adjusted migration

Initial bayer app

Show Pack Classification

Adjusted docker compose to bayer specifics

Adjusted Dockerfile for Bayer

Adding secret flags to group, add secret pools to packages

Adjusted View for Package creation

Prep configs, added Package Create Modal

wip

More on PES

wip

wip

Wip

minor

PW interactions

API PES

wip

Make Select Widget reflect required

make required generallay available

Update UI if pathway mode is set to build

Added ais

circle adjustments

Initial Zoom, fix AD Creation

wip

auth log, bb4g fix

missing import

Added viz hint if PES is part of reaction

Add Edge check for pes

flip boolean

...

pes

Added extra

...

In / Out Edges Viz, Submitting Button Text

...

Make PES Link clickable

Return proper http response instead of error

Fixed error return, removed unused options

Fix PES Link HTML for other entities

Fixed molfile assignment, adjusted Export

Package Export/Import cycle

highlight Description links

implemented non persistent

Harmonised proposed field in Json output

Added pesLink field to PW Api output

PES Fields in API Output

removed debug

Fix Classification import, Fix PES Deserialization

underline pes link in templates

Fix alter name/desc for node, make /node /edge funcitonal

provide setting link and copy button

Implemented Compound Names / Reaction Names View Option

Unconnected Nodes

Make links thicker, reduce timeout trigger time

Show proposed info in popover

Pathway Build no stereo removal

Include probs in reaction name option viz

Detect clicks outside nodes/edges

.gitea/workflows/build-image.yaml

@@ -1,62 +0,0 @@
-name: Build Docker Image
-
-# Trigger when a PR to main/develop is completed.
-on:
-  pull_request:
-    branches:
-      - main
-      - develop
-    types:
-      - closed
-
-jobs:
-  build-and-push:
-    if: ${{ github.event.pull_request.merged == true }}
-    runs-on: ubuntu-latest
-    steps:
-      # Fetch the repository content for the Docker build context.
-      - name: Checkout repository
-        uses: actions/checkout@v4
-
-      # Enable Buildx for BuildKit features (incl. SSH mount support).
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
-
-      # Authenticate against the container registry before pushing images.
-      - name: Log in to container registry
-        uses: docker/login-action@v3
-        with:
-          registry: git.envipath.com
-          username: ${{ secrets.CI_REGISTRY_USER }}
-          password: ${{ secrets.CI_REGISTRY_PASSWORD }}
-
-      # Generate image tags/labels:
-      # - PRs targeting main get "latest" and "main-sha"
-      # - PRs targeting develop get "dev" and "dev-sha"
-      - name: Extract metadata
-        id: meta
-        uses: docker/metadata-action@v5
-        with:
-          images: git.envipath.com/envipath/envipy
-          tags: |
-            type=raw,value=latest,enable=${{ github.event.pull_request.base.ref == 'main' }}
-            type=sha,prefix=main-,enable=${{ github.event.pull_request.base.ref == 'main' }}
-            type=raw,value=dev,enable=${{ github.event.pull_request.base.ref == 'develop' }}
-            type=sha,prefix=dev-,enable=${{ github.event.pull_request.base.ref == 'develop' }}
-
-      # Load SSH key so Docker can pull private git+ssh dependencies during build.
-      - name: Setup SSH for private git dependencies
-        uses: webfactory/ssh-agent@v0.9.0
-        with:
-          ssh-private-key: ${{ secrets.ENVIPY_CI_PRIVATE_KEY }}
-
-      # Build and push the production image; forward SSH agent without registry cache reuse.
-      - name: Build and push Docker image
-        uses: docker/build-push-action@v5
-        with:
-          context: .
-          file: Dockerfile
-          push: true
-          ssh: default
-          tags: ${{ steps.meta.outputs.tags }}
-          labels: ${{ steps.meta.outputs.labels }}

Dockerfile

@@ -60,10 +60,6 @@ COPY tests tests
 COPY utilities utilities
 COPY manage.py .
 
-# Used to run migrations etc
-COPY entrypoint.sh entrypoint.sh
-RUN chmod +x entrypoint.sh
-
 # Install frontend deps
 COPY package.json pnpm-lock.yaml pnpm-workspace.yaml ./
 
@@ -85,7 +81,6 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     libxext6 \
     libfontconfig1 \
     nano \
-    openjdk-21-jre-headless \
     && rm -rf /var/lib/apt/lists/*
 
 RUN useradd -ms /bin/bash django
@@ -107,5 +102,4 @@ USER django
 
 EXPOSE 8000
 
-ENTRYPOINT ["/app/entrypoint.sh"]
-CMD ["gunicorn", "envipath.wsgi:application", "--bind", "0.0.0.0:8000", "--workers", "8"]
+CMD ["gunicorn", "envipath.wsgi:application", "--bind", "0.0.0.0:8000", "--workers", "3"]

bayer/templates/modals/collections/new_package_modal.html

@@ -5,11 +5,11 @@
   class="modal"
   x-data="{
     isSubmitting: false,
-    packageClassification: '',
+    packageClassification: null,
 
     reset() {
       this.isSubmitting = false;
-      this.packageClassification = '';
+      this.packageClassification = null;
     },
 
     setFormData(data) {
@@ -114,7 +114,7 @@
             x-model="packageClassification"
             required
           >
-            <option value="" disabled>Select Classification</option>
+            <option value="null" disabled selected>Select Classification</option>
             <option value="0">Internal</option>
             <option value="10">Restricted</option>
             <option value="20">Secret</option>
@@ -131,9 +131,8 @@
             id="package-data-pool"
             name="package-data-pool"
             class="select select-bordered w-full"
-            :required="isSecret"
           >
-            <option value="" disabled>Select Data Pool</option>
+            <option value="" disabled selected>Select Data Pool</option>
               {% for obj in meta.secret_groups %}
                 <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
               {% endfor %}

bayer/templates/objects/package.html

@@ -4,7 +4,6 @@
 
   {% block action_modals %}
     {% include "modals/objects/edit_package_modal.html" %}
-    {% include "modals/objects/view_package_permissions_modal.html" %}
     {% include "modals/objects/edit_package_permissions_modal.html" %}
     {% include "modals/objects/publish_package_modal.html" %}
     {% include "modals/objects/set_license_modal.html" %}

bayer/views.py

@@ -1,40 +1,19 @@
 import base64
-import logging
 
 import requests
 from django.conf import settings as s
-from django.http import HttpResponse, HttpResponseBadRequest, HttpResponseNotAllowed
+from django.http import HttpResponse, HttpResponseBadRequest
 from django.shortcuts import redirect
 
 from bayer.models import PESCompound
 from epdb.logic import PackageManager
-from epdb.models import Pathway, Node, Group
+from epdb.models import Pathway, Node
 from epdb.views import _anonymous_or_real, error
 from utilities.decorators import package_permission_required
 
 Package = s.GET_PACKAGE_MODEL()
 
 
-logger = logging.getLogger(__name__)
-
-
-def has_secret_group(user):
-    """
-    Determines if the specified user belongs to any secret group.
-
-    This function checks whether the given user is a member of any group
-    that is marked as secret.
-
-    Args:
-        user: The user for whom the check is performed.
-
-    Returns:
-        bool: True if the user belongs to at least one secret group,
-        False otherwise.
-    """
-    return Group.objects.filter(secret=True, user_member=user).exists()
-
-
 @package_permission_required()
 def create_pes(request, package_uuid):
     current_user = _anonymous_or_real(request)
@@ -55,43 +34,29 @@ def create_pes(request, package_uuid):
 
         if pes_link:
             try:
-                pes_data = fetch_pes(request, pes_link, current_user)
+                pes_data = fetch_pes(request, pes_link)
             except ValueError as e:
-                return error(
-                    request,
-                    "Could not fetch PES",
-                    f"Could not fetch PES data for {pes_link}"
-                )
+                return HttpResponseBadRequest(f"Could not fetch PES data for {pes_link}")
 
             classification = pes_data.get("classificationLevel", "")
             if "secret" == classification.lower():
 
                 if current_package.classification_level != Package.Classification.SECRET:
-                    return error(
-                        request,
-                        "Classification Mismatch!",
-                        "Cannot create secret PESs in non-secret packages."
-                    )
+                    return HttpResponseBadRequest("Cannot create PESs for non-secret packages.")
 
-                if not current_package.data_pool or not current_package.data_pool.secret:
-                    logger.info(f"The current package does not have a secret data pool.")
-                    return error(
-                        request,
-                        "The current package does not have a secret data pool.",
-                        "Cannot create secret PESs in package without a secret data pool."
-                    )
+                data_pools = pes_data.get("dataPools")
+                if data_pools:
+                    if s.DATA_POOL_MAPPING[current_package.data_pool.name] not in data_pools:
+                        return HttpResponseBadRequest(
+                            f"PES data pool {s.DATA_POOL_MAPPING[current_package.data_pool.name]} not found in PES data")
 
             pes = PESCompound.create(current_package, pes_data, compound_name, compound_description)
 
             return redirect(pes.url)
         else:
-            return error(
-                request,
-                "No PES link received",
-                "Please provide a PES link."
-            )
+            return HttpResponseBadRequest("Please provide a PES link.")
     else:
-        return HttpResponseNotAllowed(["POST"])
+        pass
 
 
 @package_permission_required()
@@ -115,39 +80,25 @@ def create_pes_node(request, package_uuid, pathway_uuid):
 
         if pes_link:
             try:
-                pes_data = fetch_pes(request, pes_link, current_user)
+                pes_data = fetch_pes(request, pes_link)
             except ValueError as e:
-                return error(
-                    request,
-                    "Could not fetch PES",
-                    f"Could not fetch PES data for {pes_link}"
-                )
+                return HttpResponseBadRequest(f"Could not fetch PES data for {pes_link}")
 
             classification = pes_data.get("classificationLevel", "")
             if "secret" == classification.lower():
 
                 if current_package.classification_level != Package.Classification.SECRET:
-                    return error(
-                        request,
-                        "Classification Mismatch!",
-                        "Cannot create secret PESs in non-secret packages."
-                    )
+                    return HttpResponseBadRequest("Cannot create PESs for non-secret packages.")
 
-                if not current_package.data_pool or not current_package.data_pool.secret:
-                    logger.info(f"The current package does not have a secret data pool.")
-                    return error(
-                        request,
-                        "The current package does not have a secret data pool.",
-                        "Cannot create secret PESs in package without a secret data pool."
-                    )
+                data_pools = pes_data.get("dataPools")
+                if data_pools:
+                    if s.DATA_POOL_MAPPING[current_package.data_pool.name] not in data_pools:
+                        return HttpResponseBadRequest(
+                            f"PES data pool {s.DATA_POOL_MAPPING[current_package.data_pool.name]} not found in PES data")
 
             pes = PESCompound.create(current_package, pes_data, compound_name, compound_description)
 
-            node_qs = Node.objects.filter(
-                pathway=current_pathway,
-                default_node_label=pes.default_structure
-            )
-
+            node_qs = Node.objects.filter(pathway=current_pathway, default_node_label=pes.default_structure)
             if node_qs.exists():
                 return redirect(current_pathway.url)
 
@@ -165,91 +116,58 @@ def create_pes_node(request, package_uuid, pathway_uuid):
             return redirect(current_pathway.url)
 
         else:
-            return error(
-                request,
-                "No PES link received",
-                "Please provide a PES link."
-            )
+            return HttpResponseBadRequest("Please provide a PES link.")
     else:
-        return HttpResponseNotAllowed(["POST"])
+        pass
 
 
-def get_application_token(prod: bool) -> str:
-    scope = f"{s.PROD_PES_SCOPE if prod else s.NON_PROD_PES_SCOPE}/.default"
+def fetch_pes(request, pes_url) -> dict:
+    from epauth.views import get_access_token_from_request
+    token = get_access_token_from_request(request)
 
-    url = f"https://login.microsoftonline.com/{s.MS_ENTRA_TENANT_ID}/oauth2/v2.0/token"
-    data = {
-        "grant_type": "client_credentials",
-        "client_id": s.MS_ENTRA_CLIENT_ID,
-        "client_secret": s.MS_ENTRA_CLIENT_SECRET,
-        "scope": scope,
-    }
+    if token is None:
+        token = pes_url.split('/')[-1] == 'dummy'
 
-    try:
-        response = requests.post(url, data=data)
-        response.raise_for_status()
-        return response.json()["access_token"]
-    except requests.exceptions.HTTPError as e:
-        logger.error(f"Could not fetch application token: {e}")
-        raise ValueError(f"Could not fetch application token!")
+    if token:
+        for k, v in s.PES_API_MAPPING.items():
+            if pes_url.startswith(k):
+                pes_id = pes_url.split('/')[-1]
 
-
-def fetch_pes(request, pes_url, user) -> dict:
-
-    for k, v in s.PES_API_MAPPING.items():
-        if pes_url.startswith(k):
-
-            prod = "cropkey-np" not in pes_url
-
-            pes_id = pes_url.split('/')[-1]
-
-            if pes_id == 'dummy':
-                import json
-                res_data = json.load(open(s.BASE_DIR / "fixtures/pes.json"))
-                res_data["pes_url"] = pes_url
-                return res_data
-            else:
-                headers = {
-                    "accept": "*/*",
-                    "authorization": "Bearer " + get_application_token(prod),
-                }
-
-                # Restrict request if user is not part of any secret group
-                if not has_secret_group(user):
-                    headers["app-classification-level-restriction"] = "restrict-pes-secret-structure-access"
-
-
-                params = {"pes_reg_entity_corporate_id": pes_id}
-
-                res = requests.get(v, headers=headers, params=params, proxies=s.PROXIES or None)
-
-                try:
-                    res.raise_for_status()
-                    pes_data = res.json()
-
-                    # Handle missing response
-                    if "detail" in pes_data and "The following PES Reg Entities Corporate Ids could not be found" in pes_data["detail"]:
-                        raise ValueError(f"PES with id {pes_id} not found")
-
-                    # Ensure we have a entity
-                    if len(pes_data) == 0:
-                        raise ValueError(f"PES with id {pes_id} not found")
-
-                    res_data = pes_data[0]
+                if pes_id == 'dummy':
+                    import json
+                    res_data = json.load(open(s.BASE_DIR / "fixtures/pes.json"))
                     res_data["pes_url"] = pes_url
                     return res_data
+                else:
+                    headers = {"Authorization": f"Bearer {token['access_token']}"}
+                    params = {"pes_reg_entity_corporate_id": pes_id}
 
-                except requests.exceptions.HTTPError as e:
-                    raise ValueError(f"Error fetching PES with id {pes_id}: {e}")
+                    res = requests.get(v, headers=headers, params=params, proxies=s.PROXIES or None)
 
