adjusted migration

Initial bayer app

Show Pack Classification

Adjusted docker compose to bayer specifics

Adjusted Dockerfile for Bayer

Adding secret flags to group, add secret pools to packages

Adjusted View for Package creation

Prep configs, added Package Create Modal

wip

More on PES

wip

wip

Dockerfile

@@ -30,13 +30,12 @@ RUN mkdir -p -m 0700 /root/.ssh \
     && ssh-keyscan git.envipath.com >> /root/.ssh/known_hosts
 
 # We'll need access to private repos, let docker make use of host ssh agent and use it like:
-# docker build --ssh default -t envipath/envipy-bayer:1.0 .
+# docker build --ssh default -t envipath/envipy:1.0 .
 RUN --mount=type=ssh \
     uv sync --locked --extra ms-login --extra pepper-plugin
 
 # Now copy source and do a final sync to install the project itself
 # Ensure .dockerignore is reasonable
-COPY bb4g bb4g
 COPY biotransformer biotransformer
 COPY bayer bayer
 COPY bridge bridge

bayer/epdb_hooks.py

@@ -13,14 +13,6 @@ register_template(
     "modals.collections.compound",
     "modals/collections/new_pes_modal.html",
 )
-register_template(
-    "epdb.actions.objects.pathway.add",
-    "actions/objects/pathway_add_pes.html",
-)
-register_template(
-    "epdb.modals.objects.pathway.add",
-    "modals/objects/add_pathway_pes_node_modal.html"
-)
 
 # PES Viz
 register_template(

bayer/templates/actions/objects/pathway_add_pes.html

@@ -1,8 +0,0 @@
-<li>
-  <a
-    class="button"
-    onclick="document.getElementById('add_pathway_pes_node_modal').showModal(); return false;"
-  >
-    <i class="glyphicon glyphicon-plus"></i> Add PES</a
-  >
-</li>

bayer/views.py

@@ -103,15 +103,20 @@ def create_pes_node(request, package_uuid, pathway_uuid):
 
 
 def fetch_pes(request, pes_url) -> dict:
+    proxies = {
+        "http": "http://10.185.190.100:8080",
+        "https": "http://10.185.190.100:8080",
+    }
+
     from epauth.views import get_access_token_from_request
     token = get_access_token_from_request(request)
 
-    if token:
+    if token or True:
         for k, v in s.PES_API_MAPPING.items():
             if pes_url.startswith(k):
                 pes_id = pes_url.split('/')[-1]
 
-                if pes_id == 'dummy':
+                if pes_id == 'dummy' or True:
                     import json
                     res_data = json.load(open(s.BASE_DIR / "fixtures/pes.json"))
                     res_data["pes_url"] = pes_url
@@ -120,7 +125,7 @@ def fetch_pes(request, pes_url) -> dict:
                     headers = {"Authorization": f"Bearer {token['access_token']}"}
                     params = {"pes_reg_entity_corporate_id": pes_id}
 
-                    res = requests.get(v, headers=headers, params=params, proxies=s.PROXIES or None)
+                    res = requests.get(v, headers=headers, params=params, proxies=proxies)
 
                     try:
                         res.raise_for_status()

bb4g/__init__.py

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

bridge/contracts.py

@@ -254,15 +254,7 @@ class Classifier(Plugin):
     def parse_config(cls, data: dict | None = None) -> EnviPyModel | None:
         if cls.Config is None:
             return None
-
+        return cls.Config(**(data or {}))
-        # remove empty strings a.k.a unset params to not overwrite defaults
-        cpy = {}
-        if data is not None:
-            for k, v in data.items():
-                if v != "":
-                    cpy[k] = v
-
-        return cls.Config(**cpy)
 
     @classmethod
     def create(cls, data: dict | None = None):

envipath/settings.py

@@ -143,12 +143,6 @@ if os.environ.get("USE_TEMPLATE_DB", False) == "True":
         "TEMPLATE": os.environ["TEMPLATE_DB"],
     }
 
-CACHES = {
-    "default": {
-        "BACKEND": "django.core.cache.backends.locmem.LocMemCache",
-        "LOCATION": "unique-snowflake",
-    }
-}
 
