c6cb1", size = 460446, upload-time = "2026-03-31T21:58:10.945Z" },
-    { url = "https://files.pythonhosted.org/packages/97/8a/12ca489246ca1faaf5432844adbfce7ff2cc4997733e0af120869345643a/aiohttp-3.13.3-cp313-cp313-macosx_10_13_universal2.whl", hash = "sha256:5dff64413671b0d3e7d5918ea490bdccb97a4ad29b3f311ed423200b2203e01c", size = 734190, upload-time = "2026-01-03T17:30:45.832Z" },
+    { url = "https://files.pythonhosted.org/packages/78/e9/d76bf503005709e390122d34e15256b88f7008e246c4bdbe915cd4f1adce/aiohttp-3.13.5-cp313-cp313-macosx_10_13_universal2.whl", hash = "sha256:a5029cc80718bbd545123cd8fe5d15025eccaaaace5d0eeec6bd556ad6163d61", size = 742930, upload-time = "2026-03-31T21:58:13.155Z" },
-    { url = "https://files.pythonhosted.org/packages/32/08/de43984c74ed1fca5c014808963cc83cb00d7bb06af228f132d33862ca76/aiohttp-3.13.3-cp313-cp313-macosx_10_13_x86_64.whl", hash = "sha256:87b9aab6d6ed88235aa2970294f496ff1a1f9adcd724d800e9b952395a80ffd9", size = 491783, upload-time = "2026-01-03T17:30:47.466Z" },
+    { url = "https://files.pythonhosted.org/packages/57/00/4b7b70223deaebd9bb85984d01a764b0d7bd6526fcdc73cca83bcbe7243e/aiohttp-3.13.5-cp313-cp313-macosx_10_13_x86_64.whl", hash = "sha256:4bb6bf5811620003614076bdc807ef3b5e38244f9d25ca5fe888eaccea2a9832", size = 496927, upload-time = "2026-03-31T21:58:15.073Z" },
-    { url = "https://files.pythonhosted.org/packages/17/f8/8dd2cf6112a5a76f81f81a5130c57ca829d101ad583ce57f889179accdda/aiohttp-3.13.3-cp313-cp313-macosx_11_0_arm64.whl", hash = "sha256:425c126c0dc43861e22cb1c14ba4c8e45d09516d0a3ae0a3f7494b79f5f233a3", size = 490704, upload-time = "2026-01-03T17:30:49.373Z" },
+    { url = "https://files.pythonhosted.org/packages/9c/f5/0fb20fb49f8efdcdce6cd8127604ad2c503e754a8f139f5e02b01626523f/aiohttp-3.13.5-cp313-cp313-macosx_11_0_arm64.whl", hash = "sha256:a84792f8631bf5a94e52d9cc881c0b824ab42717165a5579c760b830d9392ac9", size = 497141, upload-time = "2026-03-31T21:58:17.009Z" },
-    { url = "https://files.pythonhosted.org/packages/6d/40/a46b03ca03936f832bc7eaa47cfbb1ad012ba1be4790122ee4f4f8cba074/aiohttp-3.13.3-cp313-cp313-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:7f9120f7093c2a32d9647abcaf21e6ad275b4fbec5b55969f978b1a97c7c86bf", size = 1720652, upload-time = "2026-01-03T17:30:50.974Z" },
+    { url = "https://files.pythonhosted.org/packages/3b/86/b7c870053e36a94e8951b803cb5b909bfbc9b90ca941527f5fcafbf6b0fa/aiohttp-3.13.5-cp313-cp313-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:57653eac22c6a4c13eb22ecf4d673d64a12f266e72785ab1c8b8e5940d0e8090", size = 1732476, upload-time = "2026-03-31T21:58:18.925Z" },
-    { url = "https://files.pythonhosted.org/packages/f7/7e/917fe18e3607af92657e4285498f500dca797ff8c918bd7d90b05abf6c2a/aiohttp-3.13.3-cp313-cp313-manylinux2014_armv7l.manylinux_2_17_armv7l.manylinux_2_31_armv7l.whl", hash = "sha256:697753042d57f4bf7122cab985bf15d0cef23c770864580f5af4f52023a56bd6", size = 1692014, upload-time = "2026-01-03T17:30:52.729Z" },
+    { url = "https://files.pythonhosted.org/packages/b5/e5/4e161f84f98d80c03a238671b4136e6530453d65262867d989bbe78244d0/aiohttp-3.13.5-cp313-cp313-manylinux2014_armv7l.manylinux_2_17_armv7l.manylinux_2_31_armv7l.whl", hash = "sha256:e5e5f7debc7a57af53fdf5c5009f9391d9f4c12867049d509bf7bb164a6e295b", size = 1706507, upload-time = "2026-03-31T21:58:21.094Z" },
-    { url = "https://files.pythonhosted.org/packages/71/b6/cefa4cbc00d315d68973b671cf105b21a609c12b82d52e5d0c9ae61d2a09/aiohttp-3.13.3-cp313-cp313-manylinux2014_ppc64le.manylinux_2_17_ppc64le.manylinux_2_28_ppc64le.whl", hash = "sha256:6de499a1a44e7de70735d0b39f67c8f25eb3d91eb3103be99ca0fa882cdd987d", size = 1759777, upload-time = "2026-01-03T17:30:54.537Z" },
+    { url = "https://files.pythonhosted.org/packages/d4/56/ea11a9f01518bd5a2a2fcee869d248c4b8a0cfa0bb13401574fa31adf4d4/aiohttp-3.13.5-cp313-cp313-manylinux2014_ppc64le.manylinux_2_17_ppc64le.manylinux_2_28_ppc64le.whl", hash = "sha256:c719f65bebcdf6716f10e9eff80d27567f7892d8988c06de12bbbd39307c6e3a", size = 1773465, upload-time = "2026-03-31T21:58:23.159Z" },
-    { url = "https://files.pythonhosted.org/packages/fb/e3/e06ee07b45e59e6d81498b591fc589629be1553abb2a82ce33efe2a7b068/aiohttp-3.13.3-cp313-cp313-manylinux2014_s390x.manylinux_2_17_s390x.manylinux_2_28_s390x.whl", hash = "sha256:37239e9f9a7ea9ac5bf6b92b0260b01f8a22281996da609206a84df860bc1261", size = 1861276, upload-time = "2026-01-03T17:30:56.512Z" },
+    { url = "https://files.pythonhosted.org/packages/eb/40/333ca27fb74b0383f17c90570c748f7582501507307350a79d9f9f3c6eb1/aiohttp-3.13.5-cp313-cp313-manylinux2014_s390x.manylinux_2_17_s390x.manylinux_2_28_s390x.whl", hash = "sha256:d97f93fdae594d886c5a866636397e2bcab146fd7a132fd6bb9ce182224452f8", size = 1873523, upload-time = "2026-03-31T21:58:25.59Z" },
-    { url = "https://files.pythonhosted.org/packages/7c/24/75d274228acf35ceeb2850b8ce04de9dd7355ff7a0b49d607ee60c29c518/aiohttp-3.13.3-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:f76c1e3fe7d7c8afad7ed193f89a292e1999608170dcc9751a7462a87dfd5bc0", size = 1743131, upload-time = "2026-01-03T17:30:58.256Z" },
