API PES

PW interactions
minor
2026-05-12 13:16:39 +02:00 · 2026-05-12 13:16:39 +02:00 · 2026-05-12 13:16:39 +02:00 · 2026-05-12 13:16:39 +02:00 · 2026-05-12 13:16:39 +02:00 · 2026-05-12 21:04:56 +12:00
39 changed files with 936 additions and 342 deletions
--- a/5
+++ b/5
@ -30,14 +30,15 @@ RUN mkdir -p -m 0700 /root/.ssh \
    && ssh-keyscan git.envipath.com >> /root/.ssh/known_hosts

 # We'll need access to private repos, let docker make use of host ssh agent and use it like:
-# docker build --ssh default -t envipath/envipy:1.0 .
+# docker build --ssh default -t envipath/envipy-bayer:1.0 .
 RUN --mount=type=ssh \
    uv sync --locked --extra ms-login --extra pepper-plugin

 # Now copy source and do a final sync to install the project itself
 # Ensure .dockerignore is reasonable
-COPY bayer bayer
+COPY bb4g bb4g
 COPY biotransformer biotransformer
+COPY bayer bayer
 COPY bridge bridge
 COPY envipath envipath
 COPY epapi epapi
--- a/bayer/epdb_hooks.py
+++ b/bayer/epdb_hooks.py
@ -13,6 +13,14 @@ register_template(
    "modals.collections.compound",
    "modals/collections/new_pes_modal.html",
 )
+register_template(
+    "epdb.actions.objects.pathway.add",
+    "actions/objects/pathway_add_pes.html",
+)
+register_template(
+    "epdb.modals.objects.pathway.add",
+    "modals/objects/add_pathway_pes_node_modal.html"
+)

 # PES Viz
 register_template(
--- a/bayer/templates/actions/objects/pathway_add_pes.html
+++ b/bayer/templates/actions/objects/pathway_add_pes.html
@ -0,0 +1,8 @@
+<li>
+  <a
+    class="button"
+    onclick="document.getElementById('add_pathway_pes_node_modal').showModal(); return false;"
+  >
+    <i class="glyphicon glyphicon-plus"></i> Add PES</a
+  >
+</li>
--- a/bayer/views.py
+++ b/bayer/views.py
@ -103,20 +103,15 @@ def create_pes_node(request, package_uuid, pathway_uuid):


 def fetch_pes(request, pes_url) -> dict:
-    proxies = {
-        "http": "http://10.185.190.100:8080",
-        "https": "http://10.185.190.100:8080",
-    }
-
    from epauth.views import get_access_token_from_request
    token = get_access_token_from_request(request)

-    if token or True:
+    if token:
        for k, v in s.PES_API_MAPPING.items():
            if pes_url.startswith(k):
                pes_id = pes_url.split('/')[-1]

-                if pes_id == 'dummy' or True:
+                if pes_id == 'dummy':
                    import json
                    res_data = json.load(open(s.BASE_DIR / "fixtures/pes.json"))
                    res_data["pes_url"] = pes_url
@ -125,7 +120,7 @@ def fetch_pes(request, pes_url) -> dict:
                    headers = {"Authorization": f"Bearer {token['access_token']}"}
                    params = {"pes_reg_entity_corporate_id": pes_id}

-                    res = requests.get(v, headers=headers, params=params, proxies=proxies)
+                    res = requests.get(v, headers=headers, params=params, proxies=s.PROXIES or None)