 # Password validation
 # https://docs.djangoproject.com/en/4.2/ref/settings/#auth-password-validators
@@ -480,14 +474,3 @@ if DATA_POOL_MAPPING:
 else:
     DATA_POOL_MAPPING = {}
 
-PROXIES = {}
-if os.environ.get("HTTP_PROXY"):
-    PROXIES["http"] = os.environ.get("HTTP_PROXY")
-    PROXIES["https"] = os.environ.get("HTTPS_PROXY")
-
-# BB4g
-BB4G_URL = os.environ.get("BB4G_URL")
-BB4G_TENANT_ID = os.environ.get("BB4G_TENANT_ID")
-BB4G_CLIENT_ID = os.environ.get("BB4G_CLIENT_ID")
-BB4G_CLIENT_SECRET = os.environ.get("BB4G_CLIENT_SECRET")
-BB4G_SCOPE = os.environ.get("BB4G_SCOPE")

epauth/urls.py

@@ -5,5 +5,4 @@ from . import views
 urlpatterns = [
     path("entra/login/", views.entra_login, name="entra_login"),
     path("auth/redirect/", views.entra_callback, name="entra_callback"),
-    path("auth/token/", views.get_token, name="get_token"),
 ]

epauth/views.py

@@ -2,11 +2,9 @@ import msal
 from django.conf import settings as s
 from django.contrib.auth import get_user_model
 from django.contrib.auth import login
-from django.http import HttpResponse
 from django.shortcuts import redirect
 
-from epdb.logic import UserManager, GroupManager
+from epdb.logic import UserManager
-from epdb.models import Group
 
 
 def get_msal_app_with_cache(request):
@@ -83,12 +81,10 @@ def entra_callback(request):
     login(request, u)
 
     # EDIT START
-
     # Ensure groups exists in eP
     for id, name in s.ENTRA_SECRET_GROUPS.items():
         if not Group.objects.filter(uuid=id).exists():
-            g = GroupManager.create_group(User.objects.get(username="admin"), name, f"Synced Entra Group {name} ",
+            g = GroupManager.create_group(User.objects.get(username="admin"), name, f"Synced Entra Group {name} ", uuid=id)
-                                          uuid=id)
         else:
             g = Group.objects.get(uuid=id)
         # Ensure its secret
@@ -97,8 +93,7 @@ def entra_callback(request):
 
     for id, name in s.ENTRA_GROUPS.items():
         if not Group.objects.filter(uuid=id).exists():
-            g = GroupManager.create_group(User.objects.get(username="admin"), name, f"Synced Entra Group {name} ",
+            g = GroupManager.create_group(User.objects.get(username="admin"), name, f"Synced Entra Group {name} ", uuid=id)
-                                          uuid=id)
         else:
             g = Group.objects.get(uuid=id)
 
@@ -116,11 +111,6 @@ def get_access_token_from_request(request, scopes=None):
     """
     Get an access token from the request using MSAL token cache.
     """
-
-    # Check if auth via Access Token
-    if request.headers.get("Authorization"):
-        return {"access_token": request.headers.get("Authorization").split(" ")[1]}
-
     if scopes is None:
         scopes = s.MS_ENTRA_SCOPES
 
@@ -162,9 +152,3 @@ def get_access_token_from_request(request, scopes=None):
         return result
 
     return None
-
-
-def get_token(request):
-    token = get_access_token_from_request(request)
-    msg = f"{token}"
-    return HttpResponse(msg, content_type='text/plain')

epdb/legacy_api.py

@@ -1,17 +1,19 @@
+import hashlib
 from collections import defaultdict
 from typing import Any, Dict, List, Optional
 
 import jwt
-import nh3
 import requests
+
+import nh3
 from django.conf import settings as s
 from django.contrib.auth import get_user_model
-from django.core.cache import cache
 from django.http import HttpResponse, JsonResponse
 from django.shortcuts import redirect
-from jwt import InvalidIssuerError
 from ninja import Field, Form, Query, Router, Schema
+from ninja.errors import HttpError
 from ninja.security import HttpBearer
+from ninja.security import SessionAuth
 
 from utilities.chem import FormatConverter
 from utilities.misc import PackageExporter
@@ -49,26 +51,6 @@ from .models import (
 Package = s.GET_PACKAGE_MODEL()
 
