[Feature] Management Command to Compute and Store Reaction <-> Rule Associations (#453)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#453

.gitea/workflows/build-image.yaml

@@ -0,0 +1,62 @@
+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

@@ -58,6 +58,10 @@ 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 ./
 
@@ -100,4 +104,5 @@ USER django
 
 EXPOSE 8000
 
-CMD ["gunicorn", "envipath.wsgi:application", "--bind", "0.0.0.0:8000", "--workers", "3"]
+ENTRYPOINT ["/app/entrypoint.sh"]
+CMD ["gunicorn", "envipath.wsgi:application", "--bind", "0.0.0.0:8000", "--workers", "8"]

bridge/contracts.py

@@ -1,4 +1,5 @@
 import enum
+from typing import Any, Dict
 from abc import ABC, abstractmethod
 
 from envipy_additional_information import EnviPyModel
@@ -69,6 +70,12 @@ 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:
@@ -300,6 +307,12 @@ 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

@@ -0,0 +1,9 @@
+#!/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

@@ -340,6 +340,7 @@ DEFAULT_MODEL_PARAMS = {
 DEFAULT_MAX_NUMBER_OF_NODES = 50
 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"

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
-from ..dal import get_scenario_for_read, get_scenario_for_write
+from epdb.models import AdditionalInformation, Scenario, Node
+from ..dal import get_scenario_for_read, get_scenario_for_write, get_package_for_write
 
 logger = logging.getLogger(__name__)
 
@@ -58,6 +58,61 @@ 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.scenarios.all(), key=lambda item: item.pk):
+        for scenario in sorted(node.get_scenarios(), 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(

epdb/legacy_api.py

@@ -46,6 +46,10 @@ from .models import (
 Package = s.GET_PACKAGE_MODEL()
 
 
+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):
@@ -1620,7 +1624,7 @@ 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, str]] = []
+    proposed: List[Dict[str, Any]] = []
     smiles: str = Field(None, alias="smiles")
     pseudo: bool = Field(False, alias="pseudo")
 
@@ -2291,3 +2295,42 @@ 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

@@ -44,7 +44,7 @@ class EPDBURLParser:
     MODEL_PATTERNS = {
         "epdb.User": re.compile(rf"^.*/user/{UUID_PATTERN}"),
         "epdb.Group": re.compile(rf"^.*/group/{UUID_PATTERN}"),
-        "epdb.Package": re.compile(rf"^.*/package/{UUID_PATTERN}"),
+        s.EPDB_PACKAGE_MODEL: 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}"
@@ -94,7 +94,7 @@ class EPDBURLParser:
 
     def contains_package_url(self):
         return (
-            bool(self.MODEL_PATTERNS["epdb.Package"].findall(self.url))
+            bool(self.MODEL_PATTERNS[s.EPDB_PACKAGE_MODEL].findall(self.url))
             and not self.is_package_url()
         )
 
@@ -122,7 +122,7 @@ class EPDBURLParser:
             "epdb.EPModel",
             "epdb.Pathway",
             # 1st level
-            "epdb.Package",
+            s.EPDB_PACKAGE_MODEL,
             "epdb.Setting",
             "epdb.Group",
             "epdb.User",
@@ -144,7 +144,7 @@ class EPDBURLParser:
 
         hierarchy_order = [
             # 1st level
-            "epdb.Package",
+            s.EPDB_PACKAGE_MODEL,
             "epdb.Setting",
             "epdb.Group",
             "epdb.User",
@@ -1805,12 +1805,51 @@ 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
@@ -1831,6 +1870,7 @@ class SPathway(object):
 
             if edge.probability:
                 e["probability"] = edge.probability
+                e["multiGenProbability"] = bayes_probs[edge]
 
             edges.append(e)
 

epdb/management/commands/localize_urls.py

@@ -44,15 +44,19 @@ class Command(BaseCommand):
             "EPModel",
             "ApplicabilityDomain",
             "EnzymeLink",
+            "AdditionalInformation",
         ]
         for model in MODELS:
             obj_cls = apps.get_model("epdb", model)
-            obj_cls.objects.update(
-                url=Replace(F("url"), Value(options["old"]), Value(options["new"]))
+
+            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"])
                 )
+
             if issubclass(obj_cls, EnviPathModel):
-                obj_cls.objects.update(
-                    kv=Cast(
+                update_fields["kv"] = Cast(
                     Replace(
                         Cast(F("kv"), output_field=TextField()),
                         Value(options["old"]),
@@ -60,4 +64,5 @@ class Command(BaseCommand):
                     ),
                     output_field=JSONField(),
                 )
-                )
+
+            obj_cls.objects.update(**update_fields)

epdb/management/commands/reaction_rule_mapping.py

@@ -0,0 +1,97 @@
+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

@@ -0,0 +1,113 @@
+# 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

@@ -0,0 +1,63 @@
+# 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

@@ -0,0 +1,37 @@
+# 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

@@ -854,9 +854,15 @@ 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])
-        ).order_by("name")
+                | Reaction.objects.filter(
+                    package=self.package, products__in=[self.default_structure]
+                )
+            )
+            .distinct()
+            .order_by("name")
+        )
 