                    try:
                        res.raise_for_status()
--- a/bb4g/init.py
+++ b/bb4g/init.py
@ -0,0 +1,183 @@
+import json
+import math
+from datetime import datetime
+from typing import List
+import enum
+import requests
+from django.conf import settings as s
+from envipy_additional_information import EnviPyModel, UIConfig, WidgetType
+from envipy_additional_information import register
+
+from bridge.contracts import Classifier  # noqa: I001
+from bridge.dto import (
+    BuildResult,
+    EnviPyDTO,
+    EvaluationResult,
+    RunResult,
+    TransformationProductPrediction,
+)  # noqa: I001
+
+class SamplingAlgorithm(enum.Enum):
+    EXACT = "exact"
+
+
+@register("bb4gconfig")
+class BB4GConfig(EnviPyModel):
+    sampling_algorithm: SamplingAlgorithm = SamplingAlgorithm.EXACT
+    cutoff: int = -5
+
+    class UI:
+        title = "BB4G Configuration"
+        sampling_algorithm = UIConfig(
+            widget=WidgetType.SELECT,
+            label="BB4G Sampling Algorithm",
+            order=1,
+            placeholder="If unset defaults to 'exact'"
+        )
+        cutoff = UIConfig(
+            widget=WidgetType.NUMBER,
+            label="BB4G Cutoff",
+            order=2,
+            placeholder="If unset defaults to -5"
+        )
+
+
+# Once stable these will be exposed by enviPy-plugins lib
+class BB4G(Classifier):
+    Config = BB4GConfig
+
+    def __init__(self, config: BB4GConfig | None = None):
+        super().__init__(config)
+        self.url = f"{s.BB4G_URL}"
+
+        self.token = self.acquire_token()
+        self.header = {
+            "Authorization": f"Bearer {self.token}",
+            "Content-Type": "application/json",
+        }
+
+    def acquire_token(self):
+        BB4G_TENANT_ID = s.BB4G_TENANT_ID
+        BB4G_CLIENT_ID = s.BB4G_CLIENT_ID
+        BB4G_CLIENT_SECRET = s.BB4G_CLIENT_SECRET
+        BB4G_SCOPE = s.BB4G_SCOPE
+
+        BB4G_TOKEN_URL = f"https://login.microsoftonline.com/{BB4G_TENANT_ID}/oauth2/v2.0/token"
+
+        payload = {
+            "client_id": BB4G_CLIENT_ID,
+            "client_secret": BB4G_CLIENT_SECRET,
+            "scope": BB4G_SCOPE,
+            "grant_type": "client_credentials"
+        }
+
+        # No Proxy required, URL is whitelisted
+        res = requests.post(BB4G_TOKEN_URL, data=payload)
+
+        res.raise_for_status()
+
+        return res.json()["access_token"]
+
+    def start(self):
+        header = {
+            "Authorization": f"Bearer {self.token}",
+            "Content-Type": "application/json",
+        }
+
+        started = False
+        retries = 0
+        while not started and retries < 5:
+            res = requests.post(f"{self.url}/start", headers=header, data={}, proxies=s.PROXIES or None)
+
+            if res.status_code == 200:
+                started = True
+            elif res.status_code in [500, 502]:
+                retries += 1
+                import time
+                time.sleep(5)
+            else:
+                raise ValueError(f"Unexpected status code: {res.status_code}")
+
+    @classmethod
+    def requires_rule_packages(cls) -> bool:
+        return False
+
+    @classmethod
+    def requires_data_packages(cls) -> bool:
+        return False
+
+    @classmethod
+    def identifier(cls) -> str:
+        return "bb4g"
+
+    @classmethod
+    def name(cls) -> str:
+        return "BB4G Template Free Model"
+
+    @classmethod
+    def display(cls) -> str:
+        return "BB4G Template Free Model"
+
+    def build(self, eP: EnviPyDTO, *args, **kwargs) -> BuildResult | None:
+        return
+
+    def run(self, eP: EnviPyDTO, *args, **kwargs) -> RunResult:
+
+        # Ensure Service is running
+        self.start()
+
+        smiles = [c.smiles for c in eP.get_compounds()]
+        preds = self._post(smiles)
+
+        results = []
+
+        for substrate in preds.keys():
+            results.append(
+                TransformationProductPrediction(
+                    substrate=substrate,
+                    products=preds[substrate],
+                )
+            )
+
+        return RunResult(
+            producer=eP.get_context().url,
+            description=f"Generated at {datetime.now()}",
+            result=results,
+        )
+
+    def evaluate(self, eP: EnviPyDTO, *args, **kwargs) -> EvaluationResult:
+        pass
+
+    def build_and_evaluate(self, eP: EnviPyDTO, *args, **kwargs) -> EvaluationResult:
+        pass
+
+    def _post(self, smiles: List[str]) -> dict[str, dict[str, float]]:
+        header = {
+            "Authorization": f"Bearer {self.token}",
+            "Content-Type": "application/json",
+        }
+
+        result = {}
+
+        for smi in smiles:
+            data = {
+                "smiles": smi,
+                "sampling_alg": self.config.sampling_algorithm.value,
+                "cutoff": self.config.cutoff,
+            }
+
+            resp = requests.post(f"{self.url}/compute", headers=header, data=json.dumps(data), proxies=s.PROXIES or None)
+
+            resp.raise_for_status()
+
+            for substrate, predictions in resp.json().items():
+                preds = {}
+
+                for pred in predictions:
+                    prod = pred["prediction"]
+                    prob = math.exp(pred["log_likelihood"])
+                    preds[prod] = prob
+
+                result[substrate] = preds
+
+        return result
--- a/bridge/contracts.py
+++ b/bridge/contracts.py
@ -254,7 +254,15 @@ class Classifier(Plugin):
    def parse_config(cls, data: dict | None = None) -> EnviPyModel | None:
        if cls.Config is None:
            return None
-        return cls.Config(**(data or {}))
+
+        # remove empty strings a.k.a unset params to not overwrite defaults
+        cpy = {}
+        if data is not None:
+            for k, v in data.items():
+                if v != "":
+                    cpy[k] = v
+
+        return cls.Config(**cpy)

    @classmethod
    def create(cls, data: dict | None = None):
--- a/envipath/settings.py
+++ b/envipath/settings.py
@ -143,6 +143,12 @@ if os.environ.get("USE_TEMPLATE_DB", False) == "True":
        "TEMPLATE": os.environ["TEMPLATE_DB"],
    }

