[Feature] Integrate DOI Links, Handle Cycles in Pathway Viz (#407)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#407

Dockerfile

@@ -36,11 +36,13 @@ RUN --mount=type=ssh \
 
 # Now copy source and do a final sync to install the project itself
 # Ensure .dockerignore is reasonable
+COPY biotransformer biotransformer
 COPY bridge bridge
 COPY envipath envipath
 COPY epapi epapi
 COPY epauth epauth
 COPY epdb epdb
+COPY epiuclid epiuclid
 COPY fixtures fixtures
 COPY migration migration
 COPY pepper pepper

envipath/urls.py

@@ -40,6 +40,9 @@ if "migration" in s.INSTALLED_APPS:
 if s.MS_ENTRA_ENABLED:
     urlpatterns.append(path(f"{PATH_PREFIX}", include("epauth.urls")))
 
+if s.TENANT != "public":
+    urlpatterns.append(path(f"{PATH_PREFIX}", include(f"{s.TENANT}.urls")))
+
 # Custom error handlers
 handler400 = "epdb.views.handler400"
 handler403 = "epdb.views.handler403"

epapi/v1/endpoints/joblogs.py

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

epapi/v1/router.py

@@ -15,6 +15,7 @@ from .endpoints import (
     additional_information,
     settings,
     groups,
+    joblogs,
 )
 
 # Main router with authentication
@@ -37,6 +38,7 @@ router.add_router("", structure.router)
 router.add_router("", additional_information.router)
 router.add_router("", settings.router)
 router.add_router("", groups.router)
+router.add_router("", joblogs.router)
 
 if s.IUCLID_EXPORT_ENABLED:
     from epiuclid.api import router as iuclid_router

epapi/v1/schemas.py

@@ -1,7 +1,10 @@
-from ninja import FilterSchema, FilterLookup, Schema
+from datetime import datetime
 from typing import Annotated, Optional, List, Dict, Any
 from uuid import UUID
 
+from django.urls import reverse
+from ninja import Field, FilterSchema, FilterLookup, Schema
+
 
 # Filter schema for query parameters
 class ReviewStatusFilter(FilterSchema):
@@ -133,3 +136,23 @@ class GroupOutSchema(Schema):
     url: str = ""
     name: str
     description: str
+
+
+class SimpleUserOutSchema(Schema):
+    uuid: UUID
+    url: str
+    name: str = Field(alias="username")
+
+
+class JobLogOutSchema(Schema):
+    user: SimpleUserOutSchema
+    id: UUID = Field(alias="task_id")
+    url: str
+    name: str = Field(alias="job_name")
+    created: datetime = Field(alias="created")
+    status: str = Field(alias="status")
+    done: Optional[datetime] = Field(None, alias="done_at")
+
+    @staticmethod
+    def resolve_url(obj):
+        return reverse("job detail", kwargs={"job_uuid": obj.task_id})

epauth/views.py

@@ -1,12 +1,32 @@
 import msal
 from django.conf import settings as s
+from django.contrib.auth import get_user_model
 from django.contrib.auth import login
 from django.shortcuts import redirect
-from django.contrib.auth import get_user_model
 
 from epdb.logic import UserManager
 
 
+def get_msal_app_with_cache(request):
+    """
+    Create MSAL app with session-based token cache.
+    """
+    cache = msal.SerializableTokenCache()
+
+    # Load cache from session if it exists
+    if request.session.get("msal_token_cache"):
+        cache.deserialize(request.session["msal_token_cache"])
+
+    msal_app = msal.ConfidentialClientApplication(
+        client_id=s.MS_ENTRA_CLIENT_ID,
+        client_credential=s.MS_ENTRA_CLIENT_SECRET,
+        authority=s.MS_ENTRA_AUTHORITY,
+        token_cache=cache,
+    )
+
+    return msal_app, cache
+
+
 def entra_login(request):
     msal_app = msal.ConfidentialClientApplication(
         client_id=s.MS_ENTRA_CLIENT_ID,
@@ -23,11 +43,7 @@ def entra_login(request):
 
 
 def entra_callback(request):
-    msal_app = msal.ConfidentialClientApplication(
-        client_id=s.MS_ENTRA_CLIENT_ID,
-        client_credential=s.MS_ENTRA_CLIENT_SECRET,
-        authority=s.MS_ENTRA_AUTHORITY,
-    )
+    msal_app, cache = get_msal_app_with_cache(request)
 
     flow = request.session.pop("msal_auth_flow", None)
     if not flow:
@@ -36,11 +52,18 @@ def entra_callback(request):
     # Acquire token using the flow and callback request
     result = msal_app.acquire_token_by_auth_code_flow(flow, request.GET)
 