+    { url = "https://files.pythonhosted.org/packages/f0/d2/e2f77eef1acb7111405433c707dc735e63f67a56e176e72e9e7a2cd3f493/aiohttp-3.13.5-cp313-cp313-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:3df334e39d4c2f899a914f1dba283c1aadc311790733f705182998c6f7cae665", size = 1754113, upload-time = "2026-03-31T21:58:27.624Z" },
-    { url = "https://files.pythonhosted.org/packages/04/98/3d21dde21889b17ca2eea54fdcff21b27b93f45b7bb94ca029c31ab59dc3/aiohttp-3.13.3-cp313-cp313-manylinux_2_31_riscv64.manylinux_2_39_riscv64.whl", hash = "sha256:fc290605db2a917f6e81b0e1e0796469871f5af381ce15c604a3c5c7e51cb730", size = 1556863, upload-time = "2026-01-03T17:31:00.445Z" },
+    { url = "https://files.pythonhosted.org/packages/fb/56/3f653d7f53c89669301ec9e42c95233e2a0c0a6dd051269e6e678db4fdb0/aiohttp-3.13.5-cp313-cp313-manylinux_2_31_riscv64.manylinux_2_39_riscv64.whl", hash = "sha256:fe6970addfea9e5e081401bcbadf865d2b6da045472f58af08427e108d618540", size = 1562351, upload-time = "2026-03-31T21:58:29.918Z" },
-    { url = "https://files.pythonhosted.org/packages/9e/84/da0c3ab1192eaf64782b03971ab4055b475d0db07b17eff925e8c93b3aa5/aiohttp-3.13.3-cp313-cp313-musllinux_1_2_aarch64.whl", hash = "sha256:4021b51936308aeea0367b8f006dc999ca02bc118a0cc78c303f50a2ff6afb91", size = 1682793, upload-time = "2026-01-03T17:31:03.024Z" },
+    { url = "https://files.pythonhosted.org/packages/ec/a6/9b3e91eb8ae791cce4ee736da02211c85c6f835f1bdfac0594a8a3b7018c/aiohttp-3.13.5-cp313-cp313-musllinux_1_2_aarch64.whl", hash = "sha256:7becdf835feff2f4f335d7477f121af787e3504b48b449ff737afb35869ba7bb", size = 1693205, upload-time = "2026-03-31T21:58:32.214Z" },
-    { url = "https://files.pythonhosted.org/packages/ff/0f/5802ada182f575afa02cbd0ec5180d7e13a402afb7c2c03a9aa5e5d49060/aiohttp-3.13.3-cp313-cp313-musllinux_1_2_armv7l.whl", hash = "sha256:49a03727c1bba9a97d3e93c9f93ca03a57300f484b6e935463099841261195d3", size = 1716676, upload-time = "2026-01-03T17:31:04.842Z" },
+    { url = "https://files.pythonhosted.org/packages/98/fc/bfb437a99a2fcebd6b6eaec609571954de2ed424f01c352f4b5504371dd3/aiohttp-3.13.5-cp313-cp313-musllinux_1_2_armv7l.whl", hash = "sha256:676e5651705ad5d8a70aeb8eb6936c436d8ebbd56e63436cb7dd9bb36d2a9a46", size = 1730618, upload-time = "2026-03-31T21:58:34.728Z" },
-    { url = "https://files.pythonhosted.org/packages/3f/8c/714d53bd8b5a4560667f7bbbb06b20c2382f9c7847d198370ec6526af39c/aiohttp-3.13.3-cp313-cp313-musllinux_1_2_ppc64le.whl", hash = "sha256:3d9908a48eb7416dc1f4524e69f1d32e5d90e3981e4e37eb0aa1cd18f9cfa2a4", size = 1733217, upload-time = "2026-01-03T17:31:06.868Z" },
+    { url = "https://files.pythonhosted.org/packages/e4/b6/c8534862126191a034f68153194c389addc285a0f1347d85096d349bbc15/aiohttp-3.13.5-cp313-cp313-musllinux_1_2_ppc64le.whl", hash = "sha256:9b16c653d38eb1a611cc898c41e76859ca27f119d25b53c12875fd0474ae31a8", size = 1745185, upload-time = "2026-03-31T21:58:36.909Z" },
-    { url = "https://files.pythonhosted.org/packages/7d/79/e2176f46d2e963facea939f5be2d26368ce543622be6f00a12844d3c991f/aiohttp-3.13.3-cp313-cp313-musllinux_1_2_riscv64.whl", hash = "sha256:2712039939ec963c237286113c68dbad80a82a4281543f3abf766d9d73228998", size = 1552303, upload-time = "2026-01-03T17:31:08.958Z" },
+    { url = "https://files.pythonhosted.org/packages/0b/93/4ca8ee2ef5236e2707e0fd5fecb10ce214aee1ff4ab307af9c558bda3b37/aiohttp-3.13.5-cp313-cp313-musllinux_1_2_riscv64.whl", hash = "sha256:999802d5fa0389f58decd24b537c54aa63c01c3219ce17d1214cbda3c2b22d2d", size = 1557311, upload-time = "2026-03-31T21:58:39.38Z" },
-    { url = "https://files.pythonhosted.org/packages/ab/6a/28ed4dea1759916090587d1fe57087b03e6c784a642b85ef48217b0277ae/aiohttp-3.13.3-cp313-cp313-musllinux_1_2_s390x.whl", hash = "sha256:7bfdc049127717581866fa4708791220970ce291c23e28ccf3922c700740fdc0", size = 1763673, upload-time = "2026-01-03T17:31:10.676Z" },
+    { url = "https://files.pythonhosted.org/packages/57/ae/76177b15f18c5f5d094f19901d284025db28eccc5ae374d1d254181d33f4/aiohttp-3.13.5-cp313-cp313-musllinux_1_2_s390x.whl", hash = "sha256:ec707059ee75732b1ba130ed5f9580fe10ff75180c812bc267ded039db5128c6", size = 1773147, upload-time = "2026-03-31T21:58:41.476Z" },
-    { url = "https://files.pythonhosted.org/packages/e8/35/4a3daeb8b9fab49240d21c04d50732313295e4bd813a465d840236dd0ce1/aiohttp-3.13.3-cp313-cp313-musllinux_1_2_x86_64.whl", hash = "sha256:8057c98e0c8472d8846b9c79f56766bcc57e3e8ac7bfd510482332366c56c591", size = 1721120, upload-time = "2026-01-03T17:31:12.575Z" },
+    { url = "https://files.pythonhosted.org/packages/01/a4/62f05a0a98d88af59d93b7fcac564e5f18f513cb7471696ac286db970d6a/aiohttp-3.13.5-cp313-cp313-musllinux_1_2_x86_64.whl", hash = "sha256:2d6d44a5b48132053c2f6cd5c8cb14bc67e99a63594e336b0f2af81e94d5530c", size = 1730356, upload-time = "2026-03-31T21:58:44.049Z" },
-    { url = "https://files.pythonhosted.org/packages/bc/9f/d643bb3c5fb99547323e635e251c609fbbc660d983144cfebec529e09264/aiohttp-3.13.3-cp313-cp313-win32.whl", hash = "sha256:1449ceddcdbcf2e0446957863af03ebaaa03f94c090f945411b61269e2cb5daf", size = 427383, upload-time = "2026-01-03T17:31:14.382Z" },