+CACHES = {
+    "default": {
+        "BACKEND": "django.core.cache.backends.locmem.LocMemCache",
+        "LOCATION": "unique-snowflake",
+    }
+}

 # Password validation
 # https://docs.djangoproject.com/en/4.2/ref/settings/#auth-password-validators
@ -474,3 +480,14 @@ if DATA_POOL_MAPPING:
 else:
    DATA_POOL_MAPPING = {}

+PROXIES = {}
+if os.environ.get("HTTP_PROXY"):
+    PROXIES["http"] = os.environ.get("HTTP_PROXY")
+    PROXIES["https"] = os.environ.get("HTTPS_PROXY")
+
+# BB4g
+BB4G_URL = os.environ.get("BB4G_URL")
+BB4G_TENANT_ID = os.environ.get("BB4G_TENANT_ID")
+BB4G_CLIENT_ID = os.environ.get("BB4G_CLIENT_ID")
+BB4G_CLIENT_SECRET = os.environ.get("BB4G_CLIENT_SECRET")
+BB4G_SCOPE = os.environ.get("BB4G_SCOPE")
--- a/envipath/urls.py
+++ b/envipath/urls.py
@ -41,9 +41,7 @@ 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"))
-    )
+    urlpatterns.append(path(f"{PATH_PREFIX}", include(f"{s.TENANT}.urls")))

 # Custom error handlers
 handler400 = "epdb.views.handler400"
--- a/epauth/urls.py
+++ b/epauth/urls.py
@ -5,4 +5,5 @@ from . import views
 urlpatterns = [
    path("entra/login/", views.entra_login, name="entra_login"),
    path("auth/redirect/", views.entra_callback, name="entra_callback"),
+    path("auth/token/", views.get_token, name="get_token"),
 ]
--- a/epauth/views.py
+++ b/epauth/views.py
@ -2,6 +2,7 @@ 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.http import HttpResponse
 from django.shortcuts import redirect

 from epdb.logic import UserManager, GroupManager
@ -22,7 +23,7 @@ def get_msal_app_with_cache(request):
        client_id=s.MS_ENTRA_CLIENT_ID,
        client_credential=s.MS_ENTRA_CLIENT_SECRET,
        authority=s.MS_ENTRA_AUTHORITY,
-        token_cache=cache
+        token_cache=cache,
    )

    return msal_app, cache
@ -59,9 +60,12 @@ def entra_callback(request):

    claims = result["id_token_claims"]

-    user_name = claims["name"]
-    user_email = claims.get("emailaddress", claims["email"])
-    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()
@ -79,6 +83,7 @@ def entra_callback(request):
    login(request, u)

    # EDIT START
+
    # Ensure groups exists in eP
    for id, name in s.ENTRA_SECRET_GROUPS.items():
        if not Group.objects.filter(uuid=id).exists():
@ -111,6 +116,11 @@ def get_access_token_from_request(request, scopes=None):
    """
    Get an access token from the request using MSAL token cache.
    """
+
+    # Check if auth via Access Token
+    if request.headers.get("Authorization"):
+        return {"access_token": request.headers.get("Authorization").split(" ")[1]}
+
    if scopes is None:
        scopes = s.MS_ENTRA_SCOPES

@ -142,10 +152,7 @@ def get_access_token_from_request(request, scopes=None):
        return None

    # Try to acquire token silently from cache
-    result = msal_app.acquire_token_silent(
-        scopes=scopes,
-        account=user_account
-    )
+    result = msal_app.acquire_token_silent(scopes=scopes, account=user_account)

    # Save cache changes back to session
    if cache.has_state_changed:
@ -155,3 +162,9 @@ def get_access_token_from_request(request, scopes=None):
        return result

    return None
+
+
+def get_token(request):
+    token = get_access_token_from_request(request)
+    msg = f"{token}"
+    return HttpResponse(msg, content_type='text/plain')
--- a/epdb/admin.py
+++ b/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
--- a/epdb/legacy_api.py
+++ b/epdb/legacy_api.py
@ -1,19 +1,17 @@
-import hashlib
 from collections import defaultdict
 from typing import Any, Dict, List, Optional

 import jwt
-import requests
-
 import nh3
+import requests
 from django.conf import settings as s
 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.errors import HttpError
 from ninja.security import HttpBearer
-from ninja.security import SessionAuth

 from utilities.chem import FormatConverter
 from utilities.misc import PackageExporter
@ -51,6 +49,26 @@ from .models import (
 Package = s.GET_PACKAGE_MODEL()