+    # Save the token cache to session
+    if cache.has_state_changed:
+        request.session["msal_token_cache"] = cache.serialize()
+
     claims = result["id_token_claims"]
 
-    user_name = claims["name"]
-    user_email = claims["emailaddress"]
-    user_oid = claims["oid"]
+    user_name = claims.get("name")
+    user_email = claims.get("emailaddress", claims.get("email"))
+    user_oid = claims.get("oid")
+
+    if not all([user_name, user_email, user_oid]):
+        raise ValueError("Missing required claims in ID token")
 
     # Get implementing class
     User = get_user_model()
@@ -57,4 +80,51 @@ def entra_callback(request):
 
     login(request, u)
 
-    return redirect("/")  # Handle errors
+    return redirect(s.SERVER_URL)  # Handle errors
+
+
+def get_access_token_from_request(request, scopes=None):
+    """
+    Get an access token from the request using MSAL token cache.
+    """
+    if scopes is None:
+        scopes = s.MS_ENTRA_SCOPES
+
+    # Get user from request (must be authenticated)
+    if not request.user.is_authenticated:
+        return None
+
+    # Create MSAL app with persistent cache
+    msal_app, cache = get_msal_app_with_cache(request)
+
+    # Try to get accounts from cache
+    accounts = msal_app.get_accounts()
+
+    if not accounts:
+        return None
+
+    # Find the account that matches the current user
+    user_account = None
+    for account in accounts:
+        if account.get("local_account_id") == str(request.user.uuid):
+            user_account = account
+            break
+
+    # If no matching account found, use the first available account
+    if not user_account and accounts:
+        user_account = accounts[0]
+
+    if not user_account:
+        return None
+
+    # Try to acquire token silently from cache
+    result = msal_app.acquire_token_silent(scopes=scopes, account=user_account)
+
+    # Save cache changes back to session
+    if cache.has_state_changed:
+        request.session["msal_token_cache"] = cache.serialize()
+
+    if result and "access_token" in result:
+        return result
+
+    return None

epdb/admin.py

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

epdb/legacy_api.py

@@ -386,23 +386,50 @@ class PackageSchema(Schema):
 
     @staticmethod
     def resolve_readers(obj: Package):
-        users = User.objects.filter(
-            id__in=UserPackagePermission.objects.filter(
-                package=obj, permission=UserPackagePermission.READ[0]
-            ).values_list("user", flat=True)
-        ).distinct()
+        readers = []
 
-        return [{u.id: u.get_name()} for u in users]
+        user_ids = UserPackagePermission.objects.filter(package=obj).values_list("user", flat=True)
+
+        users = User.objects.filter(id__in=user_ids).distinct()
+
+        for u in users:
+            readers.append({"id": str(u.url), "identifier": "user", "name": u.get_name()})
+
+        group_ids = GroupPackagePermission.objects.filter(package=obj).values_list(
+            "group", flat=True
+        )
+
+        groups = Group.objects.filter(id__in=group_ids).distinct()
+
+        for g in groups:
+            readers.append({"id": str(g.url), "identifier": "group", "name": g.get_name()})
+
+        return readers
 
     @staticmethod
     def resolve_writers(obj: Package):
-        users = User.objects.filter(
-            id__in=UserPackagePermission.objects.filter(
-                package=obj, permission=UserPackagePermission.WRITE[0]
-            ).values_list("user", flat=True)
-        ).distinct()
+        writers = []
 