 
-def get_cached_jwks(tenant_id: str, force=False) -> Dict:
-    """Get JWKS using Django cache"""
-    cache_key = f"jwks_{tenant_id}"
-
-    jwks = cache.get(cache_key)
-
-    if jwks is None or force:
-        # Cache miss, fetch new keys
-        jwks_uri = f"https://login.microsoftonline.com/{tenant_id}/discovery/v2.0/keys"
-        response = requests.get(jwks_uri)
-        response.raise_for_status()
-
-        jwks = response.json()
-
-        # Cache for 1 hour (3600 seconds)
-        cache.set(cache_key, jwks, 3600)
-
-    return jwks
-
-
 def get_package_for_write(user, package_uuid):
     p = PackageManager.get_package_by_id(user, package_uuid)
     if not PackageManager.writable(user, p):
@@ -86,7 +68,9 @@ def validate_token(token: str) -> dict:
     TENANT_ID = s.MS_ENTRA_TENANT_ID
     CLIENT_ID = s.MS_ENTRA_CLIENT_ID
 
-    jwks = get_cached_jwks(TENANT_ID)
+    # Fetch Microsoft's public keys
+    jwks_uri = f"https://login.microsoftonline.com/{TENANT_ID}/discovery/v2.0/keys"
+    jwks = requests.get(jwks_uri).json()
 
     header = jwt.get_unverified_header(token)
 
@@ -94,21 +78,13 @@ def validate_token(token: str) -> dict:
         next(k for k in jwks["keys"] if k["kid"] == header["kid"])
     )
 
-    # Handle V1 and V2 tokens
+    claims = jwt.decode(
-    try:
+        token,
-        claims = jwt.decode(
+        public_key,
-            token,
+        algorithms=["RS256"],
-            public_key,
+        audience=[CLIENT_ID, f"api://{CLIENT_ID}"],
-            algorithms=["RS256"],
+        issuer=f"https://sts.windows.net/{TENANT_ID}/",
-            audience=[CLIENT_ID, f"api://{CLIENT_ID}"],
+    )
-            issuer=[
-                f"https://sts.windows.net/{TENANT_ID}/",
-                f"https://login.microsoftonline.com/{TENANT_ID}/v2.0"
-            ]
-        )
-    except Exception as e:
-        raise ValueError(f"Token verification failed! - {e}")
-
     return claims
 
 
@@ -820,7 +796,6 @@ class CreateCompound(Schema):
     compoundName: str | None = None
     compoundDescription: str | None = None
     inchi: str | None = None
-    pesLink: str | None = None
 
 
 @router.post("/package/{uuid:package_uuid}/compound")
@@ -832,28 +807,9 @@ def create_package_compound(
     try:
         p = get_package_for_write(request.user, package_uuid)
         # inchi is not used atm
-
+        c = Compound.create(
-        if c.pesLink is not None:
+            p, c.compoundSmiles, c.compoundName, c.compoundDescription, inchi=c.inchi
-            from bayer.views import fetch_pes
+        )
-            from bayer.models import PESCompound
-
-            try:
-                pes_data = fetch_pes(request, c.pesLink)
-            except ValueError as e:
-                return 400, {"message": f"Could not fetch PES data for {c.pesLink}"}
-
-            classification = pes_data.get("classificationLevel", "")
-            if "secret" == classification.lower():
-                data_pools = pes_data.get("dataPools")
-                if data_pools:
-                    if s.DATA_POOL_MAPPING[p.data_pool.name] not in data_pools:
-                        return 400, { "messsage": f"PES data pool {s.DATA_POOL_MAPPING[p.data_pool.name]} not found in PES data"}
-
-            c = PESCompound.create(p, pes_data, c.compoundName, c.compoundDescription)
-        else:
-            c = Compound.create(
-                p, c.compoundSmiles, c.compoundName, c.compoundDescription, inchi=c.inchi
-            )
         return redirect(c.url)
     except ValueError as e:
         return 400, {"message": str(e)}
@@ -1874,7 +1830,6 @@ class CreateNode(Schema):
     nodeName: str | None = None
     nodeReason: str | None = None
     nodeDepth: str | None = None
-    pesLink: str | None = None
 