+def get_cached_jwks(tenant_id: str, force=False) -> Dict:
+    """Get JWKS using Django cache"""
+    cache_key = f"jwks_{tenant_id}"
+
+    jwks = cache.get(cache_key)
+
+    if jwks is None or force:
+        # Cache miss, fetch new keys
+        jwks_uri = f"https://login.microsoftonline.com/{tenant_id}/discovery/v2.0/keys"
+        response = requests.get(jwks_uri)
+        response.raise_for_status()
+
+        jwks = response.json()
+
+        # Cache for 1 hour (3600 seconds)
+        cache.set(cache_key, jwks, 3600)
+
+    return jwks
+
+
 def get_package_for_write(user, package_uuid):
    p = PackageManager.get_package_by_id(user, package_uuid)
    if not PackageManager.writable(user, p):
@ -68,9 +86,7 @@ def validate_token(token: str) -> dict:
    TENANT_ID = s.MS_ENTRA_TENANT_ID
    CLIENT_ID = s.MS_ENTRA_CLIENT_ID

-    # Fetch Microsoft's public keys
-    jwks_uri = f"https://login.microsoftonline.com/{TENANT_ID}/discovery/v2.0/keys"
-    jwks = requests.get(jwks_uri).json()
+    jwks = get_cached_jwks(TENANT_ID)

    header = jwt.get_unverified_header(token)

@ -78,13 +94,21 @@ def validate_token(token: str) -> dict:
        next(k for k in jwks["keys"] if k["kid"] == header["kid"])
    )

+    # Handle V1 and V2 tokens
+    try:
        claims = jwt.decode(
            token,
            public_key,
            algorithms=["RS256"],
            audience=[CLIENT_ID, f"api://{CLIENT_ID}"],
-        issuer=f"https://sts.windows.net/{TENANT_ID}/",
+            issuer=[
+                f"https://sts.windows.net/{TENANT_ID}/",
+                f"https://login.microsoftonline.com/{TENANT_ID}/v2.0"
+            ]
        )
+    except Exception as e:
+        raise ValueError(f"Token verification failed! - {e}")
+
    return claims


@ -796,6 +820,7 @@ class CreateCompound(Schema):
    compoundName: str | None = None
    compoundDescription: str | None = None
    inchi: str | None = None
+    pesLink: str | None = None


@router.post("/package/{uuid:package_uuid}/compound")
@ -807,6 +832,25 @@ def create_package_compound(
    try:
        p = get_package_for_write(request.user, package_uuid)
        # inchi is not used atm
+
+        if c.pesLink is not None:
+            from bayer.views import fetch_pes
+            from bayer.models import PESCompound
+
+            try:
+                pes_data = fetch_pes(request, c.pesLink)
+            except ValueError as e:
+                return 400, {"message": f"Could not fetch PES data for {c.pesLink}"}
+
+            classification = pes_data.get("classificationLevel", "")
+            if "secret" == classification.lower():
+                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:
            c = Compound.create(
                p, c.compoundSmiles, c.compoundName, c.compoundDescription, inchi=c.inchi
            )
@ -1830,6 +1874,7 @@ class CreateNode(Schema):
    nodeName: str | None = None
    nodeReason: str | None = None
    nodeDepth: str | None = None
+    pesLink: str | None = None


@router.post(
@ -1841,14 +1886,43 @@ def add_pathway_node(request, package_uuid, pathway_uuid, n: Form[CreateNode]):
        p = get_package_for_write(request.user, package_uuid)
        pw = Pathway.objects.get(package=p, uuid=pathway_uuid)

+        if n.pesLink:
+            from bayer.views import fetch_pes
+            from bayer.models import PESCompound
+
+            try:
+                pes_data = fetch_pes(request, c.pesLink)
+            except ValueError as e:
+                return 400, {"message": f"Could not fetch PES data for {c.pesLink}"}
+
+            classification = pes_data.get("classificationLevel", "")
+            if "secret" == classification.lower():
+                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)
+
+            node = Node()
+            node.stereo_removed = False
+            node.pathway = pw
+            node.depth = 0
+
+            node.default_node_label = c.default_structure
+            node.save()
+
+            node.node_labels.add(c.default_structure)
+            node.save()
+        else:
            if n.nodeDepth is not None and n.nodeDepth.strip() != "":
                node_depth = int(n.nodeDepth)
            else:
                node_depth = -1

-        n = Node.create(pw, n.nodeAsSmiles, node_depth, n.nodeName, n.nodeReason)
+            node = Node.create(pw, n.nodeAsSmiles, node_depth, n.nodeName, n.nodeReason)

-        return redirect(n.url)
+        return redirect(node.url)
    except ValueError:
        return 403, {"message": "Adding node failed!"}

@ -2000,6 +2074,9 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
            description=e.edgeReason,
        )

+        # Update depths as sideeffect of above operation
+        pw.update_depths()
+
        return redirect(new_e.url)
    except ValueError:
        return 403, {"message": "Adding Edge failed!"}
--- a/epdb/logic.py
+++ b/epdb/logic.py
@ -346,7 +346,9 @@ class PackageManager(object):

    @staticmethod
    def readable(user, package):
-        return PackageManager.has_package_permission(user, package, "read")
+        return (
+            PackageManager.has_package_permission(user, package, "read") | package.reviewed is True
+        )

