wip

Dockerfile

@@ -30,21 +30,19 @@ 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
+COPY biotransformer biotransformer
 COPY envipath envipath
 COPY epapi epapi
 COPY epauth epauth
 COPY epdb epdb
-COPY epiuclid epiuclid
 COPY fixtures fixtures
 COPY migration migration
 COPY pepper pepper

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/migrations/0003_package_data_pool.py

@@ -0,0 +1,20 @@
+# Generated by Django 6.0.3 on 2026-04-14 19:07
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('bayer', '0002_initial'),
+        ('epdb', '0023_alter_compoundstructure_options_and_more'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='package',
+            name='data_pool',
+            field=models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.group', verbose_name='Data pool'),
+        ),
+    ]

bayer/migrations/0004_pescompound_pesstructure.py

@@ -1,4 +1,4 @@
-# Generated by Django 6.0.3 on 2026-04-17 21:22
+# Generated by Django 6.0.3 on 2026-04-15 20:03
 
 import django.db.models.deletion
 from django.db import migrations, models
@@ -7,7 +7,7 @@ from django.db import migrations, models
 class Migration(migrations.Migration):
 
     dependencies = [
-        ('bayer', '0002_initial'),
+        ('bayer', '0003_package_data_pool'),
         ('epdb', '0023_alter_compoundstructure_options_and_more'),
     ]
 
@@ -26,16 +26,10 @@ class Migration(migrations.Migration):
             name='PESStructure',
             fields=[
                 ('compoundstructure_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.compoundstructure')),
-                ('pes_link', models.URLField(verbose_name='PES Link')),
             ],
             options={
                 'abstract': False,
             },
             bases=('epdb.compoundstructure',),
         ),
-        migrations.AddField(
-            model_name='package',
-            name='data_pool',
-            field=models.ForeignKey(blank=True, default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, to='epdb.group', verbose_name='Data pool'),
-        ),
     ]

bayer/migrations/0005_pesstructure_pes_link.py

@@ -0,0 +1,19 @@
+# Generated by Django 6.0.3 on 2026-04-16 08:43
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('bayer', '0004_pescompound_pesstructure'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='pesstructure',
+            name='pes_link',
+            field=models.URLField(default=None, verbose_name='PES Link'),
+            preserve_default=False,
+        ),
+    ]

bayer/models.py

@@ -15,7 +15,6 @@ from epdb.models import (
     SimpleAmbitRule,
     SimpleRDKitRule,
 )
-from utilities.chem import FormatConverter
 
 
 class Package(EnviPathModel):
@@ -115,9 +114,7 @@ class PESCompound(Compound):
 
         # Check if we find a direct match for a given pes_link
         if PESStructure.objects.filter(pes_link=pes_url, compound__package=package).exists():
-            # Due to normalization we might end up in having multiple structures
+            return PESStructure.objects.get(pes_link=pes_url, compound__package=package).compound
-            # All of them point to the same compound -> pick any
-            return PESStructure.objects.filter(pes_link=pes_url, compound__package=package).first().compound
 
         # Generate Compound
         c = PESCompound()
@@ -138,37 +135,19 @@ class PESCompound(Compound):
 
         c.save()
 
-        molfile = pes_data.get("representativeStructures", [{}])[0].get("ctab")
-
-        if molfile is None:
-            raise ValueError("PES data does not contain a valid mol file!")
-
-        smiles = FormatConverter.to_smiles(FormatConverter.from_molfile(molfile))
-
-        standardized_smiles = FormatConverter.standardize(smiles, remove_stereo=True)
-
         is_standardized = standardized_smiles == smiles
 
         if not is_standardized:
-            _ = PESStructure.create(
+            _ = CompoundStructure.create(
                 c,
-                pes_url,
-                molfile,
                 standardized_smiles,
                 name="Normalized structure of {}".format(name),
                 description="{} (in its normalized form)".format(description),
                 normalized_structure=True,
             )
 
-
+        cs = CompoundStructure.create(
-        cs = PESStructure.create(
+            c, smiles, name=name, description=description, normalized_structure=is_standardized
-            c,
-            pes_url,
-            molfile,
-            smiles,
-            name=name,
-            description=description,
-            normalized_structure=is_standardized
         )
 
         c.default_structure = cs
@@ -180,53 +159,6 @@ class PESCompound(Compound):
 class PESStructure(CompoundStructure):
     pes_link = models.URLField(blank=False, null=False, verbose_name="PES Link")
 
-    @staticmethod
-    @transaction.atomic
-    def create(
-            compound: Compound,
-            pes_link: str,
-            mol_file: str,
-            smiles: str,
-            name: str = None,
-            description: str = None,
-            *args,
-            **kwargs
-    ):
-        if compound.pk is None:
-            raise ValueError("Unpersisted Compound! Persist compound first!")
-
-        cs = PESStructure()
-        # Clean for potential XSS
-        if name is not None:
-            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()
-
-        cs.smiles = smiles
-        cs.mol_file = mol_file
-        cs.pes_link = pes_link
-        cs.compound = compound
-
-        if "normalized_structure" in kwargs:
-            cs.normalized_structure = kwargs["normalized_structure"]
-
-        cs.save()
-
-        return cs
-
-    @transaction.atomic
-    def add_structure(
-        self,
-        smiles: str,
-        name: str = None,
-        description: str = None,
-        default_structure: bool = False,
-        *args,
-        **kwargs,
-    ) -> "CompoundStructure":
-        raise ValueError("Not supported!")
-
     def d3_json(self):
         return {
             "is_pes": True,

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/templates/modals/collections/new_pes_modal.html

@@ -154,7 +154,7 @@
       <button
         type="button"
         class="btn btn-primary"
-        @click="submit('new-pes-modal-form')"
+        @click="submit('new-compound-modal-form')"
         :disabled="isSubmitting"
       >
         <span x-show="!isSubmitting">Submit</span>