-    raise ValueError(f"Unknown URL {pes_url}")
+                    try:
+                        res.raise_for_status()
+                        pes_data = res.json()
+
+                        if len(pes_data) == 0:
+                            raise ValueError(f"PES with id {pes_id} not found")
+
+                        res_data = pes_data[0]
+                        res_data["pes_url"] = pes_url
+                        return res_data
+
+                    except requests.exceptions.HTTPError as e:
+                        raise ValueError(f"Error fetching PES with id {pes_id}: {e}")
+        else:
+            raise ValueError(f"Unknown URL {pes_url}")
+    else:
+        raise ValueError("Could not fetch access token from request.")
 
 
 def visualize_pes(request):
     pes_link = request.GET.get('pesLink')
 
     if pes_link:
-        pes_data = fetch_pes(request, pes_link, request.user)
+        pes_data = fetch_pes(request, pes_link)
 
         representations = pes_data.get('representations')
 

bridge/contracts.py

@@ -1,5 +1,4 @@
 import enum
-from typing import Any, Dict
 from abc import ABC, abstractmethod
 
 from envipy_additional_information import EnviPyModel
@@ -70,12 +69,6 @@ class Plugin(ABC):
 
 
 class Property(Plugin):
-    def parameters(self) -> Dict[str, Any]:
-        """
-        Returns the parameters of the PropertyPlugin.
-        """
-        return {}
-
     @classmethod
     @abstractmethod
     def requires_rule_packages(cls) -> bool:
@@ -307,12 +300,6 @@ class Classifier(Plugin):
         """
         pass
 
-    def parameters(self) -> Dict[str, Any]:
-        """
-        Returns the parameters of the ClassifierPlugin.
-        """
-        return {}
-
     @abstractmethod
     def build(self, eP: EnviPyDTO, *args, **kwargs) -> BuildResult | None:
         """

entrypoint.sh

@@ -1,9 +0,0 @@
-#!/bin/bash
-set -e
-
-if [ "${SKIP_DJANGO_SETUP:-false}" != "true" ]; then
-  python manage.py migrate --no-input
-  python manage.py collectstatic --no-input
-fi
-
-exec "$@"

envipath/settings.py

@@ -357,7 +357,6 @@ DEFAULT_MODEL_PARAMS = {
 DEFAULT_MAX_NUMBER_OF_NODES = 9999
 DEFAULT_MAX_DEPTH = 8
 DEFAULT_MODEL_THRESHOLD = 0.25
-BATCH_PREDICT_MAX_COMPOUNDS = 150
 
 # Loading Plugins
 PLUGINS_ENABLED = os.environ.get("PLUGINS_ENABLED", "False") == "True"
@@ -445,8 +444,6 @@ if MS_ENTRA_ENABLED:
     MS_ENTRA_AUTHORITY = f"https://login.microsoftonline.com/{MS_ENTRA_TENANT_ID}"
     MS_ENTRA_REDIRECT_URI = os.environ["MS_REDIRECT_URI"]
     MS_ENTRA_SCOPES = os.environ.get("MS_SCOPES", "").split(",")
-    NON_PROD_PES_SCOPE = os.environ.get("NON_PROD_PES_SCOPE")
-    PROD_PES_SCOPE = os.environ.get("PROD_PES_SCOPE")
 
 # Site ID 10 -> beta.envipath.org
 MATOMO_SITE_ID = os.environ.get("MATOMO_SITE_ID", "10")

epapi/v1/endpoints/additional_information.py

@@ -9,8 +9,8 @@ from envipy_additional_information import registry
 from envipy_additional_information.groups import GroupEnum
 from epapi.utils.schema_transformers import build_rjsf_output
 from epapi.utils.validation_errors import handle_validation_error
-from epdb.models import AdditionalInformation, Scenario, Node
-from ..dal import get_scenario_for_read, get_scenario_for_write, get_package_for_write
+from epdb.models import AdditionalInformation
+from ..dal import get_scenario_for_read, get_scenario_for_write
 
 logger = logging.getLogger(__name__)
 
@@ -58,61 +58,6 @@ def list_scenario_info(request, scenario_uuid: UUID):
     return result
 
 
-@router.post("/information/{model_name}/")
-def add_object_info(request, model_name: str, payload: Dict[str, Any] = Body(...)):
-    from epdb.views import EPDBURLParser
-
-    cls = registry.get_model(model_name.lower())
-    if not cls:
-        raise HttpError(404, f"Unknown model: {model_name}")
-
-    try:
-        instance = cls(**payload)  # Pydantic validates
-    except ValidationError as e:
-        handle_validation_error(e)
-
-    if "attach_obj_url" in payload:
-        url_parser = EPDBURLParser(payload["attach_obj_url"])
-
-        if url_parser.contains_package_url():
-            package = get_package_for_write(request.user, url_parser.get_objects()[0].uuid)
-            attach_obj = url_parser.get_object()
-
-            if "scenario_uuid" in payload:
-                scenario = get_scenario_for_read(request.user, payload["scenario_uuid"])
-            else:
-                scenario = Scenario.create(
-                    package,
-                    name=f"Scenario {Scenario.objects.filter(package=package).count() + 1}",
-                    description="no description",
-                    scenario_date=None,
-                    scenario_type=None,
-                    additional_information=[],
-                )
-
-            if isinstance(attach_obj, Node):
-                ai = add_info_to_node(package, instance, scenario, attach_obj)
-            else:
-                raise HttpError(404, f"Bad request - Not implemented for {type(attach_obj)}!")
-
-            return {"status": "created", "uuid": ai.uuid}
-
-    raise HttpError(404, "Bad request!")
-
-
-def add_info_to_node(package, add_inf, scenario, node):
-    ai = AdditionalInformation.create(
-        package,
-        add_inf,
-        scenario=scenario,
-        content_object=node,
-    )
-
-    node.pathway.scenarios.add(scenario)
-
-    return ai
-
-
 @router.post("/scenario/{uuid:scenario_uuid}/information/{model_name}/")
 def add_scenario_info(
     request, scenario_uuid: UUID, model_name: str, payload: Dict[str, Any] = Body(...)

epapi/v1/interfaces/iuclid/projections.py

@@ -56,7 +56,7 @@ def get_pathway_for_iuclid_export(user, pathway_uuid: UUID) -> PathwayExportDTO:
 
         ai_for_node = []
         scenario_entries: list[PathwayScenarioDTO] = []
-        for scenario in sorted(node.get_scenarios(), key=lambda item: item.pk):
+        for scenario in sorted(node.scenarios.all(), key=lambda item: item.pk):
             ai_for_scenario = list(scenario.get_additional_information(direct_only=True))
             ai_for_node.extend(ai_for_scenario)
             scenario_entries.append(

epauth/views.py

@@ -1,5 +1,3 @@
-import logging
-
 import msal
 from django.conf import settings as s
 from django.contrib.auth import get_user_model
@@ -9,9 +7,6 @@ from django.shortcuts import redirect
 
 from epdb.logic import UserManager, GroupManager
 from epdb.models import Group
-from epdb.views import get_remote_address, error
-
-auth_log = logging.getLogger("auth")
 
 
 def get_msal_app_with_cache(request):
@@ -35,9 +30,6 @@ def get_msal_app_with_cache(request):
 
 
 def entra_login(request):
-
-    auth_log.info(f"Login request from {get_remote_address(request)}")
-
     msal_app = msal.ConfidentialClientApplication(
         client_id=s.MS_ENTRA_CLIENT_ID,
         client_credential=s.MS_ENTRA_CLIENT_SECRET,
@@ -62,28 +54,14 @@ def entra_callback(request):
     # Acquire token using the flow and callback request
     result = msal_app.acquire_token_by_auth_code_flow(flow, request.GET)
 
-    if "error" in result:
-        auth_log.error(f"Login attempt by {get_remote_address(request)} failed due to {result['error']}")
-        return redirect("/")
-
     # Save the token cache to session
     if cache.has_state_changed:
         request.session["msal_token_cache"] = cache.serialize()
 
     claims = result["id_token_claims"]
 
-    if claims.get("roles") is None or claims.get("roles") == [] or "envipath_registered_user" not in claims.get("roles"):
-        auth_log.error(f"Login attempt by {get_remote_address(request)} failed due to missing role")
-        return error(
-            request,
-            "Login Failed",
-            "The user is not authenticated. A reason for this might be a missing assignment to the respective enviPath group.",
-            403,
-        )
-
     user_name = claims.get("name")
-    # preferred_username is a fallback for 2nd CWID
-    user_email = claims.get("emailaddress", claims.get("email", claims.get("preferred_username")))
+    user_email = claims.get("emailaddress", claims.get("email"))
     user_oid = claims.get("oid")
 
     if not all([user_name, user_email, user_oid]):
@@ -92,7 +70,6 @@ def entra_callback(request):
     # Get implementing class
     User = get_user_model()
 
-    registered = False
     if User.objects.filter(uuid=user_oid).exists():
         u = User.objects.get(uuid=user_oid)
 
@@ -101,11 +78,8 @@ def entra_callback(request):
             u.save()
 
     else:
-        auth_log.info(f"Registering {user_name} with OID {user_oid}")
         u = UserManager.create_user(user_name, user_email, None, uuid=user_oid, is_active=True)
-        registered = True
 
-    auth_log.info(f"User {user_name} {'(admin) ' if u.is_superuser else ''}with OID {user_oid} successfully logged in as {u.username} from {get_remote_address(request)}")
     login(request, u)
 
     # EDIT START
@@ -128,31 +102,10 @@ def entra_callback(request):
         else:
             g = Group.objects.get(uuid=id)
 
-    sync_groups = list(s.ENTRA_GROUPS.keys()) + list(s.ENTRA_SECRET_GROUPS.keys())
-    user_groups = claims.get("groups", [])
-
-    for uuid in sync_groups:
-        if uuid in user_groups:
-            g = Group.objects.get(uuid=uuid)
-            if not g.user_member.contains(u):
-                g.user_member.add(u)
-                auth_log.info(f"Login Group Sync: Adding {u.username} to Group {g.name} ({ uuid })")
-        else:
-            g = Group.objects.get(uuid=uuid)
-            if g.user_member.contains(u):
-                g.user_member.remove(u)
-                auth_log.info(f"Login Group Sync: Removing {u.username} from Group {g.name} ({ uuid })")
-
-    if registered:
-        # #72 make package secret if user is part of a secret group
-        for id, name in s.ENTRA_SECRET_GROUPS.items():
-            group = Group.objects.get(uuid=id)
-            if group.user_member.contains(u):
-                # User is eligible for secrete
-                pack = u.default_package
-                pack.data_pool = group
-                pack.classification_level = pack.Classification.SECRET
-                pack.save()
+    for group_uuid in claims.get("groups", []):
+        if Group.objects.filter(uuid=group_uuid).exists():
+            g = Group.objects.get(uuid=group_uuid)
+            g.user_member.add(u)
 
     # EDIT END
 

epdb/legacy_api.py

@@ -1,4 +1,3 @@
-import logging
 from collections import defaultdict
 from typing import Any, Dict, List, Optional
 
@@ -10,11 +9,13 @@ from django.contrib.auth import get_user_model
 from django.core.cache import cache
 from django.http import HttpResponse, JsonResponse
 from django.shortcuts import redirect
+from jwt import InvalidIssuerError
 from ninja import Field, Form, Query, Router, Schema
 from ninja.security import HttpBearer
 
 from utilities.chem import FormatConverter
 from utilities.misc import PackageExporter
+
 from .logic import (
     EPDBURLParser,
     GroupManager,
@@ -45,12 +46,9 @@ from .models import (
     User,
     UserPackagePermission,
 )
-from .views import delete_with_log, get_remote_address
 
 Package = s.GET_PACKAGE_MODEL()
 
-auth_log = logging.getLogger("auth")
-
 
 def get_cached_jwks(tenant_id: str, force=False) -> Dict:
     """Get JWKS using Django cache"""
@@ -72,10 +70,6 @@ def get_cached_jwks(tenant_id: str, force=False) -> Dict:
     return jwks
 
 
-def get_package_for_read(user, package_uuid):
-    return PackageManager.get_package_by_id(user, package_uuid)
-
-
 def get_package_for_write(user, package_uuid):
     p = PackageManager.get_package_by_id(user, package_uuid)
     if not PackageManager.writable(user, p):
@@ -122,22 +116,15 @@ def validate_token(token: str) -> dict:
 class MSBearerTokenAuth(HttpBearer):
 
     def authenticate(self, request, token):
-
-        auth_log.info(f"Authentication request by {get_remote_address(request)}")
-
         if token is None:
             return None
 
         claims = validate_token(token)
 
         if not User.objects.filter(uuid=claims['oid']).exists():
-            auth_log.info(f"Authentication request by {get_remote_address(request)} failed!")
             return None
 
-        user = User.objects.get(uuid=claims['oid'])
-        request.user = user
-        auth_log.info(
-            f"User {user.username} {'(admin) ' if user.is_superuser else ''}with OID {user.uuid} successfully logged in as {user.username} from {get_remote_address(request)}")
+        request.user = User.objects.get(uuid=claims['oid'])
         return request.user
 
 
@@ -571,10 +558,7 @@ def update_package(request, package_uuid, pack: Form[UpdatePackage]):
 
         if pack.hiddenMethod:
             if pack.hiddenMethod == "DELETE":
-                if PackageManager.administrable(request.user, p):
-                    delete_with_log(request, p)
-                else:
-                    raise ValueError("You do not have the rights to delete this Package!")
+                p.delete()
 
         elif pack.packageDescription is not None:
             description = nh3.clean(pack.packageDescription, tags=s.ALLOWED_HTML_TAGS).strip()
@@ -611,7 +595,7 @@ def delete_package(request, package_uuid):
         p = PackageManager.get_package_by_id(request.user, package_uuid)
 
         if PackageManager.administrable(request.user, p):
-            delete_with_log(request, p)
+            p.delete()
             return redirect(f"{s.SERVER_URL}/package")
         else:
             raise ValueError("You do not have the rights to delete this Package!")
@@ -889,7 +873,7 @@ def create_package_compound(
             from bayer.models import PESCompound
 
             try:
-                pes_data = fetch_pes(request, c.pesLink, request.user)
+                pes_data = fetch_pes(request, c.pesLink)
             except ValueError as e:
                 return 400, {"message": f"Could not fetch PES data for {c.pesLink}"}
 
@@ -897,11 +881,12 @@ def create_package_compound(
             if "secret" == classification.lower():
 
                 if p.classification_level != Package.Classification.SECRET:
-                    return 400, {"message": "Cannot create secret PESs in non-secret packages."}
-
-                if not p.data_pool or not p.data_pool.secret:
-                    return 400, {"message": "Cannot create secret PESs in package without a secret data pool."}
+                    return 400, {"Cannot create PESs for non-secret packages."}
 