    @staticmethod
    def writable(user, package):
@ -1063,52 +1065,9 @@ 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
--- a/epdb/migrations/0023_alter_compoundstructure_options_and_more.py
+++ b/epdb/migrations/0023_alter_compoundstructure_options_and_more.py
@ -1,55 +1,54 @@
-# Generated by Django 6.0.3 on 2026-04-17 21:22
+# 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'),
+        ("epdb", "0022_alter_classifierpluginmodel_data_packages_and_more"),
    ]

    operations = [
        migrations.AlterModelOptions(
-            name='compoundstructure',
+            name="compoundstructure",
            options={},
        ),
        migrations.AlterModelOptions(
-            name='epmodel',
+            name="epmodel",
            options={},
        ),
        migrations.AlterModelOptions(
-            name='parallelrule',
+            name="parallelrule",
            options={},
        ),
        migrations.AlterModelOptions(
-            name='rule',
+            name="rule",
            options={},
        ),
        migrations.AlterModelOptions(
-            name='sequentialrule',
+            name="sequentialrule",
            options={},
        ),
        migrations.AlterModelOptions(
-            name='simpleambitrule',
+            name="simpleambitrule",
            options={},
        ),
        migrations.AlterModelOptions(
-            name='simplerdkitrule',
+            name="simplerdkitrule",
            options={},
        ),
        migrations.AlterModelOptions(
-            name='simplerule',
+            name="simplerule",
            options={},
        ),
        migrations.AddField(
-            model_name='compoundstructure',
-            name='molfile',
-            field=models.TextField(blank=True, null=True, verbose_name='Molfile'),
+            model_name="compoundstructure",
+            name="molfile",
+            field=models.TextField(blank=True, null=True, verbose_name="Molfile"),
        ),
        migrations.AddField(
-            model_name='group',
-            name='secret',
-            field=models.BooleanField(default=False, verbose_name='Secret Group'),
+            model_name="group",
+            name="secret",
+            field=models.BooleanField(default=False, verbose_name="Secret Group"),
        ),
    ]
--- a/epdb/migrations/0024_user_contacted.py
+++ b/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),
+        ),
+    ]
--- a/epdb/migrations/0025_auto_20260511_2025.py
+++ b/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,
+    "SFOÂ²": 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),
+    ]
--- a/epdb/models.py
+++ b/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"]
@ -2185,6 +2186,56 @@ 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()
+
+        for n in self.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:
+                    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:
+                for e in self.edges:
+                    if n in e.start_nodes.all():
+                        for p in e.end_nodes.all():
+                            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:
+                    n.depth = depth
+                    n.save()
+

 class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin):
    pathway = models.ForeignKey(
@ -2226,7 +2277,9 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
            if isinstance(ai.get(), PropertyPrediction):
                predicted_properties[ai.get().__class__.__name__].append(ai.data)

-        extra_structure_data = self.default_node_label.d3_json()
+        # 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,
@ -2237,7 +2290,7 @@ 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()],
@ -2250,9 +2303,9 @@ 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,
        }

-        res.update(**extra_structure_data)
        return res

    @staticmethod
--- a/epdb/views.py
+++ b/epdb/views.py
@ -937,12 +937,14 @@ def package_models(request, package_uuid):
                "requires_rule_packages": True,
                "requires_data_packages": True,
            },
-            "EnviFormer": {
+        }
+
+        if s.ENVIFORMER_PRESENT:
+            context["model_types"]["EnviFormer"] = {
                "type": "enviformer",
                "requires_rule_packages": False,
                "requires_data_packages": True,
            },
-        }

        if s.FLAGS.get("PLUGINS", False):
            for k, v in s.CLASSIFIER_PLUGINS.items():
@ -2537,6 +2539,9 @@ 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:
--- a/pepper/init.py
+++ b/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
--- a/pepper/impl/pepper.py
+++ b/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")
            )
--- a/static/js/pw.js
+++ b/static/js/pw.js
@ -605,7 +605,36 @@ function draw(pathway, elem) {
        // Check if target is pseudo and draw marker only if not pseudo
        .attr("class", d => d.target.pseudo ? "link_no_arrow" : "link")
        .attr("marker-end", d => d.target.pseudo ? '' : d.multi_step ? 'url(#doublearrow)' : 'url(#arrow)')
+      .on("click", function(event, d) {
+          const wasHighlighted = d3.select(this).classed("highlighted");

+          d3.selectAll("line").classed("highlighted", false);
+
+          if (!wasHighlighted) {
+              const toHighlight = [];
+              toHighlight.push(d.el);
+
+              if (d.source.pseudo || d.target.pseudo) {
+                  if (d.target.pseudo) {
+                      d3.selectAll("line").each(e => {
+                          if (e !== undefined && e.source.id === d.target.id) {
+                              toHighlight.push(e.el);
+                          }
+                      });
+                  } else {
+                      d3.selectAll("line").each(e => {
+                          if (e !== undefined && (e.target.id === d.source.id || e.source.id === d.source.id)) {
+                              toHighlight.push(e.el);
+                          }
+                      });
+                  }
+              }
+
+              for (const e of toHighlight) {
+                  d3.select(e).classed("highlighted", true);
+              }
+          }
+      })

