API PES

Initial bayer app

Show Pack Classification

Adjusted docker compose to bayer specifics

Adjusted Dockerfile for Bayer

Adding secret flags to group, add secret pools to packages

Adjusted View for Package creation

Prep configs, added Package Create Modal

wip

More on PES

wip

wip

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}"

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__)
@@ -37,4 +36,4 @@ register_template(
 register_template(
     "epdb.objects.node.viz",
     "objects/node_viz.html",
-)
+)

bayer/models.py

@@ -185,7 +185,7 @@ class PESStructure(CompoundStructure):
     def create(
             compound: Compound,
             pes_link: str,
-            molfile: str,
+            mol_file: str,
             smiles: str,
             name: str = None,
             description: str = None,
@@ -204,7 +204,7 @@ class PESStructure(CompoundStructure):
             cs.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
 
         cs.smiles = smiles
-        cs.molfile = molfile
+        cs.mol_file = mol_file
         cs.pes_link = pes_link
         cs.compound = compound
 
@@ -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/objects/compound_structure_viz.html

@@ -3,11 +3,7 @@
   <div class="collapse-arrow bg-base-200 collapse">
     <input type="checkbox" checked />
     <div class="collapse-title text-xl font-medium">Link to PES</div>
-    <div class="collapse-content">
+    <div class="collapse-content">{{ compound_structure.pes_link }}</div>
-      <p>
-        <a href="{{ compound_structure.pes_link }}" class="hover:bg-base-200">{{ compound_structure.pes_link }}</a>
-      </p>
-    </div>
   </div>
 
   <!-- Image Representation -->

bayer/templates/objects/compound_viz.html

@@ -3,11 +3,7 @@
   <div class="collapse-arrow bg-base-200 collapse">
     <input type="checkbox" checked />
     <div class="collapse-title text-xl font-medium">Link to PES</div>
-    <div class="collapse-content">
+    <div class="collapse-content">{{ compound.default_structure.pes_link }}</div>
-      <p>
-        <a href="{{ compound.default_structure.pes_link }}" class="hover:bg-base-200">{{ compound.default_structure.pes_link }}</a>
-      </p>
-    </div>
   </div>
 
   <!-- Image Representation -->

bayer/templates/objects/node_viz.html

@@ -3,11 +3,7 @@
   <div class="collapse-arrow bg-base-200 collapse">
     <input type="checkbox" checked />
     <div class="collapse-title text-xl font-medium">Link to PES</div>
-    <div class="collapse-content">
+    <div class="collapse-content">{{ node.default_node_label.pes_link }}</div>
-      <p>
-        <a href="{{ node.default_node_label.pes_link }}" class="hover:bg-base-200">{{ node.default_node_label.pes_link }}</a>
-      </p>
-    </div>
   </div>
 
   <!-- Image Representation -->

bayer/views.py

@@ -2,13 +2,14 @@ import base64
 
 import requests
 from django.conf import settings as s
-from django.http import HttpResponse, HttpResponseBadRequest
+from django.core.exceptions import BadRequest
+from django.http import HttpResponse
 from django.shortcuts import redirect
 
 from bayer.models import PESCompound
 from epdb.logic import PackageManager
 from epdb.models import Pathway, Node
-from epdb.views import _anonymous_or_real, error
+from epdb.views import _anonymous_or_real
 from utilities.decorators import package_permission_required
 
 Package = s.GET_PACKAGE_MODEL()
@@ -22,11 +23,7 @@ def create_pes(request, package_uuid):
     if request.method == "POST":
 
         if current_package.classification_level == Package.Classification.INTERNAL:
-            return error(
+            raise BadRequest("Cannot create PESs for internal packages.")
-                request,
-                f'Creation of PESs for package {current_package.name} failed!',
-                "Creating PESs for internal packages is not allowed.",
-            )
 
         compound_name = request.POST.get('compound-name')
         compound_description = request.POST.get('compound-description')
@@ -36,25 +33,21 @@ def create_pes(request, package_uuid):
             try:
                 pes_data = fetch_pes(request, pes_link)
             except ValueError as e:
-                return HttpResponseBadRequest(f"Could not fetch PES data for {pes_link}")
+                return BadRequest(f"Could not fetch PES data for {pes_link}")
 
             classification = pes_data.get("classificationLevel", "")
             if "secret" == classification.lower():
-
-                if current_package.classification_level != Package.Classification.SECRET:
-                    return HttpResponseBadRequest("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:
-                        return HttpResponseBadRequest(
+                        return BadRequest(
                             f"PES data pool {s.DATA_POOL_MAPPING[current_package.data_pool.name]} not found in PES data")
 
             pes = PESCompound.create(current_package, pes_data, compound_name, compound_description)
 
             return redirect(pes.url)
         else:
-            return HttpResponseBadRequest("Please provide a PES link.")
+            return BadRequest("Please provide a PES link.")
     else:
         pass
 
@@ -68,11 +61,7 @@ def create_pes_node(request, package_uuid, pathway_uuid):
     if request.method == "POST":
 
         if current_package.classification_level == Package.Classification.INTERNAL:
-            return error(
+            raise BadRequest("Cannot create PESs for internal packages.")
-                request,
-                f'Creation of PESs for package {current_package.name} failed!',
-                "Creating PESs for internal packages is not allowed.",
-            )
 
         compound_name = request.POST.get('compound-name')
         compound_description = request.POST.get('compound-description')
@@ -82,26 +71,18 @@ def create_pes_node(request, package_uuid, pathway_uuid):
             try:
                 pes_data = fetch_pes(request, pes_link)
             except ValueError as e:
-                return HttpResponseBadRequest(f"Could not fetch PES data for {pes_link}")
+                return BadRequest(f"Could not fetch PES data for {pes_link}")
 
             classification = pes_data.get("classificationLevel", "")
             if "secret" == classification.lower():
-
-                if current_package.classification_level != Package.Classification.SECRET:
-                    return HttpResponseBadRequest("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:
-                        return HttpResponseBadRequest(
+                        return BadRequest(
                             f"PES data pool {s.DATA_POOL_MAPPING[current_package.data_pool.name]} not found in PES data")
 
             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
@@ -116,7 +97,7 @@ def create_pes_node(request, package_uuid, pathway_uuid):
             return redirect(current_pathway.url)
 
         else:
-            return HttpResponseBadRequest("Please provide a PES link.")
+            return BadRequest("Please provide a PES link.")
     else:
         pass
 
@@ -125,9 +106,6 @@ def fetch_pes(request, pes_url) -> dict:
     from epauth.views import get_access_token_from_request
     token = get_access_token_from_request(request)
 
-    if token is None:
-        token = pes_url.split('/')[-1] == 'dummy'
-
     if token:
         for k, v in s.PES_API_MAPPING.items():
             if pes_url.startswith(k):

bb4g/__init__.py

@@ -1,13 +1,12 @@
-import enum
 import json
-import logging
 import math
 from datetime import datetime
 from typing import List
-
+import enum
 import requests
 from django.conf import settings as s
-from envipy_additional_information import register, EnviPyModel, UIConfig, WidgetType
+from envipy_additional_information import EnviPyModel, UIConfig, WidgetType
+from envipy_additional_information import register
 
 from bridge.contracts import Classifier  # noqa: I001
 from bridge.dto import (
@@ -18,9 +17,6 @@ from bridge.dto import (
     TransformationProductPrediction,
 )  # noqa: I001
 
-logger = logging.getLogger("epdb")
-
-
 class SamplingAlgorithm(enum.Enum):
     EXACT = "exact"
 
@@ -89,13 +85,14 @@ class BB4G(Classifier):
         }
 
         started = False
-
+        retries = 0
-        while not started:
+        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:
@@ -169,30 +166,18 @@ class BB4G(Classifier):
                 "cutoff": self.config.cutoff,
             }
 
-            retries = 0
+            resp = requests.post(f"{self.url}/compute", headers=header, data=json.dumps(data), proxies=s.PROXIES or None)
-            while retries < 100:
-                resp = requests.post(f"{self.url}/compute", headers=header, data=json.dumps(data),
-                                     proxies=s.PROXIES or None)
 
-                if resp.status_code == 418:
+            resp.raise_for_status()
-                    retries += 1
-                    logger.info(f"BB4G predict hit a 418, retrying in 60 seconds")
-                    import time
-                    time.sleep(3)
-                    continue
 
-                resp.raise_for_status()
+            for substrate, predictions in resp.json().items():
+                preds = {}
 
-                for substrate, predictions in resp.json().items():
+                for pred in predictions:
-                    preds = {}
+                    prod = pred["prediction"]
+                    prob = math.exp(pred["log_likelihood"])
+                    preds[prod] = prob
 
-                    for pred in predictions:
+                result[substrate] = preds
-                        prod = pred["prediction"]
-                        prob = math.exp(pred["log_likelihood"])
-                        preds[prod] = prob
-
-                    result[substrate] = preds
-
-                break
 
         return result

bridge/contracts.py

@@ -261,6 +261,7 @@ class Classifier(Plugin):
             for k, v in data.items():
                 if v != "":
                     cpy[k] = v
+
         return cls.Config(**cpy)
 
     @classmethod

docker-compose.dev.yml

@@ -25,14 +25,25 @@ services:
       - ep_bayer_redis_data:/data
 
   biotransformer3:
-    image: git.envipath.com/envipath/biotransformer3:1.0
+    image: envipath/biotransformer3:1.0
     container_name: epbiotransformer3
 