+                data_pools = pes_data.get("dataPools")
+                if data_pools:
+                    if s.DATA_POOL_MAPPING[p.data_pool.name] not in data_pools:
+                        return 400, { "messsage": f"PES data pool {s.DATA_POOL_MAPPING[p.data_pool.name]} not found in PES data"}
 
             c = PESCompound.create(p, pes_data, c.compoundName, c.compoundDescription)
         else:
@@ -1720,7 +1705,7 @@ class PathwayNode(Schema):
     image: str = Field(None, alias="image")
     imageSize: int = Field(None, alias="image_size")
     name: str = Field(None, alias="name")
-    proposed: List[Dict[str, Any]] = []
+    proposed: List[Dict[str, str]] = []
     smiles: str = Field(None, alias="smiles")
     pseudo: bool = Field(False, alias="pseudo")
     pesLink: str | None = Field(None, alias="pes_link")
@@ -1892,7 +1877,7 @@ def delete_pathway(request, package_uuid, pathway_uuid):
         p = get_package_for_write(request.user, package_uuid)
 
         pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
-        delete_with_log(request, pw)
+        pw.delete()
         return redirect(f"{p.url}/pathway")
 
     except ValueError:
@@ -1990,7 +1975,7 @@ def get_package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
 
 
 class CreateNode(Schema):
-    nodeAsSmiles: str | None = None
+    nodeAsSmiles: str
     nodeAsMolFile: str | None = None
     nodeName: str | None = None
     nodeReason: str | None = None
@@ -2014,7 +1999,7 @@ def add_pathway_node(request, package_uuid, pathway_uuid, n: Form[CreateNode]):
             from bayer.models import PESCompound
 
             try:
-                pes_data = fetch_pes(request, n.pesLink, request.user)
+                pes_data = fetch_pes(request, n.pesLink)
             except ValueError as e:
                 return 400, {"message": f"Could not fetch PES data for {n.pesLink}"}
 
@@ -2022,10 +2007,14 @@ def add_pathway_node(request, package_uuid, pathway_uuid, n: Form[CreateNode]):
             if "secret" == classification.lower():
 
                 if p.classification_level != Package.Classification.SECRET:
-                    return 400, {"message": "Cannot create secret PESs in non-secret packages."}
+                    return 400, "Cannot create PESs for non-secret packages."
 
-                if not p.data_pool or not p.data_pool.secret:
-                    return 400, {"message": "Cannot create secret PESs in package without a secret data pool."}
+                data_pools = pes_data.get("dataPools")
+                if data_pools:
+                    if s.DATA_POOL_MAPPING[p.data_pool.name] not in data_pools:
+                        return 400, {
+                            "messsage": f"PES data pool {s.DATA_POOL_MAPPING[p.data_pool.name]} not found in PES data"
+                        }
 
             c = PESCompound.create(p, pes_data, n.nodeName, n.nodeReason)
 
@@ -2070,7 +2059,7 @@ def delete_node(request, package_uuid, pathway_uuid, node_uuid):
 
         pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
         n = Node.objects.get(pathway=pw, uuid=node_uuid)
-        delete_with_log(request, n)
+        n.delete()
         return redirect(f"{pw.url}/node")
 
     except ValueError:
@@ -2230,7 +2219,7 @@ def delete_edge(request, package_uuid, pathway_uuid, edge_uuid):
 
         pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
         e = Edge.objects.get(pathway=pw, uuid=edge_uuid)
-        delete_with_log(request, e)
+        e.delete()
         return redirect(f"{pw.url}/edge")
 
     except ValueError:
@@ -2434,42 +2423,3 @@ def predict(request, np: Form[NonPersistent]):
         return 403, {
             "message": f"Getting Setting with id {np.setting_url} failed due to insufficient rights!"
         }
-
-
-##########
-# Export #
-##########
-class PackageExportInSchema(Schema):
-    package_uuid: str
-    additional_information_types: List[str] | None = None
-
-
-@router.get("/export", response={200: Any, 403: Error})
-def export(request, q: Query[PackageExportInSchema]):
-    try:
-        p = get_package_for_read(request.user, q.package_uuid)
-
-        from envipy_additional_information import registry
-        from utilities.misc import PathwayExporter
-
-        ai_types = []
-        if q.additional_information_types is not None:
-            for ai_type in q.additional_information_types:
-                if registry.get_model(ai_type) is None:
-                    return 400, {
-                        "message": f"Exporting Package with id {q.package_uuid} failed as {ai_type} is not a valid additional information type!"
-                    }
-                ai_types.append(ai_type)
-
-        exporter = PathwayExporter(p, add_infs_to_export=ai_types)
-        res = exporter.do_export()
-
-        filename = f"{p.get_name().replace(' ', '_')}_{p.uuid}.tsv"
-        response = HttpResponse(res, content_type="text/csv")
-        response["Content-Disposition"] = f'attachment; filename="{filename}"'
-
-        return response
-    except ValueError:
-        return 403, {
-            "message": f"Exporting Package with id {q.package_uuid} failed due to insufficient rights!"
-        }

epdb/logic.py

@@ -35,7 +35,6 @@ from utilities.chem import FormatConverter
 from utilities.misc import PackageExporter, PackageImporter
 
 logger = logging.getLogger(__name__)
-auth_log = logging.getLogger("auth")
 
 Package = s.GET_PACKAGE_MODEL()
 
@@ -46,7 +45,7 @@ class EPDBURLParser:
     MODEL_PATTERNS = {
         "epdb.User": re.compile(rf"^.*/user/{UUID_PATTERN}"),
         "epdb.Group": re.compile(rf"^.*/group/{UUID_PATTERN}"),
-        s.EPDB_PACKAGE_MODEL: re.compile(rf"^.*/package/{UUID_PATTERN}"),
+        "epdb.Package": re.compile(rf"^.*/package/{UUID_PATTERN}"),
         "epdb.Compound": re.compile(rf"^.*/package/{UUID_PATTERN}/compound/{UUID_PATTERN}"),
         "epdb.CompoundStructure": re.compile(
             rf"^.*/package/{UUID_PATTERN}/compound/{UUID_PATTERN}/structure/{UUID_PATTERN}"
@@ -96,7 +95,7 @@ class EPDBURLParser:
 
     def contains_package_url(self):
         return (
-            bool(self.MODEL_PATTERNS[s.EPDB_PACKAGE_MODEL].findall(self.url))
+            bool(self.MODEL_PATTERNS["epdb.Package"].findall(self.url))
             and not self.is_package_url()
         )
 
@@ -124,7 +123,7 @@ class EPDBURLParser:
             "epdb.EPModel",
             "epdb.Pathway",
             # 1st level
-            s.EPDB_PACKAGE_MODEL,
+            "epdb.Package",
             "epdb.Setting",
             "epdb.Group",
             "epdb.User",
@@ -146,7 +145,7 @@ class EPDBURLParser:
 
         hierarchy_order = [
             # 1st level
-            s.EPDB_PACKAGE_MODEL,
+            "epdb.Package",
             "epdb.Setting",
             "epdb.Group",
             "epdb.User",
@@ -317,19 +316,13 @@ class GroupManager(object):
         if isinstance(member, Group):
             if add_or_remove == "add":
                 group.group_member.add(member)
-                auth_log.info(f"{caller.username} ({caller.url}) adds {member.name} ({member.url}) to {group.name} ({group.url})")
             else:
                 group.group_member.remove(member)
-                auth_log.info(
-                    f"{caller.username} ({caller.url}) removes {member.name} ({member.url}) from {group.name} ({group.url})")
         else:
             if add_or_remove == "add":
                 group.user_member.add(member)
-                auth_log.info(f"{caller.username} ({caller.url}) adds {member.username} ({member.url}) to {group.name} ({group.url})")
             else:
                 group.user_member.remove(member)
-                auth_log.info(
-                    f"{caller.username} ({caller.url}) removes {member.username} ({member.url}) from {group.name} ({group.url})")
 
         group.save()
 
@@ -585,11 +578,9 @@ class PackageManager(object):
         if isinstance(grantee, User):
             perm_cls = UserPackagePermission
             data["user"] = grantee
-            grantee_name = grantee.username
         else:
             perm_cls = GroupPackagePermission
             data["group"] = grantee
-            grantee_name = grantee.name
 
         if new_perm is None:
             qs = perm_cls.objects.filter(**data)
@@ -598,23 +589,11 @@ class PackageManager(object):
             if qs.count() != 0:
                 logger.info(f"Deleting Perm {qs.first()}")
                 qs.delete()
-                auth_log.info(f"{caller.username} ({caller.url}) revokes {grantee_name} ({grantee.url}) all Permissions on {package.name} ({package.url})")
             else:
                 logger.debug(f"No Permission object for {perm_cls} with filter {data} found!")
         else:
-            old_perm = None
-            old_perms_qs = perm_cls.objects.filter(**data)
-
-            if old_perms_qs.exists():
-                old_perm = old_perms_qs.first().permission
-
             _ = perm_cls.objects.update_or_create(defaults={"permission": new_perm}, **data)
 
-            if old_perm is None:
-                auth_log.info(f"{caller.username} ({caller.url}) grants {grantee_name} ({grantee.url}) '{new_perm}' Permissions on {package.name} ({package.url})")
-            else:
-                auth_log.info(f"{caller.username} ({caller.url}) set {grantee_name} ({grantee.url}) Permissions from '{old_perm}' to '{new_perm}' on {package.name} ({package.url})")
-
     @staticmethod
     def grant_read(caller: User, package: Package, grantee: Union[User, Group]):
         PackageManager.update_permissions(caller, package, grantee, Permission.READ[0])
@@ -1896,51 +1875,12 @@ class SPathway(object):
 
         logger.info("Update done!")
 
-    def compute_bayes_probabilities(self) -> Dict[SEdge, float]:
-        """
-        Computes Bayes-adjusted probabilities for all edges in the pathway
-        by iterating level by level from depth 0 upwards, keyed on educt depth.
-
-        Returns:
-            A dict mapping each SEdge to its Bayes-adjusted probability.
-        """
-        bayes_probs: Dict[SEdge, float] = {}
-
-        # Group edges by their educt depth
-        edges_by_depth: Dict[int, List[SEdge]] = {}
-        for edge in self.edges:
-            d = edge.educts[0].depth
-            edges_by_depth.setdefault(d, []).append(edge)
-
-        for depth in sorted(edges_by_depth.keys()):
-            for edge in edges_by_depth[depth]:
-                if depth == 0:
-                    bayes_probs[edge] = edge.probability
-                else:
-                    predecessor_edges = [e for e in self.edges if edge.educts[0] in e.products]
-
-                    if not predecessor_edges or not all(
-                        e in bayes_probs for e in predecessor_edges
-                    ):
-                        # Predecessor not computed yet (e.g. same-depth product),
-                        # fall back to raw probability
-                        bayes_probs[edge] = edge.probability
-                    else:
-                        predecessor_avg = sum(bayes_probs[e] for e in predecessor_edges) / len(
-                            predecessor_edges
-                        )
-                        bayes_probs[edge] = predecessor_avg * edge.probability
-
-        return bayes_probs
-
     def to_json(self):
         nodes = []
         edges = []
 
         idx_lookup = {}
 
-        bayes_probs = self.compute_bayes_probabilities()
-
         for i, smiles in enumerate(self.smiles_to_node):
             n = self.smiles_to_node[smiles]
             idx_lookup[smiles] = i
@@ -1961,7 +1901,6 @@ class SPathway(object):
 
             if edge.probability:
                 e["probability"] = edge.probability
-                e["multiGenProbability"] = bayes_probs[edge]
 
             edges.append(e)
 

epdb/management/commands/localize_urls.py

@@ -44,25 +44,20 @@ class Command(BaseCommand):
             "EPModel",
             "ApplicabilityDomain",
             "EnzymeLink",
-            "AdditionalInformation",
         ]
         for model in MODELS:
             obj_cls = apps.get_model("epdb", model)
-
-            update_fields = {"url": Replace(F("url"), Value(options["old"]), Value(options["new"]))}
-            if hasattr(obj_cls, "description"):
-                update_fields["description"] = Replace(
-                    F("description"), Value(options["old"]), Value(options["new"])
-                )
-
+            obj_cls.objects.update(
+                url=Replace(F("url"), Value(options["old"]), Value(options["new"]))
+            )
             if issubclass(obj_cls, EnviPathModel):
-                update_fields["kv"] = Cast(
-                    Replace(
-                        Cast(F("kv"), output_field=TextField()),
-                        Value(options["old"]),
-                        Value(options["new"]),
-                    ),
-                    output_field=JSONField(),
+                obj_cls.objects.update(
+                    kv=Cast(
+                        Replace(
+                            Cast(F("kv"), output_field=TextField()),
+                            Value(options["old"]),
+                            Value(options["new"]),
+                        ),
+                        output_field=JSONField(),
+                    )
                 )
-
-            obj_cls.objects.update(**update_fields)

epdb/management/commands/reaction_rule_mapping.py

@@ -1,97 +0,0 @@
-import logging
-
-from django.core.management.base import BaseCommand
-from django.db import transaction
-from uuid import uuid4
-from epdb.models import Package, ReactionExplanation
-from utilities.chem import FormatConverter
-from django.utils import timezone
-
-
-logger = logging.getLogger(__name__)
-
-
-class Command(BaseCommand):
-    def add_arguments(self, parser):
-        parser.add_argument(
-            "--rule-package",
-            action="append",
-            default=["32de3cf4-e3e6-4168-956e-32fa5ddb0ce1"],
-            type=str,
-            help="UUID to process. Can be specified multiple times.",
-        )
-
-        parser.add_argument(
-            "--reaction-package",
-            action="append",
-            default=[
-                "32de3cf4-e3e6-4168-956e-32fa5ddb0ce1",  # BBD
-                "f05e38d8-e9b4-4c3e-b0d8-9ab29966eccf",  # Sediment
-                "521c547a-fd2a-491c-ad5b-7eaa1577fb65",  # Sludge
-                "5882df9c-dae1-4d80-a40e-db4724271456",  # Soil
-                "87a49584-d937-482c-9c33-25928dcb02a8",  # PFAS
-            ],
-            type=str,
-            help="UUID to process. Can be specified multiple times.",
-        )
-
-        parser.add_argument(
-            "--dry-run",
-            default=False,
-            action="store_true",
-            help="Perform dry run",
-        )
-
-    @transaction.atomic
-    def handle(self, *args, **options):
-        RUN_UUID = uuid4()
-        RUN_START = timezone.now()
-
-        rule_packages = Package.objects.filter(uuid__in=options["rule_package"])
-        reaction_packages = Package.objects.filter(uuid__in=options["reaction_package"])
-
-        rules = []
-        for rule_package in rule_packages:
-            rules.extend(rule_package.get_applicable_rules())
-
-        reactions = []
-        for reaction_package in reaction_packages:
-            reactions.extend(reaction_package.reactions)
-
-        logger.debug(f"Collected {len(rules)} rules and {len(reactions)} reactions.")
-
-        for i, reaction in enumerate(reactions):
-            logger.debug(f"Reaction {i} / {len(reactions)}")
-            for j, rule in enumerate(rules):
-                reactants, products = reaction.smirks().split(">>")
-
-                if len(reactants.split(".")) > 1:
-                    logger.debug(f"Skipping reaction {reaction.uuid} as it has multiple reactants.")
-                    break
-
-                products = products.split(".")
-
-                # Run reaction with rule
-                rule_products = rule.apply(reactants)
-
-                # Check if products match (in both directions if extras are not allowed)
-                for product_set in rule_products:
-                    covered, exact = FormatConverter.smiles_covered_by(
-                        products,
-                        product_set.product_set,
-                        standardize=True,
-                        canonicalize_tautomers=True,
-                        return_exact_match=True,
-                    )
-
-                    if covered and not options["dry-run"]:
-                        logger.debug(f"Reaction {reaction.uuid} explained by rule {rule.uuid}")
-                        re = ReactionExplanation()
-                        re.run_uuid = RUN_UUID
-                        re.run_start = RUN_START
-                        re.reaction = reaction
-                        re.rule = rule
-                        re.exact = exact
-                        re.save()
-                        # Its explained, if there are more sets skip them
-                        break

