wip

Dockerfile

@@ -6,23 +6,18 @@ ENV PYTHONDONTWRITEBYTECODE=1 \
 
 WORKDIR /app
 
-
 RUN apt-get update && apt-get install -y --no-install-recommends \
     build-essential \
     libpq-dev \
     curl \
     openssh-client \
     git \
-    ca-certificates \
+    nodejs \
+    npm \
     && rm -rf /var/lib/apt/lists/*
 
-# Install Node 22 + pnpm
+# Install pnpm
-RUN curl -fsSL https://deb.nodesource.com/setup_22.x | bash - \
+RUN npm install -g pnpm
-    && apt-get update \
-    && apt-get install -y --no-install-recommends nodejs \
-    && corepack enable \
-    && corepack prepare pnpm@latest --activate \
-    && rm -rf /var/lib/apt/lists/*
 
 RUN curl -LsSf https://astral.sh/uv/install.sh | sh
 ENV PATH="/root/.local/bin:${PATH}"
@@ -35,13 +30,12 @@ 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 bridge bridge

bayer/additional_information/__init__.py

@@ -1,178 +0,0 @@
-import enum
-from typing import Optional
-
-from envipy_additional_information import GroupEnum as G
-from envipy_additional_information import SubcategoryEnum as S
-from envipy_additional_information import (
-    register,
-    register_parser_command,
-    EnviPyModel,
-    # EnviPyModelParser,
-    Interval,
-    UIConfig,
-    IntervalConfig,
-    WidgetType,
-    registry,
-)
-
-
-@register(keyname="compoundlabel", groups=[S.MISC, G.SLUDGE, G.SEDIMENT, G.SOIL])
-class CompoundLabel(EnviPyModel):
-    label: str
-
-    class UI:
-        title = "Compound Label"
-        label = UIConfig(widget=WidgetType.TEXT, label="Label", order=1)
-
-
-# TODO Expose EnviPyModelParser in lib and subclass
-@register_parser_command("compoundlabel")
-class CompoundLabelParser:
-    @staticmethod
-    def from_string(data: str) -> CompoundLabel:
-        return CompoundLabel(label=data)
-
-
-@register(keyname="studywaterstoragecapacity", groups=[S.MISC, G.SLUDGE, G.SEDIMENT, G.SOIL])
-class StudyWaterStorageCapacity(EnviPyModel):
-    capacity: str
-
-    class UI:
-        title = "Study Water Storage Capacity"
-        capacity = UIConfig(widget=WidgetType.TEXT, label="Study Water Storage Capacity", order=1)
-
-
-# TODO Expose EnviPyModelParser in lib and subclass
-@register_parser_command("studywst")
-class StudyWaterStorageCapacityParser:
-    @staticmethod
-    def from_string(data: str) -> StudyWaterStorageCapacity:
-        return StudyWaterStorageCapacity(capacity=data)
-
-
-class ObservationType(enum.Enum):
-    OBSERVED = "observed"
-    APPLIED = "applied"
-    NA = 'NA'
-
-
-@register(keyname="observation", groups=[S.MISC, G.SLUDGE, G.SEDIMENT, G.SOIL])
-class Observation(EnviPyModel):
-    type: ObservationType
-    min_value: Optional[float] = None
-    max_value: Optional[float] = None
-
-    class UI:
-        title = "Observation"
-        type = UIConfig(widget=WidgetType.SELECT, label="Observed or Applied", order=1)
-        min_value = UIConfig(widget=WidgetType.NUMBER, label="Min Value", order=2)
-        max_value = UIConfig(widget=WidgetType.NUMBER, label="Max Value", order=3)
-
-
-# TODO Expose EnviPyModelParser in lib and subclass
-@register_parser_command("observation")
-class ObservationParser:
-    @staticmethod
-    def from_string(data: str) -> Observation:
-        parts = data.split(";")
-
-        observation_type = ObservationType(parts[0])
-        min_value = None
-        if parts[1]:
-            try:
-                min_value = float(parts[1])
-            except ValueError:
-                pass
-
-        max_value = None
-        if parts[2]:
-            try:
-                max_value = float(parts[2])
-            except ValueError:
-                pass
-
-        return Observation(type=observation_type, min_value=min_value, max_value=max_value)
-
-
-@register(keyname="kinetics", groups=[S.MISC, G.SLUDGE, G.SEDIMENT, G.SOIL])
-class Kinetics(EnviPyModel):
-    dt50: Interval[float]
-    normalized_dt50: bool
-    chi2err: Optional[float] = None
-    t_test: Optional[float] = None
-    swarc: Optional[float] = None
-    visual_fit: Optional[int] = None
-    comment: str
-    source: str
-    kinetic_model: str
-    k1: Optional[float] = None
-    k2: Optional[float] = None
-    g: Optional[float] = None
-    tb: Optional[float] = None
-    alpha: Optional[float] = None
-    beta: Optional[float] = None
-
-    class UI:
-        title = "Kinetics"
-
-        # Field config
-        dt50 = IntervalConfig(label="DT50 Range", order=1, unit="d")
-        normalized_dt50 = UIConfig(widget=WidgetType.CHECKBOX, label="Normalized DT50", order=2)
-        chi2err = UIConfig(widget=WidgetType.NUMBER, label="Chi2err", order=3)
-        t_test = UIConfig(widget=WidgetType.NUMBER, label="T-Test", order=4)
-        swarc = UIConfig(widget=WidgetType.NUMBER, label="SWARC", order=5)
-        visual_fit = UIConfig(widget=WidgetType.NUMBER, label="Visual Fit", order=6)
-        comment = UIConfig(widget=WidgetType.TEXTAREA, label="Comments", order=7)
-        source = UIConfig(widget=WidgetType.TEXT, label="Source", order=8)
-        kinetic_model = UIConfig(widget=WidgetType.SELECT, label="Kinetic Model", order=9)
-        k1 = UIConfig(widget=WidgetType.NUMBER, label="K1", order=10)
-        k2 = UIConfig(widget=WidgetType.NUMBER, label="K2", order=11)
-        g = UIConfig(widget=WidgetType.NUMBER, label="G", order=12)
-        tb = UIConfig(widget=WidgetType.NUMBER, label="TB", order=13)
-        alpha = UIConfig(widget=WidgetType.NUMBER, label="Alpha", order=14)
-        beta = UIConfig(widget=WidgetType.NUMBER, label="Beta", order=15)
-
-
-# TODO Expose EnviPyModelParser in lib and subclass
-@register_parser_command("kineticevaluation")
-class KinecticsParser:
-    @staticmethod
-    def from_string(data: str) -> Kinetics:
-        parts = data.split(";")
-        dt50 = registry.get_parser("interval").from_string(parts[0])
-        normalized_dt50 = parts[1] == "true"
-        chi2err = float(parts[2]) if parts[2] else None
-        t_test = float(parts[3]) if parts[3] else None
-        swarc = float(parts[4]) if parts[4] else None
-        visual_fit = int(parts[5]) if parts[5] else None
-        comment = parts[6]
-        source = parts[7]
-        kinetic_model = parts[8]
-        k1 = float(parts[9]) if parts[9] else None
-        k2 = float(parts[10]) if parts[10] else None
-        g = float(parts[11]) if parts[11] else None
-        tb = float(parts[12]) if parts[12] else None
-        alpha = float(parts[13]) if parts[13] else None
-        beta = float(parts[14]) if parts[14] else None
-
-        return Kinetics(
-            dt50=dt50,
-            normalized_dt50=normalized_dt50,
-            chi2err=chi2err,
-            t_test=t_test,
-            swarc=swarc,
-            visual_fit=visual_fit,
-            comment=comment,
-            source=source,
-            kinetic_model=kinetic_model,
-            k1=k1,
-            k2=k2,
-            g=g,
-            tb=tb,
-            alpha=alpha,
-            beta=beta,
-        )
-
-
-if __name__ == '__main__':
-    print(KinecticsParser.from_string("187.0 - 187.0;false;;;;;;;AFO;;;;;;"))