 
 @router.post(
@@ -1886,43 +1841,14 @@ def add_pathway_node(request, package_uuid, pathway_uuid, n: Form[CreateNode]):
         p = get_package_for_write(request.user, package_uuid)
         pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
 
-        if n.pesLink:
+        if n.nodeDepth is not None and n.nodeDepth.strip() != "":
-            from bayer.views import fetch_pes
+            node_depth = int(n.nodeDepth)
-            from bayer.models import PESCompound
-
-            try:
-                pes_data = fetch_pes(request, c.pesLink)
-            except ValueError as e:
-                return 400, {"message": f"Could not fetch PES data for {c.pesLink}"}
-
-            classification = pes_data.get("classificationLevel", "")
-            if "secret" == classification.lower():
-                data_pools = pes_data.get("dataPools")
-                if data_pools:
-                    if s.DATA_POOL_MAPPING[p.data_pool.name] not in data_pools:
-                        return 400, { "messsage": f"PES data pool {s.DATA_POOL_MAPPING[p.data_pool.name]} not found in PES data"}
-
-            c = PESCompound.create(p, pes_data, c.compoundName, c.compoundDescription)
-
-            node = Node()
-            node.stereo_removed = False
-            node.pathway = pw
-            node.depth = 0
-
-            node.default_node_label = c.default_structure
-            node.save()
-
-            node.node_labels.add(c.default_structure)
-            node.save()
         else:
-            if n.nodeDepth is not None and n.nodeDepth.strip() != "":
+            node_depth = -1
-                node_depth = int(n.nodeDepth)
-            else:
-                node_depth = -1
 
-            node = Node.create(pw, n.nodeAsSmiles, node_depth, n.nodeName, n.nodeReason)
+        n = Node.create(pw, n.nodeAsSmiles, node_depth, n.nodeName, n.nodeReason)
 
-        return redirect(node.url)
+        return redirect(n.url)
     except ValueError:
         return 403, {"message": "Adding node failed!"}
 
@@ -2074,9 +2000,6 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
             description=e.edgeReason,
         )
 
-        # Update depths as sideeffect of above operation
-        pw.update_depths()
-
         return redirect(new_e.url)
     except ValueError:
         return 403, {"message": "Adding Edge failed!"}

epdb/logic.py

@@ -1065,9 +1065,52 @@ class PackageManager(object):
 
         print("Fixing Node depths...")
         total_pws = Pathway.objects.filter(package=pack).count()
-
         for p, pw in enumerate(Pathway.objects.filter(package=pack)):
-            pw.update_depths()
+            in_count = defaultdict(lambda: 0)
+            out_count = defaultdict(lambda: 0)
+
+            for e in pw.edges:
+                # TODO check if this will remain
+                for react in e.start_nodes.all():
+                    out_count[str(react.uuid)] += 1
+
+                for prod in e.end_nodes.all():
+                    in_count[str(prod.uuid)] += 1
+
+            root_nodes = []
+            for n in pw.nodes:
+                num_parents = in_count[str(n.uuid)]
+                if num_parents == 0:
+                    # must be a root node or unconnected node
+                    if n.depth != 0:
+                        n.depth = 0
+                        n.save()
+
+                    # Only root node may have children
+                    if out_count[str(n.uuid)] > 0:
+                        root_nodes.append(n)
+
+            levels = [root_nodes]
+            seen = set()
+            # Do a bfs to determine depths starting with level 0 a.k.a. root nodes
+            for i, level_nodes in enumerate(levels):
+                new_level = []
+                for n in level_nodes:
+                    for e in n.out_edges.all():
+                        for prod in e.end_nodes.all():
+                            if str(prod.uuid) not in seen:
+                                old_depth = prod.depth
+                                if old_depth != i + 1:
+                                    prod.depth = i + 1
+                                    prod.save()
+
+                                new_level.append(prod)
+
+                    seen.add(str(n.uuid))
+
+                if new_level:
+                    levels.append(new_level)
+
             print(f"{p + 1}/{total_pws} fixed.", end="\r")
 
