wip

Dockerfile

@@ -30,15 +30,14 @@ 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-bayer:1.0 .
+# docker build --ssh default -t envipath/envipy: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 bb4g bb4g
-COPY biotransformer biotransformer
 COPY bayer bayer
+COPY biotransformer biotransformer
 COPY bridge bridge
 COPY envipath envipath
 COPY epapi epapi

bayer/epdb_hooks.py

@@ -13,14 +13,6 @@ 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(

bayer/templates/actions/objects/pathway_add_pes.html

@@ -1,8 +0,0 @@
-<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>

bayer/views.py

@@ -103,15 +103,20 @@ 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:
+    if token or True:
         for k, v in s.PES_API_MAPPING.items():
             if pes_url.startswith(k):
                 pes_id = pes_url.split('/')[-1]
 
-                if pes_id == 'dummy':
+                if pes_id == 'dummy' or True:
                     import json
                     res_data = json.load(open(s.BASE_DIR / "fixtures/pes.json"))
                     res_data["pes_url"] = pes_url
@@ -120,7 +125,7 @@ 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=s.PROXIES or None)
+                    res = requests.get(v, headers=headers, params=params, proxies=proxies)
 
                     try:
                         res.raise_for_status()

bb4g/__init__.py

@@ -1,183 +0,0 @@
-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

bridge/contracts.py

@@ -254,15 +254,7 @@ class Classifier(Plugin):
     def parse_config(cls, data: dict | None = None) -> EnviPyModel | None:
         if cls.Config is None:
             return None
-
-        # 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)
+        return cls.Config(**(data or {}))
 
     @classmethod
     def create(cls, data: dict | None = None):

envipath/settings.py

@@ -143,12 +143,6 @@ 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
@@ -480,14 +474,3 @@ 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")

envipath/urls.py

@@ -41,7 +41,9 @@ 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"

epauth/urls.py

@@ -5,5 +5,4 @@ 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"),
 ]

epauth/views.py

@@ -2,7 +2,6 @@ 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
@@ -23,7 +22,7 @@ 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
@@ -60,12 +59,9 @@ def entra_callback(request):
 
     claims = result["id_token_claims"]
 
-    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")
+    user_name = claims["name"]
+    user_email = claims.get("emailaddress", claims["email"])
+    user_oid = claims["oid"]
 
     # Get implementing class
     User = get_user_model()
@@ -83,7 +79,6 @@ 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():
@@ -116,11 +111,6 @@ 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
 
@@ -152,7 +142,10 @@ 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:
@@ -162,9 +155,3 @@ 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')

epdb/admin.py

@@ -1,8 +1,5 @@
-import logging
-
 from django.conf import settings as s
 from django.contrib import admin
-from django.contrib import messages
 
 from .models import (
     AdditionalInformation,
@@ -32,8 +29,6 @@ from .models import (
 
 Package = s.GET_PACKAGE_MODEL()
 
-logger = logging.getLogger(__name__)
-
 
 class AdditionalInformationAdmin(admin.ModelAdmin):
     pass
@@ -50,113 +45,6 @@ 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

@@ -1,17 +1,19 @@
+import hashlib
 from collections import defaultdict
 from typing import Any, Dict, List, Optional
 
 import jwt
-import nh3
 import requests
+
+import nh3
 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
@@ -49,26 +51,6 @@ 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):
@@ -86,7 +68,9 @@ def validate_token(token: str) -> dict:
     TENANT_ID = s.MS_ENTRA_TENANT_ID
     CLIENT_ID = s.MS_ENTRA_CLIENT_ID
 
-    jwks = get_cached_jwks(TENANT_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()
 
     header = jwt.get_unverified_header(token)
 
@@ -94,21 +78,13 @@ 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}/",
-                f"https://login.microsoftonline.com/{TENANT_ID}/v2.0"
-            ]
-        )
-    except Exception as e:
-        raise ValueError(f"Token verification failed! - {e}")
-
+    claims = jwt.decode(
+        token,
+        public_key,
+        algorithms=["RS256"],
+        audience=[CLIENT_ID, f"api://{CLIENT_ID}"],
+        issuer=f"https://sts.windows.net/{TENANT_ID}/",
+    )
     return claims
 