+#  web:
+#    image: envipath/envipy-bayer:1.0
+#    container_name: epdjango
+#    ports:
+#      - "127.0.0.1:8000:8000"
+#    env_file:
+#      - .env
+#    command: gunicorn envipath.wsgi:application --bind 0.0.0.0:8000 --workers 3
+#    volumes:
+#      - ep_bayer_data:/opt/enviPy/
+
   celery_worker:
-    image: git.envipath.com/envipath/envipy-bayer:1.2
+    image: envipath/envipy-bayer:1.0
     container_name: epcelery
     env_file:
-      - .env
+      - .env.dev
     command: celery -A envipath worker --concurrency=6 -Q model,predict,background --pool threads
     volumes:
       - ep_bayer_data:/opt/enviPy/

envipath/settings.py

@@ -275,12 +275,6 @@ 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 +295,6 @@ LOGGING = {
             "propagate": True,
             "level": os.environ.get("LOG_LEVEL", "INFO"),
         },
-        "auth": {
-            "handlers": ["auth_file"],
-            "propagate": True,
-            "level": os.environ.get("LOG_LEVEL", "INFO"),
-        }
     },
 }
 
@@ -354,7 +343,7 @@ DEFAULT_MODEL_PARAMS = {
     "num_chains": 10,
 }
 
-DEFAULT_MAX_NUMBER_OF_NODES = 9999
+DEFAULT_MAX_NUMBER_OF_NODES = 50
 DEFAULT_MAX_DEPTH = 8
 DEFAULT_MODEL_THRESHOLD = 0.25
 
@@ -502,5 +491,3 @@ 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})

epdb/exceptions.py

@@ -1,5 +0,0 @@
-class InvalidSMILESException(Exception):
-    pass
-
-class PackageImportException(Exception):
-    pass

epdb/legacy_api.py

@@ -439,50 +439,23 @@ 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):
@@ -633,14 +606,9 @@ class CompoundSchema(Schema):
     reviewStatus: str = Field(False, alias="review_status")
     scenarios: List["SimpleScenario"] = Field([], alias="scenarios")
     structures: List["CompoundStructureSchema"] = []
-    pesLink: str | None = Field(None, alias="pes_link")
 
     @staticmethod
-    def resolve_pes_link(obj: Compound):
+    def resolve_review_status(obj: CompoundStructure):
-        return getattr(obj.default_structure, "pes_link", None)
-
-    @staticmethod
-    def resolve_review_status(obj: Compound):
         return "reviewed" if obj.package.reviewed else "unreviewed"
 
     @staticmethod
@@ -714,7 +682,6 @@ class CompoundStructureSchema(Schema):
     reviewStatus: str = Field(None, alias="review_status")
     scenarios: List["SimpleScenario"] = Field([], alias="scenarios")
     smiles: str = Field(None, alias="smiles")
-    pesLink: str | None = Field(None, alias="pes_link")
 
     @staticmethod
     def resolve_review_status(obj: CompoundStructure):
@@ -877,10 +844,6 @@ def create_package_compound(
 
             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:
@@ -909,27 +872,6 @@ 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}"
 )
@@ -1456,7 +1398,6 @@ 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"
@@ -1600,56 +1541,28 @@ 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}")
@@ -1693,15 +1606,13 @@ class PathwayNode(Schema):
     dt50s: List[Dict[str, str]] = Field([], alias="dt50s")
     engineeredIntermediate: bool = Field(None, alias="engineered_intermediate")
     id: str = Field(None, alias="url")
-    idcomp: str = Field(None, alias="node_label_id")
+    idcomp: str = Field(None, alias="default_node_label.url")
-    idreact: str = Field(None, alias="node_label_id")
+    idreact: str = Field(None, alias="default_node_label.url")
     image: str = Field(None, alias="image")
     imageSize: int = Field(None, alias="image_size")
     name: str = Field(None, alias="name")
     proposed: List[Dict[str, str]] = Field([], alias="proposed_intermediate")
-    smiles: str = Field(None, alias="smiles")
+    smiles: str = Field(None, alias="default_node_label.smiles")
-    pseudo: bool = Field(False, alias="pseudo")
-    pesLink: str | None = Field(None, alias="pes_link")
 
     @staticmethod
     def resolve_atom_count(obj: Node):
@@ -1714,10 +1625,24 @@ class PathwayNode(Schema):
         # TODO
         return []
 
+    @staticmethod
+    def resolve_engineered_intermediate(obj: Node):
+        # TODO
+        return False
+
+    @staticmethod
+    def resolve_image(obj: Node):
+        return f"{obj.default_node_label.url}?image=svg"
+
     @staticmethod
     def resolve_image_size(obj: Node):
         return 400
 
+    @staticmethod
+    def resolve_proposed_intermediate(obj: Node):
+        # TODO
+        return []
+
 
 class PathwaySchema(Schema):
     aliases: List[str] = Field([], alias="aliases")
@@ -1841,29 +1766,6 @@ 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:
@@ -1977,42 +1879,30 @@ class CreateNode(Schema):
 
 @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.pesLink:
             from bayer.views import fetch_pes
             from bayer.models import PESCompound
 
             try:
-                pes_data = fetch_pes(request, n.pesLink)
+                pes_data = fetch_pes(request, c.pesLink)
             except ValueError as e:
-                return 400, {"message": f"Could not fetch PES data for {n.pesLink}"}
+                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, {
+                        return 400, { "messsage": f"PES data pool {s.DATA_POOL_MAPPING[p.data_pool.name]} not found in PES data"}
-                            "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)
+            c = PESCompound.create(p, pes_data, c.compoundName, c.compoundDescription)
-
-            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
@@ -2175,10 +2065,6 @@ 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,
@@ -2186,12 +2072,8 @@ 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!"}
@@ -2385,31 +2267,3 @@ def get_setting(request, setting_uuid):
         return 403, {
             "message": f"Getting Setting with id {setting_uuid} failed due to insufficient rights!"
         }
-
-
-########
-# Util #
-########
-class NonPersistent(Schema):
-    smiles: str
-    setting_url: str = Field(..., alias="settingUri")
-
-
-@router.post("/util", response={200: Any, 403: Error})
-def predict(request, np: Form[NonPersistent]):
-    try:
-        print(request.user)
-        print(np.setting_url)
-        setting = SettingManager.get_setting_by_url(request.user, np.setting_url)
-
-        from epdb.logic import SPathway
-
-        spw = SPathway(prediction_setting=setting, root_nodes=[np.smiles])
-        spw.predict()
-
-        return spw.to_json()
-
-    except ValueError:
-        return 403, {
-            "message": f"Getting Setting with id {np.setting_url} failed due to insufficient rights!"
-        }

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
@@ -1078,8 +1121,10 @@ class PackageManager(object):
         data: Dict[str, Any],
         owner: User,
         preserve_uuids=False,
+        add_import_timestamp=True,
+        trust_reviewed=False,
     ) -> Package:
-        importer = PackageImporter(data, preserve_uuids)
+        importer = PackageImporter(data, preserve_uuids, add_import_timestamp, trust_reviewed)
         imported_package = importer.do_import()
 
         up = UserPackagePermission()
@@ -1896,12 +1941,6 @@ class SPathway(object):
                 "to": to_indices,
             }
 
-            if edge.rule:
-                e["rule"] = edge.rule.simple_json()
-
-            if edge.probability:
-                e["probability"] = edge.probability
-
             edges.append(e)
 
         return {

epdb/management/commands/bootstrap.py

@@ -99,15 +99,11 @@ class Command(BaseCommand):
                 new_license.image_link = f"https://licensebuttons.net/l/{cc_string}/4.0/88x31.png"
                 new_license.save()
 
-    def import_package(self, data, owner, all_envipath_user_group):
+    def import_package(self, data, owner):
-        p = PackageManager.import_legacy_package(
+        return PackageManager.import_legacy_package(
             data, owner, keep_ids=True, add_import_timestamp=False, trust_reviewed=True
         )
 
-        PackageManager.grant_read(owner, p, all_envipath_user_group)
-
-        return p
-
     def create_default_setting(self, owner, packages):
         s = SettingManager.create_setting(
             owner,
@@ -202,7 +198,7 @@ class Command(BaseCommand):
                     s.BASE_DIR / "fixtures" / "packages" / "2025-07-18" / p, encoding="utf-8"
                 ).read()
             )
-            imported_package = self.import_package(package_data, admin, g)
+            imported_package = self.import_package(package_data, admin)
             mapping[p.replace(".json", "")] = imported_package
 
         setting = self.create_default_setting(admin, [mapping["EAWAG-BBD"]])

epdb/migrations/0025_auto_20260511_2025.py

@@ -1,57 +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,
-    "other": HalfLifeModel.OTHER,
-}
-
-
-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/migrations/0027_alter_compound_aliases_and_more.py