bayer/templates/modals/objects/add_pathway_pes_node_modal.html

@@ -1,174 +0,0 @@
-{% load static %}
-
-<dialog
-  id="add_pathway_pes_node_modal"
-  class="modal"
-  x-data="{
-    isSubmitting: false,
-    pesLink: null,
-    pesVizHtml: '',
-
-    reset() {
-      this.isSubmitting = false;
-    },
-
-    get isPESSet() {
-      console.log(this.pesLink);
-      return this.pesLink !== null;
-    },
-
-    updatePesViz() {
-      if (!this.isPESSet) {
-        this.pesVizHtml = '';
-        return;
-      }
-
-      const img = new Image();
-      img.src = '{% url 'depict_pes' %}?pesLink=' + encodeURIComponent(this.pesLink);
-      img.style.width = '100%';
-      img.style.height = '100%';
-      img.style.objectFit = 'cover';
-
-      img.onload = () => {
-        this.pesVizHtml = img.outerHTML;
-      };
-
-      img.onerror = () => {
-        this.pesVizHtml = `
-          <div class='alert alert-error' role='alert'>
-            <h4 class='alert-heading'>Could not render PES!</h4>
-            <p>Could not render PES - Do you have access?</p>
-          </div>`;
-      };
-    },
-
-    submit(formId) {
-      const form = document.getElementById(formId);
-
-      // Remove previously injected inputs
-      form.querySelectorAll('.dynamic-param').forEach(el => el.remove());
-
-      // Add values from dynamic form into the html form
-      if (this.formData) {
-        Object.entries(this.formData).forEach(([key, value]) => {
-          const input = document.createElement('input');
-          input.type = 'hidden';
-          input.name = key;
-          input.value = value;
-          input.classList.add('dynamic-param');
-
-          form.appendChild(input);
-        });
-      }
-
-      if (form && form.checkValidity()) {
-        this.isSubmitting = true;
-        form.submit();
-      } else if (form) {
-        form.reportValidity();
-      }
-    }
-  }"
-  @close="reset()"
->
-  <div class="modal-box max-w-3xl">
-  <!-- Header -->
-  <h3 class="text-lg font-bold">New PES</h3>
-
-    <!-- Close button (X) -->
-    <form method="dialog">
-      <button
-        class="btn btn-sm btn-circle btn-ghost absolute top-2 right-2"
-        :disabled="isSubmitting"
-      >
-        ✕
-      </button>
-    </form>
-
-    <!-- Body -->
-    <div class="py-4">
-      <form
-        id="new-pes-node-modal-form"
-        accept-charset="UTF-8"
-        action="{% url 'create pes node' current_object.package.uuid current_object.uuid  %}"
-        method="post"
-      >
-        {% csrf_token %}
-
-        <div class="form-control mb-3">
-          <label class="label" for="compound-name">
-            <span class="label-text">Name</span>
-          </label>
-          <input
-            id="compound-name"
-            class="input input-bordered w-full"
-            name="compound-name"
-            placeholder="Name"
-            required
-          />
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label" for="compound-description">
-            <span class="label-text">Description</span>
-          </label>
-          <input
-            id="compound-description"
-            class="input input-bordered w-full"
-            name="compound-description"
-            placeholder="Description"
-          />
-        </div>
-
-        <div class="form-control mb-3">
-          <label class="label" for="pes-link">
-            <span class="label-text">Link to PES</span>
-          </label>
-          <input
-            id="pes-link"
-            name="pes-link"
-            type="text"
-            class="input input-bordered w-full"
-            placeholder="Link to PES e.g. https://pesregapp-test.cropkey-np.ag/entities/PES-000126"
-            x-model="pesLink"
-            @input="updatePesViz()"
-            required
-          />
-        </div>
-
-        <div id="pes-viz" class="mb-3" x-html="pesVizHtml"></div>
-
-      </form>
-    </div>
-
-    <!-- Footer -->
-    <div class="modal-action">
-      <button
-        type="button"
-        class="btn"
-        onclick="this.closest('dialog').close()"
-        :disabled="isSubmitting"
-      >
-        Close
-      </button>
-      <button
-        type="button"
-        class="btn btn-primary"
-        @click="submit('new-pes-node-modal-form')"
-        :disabled="isSubmitting"
-      >
-        <span x-show="!isSubmitting">Submit</span>
-        <span
-          x-show="isSubmitting"
-          class="loading loading-spinner loading-sm"
-        ></span>
-        <span x-show="isSubmitting">Creating...</span>
-      </button>
-    </div>
-  </div>
-
-  <!-- Backdrop -->
-  <form method="dialog" class="modal-backdrop">
-    <button :disabled="isSubmitting">close</button>
-  </form>
-</dialog>

bayer/templates/objects/compound_structure_viz.html

@@ -1,11 +1,4 @@
 {% if compound_structure.pes_link %}
-  <!-- PES -->
-  <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">{{ compound_structure.pes_link }}</div>
-  </div>
-
   <!-- Image Representation -->
   <div class="collapse-arrow bg-base-200 collapse">
     <input type="checkbox" checked />

bayer/templates/objects/compound_viz.html

@@ -1,11 +1,4 @@
 {% if compound.default_structure.pes_link %}
-  <!-- PES -->
-  <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">{{ compound.default_structure.pes_link }}</div>
-  </div>
-
   <!-- Image Representation -->
   <div class="collapse-arrow bg-base-200 collapse">
     <input type="checkbox" checked />

bayer/templates/objects/node_viz.html

@@ -1,11 +1,4 @@
 {% if node.default_node_label.pes_link %}
-  <!-- PES -->
-  <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">{{ node.default_node_label.pes_link }}</div>
-  </div>
-
   <!-- Image Representation -->
   <div class="collapse-arrow bg-base-200 collapse">
     <input type="checkbox" checked />

bayer/templates/objects/package.html

@@ -1,5 +1,5 @@
 {% extends "framework_modern.html" %}
-{% load static %}
+
 {% block content %}
 
   {% block action_modals %}
@@ -16,7 +16,7 @@
     <div class="card bg-base-100">
       <div class="card-body">
         <div class="flex items-center justify-between">
-          <h2 class="card-title text-2xl">{{ package.name }} {% if meta.url_contains_package and meta.current_package.get_classification_level_display == "Restricted" %}<img src="{% static 'images/restricted_mid.png' %}" width="100">{% elif meta.url_contains_package and meta.current_package.get_classification_level_display == "Secret" %}<img src="{% static 'images/secret_mid.png' %}" width="60">{% endif %}</h2>
+          <h2 class="card-title text-2xl">{{ package.name }} - ({{ package.get_classification_level_display }})</h2>
           <div id="actionsButton" class="dropdown dropdown-e nd hidden">
             <div tabindex="0" role="button" class="btn btn-ghost btn-sm">
               <svg

bayer/templates/static/login.html

@@ -1,5 +1,5 @@
 {% extends "static/login_base.html" %}
-{% load static %}
+
 {% block title %}enviPath - Sign In{% endblock %}
 
 {% block extra_styles %}
@@ -31,18 +31,13 @@
 {% endblock %}
 
 {% block content %}
-  <div>
+  <div class="card bg-base-200 mb-6 ">
-  <img src="{% static 'images/bayer-logo.svg' %}">
+    <div class="card-body">
-
+      <h3 class="card-title">Welcome to the new enviPath!</h3>
     </div>
-  <div class="flex flex-col space-y-4 ...">
-    <div><p></p></div>
-  <div><p></p></div>
-
   </div>
-
   <!-- Tab Navigation -->
-  <div class="border-base-300 mb-6 border-b" hidden>
+  <div class="border-base-300 mb-6 border-b">
     <div class="flex justify-start">
       <input
         type="radio"

bayer/urls.py

@@ -7,13 +7,8 @@ UUID = "[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}"
 urlpatterns = [
     re_path(r"^depict_pes$", v.visualize_pes, name="depict_pes"),
     re_path(
-        rf"^package/(?P<package_uuid>{UUID})/pes$",
+        rf"^package/(?P<package_uuid>{UUID})/compound$",
         v.create_pes,
         name="create pes",
     ),
-    re_path(
-        rf"^package/(?P<package_uuid>{UUID})/pathway/(?P<pathway_uuid>{UUID})/pes$",
-        v.create_pes_node,
-        name="create pes node",
-    ),
 ]

bayer/views.py

@@ -8,12 +8,9 @@ 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
 from utilities.decorators import package_permission_required
 