+    { url = "https://files.pythonhosted.org/packages/e4/85/fc8601f59dfa8c9523808281f2da571f8b4699685f9809a228adcc90838d/aiohttp-3.13.5-cp313-cp313-win32.whl", hash = "sha256:329f292ed14d38a6c4c435e465f48bebb47479fd676a0411936cc371643225cc", size = 432637, upload-time = "2026-03-31T21:58:46.167Z" },
-    { url = "https://files.pythonhosted.org/packages/4e/f1/ab0395f8a79933577cdd996dd2f9aa6014af9535f65dddcf88204682fe62/aiohttp-3.13.3-cp313-cp313-win_amd64.whl", hash = "sha256:693781c45a4033d31d4187d2436f5ac701e7bbfe5df40d917736108c1cc7436e", size = 453899, upload-time = "2026-01-03T17:31:15.958Z" },
+    { url = "https://files.pythonhosted.org/packages/c0/1b/ac685a8882896acf0f6b31d689e3792199cfe7aba37969fa91da63a7fa27/aiohttp-3.13.5-cp313-cp313-win_amd64.whl", hash = "sha256:69f571de7500e0557801c0b51f4780482c0ec5fe2ac851af5a92cfce1af1cb83", size = 458896, upload-time = "2026-03-31T21:58:48.119Z" },
-    { url = "https://files.pythonhosted.org/packages/99/36/5b6514a9f5d66f4e2597e40dea2e3db271e023eb7a5d22defe96ba560996/aiohttp-3.13.3-cp314-cp314-macosx_10_13_universal2.whl", hash = "sha256:ea37047c6b367fd4bd632bff8077449b8fa034b69e812a18e0132a00fae6e808", size = 737238, upload-time = "2026-01-03T17:31:17.909Z" },
+    { url = "https://files.pythonhosted.org/packages/5d/ce/46572759afc859e867a5bc8ec3487315869013f59281ce61764f76d879de/aiohttp-3.13.5-cp314-cp314-macosx_10_13_universal2.whl", hash = "sha256:eb4639f32fd4a9904ab8fb45bf3383ba71137f3d9d4ba25b3b3f3109977c5b8c", size = 745721, upload-time = "2026-03-31T21:58:50.229Z" },
-    { url = "https://files.pythonhosted.org/packages/f7/49/459327f0d5bcd8c6c9ca69e60fdeebc3622861e696490d8674a6d0cb90a6/aiohttp-3.13.3-cp314-cp314-macosx_10_13_x86_64.whl", hash = "sha256:6fc0e2337d1a4c3e6acafda6a78a39d4c14caea625124817420abceed36e2415", size = 492292, upload-time = "2026-01-03T17:31:19.919Z" },
+    { url = "https://files.pythonhosted.org/packages/13/fe/8a2efd7626dbe6049b2ef8ace18ffda8a4dfcbe1bcff3ac30c0c7575c20b/aiohttp-3.13.5-cp314-cp314-macosx_10_13_x86_64.whl", hash = "sha256:7e5dc4311bd5ac493886c63cbf76ab579dbe4641268e7c74e48e774c74b6f2be", size = 497663, upload-time = "2026-03-31T21:58:52.232Z" },
-    { url = "https://files.pythonhosted.org/packages/e8/0b/b97660c5fd05d3495b4eb27f2d0ef18dc1dc4eff7511a9bf371397ff0264/aiohttp-3.13.3-cp314-cp314-macosx_11_0_arm64.whl", hash = "sha256:c685f2d80bb67ca8c3837823ad76196b3694b0159d232206d1e461d3d434666f", size = 493021, upload-time = "2026-01-03T17:31:21.636Z" },
+    { url = "https://files.pythonhosted.org/packages/9b/91/cc8cc78a111826c54743d88651e1687008133c37e5ee615fee9b57990fac/aiohttp-3.13.5-cp314-cp314-macosx_11_0_arm64.whl", hash = "sha256:756c3c304d394977519824449600adaf2be0ccee76d206ee339c5e76b70ded25", size = 499094, upload-time = "2026-03-31T21:58:54.566Z" },
-    { url = "https://files.pythonhosted.org/packages/54/d4/438efabdf74e30aeceb890c3290bbaa449780583b1270b00661126b8aae4/aiohttp-3.13.3-cp314-cp314-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:48e377758516d262bde50c2584fc6c578af272559c409eecbdd2bae1601184d6", size = 1717263, upload-time = "2026-01-03T17:31:23.296Z" },
+    { url = "https://files.pythonhosted.org/packages/0a/33/a8362cb15cf16a3af7e86ed11962d5cd7d59b449202dc576cdc731310bde/aiohttp-3.13.5-cp314-cp314-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:ecc26751323224cf8186efcf7fbcbc30f4e1d8c7970659daf25ad995e4032a56", size = 1726701, upload-time = "2026-03-31T21:58:56.864Z" },
-    { url = "https://files.pythonhosted.org/packages/71/f2/7bddc7fd612367d1459c5bcf598a9e8f7092d6580d98de0e057eb42697ad/aiohttp-3.13.3-cp314-cp314-manylinux2014_armv7l.manylinux_2_17_armv7l.manylinux_2_31_armv7l.whl", hash = "sha256:34749271508078b261c4abb1767d42b8d0c0cc9449c73a4df494777dc55f0687", size = 1669107, upload-time = "2026-01-03T17:31:25.334Z" },
+    { url = "https://files.pythonhosted.org/packages/45/0c/c091ac5c3a17114bd76cbf85d674650969ddf93387876cf67f754204bd77/aiohttp-3.13.5-cp314-cp314-manylinux2014_armv7l.manylinux_2_17_armv7l.manylinux_2_31_armv7l.whl", hash = "sha256:10a75acfcf794edf9d8db50e5a7ec5fc818b2a8d3f591ce93bc7b1210df016d2", size = 1683360, upload-time = "2026-03-31T21:58:59.072Z" },
-    { url = "https://files.pythonhosted.org/packages/00/5a/1aeaecca40e22560f97610a329e0e5efef5e0b5afdf9f857f0d93839ab2e/aiohttp-3.13.3-cp314-cp314-manylinux2014_ppc64le.manylinux_2_17_ppc64le.manylinux_2_28_ppc64le.whl", hash = "sha256:82611aeec80eb144416956ec85b6ca45a64d76429c1ed46ae1b5f86c6e0c9a26", size = 1760196, upload-time = "2026-01-03T17:31:27.394Z" },
+    { url = "https://files.pythonhosted.org/packages/23/73/bcee1c2b79bc275e964d1446c55c54441a461938e70267c86afaae6fba27/aiohttp-3.13.5-cp314-cp314-manylinux2014_ppc64le.manylinux_2_17_ppc64le.manylinux_2_28_ppc64le.whl", hash = "sha256:0f7a18f258d124cd678c5fe072fe4432a4d5232b0657fca7c1847f599233c83a", size = 1773023, upload-time = "2026-03-31T21:59:01.776Z" },
-    { url = "https://files.pythonhosted.org/packages/f8/f8/0ff6992bea7bd560fc510ea1c815f87eedd745fe035589c71ce05612a19a/aiohttp-3.13.3-cp314-cp314-manylinux2014_s390x.manylinux_2_17_s390x.manylinux_2_28_s390x.whl", hash = "sha256:2fff83cfc93f18f215896e3a190e8e5cb413ce01553901aca925176e7568963a", size = 1843591, upload-time = "2026-01-03T17:31:29.238Z" },