-        return [{u.id: u.get_name()} for u in users]
+        user_ids = UserPackagePermission.objects.filter(
+            package=obj,
+            permission__in=[UserPackagePermission.WRITE[0], UserPackagePermission.ALL[0]],
+        ).values_list("user", flat=True)
+
+        users = User.objects.filter(id__in=user_ids).distinct()
+
+        for u in users:
+            writers.append({"id": str(u.url), "identifier": "user", "name": u.get_name()})
+
+        group_ids = GroupPackagePermission.objects.filter(
+            package=obj, permission=[UserPackagePermission.WRITE[0], UserPackagePermission.ALL[0]]
+        ).values_list("group", flat=True)
+
+        groups = Group.objects.filter(id__in=group_ids).distinct()
+
+        for g in groups:
+            writers.append({"id": str(g.url), "identifier": "group", "name": g.get_name()})
+
+        return writers
 
     @staticmethod
     def resolve_review_comment(obj):
@@ -799,6 +826,27 @@ def delete_compound(request, package_uuid, compound_uuid):
         }
 
 
+class CreateCompoundStructure(Schema):
+    smiles: str
+    name: str | None = None
+    description: str | None = None
+    inchi: str | None = None
+    molfile: str | None = None
+
+
+@router.post("/package/{uuid:package_uuid}/compound/{uuid:compound_uuid}/structure")
+def create_package_compound_structure(
+    request, package_uuid, compound_uuid, structure: Form[CreateCompoundStructure]
+):
+    try:
+        p = get_package_for_write(request.user, package_uuid)
+        c = Compound.objects.get(package=p, uuid=compound_uuid)
+        cs = CompoundStructure.create(c, structure.smiles, structure.name, structure.description)
+        return redirect(cs.url)
+    except ValueError as e:
+        return 400, {"message": str(e)}
+
+
 @router.delete(
     "/package/{uuid:package_uuid}/compound/{uuid:compound_uuid}/structure/{uuid:structure_uuid}"
 )
@@ -1325,6 +1373,7 @@ class ScenarioSchema(Schema):
     aliases: List[str] = Field([], alias="aliases")
     collection: Dict["str", List[Dict[str, Any]]] = Field([], alias="collection")
     collectionID: Optional[str] = None
+    date: str = Field(None, alias="scenario_date")
     description: str = Field(None, alias="description")
     id: str = Field(None, alias="url")
     identifier: str = "scenario"
@@ -1468,6 +1517,7 @@ def create_package_additional_information(request, package_uuid):
         scen = request.POST.get("scenario")
         scenario = Scenario.objects.get(package=p, url=scen)
 
+        if request.POST.get("adInfoTypes[]"):
             url_parser = EPDBURLParser(request.POST.get("attach_obj"))
             attach_obj = url_parser.get_object()
 
@@ -1491,6 +1541,33 @@ def create_package_additional_information(request, package_uuid):
                     content_object=attach_obj,
                 )
 
+        elif request.POST.get("ais"):
+            import json
+
+            parsed_ais = json.loads(request.POST.get("ais"))
+
+            for ai_type, ais in parsed_ais.items():
+                for ai in ais:
+                    attach_obj = None
+                    if ai.get("related"):
+                        url_parser = EPDBURLParser(ai.get("related").get("url"))
+                        attach_obj = url_parser.get_object()
+
+                        if not hasattr(attach_obj, "additional_information"):
+                            raise ValueError("Can't attach additional information to this object!")
+
+                        if not attach_obj.url.startswith(p.url):
+                            raise ValueError(
+                                "Additional Information can only be set to objects stored in the same package!"
+                            )
+
+                    AdditionalInformation.create(
+                        p,
+                        AdditionalInformation.from_dict(ai_type, ai),
+                        scenario=scenario,
+                        content_object=attach_obj,
+                    )
+
         # TODO implement additional information endpoint ?
         return redirect(f"{scenario.url}")
     except ValueError:
@@ -1540,6 +1617,7 @@ class PathwayNode(Schema):
     name: str = Field(None, alias="name")
     proposed: List[Dict[str, str]] = Field([], alias="proposed_intermediate")
     smiles: str = Field(None, alias="default_node_label.smiles")
+    pseudo: bool = Field(False, alias="pseudo")
 