epdb/migrations/0028_auto_20260812_0902.py

@@ -1,113 +0,0 @@
-# Generated by Django 6.0.3 on 2026-08-12 09:02
-
-from django.conf import settings as s
-from django.db import migrations
-from envipy_additional_information import Likelihood, RuleLikelihood
-
-NEW_RULE = {
-    "parent": "bt0005",
-    "name": "bt0005-3667",
-    "description": "vic-unsubstituted Aromatic > vic-Dihydroxyaromatic",
-    "smirks": "[#8:7]([H])-[#6:1]([H])-1-[#6:2]=[#6:3]-[#6:4]=[#6:5]-[#6:6]([H])-1-[#8:8]([H])>>[#8:7]([H])-[#6:1]=1-[#6:2]=[#6:3]-[#6:4]=[#6:5]-[#6:6]=1-[#8:8]([H])",
-    "scenario_name": "bt0005-3667 aerobic likelihood",
-    "scenario_aerobic_likelihood": RuleLikelihood(likelihood=Likelihood.LIKELY),
-}
-
-RULE_FIXES = {
-    "bt0005-4282": "[c:1]([H])1:[c:2]([H]):[#6,#7;a:3]:[c:4]:[c:5]:[c:6]1>>[c:1]([#8])1:[c:2]([#8]):[#6,#7;a:3]:[c:4]:[c:5]:[c:6]1",
-    "bt0014-4215": "[c:1]([H])1[c:8][#6,#7;a:7][c:6][c:5][c:4]1[#8;!$([OH]c:[#6,#7;a:7]([OH])):9]([H])>>[#8:9]([H])[c:4]1:[c:5]:[c:6]:[#6,#7;a:7]:[c:8]:[c:1]1[#8]([H])",
-    # "bt0063-3938": "[#1,#6:6][#7;X3;!$(NC1CC1)!$([N][C]=O)!$([!#8]CNC=O):1]([#1,#6:7])[#6;A;X4:2][H:3]>>[#1,#6:6][#7;X3:1]([H:3])(=[#1,#6:7]).[#6;A:2]=O",
-    # CN1C=NC2=C1C(=O)N(C)C(=O)N2 not working anymore with bt0063-3938 if change above is applied
-    "bt0063-3938": "[#1,#6:6][#7;X3;!$(NC1CC1)!$([N][C]=O)!$([!#8]CNC=O):1]([#1,#6:7])[#6;A;X4:2][H:3]>>[#1,#6:6][#7;X3:1]([#1,#6:7])[H:3].[#6;A:2]=O",
-    "bt0068-3564": "[#7:4]!@-[#6:2](!@-[#7:1])=[O:5]>>[#7:4]-[#6:2](-[O+0H1])=[O:5].[#7H1:1]",
-    "bt0180-2844": "[H][C:2]([#6:5]([H])([H])([H]))([#1,#6:4])!@-[#6:1]([H])([H])-[#6:3](-[#8-:8])=[O:6]>>[#6:5]([H])([H])([H])\\[#6:2](-[#1,#6:4])=[#6H:1]\\[#6:3](-[#8-:8])=[O:6]",
-    "bt0181-1278": "[#8-:1]-[#6:2](=[O:11])-[#6:7]=[#6:8]-[#6:3](-[H])=[#6:5](-Cl)-[#6:6](-[#8-:10])=[O:9]>>[O+0H1:10]-[#6:6](=[O:9])-[#6:5]=[#6:3]-1-[O+0:1]-[#6:2](=[O:11])-[#6:7]=[#6:8]-1",
-    "bt0298-3335": "[#6:1][N+:2]#[C:3]>>[#6:1]-[#7H2:2]-[#6:3]=O",
-    "bt0322-3393": "[H:10]\\[#6:6](=[#6:9](/[#6:1]([H])([H])([H]))-[#6:11]-[#6:12]-[#6:13]=[#6:14])-[#6:5](-[#16:7])=[O:8]>>[H:10]\\[#6:6](-[#6:5](-[#16:7])=[O:8])=[#6:9](\\[#6:11]-[#6:12]-[#6:13]=[#6:14])-[#6:1]-[#6](-[#8-])=O",
-    "bt0343-2675": "[#8-]-[#6](=O)-[c:1]1[c:6][cH:7][c:8](-[#7H2,#8H1:9])[cH:10][c:11]1>>[#8H][c:1]1[c:6][c:7][c:8]([*:9])[c:10][c:11]1",
-    "bt0350-3319": "[#6:6][#7:3][#6;!R:2]=[#7;!R:1][#6:5]>>[#6:5][#7:1][#6:2]=O.[#6:6][#7:3]",  # Trig before 5 -> all of them shouldn't
-    "bt0374-4081": "[cH:4]1[c:16][c:15][c:14][c:13][c:3]1[#7,#8:2][c:1]1[c:8][c:9][c:10][c:11][c:12]1>>[#7,#8:2]-[c:1]1[c:12][c:11][c:10][c:9][c:8]1[c:13]1[c:14][c:15][c:16][c:4](-[#8])[c:3]1-[#8]",
-    "bt0378-3188": "[#8-:7][c:1]1[c:6]([#7+]([#8-])=O)[c:5][c:4]([#7+:9]([#8-])=O)[c:3][c:2]1([#7+:8]([#8-])=O)>>[#8+0:7]=[#6:1]1-[#6:6]-[#6:5]-[#6:4]([#7+:9]([#8-])=O)-[#6:3]-[#6:2]1([#7+:8]([#8-])=O)",
-    "bt0379-3190": "[#9,#17,#35,#53]-[#6:1](-[H])-1-[#6:5]-,=[#6:6]-[#6:7]-,=[#6:8]-[#6:2](-[H])-1-[#9,#17,#35,#53]>>[#6:6]~1-[#6:7]~[#6:8]-[#6:2]=[#6:1]-[#6:5]~1",
-    "bt0393-3367": "[#6:5]-[#6:1](-[#7:2](-[H])(-[H]))=[S+:3]-[#8-:6]>>[#6:5]-[#6:1](=[#7H1:2])-[S+0:3](=[O])-[#8+0H1:6]",
-}
-
-
-def forward_func(apps, schema_editor):
-    ContentType = apps.get_model("contenttypes", "ContentType")
-
-    pkg_class = s.EPDB_PACKAGE_MODEL
-
-    if len(pkg_class.split(".")) != 2:
-        raise ValueError(
-            f"EPDB_PACKAGE_MODEL must be of the form 'app_label.model_name', got {pkg_class}"
-        )
-
-    app_label, model_name = pkg_class.split(".")
-    Package = apps.get_model(app_label, model_name)
-    SimpleAmbitRule = apps.get_model("epdb", "SimpleAmbitRule")
-    ParallelRule = apps.get_model("epdb", "ParallelRule")
-    Scenario = apps.get_model("epdb", "Scenario")
-    AdditionalInformation = apps.get_model("epdb", "AdditionalInformation")
-    simple_ambit_rule_ct = ContentType.objects.get_for_model(SimpleAmbitRule)
-
-    if Package.objects.filter(name="EAWAG-BBD").exists():
-        p = Package.objects.get(name="EAWAG-BBD")
-
-        if not SimpleAmbitRule.objects.filter(package=p, name=NEW_RULE["name"]).exists():
-            # Create Missing Rule
-            new_sr = SimpleAmbitRule()
-            new_sr.polymorphic_ctype = simple_ambit_rule_ct
-            new_sr.package = p
-            new_sr.name = NEW_RULE["name"]
-            new_sr.description = NEW_RULE["description"]
-            new_sr.smirks = NEW_RULE["smirks"]
-            new_sr.save()
-
-            new_sr.url = "{}/simple-ambit-rule/{}".format(new_sr.package.url, new_sr.uuid)
-            new_sr.save()
-
-            # Add likelihood
-            new_scen = Scenario()
-            new_scen.package = p
-            new_scen.name = NEW_RULE["scenario_name"]
-            new_scen.save()
-
-            new_scen.url = "{}/scenario/{}".format(new_scen.package.url, new_scen.uuid)
-            new_scen.save()
-
-            ai = NEW_RULE["scenario_aerobic_likelihood"]
-            new_add_inf = AdditionalInformation()
-            new_add_inf.package = p
-            new_add_inf.type = ai.__class__.__name__
-            new_add_inf.data = ai.model_dump(mode="json")
-            new_add_inf.scenario = new_scen
-            new_add_inf.save()
-
-            new_add_inf.url = "{}/additional-information/{}".format(
-                new_add_inf.scenario.url, new_add_inf.uuid
-            )
-            new_add_inf.save()
-
-            # Link Scenario
-            new_sr.scenarios.add(new_scen)
-
-            # Link to bt0005
-            pr = ParallelRule.objects.get(package=p, name="bt0005")
-            pr.simple_rules.add(new_sr)
-
-        # Update others
-        for rule_name, smirks in RULE_FIXES.items():
-            sr = SimpleAmbitRule.objects.get(package=p, name=rule_name)
-            sr.smirks = smirks
-            sr.save()
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0027_alter_compound_aliases_and_more"),
-    ]
-
-    operations = [
-        migrations.RunPython(forward_func, reverse_code=migrations.RunPython.noop),
-    ]

epdb/migrations/0029_reactionexplanation_reaction_explained_by.py

@@ -1,63 +0,0 @@
-# Generated by Django 6.0.3 on 2026-08-13 09:58
-
-import django.db.models.deletion
-import django.utils.timezone
-import model_utils.fields
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0028_auto_20260812_0902"),
-    ]
-
-    operations = [
-        migrations.CreateModel(
-            name="ReactionExplanation",
-            fields=[
-                (
-                    "id",
-                    models.BigAutoField(
-                        auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
-                    ),
-                ),
-                (
-                    "created",
-                    model_utils.fields.AutoCreatedField(
-                        default=django.utils.timezone.now, editable=False, verbose_name="created"
-                    ),
-                ),
-                (
-                    "modified",
-                    model_utils.fields.AutoLastModifiedField(
-                        default=django.utils.timezone.now, editable=False, verbose_name="modified"
-                    ),
-                ),
-                ("run_uuid", models.UUIDField()),
-                ("run_start", models.DateTimeField()),
-                ("exact", models.BooleanField(default=False)),
-                (
-                    "reaction",
-                    models.ForeignKey(
-                        on_delete=django.db.models.deletion.CASCADE, to="epdb.reaction"
-                    ),
-                ),
-                (
-                    "rule",
-                    models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to="epdb.rule"),
-                ),
-            ],
-            options={
-                "abstract": False,
-            },
-        ),
-        migrations.AddField(
-            model_name="reaction",
-            name="explained_by",
-            field=models.ManyToManyField(
-                related_name="explained_reactions",
-                through="epdb.ReactionExplanation",
-                to="epdb.rule",
-            ),
-        ),
-    ]

epdb/migrations/0030_auto_20260814_0741.py

@@ -1,37 +0,0 @@
-# Generated by Django 6.0.3 on 2026-08-14 07:41
-
-from django.db import migrations
-
-
-def forward_func(apps, schema_editor):
-    ContentType = apps.get_model("contenttypes", "ContentType")
-    AdditionalInformation = apps.get_model("epdb", "AdditionalInformation")
-
-    models = {}
-
-    for c in ContentType.objects.all():
-        try:
-            models[(c.app_label, c.model)] = apps.get_model(c.app_label, c.model)
-        except Exception:
-            pass
-
-    for ai in AdditionalInformation.objects.all():
-        if ai.url is None:
-            if ai.content_type is None:
-                ai.url = "{}/additional-information/{}".format(ai.scenario.url, ai.uuid)
-            else:
-                model = models[(ai.content_type.app_label, ai.content_type.model)]
-                obj = model.objects.get(pk=ai.object_id)
-                ai.url = "{}/additional-information/{}".format(obj.url, ai.uuid)
-
-            ai.save()
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0029_reactionexplanation_reaction_explained_by"),
-    ]
-
-    operations = [
-        migrations.RunPython(forward_func, reverse_code=migrations.RunPython.noop),
-    ]

epdb/models.py

@@ -859,15 +859,9 @@ class Compound(
     @property
     def related_reactions(self):
         return (
-            (
-                Reaction.objects.filter(package=self.package, educts__in=[self.default_structure])
-                | Reaction.objects.filter(
-                    package=self.package, products__in=[self.default_structure]
-                )
-            )
-            .distinct()
-            .order_by("name")
-        )
+            Reaction.objects.filter(package=self.package, educts__in=[self.default_structure])
+            | Reaction.objects.filter(package=self.package, products__in=[self.default_structure])
+        ).order_by("name")
 
     @property
     def related_nodes(self):
@@ -1741,14 +1735,6 @@ class SequentialRuleOrdering(models.Model):
     order_index = models.IntegerField(null=False, blank=False)
 
 
-class ReactionExplanation(TimeStampedModel):
-    run_uuid = models.UUIDField(null=False, blank=False)
-    run_start = models.DateTimeField(null=False, blank=False)
-    reaction = models.ForeignKey("epdb.Reaction", on_delete=models.CASCADE)
-    rule = models.ForeignKey("epdb.Rule", on_delete=models.CASCADE)
-    exact = models.BooleanField(default=False)
-
-
 class Reaction(
     EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin, AdditionalInformationMixin
 ):
@@ -1774,12 +1760,6 @@ class Reaction(
 
     external_identifiers = GenericRelation("ExternalIdentifier")
 