+    { url = "https://files.pythonhosted.org/packages/c7/ef/720e639df03004fee2d869f771799d8c23046dec47d5b81e396c7cda583a/aiohttp-3.13.5-cp314-cp314-manylinux2014_s390x.manylinux_2_17_s390x.manylinux_2_28_s390x.whl", hash = "sha256:df6104c009713d3a89621096f3e3e88cc323fd269dbd7c20afe18535094320be", size = 1853795, upload-time = "2026-03-31T21:59:04.568Z" },
-    { url = "https://files.pythonhosted.org/packages/e3/d1/e30e537a15f53485b61f5be525f2157da719819e8377298502aebac45536/aiohttp-3.13.3-cp314-cp314-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:bbe7d4cecacb439e2e2a8a1a7b935c25b812af7a5fd26503a66dadf428e79ec1", size = 1720277, upload-time = "2026-01-03T17:31:31.053Z" },
+    { url = "https://files.pythonhosted.org/packages/bd/c9/989f4034fb46841208de7aeeac2c6d8300745ab4f28c42f629ba77c2d916/aiohttp-3.13.5-cp314-cp314-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:241a94f7de7c0c3b616627aaad530fe2cb620084a8b144d3be7b6ecfe95bae3b", size = 1730405, upload-time = "2026-03-31T21:59:07.221Z" },
-    { url = "https://files.pythonhosted.org/packages/84/45/23f4c451d8192f553d38d838831ebbc156907ea6e05557f39563101b7717/aiohttp-3.13.3-cp314-cp314-manylinux_2_31_riscv64.manylinux_2_39_riscv64.whl", hash = "sha256:b928f30fe49574253644b1ca44b1b8adbd903aa0da4b9054a6c20fc7f4092a25", size = 1548575, upload-time = "2026-01-03T17:31:32.87Z" },
+    { url = "https://files.pythonhosted.org/packages/ce/75/ee1fd286ca7dc599d824b5651dad7b3be7ff8d9a7e7b3fe9820d9180f7db/aiohttp-3.13.5-cp314-cp314-manylinux_2_31_riscv64.manylinux_2_39_riscv64.whl", hash = "sha256:c974fb66180e58709b6fc402846f13791240d180b74de81d23913abe48e96d94", size = 1558082, upload-time = "2026-03-31T21:59:09.484Z" },
-    { url = "https://files.pythonhosted.org/packages/6a/ed/0a42b127a43712eda7807e7892c083eadfaf8429ca8fb619662a530a3aab/aiohttp-3.13.3-cp314-cp314-musllinux_1_2_aarch64.whl", hash = "sha256:7b5e8fe4de30df199155baaf64f2fcd604f4c678ed20910db8e2c66dc4b11603", size = 1679455, upload-time = "2026-01-03T17:31:34.76Z" },
+    { url = "https://files.pythonhosted.org/packages/c3/20/1e9e6650dfc436340116b7aa89ff8cb2bbdf0abc11dfaceaad8f74273a10/aiohttp-3.13.5-cp314-cp314-musllinux_1_2_aarch64.whl", hash = "sha256:6e27ea05d184afac78aabbac667450c75e54e35f62238d44463131bd3f96753d", size = 1692346, upload-time = "2026-03-31T21:59:12.068Z" },
-    { url = "https://files.pythonhosted.org/packages/2e/b5/c05f0c2b4b4fe2c9d55e73b6d3ed4fd6c9dc2684b1d81cbdf77e7fad9adb/aiohttp-3.13.3-cp314-cp314-musllinux_1_2_armv7l.whl", hash = "sha256:8542f41a62bcc58fc7f11cf7c90e0ec324ce44950003feb70640fc2a9092c32a", size = 1687417, upload-time = "2026-01-03T17:31:36.699Z" },
+    { url = "https://files.pythonhosted.org/packages/d8/40/8ebc6658d48ea630ac7903912fe0dd4e262f0e16825aa4c833c56c9f1f56/aiohttp-3.13.5-cp314-cp314-musllinux_1_2_armv7l.whl", hash = "sha256:a79a6d399cef33a11b6f004c67bb07741d91f2be01b8d712d52c75711b1e07c7", size = 1698891, upload-time = "2026-03-31T21:59:14.552Z" },
-    { url = "https://files.pythonhosted.org/packages/c9/6b/915bc5dad66aef602b9e459b5a973529304d4e89ca86999d9d75d80cbd0b/aiohttp-3.13.3-cp314-cp314-musllinux_1_2_ppc64le.whl", hash = "sha256:5e1d8c8b8f1d91cd08d8f4a3c2b067bfca6ec043d3ff36de0f3a715feeedf926", size = 1729968, upload-time = "2026-01-03T17:31:38.622Z" },
+    { url = "https://files.pythonhosted.org/packages/d8/78/ea0ae5ec8ba7a5c10bdd6e318f1ba5e76fcde17db8275188772afc7917a4/aiohttp-3.13.5-cp314-cp314-musllinux_1_2_ppc64le.whl", hash = "sha256:c632ce9c0b534fbe25b52c974515ed674937c5b99f549a92127c85f771a78772", size = 1742113, upload-time = "2026-03-31T21:59:17.068Z" },
-    { url = "https://files.pythonhosted.org/packages/11/3b/e84581290a9520024a08640b63d07673057aec5ca548177a82026187ba73/aiohttp-3.13.3-cp314-cp314-musllinux_1_2_riscv64.whl", hash = "sha256:90455115e5da1c3c51ab619ac57f877da8fd6d73c05aacd125c5ae9819582aba", size = 1545690, upload-time = "2026-01-03T17:31:40.57Z" },
+    { url = "https://files.pythonhosted.org/packages/8a/66/9d308ed71e3f2491be1acb8769d96c6f0c47d92099f3bc9119cada27b357/aiohttp-3.13.5-cp314-cp314-musllinux_1_2_riscv64.whl", hash = "sha256:fceedde51fbd67ee2bcc8c0b33d0126cc8b51ef3bbde2f86662bd6d5a6f10ec5", size = 1553088, upload-time = "2026-03-31T21:59:19.541Z" },
-    { url = "https://files.pythonhosted.org/packages/f5/04/0c3655a566c43fd647c81b895dfe361b9f9ad6d58c19309d45cff52d6c3b/aiohttp-3.13.3-cp314-cp314-musllinux_1_2_s390x.whl", hash = "sha256:042e9e0bcb5fba81886c8b4fbb9a09d6b8a00245fd8d88e4d989c1f96c74164c", size = 1746390, upload-time = "2026-01-03T17:31:42.857Z" },
+    { url = "https://files.pythonhosted.org/packages/da/a6/6cc25ed8dfc6e00c90f5c6d126a98e2cf28957ad06fa1036bd34b6f24a2c/aiohttp-3.13.5-cp314-cp314-musllinux_1_2_s390x.whl", hash = "sha256:f92995dfec9420bb69ae629abf422e516923ba79ba4403bc750d94fb4a6c68c1", size = 1757976, upload-time = "2026-03-31T21:59:22.311Z" },
-    { url = "https://files.pythonhosted.org/packages/1f/53/71165b26978f719c3419381514c9690bd5980e764a09440a10bb816ea4ab/aiohttp-3.13.3-cp314-cp314-musllinux_1_2_x86_64.whl", hash = "sha256:2eb752b102b12a76ca02dff751a801f028b4ffbbc478840b473597fc91a9ed43", size = 1702188, upload-time = "2026-01-03T17:31:44.984Z" },