 
@@ -820,7 +796,6 @@ 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")
@@ -832,28 +807,9 @@ 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
-            )
+        c = Compound.create(
+            p, c.compoundSmiles, c.compoundName, c.compoundDescription, inchi=c.inchi
+        )
         return redirect(c.url)
     except ValueError as e:
         return 400, {"message": str(e)}
@@ -1874,7 +1830,6 @@ class CreateNode(Schema):
     nodeName: str | None = None
     nodeReason: str | None = None
     nodeDepth: str | None = None
-    pesLink: str | None = None
 
 
 @router.post(
@@ -1886,43 +1841,14 @@ 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()
+        if n.nodeDepth is not None and n.nodeDepth.strip() != "":
+            node_depth = int(n.nodeDepth)
         else:
-            if n.nodeDepth is not None and n.nodeDepth.strip() != "":
-                node_depth = int(n.nodeDepth)
-            else:
-                node_depth = -1
+            node_depth = -1
 
-            node = Node.create(pw, n.nodeAsSmiles, node_depth, n.nodeName, n.nodeReason)
+        n = Node.create(pw, n.nodeAsSmiles, node_depth, n.nodeName, n.nodeReason)
 
-        return redirect(node.url)
+        return redirect(n.url)
     except ValueError:
         return 403, {"message": "Adding node failed!"}
 
@@ -2074,9 +2000,6 @@ 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!"}

epdb/logic.py

@@ -95,8 +95,8 @@ class EPDBURLParser:
 
     def contains_package_url(self):
         return (
-            bool(self.MODEL_PATTERNS["epdb.Package"].findall(self.url))
-            and not self.is_package_url()
+                bool(self.MODEL_PATTERNS["epdb.Package"].findall(self.url))
+                and not self.is_package_url()
         )
 
     def is_user_url(self) -> bool:
@@ -188,7 +188,7 @@ class UserManager(object):
     @staticmethod
     @transaction.atomic
     def create_user(
-        username, email, password, set_setting=True, add_to_group=True, *args, **kwargs
+            username, email, password, set_setting=True, add_to_group=True, *args, **kwargs
     ):
         # Clean for potential XSS
         clean_username = nh3.clean(username).strip()
@@ -346,9 +346,7 @@ class PackageManager(object):
 
     @staticmethod
     def readable(user, package):
-        return (
-            PackageManager.has_package_permission(user, package, "read") | package.reviewed is True
-        )
+        return PackageManager.has_package_permission(user, package, "read")
 
     @staticmethod
     def writable(user, package):
@@ -378,13 +376,13 @@ class PackageManager(object):
         valid_perms = perms.get(permission)
 
         if (
-            UserPackagePermission.objects.filter(
-                package=package, user=user, permission__in=valid_perms
-            ).exists()
-            or GroupPackagePermission.objects.filter(
-                package=package, group__in=groups, permission__in=valid_perms
-            ).exists()
-            or user.is_superuser
+                UserPackagePermission.objects.filter(
+                    package=package, user=user, permission__in=valid_perms
+                ).exists()
+                or GroupPackagePermission.objects.filter(
+            package=package, group__in=groups, permission__in=valid_perms
+        ).exists()
+                or user.is_superuser
         ):
             return True
 
@@ -562,7 +560,7 @@ class PackageManager(object):
     @staticmethod
     @transaction.atomic
     def update_permissions(
-        caller: User, package: Package, grantee: Union[User, Group], new_perm: Optional[str]
+            caller: User, package: Package, grantee: Union[User, Group], new_perm: Optional[str]
     ):
         caller_perm = None
         if not caller.is_superuser:
@@ -605,7 +603,7 @@ class PackageManager(object):
     @staticmethod
     @transaction.atomic
     def import_legacy_package(
-        data: dict, owner: User, keep_ids=False, add_import_timestamp=True, trust_reviewed=False
+            data: dict, owner: User, keep_ids=False, add_import_timestamp=True, trust_reviewed=False
     ):
         from collections import defaultdict
         from datetime import datetime
@@ -685,7 +683,7 @@ class PackageManager(object):
             # Check if parent exists and park this Scenario to convert it later into an
             # AdditionalInformation object
             for ex in scenario.get("additionalInformationCollection", {}).get(
-                "additionalInformation", []
+                    "additionalInformation", []
             ):
                 if ex["name"] == "referringscenario":
                     postponed_scens[ex["data"]].append(scenario)
@@ -708,7 +706,7 @@ class PackageManager(object):
             mapping[scenario["id"]] = scen.uuid
 