@@ -1,150 +0,0 @@
-# Generated by Django 6.0.3 on 2026-07-01 20:59
-
-import django.contrib.postgres.fields
-import django.db.models.deletion
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0026_auto_20260602_1718"),
-    ]
-
-    operations = [
-        migrations.AlterField(
-            model_name="compound",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="compound",
-            name="default_structure",
-            field=models.ForeignKey(
-                null=True,
-                on_delete=django.db.models.deletion.SET_NULL,
-                related_name="compound_default_structure",
-                to="epdb.compoundstructure",
-                verbose_name="Default Structure",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="compound",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="compoundstructure",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="compoundstructure",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="edge",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="edge",
-            name="edge_label",
-            field=models.ForeignKey(
-                null=True,
-                on_delete=django.db.models.deletion.CASCADE,
-                to="epdb.reaction",
-                verbose_name="Edge label",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="edge",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="node",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="node",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="pathway",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="pathway",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="reaction",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="reaction",
-            name="medline_references",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(),
-                blank=True,
-                null=True,
-                verbose_name="Medline References",
-            ),
-        ),
-        migrations.AlterField(
-            model_name="reaction",
-            name="rules",
-            field=models.ManyToManyField(
-                blank=True, related_name="reaction_rule", to="epdb.rule", verbose_name="Rule"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="reaction",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="rule",
-            name="aliases",
-            field=django.contrib.postgres.fields.ArrayField(
-                base_field=models.TextField(), blank=True, default=list, verbose_name="Aliases"
-            ),
-        ),
-        migrations.AlterField(
-            model_name="rule",
-            name="scenarios",
-            field=models.ManyToManyField(
-                blank=True, to="epdb.scenario", verbose_name="Attached Scenarios"
-            ),
-        ),
-    ]

epdb/models.py

@@ -31,7 +31,6 @@ from sklearn.model_selection import ShuffleSplit
 
 from bridge.contracts import Property
 from bridge.dto import RunResult, PropertyPrediction
-from epdb.exceptions import InvalidSMILESException
 from utilities.chem import FormatConverter, IndigoUtils, PredictionResult, ProductSet
 from utilities.ml import (
     ApplicabilityDomainPCA,
@@ -577,10 +576,6 @@ class ReactionIdentifierMixin(ExternalIdentifierMixin):
     def get_uniprot_identifiers(self):
         return self.get_external_identifier("UniProt")
 
-    def contains_pes(self):
-        from bayer.models import PESStructure
-        return any([isinstance(o, PESStructure) for o in self.educts.all()]) or any(
-            [isinstance(o, PESStructure) for o in self.products.all()])
 
 ##############
 # EP Objects #
@@ -637,7 +632,7 @@ class EnviPathModel(TimeStampedModel):
 
 class AliasMixin(models.Model):
     aliases = ArrayField(
-        models.TextField(blank=False, null=False), verbose_name="Aliases", default=list, blank=True
+        models.TextField(blank=False, null=False), verbose_name="Aliases", default=list
     )
 
     @transaction.atomic
@@ -660,9 +655,7 @@ class AliasMixin(models.Model):
 
 
 class ScenarioMixin(models.Model):
-    scenarios = models.ManyToManyField(
+    scenarios = models.ManyToManyField("epdb.Scenario", verbose_name="Attached Scenarios")
-        "epdb.Scenario", verbose_name="Attached Scenarios", blank=True
-    )
 
     @transaction.atomic
     def set_scenarios(self, scenarios: List["Scenario"]):
@@ -788,7 +781,7 @@ class Compound(
         "CompoundStructure",
         verbose_name="Default Structure",
         related_name="compound_default_structure",
-        on_delete=models.SET_NULL,
+        on_delete=models.CASCADE,
         null=True,
     )
 
@@ -865,17 +858,13 @@ class Compound(
         package: "Package", smiles: str, name: str = None, description: str = None, *args, **kwargs
     ) -> "Compound":
         if smiles is None or smiles.strip() == "":
-            raise InvalidSMILESException("SMILES is required")
+            raise ValueError("SMILES is required")
 
         smiles = smiles.strip()
 
         parsed = FormatConverter.from_smiles(smiles)
         if parsed is None:
-            raise InvalidSMILESException("Given SMILES is invalid")
+            raise ValueError("Given SMILES is invalid")
-
-        if name is not None:
-            # Clean for potential XSS
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
 
         standardized_smiles = FormatConverter.standardize(smiles, remove_stereo=True)
 
@@ -887,14 +876,7 @@ class Compound(
 
         # Check if we find a direct match for a given SMILES
         if qs.exists():
-            found_structure = qs.first()
+            return qs.first().compound
-            found_compound = found_structure.compound
-
-            if name:
-                found_structure.add_alias(name)
-                found_compound.add_alias(name)
-
-            return found_compound
 
 
         qs = CompoundStructure.objects.filter(smiles=standardized_smiles, compound__package=package)
@@ -904,19 +886,16 @@ class Compound(
         # Check if we can find the standardized one
         if qs.exists():
             # TODO should we add a structure?
-            found_structure = qs.first()
+            return qs.first().compound
-            found_compound = found_structure.compound
-
-            if name:
-                found_structure.add_alias(name)
-                found_compound.add_alias(name)
-
-            return found_compound
 
         # Generate Compound
         c = Compound()
         c.package = package
 
+        if name is not None:
+            # Clean for potential XSS
+            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+
         if name is None or name == "":
             name = f"Compound {Compound.objects.filter(package=package).count() + 1}"
 
@@ -1167,27 +1146,18 @@ class CompoundStructure(
     @staticmethod
     @transaction.atomic
     def create(
-        compound: Compound, smiles: str, name: str = None, description: str = None, molfile: str = None, *args, **kwargs
+        compound: Compound, smiles: str, name: str = None, description: str = None, *args, **kwargs
     ):
-        # Clean for potential XSS
-        if name is not None:
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-
         if CompoundStructure.objects.filter(compound=compound, smiles=smiles).exists():
-            found_cs = CompoundStructure.objects.get(compound=compound, smiles=smiles)
+            return CompoundStructure.objects.get(compound=compound, smiles=smiles)
-
-            if name:
-                found_cs.add_alias(name)
-
-            return found_cs
 
         if compound.pk is None:
             raise ValueError("Unpersisted Compound! Persist compound first!")
 
         cs = CompoundStructure()
-
+        # Clean for potential XSS
         if name is not None:
-            cs.name = name
+            cs.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
 
         if description is not None:
             cs.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
@@ -1195,10 +1165,6 @@ class CompoundStructure(
         cs.smiles = smiles
         cs.compound = compound
 
-        # Check if molfile is present and valid
-        if molfile is not None and FormatConverter.from_molfile(molfile) is not None:
-            cs.molfile = molfile
-
         if "normalized_structure" in kwargs:
             cs.normalized_structure = kwargs["normalized_structure"]
 
@@ -1216,8 +1182,6 @@ class CompoundStructure(
 
     @property
     def as_svg(self, width: int = 800, height: int = 400):
-        if self.molfile is not None and self.molfile.strip() != "":
-            return IndigoUtils.mol_to_svg(self.molfile, width=width, height=height)
         return IndigoUtils.mol_to_svg(self.smiles, width=width, height=height)
 
     @property
@@ -1415,9 +1379,6 @@ class SimpleAmbitRule(SimpleRule):
         if not FormatConverter.is_valid_smirks(smirks):
             raise ValueError(f'SMIRKS "{smirks}" is invalid!')
 
-        if name is not None:
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-
         query = SimpleAmbitRule.objects.filter(package=package, smirks=smirks)
 
         if reactant_filter_smarts is not None and reactant_filter_smarts.strip() != "":
@@ -1429,17 +1390,14 @@ class SimpleAmbitRule(SimpleRule):
         if query.exists():
             if query.count() > 1:
                 logger.error(f"More than one rule matched this one! {query}")
-
+            return query.first()
-            found_rule = query.first()
-
-            if name:
-                found_rule.add_alias(name)
-
-            return found_rule
 
         r = SimpleAmbitRule()
         r.package = package
 
+        if name is not None:
+            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+
         if name is None or name == "":
             name = f"Rule {Rule.objects.filter(package=package).count() + 1}"
 
@@ -1660,15 +1618,10 @@ class Reaction(
     products = models.ManyToManyField(
         "epdb.CompoundStructure", verbose_name="Products", related_name="reaction_products"
     )
-    rules = models.ManyToManyField(
+    rules = models.ManyToManyField("epdb.Rule", verbose_name="Rule", related_name="reaction_rule")
-        "epdb.Rule", verbose_name="Rule", related_name="reaction_rule", blank=True
-    )
     multi_step = models.BooleanField(verbose_name="Multistep Reaction")
     medline_references = ArrayField(
-        models.TextField(blank=False, null=False),
+        models.TextField(blank=False, null=False), null=True, verbose_name="Medline References"
-        null=True,
-        verbose_name="Medline References",
-        blank=True,
     )
 
     external_identifiers = GenericRelation("ExternalIdentifier")
@@ -1685,13 +1638,8 @@ class Reaction(
         educts: Union[List[str], List[CompoundStructure]] = None,
         products: Union[List[str], List[CompoundStructure]] = None,
         rules: Union[Rule | List[Rule]] = None,
-        multi_step: bool = False,
+        multi_step: bool = True,
     ):
-
-        # Clean for potential XSS
-        if name is not None and name.strip() != "":
-            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
-
         _educts = []
         _products = []
 
@@ -1746,21 +1694,16 @@ class Reaction(
                 logger.error(
                     f"Found more than one reaction for given input! {existing_reaction_qs}"
                 )
-
+            return existing_reaction_qs.first()
-            found_reaction = existing_reaction_qs.first()
-
-            if name:
-                found_reaction.add_alias(name)
-
-            return found_reaction
 
         r = Reaction()
         r.package = package
 
-        if r is not None:
+        # Clean for potential XSS
-            r.name = name
+        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
@@ -1838,7 +1781,7 @@ 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):
@@ -1951,9 +1894,6 @@ 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)
@@ -2231,7 +2171,7 @@ 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)
 
@@ -2246,68 +2186,6 @@ 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(
@@ -2360,12 +2238,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             "node_label_id": self.default_node_label.url,
             "image": f"{self.url}?image=svg",
             "image_svg": IndigoUtils.mol_to_svg(
-                self.default_node_label.molfile
+                self.default_node_label.smiles, width=40, height=40
-                if self.default_node_label.molfile is not None
-                and self.default_node_label.molfile.strip()
-                else self.default_node_label.smiles,
-                width=40,
-                height=40,
             ),
             "image_type": "svg",
             "name": self.get_name(),
@@ -2379,7 +2252,6 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             },
             "predicted_properties": predicted_properties,
             "is_engineered_intermediate": self.kv.get("is_engineered_intermediate", False),
-            "proposed": self.is_proposed_intermediate(),
             "timeseries": self.get_timeseries_data(),
             **structure_data,
         }
@@ -2420,17 +2292,12 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
 