-Package = s.GET_PACKAGE_MODEL()
-
 
 @package_permission_required()
 def create_pes(request, package_uuid):
@@ -21,10 +18,6 @@ def create_pes(request, package_uuid):
     current_package = PackageManager.get_package_by_id(current_user, package_uuid)
 
     if request.method == "POST":
-
-        if current_package.classification_level == Package.Classification.INTERNAL:
-            raise BadRequest("Cannot create PESs for internal packages.")
-
         compound_name = request.POST.get('compound-name')
         compound_description = request.POST.get('compound-description')
         pes_link = request.POST.get('pes-link')
@@ -35,14 +28,6 @@ def create_pes(request, package_uuid):
             except ValueError as e:
                 return BadRequest(f"Could not fetch PES data for {pes_link}")
 
-            classification = pes_data.get("classificationLevel", "")
-            if "secret" == classification.lower():
-                data_pools = pes_data.get("dataPools")
-                if data_pools:
-                    if s.DATA_POOL_MAPPING[current_package.data_pool.name] not in data_pools:
-                        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)
@@ -52,66 +37,22 @@ def create_pes(request, package_uuid):
         pass
 
 
-@package_permission_required()
-def create_pes_node(request, package_uuid, pathway_uuid):
-    current_user = _anonymous_or_real(request)
-    current_package = PackageManager.get_package_by_id(current_user, package_uuid)
-    current_pathway = Pathway.objects.get(package=current_package, uuid=pathway_uuid)
-
-    if request.method == "POST":
-
-        if current_package.classification_level == Package.Classification.INTERNAL:
-            raise BadRequest("Cannot create PESs for internal packages.")
-
-        compound_name = request.POST.get('compound-name')
-        compound_description = request.POST.get('compound-description')
-        pes_link = request.POST.get('pes-link')
-
-        if pes_link:
-            try:
-                pes_data = fetch_pes(request, pes_link)
-            except ValueError as e:
-                return BadRequest(f"Could not fetch PES data for {pes_link}")
-
-            classification = pes_data.get("classificationLevel", "")
-            if "secret" == classification.lower():
-                data_pools = pes_data.get("dataPools")
-                if data_pools:
-                    if s.DATA_POOL_MAPPING[current_package.data_pool.name] not in data_pools:
-                        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)
-
-            n = Node()
-            n.stereo_removed = False
-            n.pathway = current_pathway
-            n.depth = 0
-
-            n.default_node_label = pes.default_structure
-            n.save()
-
-            n.node_labels.add(pes.default_structure)
-            n.save()
-
-            return redirect(current_pathway.url)
-
-        else:
-            return BadRequest("Please provide a PES link.")
-    else:
-        pass
-
 
 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 +61,7 @@ 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")

envipath/urls.py

@@ -41,7 +41,9 @@ if s.MS_ENTRA_ENABLED:
     urlpatterns.append(path(f"{PATH_PREFIX}", include("epauth.urls")))
 
 if s.TENANT != "public":
-    urlpatterns.append(path(f"{PATH_PREFIX}", include(f"{s.TENANT}.urls")))
+    urlpatterns.append(
+        path(f"{PATH_PREFIX}", include(f"{s.TENANT}.urls"))
+    )
 
 # Custom error handlers
 handler400 = "epdb.views.handler400"

epauth/urls.py

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

epauth/views.py

@@ -2,7 +2,6 @@ import msal
 from django.conf import settings as s
 from django.contrib.auth import get_user_model
 from django.contrib.auth import login
-from django.http import HttpResponse
 from django.shortcuts import redirect
 
 from epdb.logic import UserManager, GroupManager
@@ -23,7 +22,7 @@ def get_msal_app_with_cache(request):
         client_id=s.MS_ENTRA_CLIENT_ID,
         client_credential=s.MS_ENTRA_CLIENT_SECRET,
         authority=s.MS_ENTRA_AUTHORITY,
-        token_cache=cache,
+        token_cache=cache
     )
 
     return msal_app, cache
@@ -60,12 +59,9 @@ def entra_callback(request):
 
     claims = result["id_token_claims"]
 
-    user_name = claims.get("name")
+    user_name = claims["name"]
-    user_email = claims.get("emailaddress", claims.get("email"))
+    user_email = claims.get("emailaddress", claims["email"])
-    user_oid = claims.get("oid")
+    user_oid = claims["oid"]
-
-    if not all([user_name, user_email, user_oid]):
-        raise ValueError("Missing required claims in ID token")
 
     # Get implementing class
     User = get_user_model()
@@ -83,7 +79,6 @@ def entra_callback(request):
     login(request, u)
 
     # EDIT START
-
     # Ensure groups exists in eP
     for id, name in s.ENTRA_SECRET_GROUPS.items():
         if not Group.objects.filter(uuid=id).exists():
@@ -116,11 +111,6 @@ def get_access_token_from_request(request, scopes=None):
     """
     Get an access token from the request using MSAL token cache.
     """
-
-    # Check if auth via Access Token
-    if request.headers.get("Authorization"):
-        return {"access_token": request.headers.get("Authorization").split(" ")[1]}
-
     if scopes is None:
         scopes = s.MS_ENTRA_SCOPES
 
@@ -152,7 +142,10 @@ def get_access_token_from_request(request, scopes=None):
         return None
 
     # Try to acquire token silently from cache
-    result = msal_app.acquire_token_silent(scopes=scopes, account=user_account)
+    result = msal_app.acquire_token_silent(
+        scopes=scopes,
+        account=user_account
+    )
 
     # Save cache changes back to session
     if cache.has_state_changed:
@@ -162,9 +155,3 @@ def get_access_token_from_request(request, scopes=None):
         return result
 
     return None
-
-
-def get_token(request):
-    token = get_access_token_from_request(request)
-    msg = f"{token}"
-    return HttpResponse(msg, content_type='text/plain')

epdb/admin.py

@@ -1,8 +1,5 @@
-import logging
-
 from django.conf import settings as s
 from django.contrib import admin
-from django.contrib import messages
 
 from .models import (
     AdditionalInformation,
@@ -32,8 +29,6 @@ from .models import (
 
 Package = s.GET_PACKAGE_MODEL()
 
-logger = logging.getLogger(__name__)
-
 
 class AdditionalInformationAdmin(admin.ModelAdmin):
     pass
@@ -50,113 +45,6 @@ class UserAdmin(admin.ModelAdmin):
         "date_joined",
     ]
 