             for ex in scenario.get("additionalInformationCollection", {}).get(
-                "additionalInformation", []
+                    "additionalInformation", []
             ):
                 name = ex["name"]
                 addinf_data = ex["data"]
@@ -977,7 +975,7 @@ class PackageManager(object):
         for parent, children in postponed_scens.items():
             for child in children:
                 for ex in child.get("additionalInformationCollection", {}).get(
-                    "additionalInformation", []
+                        "additionalInformation", []
                 ):
                     child_id = child["id"]
                     name = ex["name"]
@@ -1065,9 +1063,52 @@ 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)):
-            pw.update_depths()
+            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)
+
             print(f"{p + 1}/{total_pws} fixed.", end="\r")
 
         return pack
@@ -1075,11 +1116,11 @@ class PackageManager(object):
     @staticmethod
     @transaction.atomic
     def import_package(
-        data: Dict[str, Any],
-        owner: User,
-        preserve_uuids=False,
-        add_import_timestamp=True,
-        trust_reviewed=False,
+            data: Dict[str, Any],
+            owner: User,
+            preserve_uuids=False,
+            add_import_timestamp=True,
+            trust_reviewed=False,
     ) -> Package:
         importer = PackageImporter(data, preserve_uuids, add_import_timestamp, trust_reviewed)
         imported_package = importer.do_import()
@@ -1094,7 +1135,7 @@ class PackageManager(object):
 
     @staticmethod
     def export_package(
-        package: Package, include_models: bool = False, include_external_identifiers: bool = True
+            package: Package, include_models: bool = False, include_external_identifiers: bool = True
     ) -> Dict[str, Any]:
         return PackageExporter(package).do_export()
 
@@ -1121,10 +1162,10 @@ class SettingManager(object):
         s = Setting.objects.get(uuid=setting_id)
 
         if (
-            s.global_default
-            or s.public
-            or user.is_superuser
-            or UserSettingPermission.objects.filter(user=user, setting=s).exists()
+                s.global_default
+                or s.public
+                or user.is_superuser
+                or UserSettingPermission.objects.filter(user=user, setting=s).exists()
         ):
             return s
 
@@ -1134,24 +1175,24 @@ class SettingManager(object):
     def get_all_settings(user):
         sp = UserSettingPermission.objects.filter(user=user).values("setting")
         return (
-            Setting.objects.filter(id__in=sp)
-            | Setting.objects.filter(public=True)
-            | Setting.objects.filter(global_default=True)
+                Setting.objects.filter(id__in=sp)
+                | Setting.objects.filter(public=True)
+                | Setting.objects.filter(global_default=True)
         ).distinct()
 
     @staticmethod
     @transaction.atomic
     def create_setting(
-        user: User,
-        name: str = None,
-        description: str = None,
-        max_nodes: int = None,
-        max_depth: int = None,
-        rule_packages: List[Package] | None = None,
-        model: EPModel = None,
-        model_threshold: float = None,
-        expansion_scheme: ExpansionSchemeChoice = ExpansionSchemeChoice.BFS,
-        property_models: List["PropertyPluginModel"] | None = None,
+            user: User,
+            name: str = None,
+            description: str = None,
+            max_nodes: int = None,
+            max_depth: int = None,
+            rule_packages: List[Package] | None = None,
+            model: EPModel = None,
+            model_threshold: float = None,
+            expansion_scheme: ExpansionSchemeChoice = ExpansionSchemeChoice.BFS,
+            property_models: List["PropertyPluginModel"] | None = None,
     ):
         new_s = Setting()
 