bayer/epdb_hooks.py

@@ -1,6 +1,5 @@
 import logging
 
-from bayer import additional_information  # noqa: F401
 from epdb.template_registry import register_template
 
 logger = logging.getLogger(__name__)
@@ -14,14 +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(
@@ -37,4 +28,4 @@ register_template(
 register_template(
     "epdb.objects.node.viz",
     "objects/node_viz.html",
-)
+)

bayer/models.py

@@ -232,6 +232,5 @@ class PESStructure(CompoundStructure):
             "is_pes": True,
             "pes_link": self.pes_link,
             # Will overwrite image from Node
-            "image": f"{reverse('depict_pes')}?pesLink={urllib.parse.quote(self.pes_link)}",
+            "image": f"{reverse("depict_pes")}?pesLink={urllib.parse.quote(self.pes_link)}"
-            "image_type": "png",
         }

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

@@ -37,10 +37,6 @@ def create_pes(request, package_uuid):
 
             classification = pes_data.get("classificationLevel", "")
             if "secret" == classification.lower():
-
-                if current_package.classification_level != Package.Classification.SECRET:
-                    return BadRequest("Cannot create PESs for non-secret packages.")
-
                 data_pools = pes_data.get("dataPools")
                 if data_pools:
                     if s.DATA_POOL_MAPPING[current_package.data_pool.name] not in data_pools:
@@ -79,10 +75,6 @@ def create_pes_node(request, package_uuid, pathway_uuid):
 
             classification = pes_data.get("classificationLevel", "")
             if "secret" == classification.lower():
-
-                if current_package.classification_level != Package.Classification.SECRET:
-                    return BadRequest("Cannot create PESs for non-secret packages.")
-
                 data_pools = pes_data.get("dataPools")
                 if data_pools:
                     if s.DATA_POOL_MAPPING[current_package.data_pool.name] not in data_pools:
@@ -91,10 +83,6 @@ def create_pes_node(request, package_uuid, pathway_uuid):
 
             pes = PESCompound.create(current_package, pes_data, compound_name, compound_description)
 
-            node_qs = Node.objects.filter(pathway=current_pathway, default_node_label=pes.default_structure)
-            if node_qs.exists():
-                return redirect(current_pathway.url)
-
             n = Node()
             n.stereo_removed = False
             n.pathway = current_pathway
@@ -115,15 +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
@@ -132,7 +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

@@ -1,199 +0,0 @@
-import enum
-import json
-import logging
-import math
-from datetime import datetime
-from typing import List
-
-import requests
-from django.conf import settings as s
-from envipy_additional_information import register, EnviPyModel, UIConfig, WidgetType
-
-from bridge.contracts import Classifier  # noqa: I001
-from bridge.dto import (
-    BuildResult,
-    EnviPyDTO,
-    EvaluationResult,
-    RunResult,
-    TransformationProductPrediction,
-)  # noqa: I001
-
-logger = logging.getLogger("epdb")
-
-
-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)
-            logger.info(f"Starting BB4G: {res.status_code}")
-            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,
-            }
-
-            retries = 0
-            while retries < 5:
-                resp = requests.post(f"{self.url}/compute", headers=header, data=json.dumps(data),
-                                     proxies=s.PROXIES or None)
-
-                if resp.status_code == 418:
-                    retries += 1
-                    logger.info(f"BB4G predict hit a 418, retrying in 60 seconds")
-                    import time
-                    time.sleep(60)
-                    continue
-
-                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
-
-                break
-
-        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
-
+        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):

docker-compose.dev.yml

@@ -25,7 +25,7 @@ services:
       - ep_bayer_redis_data:/data
 
   biotransformer3:
-    image: git.envipath.com/envipath/biotransformer3:1.0
+    image: envipath/biotransformer3:1.0
     container_name: epbiotransformer3
 