+    { url = "https://files.pythonhosted.org/packages/c1/2b/cce5b0ffe0de99c83e5e36d8f828e4161e415660a9f3e58339d07cce3006/aiohttp-3.13.5-cp314-cp314-musllinux_1_2_x86_64.whl", hash = "sha256:20ae0ff08b1f2c8788d6fb85afcb798654ae6ba0b747575f8562de738078457b", size = 1712444, upload-time = "2026-03-31T21:59:24.635Z" },
-    { url = "https://files.pythonhosted.org/packages/29/a7/cbe6c9e8e136314fa1980da388a59d2f35f35395948a08b6747baebb6aa6/aiohttp-3.13.3-cp314-cp314-win32.whl", hash = "sha256:b556c85915d8efaed322bf1bdae9486aa0f3f764195a0fb6ee962e5c71ef5ce1", size = 433126, upload-time = "2026-01-03T17:31:47.463Z" },
+    { url = "https://files.pythonhosted.org/packages/6c/cf/9e1795b4160c58d29421eafd1a69c6ce351e2f7c8d3c6b7e4ca44aea1a5b/aiohttp-3.13.5-cp314-cp314-win32.whl", hash = "sha256:b20df693de16f42b2472a9c485e1c948ee55524786a0a34345511afdd22246f3", size = 438128, upload-time = "2026-03-31T21:59:27.291Z" },
-    { url = "https://files.pythonhosted.org/packages/de/56/982704adea7d3b16614fc5936014e9af85c0e34b58f9046655817f04306e/aiohttp-3.13.3-cp314-cp314-win_amd64.whl", hash = "sha256:9bf9f7a65e7aa20dd764151fb3d616c81088f91f8df39c3893a536e279b4b984", size = 459128, upload-time = "2026-01-03T17:31:49.2Z" },
+    { url = "https://files.pythonhosted.org/packages/22/4d/eaedff67fc805aeba4ba746aec891b4b24cebb1a7d078084b6300f79d063/aiohttp-3.13.5-cp314-cp314-win_amd64.whl", hash = "sha256:f85c6f327bf0b8c29da7d93b1cabb6363fb5e4e160a32fa241ed2dce21b73162", size = 464029, upload-time = "2026-03-31T21:59:29.429Z" },
-    { url = "https://files.pythonhosted.org/packages/6c/2a/3c79b638a9c3d4658d345339d22070241ea341ed4e07b5ac60fb0f418003/aiohttp-3.13.3-cp314-cp314t-macosx_10_13_universal2.whl", hash = "sha256:05861afbbec40650d8a07ea324367cb93e9e8cc7762e04dd4405df99fa65159c", size = 769512, upload-time = "2026-01-03T17:31:51.134Z" },
+    { url = "https://files.pythonhosted.org/packages/79/11/c27d9332ee20d68dd164dc12a6ecdef2e2e35ecc97ed6cf0d2442844624b/aiohttp-3.13.5-cp314-cp314t-macosx_10_13_universal2.whl", hash = "sha256:1efb06900858bb618ff5cee184ae2de5828896c448403d51fb633f09e109be0a", size = 778758, upload-time = "2026-03-31T21:59:31.547Z" },
-    { url = "https://files.pythonhosted.org/packages/29/b9/3e5014d46c0ab0db8707e0ac2711ed28c4da0218c358a4e7c17bae0d8722/aiohttp-3.13.3-cp314-cp314t-macosx_10_13_x86_64.whl", hash = "sha256:2fc82186fadc4a8316768d61f3722c230e2c1dcab4200d52d2ebdf2482e47592", size = 506444, upload-time = "2026-01-03T17:31:52.85Z" },
+    { url = "https://files.pythonhosted.org/packages/04/fb/377aead2e0a3ba5f09b7624f702a964bdf4f08b5b6728a9799830c80041e/aiohttp-3.13.5-cp314-cp314t-macosx_10_13_x86_64.whl", hash = "sha256:fee86b7c4bd29bdaf0d53d14739b08a106fdda809ca5fe032a15f52fae5fe254", size = 512883, upload-time = "2026-03-31T21:59:34.098Z" },
-    { url = "https://files.pythonhosted.org/packages/90/03/c1d4ef9a054e151cd7839cdc497f2638f00b93cbe8043983986630d7a80c/aiohttp-3.13.3-cp314-cp314t-macosx_11_0_arm64.whl", hash = "sha256:0add0900ff220d1d5c5ebbf99ed88b0c1bbf87aa7e4262300ed1376a6b13414f", size = 510798, upload-time = "2026-01-03T17:31:54.91Z" },
+    { url = "https://files.pythonhosted.org/packages/bb/a6/aa109a33671f7a5d3bd78b46da9d852797c5e665bfda7d6b373f56bff2ec/aiohttp-3.13.5-cp314-cp314t-macosx_11_0_arm64.whl", hash = "sha256:20058e23909b9e65f9da62b396b77dfa95965cbe840f8def6e572538b1d32e36", size = 516668, upload-time = "2026-03-31T21:59:36.497Z" },
-    { url = "https://files.pythonhosted.org/packages/ea/76/8c1e5abbfe8e127c893fe7ead569148a4d5a799f7cf958d8c09f3eedf097/aiohttp-3.13.3-cp314-cp314t-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:568f416a4072fbfae453dcf9a99194bbb8bdeab718e08ee13dfa2ba0e4bebf29", size = 1868835, upload-time = "2026-01-03T17:31:56.733Z" },
+    { url = "https://files.pythonhosted.org/packages/79/b3/ca078f9f2fa9563c36fb8ef89053ea2bb146d6f792c5104574d49d8acb63/aiohttp-3.13.5-cp314-cp314t-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:8cf20a8d6868cb15a73cab329ffc07291ba8c22b1b88176026106ae39aa6df0f", size = 1883461, upload-time = "2026-03-31T21:59:38.723Z" },
-    { url = "https://files.pythonhosted.org/packages/8e/ac/984c5a6f74c363b01ff97adc96a3976d9c98940b8969a1881575b279ac5d/aiohttp-3.13.3-cp314-cp314t-manylinux2014_armv7l.manylinux_2_17_armv7l.manylinux_2_31_armv7l.whl", hash = "sha256:add1da70de90a2569c5e15249ff76a631ccacfe198375eead4aadf3b8dc849dc", size = 1720486, upload-time = "2026-01-03T17:31:58.65Z" },
+    { url = "https://files.pythonhosted.org/packages/b7/e3/a7ad633ca1ca497b852233a3cce6906a56c3225fb6d9217b5e5e60b7419d/aiohttp-3.13.5-cp314-cp314t-manylinux2014_armv7l.manylinux_2_17_armv7l.manylinux_2_31_armv7l.whl", hash = "sha256:330f5da04c987f1d5bdb8ae189137c77139f36bd1cb23779ca1a354a4b027800", size = 1747661, upload-time = "2026-03-31T21:59:41.187Z" },
-    { url = "https://files.pythonhosted.org/packages/b2/9a/b7039c5f099c4eb632138728828b33428585031a1e658d693d41d07d89d1/aiohttp-3.13.3-cp314-cp314t-manylinux2014_ppc64le.manylinux_2_17_ppc64le.manylinux_2_28_ppc64le.whl", hash = "sha256:10b47b7ba335d2e9b1239fa571131a87e2d8ec96b333e68b2a305e7a98b0bae2", size = 1847951, upload-time = "2026-01-03T17:32:00.989Z" },