     @property
     def as_svg(self):
-        if (
-            self.default_node_label.molfile is not None
-            and self.default_node_label.molfile.strip() != ""
-        ):
-            return IndigoUtils.mol_to_svg(self.default_node_label.molfile)
         return IndigoUtils.mol_to_svg(self.default_node_label.smiles)
 
     def get_timeseries_data(self):
         for ai in self.additional_information.all():
-            if ai.type == "OECD301FTimeSeries":
+            if ai.__class__.__name__ == "OECD301FTimeSeries":
-                return ai.get().model_dump(mode="json")
+                return ai.model_dump(mode="json")
 
         return None
 
@@ -2453,26 +2320,6 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
 
         return data
 
-    def is_proposed_intermediate(self):
-        collected = defaultdict(dict)
-        for ai in self.additional_information.filter(
-                type__in=["ProposedIntermediate", "TransformationProductImportance", "Confidence"]
-                , scenario__isnull=False
-        ):
-            collected[str(ai.scenario.uuid)]["scenarioId"] = ai.scenario.url
-            collected[str(ai.scenario.uuid)]["scenarioName"] = ai.scenario.name
-
-            if ai.type == "ProposedIntermediate":
-                collected[str(ai.scenario.uuid)]["proposed"] = True
-
-            if ai.type == "Confidence":
-                collected[str(ai.scenario.uuid)]["Confidence"] = ai.get().level
-
-            if ai.type == "TransformationProductImportance":
-                collected[str(ai.scenario.uuid)]["Transformation product importance"] = ai.get().importance.value
-
-        return list(collected.values())
-
     def simple_json(self, include_description=False):
         res = super().simple_json()
         name = res.get("name", None)
@@ -2487,7 +2334,7 @@ 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"
@@ -2566,8 +2413,6 @@ 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
@@ -2597,7 +2442,7 @@ 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
@@ -4605,22 +4450,18 @@ 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

@@ -19,7 +19,6 @@ from sentry_sdk import capture_exception
 
 from utilities.chem import FormatConverter, IndigoUtils
 from utilities.decorators import package_permission_required
-from .exceptions import InvalidSMILESException
 
 from .logic import (
     EPDBURLParser,
@@ -786,11 +785,6 @@ def models(request):
             {"Model": s.SERVER_URL + "/model"},
         ]
 
-        context["entity_type"] = "model"
-        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/models/"
-        context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
-        context["list_title"] = "models"
-
         # Keep model_types for potential modal/action use
         context["model_types"] = {
             "ML Relative Reasoning": {
@@ -803,14 +797,12 @@ def models(request):
                 "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():
@@ -818,9 +810,6 @@ def models(request):
                     "type": k,
                     "requires_rule_packages": v.requires_rule_packages(),
                     "requires_data_packages": v.requires_data_packages(),
-                    "additional_parameters": v.Config.__name__.lower()
-                    if v.Config.__name__ != ""
-                    else None,
                 }
             for k, v in s.PROPERTY_PLUGINS.items():
                 context["model_types"][v.display()] = {
@@ -829,6 +818,12 @@ def models(request):
                     "requires_data_packages": v.requires_data_packages(),
                 }
 
+        # Context for paginated template
+        context["entity_type"] = "model"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/models/"
+        context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
+        context["list_title"] = "models"
+
         return render(request, "collections/models_paginated.html", context)
 
     elif request.method == "POST":
@@ -943,12 +938,13 @@ def package_models(request, package_uuid):
                 "requires_data_packages": True,
             },
         }
+
         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():
@@ -1124,11 +1120,6 @@ def package_model(request, package_uuid, model_uuid):
                             }
                         )
 
-                        # Sort data by prob desc
-                        res["pred"] = sorted(
-                            res["pred"], key=lambda x: x["probability"], reverse=True
-                        )
-
                 return JsonResponse(res, safe=False)
 
             elif half_life:
@@ -1232,7 +1223,9 @@ def package(request, package_uuid):
     if request.method == "GET":
         if request.GET.get("export", False) == "true":
             filename = f"{current_package.get_name().replace(' ', '_')}_{current_package.uuid}.json"
-            pack_json = PackageManager.export_package(current_package)
+            pack_json = PackageManager.export_package(
+                current_package, include_models=False, include_external_identifiers=False
+            )
             response = JsonResponse(pack_json, content_type="application/json")
             response["Content-Disposition"] = f'attachment; filename="{filename}"'
 
@@ -2368,13 +2361,7 @@ def package_pathway_nodes(request, package_uuid, pathway_uuid):
         node_description = request.POST.get("node-description")
 
         node_smiles = request.POST.get("node-smiles").strip()
-
+        current_pathway.add_node(node_smiles, name=node_name, description=node_description)
-        try:
-            current_pathway.add_node(node_smiles, name=node_name, description=node_description)
-        except InvalidSMILESException:
-            return error(
-                request, "Node creation failed!", f"Given SMILES ({node_smiles}) is invalid"
-            )
 
         return redirect(current_pathway.url)
 
@@ -2482,22 +2469,7 @@ def package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
 
             return JsonResponse({"success": current_node.url})
 
-        new_node_name = request.POST.get("node-name")
+        return HttpResponseBadRequest()
-        new_node_description = request.POST.get("node-description")
-
-        if any([new_node_name, new_node_description]):
-            if new_node_name is not None and new_node_name.strip() != "":
-                new_node_name = nh3.clean(new_node_name.strip(), tags=s.ALLOWED_HTML_TAGS).strip()
-                current_node.name = new_node_name
-
-            if new_node_description is not None and new_node_description.strip() != "":
-                new_node_description = nh3.clean(new_node_description.strip(), tags=s.ALLOWED_HTML_TAGS).strip()
-                current_node.description = new_node_description
-
-            current_node.save()
-            return redirect(current_node.url)
-
-        return error(request, "Node update failed!", "No changes were made to the node")
     else:
         return HttpResponseNotAllowed(["GET", "POST"])
 
@@ -2567,9 +2539,6 @@ 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:
@@ -3029,15 +2998,9 @@ def settings(request):
         new_default = request.POST.get("prediction-setting-new-default", "off") == "on"
 
         # min 2, max s.DEFAULT_MAX_NUMBER_OF_NODES
-        temp_max_nodes = request.POST.get("prediction-setting-max-nodes")
-        if temp_max_nodes is None or temp_max_nodes == "" or int(temp_max_nodes) == -1:
-            temp_max_nodes = s.DEFAULT_MAX_NUMBER_OF_NODES
-        else:
-            temp_max_nodes = int(request.POST.get("prediction-setting-max-nodes", 1))
-
         max_nodes = min(
             max(
-                temp_max_nodes,
+                int(request.POST.get("prediction-setting-max-nodes", 1)),
                 2,
             ),
             s.DEFAULT_MAX_NUMBER_OF_NODES,
@@ -3058,7 +3021,6 @@ def settings(request):
 
             model_uuid = model_url.split("/")[-1]
             params["model"] = EPModel.objects.get(uuid=model_uuid)
-            # TODO Check if removed if request contains "" or not at all
             params["model_threshold"] = request.POST.get(
                 "model-based-prediction-setting-threshold", s.DEFAULT_MODEL_THRESHOLD
             )
@@ -3148,21 +3110,12 @@ 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")

migration/views.py

@@ -65,25 +65,6 @@ def run_both_engines(SMILES, SMIRKS):
 
 
 def migration(request):
-    accepted_diffs = [
-        "bt0055-3469.1",
-        "bt0056-2685",
-        "bt0193-4263",
-        "bt0231-1871.1",
-        "bt0242-3803",
-        "bt0254-4224.1",
-        "bt0254-4224.2",
-        "bt0291-1129",
-        "bt0337-3543",
-        "bt0391-4285",
-        "bt0402-3576",
-        "bt0404-3928",
-        "bt0416-4269",
-        "bt0432-4254",
-        "bt0337-4117",
-        "bt0322-3393",
-    ]
-
     if request.method == "GET":
         context = get_base_context(request)
 
@@ -128,11 +109,11 @@ def migration(request):
                         ),
                         "id": str(r.uuid),
                         "url": r.url,
-                        "status": res or r.name in accepted_diffs,
+                        "status": res,
                     }
                 )
 
-                if res or r.name in accepted_diffs:
+                if res:
                     success += 1
                 else:
                     error += 1
@@ -154,16 +135,7 @@ def migration(request):
 
         for r in migration_status["results"]:
             r["detail_url"] = r["detail_url"].replace("http://localhost:8000", s.SERVER_URL)
-            if r["name"] in accepted_diffs:
-                r["status"] = True
 
-        migration_status["results"] = sorted(
-            migration_status["results"], key=lambda x: (x["status"], x["name"])
-        )
-
-        num_success = sum([int(x["status"]) for x in migration_status["results"]])
-        migration_status["success"] = num_success
-        migration_status["error"] = migration_status["total"] - num_success
         context.update(**migration_status)
 
         return render(request, "migration.html", context)

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/css/input.css

@@ -34,12 +34,3 @@
 }
 
 @import "./daisyui-theme.css";
-
-select.select[multiple] {
-  display: block;
-  white-space: normal;
-}
-
-p a {
-  @apply underline;
-}