-    actions = ["send_welcome_mail", "send_affiliation_mail"]
-
-    @admin.action(description="Send welcome mail")
-    def send_welcome_mail(self, request, queryset):
-        from django.core.mail import EmailMultiAlternatives
-
-        tpl = """Hello {username},
-
-Your account has been successfully activated.
-
-To log in, please visit
-https://envipath.org/password_reset/
-and request a new password.
-
-If you have any questions or feedback, feel free to visit our community forum at
-https://community.envipath.org/.
-You do not need to register again for the forum - you can log in using your enviPath account by clicking "Log In" and then "Log in with enviPath."
-
-Best regards,
-
-The enviPath Team"""
-
-        users = []
-
-        for user in queryset:
-            if user.is_active:
-                logger.info(f"{user.username} already active - not sending mail again")
-                continue
-            try:
-                msg = EmailMultiAlternatives(
-                    "Your enviPath Account Is Now Active",
-                    tpl.format(username=user.username),
-                    "admin@envipath.org",
-                    [user.email],
-                    bcc=["admin@envipath.org"],
-                )
-
-                msg.send(fail_silently=False)
-
-                user.is_active = True
-                user.password = "ASDF"
-                user.save()
-
-                users.append(user)
-                logger.info(f"{user.username} -> {user.email} mail sent")
-            except Exception as e:
-                logger.info(f"Error sending mail to {user.username}: {e}")
-
-        self.message_user(
-            request, f"Sent welcome mail to {[u.email for u in users]}", messages.SUCCESS
-        )
-
-    @admin.action(description="Send affiliation mail")
-    def send_affiliation_mail(self, request, queryset):
-        from django.core.mail import EmailMultiAlternatives
-
-        tpl = """Dear {username},
-
-Thank you for your interest in enviPath!
-
-Please note that the public enviPath system is intended for non-commercial use only.
-We see that you registered using the email address {email}.
-If possible, we kindly ask you to register using an official email address that reflects your affiliation (e.g., a university, NGO, or research organization).
-
-If you would like us to update your account, simply reply to this email and let us know which address we should use.
-We will then change it in our system, and you will receive a password reset email at the new address.
-
-If you are registering with a company email address and are interested in commercial use, you are very welcome to book a meeting with us so we can discuss how we can best support you.
-To book a meeting, please visit https://envipath.com/book
-
-If changing to an affiliation email address is not possible, please contact us at registration@envipath.org
-
-Best regards,
-
-enviPath team"""
-
-        users = []
-
-        for user in queryset:
-            if user.is_active or user.contacted:
-                logger.info(
-                    f"{user.username} already active or already contacted - not sending mail again"
-                )
-                continue
-            try:
-                msg = EmailMultiAlternatives(
-                    "Regarding your enviPath registration",
-                    tpl.format(username=user.username, email=user.email),
-                    "admin@envipath.org",
-                    [user.email],
-                    bcc=["admin@envipath.org"],
-                )
-
-                msg.send(fail_silently=False)
-
-                user.contacted = True
-                user.save()
-
-                users.append(user)
-                logger.info(f"{user.username} -> {user.email} affiliation mail sent")
-            except Exception as e:
-                logger.info(f"Error sending mail to {user.username}: {e}")
-
-        self.message_user(
-            request, f"Sent affiliation mail to {[u.email for u in users]}", messages.SUCCESS
-        )
-
 
 class UserPackagePermissionAdmin(admin.ModelAdmin):
     pass

epdb/legacy_api.py

@@ -1,17 +1,19 @@
+import hashlib
 from collections import defaultdict
 from typing import Any, Dict, List, Optional
 
 import jwt
-import nh3
 import requests
+
+import nh3
 from django.conf import settings as s
 from django.contrib.auth import get_user_model
-from django.core.cache import cache
 from django.http import HttpResponse, JsonResponse
 from django.shortcuts import redirect
-from jwt import InvalidIssuerError
 from ninja import Field, Form, Query, Router, Schema
+from ninja.errors import HttpError
 from ninja.security import HttpBearer
+from ninja.security import SessionAuth
 
 from utilities.chem import FormatConverter
 from utilities.misc import PackageExporter
@@ -49,26 +51,6 @@ from .models import (
 Package = s.GET_PACKAGE_MODEL()
 
 
-def get_cached_jwks(tenant_id: str, force=False) -> Dict:
-    """Get JWKS using Django cache"""
-    cache_key = f"jwks_{tenant_id}"
-
-    jwks = cache.get(cache_key)
-
-    if jwks is None or force:
-        # Cache miss, fetch new keys
-        jwks_uri = f"https://login.microsoftonline.com/{tenant_id}/discovery/v2.0/keys"
-        response = requests.get(jwks_uri)
-        response.raise_for_status()
-
-        jwks = response.json()
-
-        # Cache for 1 hour (3600 seconds)
-        cache.set(cache_key, jwks, 3600)
-
-    return jwks
-
-
 def get_package_for_write(user, package_uuid):
     p = PackageManager.get_package_by_id(user, package_uuid)
     if not PackageManager.writable(user, p):
@@ -86,7 +68,9 @@ def validate_token(token: str) -> dict:
     TENANT_ID = s.MS_ENTRA_TENANT_ID
     CLIENT_ID = s.MS_ENTRA_CLIENT_ID
 
-    jwks = get_cached_jwks(TENANT_ID)
+    # Fetch Microsoft's public keys
+    jwks_uri = f"https://login.microsoftonline.com/{TENANT_ID}/discovery/v2.0/keys"
+    jwks = requests.get(jwks_uri).json()
 
     header = jwt.get_unverified_header(token)
 
@@ -94,21 +78,13 @@ def validate_token(token: str) -> dict:
         next(k for k in jwks["keys"] if k["kid"] == header["kid"])
     )
 
-    # Handle V1 and V2 tokens
-    try:
     claims = jwt.decode(
         token,
         public_key,
         algorithms=["RS256"],
         audience=[CLIENT_ID, f"api://{CLIENT_ID}"],
-            issuer=[
+        issuer=f"https://sts.windows.net/{TENANT_ID}/",
-                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")
@@ -832,25 +807,6 @@ def create_package_compound(
     try:
         p = get_package_for_write(request.user, package_uuid)
         # inchi is not used atm
-
-        if c.pesLink is not None:
-            from bayer.views import fetch_pes
-            from bayer.models import PESCompound
-
-            try:
-                pes_data = fetch_pes(request, c.pesLink)
-            except ValueError as e:
-                return 400, {"message": f"Could not fetch PES data for {c.pesLink}"}
-
-            classification = pes_data.get("classificationLevel", "")
-            if "secret" == classification.lower():
-                data_pools = pes_data.get("dataPools")
-                if data_pools:
-                    if s.DATA_POOL_MAPPING[p.data_pool.name] not in data_pools:
-                        return 400, { "messsage": f"PES data pool {s.DATA_POOL_MAPPING[p.data_pool.name]} not found in PES data"}
-
-            c = PESCompound.create(p, pes_data, c.compoundName, c.compoundDescription)
-        else:
         c = Compound.create(
             p, c.compoundSmiles, c.compoundName, c.compoundDescription, inchi=c.inchi
         )
@@ -1874,7 +1830,6 @@ class CreateNode(Schema):
     nodeName: str | None = None
     nodeReason: str | None = None
     nodeDepth: str | None = None
-    pesLink: str | None = None
 
 
 @router.post(
@@ -1886,43 +1841,14 @@ def add_pathway_node(request, package_uuid, pathway_uuid, n: Form[CreateNode]):
         p = get_package_for_write(request.user, package_uuid)
         pw = Pathway.objects.get(package=p, uuid=pathway_uuid)
 