@@ -1230,8 +1271,8 @@ class SearchManager(object):
         pathway_qs = Pathway.objects.filter(
             Q(package__in=packages)
             & (
-                Q(edge__edge_label__educts__inchikey=searchterm)
-                | Q(edge__edge_label__products__inchikey=searchterm)
+                    Q(edge__edge_label__educts__inchikey=searchterm)
+                    | Q(edge__edge_label__products__inchikey=searchterm)
             )
         ).distinct()
 
@@ -1269,8 +1310,8 @@ class SearchManager(object):
         pathway_qs = Pathway.objects.filter(
             Q(package__in=packages)
             & (
-                Q(edge__edge_label__educts__smiles=searchterm)
-                | Q(edge__edge_label__products__smiles=searchterm)
+                    Q(edge__edge_label__educts__smiles=searchterm)
+                    | Q(edge__edge_label__products__smiles=searchterm)
             )
         ).distinct()
 
@@ -1306,15 +1347,15 @@ class SearchManager(object):
         reactions_qs = Reaction.objects.filter(
             Q(package__in=packages)
             & (
-                Q(educts__inchikey__startswith=inchi_front)
-                | Q(products__inchikey__startswith=inchi_front)
+                    Q(educts__inchikey__startswith=inchi_front)
+                    | Q(products__inchikey__startswith=inchi_front)
             )
         ).distinct()
         pathway_qs = Pathway.objects.filter(
             Q(package__in=packages)
             & (
-                Q(edge__edge_label__educts__inchikey__startswith=inchi_front)
-                | Q(edge__edge_label__products__inchikey__startswith=inchi_front)
+                    Q(edge__edge_label__educts__inchikey__startswith=inchi_front)
+                    | Q(edge__edge_label__products__inchikey__startswith=inchi_front)
             )
         ).distinct()
 
@@ -1352,8 +1393,8 @@ class SearchManager(object):
         pathway_qs = Pathway.objects.filter(
             Q(package__in=packages)
             & (
-                Q(edge__edge_label__educts__canonical_smiles=searchterm)
-                | Q(edge__edge_label__products__canonical_smiles=searchterm)
+                    Q(edge__edge_label__educts__canonical_smiles=searchterm)
+                    | Q(edge__edge_label__products__canonical_smiles=searchterm)
             )
         ).distinct()
 
@@ -1428,11 +1469,11 @@ class SNode(object):
 
 class SEdge(object):
     def __init__(
-        self,
-        educts: Union[SNode, List[SNode]],
-        products: Union[SNode | List[SNode]],
-        rule: Optional["Rule"] = None,
-        probability: Optional[float] = None,
+            self,
+            educts: Union[SNode, List[SNode]],
+            products: Union[SNode | List[SNode]],
+            rule: Optional["Rule"] = None,
+            probability: Optional[float] = None,
     ):
         if not isinstance(educts, list):
             educts = [educts]
@@ -1464,11 +1505,11 @@ class SEdge(object):
             return False
 
         if (
-            self.rule is not None
-            and other.rule is None
-            or self.rule is None
-            and other.rule is not None
-            or self.rule != other.rule
+                self.rule is not None
+                and other.rule is None
+                or self.rule is None
+                and other.rule is not None
+                or self.rule != other.rule
         ):
             return False
 
@@ -1476,8 +1517,8 @@ class SEdge(object):
             return False
 
         for n1, n2 in zip(
-            sorted(self.educts, key=lambda x: x.smiles),
-            sorted(other.educts, key=lambda x: x.smiles),
+                sorted(self.educts, key=lambda x: x.smiles),
+                sorted(other.educts, key=lambda x: x.smiles),
         ):
             if n1.smiles != n2.smiles:
                 return False
@@ -1486,8 +1527,8 @@ class SEdge(object):
             return False
 
         for n1, n2 in zip(
-            sorted(self.products, key=lambda x: x.smiles),
-            sorted(other.products, key=lambda x: x.smiles),
+                sorted(self.products, key=lambda x: x.smiles),
+                sorted(other.products, key=lambda x: x.smiles),
         ):
             if n1.smiles != n2.smiles:
                 return False
@@ -1500,10 +1541,10 @@ class SEdge(object):
 
 class SPathway(object):
     def __init__(
-        self,
-        root_nodes: Optional[Union[str, SNode, List[str | SNode]]] = None,
-        persist: Optional["Pathway"] = None,
-        prediction_setting: Optional[Setting] = None,
+            self,
+            root_nodes: Optional[Union[str, SNode, List[str | SNode]]] = None,
+            persist: Optional["Pathway"] = None,
+            prediction_setting: Optional[Setting] = None,
     ):
         self.root_nodes = []
 