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/alpine/pagination.js

@@ -5,125 +5,6 @@
  */
 
 document.addEventListener('alpine:init', () => {
-
-  const basePagination = (
-    items,
-    currentPage,
-    totalPages,
-    totalItems,
-    perPage,
-    isReviewed,
-    instanceId
-  ) => ({
-    items,
-    currentPage,
-    totalPages,
-    totalItems,
-    perPage,
-    isReviewed,
-    instanceId,
-
-    get paginatedItems() {
-      return this.items;
-    },
-
-    get showingStart() {
-      if (this.totalItems === 0) return 0;
-      return (this.currentPage - 1) * this.perPage + 1;
-    },
-
-    get showingEnd() {
-      if (this.totalItems === 0) return 0;
-      return Math.min((this.currentPage - 1) * this.perPage + this.items.length, this.totalItems);
-    },
-
-    nextPage() {
-      if (this.currentPage < this.totalPages) {
-        this.fetchPage(this.currentPage + 1);
-      }
-    },
-
-    prevPage() {
-      if (this.currentPage > 1) {
-        this.fetchPage(this.currentPage - 1);
-      }
-    },
-
-    goToPage(page) {
-      if (page >= 1 && page <= this.totalPages) {
-        this.fetchPage(page);
-      }
-    },
-
-    get pageNumbers() {
-      const pages = [];
-      const total = this.totalPages;
-      const current = this.currentPage;
-
-      if (total === 0) {
-        return pages;
-      }
-
-      if (total <= 7) {
-        for (let i = 1; i <= total; i++) {
-          pages.push({ page: i, isEllipsis: false, key: `${this.instanceId}-page-${i}` });
-        }
-      } else {
-        pages.push({ page: 1, isEllipsis: false, key: `${this.instanceId}-page-1` });
-
-        let rangeStart;
-        let rangeEnd;
-
-        if (current <= 4) {
-          rangeStart = 2;
-          rangeEnd = 5;
-        } else if (current >= total - 3) {
-          rangeStart = total - 4;
-          rangeEnd = total - 1;
-        } else {
-          rangeStart = current - 1;
-          rangeEnd = current + 1;
-        }
-
-        if (rangeStart > 2) {
-          pages.push({ page: '...', isEllipsis: true, key: `${this.instanceId}-ellipsis-start` });
-        }
-
-        for (let i = rangeStart; i <= rangeEnd; i++) {
-          pages.push({ page: i, isEllipsis: false, key: `${this.instanceId}-page-${i}` });
-        }
-
-        if (rangeEnd < total - 1) {
-          pages.push({ page: '...', isEllipsis: true, key: `${this.instanceId}-ellipsis-end` });
-        }
-
-        pages.push({ page: total, isEllipsis: false, key: `${this.instanceId}-page-${total}` });
-      }
-
-      return pages;
-    }
-  });
-
-  Alpine.data('paginatedList',
-    (items, options = {}) => ({
-      ...basePagination(items,1, 0, 0, options.perPage || 50, options.isReviewed || false, options.instanceId || Math.random().toString(36).substring(2, 9),),
-
-      init() {
-        this.fetchPage(1);
-      },
-
-      async fetchPage(page) {
-        this.totalItems = this.items.length;
-        this.totalPages = Math.ceil(this.items.length / this.perPage);
-        this.currentPage = page
-
-        const start = page * this.perPage - this.perPage;
-        const end = page * this.perPage;
-        return this.items.slice(start, end);
-      }
-
-    }));
-
   Alpine.data('remotePaginatedList', (options = {}) => ({
     items: [],
     currentPage: 1,

static/js/pw.js

@@ -1,37 +1,5 @@
 console.log("loaded pw.js")
 
-function findPaths(source_idx, links) {
-    const resultLinks = new Set();
-    const visited = new Set();
-    // Helper function for depth-first search
-    function dfs(current) {
-
-        if (visited.has(current)) {
-            return;
-        }
-
-        if (links.filter(link => link.target.id === current).length === 0) {
-            return;
-        }
-
-        visited.add(current);
-        links.forEach(link => {
-            if (
-                link.target.id === current &&
-                !visited.has(link.source.id) &&
-                link.source.id !== link.target.id // Avoid self-loops
-            ) {
-                resultLinks.add(link); // Add link to result
-                dfs(link.source.id);
-            }
-        });
-        visited.delete(current);
-    }
-    // Start DFS
-    dfs(source_idx);
-    return Array.from(resultLinks);
-}
-
 function predictFromNode(url) {
     fetch("", {
         method: "POST",
@@ -55,7 +23,6 @@ function predictFromNode(url) {
 // elem = 'vizdiv'
 function draw(pathway, elem) {
 
-    const initialzoom = 2.5
     const nodeRadius = 20;
     const linkDistance = 100;
     const chargeStrength = -200;
@@ -67,9 +34,6 @@ function draw(pathway, elem) {
         const horizontalSpacing = 75; // horizontal space between nodes
         const depthMap = new Map();
 
-        // Avoid leaving unconnected Nodes leaving the viewport
-        nodes.forEach(node => {if (node.depth < 0)  node.depth = 0;});
-
         // Sort nodes by depth first to minimize crossings
         const sortedNodes = [...nodes].sort((a, b) => a.depth - b.depth);
 
@@ -99,7 +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);
         });
     }
@@ -137,30 +101,12 @@ 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})`);
-
-        linkText
-         .attr("x", d => (d.source.x + d.target.x) / 2)
-         .attr("y", d => (d.source.y + d.target.y) / 2);
     }
 
     function dragstarted(event, d) {
@@ -263,7 +209,7 @@ function draw(pathway, elem) {
     }
 
     // Wait before showing popup (ms)
-    var popupWaitBeforeShow = 500;
+    var popupWaitBeforeShow = 1000;
 
     // Custom popover element
     let popoverTimeout = null;
@@ -517,7 +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>"
                         }
                     }
                 }
@@ -617,8 +563,6 @@ function draw(pathway, elem) {
     // 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);
@@ -637,11 +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));
-            // }
+            }
         }
     });
 
@@ -654,68 +598,43 @@ function draw(pathway, elem) {
         .on("tick", ticked);
 
     // Kanten zeichnen
-    const linkGroup = zoomable.append("g")
+    const link = zoomable.append("g")
-      .selectAll("g")
+        .selectAll("line")
-      .data(links)
+        .data(links)
-      .enter()
+        .enter().append("line")
-      .append("g")
+        // Check if target is pseudo and draw marker only if not pseudo
-      .attr("class", "link-group");
+        .attr("class", d => d.target.pseudo ? "link_no_arrow" : "link")
-
+        .attr("marker-end", d => d.target.pseudo ? '' : d.multi_step ? 'url(#doublearrow)' : 'url(#arrow)')
-    const link = linkGroup
-      .append("path")
-      .attr("class", d => d.target.pseudo ? "link_no_arrow" : "link")
-      .attr("marker-end", d => d.target.pseudo ? "" : "url(#arrow)")
-      .attr("fill", "none")
-
-      // 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 => {
-        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);
+
+          d3.selectAll("line").classed("highlighted", false);
+
           if (!wasHighlighted) {
-            const toHighlight = [];
+              const toHighlight = [];
-            toHighlight.push(d.el);
+              toHighlight.push(d.el);
 
-            if (d.source.pseudo || d.target.pseudo) {
+              if (d.source.pseudo || d.target.pseudo) {
-              if (d.target.pseudo) {
+                  if (d.target.pseudo) {
-                d3.selectAll("path").each(e => {
+                      d3.selectAll("line").each(e => {
-                  if (e !== undefined && e.source.id === d.target.id) {
+                          if (e !== undefined && e.source.id === d.target.id) {
-                    toHighlight.push(e.el);
+                              toHighlight.push(e.el);
+                          }
+                      });
+                  } else {
+                      d3.selectAll("line").each(e => {
+                          if (e !== undefined && (e.target.id === d.source.id || e.source.id === d.source.id)) {
+                              toHighlight.push(e.el);
+                          }
+                      });
                   }
-                });
-              } 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) {
+              for (const e of toHighlight) {
-              d3.select(e).classed("highlighted", true);
+                  d3.select(e).classed("highlighted", true);
-            }
+              }
           }
-        });
+      })
-
-    const linkText = linkGroup
-      .append("text")
-      .attr("class", "link-label")
-      .attr("text-anchor", "middle")
-      .attr("dy", -6)
-      .style("font-size", "4px")
-      .style("pointer-events", "none")
-      .style("display", "none")
-      .text(d => d.name)
-      .attr("x", d => (d.source.x + d.target.x) / 2)
-      .attr("y", d => (d.source.y + d.target.y) / 2);
 
     // add element to links array
     link.each(function (d) {
@@ -732,41 +651,16 @@ function draw(pathway, elem) {
         .call(d3.drag()
             .on("start", dragstarted)
             .on("drag", dragged)
-            .on("end", dragended)
+            .on("end", dragended))
-        )
         .on("click", function (event, d) {
-          const wasHighlighted = d3.select(this).select("circle").classed("highlighted");
+            const wasHighlighted = d3.select(this).select("circle").classed("highlighted");
-          d3.selectAll('circle.highlighted').classed('highlighted', false);
-          d3.selectAll("path").classed("inedge", false);
-          d3.selectAll("path").classed("outedge", false);
 
-          if (!wasHighlighted) {
+            d3.selectAll('circle.highlighted').classed('highlighted', false);
-            d3.select(this).select("circle").classed("highlighted", !d3.select(this).select("circle").classed("highlighted"));
-            const inEdges = findPaths(d.id, links);
-            const outEdges = []
-            // Colorize out edges green
-            for (const l of links) {
-              if (l.source.id === d.id) {
-                outEdges.push(l);
-                if (l.target.pseudo) {
-                  for (const l2 of links) {
-                    if (l.target.id === l2.source.id) {
-                      outEdges.push(l2);
-                    }
-                  }
-                }
-              }
-            }
 