 #  web:
@@ -40,7 +40,7 @@ services:
 #      - ep_bayer_data:/opt/enviPy/
 
   celery_worker:
-    image: git.envipath.com/envipath/envipy-bayer:1.0
+    image: envipath/envipy-bayer:1.0
     container_name: epcelery
     env_file:
       - .env.dev

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
@@ -275,12 +269,6 @@ LOGGING = {
             "filename": os.path.join(LOG_DIR, "debug.log"),
             "formatter": "simple",
         },
-        "auth_file": {
-            "level": "INFO",  # Or higher
-            "class": "logging.FileHandler",
-            "filename": os.path.join(LOG_DIR, "auth.log"),
-            "formatter": "simple",
-        }
     },
     "loggers": {
         # For everything under epdb/ loaded via getlogger(__name__)
@@ -301,11 +289,6 @@ LOGGING = {
             "propagate": True,
             "level": os.environ.get("LOG_LEVEL", "INFO"),
         },
-        "auth": {
-            "handlers": ["auth_file"],
-            "propagate": True,
-            "level": os.environ.get("LOG_LEVEL", "INFO"),
-        }
     },
 }
 
@@ -491,16 +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")
-
-os.environ["NO_PROXY"] = "localhost,127.0.0.1,epbiotransformer3"

epapi/v1/endpoints/joblogs.py

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

epapi/v1/router.py

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

epapi/v1/schemas.py

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

epauth/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

@@ -2,11 +2,9 @@ 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
+from epdb.logic import UserManager
-from epdb.models import Group
 
 
 def get_msal_app_with_cache(request):
@@ -83,12 +81,10 @@ 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():
-            g = GroupManager.create_group(User.objects.get(username="admin"), name, f"Synced Entra Group {name} ",
+            g = GroupManager.create_group(User.objects.get(username="admin"), name, f"Synced Entra Group {name} ", uuid=id)
-                                          uuid=id)
         else:
             g = Group.objects.get(uuid=id)
         # Ensure its secret
@@ -97,8 +93,7 @@ def entra_callback(request):
 
     for id, name in s.ENTRA_GROUPS.items():
         if not Group.objects.filter(uuid=id).exists():
-            g = GroupManager.create_group(User.objects.get(username="admin"), name, f"Synced Entra Group {name} ",
+            g = GroupManager.create_group(User.objects.get(username="admin"), name, f"Synced Entra Group {name} ", uuid=id)
-                                          uuid=id)
         else:
             g = Group.objects.get(uuid=id)
 
@@ -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
 
@@ -162,9 +152,3 @@ 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
+    claims = jwt.decode(
-    try:
+        token,
-        claims = jwt.decode(
+        public_key,
-            token,
+        algorithms=["RS256"],
-            public_key,
+        audience=[CLIENT_ID, f"api://{CLIENT_ID}"],
-            algorithms=["RS256"],
+        issuer=f"https://sts.windows.net/{TENANT_ID}/",
-            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}")
-
     return claims
 
 
@@ -439,50 +415,23 @@ class PackageSchema(Schema):
 
     @staticmethod
     def resolve_readers(obj: Package):
-        readers = []
+        users = User.objects.filter(
+            id__in=UserPackagePermission.objects.filter(
+                package=obj, permission=UserPackagePermission.READ[0]
+            ).values_list("user", flat=True)
+        ).distinct()
 
-        user_ids = UserPackagePermission.objects.filter(package=obj).values_list("user", flat=True)
+        return [{u.id: u.get_name()} for u in users]
-
-        users = User.objects.filter(id__in=user_ids).distinct()
-
-        for u in users:
-            readers.append({"id": str(u.url), "identifier": "user", "name": u.get_name()})
-
-        group_ids = GroupPackagePermission.objects.filter(package=obj).values_list(
-            "group", flat=True
-        )
-
-        groups = Group.objects.filter(id__in=group_ids).distinct()
-
-        for g in groups:
-            readers.append({"id": str(g.url), "identifier": "group", "name": g.get_name()})
-
-        return readers
 
     @staticmethod
     def resolve_writers(obj: Package):
-        writers = []
+        users = User.objects.filter(
+            id__in=UserPackagePermission.objects.filter(
+                package=obj, permission=UserPackagePermission.WRITE[0]
+            ).values_list("user", flat=True)
+        ).distinct()
 
-        user_ids = UserPackagePermission.objects.filter(
+        return [{u.id: u.get_name()} for u in users]
-            package=obj,
-            permission__in=[UserPackagePermission.WRITE[0], UserPackagePermission.ALL[0]],
-        ).values_list("user", flat=True)
-
-        users = User.objects.filter(id__in=user_ids).distinct()
-
-        for u in users:
-            writers.append({"id": str(u.url), "identifier": "user", "name": u.get_name()})
-
-        group_ids = GroupPackagePermission.objects.filter(
-            package=obj, permission=[UserPackagePermission.WRITE[0], UserPackagePermission.ALL[0]]
-        ).values_list("group", flat=True)
-
-        groups = Group.objects.filter(id__in=group_ids).distinct()
-
-        for g in groups:
-            writers.append({"id": str(g.url), "identifier": "group", "name": g.get_name()})
-
-        return writers
 
     @staticmethod
     def resolve_review_comment(obj):
@@ -847,7 +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")
@@ -859,32 +807,9 @@ def create_package_compound(
     try:
         p = get_package_for_write(request.user, package_uuid)
         # inchi is not used atm
-
+        c = Compound.create(
-        if c.pesLink is not None:
+            p, c.compoundSmiles, c.compoundName, c.compoundDescription, inchi=c.inchi
-            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():
-
-                if p.classification_level != Package.Classification.SECRET:
-                    return 400, {"Cannot create PESs for non-secret packages."}
-
-                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
-            )
         return redirect(c.url)
     except ValueError as e:
         return 400, {"message": str(e)}
@@ -903,27 +828,6 @@ def delete_compound(request, package_uuid, compound_uuid):
         }
 