+    { url = "https://files.pythonhosted.org/packages/33/b9/cd6fe579bed34a906d3d783fe60f2fa297ef55b27bb4538438ee49d4dc41/aiohttp-3.13.5-cp314-cp314t-manylinux2014_ppc64le.manylinux_2_17_ppc64le.manylinux_2_28_ppc64le.whl", hash = "sha256:6f1cbf0c7926d315c3c26c2da41fd2b5d2fe01ac0e157b78caefc51a782196cf", size = 1863800, upload-time = "2026-03-31T21:59:43.84Z" },
-    { url = "https://files.pythonhosted.org/packages/3c/02/3bec2b9a1ba3c19ff89a43a19324202b8eb187ca1e928d8bdac9bbdddebd/aiohttp-3.13.3-cp314-cp314t-manylinux2014_s390x.manylinux_2_17_s390x.manylinux_2_28_s390x.whl", hash = "sha256:3dd4dce1c718e38081c8f35f323209d4c1df7d4db4bab1b5c88a6b4d12b74587", size = 1941001, upload-time = "2026-01-03T17:32:03.122Z" },
+    { url = "https://files.pythonhosted.org/packages/c0/3f/2c1e2f5144cefa889c8afd5cf431994c32f3b29da9961698ff4e3811b79a/aiohttp-3.13.5-cp314-cp314t-manylinux2014_s390x.manylinux_2_17_s390x.manylinux_2_28_s390x.whl", hash = "sha256:53fc049ed6390d05423ba33103ded7281fe897cf97878f369a527070bd95795b", size = 1958382, upload-time = "2026-03-31T21:59:46.187Z" },
-    { url = "https://files.pythonhosted.org/packages/37/df/d879401cedeef27ac4717f6426c8c36c3091c6e9f08a9178cc87549c537f/aiohttp-3.13.3-cp314-cp314t-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:34bac00a67a812570d4a460447e1e9e06fae622946955f939051e7cc895cfab8", size = 1797246, upload-time = "2026-01-03T17:32:05.255Z" },
+    { url = "https://files.pythonhosted.org/packages/66/1d/f31ec3f1013723b3babe3609e7f119c2c2fb6ef33da90061a705ef3e1bc8/aiohttp-3.13.5-cp314-cp314t-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:898703aa2667e3c5ca4c54ca36cd73f58b7a38ef87a5606414799ebce4d3fd3a", size = 1803724, upload-time = "2026-03-31T21:59:48.656Z" },
-    { url = "https://files.pythonhosted.org/packages/8d/15/be122de1f67e6953add23335c8ece6d314ab67c8bebb3f181063010795a7/aiohttp-3.13.3-cp314-cp314t-manylinux_2_31_riscv64.manylinux_2_39_riscv64.whl", hash = "sha256:a19884d2ee70b06d9204b2727a7b9f983d0c684c650254679e716b0b77920632", size = 1627131, upload-time = "2026-01-03T17:32:07.607Z" },
+    { url = "https://files.pythonhosted.org/packages/0e/b4/57712dfc6f1542f067daa81eb61da282fab3e6f1966fca25db06c4fc62d5/aiohttp-3.13.5-cp314-cp314t-manylinux_2_31_riscv64.manylinux_2_39_riscv64.whl", hash = "sha256:0494a01ca9584eea1e5fbd6d748e61ecff218c51b576ee1999c23db7066417d8", size = 1640027, upload-time = "2026-03-31T21:59:51.284Z" },
-    { url = "https://files.pythonhosted.org/packages/12/12/70eedcac9134cfa3219ab7af31ea56bc877395b1ac30d65b1bc4b27d0438/aiohttp-3.13.3-cp314-cp314t-musllinux_1_2_aarch64.whl", hash = "sha256:5f8ca7f2bb6ba8348a3614c7918cc4bb73268c5ac2a207576b7afea19d3d9f64", size = 1795196, upload-time = "2026-01-03T17:32:09.59Z" },
+    { url = "https://files.pythonhosted.org/packages/25/3c/734c878fb43ec083d8e31bf029daae1beafeae582d1b35da234739e82ee7/aiohttp-3.13.5-cp314-cp314t-musllinux_1_2_aarch64.whl", hash = "sha256:6cf81fe010b8c17b09495cbd15c1d35afbc8fb405c0c9cf4738e5ae3af1d65be", size = 1806644, upload-time = "2026-03-31T21:59:53.753Z" },
-    { url = "https://files.pythonhosted.org/packages/32/11/b30e1b1cd1f3054af86ebe60df96989c6a414dd87e27ad16950eee420bea/aiohttp-3.13.3-cp314-cp314t-musllinux_1_2_armv7l.whl", hash = "sha256:b0d95340658b9d2f11d9697f59b3814a9d3bb4b7a7c20b131df4bcef464037c0", size = 1782841, upload-time = "2026-01-03T17:32:11.445Z" },
+    { url = "https://files.pythonhosted.org/packages/20/a5/f671e5cbec1c21d044ff3078223f949748f3a7f86b14e34a365d74a5d21f/aiohttp-3.13.5-cp314-cp314t-musllinux_1_2_armv7l.whl", hash = "sha256:c564dd5f09ddc9d8f2c2d0a301cd30a79a2cc1b46dd1a73bef8f0038863d016b", size = 1791630, upload-time = "2026-03-31T21:59:56.239Z" },
-    { url = "https://files.pythonhosted.org/packages/88/0d/d98a9367b38912384a17e287850f5695c528cff0f14f791ce8ee2e4f7796/aiohttp-3.13.3-cp314-cp314t-musllinux_1_2_ppc64le.whl", hash = "sha256:a1e53262fd202e4b40b70c3aff944a8155059beedc8a89bba9dc1f9ef06a1b56", size = 1795193, upload-time = "2026-01-03T17:32:13.705Z" },
+    { url = "https://files.pythonhosted.org/packages/0b/63/fb8d0ad63a0b8a99be97deac8c04dacf0785721c158bdf23d679a87aa99e/aiohttp-3.13.5-cp314-cp314t-musllinux_1_2_ppc64le.whl", hash = "sha256:2994be9f6e51046c4f864598fd9abeb4fba6e88f0b2152422c9666dcd4aea9c6", size = 1809403, upload-time = "2026-03-31T21:59:59.103Z" },
-    { url = "https://files.pythonhosted.org/packages/43/a5/a2dfd1f5ff5581632c7f6a30e1744deda03808974f94f6534241ef60c751/aiohttp-3.13.3-cp314-cp314t-musllinux_1_2_riscv64.whl", hash = "sha256:d60ac9663f44168038586cab2157e122e46bdef09e9368b37f2d82d354c23f72", size = 1621979, upload-time = "2026-01-03T17:32:15.965Z" },
+    { url = "https://files.pythonhosted.org/packages/59/0c/bfed7f30662fcf12206481c2aac57dedee43fe1c49275e85b3a1e1742294/aiohttp-3.13.5-cp314-cp314t-musllinux_1_2_riscv64.whl", hash = "sha256:157826e2fa245d2ef46c83ea8a5faf77ca19355d278d425c29fda0beb3318037", size = 1634924, upload-time = "2026-03-31T22:00:02.116Z" },