-            for (const e of inEdges) {
+            if (!wasHighlighted) {
-              d3.select(e.el).classed("inedge", true);
+                d3.select(this).select("circle").classed("highlighted", !d3.select(this).select("circle").classed("highlighted"));
             }
-
+        })
-            for (const e of outEdges) {
-              d3.select(e.el).classed("outedge", true);
-            }
-          }
-        });
 
     // Kreise für die Knoten hinzufügen
     node.append("circle")
@@ -840,14 +734,14 @@ function draw(pathway, elem) {
 
 function serializeSVG(svgElement) {
 
-    svgElement.querySelectorAll("path.link").forEach(line => {
+    svgElement.querySelectorAll("line.link").forEach(line => {
         const style = getComputedStyle(line);
         line.setAttribute("stroke", style.stroke);
         line.setAttribute("stroke-width", style.strokeWidth);
         line.setAttribute("fill", style.fill);
     });
 
-    svgElement.querySelectorAll("path.link_no_arrow").forEach(line => {
+    svgElement.querySelectorAll("line.link_no_arrow").forEach(line => {
         const style = getComputedStyle(line);
         line.setAttribute("stroke", style.stroke);
         line.setAttribute("stroke-width", style.strokeWidth);

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/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/packages_paginated.html

@@ -3,73 +3,73 @@
 {% block page_title %}Packages{% endblock %}
 
 {% block action_button %}
-  <div class="flex items-center gap-2">
+    <div class="flex items-center gap-2">
-    <button
+      <button
-      type="button"
+        type="button"
-      class="btn btn-primary btn-sm"
+        class="btn btn-primary btn-sm"
-      id="new-package-button"
+        id="new-package-button"
-      onclick="document.getElementById('new_package_modal').showModal(); return false;"
+        onclick="document.getElementById('new_package_modal').showModal(); return false;"
-    >
-      <svg
-        xmlns="http://www.w3.org/2000/svg"
-        width="24"
-        height="24"
-        viewBox="0 0 24 24"
-        fill="none"
-        stroke="currentColor"
-        stroke-width="2"
-        stroke-linecap="round"
-        stroke-linejoin="round"
-        class="lucide lucide-folder-plus-icon lucide-folder-plus"
       >
-        <path d="M12 10v6" />
-        <path d="M9 13h6" />
-        <path
-          d="M20 20a2 2 0 0 0 2-2V8a2 2 0 0 0-2-2h-7.9a2 2 0 0 1-1.69-.9L9.6 3.9A2 2 0 0 0 7.93 3H4a2 2 0 0 0-2 2v13a2 2 0 0 0 2 2Z"
-        />
-      </svg>
-    </button>
-    <div class="dropdown dropdown-end">
-      <div tabindex="0" role="button" class="btn btn-sm">
-        Import
         <svg
           xmlns="http://www.w3.org/2000/svg"
-          width="16"
+          width="24"
-          height="16"
+          height="24"
           viewBox="0 0 24 24"
           fill="none"
           stroke="currentColor"
           stroke-width="2"
           stroke-linecap="round"
           stroke-linejoin="round"
-          class="lucide lucide-chevron-down ml-1"
+          class="lucide lucide-folder-plus-icon lucide-folder-plus"
         >
-          <path d="m6 9 6 6 6-6" />
+          <path d="M12 10v6" />
+          <path d="M9 13h6" />
+          <path
+            d="M20 20a2 2 0 0 0 2-2V8a2 2 0 0 0-2-2h-7.9a2 2 0 0 1-1.69-.9L9.6 3.9A2 2 0 0 0 7.93 3H4a2 2 0 0 0-2 2v13a2 2 0 0 0 2 2Z"
+          />
         </svg>
+      </button>
+      <div class="dropdown dropdown-end">
+        <div tabindex="0" role="button" class="btn btn-sm">
+          Import
+          <svg
+            xmlns="http://www.w3.org/2000/svg"
+            width="16"
+            height="16"
+            viewBox="0 0 24 24"
+            fill="none"
+            stroke="currentColor"
+            stroke-width="2"
+            stroke-linecap="round"
+            stroke-linejoin="round"
+            class="lucide lucide-chevron-down ml-1"
+          >
+            <path d="m6 9 6 6 6-6" />
+          </svg>
+        </div>
+        <ul
+          tabindex="-1"
+          class="dropdown-content menu bg-base-100 rounded-box z-50 w-56 p-2"
+        >
+          <li>
+            <a
+              role="button"
+              onclick="document.getElementById('import_package_modal').showModal(); return false;"
+            >
+              Import Package from JSON
+            </a>
+          </li>
+          <li>
+            <a
+              role="button"
+              onclick="document.getElementById('import_legacy_package_modal').showModal(); return false;"
+            >
+              Import Package from legacy JSON
+            </a>
+          </li>
+        </ul>
       </div>
-      <ul
-        tabindex="-1"
-        class="dropdown-content menu bg-base-100 rounded-box z-50 w-56 p-2"
-      >
-        <li>
-          <a
-            role="button"
-            onclick="document.getElementById('import_package_modal').showModal(); return false;"
-          >
-            Import Package from JSON
-          </a>
-        </li>
-        <li>
-          <a
-            role="button"
-            onclick="document.getElementById('import_legacy_package_modal').showModal(); return false;"
-          >
-            Import Package from legacy JSON
-          </a>
-        </li>
-      </ul>
     </div>
-  </div>
 {% 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/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 or not meta.url_contains_package  %}
     <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/objects/add_pathway_edge_modal.html

@@ -5,7 +5,6 @@
   x-data="{
     isSubmitting: false,
     reactionImageUrl: '',
-    pes: false,
 
     reset() {
       this.isSubmitting = false;
@@ -16,30 +15,20 @@
       const substratesSelect = document.getElementById('add_pathway_edge_substrates');
       const productsSelect = document.getElementById('add_pathway_edge_products');
 
-      const pesLinks = [];
-
       const substrates = [];
       for (const option of substratesSelect.selectedOptions) {
         substrates.push(option.dataset.smiles);
-        if (option.dataset.pes === 'true') {
-          pesLinks.push(option.dataset.pes);
-        }
       }
 
       const products = [];
       for (const option of productsSelect.selectedOptions) {
         products.push(option.dataset.smiles);
-        if (option.dataset.pes === 'true') {
-          pesLinks.push(option.dataset.pes);
-        }
       }
 
       if (substrates.length > 0 && products.length > 0) {
         const reaction = substrates.join('.') + '>>' + products.join('.');
         this.reactionImageUrl = '{% url "depict" %}?smirks=' + encodeURIComponent(reaction);
-        this.pes = pesLinks.length > 0;
       } else {
-        this.pes = false;
         this.reactionImageUrl = '';
       }
     },
@@ -117,7 +106,6 @@
                 {% for n in pathway.nodes %}
                   <option
                     data-smiles="{{ n.default_node_label.smiles }}"
-                    data-pes="{% if n.default_node_label.pes_link %}true{% else %}false{% endif %}"
                     value="{{ n.url }}"
                   >
                     {{ n.default_node_label.name|safe }}
@@ -144,7 +132,6 @@
                 {% for n in pathway.nodes %}
                   <option
                     data-smiles="{{ n.default_node_label.smiles }}"
-                    data-pes="{% if n.default_node_label.pes_link %}true{% else %}false{% endif %}"
                     value="{{ n.url }}"
                   >
                     {{ n.default_node_label.name|safe }}
@@ -157,9 +144,6 @@
 
         <div class="mb-3" x-show="reactionImageUrl" x-cloak>
           <img :src="reactionImageUrl" class="w-full" alt="Reaction preview" />
-          <div x-show="pes">
-            <span class='alert alert-info alert-soft'>The reaction contains a partially elucidated structure!</br>For visualization the representative structure is used. The pathway itself will show the actual partially elucidated structure.</span>
-          </div>
         </div>
       </form>
     </div>

templates/modals/objects/delete_pathway_edge_modal.html

@@ -5,7 +5,8 @@
   class="modal"
   x-data="modalForm({ state: { selectedEdge: '', imageUrl: '' } })"
   @modal-opened.window="
-   const links = d3.selectAll('path.highlighted');
+   const links = d3.selectAll('line.highlighted');
+  console.log(links);
    if (!links.empty()) {
         const el = links.node();
         const selectElement = document.getElementById('delete_pathway_edge_edges');
@@ -17,7 +18,9 @@
                 break;
             }
         }
+
         selectElement.dispatchEvent(new Event('change'));
+
    }
   "
   @close="reset()"

templates/modals/objects/delete_pathway_node_modal.html

@@ -6,14 +6,17 @@
   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'));
    }
   "

templates/objects/edge.html

@@ -82,9 +82,6 @@
       <div class="collapse-content">
         <div class="flex justify-center">{{ edge.edge_label.as_svg|safe }}</div>
       </div>
-      {% if edge.edge_label.contains_pes %}
-        <span class='alert alert-info alert-soft'>The reaction contains a partially elucidated structure!</br>For visualization the representative structure is used. The pathway itself will show the actual partially elucidated structure.</span>
-      {% endif %}
     </div>
 