-    explained_by = models.ManyToManyField(
-        "epdb.Rule",
-        through="ReactionExplanation",
-        related_name="explained_reactions",
-    )
-
     def _url(self):
         return "{}/reaction/{}".format(self.package.url, self.uuid)
 
@@ -2193,7 +2173,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
 
             row += [cs.smiles, cs.get_name(), n.depth]
 
-            edges = self.edges.filter(end_nodes=n)
+            edges = self.edges.filter(end_nodes__in=[n])
             if len(edges):
                 for e in edges:
                     _row = row.copy()
@@ -2486,7 +2466,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             "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.get_scenarios()],
+            "scenarios": [{"name": s.get_name(), "url": s.url} for s in self.scenarios.all()],
             "app_domain": {
                 "inside_app_domain": app_domain_data["assessment"]["inside_app_domain"]
                 if app_domain_data
@@ -2605,7 +2585,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
                 collected[str(ai.scenario.uuid)]["proposed"] = True
 
             if ai.type == "Confidence":
-                collected[str(ai.scenario.uuid)]["Confidence"] = ai.get().level.value
+                collected[str(ai.scenario.uuid)]["Confidence"] = ai.get().level
 
             if ai.type == "TransformationProductImportance":
                 collected[str(ai.scenario.uuid)]["Transformation product importance"] = (
@@ -2614,15 +2594,6 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
 
         return list(collected.values())
 
-    def get_scenarios(self):
-        qs = self.scenarios.all()
-        qs |= Scenario.objects.filter(
-            id__in=self.additional_information.filter(scenario__isnull=False)
-            .values_list("scenario", flat=True)
-            .distinct()
-        )
-        return qs.distinct()
-
 
 class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin):
     pathway = models.ForeignKey(
@@ -2878,58 +2849,6 @@ class PackageBasedModel(EPModel):
 
         return res
 
-    def parameters(self):
-        params = {
-            "Model Evaluation Threshold": f"{self.threshold:.2f}",
-            "Multi Gen Evaluation": "Yes" if self.multigen_eval else "No",
-        }
-
-        if self.app_domain:
-            params["Applicability Domain Num Neighbors"] = f"{self.app_domain.num_neighbours:.2f}"
-            params["Applicability Domain Reliability Threshold"] = (
-                f"{self.app_domain.reliability_threshold:.2f}"
-            )
-            params["Applicability Domain Local Compatibility Threshold"] = (
-                f"{self.app_domain.local_compatibilty_threshold:.2f}"
-            )
-
-        return params
-
-    def statistics(self):
-        from sklearn.metrics import auc
-
-        recall = list(self.eval_results["average_recall_per_threshold"].values())
-        precision = list(self.eval_results["average_precision_per_threshold"].values())
-        mg_recall = list(
-            self.eval_results.get("multigen_average_recall_per_threshold", {}).values()
-        )
-        mg_precision = list(
-            self.eval_results.get("multigen_average_precision_per_threshold", {}).values()
-        )
-
-        return {
-            "accuracy": [
-                self.eval_results["average_accuracy"],
-                self.eval_results.get("multigen_average_accuracy"),
-            ],
-            "precision": [
-                self.eval_results["average_precision_per_threshold"][f"{self.threshold:.2f}"],
-                self.eval_results.get("multigen_average_precision_per_threshold", {}).get(
-                    f"{self.threshold:.2f}"
-                ),
-            ],
-            "recall": [
-                self.eval_results["average_recall_per_threshold"][f"{self.threshold:.2f}"],
-                self.eval_results.get("multigen_average_recall_per_threshold", {}).get(
-                    f"{self.threshold:.2f}"
-                ),
-            ],
-            "Area under PR Curve": [
-                auc(recall, precision),
-                auc(mg_recall, mg_precision) if self.multigen_eval else None,
-            ],
-        }
-
     @cached_property
     def applicable_rules(self) -> List["Rule"]:
         """
@@ -3086,14 +3005,7 @@ class PackageBasedModel(EPModel):
 
             prec, rec = dict(), dict()
 
-            thresholds = list(np.arange(0, 1.05, 0.05))
-
-            # Add specific threshold set during object creation if not already present
-            if np.float64(threshold) not in thresholds:
-                thresholds.append(np.float64(threshold))
-                thresholds.sort()
-
-            for t in thresholds:
+            for t in np.arange(0, 1.05, 0.05):
                 temp_thresholded = (y_pred_filtered >= t).astype(int)
                 prec[f"{t:.2f}"] = precision_score(
                     y_test_filtered, temp_thresholded, zero_division=0
@@ -3103,12 +3015,7 @@ class PackageBasedModel(EPModel):
             return acc, prec, rec
 
         def evaluate_mg(model, pathways: Union[QuerySet["Pathway"] | List["Pathway"]], threshold):
-            thresholds = list(np.arange(0, 1.05, 0.05))
-
-            # Add specific threshold set during object creation if not already present
-            if np.float64(threshold) not in thresholds:
-                thresholds.append(np.float64(threshold))
-                thresholds.sort()
+            thresholds = np.arange(0.1, 1.1, 0.1)
 
             precision = {f"{t:.2f}": [] for t in thresholds}
             recall = {f"{t:.2f}": [] for t in thresholds}
@@ -3134,7 +3041,7 @@ class PackageBasedModel(EPModel):
 
             s = Setting()
             s.model = mod
-            s.model_threshold = 0.0
+            s.model_threshold = thresholds.min()
             s.max_depth = 10
             s.max_nodes = 50
 
@@ -3158,17 +3065,14 @@ class PackageBasedModel(EPModel):
             for t in thresholds:
                 for true, pred in zip(pathways, pred_pathways):
                     acc, pre, rec = multigen_eval(true, pred, t)
-
-                    if f"{t:.2f}" == f"{threshold:.2f}":
-                        mg_acc += acc
-
+                    if abs(t - threshold) < 0.01:
+                        mg_acc = acc
                     precision[f"{t:.2f}"].append(pre)
                     recall[f"{t:.2f}"].append(rec)
 
-            avg_mg_acc = mg_acc / len(root_compounds)
             precision = {k: sum(v) / len(v) if len(v) > 0 else 0 for k, v in precision.items()}
             recall = {k: sum(v) / len(v) if len(v) > 0 else 0 for k, v in recall.items()}
-            return avg_mg_acc, precision, recall
+            return mg_acc, precision, recall
 
         # If there are eval packages perform single generation evaluation on them instead of random splits
         if self.eval_packages.count() > 0:
@@ -4300,9 +4204,6 @@ class ClassifierPluginModel(PackageBasedModel):
         instance = impl(conf)
         return instance
 
-    def parameters(self):
-        return self.instance().parameters()
-
     def build_dataset(self):
         """
         Required by general model contract but actual implementation resides in plugin.
@@ -4523,9 +4424,6 @@ class PropertyPluginModel(PackageBasedModel):
         instance = impl()
         return instance
 
-    def parameters(self):
-        return self.instance().parameters()
-
     def build_dataset(self):
         """
         Required by general model contract but actual implementation resides in plugin.

epdb/tasks.py

@@ -477,7 +477,8 @@ def batch_predict(
             limit=None,
             setting_overrides={
                 "max_nodes": num_tps,
-                "model_threshold": 0.0,
+                "max_depth": num_tps,
+                "model_threshold": 0.001,
             },
         )
 

epdb/views.py

@@ -61,7 +61,6 @@ from .models import (
 )
 
 logger = logging.getLogger(__name__)
-auth_log = logging.getLogger("auth")
 
 Package = s.GET_PACKAGE_MODEL()
 
@@ -72,18 +71,6 @@ def log_post_params(request):
             logger.debug(f"{k}\t{v}")
 
 
-def get_remote_address(request):
-    remote_address = ""
-
-    if request is not None:
-        remote_address = request.META.get("HTTP_X_FORWARDED_FOR")
-
-        if not remote_address:
-            remote_address = request.META.get("REMOTE_ADDR", "")
-
-    return remote_address
-
-
 def get_error_handler_context(request, for_user=None) -> Dict[str, Any]:
     current_user = _anonymous_or_real(request)
 
@@ -160,20 +147,6 @@ def handler500(request):
     return render(request, "errors/error.html", context, status=500)
 
 
-def delete_with_log(request, obj):
-    caller = request.user
-    obj_type = obj.__class__.__name__
-
-    try:
-        obj.delete()
-        auth_log.info(f"{caller.username} ({caller.url}) deleted {obj_type}: {obj.name} ({obj.url})")
-    except Exception as e:
-        logger.info(f"Tried to delete {obj_type}: {obj.name} ({obj.url}) but deletion failed! Exception {e}")
-        auth_log.info(
-            f"{caller.username} ({caller.url}) tried to delete {obj_type}: {obj.name} ({obj.url}) but deletion failed!")
-        raise e
-
-
 def login(request):
     context = get_base_context(request)
 
@@ -232,18 +205,11 @@ def login(request):
         if user is not None:
             login(request, user)
 
-            if user.is_superuser:
-                auth_log.error(f"admin ({user.username}) login attempt by {get_remote_address(request)} successful")
-
             if next := request.POST.get("next"):
                 return redirect(next)
 
             return redirect(reverse("index"))
         else:
-            if _user := User.objects.get(email=email):
-                if _user.is_superuser:
-                    auth_log.error(f"admin ({_user.username}) login attempt by {get_remote_address(request)} failed")
-
             context["message"] = "Login failed!"
             return render(request, "static/login.html", context)
     else:
@@ -424,7 +390,7 @@ def get_base_context(request, for_user=None) -> Dict[str, Any]:
             "external_databases": ExternalDatabase.get_databases(),
             "site_id": s.MATOMO_SITE_ID,
             # EDIT START
-            "secret_groups": Group.objects.filter(secret=True, user_member=current_user),
+            "secret_groups": Group.objects.filter(secret=True),
             # EDIT END
         },
     }
@@ -560,7 +526,6 @@ def batch_predict_pathway(request):
     context = get_base_context(request)
     context["title"] = "enviPath - Batch Predict Pathway"
     context["meta"]["current_package"] = context["meta"]["user"].default_package
-    context["batch_predict_max_compounds"] = s.BATCH_PREDICT_MAX_COMPOUNDS
 
     return render(request, "batch_predict_pathway.html", context)
 
@@ -1145,23 +1110,19 @@ def package_model(request, package_uuid, model_uuid):
                 for pr in pred_res:
                     if len(pr) > 0:
                         products = []
-
                         for prod_set in pr.product_sets:
                             logger.debug(f"Checking {prod_set}")
                             products.append(tuple([x for x in prod_set]))
 
-                        products = list(set(products))
-
-                        for prod in products:
-                            res["pred"].append(
-                                {
-                                    "products": list(prod),
-                                    "probability": pr.probability,
-                                    "btrule": {k: getattr(pr.rule, k) for k in ["url", "name"]}
-                                    if pr.rule is not None
-                                    else None,
-                                }
-                            )
+                        res["pred"].append(
+                            {
+                                "products": list(set(products)),
+                                "probability": pr.probability,
+                                "btrule": {k: getattr(pr.rule, k) for k in ["url", "name"]}
+                                if pr.rule is not None
+                                else None,
+                            }
+                        )
 
                         # Sort data by prob desc
                         res["pred"] = sorted(
@@ -1320,8 +1281,7 @@ def package(request, package_uuid):
                         "You cannot delete the default package. If you want to delete this package you have to set another default package first.",
                     )
 
-                delete_with_log(request, current_package)
-
+                logger.debug(current_package.delete())
                 return redirect(s.SERVER_URL + "/package")
             elif hidden == "publish-package":
                 for g in Group.objects.filter(public=True):
@@ -1989,21 +1949,6 @@ def package_reactions(request, package_uuid):
         reaction_name = request.POST.get("reaction-name")
         reaction_description = request.POST.get("reaction-description")
         reaction_smiles = request.POST.get("reaction-smiles")
-
-        if reaction_smiles is None or reaction_smiles.strip() == "":
-            return error(
-                request,
-                "Reaction SMILES is empty / missing",
-                "No reaction SMILES provided. Please provide a SMILES for the reaction.",
-            )
-
-        if not FormatConverter.is_valid_smirks(reaction_smiles):
-            return error(
-                request,
-                "Reaction SMILES is invalid",
-                f"The provided reactions SMILES {reaction_smiles} is invalid",
-            )
-
         educts = reaction_smiles.split(">>")[0].split(".")
         products = reaction_smiles.split(">>")[1].split(".")
 