    // add element to links array
    link.each(function (d) {
@ -624,7 +653,13 @@ function draw(pathway, elem) {
            .on("drag", dragged)
            .on("end", dragended))
        .on("click", function (event, d) {
+            const wasHighlighted = d3.select(this).select("circle").classed("highlighted");
+
+            d3.selectAll('circle.highlighted').classed('highlighted', false);
+
+            if (!wasHighlighted) {
                d3.select(this).select("circle").classed("highlighted", !d3.select(this).select("circle").classed("highlighted"));
+            }
        })

    // Kreise für die Knoten hinzufügen
@ -637,14 +672,7 @@ function draw(pathway, elem) {
    node.filter(d => !d.pseudo).each(function (d, i) {
        const g = d3.select(this);

-        if (d.is_pes) {
-            g.append("svg:image")
-              .attr("xlink:href", d.image)
-              .attr("width", 40)
-              .attr("height", 40)
-              .attr("x", -20)
-              .attr("y", -20);
-        } else {
+        if (d.image_type === "svg") {
            // Parse the SVG string
            const parser = new DOMParser();
            const svgDoc = parser.parseFromString(d.image_svg, "image/svg+xml");
@ -683,6 +711,15 @@ 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);
        }

    });
--- a/templates/actions/objects/pathway.html
+++ b/templates/actions/objects/pathway.html
@ -1,3 +1,5 @@
+{% load envipytags %}
+
 {% if meta.can_edit %}
  <li>
    <a
@ -7,14 +9,6 @@
      <i class="glyphicon glyphicon-plus"></i> Add Compound</a
    >
  </li>
-  <li>
-    <a
-      class="button"
-      onclick="document.getElementById('add_pathway_pes_node_modal').showModal(); return false;"
-    >
-      <i class="glyphicon glyphicon-plus"></i> Add PES</a
-    >
-  </li>
  <li>
    <a
      class="button"
@ -23,7 +17,12 @@
      <i class="glyphicon glyphicon-plus"></i> Add Reaction</a
    >
  </li>
-  <li role="separator" class="divider"></li>
+  {% epdb_slot_templates "epdb.actions.objects.pathway.add" as action_button_templates %}
+
+  {% for tpl in action_button_templates %}
+    {% include tpl %}
+  {% endfor %}
+  <li role="separator" class="divider h-px"></li>
 {% endif %}
 <li>
  <a
@ -75,7 +74,7 @@
      Rules</a
    >
  </li>
-  <li role="separator" class="divider"></li>
+  <li role="separator" class="divider h-px"></li>
  <li>
    <a
      class="button"
@ -100,11 +99,16 @@
      <i class="glyphicon glyphicon-plus"></i> Set Aliases</a
    >
  </li>
-  <li role="separator" class="divider"></li>
+  <li role="separator" class="divider h-px"></li>
  <li>
    <a
      class="button"
-      onclick="document.getElementById('delete_pathway_node_modal').showModal(); return false;"
+      onclick="
+      const modal = document.getElementById('delete_pathway_node_modal');
+      modal.showModal();
+      window.dispatchEvent(new Event('modal-opened'));
+      return false;
+      "
    >
      <i class="glyphicon glyphicon-trash"></i> Delete Compound</a
    >
@ -112,7 +116,12 @@
  <li>
    <a
      class="button"
-      onclick="document.getElementById('delete_pathway_edge_modal').showModal(); return false;"
+      onclick="
+      const modal = document.getElementById('delete_pathway_edge_modal');
+      modal.showModal();
+      window.dispatchEvent(new Event('modal-opened'));
+      return false;
+      "
    >
      <i class="glyphicon glyphicon-trash"></i> Delete Reaction</a
    >
--- a/templates/collections/compounds_paginated.html
+++ b/templates/collections/compounds_paginated.html
@ -5,7 +5,7 @@

 {% block action_button %}
  <div class="flex items-center gap-2">
-    {% if meta.can_edit %}
+    {% if meta.can_edit or not meta.url_contains_package %}
      <button
        type="button"
        class="btn btn-primary btn-sm"
--- a/templates/collections/models_paginated.html
+++ b/templates/collections/models_paginated.html
@ -3,7 +3,8 @@
 {% block page_title %}Models{% endblock %}

 {% block action_button %}
-  {% if meta.can_edit and meta.enabled_features.MODEL_BUILDING %}
+  {% if meta.can_edit or not meta.url_contains_package %}
+    {% if meta.enabled_features.MODEL_BUILDING %}
      <button
        type="button"
        class="btn btn-primary btn-sm"
@ -12,6 +13,7 @@
        New Model
      </button>
    {% endif %}
+  {% endif %}
 {% endblock action_button %}