-        if n.pesLink:
-            from bayer.views import fetch_pes
-            from bayer.models import PESCompound
-
-            try:
-                pes_data = fetch_pes(request, c.pesLink)
-            except ValueError as e:
-                return 400, {"message": f"Could not fetch PES data for {c.pesLink}"}
-
-            classification = pes_data.get("classificationLevel", "")
-            if "secret" == classification.lower():
-                data_pools = pes_data.get("dataPools")
-                if data_pools:
-                    if s.DATA_POOL_MAPPING[p.data_pool.name] not in data_pools:
-                        return 400, { "messsage": f"PES data pool {s.DATA_POOL_MAPPING[p.data_pool.name]} not found in PES data"}
-
-            c = PESCompound.create(p, pes_data, c.compoundName, c.compoundDescription)
-
-            node = Node()
-            node.stereo_removed = False
-            node.pathway = pw
-            node.depth = 0
-
-            node.default_node_label = c.default_structure
-            node.save()
-
-            node.node_labels.add(c.default_structure)
-            node.save()
-        else:
         if n.nodeDepth is not None and n.nodeDepth.strip() != "":
             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!"}
 
@@ -2032,16 +1958,13 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
         educts = []
         products = []
 
-        subclasses = CompoundStructure.__subclasses__()
-
         if e.edgeAsSmirks:
             for ed in e.edgeAsSmirks.split(">>")[0].split("\\."):
                 stand_ed = FormatConverter.standardize(ed, remove_stereo=True)
                 educts.append(
                     Node.objects.get(
                         pathway=pw,
-                        default_node_label=CompoundStructure.objects.not_instance_of(*subclasses).
+                        default_node_label=CompoundStructure.objects.get(
-                        get(
                             compound__package=p, smiles=stand_ed
                         ).compound.default_structure,
                     )
@@ -2052,8 +1975,7 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
                 products.append(
                     Node.objects.get(
                         pathway=pw,
-                        default_node_label=CompoundStructure.objects.not_instance_of(*subclasses).
+                        default_node_label=CompoundStructure.objects.get(
-                        get(
                             compound__package=p, smiles=stand_pr
                         ).compound.default_structure,
                     )
@@ -2074,12 +1996,9 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
             description=e.edgeReason,
         )
 
-        # Update depths as sideeffect of above operation
-        pw.update_depths()
-
         return redirect(new_e.url)
     except ValueError:
-        return 403, {"message": "Adding Edge failed!"}
+        return 403, {"message": "Adding node failed!"}
 
 
 @router.delete("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}/edge/{uuid:edge_uuid}")

epdb/logic.py

@@ -7,7 +7,6 @@ import nh3
 from django.conf import settings as s
 from django.contrib.auth import get_user_model
 from django.db import transaction
-from django.db.models import QuerySet
 from pydantic import ValidationError
 
 from epdb.models import (
@@ -346,17 +345,52 @@ class PackageManager(object):
 
     @staticmethod
     def readable(user, package):
-        return (
+        if (
-            PackageManager.has_package_permission(user, package, "read") | package.reviewed is True
+            UserPackagePermission.objects.filter(package=package, user=user).exists()
+            or GroupPackagePermission.objects.filter(
+                package=package, group__in=GroupManager.get_groups(user)
             )
+            or package.reviewed is True
+            or user.is_superuser
+        ):
+            return True
+
+        return False
 
     @staticmethod
     def writable(user, package):
-        return PackageManager.has_package_permission(user, package, "write")
+        if (
+            UserPackagePermission.objects.filter(
+                package=package, user=user, permission=Permission.WRITE[0]
+            ).exists()
+            or GroupPackagePermission.objects.filter(
+                package=package,
+                group__in=GroupManager.get_groups(user),
+                permission=Permission.WRITE[0],
+            ).exists()
+            or UserPackagePermission.objects.filter(
+                package=package, user=user, permission=Permission.ALL[0]
+            ).exists()
+            or user.is_superuser
+        ):
+            return True
+        return False
 
     @staticmethod
     def administrable(user, package):
-        return PackageManager.has_package_permission(user, package, "all")
+        if (
+            UserPackagePermission.objects.filter(
+                package=package, user=user, permission=Permission.ALL[0]
+            ).exists()
+            or GroupPackagePermission.objects.filter(
+                package=package,
+                group__in=GroupManager.get_groups(user),
+                permission=Permission.ALL[0],
+            ).exists()
+            or user.is_superuser
+        ):
+            return True
+        return False
 
     @staticmethod
     def has_package_permission(user: "User", package: Union[str, UUID, "Package"], permission: str):
@@ -365,14 +399,6 @@ class PackageManager(object):
 
         groups = GroupManager.get_groups(user)
 
-        # EDIT START
-
-        if package.classification_level == Package.Classification.SECRET:
-            if package.data_pool not in groups:
-                return False
-
-        # EDIT END
-
         perms = {"all": ["all"], "write": ["all", "write"], "read": ["all", "write", "read"]}
 
         valid_perms = perms.get(permission)
@@ -415,7 +441,6 @@ class PackageManager(object):
         try:
             p = Package.objects.get(uuid=package_id)
             if PackageManager.readable(user, p):
-                p = PackageManager.check_package_classification(user, p)
                 return p
             else:
                 # FIXME: use custom exception to be translatable to 403 in API
@@ -425,37 +450,6 @@ class PackageManager(object):
         except Package.DoesNotExist:
             raise ValueError("Package with ID {} does not exist!".format(package_id))
 
-    # EDIT START
-
-    @staticmethod
-    def check_package_classification(user, pack: Package):
-        if pack.classification_level == Package.Classification.SECRET:
-            if pack.data_pool.user_member.filter(id=user.id).exists():
-                return pack
-
-            raise ValueError("Package is secret and not accessible to user!")
-
-        else:
-            return pack
-
-
-    @staticmethod
-    def check_package_classifications(user, package_qs: QuerySet[Package]):
-        non_secret = package_qs.exclude(classification_level=Package.Classification.SECRET)
-        secret = package_qs.filter(classification_level=Package.Classification.SECRET)
-
-        # TODO we should be able to do via the db
-        accessible_secret = []
-
-        for s_package in secret:
-            if s_package.data_pool.user_member.filter(id=user.id).exists():
-                accessible_secret.append(s_package.pk)
-
-        # Cannot combine a unique query with a non-unique query -> we have to call distinct
-        return Package.objects.filter(pk__in=accessible_secret).distinct() | non_secret.distinct()
-
-    # EDIT END
-
     @staticmethod
     def get_all_readable_packages(user, include_reviewed=False):
         # UserPermission only exists if at least read is granted...
@@ -480,13 +474,7 @@ class PackageManager(object):
             # remove package if user is owner and package is reviewed e.g. admin
             qs = qs.filter(reviewed=False)
 
-        qs = qs.distinct()
+        return qs.distinct()
-
-        # EDIT START
-        qs = PackageManager.check_package_classifications(user, qs)
-        # EDIT END
-
-        return qs
 
     @staticmethod
     def get_all_writeable_packages(user):
@@ -530,13 +518,11 @@ class PackageManager(object):
 
         qs = qs.filter(reviewed=False)
 
-        qs = qs.distinct()
+        return qs.distinct()
 
-        # EDIT START
+    @staticmethod
-        qs = PackageManager.check_package_classifications(user, qs)
+    def get_packages():
-        # EDIT END
+        return Package.objects.all()
-
-        return qs
 
     @staticmethod
     @transaction.atomic
@@ -1065,9 +1051,52 @@ 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/0023_alter_compoundstructure_options_and_more.py