@@ -2312,7 +2257,7 @@ def package_pathway(request, package_uuid, pathway_uuid):
     elif request.method == "POST":
         if hidden := request.POST.get("hidden", None):
             if hidden == "delete":
-                delete_with_log(request, current_pathway)
+                current_pathway.delete()
                 return redirect(current_package.url + "/pathway")
             else:
                 return HttpResponseBadRequest()
@@ -2530,7 +2475,7 @@ def package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
         if hidden := request.POST.get("hidden", None):
             if hidden == "delete":
                 # pre_delete signal will take care of edge deletion
-                delete_with_log(request, current_node)
+                current_node.delete()
 
                 return redirect(current_pathway.url)
             else:
@@ -2684,7 +2629,7 @@ def package_pathway_edge(request, package_uuid, pathway_uuid, edge_uuid):
 
         if hidden := request.POST.get("hidden", None):
             if hidden == "delete":
-                delete_with_log(request, current_edge)
+                current_edge.delete()
                 return redirect(current_pathway.url)
 
         if "selected-scenarios" in request.POST:
@@ -3046,7 +2991,7 @@ def group(request, group_uuid):
 
         if hidden := request.POST.get("hidden", None):
             if hidden == "delete":
-                delete_with_log(request, current_group)
+                current_group.delete()
                 return redirect(s.SERVER_URL + "/group")
             else:
                 return HttpResponseBadRequest()

epiuclid/serializers/pathway_mapper.py

@@ -120,6 +120,13 @@ class PathwayMapper:
             )
             bundle.reference_substances.append(ref_sub)
 
+            sub = IUCLIDSubstanceData(
+                uuid=sub_uuid,
+                name=compound.name,
+                reference_substance_uuid=ref_sub_uuid,
+            )
+            bundle.substances.append(sub)
+
         if not export.compounds:
             return bundle
 
@@ -138,16 +145,6 @@ class PathwayMapper:
         if not root_compound_pks:
             return bundle
 
-        for root_pk in root_compound_pks:
-            root_sub_uuid, root_ref_uuid = seen_compounds[root_pk]
-            bundle.substances.append(
-                IUCLIDSubstanceData(
-                    uuid=root_sub_uuid,
-                    name=compound_names[root_pk],
-                    reference_substance_uuid=root_ref_uuid,
-                )
-            )
-
         edge_templates: list[tuple[UUID, frozenset[int], tuple[int, ...], tuple[UUID, ...]]] = []
         for edge in sorted(export.edges, key=lambda item: str(item.edge_uuid)):
             parent_compound_pks = sorted(
@@ -351,8 +348,7 @@ class PathwayMapper:
 
         props = SoilPropertiesData()
 
-        for ai_obj in ai_list:
-            ai = ai_obj.get()
+        for ai in ai_list:
             if isinstance(ai, SoilTexture1) and props.soil_type is None:
                 props.soil_type = ai.type.value
             elif isinstance(ai, SoilTexture2):

epiuclid/tests/test_api.py

@@ -70,7 +70,8 @@ class IUCLIDExportAPITest(TestCase):
             names = zf.namelist()
             self.assertIn("manifest.xml", names)
             i6d_files = [n for n in names if n.endswith(".i6d")]
-            self.assertEqual(len(i6d_files), 4)
+            # 2 substances + 2 ref substances + 1 ESR = 5 i6d files
+            self.assertEqual(len(i6d_files), 5)
 
     def test_anonymous_returns_401(self):
         self.client.logout()

epiuclid/tests/test_i6z.py

@@ -7,11 +7,6 @@ from uuid import uuid4
 
 from django.test import SimpleTestCase, tag
 
-from epapi.v1.interfaces.iuclid.dto import (
-    PathwayCompoundDTO,
-    PathwayEdgeDTO,
-    PathwayExportDTO,
-)
 from epiuclid.serializers.i6z import I6ZSerializer
 from epiuclid.serializers.pathway_mapper import (
     IUCLIDDocumentBundle,
@@ -19,24 +14,9 @@ from epiuclid.serializers.pathway_mapper import (
     IUCLIDReferenceSubstanceData,
     IUCLIDSubstanceData,
     IUCLIDTransformationProductEntry,
-    PathwayMapper,
 )
 
 
-def _unlinked_documents(manifest_xml: str) -> list[tuple[str | None, str]]:
-    ns = "http://iuclid6.echa.europa.eu/namespaces/manifest/v1"
-    root = ET.fromstring(manifest_xml)
-    base = root.findtext(f"{{{ns}}}base-document-uuid")
-    linked_targets: set[str | None] = {base}
-    docs: dict[str, str | None] = {}
-    for doc in root.findall(f".//{{{ns}}}document"):
-        uuid = doc.findtext(f"{{{ns}}}uuid")
-        docs[uuid] = doc.findtext(f"{{{ns}}}type")
-        for link in doc.findall(f"{{{ns}}}links/{{{ns}}}link"):
-            linked_targets.add(link.findtext(f"{{{ns}}}ref-uuid"))
-    return [(doc_type, uuid) for uuid, doc_type in docs.items() if uuid not in linked_targets]
-
-
 def _make_bundle() -> IUCLIDDocumentBundle:
     ref_uuid = uuid4()
     sub_uuid = uuid4()
@@ -217,29 +197,3 @@ class I6ZSerializerTest(SimpleTestCase):
             }
             self.assertIn(parent_ref_key, reference_links)
             self.assertIn(product_ref_key, reference_links)
-
-    def test_multi_compound_pathway_has_no_unlinked_documents(self):
-        compounds = [
-            PathwayCompoundDTO(pk=1, name="Root", smiles="c1ccccc1"),
-            PathwayCompoundDTO(pk=2, name="P1", smiles="CCO"),
-            PathwayCompoundDTO(pk=3, name="P2", smiles="CCN"),
-            PathwayCompoundDTO(pk=4, name="P3", smiles="CCC"),
-        ]
-        export = PathwayExportDTO(
-            pathway_uuid=uuid4(),
-            pathway_name="Regression Pathway",
-            compounds=compounds,
-            edges=[
-                PathwayEdgeDTO(edge_uuid=uuid4(), start_compound_pks=[1], end_compound_pks=[2]),
-                PathwayEdgeDTO(edge_uuid=uuid4(), start_compound_pks=[1], end_compound_pks=[3]),
-                PathwayEdgeDTO(edge_uuid=uuid4(), start_compound_pks=[2], end_compound_pks=[4]),
-            ],
-            root_compound_pks=[1],
-        )
-        bundle = PathwayMapper().map(export)
-        data = I6ZSerializer().serialize(bundle)
-
-        with zipfile.ZipFile(io.BytesIO(data)) as zf:
-            manifest_xml = zf.read("manifest.xml").decode("utf-8")
-
-        self.assertEqual(_unlinked_documents(manifest_xml), [])

epiuclid/tests/test_pathway_mapper.py

@@ -31,7 +31,7 @@ class PathwayMapperTest(SimpleTestCase):
         )
         bundle = PathwayMapper().map(export)
 
-        self.assertEqual(len(bundle.substances), 1)
+        self.assertEqual(len(bundle.substances), 2)
         self.assertEqual(len(bundle.reference_substances), 2)
         self.assertEqual(len(bundle.endpoint_study_records), 1)
 
@@ -49,7 +49,8 @@ class PathwayMapperTest(SimpleTestCase):
         )
         bundle = PathwayMapper().map(export)
 
-        self.assertEqual(len(bundle.substances), 1)
+        # 2 unique compounds -> 2 substances, 2 ref substances
+        self.assertEqual(len(bundle.substances), 2)
         self.assertEqual(len(bundle.reference_substances), 2)
         # One endpoint study record per pathway
         self.assertEqual(len(bundle.endpoint_study_records), 1)

static/js/api/additional-information.js

@@ -186,40 +186,6 @@ window.AdditionalInformationApi = {
     return this._handleResponse(response, "createItem");
   },
 
-    /**
-   * Create new additional information and attach it to an object.
-
-   * @param {string} modelName - Name/type of the additional information model
-   * @param {Object} data - Data for the new item
-   * @param {string} attachObjectUrl - UUID of the object this data should be attached to
-   * @param {string} scenarioUuid - UUID of the scenario
-   * @returns {Promise<{status: string, uuid: string}>}
-   */
-  async createItemOnNonScenarioObject(modelName, data, attachObjectUrl, scenarioUuid) {
-    const sanitizedData = this.sanitizePayload(data);
-    this._log("createItemOnNonScenarioObject", { modelName, data: sanitizedData, attachObjectUrl, scenarioUuid });
-
-    sanitizedData.attach_obj_url = attachObjectUrl;
-    if (scenarioUuid) {
-      sanitizedData.scenario_uuid = scenarioUuid;
-    }
-
-
-    // Normalize model name to lowercase
-    const normalizedName = modelName.toLowerCase();
-
-    const response = await fetch(
-      `/api/v1/information/${normalizedName}/`,
-      {
-        method: "POST",
-        headers: this._buildHeaders(),
-        body: JSON.stringify(sanitizedData),
-      },
-    );
-
-    return this._handleResponse(response, "createItemOnNonScenarioObject");
-  },
-
   /**
    * Delete additional information from a scenario
    * @param {string} scenarioUuid - UUID of the scenario

templates/actions/objects/package.html

@@ -15,7 +15,6 @@
       <i class="glyphicon glyphicon-user"></i> Edit Permissions</a
     >
   </li>
-  {% if meta.current_package.get_classification_level_display != "Secret" %}
   <li>
     <a
       role="button"
@@ -24,8 +23,6 @@
       <i class="glyphicon glyphicon-bullhorn"></i> Publish Package</a
     >
   </li>
-  {% endif %}
-{% endif %}
   <li>
     <a
       role="button"
@@ -34,7 +31,6 @@
       <i class="glyphicon glyphicon-bullhorn"></i> Export Package as JSON</a
     >
   </li>
-{% if meta.can_edit %}
   <li>
     <a
       role="button"
@@ -52,13 +48,3 @@
     >
   </li>
 {% endif %}
-{% if not meta.can_edit %}
-  <li>
-    <a
-      role="button"
-      onclick="document.getElementById('view_package_permissions_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-user"></i> View Permissions</a
-    >
-  </li>
-{% endif %}

templates/actions/objects/pathway.html

@@ -83,19 +83,6 @@
       <i class="glyphicon glyphicon-edit"></i> Edit Pathway</a
     >
   </li>
-  <li>
-    <a
-      class="button"
-      onclick="
-      const modal = document.getElementById('edit_pathway_node_modal');
-      modal.showModal();
-      window.dispatchEvent(new Event('modal-opened'));
-      return false;
-      "
-    >
-      <i class="glyphicon glyphicon-edit"></i> Edit Compound</a
-    >
-  </li>
   <li>
     <a
       role="button"

templates/actions/objects/scenario.html

@@ -10,7 +10,7 @@
   <li>
     <a
       class="button"
-      onclick="document.getElementById('add_scenario_additional_information_modal').showModal(); return false;"
+      onclick="document.getElementById('add_additional_information_modal').showModal(); return false;"
     >
       <i class="glyphicon glyphicon-trash"></i> Add Additional Information</a
     >

templates/batch_predict_pathway.html

@@ -37,8 +37,7 @@
               class="text-xs text-base-content/50 border-t border-base-300 pt-3"
             >
               <strong>Format:</strong> First column = SMILES, Second column =
-              Name (headers optional) • Maximum
-              {{ batch_predict_max_compoundss|default:150 }} rows
+              Name (headers optional) • Maximum 30 rows
             </div>
           </div>
         </div>
@@ -196,7 +195,8 @@
     // Function to populate table from CSV data
     function populateTableFromCSV(csvData) {
       const lines = csvData.trim().split("\n");
-      const maxRows = Number("{{ batch_predict_max_compounds|default:150 }}");
+      const maxRows = 30;
+
       // Clear existing table
       clearTable();
 

templates/components/navbar.html

@@ -105,10 +105,6 @@
           <img src="{% static 'images/restricted_mid.png' %}" width="200">
         {% elif meta.url_contains_package and meta.current_package.get_classification_level_display == "Secret" %}
           <img src="{% static 'images/secret_mid.png' %}" width="120">
-        {% elif not meta.url_contains_package and meta.user.default_package.get_classification_level_display == "Restricted" %}
-          <img src="{% static 'images/restricted_mid.png' %}" width="200">
-        {% elif not meta.url_contains_package and meta.user.default_package.get_classification_level_display == "Secret" %}
-          <img src="{% static 'images/secret_mid.png' %}" width="120">
         {% endif %}
         {% if not public_mode %}
           <a id="search-trigger" role="button" class="cursor-pointer">

templates/errors/error.html

@@ -51,10 +51,7 @@
               </svg>
               Go Home
             </a>
-            <button
-              onclick="window.location.href = document.referrer"
-              class="btn btn-outline"
-            >
+            <button onclick="window.history.back()" class="btn btn-outline">
               <svg
                 xmlns="http://www.w3.org/2000/svg"
                 class="mr-2 h-5 w-5"

templates/modals/objects/add_additional_information_modal.html

@@ -1,7 +1,7 @@
 {% load static %}
 <!-- Add Additional Information -->
 <dialog
-  id="add_scenario_additional_information_modal"
+  id="add_additional_information_modal"
   class="modal"
   x-data="{
     isSubmitting: false,
@@ -98,7 +98,7 @@
         );
 
         // Close modal and reload page to show new item
-        document.getElementById('add_scenario_additional_information_modal').close();
+        document.getElementById('add_additional_information_modal').close();
         window.location.reload();
       } catch (err) {
         if (err.isValidationError && err.fieldErrors) {

