model stats

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

bayer/templates/modals/collections/new_package_modal.html

@@ -131,8 +131,9 @@
             id="package-data-pool"
             name="package-data-pool"
             class="select select-bordered w-full"
+            :required="isSecret"
           >
-            <option value="" disabled selected>Select Data Pool</option>
+            <option value="" disabled>Select Data Pool</option>
               {% for obj in meta.secret_groups %}
                 <option value="{{ obj.url }}">{{ obj.name|safe }}</option>
               {% endfor %}

envipath/settings.py

@@ -357,6 +357,7 @@ 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"

epauth/views.py

@@ -1,3 +1,5 @@
+import logging
+
 import msal
 from django.conf import settings as s
 from django.contrib.auth import get_user_model
@@ -7,6 +9,9 @@ from django.shortcuts import redirect
 
 from epdb.logic import UserManager, GroupManager
 from epdb.models import Group
+from epdb.views import get_remote_address
+
+auth_log = logging.getLogger("auth")
 
 
 def get_msal_app_with_cache(request):
@@ -30,6 +35,9 @@ 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,
@@ -54,6 +62,10 @@ 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()
@@ -61,7 +73,8 @@ def entra_callback(request):
     claims = result["id_token_claims"]
 
     user_name = claims.get("name")
-    user_email = claims.get("emailaddress", claims.get("email"))
+    # preferred_username is a fallback for 2nd CWID
+    user_email = claims.get("emailaddress", claims.get("email", claims.get("preferred_username")))
     user_oid = claims.get("oid")
 
     if not all([user_name, user_email, user_oid]):
@@ -70,6 +83,7 @@ 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)
 
@@ -78,8 +92,11 @@ 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
@@ -102,10 +119,31 @@ def entra_callback(request):
         else:
             g = Group.objects.get(uuid=id)
 
-    for group_uuid in claims.get("groups", []):
+    sync_groups = list(s.ENTRA_GROUPS.keys()) + list(s.ENTRA_SECRET_GROUPS.keys())
-        if Group.objects.filter(uuid=group_uuid).exists():
+    user_groups = claims.get("groups", [])
-            g = Group.objects.get(uuid=group_uuid)
+
-            g.user_member.add(u)
+    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
+                u.data_pool = group
+                u.classification_level = u.Classification.SECRET
+                u.save()
 
     # EDIT END
 

epdb/legacy_api.py

@@ -1,3 +1,4 @@
+import logging
 from collections import defaultdict
 from typing import Any, Dict, List, Optional
 
@@ -9,13 +10,11 @@ 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,
@@ -46,9 +45,12 @@ 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"""
@@ -116,15 +118,22 @@ 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
 
-        request.user = User.objects.get(uuid=claims['oid'])
+        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)}")
         return request.user
 
 
@@ -558,7 +567,10 @@ def update_package(request, package_uuid, pack: Form[UpdatePackage]):
 
         if pack.hiddenMethod:
             if pack.hiddenMethod == "DELETE":
-                p.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!")
 
         elif pack.packageDescription is not None:
             description = nh3.clean(pack.packageDescription, tags=s.ALLOWED_HTML_TAGS).strip()
@@ -595,7 +607,7 @@ def delete_package(request, package_uuid):
         p = PackageManager.get_package_by_id(request.user, package_uuid)
 
         if PackageManager.administrable(request.user, p):
-            p.delete()
+            delete_with_log(request, p)
             return redirect(f"{s.SERVER_URL}/package")
         else:
             raise ValueError("You do not have the rights to delete this Package!")
@@ -881,12 +893,11 @@ def create_package_compound(
             if "secret" == classification.lower():
 
                 if p.classification_level != Package.Classification.SECRET:
-                    return 400, {"Cannot create PESs for non-secret packages."}
+                    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."}
 
-                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:
@@ -1877,7 +1888,7 @@ 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)
-        pw.delete()
+        delete_with_log(request, pw)
         return redirect(f"{p.url}/pathway")
 
     except ValueError:
@@ -2055,7 +2066,7 @@ 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)
-        n.delete()
+        delete_with_log(request, n)
         return redirect(f"{pw.url}/node")
 
     except ValueError:
@@ -2215,7 +2226,7 @@ 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)
-        e.delete()
+        delete_with_log(request, e)
         return redirect(f"{pw.url}/edge")
 
     except ValueError:

epdb/logic.py

@@ -35,6 +35,7 @@ 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()
 
@@ -45,7 +46,7 @@ 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}"
@@ -95,7 +96,7 @@ 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()
         )
 