@@ -1,54 +1,50 @@
-# Generated by Django 6.0.3 on 2026-04-21 11:43
+# Generated by Django 6.0.3 on 2026-04-14 19:07
 
 from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
+
     dependencies = [
-        ("epdb", "0022_alter_classifierpluginmodel_data_packages_and_more"),
+        ('epdb', '0022_alter_classifierpluginmodel_data_packages_and_more'),
     ]
 
     operations = [
         migrations.AlterModelOptions(
-            name="compoundstructure",
+            name='compoundstructure',
             options={},
         ),
         migrations.AlterModelOptions(
-            name="epmodel",
+            name='epmodel',
             options={},
         ),
         migrations.AlterModelOptions(
-            name="parallelrule",
+            name='parallelrule',
             options={},
         ),
         migrations.AlterModelOptions(
-            name="rule",
+            name='rule',
             options={},
         ),
         migrations.AlterModelOptions(
-            name="sequentialrule",
+            name='sequentialrule',
             options={},
         ),
         migrations.AlterModelOptions(
-            name="simpleambitrule",
+            name='simpleambitrule',
             options={},
         ),
         migrations.AlterModelOptions(
-            name="simplerdkitrule",
+            name='simplerdkitrule',
             options={},
         ),
         migrations.AlterModelOptions(
-            name="simplerule",
+            name='simplerule',
             options={},
         ),
         migrations.AddField(
-            model_name="compoundstructure",
+            model_name='group',
-            name="molfile",
+            name='secret',
-            field=models.TextField(blank=True, null=True, verbose_name="Molfile"),
+            field=models.BooleanField(default=False, verbose_name='Secret Group'),
-        ),
-        migrations.AddField(
-            model_name="group",
-            name="secret",
-            field=models.BooleanField(default=False, verbose_name="Secret Group"),
         ),
     ]

epdb/migrations/0024_user_contacted.py

@@ -1,17 +0,0 @@
-# Generated by Django 6.0.3 on 2026-04-21 19:56
-
-from django.db import migrations, models
-
-
-class Migration(migrations.Migration):
-    dependencies = [
-        ("epdb", "0023_alter_compoundstructure_options_and_more"),
-    ]
-
-    operations = [
-        migrations.AddField(
-            model_name="user",
-            name="contacted",
-            field=models.BooleanField(blank=True, null=True),
-        ),
-    ]

epdb/migrations/0025_auto_20260511_2025.py

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

epdb/models.py

@@ -75,7 +75,6 @@ class User(AbstractUser):
         blank=False,
     )
     is_reviewer = models.BooleanField(default=False)
-    contacted = models.BooleanField(null=True, blank=True)
 
     USERNAME_FIELD = "email"
     REQUIRED_FIELDS = ["username"]
@@ -868,25 +867,18 @@ class Compound(
 
         standardized_smiles = FormatConverter.standardize(smiles, remove_stereo=True)
 
-        subclasses = CompoundStructure.__subclasses__()
-
-        qs = CompoundStructure.objects.filter(smiles=smiles, compound__package=package)
-        if subclasses:
-            qs = qs.not_instance_of(*subclasses)
-
         # Check if we find a direct match for a given SMILES
-        if qs.exists():
+        if CompoundStructure.objects.filter(smiles=smiles, compound__package=package).exists():
-            return qs.first().compound
+            return CompoundStructure.objects.get(smiles=smiles, compound__package=package).compound
-
-
-        qs = CompoundStructure.objects.filter(smiles=standardized_smiles, compound__package=package)
-        if subclasses:
-            qs = qs.not_instance_of(*subclasses)
 
         # Check if we can find the standardized one
-        if qs.exists():
+        if CompoundStructure.objects.filter(
+            smiles=standardized_smiles, compound__package=package
+        ).exists():
             # TODO should we add a structure?
-            return qs.first().compound
+            return CompoundStructure.objects.get(
+                smiles=standardized_smiles, compound__package=package
+            ).compound
 
         # Generate Compound
         c = Compound()
@@ -2186,56 +2178,6 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix
     ):
         return Edge.create(self, start_nodes, end_nodes, rule, name=name, description=description)
 
-    def update_depths(self):
-        # Collect number of in and out links per node
-        in_count = defaultdict(lambda: 0)
-        out_count = defaultdict(lambda: 0)
-
-        for e in self.edges:
-            for react in e.start_nodes.all():
-                out_count[str(react.uuid)] += 1
-
-            for prod in e.end_nodes.all():
-                in_count[str(prod.uuid)] += 1
-
-        depth_map = {}
-        depth_map[0] = list()
-
-        for n in self.nodes:
-            num_parents = in_count[str(n.uuid)]
-            if num_parents == 0:
-                # must be a root node or unconnected node
-                if n.depth != 0:
-                    n.depth = 0
-                    n.save()
-
-                # Only root node may have children
-                if out_count[str(n.uuid)] > 0:
-                    depth_map[0].append(n)
-
-        # At most depth len(nodes) is possible
-        for i in range(self.nodes.count()):
-            level_nodes = depth_map.get(i, [])
-
-            if len(level_nodes) == 0:
-                break
-
-            unique_next_level = set()
-            for n in level_nodes:
-                for e in self.edges:
-                    if n in e.start_nodes.all():
-                        for p in e.end_nodes.all():
-                            unique_next_level.add(p)
-
-            if len(unique_next_level) > 0:
-                depth_map[i + 1] = list(unique_next_level)
-
-        for depth, nodes in depth_map.items():
-            for n in nodes:
-                if n.depth != depth:
-                    n.depth = depth
-                    n.save()
-
 
 class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin):
     pathway = models.ForeignKey(
@@ -2277,9 +2219,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             if isinstance(ai.get(), PropertyPrediction):
                 predicted_properties[ai.get().__class__.__name__].append(ai.data)
 
-        # If we have Subclasses of a CompoundStructure we can overwrite keys (e.g. images)
+        extra_structure_data = self.default_node_label.d3_json()
-        # by overwriting keys
-        structure_data = self.default_node_label.d3_json()
 
         res = {
             "depth": self.depth,
@@ -2290,7 +2230,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             "image_svg": IndigoUtils.mol_to_svg(
                 self.default_node_label.smiles, width=40, height=40
             ),
-            "image_type": "svg",
+
             "name": self.get_name(),
             "smiles": self.default_node_label.smiles,
             "scenarios": [{"name": s.get_name(), "url": s.url} for s in self.scenarios.all()],
@@ -2303,9 +2243,9 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
             "predicted_properties": predicted_properties,
             "is_engineered_intermediate": self.kv.get("is_engineered_intermediate", False),
             "timeseries": self.get_timeseries_data(),
-            **structure_data,
         }
 
+        res.update(**extra_structure_data)
         return res
 
     @staticmethod

epdb/views.py

@@ -937,14 +937,12 @@ def package_models(request, package_uuid):
                 "requires_rule_packages": True,
                 "requires_data_packages": True,
             },
-        }
+            "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/images/bayer-logo.svg