templates/modals/objects/edit_pathway_node_modal.html

@@ -1,276 +0,0 @@
-{% load static %}
-<!-- Add Additional Information -->
-<dialog
-  id="edit_pathway_node_modal"
-  class="modal"
-  x-data="{
-    isSubmitting: false,
-    selectedType: '',
-    selectedScenario: '',
-    selectedNode: '',
-    schemas: {},
-    loadingSchemas: false,
-    error: null,
-    formData: null,  // Store reference to form data
-    formRenderKey: 0,  // Counter to force form re-render
-    allowedTypes: ['halflife', 'halflifews', 'proposedintermediate', 'transformationproductimportance', 'confidence'],
-    scenarios: [],
-    scenariosLoaded: false,
-
-    // Get sorted unique schema names for dropdown, excluding already-added types
-    get sortedSchemaNames() {
-      const names = Object.keys(this.schemas);
-      // Remove duplicates, exclude existing types, and sort alphabetically by display title
-      const unique = [...new Set(names)];
-      const available = unique.filter(name =>
-        this.allowedTypes.includes(name)
-      );
-      return available.sort((a, b) => {
-        const titleA = (this.schemas[a]?.schema?.['x-title'] || a).toLowerCase();
-        const titleB = (this.schemas[b]?.schema?.['x-title'] || b).toLowerCase();
-        return titleA.localeCompare(titleB);
-      });
-    },
-
-    async init() {
-      // Watch for selectedType changes
-      this.$watch('selectedType', (value) => {
-        // Reset formData when type changes and increment key to force re-render
-        this.formData = null;
-        this.formRenderKey++;
-        // Clear previous errors
-        this.error = null;
-        Alpine.store('validationErrors').clearErrors(); // No context - clears all
-      });
-
-      // Load schemas and existing items
-      try {
-        this.loadingSchemas = true;
-        const [schemasRes, scenarioRes] = await Promise.all([
-          fetch('/api/v1/information/schema/'),
-          fetch('{% url "package scenario list" meta.current_package.uuid %}', { headers: {'Accept': 'application/json' }}),
-        ]);
-
-        if (!schemasRes.ok) throw new Error('Failed to load schemas');
-        if (!scenarioRes.ok) throw new Error('Failed to load scenarios');
-
-        this.schemas = await schemasRes.json();
-        this.scenarios = await scenarioRes.json();
-        // Get unique existing types (normalize to lowercase)
-      } catch (err) {
-        this.error = err.message;
-      } finally {
-        this.loadingSchemas = false;
-      }
-    },
-
-    reset() {
-      this.isSubmitting = false;
-      this.selectedType = '';
-      this.error = null;
-      this.formData = null;
-      this.selectedScenario = '';
-      Alpine.store('validationErrors').clearErrors(); // No context - clears all
-    },
-
-    setFormData(data) {
-      // Fired from schemaRenderer
-      this.formData = data;
-    },
-
-    async submit() {
-      if (!this.selectedType) return;
-      const payload = window.AdditionalInformationApi.sanitizePayload(this.formData || {});
-
-      // Validate that form has data
-      if (!payload || Object.keys(payload).length === 0) {
-        // proposedintermediate is parameterless
-        if (!this.selectedType === 'proposedintermediate') {
-          this.error = 'Please fill in at least one field';
-          return;
-        }
-      }
-
-      this.isSubmitting = true;
-      this.error = null;
-
-      try {
-      // TODO
-        await window.AdditionalInformationApi.createItemOnNonScenarioObject(
-          this.selectedType,
-          payload,
-          this.selectedNode,
-          this.selectedScenario
-        );
-
-        // Close modal and reload page to show new item
-        document.getElementById('edit_pathway_node_modal').close();
-        window.location.reload();
-      } catch (err) {
-        if (err.isValidationError && err.fieldErrors) {
-          // No context for add modal - simple flat errors
-          Alpine.store('validationErrors').setErrors(err.fieldErrors);
-          this.error = err.message || 'Please correct the errors in the form';
-        } else {
-          this.error = err.message || 'An error occurred. Please try again.';
-        }
-      } finally {
-        this.isSubmitting = false;
-      }
-    }
-  }"
-  @close="reset()"
-  @form-data-ready="setFormData($event.detail)"
-  @modal-opened.window="
-   const el = d3.select('circle.highlighted').node();
-   if (el !== null) {
-    const selectElement = document.getElementById('edit_pathway_nodes_node');
-    for (let option of selectElement.options) {
-        if (option.value === el.__data__.url) {
-            option.selected = true;
-            break;
-        }
-    }
-    selectElement.dispatchEvent(new Event('change'));
-   }
-  "
->
-  <div class="modal-box max-w-2xl">
-    <!-- Header -->
-    <h3 class="text-lg font-bold">Edit Compound</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute top-2 right-2"
-        :disabled="isSubmitting"
-      >
-        ✕
-      </button>
-    </form>
-
-    <!-- Body -->
-    <div class="py-4">
-      <!-- Loading state -->
-      <template x-if="loadingSchemas">
-        <div class="flex items-center justify-center p-4">
-          <span class="loading loading-spinner loading-md"></span>
-        </div>
-      </template>
-
-      <!-- Error state -->
-      <template x-if="error">
-        <div class="alert alert-error mb-4">
-          <span x-text="error"></span>
-        </div>
-      </template>
-      <div class="form-control">
-        <p>
-          If no Scenario is selected a new Scenario will be created and attached
-          to this Pathway
-        </p>
-        <label class="label" for="edit_pathway_nodes_node">
-          <span class="label-text">Select Node</span>
-        </label>
-        <select
-          id="edit_pathway_nodes_node"
-          name="node"
-          class="select select-bordered w-full"
-          x-model="selectedNode"
-        >
-          {% for n in pathway.nodes %}
-            <option value="{{ n.url }}">
-              {{ n.default_node_label.name|safe }}
-            </option>
-          {% endfor %}
-        </select>
-
-        <label class="label" for="scenario-select">
-          <span class="label-text">Scenarios</span>
-        </label>
-        <select
-          id="scenario-select"
-          name="selected-scenarios"
-          class="select select-bordered w-full"
-          x-model="selectedScenario"
-        >
-          <option value="" selected disabled>Select Scenario</option>
-          <template x-for="scenario in scenarios" :key="scenario.url">
-            <option :value="scenario.url" x-text="scenario.name"></option>
-          </template>
-        </select>
-      </div>
-
-      <!-- Schema selection -->
-      <template x-if="!loadingSchemas">
-        <div>
-          <div class="form-control mb-4">
-            <label class="label" for="select-additional-information-type">
-              <span class="label-text">Select the type to add</span>
-            </label>
-            <select
-              id="select-additional-information-type"
-              class="select select-bordered w-full"
-              x-model="selectedType"
-            >
-              <option value="" selected disabled>Select the type to add</option>
-              <template x-for="name in sortedSchemaNames" :key="name">
-                <option
-                  :value="name"
-                  x-text="(schemas[name].schema && (schemas[name].schema['x-title'] || schemas[name].schema.title)) || name"
-                ></option>
-              </template>
-            </select>
-          </div>
-
-          <!-- Form renderer for selected type -->
-          <!-- Use unique key per type to force re-render -->
-          <template x-for="renderKey in [formRenderKey]" :key="renderKey">
-            <div x-show="selectedType && schemas[selectedType]">
-              <div
-                x-data="schemaRenderer({
-                  rjsf: schemas[selectedType],
-                  mode: 'edit'
-                  // No context - single form, backward compatible
-                })"
-                x-init="await init(); $dispatch('form-data-ready', data)"
-              >
-                {% include "components/schema_form.html" %}
-              </div>
-            </div>
-          </template>
-        </div>
-      </template>
-    </div>
-
-    <!-- Footer -->
-    <div class="modal-action">
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Close
-      </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="submit()"
-        :disabled="isSubmitting || loadingSchemas || !selectedType || !selectedNode"
-      >
-        <span x-show="!isSubmitting">Add</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Adding...</span>
-      </button>
-    </div>
-  </div>
-
-  <!-- Backdrop -->
-  <form method="dialog" class="modal-backdrop">
-    <button :disabled="isSubmitting">close</button>
-  </form>
-</dialog>

templates/modals/objects/view_package_permissions_modal.html

@@ -1,147 +0,0 @@
-{% load static %}
-<!-- Edit Package Permissions -->
-<dialog
-  id="view_package_permissions_modal"
-  class="modal"
-  x-data="{}"
->
-  <div class="modal-box max-w-2xl">
-    <!-- Header -->
-    <h3 class="text-lg font-bold">Current Permissions</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button class="btn btn-sm btn-circle btn-ghost absolute top-2 right-2">
-        ✕
-      </button>
-    </form>
-
-    <!-- Body -->
-    <div class="py-4">
-      <p class="mb-4">
-        Current permissions for this package.
-      </p>
-
-      <!-- User Permissions -->
-      {% if user_permissions %}
-        <div class="divider">User Permissions</div>
-        <div class="space-y-2">
-        <div class="grid grid-cols-12 gap-2 items-center">
-          <div class="col-span-5 truncate"></div>
-          <div class="col-span-2 text-center">Read</div>
-          <div class="col-span-2 text-center">Write</div>
-          <div class="col-span-2 text-center">Owner</div>
-          <div class="col-span-1"></div>
-        </div>
-          {% for up in user_permissions %}
-              <div class="grid grid-cols-12 gap-2 items-center">
-                <div class="col-span-5 truncate">
-                  {{ up.user.username }}
-                  {% if not up.user.is_active %}<i>(inactive)</i>{% endif %}
-                </div>
-                <div class="col-span-2 text-center">
-                  <input
-                    type="checkbox"
-                    name="read"
-                    id="read_{{ up.user.uuid }}"
-                    class="checkbox"
-                    {% if up.has_read %}checked{% endif %}
-                    onclick="return false;"
-                  />
-                </div>
-                <div class="col-span-2 text-center">
-                  <input
-                    type="checkbox"
-                    name="write"
-                    id="write_{{ up.user.uuid }}"
-                    class="checkbox"
-                    {% if up.has_write %}checked{% endif %}
-                    onclick="return false;"
-                  />
-                </div>
-                <div class="col-span-2 text-center">
-                  <input
-                    type="checkbox"
-                    name="owner"
-                    id="owner_{{ up.user.uuid }}"
-                    class="checkbox"
-                    {% if up.has_all %}checked{% endif %}
-                    onclick="return false;"
-                  />
-                </div>
-              </div>
-
-          {% endfor %}
-        </div>
-      {% endif %}
-
-      <!-- Group Permissions -->
-      {% if group_permissions %}
-        <div class="divider">Group Permissions</div>
-        <div class="space-y-2">
-        <div class="grid grid-cols-12 gap-2 items-center">
-          <div class="col-span-5 truncate"></div>
-          <div class="col-span-2 text-center">Read</div>
-          <div class="col-span-2 text-center">Write</div>
-          <div class="col-span-2 text-center">Owner</div>
-          <div class="col-span-1"></div>
-        </div>
-          {% for gp in group_permissions %}
-
-              <div class="grid grid-cols-12 gap-2 items-center">
-                <div class="col-span-5 truncate">
-                  {{ gp.group.name|safe }}
-                </div>
-                <div class="col-span-2 text-center">
-                  <input
-                    type="checkbox"
-                    name="read"
-                    id="read_{{ gp.group.uuid }}"
-                    class="checkbox"
-                    {% if gp.has_read %}checked{% endif %}
-                    onclick="return false;"
-                  />
-                </div>
-                <div class="col-span-2 text-center">
-                  <input
-                    type="checkbox"
-                    name="write"
-                    id="write_{{ gp.group.uuid }}"
-                    class="checkbox"
-                    {% if gp.has_write %}checked{% endif %}
-                    onclick="return false;"
-                  />
-                </div>
-                <div class="col-span-2 text-center">
-                  <input
-                    type="checkbox"
-                    name="owner"
-                    id="owner_{{ gp.group.uuid }}"
-                    class="checkbox"
-                    {% if gp.has_all %}checked{% endif %}
-                    onclick="return false;"
-                  />
-                </div>
-              </div>
-          {% endfor %}
-        </div>
-      {% endif %}
-    </div>
-
-    <!-- Footer -->
-    <div class="modal-action">
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-      >
-        Close
-      </button>
-    </div>
-  </div>
-
-  <!-- Backdrop -->
-  <form method="dialog" class="modal-backdrop">
-    <button>close</button>
-  </form>
-</dialog>

templates/objects/model/_model_base.html

@@ -117,39 +117,6 @@
           </div>
         </div>
       {% endif %}
-
-      {% if model.parameters %}
-        <!-- Model Parameters Panel -->
-        <div class="collapse-arrow bg-base-200 collapse">
-          <input type="checkbox" checked />
-          <div class="collapse-title text-xl font-medium">Model Parameters</div>
-          <div class="collapse-content">
-            <div class="flex justify-center">
-              <div
-                id="model-stats"
-                class="overflow-x-auto rounded-box shadow-md bg-base-100"
-              >
-                <table class="table table-fixed w-full">
-                  <thead class="text-base">
-                    <tr>
-                      <th class="w-3/5">Parameter</th>
-                      <th>Value</th>
-                    </tr>
-                  </thead>
-                  <tbody>
-                    {% for param, value in model.parameters.items %}
-                      <tr>
-                        <td>{{ param }}</td>
-                        <td>{{ value }}</td>
-                      </tr>
-                    {% endfor %}
-                  </tbody>
-                </table>
-              </div>
-            </div>
-          </div>
-        </div>
-      {% endif %}
     {% endblock %}
 
     {% block usemodel %}

templates/objects/model/classification_model.html

@@ -109,12 +109,12 @@
         res += "<th scope='row'>" + cnt + "</th>";
         res +=
           "<th scope='row'>" +
-          data[transformation]["products"].join(", ") +
+          data[transformation]["products"][0].join(", ") +
           "</th>";
         res +=
           "<th scope='row'>" +
           "<img width='400' src='{% url 'depict' %}?smiles=" +
-          encodeURIComponent(data[transformation]["products"].join(".")) +
+          encodeURIComponent(data[transformation]["products"][0].join(".")) +
           "'></th>";
         res +=
           "<th scope='row'>" +
@@ -313,44 +313,6 @@
                 </div>
             </div>
         {% endif %}
-
-      <!-- Model Statistics Panel -->
-      <div class="collapse-arrow bg-base-200 collapse">
-        <input type="checkbox" checked />
-        <div class="collapse-title text-xl font-medium">Model Statistics for threshold {{ model.threshold }}</div>
-        <div class="collapse-content">
-          <div class="flex justify-center">
-            <div
-              id="model-stats"
-              class="overflow-x-auto rounded-box shadow-md bg-base-100"
-            >
-              <table class="table table-fixed w-full">
-                <thead class="text-base">
-                  <tr>
-                    <th class="w-1/5">Metric</th>
-                    <th>Single Gen Value</th>
-                    {% if model.multigen_eval %}
-                      <th>Multi Gen Value</th>
-                    {% endif %}
-                  </tr>
-                </thead>
-                <tbody>
-                  {% for metric, value in model.statistics.items %}
-                    <tr>
-                      <td>{{ metric|upper }}</td>
-                      <td>{{ value.0|floatformat:3 }}</td>
-                      {% if model.multigen_eval %}
-                        <td>{{ value.1|floatformat:3 }}</td>
-                      {% endif %}
-                    </tr>
-                  {% endfor %}
-                </tbody>
-              </table>
-            </div>
-          </div>
-        </div>
-      </div>
-
     {% endif %}
     <script>
         function makeChart(selector, data) {

templates/objects/node.html

@@ -139,7 +139,7 @@
                           </tr>
                           <tr>
                             <td>Model</td>
-                            <td>{{ half_lifes.0.model.value }}</td>
+                            <td>{{ half_lifes.0.model }}</td>
                           </tr>
                         </tbody>
                       </table>

templates/objects/pathway.html

@@ -4,8 +4,6 @@
 
 {% block content %}
   <script src="https://d3js.org/d3.v7.min.js"></script>
-  <script src="{% static 'js/api/additional-information.js' %}"></script>
-
   <style>
     #vizdiv {
       width: 100%;
@@ -99,7 +97,6 @@
     {% include "modals/objects/identify_missing_rules_modal.html" %}
     {% include "modals/objects/generic_copy_object_modal.html" %}
     {% include "modals/objects/edit_pathway_modal.html" %}
-    {% include "modals/objects/edit_pathway_node_modal.html" %}
     {% include "modals/objects/generic_set_aliases_modal.html" %}
     {% include "modals/objects/generic_set_scenario_modal.html" %}
     {% include "modals/objects/delete_pathway_node_modal.html" %}
@@ -537,7 +534,7 @@
         <input type="checkbox" />
         <div class="collapse-title text-xl font-medium">Setting</div>
         <div class="collapse-content">
-          {% with setting_to_render=pathway.setting_with_overrides can_be_default=False %}
+          {% with setting_to_render=pathway.setting can_be_default=False %}
             {% include "objects/setting_template.html" %}
           {% endwith %}
         </div>

templates/objects/scenario.html

@@ -7,7 +7,7 @@
 
   {% block action_modals %}
     {% include "modals/objects/edit_scenario_modal.html" %}
-    {% include "modals/objects/add_scenario_additional_information_modal.html" %}
+    {% include "modals/objects/add_additional_information_modal.html" %}
     {% include "modals/objects/update_scenario_additional_information_modal.html" %}
     {% include "modals/objects/generic_delete_modal.html" %}
   {% endblock action_modals %}

templates/objects/user.html

@@ -95,23 +95,21 @@
     </div>
 
     <!-- Other Prediction Settings -->
-    {% if meta.available_settings|length > 1 %}
-      <div class="collapse-arrow bg-base-200 collapse">
-        <input type="checkbox" />
-        <div class="collapse-title text-xl font-medium">
-          Other Prediction Settings
-        </div>
-        <div class="collapse-content space-y-3">
-          {% for setting in meta.available_settings %}
-            {% if setting != user.default_setting %}
-              {% with setting_to_render=setting can_be_default=True %}
-                {% include "objects/setting_template.html" %}
-              {% endwith %}
-            {% endif %}
-          {% endfor %}
-        </div>
+    <div class="collapse-arrow bg-base-200 collapse">
+      <input type="checkbox" />
+      <div class="collapse-title text-xl font-medium">
+        Other Prediction Settings
       </div>
-    {% endif %}
+      <div class="collapse-content space-y-3">
+        {% for setting in meta.available_settings %}
+          {% if setting != user.default_setting %}
+            {% with setting_to_render=setting can_be_default=True %}
+              {% include "objects/setting_template.html" %}
+            {% endwith %}
+          {% endif %}
+        {% endfor %}
+      </div>
+    </div>
   </div>
 