     <!-- Reaction Description -->
@@ -95,7 +92,7 @@
         <div class="flex flex-wrap items-center justify-center gap-4">
           {% for educt in edge.start_nodes.all %}
             <a href="{{ educt.url }}" class="btn btn-outline btn-sm"
-              >{{ educt.get_name }}</a
+              >{{ educt.name }}</a
             >
           {% endfor %}
           <svg
@@ -115,7 +112,7 @@
           </svg>
           {% for product in edge.end_nodes.all %}
             <a href="{{ product.url }}" class="btn btn-outline btn-sm"
-              >{{ product.get_name }}</a
+              >{{ product.name }}</a
             >
           {% endfor %}
         </div>

templates/objects/group.html

@@ -56,9 +56,7 @@
         <ul class="menu bg-base-200 rounded-box">
           {% for um in group.user_member.all %}
             <li>
-              <a
+              <a href="{{ um.url }}" class="hover:bg-base-300"
-                href="{% if user.is_superuser %}{{ um.url }}{% else %}{{ "#" }}{% endif %}"
-                class="hover:bg-base-300"
                 >{{ um.username }}
                 {% if not um.is_active %}<i>(inactive)</i>{% endif %}</a
               >

templates/objects/node.html

@@ -55,15 +55,6 @@
       </div>
     </div>
 
-    <!-- Description -->
-    {% if node.description and node.description != "no description" %}
-      <div class="collapse-arrow bg-base-200 collapse">
-        <input type="checkbox" checked />
-        <div class="collapse-title text-xl font-medium">Description</div>
-        <div class="collapse-content">{{ node.description }}</div>
-      </div>
-    {% endif %}
-
     {% epdb_slot_templates "epdb.objects.node.viz" as viz_templates %}
 
     {% for tpl in viz_templates %}

templates/objects/pathway.html

@@ -21,7 +21,6 @@
     .link {
       stroke: #999;
       stroke-opacity: 0.6;
-      stroke-width: 1.5px;
       /* marker-end: url(#arrow); */
     }
 
@@ -73,15 +72,6 @@
       stroke: red;
       stroke-width: 3px;
     }
-
-    .inedge {
-      stroke: red;
-      stroke-width: 3px;
-    }
-    .outedge {
-      stroke: green;
-      stroke-width: 3px;
-    }
   </style>
   <script src="{% static 'js/pw.js' %}"></script>
 
@@ -121,7 +111,7 @@
       <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">
@@ -178,52 +168,6 @@
                   tabindex="0"
                   class="dropdown-content menu bg-base-100 rounded-box z-50 w-60 p-2"
                 >
-                  <li>
-                    <a id="compound-names-toggle-button" class="cursor-pointer">
-                      <svg
-                          id="compound-names-icon"
-                          xmlns="http://www.w3.org/2000/svg"
-                          width="16"
-                          height="16"
-                          viewBox="0 0 24 24"
-                          fill="none"
-                          stroke="currentColor"
-                          stroke-width="2"
-                          stroke-linecap="round"
-                          stroke-linejoin="round"
-                          class="lucide lucide-eye"
-                        >
-                          <path
-                            d="M2 12s3-7 10-7 10 7 10 7-3 7-10 7-10-7-10-7Z"
-                          />
-                          <circle cx="12" cy="12" r="3" />
-                        </svg>
-                      Compound Names
-                    </a>
-                  </li>
-                  <li>
-                    <a id="reaction-names-toggle-button" class="cursor-pointer">
-                      <svg
-                          id="reaction-names-icon"
-                          xmlns="http://www.w3.org/2000/svg"
-                          width="16"
-                          height="16"
-                          viewBox="0 0 24 24"
-                          fill="none"
-                          stroke="currentColor"
-                          stroke-width="2"
-                          stroke-linecap="round"
-                          stroke-linejoin="round"
-                          class="lucide lucide-eye"
-                        >
-                          <path
-                            d="M2 12s3-7 10-7 10 7 10 7-3 7-10 7-10-7-10-7Z"
-                          />
-                          <circle cx="12" cy="12" r="3" />
-                        </svg>
-                      Reaction Names
-                    </a>
-                  </li>
                   {% if pathway.setting.model.app_domain %}
                     <li>
                       <a id="app-domain-toggle-button" class="cursor-pointer">
@@ -249,7 +193,6 @@
                       </a>
                     </li>
                   {% endif %}
-                  {% if 1 == 0 %}
                   <li>
                     <a id="timeseries-toggle-button" class="cursor-pointer">
                       <svg
@@ -300,7 +243,6 @@
                       Show Predicted Properties
                     </a>
                   </li>
-                  {% endif %}
                 </ul>
               </div>
             </div>
@@ -425,18 +367,6 @@
               >
                 <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"
@@ -544,10 +474,6 @@
   {{ pathway.d3_json|json_script:"pathway" }}
 
   <script>
-    // Global switch for compound names view
-    var compoundNamesViewEnabled = false;
-    // Gloabl switch for reaction names view
-    var reactionNamesViewEnabled = false;
     // Global switch for app domain view
     var appDomainViewEnabled = false;
     // Global switch for timeseries view
@@ -583,67 +509,6 @@
         descContent.innerHTML = newDesc;
       }
 
-      const compoundNamesBtn = document.getElementById("compound-names-toggle-button");
-      if (compoundNamesBtn) {
-        compoundNamesBtn.addEventListener("click", function () {
-          compoundNamesViewEnabled = !compoundNamesViewEnabled;
-          const icon = document.getElementById("compound-names-icon");
-
-          if (compoundNamesViewEnabled) {
-            // Change to eye-off icon
-            icon.innerHTML =
-              '<path d="M9.88 9.88a3 3 0 1 0 4.24 4.24"/><path d="M10.73 5.08A10.43 10.43 0 0 1 12 5c7 0 10 7 10 7a13.16 13.16 0 0 1-1.67 2.68"/><path d="M6.61 6.61A13.526 13.526 0 0 0 2 12s3 7 10 7a9.74 9.74 0 0 0 5.39-1.61"/><line x1="2" x2="22" y1="2" y2="22"/>';
-
-            nodes.forEach((x) => {
-              if (x.name) {
-                d3.select(x.el)
-                  .append("text")
-                  .text(d => d.name)
-                  .attr("text-anchor", "middle")
-                  .attr("y", -20)
-                  .style("font-size", "4px");
-              }
-            });
-          } else {
-            // Change back to eye icon
-            icon.innerHTML =
-              '<path d="M2 12s3-7 10-7 10 7 10 7-3 7-10 7-10-7-10-7Z"/><circle cx="12" cy="12" r="3"/>';
-
-            nodes.forEach((x) => {
-              d3.select(x.el)
-                .select("text")
-                .remove()
-            })
-          }
-        });
-      }
-
-      const reactionNamesBtn = document.getElementById("reaction-names-toggle-button");
-      if (reactionNamesBtn) {
-        reactionNamesBtn.addEventListener("click", function () {
-          reactionNamesViewEnabled = !reactionNamesViewEnabled;
-          const icon = document.getElementById("reaction-names-icon");
-
-          if (reactionNamesViewEnabled) {
-            // Change to eye-off icon
-            icon.innerHTML =
-              '<path d="M9.88 9.88a3 3 0 1 0 4.24 4.24"/><path d="M10.73 5.08A10.43 10.43 0 0 1 12 5c7 0 10 7 10 7a13.16 13.16 0 0 1-1.67 2.68"/><path d="M6.61 6.61A13.526 13.526 0 0 0 2 12s3 7 10 7a9.74 9.74 0 0 0 5.39-1.61"/><line x1="2" x2="22" y1="2" y2="22"/>';
-
-              d3.selectAll(".link-label")
-                .style("display", null);
-
-          } else {
-            // Change back to eye icon
-            icon.innerHTML =
-              '<path d="M2 12s3-7 10-7 10 7 10 7-3 7-10 7-10-7-10-7Z"/><circle cx="12" cy="12" r="3"/>';
-
-            d3.selectAll(".link-label")
-                .style("display", "none");
-
-          }
-        });
-      }
-
       // App domain toggle
       const appDomainBtn = document.getElementById("app-domain-toggle-button");
       if (appDomainBtn) {

templates/objects/reaction.html

@@ -79,9 +79,6 @@
       <div class="collapse-content">
         <div class="flex justify-center">{{ reaction.as_svg|safe }}</div>
       </div>
-      {% if reaction.contains_pes %}
-        <span class='alert alert-info alert-soft'>The reaction contains a partially elucidated structure!</br>For visualization the representative structure is used. The pathway itself will show the actual partially elucidated structure.</span>
-      {% endif %}
     </div>
 
     <!-- Reaction Description -->

templates/objects/setting_template.html

@@ -24,76 +24,6 @@
         <td>Setting Name</td>
         <td>{{ setting_to_render.name }}</td>
       </tr>
-      <tr>
-        <td>Setting URL</td>
-        <td>
-          <a href="{{ setting_to_render.url }}" class="link link-primary">{{ setting_to_render.url }}</a>
-          <div
-            x-data="{
-              value: '{{ setting_to_render.url }}',
-              copied: false,
-
-              async copy() {
-                await navigator.clipboard.writeText(this.value)
-                this.copied = true
-
-                setTimeout(() => {
-                  this.copied = false
-                }, 1500)
-              }
-            }"
-            class="join"
-          >
-          <button
-            type="button"
-            class="btn btn-ghost"
-            :data-tip="copied ? 'Copied!' : 'Copy'"
-            @click="copy"
-            aria-label="Copy to clipboard"
-          >
-            <svg
-              x-show="!copied"
-              xmlns="http://www.w3.org/2000/svg"
-              class="h-4 w-4"
-              fill="none"
-              viewBox="0 0 24 24"
-              stroke="currentColor"
-              stroke-width="2"
-            >
-              <path
-                stroke-linecap="round"
-                stroke-linejoin="round"
-                d="M8 16H6a2 2 0 01-2-2V6a2 2 0 012-2h8a2 2 0 012 2v2"
-              />
-              <rect
-                width="12"
-                height="12"
-                x="8"
-                y="8"
-                rx="2"
-                ry="2"
-              />
-            </svg>
-
-            <svg
-              x-show="copied"
-              xmlns="http://www.w3.org/2000/svg"
-              class="h-4 w-4"
-              fill="none"
-              viewBox="0 0 24 24"
-              stroke="currentColor"
-              stroke-width="2"
-            >
-              <path
-                stroke-linecap="round"
-                stroke-linejoin="round"
-                d="M5 13l4 4L19 7"
-              />
-            </svg>
-            </button>
-          </div>
-        </td>
-      </tr>
       {% if setting_to_render.description %}
         <tr>
           <td>Setting Description</td>