     @property
     def related_nodes(self):
@@ -1724,6 +1730,14 @@ 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
 ):
@@ -1749,6 +1763,12 @@ 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)
 
@@ -2162,7 +2182,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
 
             row += [cs.smiles, cs.get_name(), n.depth]
 
-            edges = self.edges.filter(end_nodes__in=[n])
+            edges = self.edges.filter(end_nodes=n)
             if len(edges):
                 for e in edges:
                     _row = row.copy()
@@ -2455,7 +2475,7 @@ 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.scenarios.all()],
+            "scenarios": [{"name": s.get_name(), "url": s.url} for s in self.get_scenarios()],
             "app_domain": {
                 "inside_app_domain": app_domain_data["assessment"]["inside_app_domain"]
                 if app_domain_data
@@ -2574,7 +2594,7 @@ 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
+                collected[str(ai.scenario.uuid)]["Confidence"] = ai.get().level.value
 
             if ai.type == "TransformationProductImportance":
                 collected[str(ai.scenario.uuid)]["Transformation product importance"] = (
@@ -2583,6 +2603,15 @@ 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(
@@ -2838,6 +2867,58 @@ 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"]:
         """
@@ -2994,7 +3075,14 @@ class PackageBasedModel(EPModel):
 
             prec, rec = dict(), dict()
 
-            for t in np.arange(0, 1.05, 0.05):
+            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:
                 temp_thresholded = (y_pred_filtered >= t).astype(int)
                 prec[f"{t:.2f}"] = precision_score(
                     y_test_filtered, temp_thresholded, zero_division=0
@@ -3004,7 +3092,12 @@ class PackageBasedModel(EPModel):
             return acc, prec, rec
 
         def evaluate_mg(model, pathways: Union[QuerySet["Pathway"] | List["Pathway"]], threshold):
-            thresholds = np.arange(0.1, 1.1, 0.1)
+            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()
 
             precision = {f"{t:.2f}": [] for t in thresholds}
             recall = {f"{t:.2f}": [] for t in thresholds}
@@ -3030,7 +3123,7 @@ class PackageBasedModel(EPModel):
 
             s = Setting()
             s.model = mod
-            s.model_threshold = thresholds.min()
+            s.model_threshold = 0.0
             s.max_depth = 10
             s.max_nodes = 50
 
@@ -3054,14 +3147,17 @@ class PackageBasedModel(EPModel):
             for t in thresholds:
                 for true, pred in zip(pathways, pred_pathways):
                     acc, pre, rec = multigen_eval(true, pred, t)
-                    if abs(t - threshold) < 0.01:
-                        mg_acc = acc
+
+                    if f"{t:.2f}" == f"{threshold:.2f}":
+                        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 mg_acc, precision, recall
+            return avg_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:
@@ -4193,6 +4289,9 @@ 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.
@@ -4413,6 +4512,9 @@ 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

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

epdb/views.py

@@ -523,6 +523,7 @@ 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)
 
@@ -1079,13 +1080,17 @@ 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(set(products)),
+                                    "products": list(prod),
                                     "probability": pr.probability,
                                     "btrule": {k: getattr(pr.rule, k) for k in ["url", "name"]}
                                     if pr.rule is not None
@@ -1918,6 +1923,21 @@ 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(".")
 

epiuclid/serializers/pathway_mapper.py

@@ -120,13 +120,6 @@ 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
 
@@ -145,6 +138,16 @@ 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(
@@ -348,7 +351,8 @@ class PathwayMapper:
 
         props = SoilPropertiesData()
 
-        for ai in ai_list:
+        for ai_obj in ai_list:
+            ai = ai_obj.get()
             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

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

epiuclid/tests/test_i6z.py

@@ -7,6 +7,11 @@ 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,
@@ -14,9 +19,24 @@ 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()
@@ -197,3 +217,29 @@ 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), 2)
+        self.assertEqual(len(bundle.substances), 1)
         self.assertEqual(len(bundle.reference_substances), 2)
         self.assertEqual(len(bundle.endpoint_study_records), 1)
 