     @staticmethod
     def resolve_atom_count(obj: Node):
@@ -1693,6 +1771,29 @@ def create_package_pathway(
         return 403, {"message": str(e)}
 
 
+@router.post("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}")
+def update_pathway(request, package_uuid, pathway_uuid):
+    try:
+        p = get_package_for_write(request.user, package_uuid)
+
+        if request.POST.get("scenario"):
+            pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
+            scen = Scenario.objects.get(package=p, url=request.POST.get("scenario"))
+
+            pw.scenarios.add(scen)
+            pw.save()
+
+            return redirect(f"{pw.url}")
+
+        else:
+            return 400, {"message": "No scenario specified!"}
+
+    except ValueError:
+        return 403, {
+            "message": f"Deleting Pathway with id {pathway_uuid} failed due to insufficient rights!"
+        }
+
+
 @router.delete("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}")
 def delete_pathway(request, package_uuid, pathway_uuid):
     try:
@@ -1813,7 +1914,7 @@ def add_pathway_node(request, package_uuid, pathway_uuid, n: Form[CreateNode]):
         pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
 
         if n.nodeDepth is not None and n.nodeDepth.strip() != "":
-            node_depth = int(n.nodeDepth)
+            node_depth = int(float(n.nodeDepth))
         else:
             node_depth = -1
 
@@ -1958,6 +2059,10 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
             for pr in e.products.split(","):
                 products.append(Node.objects.get(pathway=pw, url=pr.strip()))
 
+        multi_step = False
+        if e.multistep and e.multistep.strip() == "true":
+            multi_step = True
+
         new_e = Edge.create(
             pathway=pw,
             start_nodes=educts,
@@ -1965,11 +2070,15 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
             rule=None,
             name=None,
             description=e.edgeReason,
+            multi_step=multi_step,
         )
 
+        # Update depths as sideeffect of above operation
+        pw.update_depths()
+
         return redirect(new_e.url)
     except ValueError:
-        return 403, {"message": "Adding node failed!"}
+        return 403, {"message": "Adding Edge failed!"}
 
 
 @router.delete("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}/edge/{uuid:edge_uuid}")

epdb/logic.py

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

epdb/migrations/0023_alter_compoundstructure_options_and_more.py

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

epdb/migrations/0024_user_contacted.py

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

epdb/migrations/0025_auto_20260511_2025.py

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

epdb/migrations/0026_auto_20260602_1718.py

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

epdb/models.py

@@ -75,6 +75,7 @@ class User(AbstractUser):
         blank=False,
     )
     is_reviewer = models.BooleanField(default=False)
+    contacted = models.BooleanField(null=True, blank=True)
 
     USERNAME_FIELD = "email"
     REQUIRED_FIELDS = ["username"]
@@ -1112,6 +1113,7 @@ class CompoundStructure(
     canonical_smiles = models.TextField(blank=False, null=False, verbose_name="Canonical SMILES")
     inchikey = models.TextField(max_length=27, blank=False, null=False, verbose_name="InChIKey")
     normalized_structure = models.BooleanField(null=False, blank=False, default=False)
+    molfile = models.TextField(blank=True, null=True, verbose_name="Molfile")
 
     external_identifiers = GenericRelation("ExternalIdentifier")
 
@@ -1208,6 +1210,9 @@ class CompoundStructure(
 
         return dict(hls)
 
+    def d3_json(self):
+        return {}
+
 
 class EnzymeLink(EnviPathModel, KEGGIdentifierMixin):
     rule = models.ForeignKey("Rule", on_delete=models.CASCADE, db_index=True)
@@ -1690,7 +1695,7 @@ class Reaction(
         if name is not None and name.strip() != "":
             r.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
 
-        if description is not None and name.strip() != "":
+        if description is not None and description.strip() != "":
             r.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
         r.multi_step = multi_step
@@ -1768,7 +1773,7 @@ class Reaction(
         return new_reaction
 
     def smirks(self):
-        return f"{'.'.join([cs.smiles for cs in self.educts.all()])}>>{'.'.join([cs.smiles for cs in self.products.all()])}"
+        return f"{'.'.join([cs.smiles for cs in self.educts.all().order_by('-pk')])}>>{'.'.join([cs.smiles for cs in self.products.all().order_by('-pk')])}"
 