         return pack

epdb/migrations/0025_auto_20260511_2025.py

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

epdb/models.py

@@ -2186,56 +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()
-
-        for n in self.nodes:
-            num_parents = in_count[str(n.uuid)]
-            if num_parents == 0:
-                # must be a root node or unconnected node
-                if n.depth != 0:
-                    n.depth = 0
-                    n.save()
-
-                # Only root node may have children
-                if out_count[str(n.uuid)] > 0:
-                    depth_map[0].append(n)
-
-        # At most depth len(nodes) is possible
-        for i in range(self.nodes.count()):
-            level_nodes = depth_map.get(i, [])
-
-            if len(level_nodes) == 0:
-                break
-
-            unique_next_level = set()
-            for n in level_nodes:
-                for e in self.edges:
-                    if n in e.start_nodes.all():
-                        for p in e.end_nodes.all():
-                            unique_next_level.add(p)
-
-            if len(unique_next_level) > 0:
-                depth_map[i + 1] = list(unique_next_level)
-
-        for depth, nodes in depth_map.items():
-            for n in nodes:
-                if n.depth != depth:
-                    n.depth = depth
-                    n.save()
-
 
 class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin):
     pathway = models.ForeignKey(

epdb/views.py

@@ -937,14 +937,12 @@ def package_models(request, package_uuid):
                 "requires_rule_packages": True,
                 "requires_data_packages": True,
             },
-        }
+            "EnviFormer": {
-
-        if s.ENVIFORMER_PRESENT:
-            context["model_types"]["EnviFormer"] = {
                 "type": "enviformer",
                 "requires_rule_packages": False,
                 "requires_data_packages": True,
             },
+        }
 
         if s.FLAGS.get("PLUGINS", False):
             for k, v in s.CLASSIFIER_PLUGINS.items():
@@ -2539,9 +2537,6 @@ def package_pathway_edges(request, package_uuid, pathway_uuid):
             substrate_nodes, product_nodes, name=edge_name, description=edge_description
         )
 
-        # Update depths as sideeffect of above operation
-        current_pathway.update_depths()
-
         return redirect(current_pathway.url)
 
     else:

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")
             )

static/js/pw.js

@@ -605,36 +605,7 @@ function draw(pathway, elem) {
         // Check if target is pseudo and draw marker only if not pseudo
         .attr("class", d => d.target.pseudo ? "link_no_arrow" : "link")
         .attr("marker-end", d => d.target.pseudo ? '' : d.multi_step ? 'url(#doublearrow)' : 'url(#arrow)')
-      .on("click", function(event, d) {
-          const wasHighlighted = d3.select(this).classed("highlighted");
 
-          d3.selectAll("line").classed("highlighted", false);
-
-          if (!wasHighlighted) {
-              const toHighlight = [];
-              toHighlight.push(d.el);
-
-              if (d.source.pseudo || d.target.pseudo) {
-                  if (d.target.pseudo) {
-                      d3.selectAll("line").each(e => {
-                          if (e !== undefined && e.source.id === d.target.id) {
-                              toHighlight.push(e.el);
-                          }
-                      });
-                  } else {
-                      d3.selectAll("line").each(e => {
-                          if (e !== undefined && (e.target.id === d.source.id || e.source.id === d.source.id)) {
-                              toHighlight.push(e.el);
-                          }
-                      });
-                  }
-              }
-
-              for (const e of toHighlight) {
-                  d3.select(e).classed("highlighted", true);
-              }
-          }
-      })
 
     // add element to links array
     link.each(function (d) {
@@ -653,13 +624,7 @@ function draw(pathway, elem) {
             .on("drag", dragged)
             .on("end", dragended))
         .on("click", function (event, d) {
-            const wasHighlighted = d3.select(this).select("circle").classed("highlighted");
+            d3.select(this).select("circle").classed("highlighted", !d3.select(this).select("circle").classed("highlighted"));
-
-            d3.selectAll('circle.highlighted').classed('highlighted', false);
-
-            if (!wasHighlighted) {
-                d3.select(this).select("circle").classed("highlighted", !d3.select(this).select("circle").classed("highlighted"));
-            }
         })
 