 {% block action_modals %}
--- a/templates/collections/packages_paginated.html
+++ b/templates/collections/packages_paginated.html
@ -3,7 +3,6 @@
 {% block page_title %}Packages{% endblock %}

 {% block action_button %}
-  {% if meta.can_edit %}
    <div class="flex items-center gap-2">
      <button
        type="button"
@ -71,7 +70,6 @@
        </ul>
      </div>
    </div>
-  {% endif %}
 {% endblock action_button %}

 {% block action_modals %}
--- a/templates/collections/pathways_paginated.html
+++ b/templates/collections/pathways_paginated.html
@ -3,7 +3,7 @@
 {% block page_title %}Pathways{% endblock %}

 {% block action_button %}
-  {% if meta.can_edit %}
+  {% if meta.can_edit or not meta.url_contains_package %}
    <div class="flex items-center gap-2">
      <a
        class="btn btn-primary btn-sm"
--- a/templates/collections/reactions_paginated.html
+++ b/templates/collections/reactions_paginated.html
@ -3,7 +3,7 @@
 {% block page_title %}Reactions{% endblock %}

 {% block action_button %}
-  {% if meta.can_edit %}
+  {% if meta.can_edit or not meta.url_contains_package %}
    <button
      type="button"
      class="btn btn-primary btn-sm"
--- a/templates/collections/rules_paginated.html
+++ b/templates/collections/rules_paginated.html
@ -3,7 +3,7 @@
 {% block page_title %}Rules{% endblock %}

 {% block action_button %}
-  {% if meta.can_edit %}
+  {% if meta.can_edit or not meta.url_contains_package %}
    <button
      type="button"
      class="btn btn-primary btn-sm"
--- a/templates/collections/scenarios_paginated.html
+++ b/templates/collections/scenarios_paginated.html
@ -11,7 +11,7 @@
 {% endblock action_modals %}

 {% block action_button %}
-  {% if meta.can_edit %}
+  {% if meta.can_edit or not meta.url_contains_package  %}
    <button
      type="button"
      class="btn btn-primary btn-sm"
--- a/templates/collections/structures_paginated.html
+++ b/templates/collections/structures_paginated.html
@ -3,7 +3,7 @@
 {% block page_title %}{{ page_title|default:"Structures" }}{% endblock %}

 {% block action_button %}
-  {% if meta.can_edit %}
+  {% if meta.can_edit or not meta.url_contains_package %}
    <button
      type="button"
      class="btn btn-primary btn-sm"
--- a/templates/modals/collections/new_prediction_setting_modal.html
+++ b/templates/modals/collections/new_prediction_setting_modal.html
@ -203,11 +203,11 @@
              id="model-based-prediction-setting-threshold"
              name="model-based-prediction-setting-threshold"
              class="input input-bordered w-full"
-              placeholder="0.25"
+              value="0.25"
              type="number"
              min="0"
              max="1"
-              step="0.05"
+              step="any"
            />
          </div>

--- a/templates/modals/objects/delete_pathway_edge_modal.html
+++ b/templates/modals/objects/delete_pathway_edge_modal.html
@ -4,6 +4,25 @@
  id="delete_pathway_edge_modal"
  class="modal"
  x-data="modalForm({ state: { selectedEdge: '', imageUrl: '' } })"
+  @modal-opened.window="
+   const links = d3.selectAll('line.highlighted');
+  console.log(links);
+   if (!links.empty()) {
+        const el = links.node();
+        const selectElement = document.getElementById('delete_pathway_edge_edges');
+        console.log(el);
+        console.log(el.__data__);
+        for (let option of selectElement.options) {
+            if (option.value === el.__data__.url) {
+                option.selected = true;
+                break;
+            }
+        }
+
+        selectElement.dispatchEvent(new Event('change'));
+
+   }
+  "
  @close="reset()"
 >
  <div class="modal-box">
--- a/templates/modals/objects/delete_pathway_node_modal.html
+++ b/templates/modals/objects/delete_pathway_node_modal.html
@ -4,6 +4,22 @@
  id="delete_pathway_node_modal"
  class="modal"
  x-data="modalForm({ state: { selectedNode: '', imageUrl: '' } })"
+  @modal-opened.window="
+   const el = d3.select('circle.highlighted').node();
+
+   if (el !== null) {
+    const selectElement = document.getElementById('delete_pathway_node_nodes');
+
+    for (let option of selectElement.options) {
+        if (option.value === el.__data__.url) {
+            option.selected = true;
+            break;
+        }
+    }
+
+    selectElement.dispatchEvent(new Event('change'));
+   }
+  "
  @close="reset()"
 >
  <div class="modal-box">
--- a/templates/objects/compound.html
+++ b/templates/objects/compound.html
@ -83,8 +83,8 @@
      <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 %}
--- a/templates/objects/compound_structure.html
+++ b/templates/objects/compound_structure.html
@ -51,8 +51,8 @@
      </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 %}
--- a/templates/objects/pathway.html
+++ b/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>
@ -75,8 +77,11 @@