 
-class CreateCompoundStructure(Schema):
-    smiles: str
-    name: str | None = None
-    description: str | None = None
-    inchi: str | None = None
-    molfile: str | None = None
-
-
-@router.post("/package/{uuid:package_uuid}/compound/{uuid:compound_uuid}/structure")
-def create_package_compound_structure(
-    request, package_uuid, compound_uuid, structure: Form[CreateCompoundStructure]
-):
-    try:
-        p = get_package_for_write(request.user, package_uuid)
-        c = Compound.objects.get(package=p, uuid=compound_uuid)
-        cs = CompoundStructure.create(c, structure.smiles, structure.name, structure.description)
-        return redirect(cs.url)
-    except ValueError as e:
-        return 400, {"message": str(e)}
-
-
 @router.delete(
     "/package/{uuid:package_uuid}/compound/{uuid:compound_uuid}/structure/{uuid:structure_uuid}"
 )
@@ -1450,7 +1354,6 @@ class ScenarioSchema(Schema):
     aliases: List[str] = Field([], alias="aliases")
     collection: Dict["str", List[Dict[str, Any]]] = Field([], alias="collection")
     collectionID: Optional[str] = None
-    date: str = Field(None, alias="scenario_date")
     description: str = Field(None, alias="description")
     id: str = Field(None, alias="url")
     identifier: str = "scenario"
@@ -1594,56 +1497,28 @@ def create_package_additional_information(request, package_uuid):
         scen = request.POST.get("scenario")
         scenario = Scenario.objects.get(package=p, url=scen)
 
-        if request.POST.get("adInfoTypes[]"):
+        url_parser = EPDBURLParser(request.POST.get("attach_obj"))
-            url_parser = EPDBURLParser(request.POST.get("attach_obj"))
+        attach_obj = url_parser.get_object()
-            attach_obj = url_parser.get_object()
 
-            if not hasattr(attach_obj, "additional_information"):
+        if not hasattr(attach_obj, "additional_information"):
-                raise ValueError("Can't attach additional information to this object!")
+            raise ValueError("Can't attach additional information to this object!")
 
-            if not attach_obj.url.startswith(p.url):
+        if not attach_obj.url.startswith(p.url):
-                raise ValueError(
+            raise ValueError(
-                    "Additional Information can only be set to objects stored in the same package!"
+                "Additional Information can only be set to objects stored in the same package!"
-                )
+            )
 
-            types = request.POST.get("adInfoTypes[]", "").split(",")
+        types = request.POST.get("adInfoTypes[]", "").split(",")
 
-            for t in types:
+        for t in types:
-                ai = build_additional_information_from_request(request, t)
+            ai = build_additional_information_from_request(request, t)
 
-                AdditionalInformation.create(
+            AdditionalInformation.create(
-                    p,
+                p,
-                    ai,
+                ai,
-                    scenario=scenario,
+                scenario=scenario,
-                    content_object=attach_obj,
+                content_object=attach_obj,
-                )
+            )
-
-        elif request.POST.get("ais"):
-            import json
-
-            parsed_ais = json.loads(request.POST.get("ais"))
-
-            for ai_type, ais in parsed_ais.items():
-                for ai in ais:
-                    attach_obj = None
-                    if ai.get("related"):
-                        url_parser = EPDBURLParser(ai.get("related").get("url"))
-                        attach_obj = url_parser.get_object()
-
-                        if not hasattr(attach_obj, "additional_information"):
-                            raise ValueError("Can't attach additional information to this object!")
-
-                        if not attach_obj.url.startswith(p.url):
-                            raise ValueError(
-                                "Additional Information can only be set to objects stored in the same package!"
-                            )
-
-                    AdditionalInformation.create(
-                        p,
-                        AdditionalInformation.from_dict(ai_type, ai),
-                        scenario=scenario,
-                        content_object=attach_obj,
-                    )
 
         # TODO implement additional information endpoint ?
         return redirect(f"{scenario.url}")
@@ -1694,7 +1569,6 @@ class PathwayNode(Schema):
     name: str = Field(None, alias="name")
     proposed: List[Dict[str, str]] = Field([], alias="proposed_intermediate")
     smiles: str = Field(None, alias="default_node_label.smiles")
-    pseudo: bool = Field(False, alias="pseudo")
 
     @staticmethod
     def resolve_atom_count(obj: Node):
@@ -1848,29 +1722,6 @@ def create_package_pathway(
         return 403, {"message": str(e)}
 
 
-@router.post("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}")
-def update_pathway(request, package_uuid, pathway_uuid):
-    try:
-        p = get_package_for_write(request.user, package_uuid)
-
-        if request.POST.get("scenario"):
-            pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
-            scen = Scenario.objects.get(package=p, url=request.POST.get("scenario"))
-
-            pw.scenarios.add(scen)
-            pw.save()
-
-            return redirect(f"{pw.url}")
-
-        else:
-            return 400, {"message": "No scenario specified!"}
-
-    except ValueError:
-        return 403, {
-            "message": f"Deleting Pathway with id {pathway_uuid} failed due to insufficient rights!"
-        }
-
-
 @router.delete("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}")
 def delete_pathway(request, package_uuid, pathway_uuid):
     try:
@@ -1979,67 +1830,25 @@ class CreateNode(Schema):
     nodeName: str | None = None
     nodeReason: str | None = None
     nodeDepth: str | None = None
-    pesLink: str | None = None
 
 
 @router.post(
     "/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}/node",
-    response={200: str | Any, 400: Error, 403: Error},
+    response={200: str | Any, 403: Error},
 )
 def add_pathway_node(request, package_uuid, pathway_uuid, n: Form[CreateNode]):
     try:
         p = get_package_for_write(request.user, package_uuid)
         pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
 