@@ -49,8 +49,7 @@ class PathwayMapperTest(SimpleTestCase):
         )
         bundle = PathwayMapper().map(export)
 
-        # 2 unique compounds -> 2 substances, 2 ref substances
-        self.assertEqual(len(bundle.substances), 2)
+        self.assertEqual(len(bundle.substances), 1)
         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

@@ -186,6 +186,40 @@ 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/pathway.html

@@ -83,6 +83,19 @@
       <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_additional_information_modal').showModal(); return false;"
+      onclick="document.getElementById('add_scenario_additional_information_modal').showModal(); return false;"
     >
       <i class="glyphicon glyphicon-trash"></i> Add Additional Information</a
     >

templates/batch_predict_pathway.html

@@ -37,7 +37,8 @@
               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 30 rows
+              Name (headers optional) • Maximum
+              {{ batch_predict_max_compoundss|default:150 }} rows
             </div>
           </div>
         </div>
@@ -195,8 +196,7 @@
     // Function to populate table from CSV data
     function populateTableFromCSV(csvData) {
       const lines = csvData.trim().split("\n");
-      const maxRows = 30;
-
+      const maxRows = Number("{{ batch_predict_max_compounds|default:150 }}");
       // Clear existing table
       clearTable();
 

templates/errors/error.html

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

templates/modals/objects/add_scenario_additional_information_modal.html

@@ -1,7 +1,7 @@
 {% load static %}
 <!-- Add Additional Information -->
 <dialog
-  id="add_additional_information_modal"
+  id="add_scenario_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_additional_information_modal').close();
+        document.getElementById('add_scenario_additional_information_modal').close();
         window.location.reload();
       } catch (err) {
         if (err.isValidationError && err.fieldErrors) {

templates/modals/objects/edit_pathway_node_modal.html

@@ -0,0 +1,276 @@
+{% 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/objects/model/_model_base.html

@@ -117,6 +117,39 @@
           </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"][0].join(", ") +
+          data[transformation]["products"].join(", ") +
           "</th>";
         res +=
           "<th scope='row'>" +
           "<img width='400' src='{% url 'depict' %}?smiles=" +
-          encodeURIComponent(data[transformation]["products"][0].join(".")) +
+          encodeURIComponent(data[transformation]["products"].join(".")) +
           "'></th>";
         res +=
           "<th scope='row'>" +
@@ -313,6 +313,44 @@
                 </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 }}</td>
+                            <td>{{ half_lifes.0.model.value }}</td>
                           </tr>
                         </tbody>
                       </table>

templates/objects/pathway.html

@@ -4,6 +4,8 @@
 
 {% 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%;
@@ -97,6 +99,7 @@
     {% 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" %}
@@ -532,7 +535,7 @@
         <input type="checkbox" />
         <div class="collapse-title text-xl font-medium">Setting</div>
         <div class="collapse-content">
-          {% with setting_to_render=pathway.setting can_be_default=False %}
+          {% with setting_to_render=pathway.setting_with_overrides 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_additional_information_modal.html" %}
+    {% include "modals/objects/add_scenario_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

@@ -95,6 +95,7 @@
     </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">
@@ -110,6 +111,7 @@
           {% endfor %}
         </div>
       </div>
+    {% endif %}
   </div>
 
   <script>

tests/test_jobs.py

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

@@ -68,6 +68,8 @@ class PredictionResult(object):
 
 
 class FormatConverter(object):
+    tautomer_enumerator = rdMolStandardize.TautomerEnumerator()
+
     @staticmethod
     def mass(smiles):
         return Descriptors.MolWt(FormatConverter.from_smiles(smiles))
@@ -240,8 +242,9 @@ class FormatConverter(object):
             Chem.RemoveStereochemistry(res_mol)
 
         if canonicalize_tautomers:
-            te = rdMolStandardize.TautomerEnumerator()  # idem
-            res_mol = te.Canonicalize(res_mol)
+            tautomers = FormatConverter.tautomer_enumerator.Enumerate(res_mol)
+            if len(tautomers) >= 1:
+                res_mol = FormatConverter.tautomer_enumerator.PickCanonical(tautomers)
 
         return Chem.MolToSmiles(res_mol, kekuleSmiles=True)
 
@@ -389,7 +392,7 @@ class FormatConverter(object):
                                 prods.append(p)
 