@@ -1,30 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<svg version="1.1" id="Layer_2" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
-	 viewBox="0 0 76 76" style="enable-background:new 0 0 76 76;" xml:space="preserve">
-<style type="text/css">
-	.st0{fill:#10384F;}
-	.st1{fill:#89D329;}
-	.st2{fill:#00BCFF;}
-</style>
-<g id="Bayer_Cross_1_">
-	<path class="st0" d="M35.9,11.3h4.4c0.5,0,0.9-0.4,0.9-0.9c0-0.5-0.4-0.9-0.9-0.9h-4.4V11.3z M35.9,15.5h4.5c0.6,0,1-0.4,1-1
-		c0-0.6-0.4-1-1-1h-4.5V15.5z M43,12.3c0.6,0.6,1,1.4,1,2.3c0,1.8-1.4,3.2-3.2,3.2h-7.3V7.3l7.2,0c1.7,0,3.1,1.4,3.1,3.1
-		C43.7,11.1,43.4,11.8,43,12.3z M44.7,30.3H42l-0.8-1.8h-5.9l-0.8,1.8h-2.7L37,19.8h2.4L44.7,30.3z M38.2,22.5l-1.8,3.8H40
-		L38.2,22.5z M41.8,32.6h3l-5.3,6.8v3.7h-2.5v-3.7l-5.3-6.8h3l3.6,4.8L41.8,32.6z M55.7,32.6v2.3h-7v1.8l6.8,0v2.3h-6.8v2h7v2.3
-		h-9.5V32.6H55.7z M63.4,39.1h-1.9v4h-2.5V32.6h6.4c1.8,0,3.2,1.5,3.2,3.3c0,1.5-1,2.7-2.3,3.1l3.1,4.1h-3L63.4,39.1z M65.2,34.8
-		h-3.6v2h3.6c0.6,0,1-0.5,1-1C66.2,35.3,65.7,34.8,65.2,34.8z M32.8,43.1h-2.7l-0.8-1.8h-5.9l-0.8,1.8h-2.7l5.3-10.5h2.4L32.8,43.1z
-		 M26.3,35.3l-1.8,3.8h3.7L26.3,35.3z M10.4,36.6h4.4c0.5,0,0.9-0.4,0.9-0.9c0-0.5-0.4-0.9-0.9-0.9l-4.4,0V36.6z M10.4,40.8h4.5
-		c0.6,0,1-0.4,1-1c0-0.6-0.4-1-1-1h-4.5V40.8z M17.5,37.6c0.6,0.6,1,1.4,1,2.3c0,1.8-1.4,3.2-3.2,3.2H7.9V32.6h7.2
-		c1.7,0,3.1,1.4,3.1,3.1C18.2,36.4,17.9,37.1,17.5,37.6z M43,45.3v2.3h-7v1.8l6.8,0v2.3h-6.8v2h7v2.3h-9.5V45.3H43z M41.2,61.6
-		c0-0.6-0.4-1-1-1h-4.3v2h4.3C40.8,62.6,41.2,62.2,41.2,61.6z M33.4,68.9V58.4h7c1.8,0,3.2,1.5,3.2,3.3c0,1.4-0.8,2.5-2,3l3.2,4.2
-		h-3l-3-4h-2.9v4H33.4z"/>
-	<path class="st1" d="M76.1,35.6C74.9,15.8,58.4,0,38.2,0C18,0,1.5,15.8,0.3,35.6c0,0.8,0.1,1.6,0.2,2.4c0.8,6.6,3.3,12.7,7.1,17.8
-		c6.9,9.4,18,15.5,30.6,15.5c-17.6,0-32-13.7-33.2-30.9c-0.1-0.8-0.1-1.6-0.1-2.4c0-0.8,0-1.6,0.1-2.4C6.2,18.4,20.6,4.7,38.2,4.7
-		c12.6,0,23.7,6.1,30.6,15.5c3.8,5.1,6.3,11.2,7.1,17.8c0.1,0.8,0.2,1.6,0.2,2.3c0-0.8,0.1-1.6,0.1-2.4
-		C76.2,37.2,76.2,36.4,76.1,35.6"/>
-	<path class="st2" d="M0.3,40.4C1.5,60.2,18,76,38.2,76c20.2,0,36.7-15.8,37.9-35.6c0-0.8-0.1-1.6-0.2-2.4
-		c-0.8-6.6-3.3-12.7-7.1-17.8c-6.9-9.4-18-15.5-30.6-15.5c17.6,0,32,13.7,33.2,30.9c0.1,0.8,0.1,1.6,0.1,2.4c0,0.8,0,1.6-0.1,2.4
-		c-1.2,17.3-15.6,30.9-33.2,30.9c-12.6,0-23.7-6.1-30.6-15.5C3.8,50.7,1.3,44.6,0.5,38c-0.1-0.8-0.2-1.6-0.2-2.3
-		c0,0.8-0.1,1.6-0.1,2.4C0.2,38.8,0.2,39.6,0.3,40.4"/>
-</g>
-</svg>

static/js/pw.js

@@ -605,36 +605,7 @@ function draw(pathway, elem) {
         // Check if target is pseudo and draw marker only if not pseudo
         .attr("class", d => d.target.pseudo ? "link_no_arrow" : "link")
         .attr("marker-end", d => d.target.pseudo ? '' : d.multi_step ? 'url(#doublearrow)' : 'url(#arrow)')
-      .on("click", function(event, d) {
-          const wasHighlighted = d3.select(this).classed("highlighted");
 
-          d3.selectAll("line").classed("highlighted", false);
-
-          if (!wasHighlighted) {
-              const toHighlight = [];
-              toHighlight.push(d.el);
-
-              if (d.source.pseudo || d.target.pseudo) {
-                  if (d.target.pseudo) {
-                      d3.selectAll("line").each(e => {
-                          if (e !== undefined && e.source.id === d.target.id) {
-                              toHighlight.push(e.el);
-                          }
-                      });
-                  } else {
-                      d3.selectAll("line").each(e => {
-                          if (e !== undefined && (e.target.id === d.source.id || e.source.id === d.source.id)) {
-                              toHighlight.push(e.el);
-                          }
-                      });
-                  }
-              }
-
-              for (const e of toHighlight) {
-                  d3.select(e).classed("highlighted", true);
-              }
-          }
-      })
 
     // add element to links array
     link.each(function (d) {
@@ -653,13 +624,7 @@ function draw(pathway, elem) {
             .on("drag", dragged)
             .on("end", dragended))
         .on("click", function (event, d) {
-            const wasHighlighted = d3.select(this).select("circle").classed("highlighted");
-
-            d3.selectAll('circle.highlighted').classed('highlighted', false);
-
-            if (!wasHighlighted) {
             d3.select(this).select("circle").classed("highlighted", !d3.select(this).select("circle").classed("highlighted"));
-            }
         })
 
     // Kreise für die Knoten hinzufügen
@@ -672,7 +637,14 @@ function draw(pathway, elem) {
     node.filter(d => !d.pseudo).each(function (d, i) {
         const g = d3.select(this);
 
-        if (d.image_type === "svg") {
+        if (d.is_pes) {
+            g.append("svg:image")
+              .attr("xlink:href", d.image)
+              .attr("width", 40)
+              .attr("height", 40)
+              .attr("x", -20)
+              .attr("y", -20);
+        } else {
             // Parse the SVG string
             const parser = new DOMParser();
             const svgDoc = parser.parseFromString(d.image_svg, "image/svg+xml");
@@ -711,15 +683,6 @@ function draw(pathway, elem) {
               .attr("height", svgHeight * scale)
               .attr("x", -svgWidth * scale / 2)
               .attr("y", -svgHeight * scale / 2);
-        } else {
-            // We have a image type different than svg
-            // include it via img url
-            g.append("svg:image")
-                .attr("xlink:href", d.image)
-                .attr("width", 40)
-                .attr("height", 40)
-                .attr("x", -20)
-                .attr("y", -20);
         }
 