-        # TODO Code Dup from bayer.views
+        if n.nodeDepth is not None and n.nodeDepth.strip() != "":
-
+            node_depth = int(n.nodeDepth)
-        if n.pesLink:
-            from bayer.views import fetch_pes
-            from bayer.models import PESCompound
-
-            try:
-                pes_data = fetch_pes(request, n.pesLink)
-            except ValueError as e:
-                return 400, {"message": f"Could not fetch PES data for {n.pesLink}"}
-
-            classification = pes_data.get("classificationLevel", "")
-            if "secret" == classification.lower():
-
-                if p.classification_level != Package.Classification.SECRET:
-                    return 400, "Cannot create PESs for non-secret packages."
-
-                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, n.nodeName, n.nodeReason)
-
-            node_qs = Node.objects.filter(pathway=pw, default_node_label=c.default_structure)
-            if node_qs.exists():
-                return redirect(pw.url)
-
-            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 = -1
-                node_depth = int(n.nodeDepth)
-            else:
-                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!"}
 
@@ -2182,10 +1991,6 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
             for pr in e.products.split(","):
                 products.append(Node.objects.get(pathway=pw, url=pr.strip()))
 
-        multi_step = False
-        if e.multistep and e.multistep.strip() == "true":
-            multi_step = True
-
         new_e = Edge.create(
             pathway=pw,
             start_nodes=educts,
@@ -2193,12 +1998,8 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
             rule=None,
             name=None,
             description=e.edgeReason,
-            multi_step=multi_step,
         )
 
-        # Update depths as sideeffect of above operation
-        pw.update_depths()
-
         return redirect(new_e.url)
     except ValueError:
         return 403, {"message": "Adding Edge failed!"}

epdb/logic.py

@@ -1065,9 +1065,52 @@ 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

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/migrations/0026_auto_20260602_1718.py

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

epdb/models.py

@@ -75,7 +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"]
@@ -1703,7 +1702,7 @@ class Reaction(
         if name is not None and name.strip() != "":
             r.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
 
-        if description is not None and description.strip() != "":
+        if description is not None and name.strip() != "":
             r.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
         r.multi_step = multi_step
@@ -1781,7 +1780,7 @@ class Reaction(
         return new_reaction
 
     def smirks(self):
-        return f"{'.'.join([cs.smiles for cs in self.educts.all().order_by('-pk')])}>>{'.'.join([cs.smiles for cs in self.products.all().order_by('-pk')])}"
+        return f"{'.'.join([cs.smiles for cs in self.educts.all()])}>>{'.'.join([cs.smiles for cs in self.products.all()])}"
 
     @property
     def as_svg(self):
@@ -1894,9 +1893,6 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
                 if n not in queue:
                     queue.append(n)
 
-        for i in queue:
-            processed.add(i)
-
         while len(queue):
             current = queue.pop()
             processed.add(current)
@@ -2174,7 +2170,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
         smiles: str,
         name: Optional[str] = None,
         description: Optional[str] = None,
-        depth: Optional[int] = -1,
+        depth: Optional[int] = 0,
     ):
         return Node.create(self, smiles, depth, name=name, description=description)
 
@@ -2189,66 +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()
-        processed = set()
-
-        data_driven_root_nodes = self.node_set.all().annotate(
-            prod_cnt=Count('edge_products'),
-            educt_cnt=Count('edge_educts')
-        ).filter(prod_cnt=0, educt_cnt__gt=0).distinct()
-
-        # Eval QuerySet
-        root_nodes_by_depth = list(self.root_nodes)
-
-        data_driven_root_nodes.update(depth=0)
-        root_nodes = [n for n in data_driven_root_nodes]
-
-        for n in root_nodes_by_depth:
-            if n not in root_nodes:
-                if len(n.edge_products.all()) == 0:
-                    root_nodes.append(n)
-
-        for n in root_nodes:
-            depth_map[0].append(n)
-
-        # At most depth len(nodes) is possible
-        for i in range(self.nodes.count()):
-            level_nodes = depth_map.get(i, [])
-
-            if len(level_nodes) == 0:
-                break
-
-            unique_next_level = set()
-            for n in level_nodes:
-                processed.add(n)
-                for e in self.edges:
-                    if n in e.start_nodes.all():
-                        for p in e.end_nodes.all():
-                            if p not in processed:
-                                unique_next_level.add(p)
-
-            if len(unique_next_level) > 0:
-                depth_map[i + 1] = list(unique_next_level)
-
-        for depth, nodes in depth_map.items():
-            for n in nodes:
-                if n.depth != depth and depth != 0:
-                    n.depth = depth
-                    n.save()
-
 
 class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin):
     pathway = models.ForeignKey(
@@ -2397,7 +2333,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
         "epdb.Pathway", verbose_name="belongs to", on_delete=models.CASCADE, db_index=True
     )
     edge_label = models.ForeignKey(
-        "epdb.Reaction", verbose_name="Edge label", null=True, on_delete=models.CASCADE
+        "epdb.Reaction", verbose_name="Edge label", null=True, on_delete=models.SET_NULL
     )
     start_nodes = models.ManyToManyField(
         "epdb.Node", verbose_name="Start Nodes", related_name="edge_educts"
@@ -2476,8 +2412,6 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
         rule: Optional[Rule] = None,
         name: Optional[str] = None,
         description: Optional[str] = None,
-        *args,
-        **kwargs,
     ):
         e = Edge()
         e.pathway = pathway
@@ -2507,7 +2441,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             educts=[n.default_node_label for n in e.start_nodes.all()],
             products=[n.default_node_label for n in e.end_nodes.all()],
             rules=rule,
-            multi_step=kwargs.get("multi_step", False),
+            multi_step=False,
         )
 
         e.edge_label = r
@@ -4515,22 +4449,18 @@ class AdditionalInformation(models.Model):
 
         return f"{self.scenario.url}/additional-information/{self.uuid}"
 
-    @staticmethod
+    def get(self) -> "EnviPyModel":
-    def from_dict(ai_type: str, ai_data: Dict[str, Any]):
         from envipy_additional_information import registry
 