     // Kreise für die Knoten hinzufügen

templates/actions/objects/pathway.html

@@ -9,6 +9,14 @@
       <i class="glyphicon glyphicon-plus"></i> Add Compound</a
     >
   </li>
+  <li>
+    <a
+      class="button"
+      onclick="document.getElementById('add_pathway_pes_node_modal').showModal(); return false;"
+    >
+      <i class="glyphicon glyphicon-plus"></i> Add PES</a
+    >
+  </li>
   <li>
     <a
       class="button"
@@ -22,7 +30,7 @@
   {% for tpl in action_button_templates %}
     {% include tpl %}
   {% endfor %}
-  <li role="separator" class="divider h-px"></li>
+  <li role="separator" class="divider"></li>
 {% endif %}
 <li>
   <a
@@ -74,7 +82,7 @@
       Rules</a
     >
   </li>
-  <li role="separator" class="divider h-px"></li>
+  <li role="separator" class="divider"></li>
   <li>
     <a
       class="button"
@@ -99,16 +107,11 @@
       <i class="glyphicon glyphicon-plus"></i> Set Aliases</a
     >
   </li>
-  <li role="separator" class="divider h-px"></li>
+  <li role="separator" class="divider"></li>
   <li>
     <a
       class="button"
-      onclick="
+      onclick="document.getElementById('delete_pathway_node_modal').showModal(); return false;"
-      const modal = document.getElementById('delete_pathway_node_modal');
-      modal.showModal();
-      window.dispatchEvent(new Event('modal-opened'));
-      return false;
-      "
     >
       <i class="glyphicon glyphicon-trash"></i> Delete Compound</a
     >
@@ -116,12 +119,7 @@
   <li>
     <a
       class="button"
-      onclick="
+      onclick="document.getElementById('delete_pathway_edge_modal').showModal(); return false;"
-      const modal = document.getElementById('delete_pathway_edge_modal');
-      modal.showModal();
-      window.dispatchEvent(new Event('modal-opened'));
-      return false;
-      "
     >
       <i class="glyphicon glyphicon-trash"></i> Delete Reaction</a
     >

templates/collections/compounds_paginated.html

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

templates/collections/models_paginated.html

@@ -3,16 +3,14 @@
 {% block page_title %}Models{% endblock %}
 
 {% block action_button %}
-  {% if meta.can_edit or not meta.url_contains_package %}
+  {% if meta.can_edit and meta.enabled_features.MODEL_BUILDING %}
-    {% if meta.enabled_features.MODEL_BUILDING %}
+    <button
-      <button
+      type="button"
-        type="button"
+      class="btn btn-primary btn-sm"
-        class="btn btn-primary btn-sm"
+      onclick="document.getElementById('new_model_modal').showModal(); return false;"
-        onclick="document.getElementById('new_model_modal').showModal(); return false;"
+    >
-      >
+      New Model
-        New Model
+    </button>
-      </button>
-    {% endif %}
   {% endif %}
 {% endblock action_button %}
 

templates/collections/packages_paginated.html

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

templates/collections/pathways_paginated.html

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

templates/collections/reactions_paginated.html

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

templates/collections/rules_paginated.html

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

templates/collections/scenarios_paginated.html

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

templates/collections/structures_paginated.html

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

templates/modals/collections/new_prediction_setting_modal.html

@@ -203,11 +203,11 @@
               id="model-based-prediction-setting-threshold"
               name="model-based-prediction-setting-threshold"
               class="input input-bordered w-full"
-              value="0.25"
+              placeholder="0.25"
               type="number"
               min="0"
               max="1"
-              step="any"
+              step="0.05"
             />
           </div>
 

templates/modals/objects/delete_pathway_edge_modal.html

@@ -4,25 +4,6 @@
   id="delete_pathway_edge_modal"
   class="modal"
   x-data="modalForm({ state: { selectedEdge: '', imageUrl: '' } })"
-  @modal-opened.window="
-   const links = d3.selectAll('line.highlighted');
-  console.log(links);
-   if (!links.empty()) {
-        const el = links.node();
-        const selectElement = document.getElementById('delete_pathway_edge_edges');
-        console.log(el);
-        console.log(el.__data__);
-        for (let option of selectElement.options) {
-            if (option.value === el.__data__.url) {
-                option.selected = true;
-                break;
-            }
-        }
-
-        selectElement.dispatchEvent(new Event('change'));
-
-   }
-  "
   @close="reset()"
 >
   <div class="modal-box">