     @property
     def as_svg(self):
@@ -1881,6 +1886,9 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                 if n not in queue:
                     queue.append(n)
 
+        for i in queue:
+            processed.add(i)
+
         while len(queue):
             current = queue.pop()
             processed.add(current)
@@ -2173,6 +2181,50 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
     ):
         return Edge.create(self, start_nodes, end_nodes, rule, name=name, description=description)
 
+    def update_depths(self):
+        # Collect number of in and out links per node
+        in_count = defaultdict(lambda: 0)
+        out_count = defaultdict(lambda: 0)
+
+        for e in self.edges:
+            for react in e.start_nodes.all():
+                out_count[str(react.uuid)] += 1
+
+            for prod in e.end_nodes.all():
+                in_count[str(prod.uuid)] += 1
+
+        depth_map = {}
+        depth_map[0] = list()
+        processed = set()
+
+        for n in self.root_nodes:
+            depth_map[0].append(n)
+
+        # At most depth len(nodes) is possible
+        for i in range(self.nodes.count()):
+            level_nodes = depth_map.get(i, [])
+
+            if len(level_nodes) == 0:
+                break
+
+            unique_next_level = set()
+            for n in level_nodes:
+                processed.add(n)
+                for e in self.edges:
+                    if n in e.start_nodes.all():
+                        for p in e.end_nodes.all():
+                            if p not in processed:
+                                unique_next_level.add(p)
+
+            if len(unique_next_level) > 0:
+                depth_map[i + 1] = list(unique_next_level)
+
+        for depth, nodes in depth_map.items():
+            for n in nodes:
+                if n.depth != depth and depth != 0:
+                    n.depth = depth
+                    n.save()
+
 
 class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin):
     pathway = models.ForeignKey(
@@ -2214,7 +2266,11 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             if isinstance(ai.get(), PropertyPrediction):
                 predicted_properties[ai.get().__class__.__name__].append(ai.data)
 
-        return {
+        # If we have Subclasses of a CompoundStructure we can overwrite keys (e.g. images)
+        # by overwriting keys
+        structure_data = self.default_node_label.d3_json()
+
+        res = {
             "depth": self.depth,
             "stereo_removed": self.stereo_removed,
             "url": self.url,
@@ -2223,6 +2279,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             "image_svg": IndigoUtils.mol_to_svg(
                 self.default_node_label.smiles, width=40, height=40
             ),
+            "image_type": "svg",
             "name": self.get_name(),
             "smiles": self.default_node_label.smiles,
             "scenarios": [{"name": s.get_name(), "url": s.url} for s in self.scenarios.all()],
@@ -2235,8 +2292,11 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             "predicted_properties": predicted_properties,
             "is_engineered_intermediate": self.kv.get("is_engineered_intermediate", False),
             "timeseries": self.get_timeseries_data(),
+            **structure_data,
         }
 
+        return res
+
     @staticmethod
     @transaction.atomic
     def create(
@@ -2392,6 +2452,8 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
         rule: Optional[Rule] = None,
         name: Optional[str] = None,
         description: Optional[str] = None,
+        *args,
+        **kwargs,
     ):
         e = Edge()
         e.pathway = pathway
@@ -2421,7 +2483,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             educts=[n.default_node_label for n in e.start_nodes.all()],
             products=[n.default_node_label for n in e.end_nodes.all()],
             rules=rule,
-            multi_step=False,
+            multi_step=kwargs.get("multi_step", False),
         )
 
         e.edge_label = r
@@ -4429,18 +4491,22 @@ class AdditionalInformation(models.Model):
 
         return f"{self.scenario.url}/additional-information/{self.uuid}"
 
-    def get(self) -> "EnviPyModel":
+    @staticmethod
+    def from_dict(ai_type: str, ai_data: Dict[str, Any]):
         from envipy_additional_information import registry
 