         MAPPING = {c.__name__: c for c in registry.list_models().values()}
         try:
-            inst = MAPPING[ai_type](**ai_data)
+            inst = MAPPING[self.type](**self.data)
         except Exception as e:
-            print(f"Error loading {ai_type}: {e}")
+            print(f"Error loading {self.type}: {e}")
             raise e
 
-        return inst
-
-    def get(self) -> "EnviPyModel":
-        inst = AdditionalInformation.from_dict(self.type, self.data)
         inst.__dict__["uuid"] = str(self.uuid)
+
         return inst
 
     def __str__(self) -> str:

epdb/views.py

@@ -937,14 +937,12 @@ 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():
@@ -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:
@@ -3113,21 +3108,12 @@ def jobs(request):
             {"Home": s.SERVER_URL},
             {"Jobs": s.SERVER_URL + "/jobs"},
         ]
-        # if current_user.is_superuser:
+        if current_user.is_superuser:
-        #     context["jobs"] = JobLog.objects.all().order_by("-created")
+            context["jobs"] = JobLog.objects.all().order_by("-created")
-        # else:
+        else:
-        #     context["jobs"] = JobLog.objects.filter(user=current_user).order_by("-created")
+            context["jobs"] = JobLog.objects.filter(user=current_user).order_by("-created")
 
-        # Context for paginated template
+        return render(request, "collections/joblog.html", context)
-        context["entity_type"] = "joblog"
-        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/joblog/"
-        context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
-        context["list_title"] = "joblog"
-        context["list_mode"] = "combined"
-
-        return render(request, "collections/joblog_paginated.html", context)
-
-        # return render(request, "collections/joblog.html", context)
 
     elif request.method == "POST":
         job_name = request.POST.get("job-name")

package.json

@@ -21,11 +21,5 @@
     "django",
     "tailwindcss",
     "daisyui"
-  ],
+  ]
-  "pnpm": {
-    "onlyBuiltDependencies": [
-      "@parcel/watcher",
-      "@tailwindcss/oxide"
-    ]
-  }
 }

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))
+        fig, ax = plt.subplots(figsize=(9, 5.5))
-        ax = fig.subplots()
         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 os.environ.get("N_PEPPER_THREADS", 1) > 1:
-        if n_threads > 1:
+            results = Parallel(n_jobs=os.environ["N_PEPPER_THREADS"])(
-            results = Parallel(n_jobs=n_threads)(
                 delayed(compute_bayes_per_group)(group[1])
                 for group in dataset.group_by("structure_id")
             )

pnpm-workspace.yaml

@@ -1,5 +1,3 @@
-allowBuilds:
-  '@parcel/watcher': true
 onlyBuiltDependencies:
   - '@parcel/watcher'
-  - '@tailwindcss/oxide'
+  - '@tailwindcss/oxide'

static/js/alpine/components/widgets.js

@@ -59,9 +59,6 @@ document.addEventListener("alpine:init", () => {
     get isEditMode() {
       return this.mode === "edit";
     },
-    get isRequired() {
-      return (this.schema.required || []).indexOf(this.fieldName) > -1
-    }
   });
 
   // Text widget
@@ -296,34 +293,6 @@ document.addEventListener("alpine:init", () => {
     }),
   );
 
-    // PubMed link widget
-  Alpine.data(
-    "doiWidget",
-    (fieldName, data, schema, uiSchema, mode, debugErrors, context = null) => ({
-      ...baseWidget(
-        fieldName,
-        data,
-        schema,
-        uiSchema,
-        mode,
-        debugErrors,
-        context,
-      ),
-
-      get value() {
-        return this.data[this.fieldName] || "";
-      },
-      set value(v) {
-        this.data[this.fieldName] = v;
-      },
-      get doiUrl() {
-        return this.value
-          ? `https://dx.doi.org/${this.value}`
-          : null;
-      },
-    }),
-  );
-
   // Compound link widget
   Alpine.data(
     "compoundWidget",

static/js/pw.js

@@ -22,7 +22,7 @@ function predictFromNode(url) {
 // data = {{ pathway.d3_json | safe }};
 // elem = 'vizdiv'
 function draw(pathway, elem) {
-    const initialzoom = 2.5
+
     const nodeRadius = 20;
     const linkDistance = 100;
     const chargeStrength = -200;
@@ -63,7 +63,7 @@ function draw(pathway, elem) {
                 node.fx = width / 2 + depthMap.get(node.depth) * horizontalSpacing - ((nodesInLevel - 1) * horizontalSpacing) / 2;
             }
 
-            node.fy = (node.depth + initialzoom + 0.5) * levelSpacing + 50;
+            node.fy = node.depth * levelSpacing + 50;
             depthMap.set(node.depth, depthMap.get(node.depth) + 1);
         });
     }
@@ -101,24 +101,10 @@ function draw(pathway, elem) {
         // Update pseudo node positions first
         updatePseudoNodePositions();
 
-        link.attr("d", d => {
+        link.attr("x1", d => d.source.x)
-            // Check if it's a self-loop (source equals target)
+            .attr("y1", d => d.source.y)
-            if (d.source.id === d.target.id) {
+            .attr("x2", d => d.target.x)
-                // Create a bezier curve for self-loops
+            .attr("y2", d => d.target.y);
-                const x = d.source.x;
-                const y = d.source.y;
-                const loopRadius = nodeRadius * 2; // Adjust size of the loop
-
-                // Create a circular path to the left of the node
-                return `M ${x},${y - nodeRadius}
-                        C ${x - loopRadius},${y - nodeRadius - loopRadius}
-                          ${x - loopRadius},${y + nodeRadius + loopRadius}
-                          ${x},${y + nodeRadius}`;
-            } else {
-                // Regular straight line for normal edges
-                return `M ${d.source.x},${d.source.y} L ${d.target.x},${d.target.y}`;
-            }
-        });
 
         node.attr("transform", d => `translate(${d.x},${d.y})`);
     }
@@ -477,7 +463,7 @@ function draw(pathway, elem) {
                     // TODO needs to be generic once we store it as AddInf
                     for (var s of n.predicted_properties["PepperPrediction"]) {
                         if (s["mean"] != null) {
-                            tempContent += "<b>DT50 predicted via Pepper:</b> " + s["mean"].toFixed(2) + " days<br>"
+                            tempContent += "<b>DT50 predicted via Pepper:</b> " + s["mean"].toFixed(2) + "<br>"
                         }
                     }
                 }
@@ -572,12 +558,11 @@ function draw(pathway, elem) {
         .scaleExtent([0.5, 5])
         .on("zoom", (event) => {
             zoomable.attr("transform", event.transform);
-        })
+        });
-
 