@@ -123,7 +124,7 @@ class EPDBURLParser:
             "epdb.EPModel",
             "epdb.Pathway",
             # 1st level
-            "epdb.Package",
+            s.EPDB_PACKAGE_MODEL,
             "epdb.Setting",
             "epdb.Group",
             "epdb.User",
@@ -145,7 +146,7 @@ class EPDBURLParser:
 
         hierarchy_order = [
             # 1st level
-            "epdb.Package",
+            s.EPDB_PACKAGE_MODEL,
             "epdb.Setting",
             "epdb.Group",
             "epdb.User",
@@ -316,13 +317,19 @@ 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}) to  {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}) adds {member.username} ({member.url}) to  {group.name} ({group.url})")
 
         group.save()
 
@@ -578,9 +585,11 @@ 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)
@@ -589,11 +598,23 @@ 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])
@@ -1875,12 +1896,51 @@ 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
@@ -1901,6 +1961,7 @@ class SPathway(object):
 
             if edge.probability:
                 e["probability"] = edge.probability
+                e["multiGenProbability"] = bayes_probs[edge]
 
             edges.append(e)
 

epdb/models.py

@@ -2815,6 +2815,21 @@ class PackageBasedModel(EPModel):
     )
     multigen_eval = models.BooleanField(null=False, blank=False, default=False)
 
+    def statistics(self):
+        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}")
+            ],
+        }
+
     @property
     def pr_curve(self):
         if self.model_status != self.FINISHED:
@@ -3014,7 +3029,14 @@ 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
@@ -3024,7 +3046,14 @@ 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()
+
+            logger.info(f"Thresholds: {thresholds}")
 
             precision = {f"{t:.2f}": [] for t in thresholds}
             recall = {f"{t:.2f}": [] for t in thresholds}
@@ -3050,7 +3079,7 @@ 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
 

epdb/views.py

@@ -61,6 +61,7 @@ from .models import (
 )
 
 logger = logging.getLogger(__name__)
+auth_log = logging.getLogger("auth")
 
 Package = s.GET_PACKAGE_MODEL()
 
@@ -71,6 +72,18 @@ 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)
 
@@ -147,6 +160,20 @@ 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)
 
@@ -205,11 +232,18 @@ 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:
@@ -390,7 +424,7 @@ 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),
+            "secret_groups": Group.objects.filter(secret=True, user_member=current_user),
             # EDIT END
         },
     }
@@ -526,6 +560,7 @@ 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)
 
@@ -1281,7 +1316,8 @@ 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.",
                     )
 
-                logger.debug(current_package.delete())
+                delete_with_log(request, current_package)
+
                 return redirect(s.SERVER_URL + "/package")
             elif hidden == "publish-package":
                 for g in Group.objects.filter(public=True):
@@ -1949,6 +1985,21 @@ 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(".")
 
@@ -2257,7 +2308,7 @@ def package_pathway(request, package_uuid, pathway_uuid):
     elif request.method == "POST":
         if hidden := request.POST.get("hidden", None):
             if hidden == "delete":
-                current_pathway.delete()
+                delete_with_log(request, current_pathway)
                 return redirect(current_package.url + "/pathway")
             else:
                 return HttpResponseBadRequest()
@@ -2475,7 +2526,7 @@ 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
-                current_node.delete()
+                delete_with_log(request, current_node)
 
                 return redirect(current_pathway.url)
             else:
@@ -2629,7 +2680,7 @@ def package_pathway_edge(request, package_uuid, pathway_uuid, edge_uuid):
 
         if hidden := request.POST.get("hidden", None):
             if hidden == "delete":
-                current_edge.delete()
+                delete_with_log(request, current_edge)
                 return redirect(current_pathway.url)
 
         if "selected-scenarios" in request.POST:
@@ -2991,7 +3042,7 @@ def group(request, group_uuid):
 
         if hidden := request.POST.get("hidden", None):
             if hidden == "delete":
-                current_group.delete()
+                delete_with_log(request, current_group)
                 return redirect(s.SERVER_URL + "/group")
             else:
                 return HttpResponseBadRequest()

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(

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), 4)
-            self.assertEqual(len(i6d_files), 5)
 
     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), 1)
-        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)

templates/actions/objects/package.html

@@ -15,6 +15,7 @@
       <i class="glyphicon glyphicon-user"></i> Edit Permissions</a
     >
   </li>
+  {% if meta.current_package.get_classification_level_display != "Secret" %}
   <li>
     <a
       role="button"
@@ -23,6 +24,7 @@
       <i class="glyphicon glyphicon-bullhorn"></i> Publish Package</a
     >
   </li>
+  {% endif %}
 {% endif %}
   <li>
     <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/components/navbar.html

@@ -105,6 +105,11 @@
           <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="200">
+
         {% endif %}
         {% if not public_mode %}
           <a id="search-trigger" role="button" class="cursor-pointer">

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/objects/model/classification_model.html

@@ -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) {