-    { url = "https://files.pythonhosted.org/packages/fa/f0/12973c382ae7c1cccbc4417e129c5bf54c374dfb85af70893646e1f0e749/aiohttp-3.13.3-cp314-cp314t-musllinux_1_2_s390x.whl", hash = "sha256:90751b8eed69435bac9ff4e3d2f6b3af1f57e37ecb0fbeee59c0174c9e2d41df", size = 1822193, upload-time = "2026-01-03T17:32:18.219Z" },
+    { url = "https://files.pythonhosted.org/packages/17/d6/fd518d668a09fd5a3319ae5e984d4d80b9a4b3df4e21c52f02251ef5a32e/aiohttp-3.13.5-cp314-cp314t-musllinux_1_2_s390x.whl", hash = "sha256:a8aca50daa9493e9e13c0f566201a9006f080e7c50e5e90d0b06f53146a54500", size = 1836119, upload-time = "2026-03-31T22:00:04.756Z" },
-    { url = "https://files.pythonhosted.org/packages/3c/5f/24155e30ba7f8c96918af1350eb0663e2430aad9e001c0489d89cd708ab1/aiohttp-3.13.3-cp314-cp314t-musllinux_1_2_x86_64.whl", hash = "sha256:fc353029f176fd2b3ec6cfc71be166aba1936fe5d73dd1992ce289ca6647a9aa", size = 1769801, upload-time = "2026-01-03T17:32:20.25Z" },
+    { url = "https://files.pythonhosted.org/packages/78/b7/15fb7a9d52e112a25b621c67b69c167805cb1f2ab8f1708a5c490d1b52fe/aiohttp-3.13.5-cp314-cp314t-musllinux_1_2_x86_64.whl", hash = "sha256:3b13560160d07e047a93f23aaa30718606493036253d5430887514715b67c9d9", size = 1772072, upload-time = "2026-03-31T22:00:07.494Z" },
-    { url = "https://files.pythonhosted.org/packages/eb/f8/7314031ff5c10e6ece114da79b338ec17eeff3a079e53151f7e9f43c4723/aiohttp-3.13.3-cp314-cp314t-win32.whl", hash = "sha256:2e41b18a58da1e474a057b3d35248d8320029f61d70a37629535b16a0c8f3767", size = 466523, upload-time = "2026-01-03T17:32:22.215Z" },
+    { url = "https://files.pythonhosted.org/packages/7e/df/57ba7f0c4a553fc2bd8b6321df236870ec6fd64a2a473a8a13d4f733214e/aiohttp-3.13.5-cp314-cp314t-win32.whl", hash = "sha256:9a0f4474b6ea6818b41f82172d799e4b3d29e22c2c520ce4357856fced9af2f8", size = 471819, upload-time = "2026-03-31T22:00:10.277Z" },
-    { url = "https://files.pythonhosted.org/packages/b4/63/278a98c715ae467624eafe375542d8ba9b4383a016df8fdefe0ae28382a7/aiohttp-3.13.3-cp314-cp314t-win_amd64.whl", hash = "sha256:44531a36aa2264a1860089ffd4dce7baf875ee5a6079d5fb42e261c704ef7344", size = 499694, upload-time = "2026-01-03T17:32:24.546Z" },
+    { url = "https://files.pythonhosted.org/packages/62/29/2f8418269e46454a26171bfdd6a055d74febf32234e474930f2f60a17145/aiohttp-3.13.5-cp314-cp314t-win_amd64.whl", hash = "sha256:18a2f6c1182c51baa1d28d68fea51513cb2a76612f038853c0ad3c145423d3d9", size = 505441, upload-time = "2026-03-31T22:00:12.791Z" },
 ]
 
 [[package]]
@@ -894,7 +894,7 @@ provides-extras = ["ms-login", "dev", "pepper-plugin"]
 [[package]]
 name = "envipy-additional-information"
 version = "0.4.2"
-source = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git?branch=develop#04f6a01b8c5cd1342464e004e0cfaec9abc13ac5" }
+source = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git?branch=develop#f2f251e0214f016760348730c45e56183d961201" }
 dependencies = [
     { name = "pydantic" },
 ]
@@ -1066,11 +1066,11 @@ wheels = [
 
 [[package]]
 name = "fsspec"
-version = "2026.2.0"
+version = "2026.3.0"
 source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/51/7c/f60c259dcbf4f0c47cc4ddb8f7720d2dcdc8888c8e5ad84c73ea4531cc5b/fsspec-2026.2.0.tar.gz", hash = "sha256:6544e34b16869f5aacd5b90bdf1a71acb37792ea3ddf6125ee69a22a53fb8bff", size = 313441, upload-time = "2026-02-05T21:50:53.743Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/e1/cf/b50ddf667c15276a9ab15a70ef5f257564de271957933ffea49d2cdbcdfb/fsspec-2026.3.0.tar.gz", hash = "sha256:1ee6a0e28677557f8c2f994e3eea77db6392b4de9cd1f5d7a9e87a0ae9d01b41", size = 313547, upload-time = "2026-03-27T19:11:14.892Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/e6/ab/fb21f4c939bb440104cc2b396d3be1d9b7a9fd3c6c2a53d98c45b3d7c954/fsspec-2026.2.0-py3-none-any.whl", hash = "sha256:98de475b5cb3bd66bedd5c4679e87b4fdfe1a3bf4d707b151b3c07e58c9a2437", size = 202505, upload-time = "2026-02-05T21:50:51.819Z" },
+    { url = "https://files.pythonhosted.org/packages/d5/1f/5f4a3cd9e4440e9d9bc78ad0a91a1c8d46b4d429d5239ebe6793c9fe5c41/fsspec-2026.3.0-py3-none-any.whl", hash = "sha256:d2ceafaad1b3457968ed14efa28798162f1638dbb5d2a6868a2db002a5ee39a4", size = 202595, upload-time = "2026-03-27T19:11:13.595Z" },
 ]
 
 [package.optional-dependencies]
@@ -2763,9 +2763,9 @@ dependencies = [
     { name = "typing-extensions", marker = "sys_platform != 'linux' and sys_platform != 'win32'" },
 ]
 wheels = [
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0-cp312-none-macosx_11_0_arm64.whl", hash = "sha256:a47b7986bee3f61ad217d8a8ce24605809ab425baf349f97de758815edd2ef54" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0-cp312-none-macosx_11_0_arm64.whl", hash = "sha256:a47b7986bee3f61ad217d8a8ce24605809ab425baf349f97de758815edd2ef54", upload-time = "2025-10-01T23:35:50Z" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0-cp313-cp313t-macosx_14_0_arm64.whl", hash = "sha256:fbe2e149c5174ef90d29a5f84a554dfaf28e003cb4f61fa2c8c024c17ec7ca58" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0-cp313-cp313t-macosx_14_0_arm64.whl", hash = "sha256:fbe2e149c5174ef90d29a5f84a554dfaf28e003cb4f61fa2c8c024c17ec7ca58", upload-time = "2025-10-01T23:35:52Z" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0-cp313-none-macosx_11_0_arm64.whl", hash = "sha256:057efd30a6778d2ee5e2374cd63a63f63311aa6f33321e627c655df60abdd390" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0-cp313-none-macosx_11_0_arm64.whl", hash = "sha256:057efd30a6778d2ee5e2374cd63a63f63311aa6f33321e627c655df60abdd390", upload-time = "2025-10-01T23:35:55Z" },