                         except ValueError as e:
-                            logger.error(f"Sanitizing and converting failed:\n{e}")
+                            logger.debug(f"Sanitizing and converting failed:\n{e}")
                             continue
 
                     if len(prods):
@@ -397,7 +400,8 @@ class FormatConverter(object):
                         pss.add(ps)
 
         except Exception as e:
-            logger.error(f"Applying {smirks} on {smiles} failed:\n{e}")
+            logger.debug(f"Applying {smirks} on {smiles} failed:\n{e}")
+            pass
 
         return list(pss)
 
@@ -444,6 +448,7 @@ 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.
@@ -482,9 +487,11 @@ class FormatConverter(object):
         if standardize:
             for smi in l_smiles:
                 try:
-                    smi = FormatConverter.standardize(
+                    smi = FormatConverter.canonicalize(
+                        FormatConverter.standardize(
                             smi, remove_stereo=True, canonicalize_tautomers=canonicalize_tautomers
                         )
+                    )
                 except Exception:
                     # :shrug:
                     # logger.debug(f'Standardizing SMILES failed for {smi}')
@@ -497,8 +504,12 @@ class FormatConverter(object):
         if standardize:
             for smi in r_smiles:
                 try:
-                    smi = FormatConverter.standardize(
-                        smi, remove_stereo=True, canonicalize_tautomers=canonicalize_tautomers
+                    smi = FormatConverter.canonicalize(
+                        FormatConverter.standardize(
+                            smi,
+                            remove_stereo=True,
+                            canonicalize_tautomers=canonicalize_tautomers,
+                        )
                     )
                 except Exception:
                     # :shrug:
@@ -507,8 +518,11 @@ 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)
 
 
 class Standardizer(ABC):

utilities/misc.py

@@ -4,11 +4,13 @@ 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
+from typing import Any, Dict, List, Optional, TYPE_CHECKING, Type
 
 from django.conf import settings as s
+from envipy_additional_information import EnviPyModel, UIConfig
 from ninja import Schema
 from pydantic import HttpUrl, ValidationError
 
@@ -132,7 +134,7 @@ class EnzymeExportSchema(RefEnzymeExportSchema):
 
 
 class EnzymeRuleExportSchema(RefRuleExportSchema):
-    enzymes: List[EnzymeExportSchema] | None = None
+    enzymes: List[EnzymeExportSchema] = []
 
     @staticmethod
     def resolve_enzymes(obj):
@@ -277,15 +279,20 @@ class PackageExportSchema(Schema):
         return AdditionalInformation.objects.filter(package=obj)
 
 
-class PackageExporter:
+class Exporter(ABC):
     def __init__(self, package: Package):
         self._raw_package = package
 
     def do_export(self):
-        return PackageExporter._export_package_as_json(self._raw_package)
+        return self._export()
 
-    @staticmethod
-    def _export_package_as_json(package: Package) -> Dict[str, Any]:
+    @abstractmethod
+    def _export(self):
+        pass
+
+
+class PackageExporter(Exporter):
+    def _export(self) -> Dict[str, Any]:
         """
         Dumps a Package and all its related objects as JSON.
 
@@ -296,11 +303,126 @@ class PackageExporter:
             Dict containing the complete package data as JSON-serializable structure
         """
 
-        data = PackageExportSchema.from_orm(package)
+        data = PackageExportSchema.from_orm(self._raw_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

@@ -238,9 +238,11 @@ class RuleBasedDataset(Dataset):
     ):
         if feat_funcs is None:
             feat_funcs = [FormatConverter.maccs]
-        _structures = set()  # Get all the structures
+
+        _structures = set()
         for r in reactions:
             _structures.update(r.educts.all())
+
             if not educts_only:
                 _structures.update(r.products.all())
 
@@ -282,17 +284,14 @@ class RuleBasedDataset(Dataset):
                     if key not in triggered:
                         continue
 
-                    # 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:
+                    if FormatConverter.smiles_covered_by(
+                        [prod.smiles for prod in r.products.all()],
+                        list(triggered[key]),
+                        standardize=True,
+                        canonicalize_tautomers=True,
+                    ):
                         observed.add(key)
+
         feat_columns = []
         for feat_func in feat_funcs:
             if isinstance(feat_func, Descriptor):
@@ -301,6 +300,7 @@ 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
@@ -334,7 +334,9 @@ 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
 
@@ -680,9 +682,13 @@ 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
@@ -696,7 +702,7 @@ class RelativeReasoning:
                             if i2 in self.winmap.get(i, []):
                                 # if thatat rule also triggered, it dominated the current
                                 # set label to 0
-                                if X[inst_idx][i2]:
+                                if immutable_res[inst_idx][i2]:
                                     res[inst_idx][i] = 0
 
         return res