@@ -1648,9 +1689,9 @@ class SPathway(object):
             # We don't have any substrate, but technically we have at least one rule that triggered.
             # If our substrate is a root node a.k.a. depth == 0 store that info in SPathway
             if (
-                len(expansion_result["transformations"]) == 0
-                and expansion_result["rule_triggered"]
-                and sub.depth == 0
+                    len(expansion_result["transformations"]) == 0
+                    and expansion_result["rule_triggered"]
+                    and sub.depth == 0
             ):
                 self.empty_due_to_threshold = True
 
@@ -1757,8 +1798,8 @@ class SPathway(object):
                         for prod in edge.products:
                             # Either is a new product or a product and we found a path with a higher prob
                             if (
-                                prod not in node_probs
-                                or current_prob * edge.probability > node_probs[prod]
+                                    prod not in node_probs
+                                    or current_prob * edge.probability > node_probs[prod]
                             ):
                                 node_probs[prod] = current_prob * edge.probability
 

epdb/migrations/0023_alter_compoundstructure_options_and_more.py

@@ -1,54 +1,55 @@
-# Generated by Django 6.0.3 on 2026-04-21 11:43
+# Generated by Django 6.0.3 on 2026-04-17 21:22
 
 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'),
         ),
     ]

epdb/migrations/0024_user_contacted.py

@@ -1,17 +0,0 @@
-# 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

@@ -1,56 +0,0 @@
-# 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/models.py

@@ -75,7 +75,6 @@ class User(AbstractUser):
         blank=False,
     )
     is_reviewer = models.BooleanField(default=False)
-    contacted = models.BooleanField(null=True, blank=True)
 
     USERNAME_FIELD = "email"
     REQUIRED_FIELDS = ["username"]
@@ -2186,56 +2185,6 @@ 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(
@@ -2277,9 +2226,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             if isinstance(ai.get(), PropertyPrediction):
                 predicted_properties[ai.get().__class__.__name__].append(ai.data)
 
-        # 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()
+        extra_structure_data = self.default_node_label.d3_json()
 
         res = {
             "depth": self.depth,
@@ -2290,7 +2237,7 @@ 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()],
@@ -2303,9 +2250,9 @@ 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

epdb/views.py

@@ -937,14 +937,12 @@ def package_models(request, package_uuid):
                 "requires_rule_packages": True,
                 "requires_data_packages": True,
             },
-        }
-
-        if s.ENVIFORMER_PRESENT:
-            context["model_types"]["EnviFormer"] = {
+            "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():
@@ -2539,9 +2537,6 @@ 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:

pepper/__init__.py

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

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

static/js/pw.js

@@ -605,36 +605,7 @@ 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) {
@@ -653,13 +624,7 @@ 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"));
-            }
+            d3.select(this).select("circle").classed("highlighted", !d3.select(this).select("circle").classed("highlighted"));
         })
 
     // Kreise für die Knoten hinzufügen
@@ -672,7 +637,14 @@ function draw(pathway, elem) {
     node.filter(d => !d.pseudo).each(function (d, i) {
         const g = d3.select(this);
 
-        if (d.image_type === "svg") {
+        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 {
             // Parse the SVG string
             const parser = new DOMParser();
             const svgDoc = parser.parseFromString(d.image_svg, "image/svg+xml");
@@ -690,7 +662,7 @@ function draw(pathway, elem) {
                 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") === `#${oldId}`
+                  u => u.getAttributeNS(XLINK_NS, "href") === `#${oldId}`
                 );
 
                 uses.forEach(u => {
@@ -707,19 +679,10 @@ function draw(pathway, elem) {
             const scale = (nodeRadius * 2) / Math.max(svgWidth, svgHeight);
 
             g.select("svg")
-                .attr("width", svgWidth * scale)
-                .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);
+              .attr("width", svgWidth * scale)
+              .attr("height", svgHeight * scale)
+              .attr("x", -svgWidth * scale / 2)
+              .attr("y", -svgHeight * scale / 2);
         }
 