 ]
 
 [[package]]
@@ -2785,19 +2785,19 @@ dependencies = [
     { name = "typing-extensions", marker = "sys_platform == 'linux' or sys_platform == 'win32'" },
 ]
 wheels = [
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp312-cp312-linux_s390x.whl", hash = "sha256:0e34e276722ab7dd0dffa9e12fe2135a9b34a0e300c456ed7ad6430229404eb5" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp312-cp312-linux_s390x.whl", hash = "sha256:0e34e276722ab7dd0dffa9e12fe2135a9b34a0e300c456ed7ad6430229404eb5", upload-time = "2025-10-01T23:33:41Z" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp312-cp312-manylinux_2_28_aarch64.whl", hash = "sha256:610f600c102386e581327d5efc18c0d6edecb9820b4140d26163354a99cd800d" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp312-cp312-manylinux_2_28_aarch64.whl", hash = "sha256:610f600c102386e581327d5efc18c0d6edecb9820b4140d26163354a99cd800d", upload-time = "2025-10-01T23:33:45Z" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp312-cp312-manylinux_2_28_x86_64.whl", hash = "sha256:cb9a8ba8137ab24e36bf1742cb79a1294bd374db570f09fc15a5e1318160db4e" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp312-cp312-manylinux_2_28_x86_64.whl", hash = "sha256:cb9a8ba8137ab24e36bf1742cb79a1294bd374db570f09fc15a5e1318160db4e", upload-time = "2025-10-01T23:33:48Z" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp312-cp312-win_amd64.whl", hash = "sha256:2be20b2c05a0cce10430cc25f32b689259640d273232b2de357c35729132256d" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp312-cp312-win_amd64.whl", hash = "sha256:2be20b2c05a0cce10430cc25f32b689259640d273232b2de357c35729132256d", upload-time = "2025-10-01T23:33:52Z" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp312-cp312-win_arm64.whl", hash = "sha256:99fc421a5d234580e45957a7b02effbf3e1c884a5dd077afc85352c77bf41434" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp312-cp312-win_arm64.whl", hash = "sha256:99fc421a5d234580e45957a7b02effbf3e1c884a5dd077afc85352c77bf41434", upload-time = "2025-10-01T23:34:10Z" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313-linux_s390x.whl", hash = "sha256:8b5882276633cf91fe3d2d7246c743b94d44a7e660b27f1308007fdb1bb89f7d" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313-linux_s390x.whl", hash = "sha256:8b5882276633cf91fe3d2d7246c743b94d44a7e660b27f1308007fdb1bb89f7d", upload-time = "2025-10-01T23:34:15Z" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313-manylinux_2_28_aarch64.whl", hash = "sha256:a5064b5e23772c8d164068cc7c12e01a75faf7b948ecd95a0d4007d7487e5f25" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313-manylinux_2_28_aarch64.whl", hash = "sha256:a5064b5e23772c8d164068cc7c12e01a75faf7b948ecd95a0d4007d7487e5f25", upload-time = "2025-10-01T23:34:19Z" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313-manylinux_2_28_x86_64.whl", hash = "sha256:8f81dedb4c6076ec325acc3b47525f9c550e5284a18eae1d9061c543f7b6e7de" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313-manylinux_2_28_x86_64.whl", hash = "sha256:8f81dedb4c6076ec325acc3b47525f9c550e5284a18eae1d9061c543f7b6e7de", upload-time = "2025-10-01T23:34:23Z" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313-win_amd64.whl", hash = "sha256:e1ee1b2346ade3ea90306dfbec7e8ff17bc220d344109d189ae09078333b0856" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313-win_amd64.whl", hash = "sha256:e1ee1b2346ade3ea90306dfbec7e8ff17bc220d344109d189ae09078333b0856", upload-time = "2025-10-01T23:34:28Z" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313-win_arm64.whl", hash = "sha256:64c187345509f2b1bb334feed4666e2c781ca381874bde589182f81247e61f88" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313-win_arm64.whl", hash = "sha256:64c187345509f2b1bb334feed4666e2c781ca381874bde589182f81247e61f88", upload-time = "2025-10-01T23:34:45Z" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313t-manylinux_2_28_aarch64.whl", hash = "sha256:af81283ac671f434b1b25c95ba295f270e72db1fad48831eb5e4748ff9840041" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313t-manylinux_2_28_aarch64.whl", hash = "sha256:af81283ac671f434b1b25c95ba295f270e72db1fad48831eb5e4748ff9840041", upload-time = "2025-10-01T23:34:50Z" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313t-manylinux_2_28_x86_64.whl", hash = "sha256:a9dbb6f64f63258bc811e2c0c99640a81e5af93c531ad96e95c5ec777ea46dab" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313t-manylinux_2_28_x86_64.whl", hash = "sha256:a9dbb6f64f63258bc811e2c0c99640a81e5af93c531ad96e95c5ec777ea46dab", upload-time = "2025-10-01T23:34:53Z" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313t-win_amd64.whl", hash = "sha256:6d93a7165419bc4b2b907e859ccab0dea5deeab261448ae9a5ec5431f14c0e64" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313t-win_amd64.whl", hash = "sha256:6d93a7165419bc4b2b907e859ccab0dea5deeab261448ae9a5ec5431f14c0e64", upload-time = "2025-10-01T23:34:58Z" },
 ]
 
 [[package]]