     // Apply zoom to the SVG element - this enables wheel zoom
     svg.call(zoom);
-    svg.call(zoom.scaleBy, initialzoom);
+
     // Also apply zoom to container to catch events that might not reach SVG
     // This ensures drag-to-pan works even when clicking on empty space
     container.call(zoom);
@@ -596,11 +581,11 @@ function draw(pathway, elem) {
         for (idx in parents) {
             p = nodes[parents[idx]]
             // console.log(p.depth)
-            // if (p.depth >= n.depth) {
+            if (p.depth >= n.depth) {
-            //     // keep the .5 steps for pseudo nodes
+                // keep the .5 steps for pseudo nodes
-            //     n.depth = n.pseudo ? p.depth + 1 : Math.floor(p.depth + 1);
+                n.depth = n.pseudo ? p.depth + 1 : Math.floor(p.depth + 1);
-            //     // console.log("Adjusting", orig_depth, Math.floor(p.depth + 1));
+                // console.log("Adjusting", orig_depth, Math.floor(p.depth + 1));
-            // }
+            }
         }
     });
 
@@ -614,47 +599,13 @@ function draw(pathway, elem) {
 
     // Kanten zeichnen
     const link = zoomable.append("g")
-        .selectAll("path")
+        .selectAll("line")
         .data(links)
-        .enter().append("path")
+        .enter().append("line")
         // 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 => {
+        .attr("marker-end", d => d.target.pseudo ? '' : d.multi_step ? 'url(#doublearrow)' : 'url(#arrow)')
-            if (d.target.pseudo) return '';
-            if (d.source.id === d.target.id) return 'url(#curve-arrow)'; // Use curve arrow for self-loops
-            return d.multi_step ? 'url(#doublearrow)' : 'url(#arrow)';
-        })
-        .attr("fill", "none")
-	.on("click", function(event, d) {
-          const wasHighlighted = d3.select(this).classed("highlighted");
 
-	  d3.selectAll("path").classed("highlighted", false);
-
-          if (!wasHighlighted) {
-              const toHighlight = [];
-              toHighlight.push(d.el);
-
-              if (d.source.pseudo || d.target.pseudo) {
-                  if (d.target.pseudo) {
-                      d3.selectAll("path").each(e => {
-                          if (e !== undefined && e.source.id === d.target.id) {
-                              toHighlight.push(e.el);
-                          }
-                      });
-                  } else {
-                      d3.selectAll("path").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) {
@@ -673,13 +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.select(this).select("circle").classed("highlighted", !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

templates/actions/objects/pathway.html

@@ -9,6 +9,14 @@
       <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"
@@ -22,7 +30,7 @@
   {% 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 +82,7 @@
       Rules</a
     >
   </li>
-  <li role="separator" class="divider h-px"></li>
+  <li role="separator" class="divider"></li>
   <li>
     <a
       class="button"
@@ -99,16 +107,11 @@
       <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="
+      onclick="document.getElementById('delete_pathway_node_modal').showModal(); return false;"
-      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
     >
@@ -116,12 +119,7 @@
   <li>
     <a
       class="button"
-      onclick="
+      onclick="document.getElementById('delete_pathway_edge_modal').showModal(); return false;"
-      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
     >

templates/collections/_joblog_paginated_list_partial.html

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

templates/collections/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/joblog_paginated.html

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

templates/collections/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.can_edit and meta.enabled_features.MODEL_BUILDING %}
-    {% if meta.enabled_features.MODEL_BUILDING %}
+    <button
-      <button
+      type="button"
-        type="button"
+      class="btn btn-primary btn-sm"
-        class="btn btn-primary btn-sm"
+      onclick="document.getElementById('new_model_modal').showModal(); return false;"
-        onclick="document.getElementById('new_model_modal').showModal(); return false;"
+    >
-      >
+      New Model
-        New Model
+    </button>
-      </button>
-    {% endif %}
   {% 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/paginated_base.html

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

templates/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/components/schema_form.html

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

templates/components/widgets/doi_link_widget.html

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

templates/components/widgets/select_widget.html

@@ -44,7 +44,6 @@
           :class="{ 'select-error': $store.validationErrors.hasError(fieldName, context) }"
           x-model="value"
           :multiple="multiple"
-          :required="isRequired"
         >
           <option value="" :selected="!value">Select...</option>
 

templates/modals/collections/new_model_modal.html

@@ -65,11 +65,11 @@
     },
 
     get showMlrr() {
-      return this.selectedType === 'ml-relative-reasoning';
+      return this.selectedType === 'mlrr';
     },
 
     get showRbrr() {
-      return this.selectedType === 'rule-based-relative-reasoning';
+      return this.selectedType === 'rbrr';
     },
 
     get showEnviformer() {

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('path.highlighted');
-
-   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/group.html