templates/modals/objects/delete_pathway_node_modal.html

@@ -4,22 +4,6 @@
   id="delete_pathway_node_modal"
   class="modal"
   x-data="modalForm({ state: { selectedNode: '', imageUrl: '' } })"
-  @modal-opened.window="
-   const el = d3.select('circle.highlighted').node();
-
-   if (el !== null) {
-    const selectElement = document.getElementById('delete_pathway_node_nodes');
-
-    for (let option of selectElement.options) {
-        if (option.value === el.__data__.url) {
-            option.selected = true;
-            break;
-        }
-    }
-
-    selectElement.dispatchEvent(new Event('change'));
-   }
-  "
   @close="reset()"
 >
   <div class="modal-box">

templates/objects/pathway.html

@@ -77,6 +77,7 @@
 
   {% block action_modals %}
     {% include "modals/objects/add_pathway_node_modal.html" %}
+    {% include "modals/objects/add_pathway_pes_node_modal.html" %}
     {% include "modals/objects/add_pathway_edge_modal.html" %}
     {% epdb_slot_templates "epdb.modals.objects.pathway.add" as add_templates %}
     {% for tpl in add_templates %}
@@ -106,12 +107,12 @@
     </div>
 
     <!-- Graphical Representation -->
-    <div class="collapse-arrow bg-base-200 collapse overflow-y-auto">
+    <div class="collapse-arrow bg-base-200 collapse">
       <input type="checkbox" checked />
       <div class="collapse-title text-xl font-medium">
         Graphical Representation
       </div>
-      <div class="collapse-content ">
+      <div class="collapse-content">
         <div class="bg-base-100 mb-2 rounded-lg p-2">
           <div class="navbar bg-base-100 rounded-lg">
             <div class="flex-1">
@@ -140,7 +141,7 @@
                 </div>
                 <ul
                   tabindex="0"
-                  class="dropdown-content menu bg-base-100 rounded-box z-50 w-96 p-2"
+                  class="dropdown-content menu bg-base-100 rounded-box z-50 w-52 p-2"
                 >
                   {% include "actions/objects/pathway.html" %}
                 </ul>

utilities/legacy.py

@@ -64,7 +64,7 @@
 
 import logging
 
-from envipy_additional_information import HalfLife, HalfLifeWS, HalfLifeModel
+from envipy_additional_information import HalfLife, HalfLifeWS
 from envipy_additional_information.information import Interval
 from envipy_additional_information.parsers import (
     AcidityParser,
@@ -473,12 +473,17 @@ def build_additional_information_from_request(request, type_):
 
             comment = get_parameter_or_empty_string(request, "comment")
             source = get_parameter_or_empty_string(request, "source")
-            # first_order = get_parameter_or_empty_string(request, "firstOrder")
+            first_order = get_parameter_or_empty_string(request, "firstOrder")
             model = get_parameter_or_empty_string(request, "model")
             fit = get_parameter_or_empty_string(request, "fit")
 
-            if model:
+            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)
 
@@ -503,10 +508,6 @@ def build_additional_information_from_request(request, type_):
             comment_ws = get_parameter_or_empty_string(request, "comment_ws")
             source_ws = get_parameter_or_empty_string(request, "source_ws")
             model_ws = get_parameter_or_empty_string(request, "model_ws")
-
-            if model_ws:
-                model_ws = HalfLifeModel(model_ws.upper())
-
             fit_ws = get_parameter_or_empty_string(request, "fit_ws")
 
             dt50_total = IntervalParser.from_string(hl_ws_total)

uv.lock

@@ -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#676dae1c5678539beac637b87e49b9dadfdfd85a" }
+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" },
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+    { url = "https://download-r2.pytorch.org/whl/cpu/torch-2.8.0%2Bcpu-cp313-cp313-linux_s390x.whl", hash = "sha256:8b5882276633cf91fe3d2d7246c743b94d44a7e660b27f1308007fdb1bb89f7d" },
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 ]
 
 [[package]]