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>
@@ -148,21 +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);
@@ -212,13 +197,7 @@
         e.preventDefault();
         const button = this;
         button.disabled = true;
-
+        button.textContent = "Predicting...";
-        // Set text depending on mode
-        if (document.getElementById("predict-submit-button").innerText === "Build") {
-          button.textContent = "Building...";
-        } else {
-          button.textContent = "Predicting...";
-        }
 
         // Get SMILES from either input or Ketcher
         const smilesInput = document.getElementById("predict-smiles");

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>

tests/test_compound_model.py

@@ -1,7 +1,5 @@
 from django.conf import settings as s
 from django.test import TestCase, override_settings
-
-from epdb.exceptions import InvalidSMILESException
 from epdb.logic import PackageManager
 from epdb.models import Compound, User, CompoundStructure
 
@@ -35,13 +33,13 @@ class CompoundTest(TestCase):
         self.assertEqual(c.description, "No Desc")
 
     def test_missing_smiles(self):
-        with self.assertRaises(InvalidSMILESException):
+        with self.assertRaises(ValueError):
             _ = Compound.create(self.package, smiles=None, name="Afoxolaner", description="No Desc")
 
-        with self.assertRaises(InvalidSMILESException):
+        with self.assertRaises(ValueError):
             _ = Compound.create(self.package, smiles="", name="Afoxolaner", description="No Desc")
 
-        with self.assertRaises(InvalidSMILESException):
+        with self.assertRaises(ValueError):
             _ = Compound.create(self.package, smiles="  ", name="Afoxolaner", description="No Desc")
 
     def test_smiles_are_trimmed(self):
@@ -98,7 +96,7 @@ class CompoundTest(TestCase):
         self.assertEqual(len(self.package.compounds), 1)
 
     def test_wrong_smiles(self):
-        with self.assertRaises(InvalidSMILESException):
+        with self.assertRaises(ValueError):
             _ = Compound.create(
                 self.package,
                 smiles="C1C(=NOC1(C2=CC(=CC(=C2)Cl)C(F)(F)F)C(F)(F)F)C3=CC=C(C=CC=CC=C43)C(=O)NCC(=O)NCC(F)(F)F",

tests/test_reaction_model.py

@@ -1,7 +1,6 @@
 from django.conf import settings as s
 from django.test import TestCase, override_settings
 
-from epdb.exceptions import InvalidSMILESException
 from epdb.logic import PackageManager
 from epdb.models import Compound, User, Reaction, Rule
 
@@ -164,7 +163,7 @@ class ReactionTest(TestCase):
         self.assertEqual(len(self.package.reactions), 1)
 
     def test_wrong_smiles(self):
-        with self.assertRaises(InvalidSMILESException):
+        with self.assertRaises(ValueError):
             _ = Reaction.create(
                 package=self.package,
                 name="Eawag BBD reaction r0001",

tests/views/test_model_views.py

@@ -46,14 +46,6 @@ class ModelViewTest(TestCase):
         )
 
         expected = [
-            {
-                "products": [["CCN(CC)C(=O)C1=CC(C=O)=CC=C1"]],
-                "probability": 0.75,
-                "btrule": {
-                    "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/2f2e0c39-e109-4836-959f-2bda2524f022",
-                    "name": "bt0001-3568",
-                },
-            },
             {
                 "products": [["O=C(O)C1=CC(CO)=CC=C1", "CCNCC"]],
                 "probability": 0.25,
@@ -70,6 +62,14 @@ class ModelViewTest(TestCase):
                     "name": "bt0243-4301",
                 },
             },
+            {
+                "products": [["CCN(CC)C(=O)C1=CC(C=O)=CC=C1"]],
+                "probability": 0.75,
+                "btrule": {
+                    "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/2f2e0c39-e109-4836-959f-2bda2524f022",
+                    "name": "bt0001-3568",
+                },
+            },
         ]
 
         actual = response.json()["pred"]

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#ad825570480bbe2f1a35c04923fede756c450751" }
+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 = [
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp312-cp312-linux_s390x.whl", hash = "sha256:0e34e276722ab7dd0dffa9e12fe2135a9b34a0e300c456ed7ad6430229404eb5", upload-time = "2025-10-01T23:33:41Z" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp312-cp312-linux_s390x.whl", hash = "sha256:0e34e276722ab7dd0dffa9e12fe2135a9b34a0e300c456ed7ad6430229404eb5" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp312-cp312-manylinux_2_28_aarch64.whl", hash = "sha256:610f600c102386e581327d5efc18c0d6edecb9820b4140d26163354a99cd800d", upload-time = "2025-10-01T23:33:45Z" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp312-cp312-manylinux_2_28_aarch64.whl", hash = "sha256:610f600c102386e581327d5efc18c0d6edecb9820b4140d26163354a99cd800d" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp312-cp312-manylinux_2_28_x86_64.whl", hash = "sha256:cb9a8ba8137ab24e36bf1742cb79a1294bd374db570f09fc15a5e1318160db4e", upload-time = "2025-10-01T23:33:48Z" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp312-cp312-manylinux_2_28_x86_64.whl", hash = "sha256:cb9a8ba8137ab24e36bf1742cb79a1294bd374db570f09fc15a5e1318160db4e" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp312-cp312-win_amd64.whl", hash = "sha256:2be20b2c05a0cce10430cc25f32b689259640d273232b2de357c35729132256d", upload-time = "2025-10-01T23:33:52Z" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp312-cp312-win_amd64.whl", hash = "sha256:2be20b2c05a0cce10430cc25f32b689259640d273232b2de357c35729132256d" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp312-cp312-win_arm64.whl", hash = "sha256:99fc421a5d234580e45957a7b02effbf3e1c884a5dd077afc85352c77bf41434", upload-time = "2025-10-01T23:34:10Z" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp312-cp312-win_arm64.whl", hash = "sha256:99fc421a5d234580e45957a7b02effbf3e1c884a5dd077afc85352c77bf41434" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313-linux_s390x.whl", hash = "sha256:8b5882276633cf91fe3d2d7246c743b94d44a7e660b27f1308007fdb1bb89f7d", upload-time = "2025-10-01T23:34:15Z" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313-linux_s390x.whl", hash = "sha256:8b5882276633cf91fe3d2d7246c743b94d44a7e660b27f1308007fdb1bb89f7d" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313-manylinux_2_28_aarch64.whl", hash = "sha256:a5064b5e23772c8d164068cc7c12e01a75faf7b948ecd95a0d4007d7487e5f25", upload-time = "2025-10-01T23:34:19Z" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313-manylinux_2_28_aarch64.whl", hash = "sha256:a5064b5e23772c8d164068cc7c12e01a75faf7b948ecd95a0d4007d7487e5f25" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313-manylinux_2_28_x86_64.whl", hash = "sha256:8f81dedb4c6076ec325acc3b47525f9c550e5284a18eae1d9061c543f7b6e7de", upload-time = "2025-10-01T23:34:23Z" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313-manylinux_2_28_x86_64.whl", hash = "sha256:8f81dedb4c6076ec325acc3b47525f9c550e5284a18eae1d9061c543f7b6e7de" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313-win_amd64.whl", hash = "sha256:e1ee1b2346ade3ea90306dfbec7e8ff17bc220d344109d189ae09078333b0856", upload-time = "2025-10-01T23:34:28Z" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313-win_amd64.whl", hash = "sha256:e1ee1b2346ade3ea90306dfbec7e8ff17bc220d344109d189ae09078333b0856" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313-win_arm64.whl", hash = "sha256:64c187345509f2b1bb334feed4666e2c781ca381874bde589182f81247e61f88", upload-time = "2025-10-01T23:34:45Z" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313-win_arm64.whl", hash = "sha256:64c187345509f2b1bb334feed4666e2c781ca381874bde589182f81247e61f88" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313t-manylinux_2_28_aarch64.whl", hash = "sha256:af81283ac671f434b1b25c95ba295f270e72db1fad48831eb5e4748ff9840041", upload-time = "2025-10-01T23:34:50Z" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313t-manylinux_2_28_aarch64.whl", hash = "sha256:af81283ac671f434b1b25c95ba295f270e72db1fad48831eb5e4748ff9840041" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313t-manylinux_2_28_x86_64.whl", hash = "sha256:a9dbb6f64f63258bc811e2c0c99640a81e5af93c531ad96e95c5ec777ea46dab", upload-time = "2025-10-01T23:34:53Z" },
+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313t-manylinux_2_28_x86_64.whl", hash = "sha256:a9dbb6f64f63258bc811e2c0c99640a81e5af93c531ad96e95c5ec777ea46dab" },
-    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313t-win_amd64.whl", hash = "sha256:6d93a7165419bc4b2b907e859ccab0dea5deeab261448ae9a5ec5431f14c0e64", upload-time = "2025-10-01T23:34:58Z" },
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 ]
 
 [[package]]