   <script>

tests/test_jobs.py

@@ -58,7 +58,7 @@ class MultiGenTest(TestCase):
 
         self.assertEqual(
             pw.setting_with_overrides.max_depth,
-            5,
+            f"{num_tps} (this is an override for this particular pathway)",
         )
         self.assertEqual(
             pw.setting_with_overrides.max_nodes,

tests/views/test_model_views.py

@@ -47,7 +47,7 @@ class ModelViewTest(TestCase):
 
         expected = [
             {
-                "products": ["CCN(CC)C(=O)C1=CC(C=O)=CC=C1"],
+                "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",
@@ -55,7 +55,7 @@ class ModelViewTest(TestCase):
                 },
             },
             {
-                "products": ["O=C(O)C1=CC(CO)=CC=C1", "CCNCC"],
+                "products": [["O=C(O)C1=CC(CO)=CC=C1", "CCNCC"]],
                 "probability": 0.25,
                 "btrule": {
                     "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/0e6e9290-b658-4450-b291-3ec19fa19206",
@@ -63,7 +63,7 @@ class ModelViewTest(TestCase):
                 },
             },
             {
-                "products": ["CCNC(=O)C1=CC(CO)=CC=C1", "CC=O"],
+                "products": [["CCNC(=O)C1=CC(CO)=CC=C1", "CC=O"]],
                 "probability": 0.0,
                 "btrule": {
                     "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/27a3a353-0b66-4228-bd16-e407949e90df",

utilities/chem.py

@@ -68,8 +68,6 @@ class PredictionResult(object):
 
 
 class FormatConverter(object):
-    tautomer_enumerator = rdMolStandardize.TautomerEnumerator()
-
     @staticmethod
     def mass(smiles):
         return Descriptors.MolWt(FormatConverter.from_smiles(smiles))
@@ -242,9 +240,8 @@ class FormatConverter(object):
             Chem.RemoveStereochemistry(res_mol)
 
         if canonicalize_tautomers:
-            tautomers = FormatConverter.tautomer_enumerator.Enumerate(res_mol)
-            if len(tautomers) >= 1:
-                res_mol = FormatConverter.tautomer_enumerator.PickCanonical(tautomers)
+            te = rdMolStandardize.TautomerEnumerator()  # idem
+            res_mol = te.Canonicalize(res_mol)
 
         return Chem.MolToSmiles(res_mol, kekuleSmiles=True)
 
@@ -392,7 +389,7 @@ class FormatConverter(object):
                                 prods.append(p)
 
                         except ValueError as e:
-                            logger.debug(f"Sanitizing and converting failed:\n{e}")
+                            logger.error(f"Sanitizing and converting failed:\n{e}")
                             continue
 
                     if len(prods):
@@ -400,8 +397,7 @@ class FormatConverter(object):
                         pss.add(ps)
 
         except Exception as e:
-            logger.debug(f"Applying {smirks} on {smiles} failed:\n{e}")
-            pass
+            logger.error(f"Applying {smirks} on {smiles} failed:\n{e}")
 
         return list(pss)
 
@@ -448,7 +444,6 @@ class FormatConverter(object):
         r_smiles: List[str],
         standardize: bool = True,
         canonicalize_tautomers: bool = True,
-        return_exact_match: bool = False,
     ) -> bool:
         """
         Check if all SMILES in the left list are covered by (contained in) the right list.
@@ -487,10 +482,8 @@ class FormatConverter(object):
         if standardize:
             for smi in l_smiles:
                 try:
-                    smi = FormatConverter.canonicalize(
-                        FormatConverter.standardize(
-                            smi, remove_stereo=True, canonicalize_tautomers=canonicalize_tautomers
-                        )
+                    smi = FormatConverter.standardize(
+                        smi, remove_stereo=True, canonicalize_tautomers=canonicalize_tautomers
                     )
                 except Exception:
                     # :shrug:
@@ -504,12 +497,8 @@ class FormatConverter(object):
         if standardize:
             for smi in r_smiles:
                 try:
-                    smi = FormatConverter.canonicalize(
-                        FormatConverter.standardize(
-                            smi,
-                            remove_stereo=True,
-                            canonicalize_tautomers=canonicalize_tautomers,
-                        )
+                    smi = FormatConverter.standardize(
+                        smi, remove_stereo=True, canonicalize_tautomers=canonicalize_tautomers
                     )
                 except Exception:
                     # :shrug:
@@ -518,11 +507,8 @@ class FormatConverter(object):
                 standardized_r_smiles.append(smi)
         else:
             standardized_r_smiles = r_smiles
-        if not return_exact_match:
-            return len(set(standardized_l_smiles).difference(set(standardized_r_smiles))) == 0
-        return len(set(standardized_l_smiles).difference(set(standardized_r_smiles))) == 0, set(
-            standardized_l_smiles
-        ) == set(standardized_r_smiles)
+
+        return len(set(standardized_l_smiles).difference(set(standardized_r_smiles))) == 0
 
 
 class Standardizer(ABC):

utilities/misc.py

@@ -4,13 +4,11 @@ import hmac
 import json
 import logging
 import uuid
-from abc import ABC, abstractmethod
 from collections import defaultdict
 from datetime import datetime
-from typing import Any, Dict, List, Optional, TYPE_CHECKING, Type
+from typing import Any, Dict, List, Optional, TYPE_CHECKING
 
 from django.conf import settings as s
-from envipy_additional_information import EnviPyModel, UIConfig
 from ninja import Schema
 from pydantic import HttpUrl, ValidationError
 
@@ -158,7 +156,7 @@ class EnzymeExportSchema(RefEnzymeExportSchema):
 
 
 class EnzymeRuleExportSchema(RefRuleExportSchema):
-    enzymes: List[EnzymeExportSchema] = []
+    enzymes: List[EnzymeExportSchema] | None = None
 
     @staticmethod
     def resolve_enzymes(obj):
@@ -271,7 +269,7 @@ class PackageExportSchema(Schema):
     @staticmethod
     def resolve_classification_level(obj):
         if isinstance(obj, dict):
-            return obj.get("classification_level", "Internal")
+            return obj["classification_level"]
         return obj.Classification(obj.classification_level).name
 
 
@@ -321,20 +319,15 @@ class PackageExportSchema(Schema):
         return AdditionalInformation.objects.filter(package=obj)
 
 
-class Exporter(ABC):
+class PackageExporter:
     def __init__(self, package: Package):
         self._raw_package = package
 
     def do_export(self):
-        return self._export()
+        return PackageExporter._export_package_as_json(self._raw_package)
 
-    @abstractmethod
-    def _export(self):
-        pass
-
-
-class PackageExporter(Exporter):
-    def _export(self) -> Dict[str, Any]:
+    @staticmethod
+    def _export_package_as_json(package: Package) -> Dict[str, Any]:
         """
         Dumps a Package and all its related objects as JSON.
 
@@ -345,126 +338,11 @@ class PackageExporter(Exporter):
             Dict containing the complete package data as JSON-serializable structure
         """
 
-        data = PackageExportSchema.from_orm(self._raw_package)
+        data = PackageExportSchema.from_orm(package)
 
         return data.model_dump(mode="json")
 
 
-class PathwayExporter(Exporter):
-    def __init__(self, package: Package, add_infs_to_export: List[str] = []):
-        super().__init__(package)
-        self._add_infs_to_export = add_infs_to_export
-
-    def _flatten_additional_information(self, ai: AdditionalInformation) -> dict[str, Any]:
-        model_cls: Type[EnviPyModel] = type(ai.get())
-
-        def _flatten(d: dict, parent_key: str = "") -> dict[str, Any]:
-            items: dict[str, Any] = {}
-            for key, value in d.items():
-                new_key = f"{parent_key}__{key.lower()}" if parent_key else key.lower()
-                if isinstance(value, dict):
-                    items.update(_flatten(value, new_key))
-                else:
-                    items[new_key] = value
-            return items
-
-        flat = _flatten(ai.data, ai.type)
-
-        ui_class = getattr(model_cls, "UI", None)
-        if ui_class is None:
-            return flat
-
-        for f in model_cls.model_fields:
-            ui_info = getattr(ui_class, f, None)
-
-            if not isinstance(ui_info, UIConfig) or ui_info.unit is None:
-                continue
-
-            flat[f"{model_cls.__name__}__{f}__unit"] = ui_info.unit
-
-        return flat
-
-    def _export(self):
-        from io import StringIO
-        from csv import DictWriter
-
-        rows = []
-
-        for pw in self._raw_package.pathways.all():
-            for n in pw.nodes:
-                for scen in pw.scenarios.all():
-                    row = {
-                        "pathway_name": pw.name,
-                        "pathway_id": str(pw.url),
-                        "node_depth": n.depth,
-                        "compound_id": str(n.default_node_label.compound.url),
-                        "pubchem_ID": n.default_node_label.pubchem_compound_id,
-                        "compound_name": n.default_node_label.compound.name,
-                        "compound_smiles": n.default_node_label.smiles,
-                        "scenario_id": str(scen.url),
-                        "scenario_name": scen.name,
-                        "scenario_type": scen.scenario_type,
-                        "scenario_description": scen.description,
-                    }
-
-                    if self._add_infs_to_export:
-                        ai_qs = AdditionalInformation.objects.filter(
-                            scenario=scen, type__in=self._add_infs_to_export
-                        )
-                    else:
-                        ai_qs = AdditionalInformation.objects.filter(scenario=scen)
-
-                    for ai in ai_qs:
-                        if ai.type == "ProposedIntermediate" and ai.content_object == n:
-                            row.update({"proposed_intermediate": True})
-                        elif ai.type == "SpikeCompound":
-                            spike = {"SpikeCompound__url": ai.get().url}
-
-                            try:
-                                struc = CompoundStructure.objects.get(
-                                    compound__package=self._raw_package, url=ai.get().url
-                                )
-                                spike["SpikeCompound__smiles"] = struc.smiles
-                            except Exception:
-                                spike["SpikeCompound__smiles"] = None
-
-                            row.update(**spike)
-                        else:
-                            row.update(self._flatten_additional_information(ai))
-                    rows.append(row)
-
-        # Get all header fields
-        all_header_fields = set()
-        for row in rows:
-            all_header_fields.update(row.keys())
-
-        # Per request the CSV should start with these fields
-        header = [
-            "pathway_name",
-            "pathway_id",
-            "node_depth",
-            "compound_id",
-            "pubchem_ID",
-            "compound_name",
-            "compound_smiles",
-            "scenario_id",
-            "scenario_name",
-            "scenario_type",
-            "scenario_description",
-        ]
-
-        # User remaining fields and place them after the predefined values in a sorted manner
-        remainder = sorted(list(all_header_fields.difference(set(header))))
-        header.extend(remainder)
-
-        buffer = StringIO()
-        writer = DictWriter(buffer, fieldnames=header, delimiter="\t")
-        writer.writeheader()
-        writer.writerows(rows)
-        buffer.seek(0)
-        return buffer.getvalue()
-
-
 class PackageImporter:
     def __init__(self, package: Dict[str, Any], preserve_uuids: bool = False):
         self.preserve_uuids = preserve_uuids

utilities/ml.py

@@ -238,11 +238,9 @@ class RuleBasedDataset(Dataset):
     ):
         if feat_funcs is None:
             feat_funcs = [FormatConverter.maccs]
-
-        _structures = set()
+        _structures = set()  # Get all the structures
         for r in reactions:
             _structures.update(r.educts.all())
-
             if not educts_only:
                 _structures.update(r.products.all())
 
@@ -284,14 +282,17 @@ class RuleBasedDataset(Dataset):
                     if key not in triggered:
                         continue
 
-                    if FormatConverter.smiles_covered_by(
-                        [prod.smiles for prod in r.products.all()],
-                        list(triggered[key]),
-                        standardize=True,
-                        canonicalize_tautomers=True,
-                    ):
+                    # standardize products from reactions for comparison
+                    standardized_products = []
+                    for cs in r.products.all():
+                        smi = cs.smiles
+                        try:
+                            smi = FormatConverter.standardize(smi, remove_stereo=True)
+                        except Exception:
+                            logger.debug(f"Standardizing SMILES failed for {smi}")
+                        standardized_products.append(smi)
+                    if len(set(standardized_products).difference(triggered[key])) == 0:
                         observed.add(key)
-
         feat_columns = []
         for feat_func in feat_funcs:
             if isinstance(feat_func, Descriptor):
@@ -300,7 +301,6 @@ class RuleBasedDataset(Dataset):
                 feats = feat_func(compounds[0].smiles)
             start_i = len(feat_columns)
             feat_columns.extend([f"feature_{start_i + i}" for i, _ in enumerate(feats)])
-
         ds_columns = (
             ["structure_id"]
             + feat_columns
@@ -334,9 +334,7 @@ class RuleBasedDataset(Dataset):
                     obs.append(None)
                 else:
                     obs.append(0)
-
             rows.append([str(comp.uuid)] + feats + trig + obs)
-
         ds = RuleBasedDataset(len(applicable_rules), ds_columns, data=rows)
         return ds
 
@@ -682,13 +680,9 @@ class RelativeReasoning:
 
     def predict(self, X):
         res = np.zeros((len(X), (self.end_index + 1 - self.start_index)))
-        immutable_res = np.zeros((len(X), (self.end_index + 1 - self.start_index)))
 
         # Loop through all instances
         for inst_idx, inst in enumerate(X):
-            for i, t in enumerate(inst[self.start_index : self.end_index + 1]):
-                immutable_res[inst_idx][i] = t
-
             # Loop through all "triggered" features
             for i, t in enumerate(inst[self.start_index : self.end_index + 1]):
                 # Set label
@@ -702,7 +696,7 @@ class RelativeReasoning:
                             if i2 in self.winmap.get(i, []):
                                 # if thatat rule also triggered, it dominated the current
                                 # set label to 0
-                                if immutable_res[inst_idx][i2]:
+                                if X[inst_idx][i2]:
                                     res[inst_idx][i] = 0
 
         return res