         MAPPING = {c.__name__: c for c in registry.list_models().values()}
         try:
-            inst = MAPPING[self.type](**self.data)
+            inst = MAPPING[ai_type](**ai_data)
         except Exception as e:
-            print(f"Error loading {self.type}: {e}")
+            print(f"Error loading {ai_type}: {e}")
             raise e
 
-        inst.__dict__["uuid"] = str(self.uuid)
+        return inst
 
+    def get(self) -> "EnviPyModel":
+        inst = AdditionalInformation.from_dict(self.type, self.data)
+        inst.__dict__["uuid"] = str(self.uuid)
         return inst
 
     def __str__(self) -> str:

epdb/views.py

@@ -2506,6 +2506,9 @@ def package_pathway_edges(request, package_uuid, pathway_uuid):
             substrate_nodes, product_nodes, name=edge_name, description=edge_description
         )
 
+        # Update depths as sideeffect of above operation
+        current_pathway.update_depths()
+
         return redirect(current_pathway.url)
 
     else:
@@ -3077,12 +3080,21 @@ def jobs(request):
             {"Home": s.SERVER_URL},
             {"Jobs": s.SERVER_URL + "/jobs"},
         ]
-        if current_user.is_superuser:
-            context["jobs"] = JobLog.objects.all().order_by("-created")
-        else:
-            context["jobs"] = JobLog.objects.filter(user=current_user).order_by("-created")
+        # if current_user.is_superuser:
+        #     context["jobs"] = JobLog.objects.all().order_by("-created")
+        # else:
+        #     context["jobs"] = JobLog.objects.filter(user=current_user).order_by("-created")
 
-        return render(request, "collections/joblog.html", context)
+        # Context for paginated template
+        context["entity_type"] = "joblog"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/joblog/"
+        context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
+        context["list_title"] = "joblog"
+        context["list_mode"] = "combined"
+
+        return render(request, "collections/joblog_paginated.html", context)
+
+        # return render(request, "collections/joblog.html", context)
 
     elif request.method == "POST":
         job_name = request.POST.get("job-name")

pepper/__init__.py

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

pepper/impl/pepper.py

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

static/js/alpine/components/widgets.js

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

static/js/pw.js

@@ -463,7 +463,7 @@ function draw(pathway, elem) {
                     // TODO needs to be generic once we store it as AddInf
                     for (var s of n.predicted_properties["PepperPrediction"]) {
                         if (s["mean"] != null) {
-                            tempContent += "<b>DT50 predicted via Pepper:</b> " + s["mean"].toFixed(2) + "<br>"
+                            tempContent += "<b>DT50 predicted via Pepper:</b> " + s["mean"].toFixed(2) + " days<br>"
                         }
                     }
                 }
@@ -581,11 +581,11 @@ function draw(pathway, elem) {
         for (idx in parents) {
             p = nodes[parents[idx]]
             // console.log(p.depth)
-            if (p.depth >= n.depth) {
-                // keep the .5 steps for pseudo nodes
-                n.depth = n.pseudo ? p.depth + 1 : Math.floor(p.depth + 1);
-                // console.log("Adjusting", orig_depth, Math.floor(p.depth + 1));
-            }
+            // if (p.depth >= n.depth) {
+            //     // keep the .5 steps for pseudo nodes
+            //     n.depth = n.pseudo ? p.depth + 1 : Math.floor(p.depth + 1);
+            //     // console.log("Adjusting", orig_depth, Math.floor(p.depth + 1));
+            // }
         }
     });
 
@@ -637,6 +637,7 @@ function draw(pathway, elem) {
     node.filter(d => !d.pseudo).each(function (d, i) {
         const g = d3.select(this);
 
+        if (d.image_type === "svg") {
             // Parse the SVG string
             const parser = new DOMParser();
             const svgDoc = parser.parseFromString(d.image_svg, "image/svg+xml");
@@ -646,19 +647,19 @@ function draw(pathway, elem) {
             const prefix = `node-${i}-`;
 