@@ -56,8 +56,8 @@
         <ul class="menu bg-base-200 rounded-box">
           {% for um in group.user_member.all %}
             <li>
-                <a href="{% if not user.is_superuser %}{{ um.url }}{% else %}{{ "#" }}{% endif %}" class="hover:bg-base-300"
+              <a href="{{ um.url }}" class="hover:bg-base-300"
-                  >{{ um.username }}
+                >{{ um.username }}
                 {% if not um.is_active %}<i>(inactive)</i>{% endif %}</a
               >
             </li>

templates/objects/pathway.html

@@ -77,6 +77,7 @@
 
   {% 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 %}
@@ -106,12 +107,12 @@
     </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 +141,7 @@
                 </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>
@@ -367,18 +368,6 @@
               >
                 <path d="M 0 0 L 10 5 L 0 10 z" fill="#999" />
               </marker>
-              <marker
-                id="curve-arrow"
-                viewBox="0 0 10 10"
-                refX="10"
-                refY="5"
-                markerWidth="6"
-                markerHeight="6"
-                orient="auto"
-                markerUnits="strokeWidth"
-              >
-                <path d="M 0 0 L 10 5 L 0 10 z" fill="#999" />
-              </marker>
               <marker
                 id="doublearrow"
                 viewBox="0 0 20 30"

templates/predict_pathway.html

@@ -105,7 +105,7 @@
         ></iframe>
       </div>
 
-      <label class="select mb-8 w-full" id="prediction-setting-label">
+      <label class="select mb-8 w-full">
         <span class="label">Predictor</span>
         <select id="prediction-setting" name="prediction-setting">
           <option disabled>Select a Setting</option>
@@ -148,22 +148,6 @@
   </div>
   {# prettier-ignore-start #}
   <script>
-    // Hide predictor selection and update button text if mode is "build"
-    function radioChange(event) {
-      if (event.target.value === "build") {
-        document.getElementById("prediction-setting-label").hidden = true;
-        document.getElementById("predict-submit-button").innerText = "Build";
-      } else {
-        document.getElementById("prediction-setting-label").hidden = false;
-        document.getElementById("predict-submit-button").innerText = "Predict";
-      }
-    }
-
-    const radioButtons = document.querySelectorAll('input[name="predict"]');
-    radioButtons.forEach(radio => {
-      radio.addEventListener('change', radioChange);
-    });
-
     // Helper function to safely get Ketcher instance from iframe
     function getKetcherInstance(iframeId) {
       const ketcherFrame = document.getElementById(iframeId);

templates/static/login_base.html

@@ -110,6 +110,8 @@
           <div
             class="text-base-content/50 flex items-center justify-center space-x-6 text-sm"
           >
+            <a href="/legal" class="link link-hover">Legal</a>
+            <span class="text-base-content/30">•</span>
             <a href="/terms" class="link link-hover">Terms of Use</a>
             <span class="text-base-content/30">•</span>
             <a href="/privacy" class="link link-hover">Privacy Policy</a>

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,
@@ -125,7 +125,6 @@ from envipy_additional_information.parsers import (
     LiquidMatrixSourceParser,
     OxygenUptakeRateParser,
     InitiatingOrganismParser,
-    PFASConfidenceParser,
 )
 
 logger = logging.getLogger(__name__)
@@ -142,7 +141,7 @@ def get_parameter(request, paramname):
     res = request.POST.get(paramname)
     if res is not None and res.strip() != "":
         return res
-    raise ValueError("Not all parameters are set!")
+    return ValueError("Not all parameters are set!")
 
 
 def get_parameter_or_empty_string(request, paramname):
@@ -474,12 +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:
+            if first_order != "":
-                model = HalfLifeModel(model.upper())
+                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)
 
@@ -504,10 +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)
@@ -674,8 +674,7 @@ def build_additional_information_from_request(request, type_):
         elif type_ == "studywst":
             # study_wst_cond = get_parameter(request, "studywstcond")
             raise ValueError("studywstcond is not yet implemented")
-        elif type_ == "pfasconfidence":
+
-            return PFASConfidenceParser.from_string(get_parameter(request, "level"))
         else:
             raise ValueError(f"No corresponding AdditionalInformation for {type_} found!")
 

uv.lock

@@ -894,7 +894,7 @@ provides-extras = ["ms-login", "dev", "pepper-plugin"]
 [[package]]
 name = "envipy-additional-information"
 version = "0.4.2"
-source = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git?branch=develop#f2f251e0214f016760348730c45e56183d961201" }
+source = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git?branch=develop#0a608c85c73a6ef5c38afea87d2b57fb43f01a70" }
 dependencies = [
     { name = "pydantic" },
 ]
@@ -2763,9 +2763,9 @@ dependencies = [
     { name = "typing-extensions", marker = "sys_platform != 'linux' and sys_platform != 'win32'" },
 ]
 wheels = [
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0-cp312-none-macosx_11_0_arm64.whl", hash = "sha256:a47b7986bee3f61ad217d8a8ce24605809ab425baf349f97de758815edd2ef54", upload-time = "2025-10-01T23:35:50Z" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0-cp312-none-macosx_11_0_arm64.whl", hash = "sha256:a47b7986bee3f61ad217d8a8ce24605809ab425baf349f97de758815edd2ef54" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0-cp313-cp313t-macosx_14_0_arm64.whl", hash = "sha256:fbe2e149c5174ef90d29a5f84a554dfaf28e003cb4f61fa2c8c024c17ec7ca58", upload-time = "2025-10-01T23:35:52Z" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0-cp313-cp313t-macosx_14_0_arm64.whl", hash = "sha256:fbe2e149c5174ef90d29a5f84a554dfaf28e003cb4f61fa2c8c024c17ec7ca58" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0-cp313-none-macosx_11_0_arm64.whl", hash = "sha256:057efd30a6778d2ee5e2374cd63a63f63311aa6f33321e627c655df60abdd390", upload-time = "2025-10-01T23:35:55Z" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0-cp313-none-macosx_11_0_arm64.whl", hash = "sha256:057efd30a6778d2ee5e2374cd63a63f63311aa6f33321e627c655df60abdd390" },
 ]
 
 [[package]]
@@ -2785,19 +2785,19 @@ dependencies = [
     { name = "typing-extensions", marker = "sys_platform == 'linux' or sys_platform == 'win32'" },
 ]
 wheels = [
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 [[package]]