     });

templates/actions/objects/pathway.html

@@ -1,5 +1,3 @@
-{% load envipytags %}
-
 {% if meta.can_edit %}
   <li>
     <a
@@ -17,12 +15,7 @@
       <i class="glyphicon glyphicon-plus"></i> Add Reaction</a
     >
   </li>
-  {% epdb_slot_templates "epdb.actions.objects.pathway.add" as action_button_templates %}
+  <li role="separator" class="divider"></li>
-
-  {% for tpl in action_button_templates %}
-    {% include tpl %}
-  {% endfor %}
-  <li role="separator" class="divider h-px"></li>
 {% endif %}
 <li>
   <a
@@ -74,7 +67,7 @@
       Rules</a
     >
   </li>
-  <li role="separator" class="divider h-px"></li>
+  <li role="separator" class="divider"></li>
   <li>
     <a
       class="button"
@@ -99,16 +92,11 @@
       <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 +104,7 @@
   <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

@@ -3,8 +3,7 @@
 {% 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
       type="button"
       class="btn btn-primary btn-sm"
@@ -13,7 +12,6 @@
       New Model
     </button>
   {% endif %}
-  {% endif %}
 {% endblock action_button %}
 
 {% block action_modals %}

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/components/navbar.html

@@ -35,7 +35,6 @@
             <use href="{% static "/images/logo-name.svg" %}#ep-logo-name" />
           </svg>
         </a>
-        <img src="{% static 'images/bayer-logo.svg' %}" width="40">
       </div>
 
       {% if not public_mode %}
@@ -101,11 +100,6 @@
       {% endif %}
 
       <div class="navbar-end">
-        {% if meta.url_contains_package and meta.current_package.get_classification_level_display == "Restricted" %}
-          <img src="{% static 'images/restricted_mid.png' %}" width="200">
-        {% elif meta.url_contains_package and meta.current_package.get_classification_level_display == "Secret" %}
-          <img src="{% static 'images/secret_mid.png' %}" width="120">
-        {% endif %}
         {% if not public_mode %}
           <a id="search-trigger" role="button" class="cursor-pointer">
             <div

templates/modals/collections/new_prediction_setting_modal.html

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

templates/modals/objects/delete_pathway_edge_modal.html

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

templates/modals/objects/delete_pathway_node_modal.html

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

templates/objects/compound.html

@@ -83,8 +83,8 @@
       <div class="collapse-content">{{ compound.description }}</div>
     </div>
 
-    <!-- Extension Slot for Viz -->
     {% epdb_slot_templates "epdb.objects.compound.viz" as viz_templates %}
+
     {% for tpl in viz_templates %}
       {% include tpl %}
     {% endfor %}

templates/objects/compound_structure.html

@@ -51,8 +51,8 @@
       </div>
     </div>
 
-    <!-- Extension Slot for Viz -->
     {% epdb_slot_templates "epdb.objects.compound_structure.viz" as viz_templates %}
+
     {% for tpl in viz_templates %}
       {% include tpl %}
     {% endfor %}

templates/objects/pathway.html

@@ -1,7 +1,5 @@
 {% extends "framework_modern.html" %}
 {% load static %}
-{% load envipytags %}
-
 {% block content %}
   <script src="https://d3js.org/d3.v7.min.js"></script>
   <style>
@@ -78,10 +76,6 @@
   {% block action_modals %}
     {% include "modals/objects/add_pathway_node_modal.html" %}
     {% include "modals/objects/add_pathway_edge_modal.html" %}
-    {% epdb_slot_templates "epdb.modals.objects.pathway.add" as add_templates %}
-    {% for tpl in add_templates %}
-      {% include tpl %}
-    {% endfor %}
     {% include "modals/objects/download_pathway_csv_modal.html" %}
     {% include "modals/objects/download_pathway_image_modal.html" %}
     {% include "modals/objects/identify_missing_rules_modal.html" %}
@@ -106,12 +100,12 @@
     </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 +134,7 @@
                 </div>
                 <ul
                   tabindex="0"
-                  class="dropdown-content menu bg-base-100 rounded-box z-50 w-96 p-2"
+                  class="dropdown-content menu bg-base-100 rounded-box z-50 w-52 p-2"
                 >
                   {% include "actions/objects/pathway.html" %}
                 </ul>

utilities/chem.py

@@ -88,10 +88,6 @@ class FormatConverter(object):
     def from_smiles(smiles):
         return Chem.MolFromSmiles(smiles)
 
-    @staticmethod
-    def from_molfile(molfile: str):
-        return Chem.MolFromMolBlock(molfile)
-
     @staticmethod
     def to_smiles(mol, canonical=False):
         return Chem.MolToSmiles(mol, canonical=canonical)
@@ -182,9 +178,11 @@ class FormatConverter(object):
 
         drawer = rdMolDraw2D.MolDraw2DCairo(*mol_size)
         opts = drawer.drawOptions()
+
         opts.clearBackground = False
         drawer.DrawMolecule(mol)
         drawer.FinishDrawing()
+
         return drawer.GetDrawingText()
 
     @staticmethod

utilities/legacy.py

@@ -64,7 +64,7 @@
 
 import logging
 
-from envipy_additional_information import HalfLife, HalfLifeWS, HalfLifeModel
+from envipy_additional_information import HalfLife, HalfLifeWS
 from envipy_additional_information.information import Interval
 from envipy_additional_information.parsers import (
     AcidityParser,
@@ -473,12 +473,17 @@ def build_additional_information_from_request(request, type_):
 
             comment = get_parameter_or_empty_string(request, "comment")
             source = get_parameter_or_empty_string(request, "source")
-            # first_order = get_parameter_or_empty_string(request, "firstOrder")
+            first_order = get_parameter_or_empty_string(request, "firstOrder")
             model = get_parameter_or_empty_string(request, "model")
             fit = get_parameter_or_empty_string(request, "fit")
 
-            if model:
+            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

@@ -17,7 +17,7 @@ wheels = [
 
 [[package]]
 name = "aiohttp"
-version = "3.13.5"
+version = "3.13.3"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "aiohappyeyeballs" },
@@ -28,76 +28,76 @@ dependencies = [
     { name = "propcache" },
     { name = "yarl" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/77/9a/152096d4808df8e4268befa55fba462f440f14beab85e8ad9bf990516918/aiohttp-3.13.5.tar.gz", hash = "sha256:9d98cc980ecc96be6eb4c1994ce35d28d8b1f5e5208a23b421187d1209dbb7d1", size = 7858271, upload-time = "2026-03-31T22:01:03.343Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/50/42/32cf8e7704ceb4481406eb87161349abb46a57fee3f008ba9cb610968646/aiohttp-3.13.3.tar.gz", hash = "sha256:a949eee43d3782f2daae4f4a2819b2cb9b0c5d3b7f7a927067cc84dafdbb9f88", size = 7844556, upload-time = "2026-01-03T17:33:05.204Z" }
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 [[package]]