             // Rename all IDs and fix <use> references
-        svgElem.querySelectorAll('[id]').forEach(el => {
+            svgElem.querySelectorAll("[id]").forEach(el => {
                 const oldId = el.id;
                 const newId = prefix + oldId;
                 el.id = newId;
 
                 const XLINK_NS = "http://www.w3.org/1999/xlink";
                 // Update <use> elements that reference this old ID
-            const uses = Array.from(svgElem.querySelectorAll('use')).filter(
-                u => u.getAttributeNS(XLINK_NS, 'href') === `#${oldId}`
+                const uses = Array.from(svgElem.querySelectorAll("use")).filter(
+                    u => u.getAttributeNS(XLINK_NS, "href") === `#${oldId}`
                 );
 
                 uses.forEach(u => {
-                u.setAttributeNS(XLINK_NS, 'href', `#${newId}`);
+                    u.setAttributeNS(XLINK_NS, "href", `#${newId}`);
                 });
             });
 
@@ -675,6 +676,17 @@ function draw(pathway, elem) {
                 .attr("height", svgHeight * scale)
                 .attr("x", -svgWidth * scale / 2)
                 .attr("y", -svgHeight * scale / 2);
+        } else {
+            // We have a image type different than svg
+            // include it via img url
+            g.append("svg:image")
+                .attr("xlink:href", d.image)
+                .attr("width", 40)
+                .attr("height", 40)
+                .attr("x", -20)
+                .attr("y", -20);
+        }
+
     });
 
     // add element to nodes array

templates/actions/objects/pathway.html

@@ -1,3 +1,5 @@
+{% load envipytags %}
+
 {% if meta.can_edit %}
   <li>
     <a
@@ -15,6 +17,11 @@
       <i class="glyphicon glyphicon-plus"></i> Add Reaction</a
     >
   </li>
+  {% epdb_slot_templates "epdb.actions.objects.pathway.add" as action_button_templates %}
+
+  {% for tpl in action_button_templates %}
+    {% include tpl %}
+  {% endfor %}
   <li role="separator" class="divider"></li>
 {% endif %}
 <li>

templates/collections/_joblog_paginated_list_partial.html

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

templates/collections/joblog_paginated.html

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

templates/collections/paginated_base.html

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

templates/components/schema_form.html

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

templates/components/widgets/doi_link_widget.html

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

templates/objects/compound.html

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

templates/objects/compound_structure.html

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

templates/objects/pathway.html

@@ -1,5 +1,7 @@
 {% extends "framework_modern.html" %}
 {% load static %}
+{% load envipytags %}
+
 {% block content %}
   <script src="https://d3js.org/d3.v7.min.js"></script>
   <style>
@@ -76,6 +78,10 @@
   {% block action_modals %}
     {% include "modals/objects/add_pathway_node_modal.html" %}
     {% include "modals/objects/add_pathway_edge_modal.html" %}
+    {% epdb_slot_templates "epdb.modals.objects.pathway.add" as add_templates %}
+    {% for tpl in add_templates %}
+      {% include tpl %}
+    {% endfor %}
     {% include "modals/objects/download_pathway_csv_modal.html" %}
     {% include "modals/objects/download_pathway_image_modal.html" %}
     {% include "modals/objects/identify_missing_rules_modal.html" %}

utilities/chem.py

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

utilities/legacy.py

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

uv.lock

@@ -17,7 +17,7 @@ wheels = [
 
 [[package]]
 name = "aiohttp"
-version = "3.13.3"
+version = "3.13.5"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "aiohappyeyeballs" },
@@ -28,76 +28,76 @@ dependencies = [
     { name = "propcache" },
     { name = "yarl" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/50/42/32cf8e7704ceb4481406eb87161349abb46a57fee3f008ba9cb610968646/aiohttp-3.13.3.tar.gz", hash = "sha256:a949eee43d3782f2daae4f4a2819b2cb9b0c5d3b7f7a927067cc84dafdbb9f88", size = 7844556, upload-time = "2026-01-03T17:33:05.204Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/77/9a/152096d4808df8e4268befa55fba462f440f14beab85e8ad9bf990516918/aiohttp-3.13.5.tar.gz", hash = "sha256:9d98cc980ecc96be6eb4c1994ce35d28d8b1f5e5208a23b421187d1209dbb7d1", size = 7858271, upload-time = "2026-03-31T22:01:03.343Z" }
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 [[package]]