     });

templates/actions/objects/pathway.html

@@ -1,5 +1,3 @@
-{% load envipytags %}
-
 {% if meta.can_edit %}
   <li>
     <a
@@ -9,6 +7,14 @@
       <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"
@@ -17,12 +23,7 @@
       <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 h-px"></li>
+  <li role="separator" class="divider"></li>
 {% endif %}
 <li>
   <a
@@ -74,7 +75,7 @@
       Rules</a
     >
   </li>
-  <li role="separator" class="divider h-px"></li>
+  <li role="separator" class="divider"></li>
   <li>
     <a
       class="button"
@@ -99,16 +100,11 @@
       <i class="glyphicon glyphicon-plus"></i> Set Aliases</a
     >
   </li>
-  <li role="separator" class="divider h-px"></li>
+  <li role="separator" class="divider"></li>
   <li>
     <a
       class="button"
-      onclick="
-      const modal = document.getElementById('delete_pathway_node_modal');
-      modal.showModal();
-      window.dispatchEvent(new Event('modal-opened'));
-      return false;
-      "
+      onclick="document.getElementById('delete_pathway_node_modal').showModal(); return false;"
     >
       <i class="glyphicon glyphicon-trash"></i> Delete Compound</a
     >
@@ -116,12 +112,7 @@
   <li>
     <a
       class="button"
-      onclick="
-      const modal = document.getElementById('delete_pathway_edge_modal');
-      modal.showModal();
-      window.dispatchEvent(new Event('modal-opened'));
-      return false;
-      "
+      onclick="document.getElementById('delete_pathway_edge_modal').showModal(); return false;"
     >
       <i class="glyphicon glyphicon-trash"></i> Delete Reaction</a
     >

templates/collections/compounds_paginated.html

@@ -5,7 +5,7 @@
 
 {% block action_button %}
   <div class="flex items-center gap-2">
-    {% if meta.can_edit or not meta.url_contains_package %}
+    {% if meta.can_edit %}
       <button
         type="button"
         class="btn btn-primary btn-sm"

templates/collections/models_paginated.html

@@ -3,16 +3,14 @@
 {% block page_title %}Models{% endblock %}
 
 {% block action_button %}
-  {% 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"
-        onclick="document.getElementById('new_model_modal').showModal(); return false;"
-      >
-        New Model
-      </button>
-    {% endif %}
+  {% if meta.can_edit and meta.enabled_features.MODEL_BUILDING %}
+    <button
+      type="button"
+      class="btn btn-primary btn-sm"
+      onclick="document.getElementById('new_model_modal').showModal(); return false;"
+    >
+      New Model
+    </button>
   {% endif %}
 {% endblock action_button %}
 

templates/collections/packages_paginated.html

@@ -3,6 +3,7 @@
 {% block page_title %}Packages{% endblock %}
 
 {% block action_button %}
+  {% if meta.can_edit %}
     <div class="flex items-center gap-2">
       <button
         type="button"
@@ -70,6 +71,7 @@
         </ul>
       </div>
     </div>
+  {% endif %}
 {% endblock action_button %}
 
 {% block action_modals %}

templates/collections/pathways_paginated.html

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

templates/collections/reactions_paginated.html

@@ -3,7 +3,7 @@
 {% block page_title %}Reactions{% endblock %}
 
 {% block action_button %}
-  {% if meta.can_edit or not meta.url_contains_package %}
+  {% if meta.can_edit %}
     <button
       type="button"
       class="btn btn-primary btn-sm"

templates/collections/rules_paginated.html

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

templates/collections/scenarios_paginated.html

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

templates/collections/structures_paginated.html

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

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"
-              value="0.25"
+              placeholder="0.25"
               type="number"
               min="0"
               max="1"
-              step="any"
+              step="0.05"
             />
           </div>
 

templates/modals/objects/delete_pathway_edge_modal.html

@@ -4,25 +4,6 @@
   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">

templates/modals/objects/delete_pathway_node_modal.html

@@ -4,22 +4,6 @@
   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">

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 %}

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 %}

templates/objects/pathway.html

@@ -1,7 +1,5 @@
 {% extends "framework_modern.html" %}
 {% load static %}
-{% load envipytags %}
-
 {% block content %}
   <script src="https://d3js.org/d3.v7.min.js"></script>
   <style>
@@ -77,11 +75,8 @@
 