  {% block action_modals %}
    {% include "modals/objects/add_pathway_node_modal.html" %}
-    {% include "modals/objects/add_pathway_pes_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" %}
@ -101,12 +106,12 @@
    </div>

    <!-- Graphical Representation -->
-    <div class="collapse-arrow bg-base-200 collapse">
+    <div class="collapse-arrow bg-base-200 collapse overflow-y-auto">
      <input type="checkbox" checked />
      <div class="collapse-title text-xl font-medium">
        Graphical Representation
      </div>
-      <div class="collapse-content">
+      <div class="collapse-content ">
        <div class="bg-base-100 mb-2 rounded-lg p-2">
          <div class="navbar bg-base-100 rounded-lg">
            <div class="flex-1">
@ -135,7 +140,7 @@
                </div>
                <ul
                  tabindex="0"
-                  class="dropdown-content menu bg-base-100 rounded-box z-50 w-52 p-2"
+                  class="dropdown-content menu bg-base-100 rounded-box z-50 w-96 p-2"
                >
                  {% include "actions/objects/pathway.html" %}
                </ul>
--- a/utilities/chem.py
+++ b/utilities/chem.py
@ -182,11 +182,9 @@ class FormatConverter(object):

        drawer = rdMolDraw2D.MolDraw2DCairo(*mol_size)
        opts = drawer.drawOptions()
-
        opts.clearBackground = False
        drawer.DrawMolecule(mol)
        drawer.FinishDrawing()
-
        return drawer.GetDrawingText()

    @staticmethod
--- a/utilities/legacy.py
+++ b/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,
@ -473,17 +473,12 @@ 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 +503,10 @@ 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)
--- a/uv.lock
+++ b/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" },
 ]
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+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]]
Author	SHA1	Message	Date
Tim Lorsbach	3b5d299128	API PES Some checks failed CI / test (pull_request) Failing after 14s Details API CI / api-tests (pull_request) Failing after 20s Details	2026-05-12 13:16:39 +02:00
Tim Lorsbach	38e901a51e	PW interactions	2026-05-12 13:16:39 +02:00
Tim Lorsbach	c92fccaf8e	minor	2026-05-12 13:16:39 +02:00
Tim Lorsbach	5eb3ebac89	Wip	2026-05-12 13:16:39 +02:00
Tim Lorsbach	d9530ce755	adjusted migration Initial bayer app Show Pack Classification Adjusted docker compose to bayer specifics Adjusted Dockerfile for Bayer Adding secret flags to group, add secret pools to packages Adjusted View for Package creation Prep configs, added Package Create Modal wip More on PES wip wip	2026-05-12 13:16:39 +02:00
jebus	1e43c298d2	[Fix] Simplify Depth adjustment (#386 ) Co-authored-by: Tim Lorsbach <tim@lorsba.ch> Reviewed-on: enviPath/enviPy#386	2026-05-12 21:04:56 +12:00
jebus	b39fc7eaf8	[Fix] Update Node depth when adding new Edges to a Pathway (#384 ) Co-authored-by: Tim Lorsbach <tim@lorsba.ch> Reviewed-on: enviPath/enviPy#384	2026-05-12 09:40:35 +12:00
jebus	a2fc9f72cb	[Feature] Make use of HalfLifeModel Enum (#383 ) Co-authored-by: Tim Lorsbach <tim@lorsba.ch> Reviewed-on: enviPath/enviPy#383	2026-05-12 09:23:56 +12:00
Tobias O	734b02767e	[Fix] Update plotting imports and thread handling in Pepper class (#382 ) - plt.subplot does not work reliably with async/ threads. - Bug in thread run that would fail with env set (string to number) Reviewed-on: enviPath/enviPy#382 Co-authored-by: Tobias O <tobias.olenyi@envipath.com> Co-committed-by: Tobias O <tobias.olenyi@envipath.com>	2026-05-12 06:43:26 +12:00
jebus	9d70db2ca2	[Fix] Wrong indentation in welcome mail (#373 ) Co-authored-by: Tim Lorsbach <tim@lorsba.ch> Reviewed-on: enviPath/enviPy#373	2026-04-22 08:47:05 +12:00
jebus	fec26d0233	[Feature] Admin Actions for Activation and Affiliation Request (#372 ) Co-authored-by: Tim Lorsbach <tim@lorsba.ch> Reviewed-on: enviPath/enviPy#372	2026-04-22 08:36:31 +12:00
jebus	689f7998eb	[Dep] Updated enviFormer, additional information lib, aiohttp, fsspec (#371 ) Co-authored-by: Tim Lorsbach <tim@lorsba.ch> Reviewed-on: enviPath/enviPy#371	2026-04-22 06:38:31 +12:00
jebus	8498e59fa1	[Feature] Changes required for non public tenants (#370 ) Co-authored-by: Tim Lorsbach <tim@lorsba.ch> Reviewed-on: enviPath/enviPy#370	2026-04-22 06:08:39 +12:00