   {% 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" %}
@@ -106,12 +101,12 @@
     </div>
 
     <!-- Graphical Representation -->
-    <div class="collapse-arrow bg-base-200 collapse overflow-y-auto">
+    <div class="collapse-arrow bg-base-200 collapse">
       <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">
@@ -140,7 +135,7 @@
                 </div>
                 <ul
                   tabindex="0"
-                  class="dropdown-content menu bg-base-100 rounded-box z-50 w-96 p-2"
+                  class="dropdown-content menu bg-base-100 rounded-box z-50 w-52 p-2"
                 >
                   {% include "actions/objects/pathway.html" %}
                 </ul>

utilities/chem.py

@@ -182,9 +182,11 @@ class FormatConverter(object):
 
         drawer = rdMolDraw2D.MolDraw2DCairo(*mol_size)
         opts = drawer.drawOptions()
+
         opts.clearBackground = False
         drawer.DrawMolecule(mol)
         drawer.FinishDrawing()
+
         return drawer.GetDrawingText()
 
     @staticmethod

utilities/legacy.py

@@ -64,7 +64,7 @@
 
 import logging
 
-from envipy_additional_information import HalfLife, HalfLifeWS, HalfLifeModel
+from envipy_additional_information import HalfLife, HalfLifeWS
 from envipy_additional_information.information import Interval
 from envipy_additional_information.parsers import (
     AcidityParser,
@@ -473,12 +473,17 @@ 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 model:
-                model = HalfLifeModel(model.upper())
+            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")
 
             return HalfLife(model=model, fit=fit, comment=comment, dt50=i, source=source)
 
@@ -503,10 +508,6 @@ 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)

uv.lock

@@ -17,7 +17,7 @@ wheels = [
 
 [[package]]
 name = "aiohttp"
-version = "3.13.5"
+version = "3.13.3"
 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/77/9a/152096d4808df8e4268befa55fba462f440f14beab85e8ad9bf990516918/aiohttp-3.13.5.tar.gz", hash = "sha256:9d98cc980ecc96be6eb4c1994ce35d28d8b1f5e5208a23b421187d1209dbb7d1", size = 7858271, upload-time = "2026-03-31T22:01:03.343Z" }
+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" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/be/6f/353954c29e7dcce7cf00280a02c75f30e133c00793c7a2ed3776d7b2f426/aiohttp-3.13.5-cp312-cp312-macosx_10_13_universal2.whl", hash = "sha256:023ecba036ddd840b0b19bf195bfae970083fd7024ce1ac22e9bba90464620e9", size = 748876, upload-time = "2026-03-31T21:57:36.319Z" },
-    { url = "https://files.pythonhosted.org/packages/f5/1b/428a7c64687b3b2e9cd293186695affc0e1e54a445d0361743b231f11066/aiohttp-3.13.5-cp312-cp312-macosx_10_13_x86_64.whl", hash = "sha256:15c933ad7920b7d9a20de151efcd05a6e38302cbf0e10c9b2acb9a42210a2416", size = 499557, upload-time = "2026-03-31T21:57:38.236Z" },
-    { url = "https://files.pythonhosted.org/packages/29/47/7be41556bfbb6917069d6a6634bb7dd5e163ba445b783a90d40f5ac7e3a7/aiohttp-3.13.5-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:ab2899f9fa2f9f741896ebb6fa07c4c883bfa5c7f2ddd8cf2aafa86fa981b2d2", size = 500258, upload-time = "2026-03-31T21:57:39.923Z" },
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 [[package]]
@@ -2785,19 +2785,19 @@ dependencies = [
     { name = "typing-extensions", marker = "sys_platform == 'linux' or sys_platform == 'win32'" },
 ]
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 ]
 
 [[package]]