wip

Dockerfile

@@ -37,12 +37,13 @@ RUN --mount=type=ssh \
 # Now copy source and do a final sync to install the project itself
 # Ensure .dockerignore is reasonable
 COPY bayer bayer
-COPY bridge bridge
 COPY biotransformer biotransformer
+COPY bridge bridge
 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/migrations/0003_package_data_pool.py

@@ -1,20 +0,0 @@
-# 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/0003_pescompound_pesstructure_package_data_pool.py

@@ -1,4 +1,4 @@
-# Generated by Django 6.0.3 on 2026-04-15 20:03
+# Generated by Django 6.0.3 on 2026-04-17 21:22
 
 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', '0003_package_data_pool'),
+        ('bayer', '0002_initial'),
         ('epdb', '0023_alter_compoundstructure_options_and_more'),
     ]
 
@@ -26,10 +26,16 @@ 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

@@ -1,19 +0,0 @@
-# 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

@@ -15,6 +15,7 @@ from epdb.models import (
     SimpleAmbitRule,
     SimpleRDKitRule,
 )
+from utilities.chem import FormatConverter
 
 
 class Package(EnviPathModel):
@@ -114,7 +115,9 @@ 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():
-            return PESStructure.objects.get(pes_link=pes_url, compound__package=package).compound
+            # Due to normalization we might end up in having multiple structures
+            # 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()
@@ -135,19 +138,37 @@ 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:
-            _ = CompoundStructure.create(
+            _ = PESStructure.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(
+
-            c, smiles, name=name, description=description, normalized_structure=is_standardized
+        cs = PESStructure.create(
+            c,
+            pes_url,
+            molfile,
+            smiles,
+            name=name,
+            description=description,
+            normalized_structure=is_standardized
         )
 
         c.default_structure = cs
@@ -159,6 +180,53 @@ 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/modals/collections/new_pes_modal.html

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

bayer/templates/modals/objects/add_pathway_pes_node_modal.html

@@ -0,0 +1,174 @@
+{% 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

@@ -1,4 +1,11 @@
 {% 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

@@ -1,4 +1,11 @@
 {% 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

@@ -1,4 +1,11 @@
 {% 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 }} - ({{ package.get_classification_level_display }})</h2>
+          <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>
           <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 %}
@@ -31,13 +31,18 @@
 {% endblock %}
 
 {% block content %}
-  <div class="card bg-base-200 mb-6 ">
+  <div>
-    <div class="card-body">
+  <img src="{% static 'images/bayer-logo.svg' %}">
-      <h3 class="card-title">Welcome to the new enviPath!</h3>
+
-    </div>
   </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">
+  <div class="border-base-300 mb-6 border-b" hidden>
     <div class="flex justify-start">
       <input
         type="radio"

bayer/urls.py

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

bayer/views.py

@@ -8,9 +8,12 @@ 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):
@@ -18,6 +21,10 @@ 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')
@@ -28,6 +35,14 @@ 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)
@@ -37,6 +52,55 @@ 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 = {

epdb/legacy_api.py

@@ -1958,13 +1958,16 @@ 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.get(
+                        default_node_label=CompoundStructure.objects.not_instance_of(*subclasses).
+                        get(
                             compound__package=p, smiles=stand_ed
                         ).compound.default_structure,
                     )
@@ -1975,7 +1978,8 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
                 products.append(
                     Node.objects.get(
                         pathway=pw,
-                        default_node_label=CompoundStructure.objects.get(
+                        default_node_label=CompoundStructure.objects.not_instance_of(*subclasses).
+                        get(
                             compound__package=p, smiles=stand_pr
                         ).compound.default_structure,
                     )
@@ -1998,7 +2002,7 @@ def add_pathway_edge(request, package_uuid, pathway_uuid, e: Form[CreateEdge]):
 
         return redirect(new_e.url)
     except ValueError:
-        return 403, {"message": "Adding node failed!"}
+        return 403, {"message": "Adding Edge failed!"}
 
 
 @router.delete("/package/{uuid:package_uuid}/pathway/{uuid:pathway_uuid}/edge/{uuid:edge_uuid}")

epdb/logic.py

@@ -7,6 +7,7 @@ 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 (
@@ -94,8 +95,8 @@ class EPDBURLParser:
 
     def contains_package_url(self):
         return (
-            bool(self.MODEL_PATTERNS["epdb.Package"].findall(self.url))
+                bool(self.MODEL_PATTERNS["epdb.Package"].findall(self.url))
-            and not self.is_package_url()
+                and not self.is_package_url()
         )
 
     def is_user_url(self) -> bool:
@@ -187,7 +188,7 @@ class UserManager(object):
     @staticmethod
     @transaction.atomic
     def create_user(
-        username, email, password, set_setting=True, add_to_group=True, *args, **kwargs
+            username, email, password, set_setting=True, add_to_group=True, *args, **kwargs
     ):
         # Clean for potential XSS
         clean_username = nh3.clean(username).strip()
@@ -345,52 +346,15 @@ class PackageManager(object):
 
     @staticmethod
     def readable(user, package):
-        if (
+        return PackageManager.has_package_permission(user, package, "read")
-            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):
-        if (
+        return PackageManager.has_package_permission(user, package, "write")
-            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):
-        if (
+        return PackageManager.has_package_permission(user, package, "all")
-            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):
@@ -399,18 +363,26 @@ 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)
 
         if (
-            UserPackagePermission.objects.filter(
+                UserPackagePermission.objects.filter(
-                package=package, user=user, permission__in=valid_perms
+                    package=package, user=user, permission__in=valid_perms
-            ).exists()
+                ).exists()
-            or GroupPackagePermission.objects.filter(
+                or GroupPackagePermission.objects.filter(
-                package=package, group__in=groups, permission__in=valid_perms
+            package=package, group__in=groups, permission__in=valid_perms
-            ).exists()
+        ).exists()
-            or user.is_superuser
+                or user.is_superuser
         ):
             return True
 
@@ -441,6 +413,7 @@ 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
@@ -450,6 +423,37 @@ 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...
@@ -474,7 +478,13 @@ class PackageManager(object):
             # remove package if user is owner and package is reviewed e.g. admin
             qs = qs.filter(reviewed=False)
 
-        return qs.distinct()
+        qs = qs.distinct()
+
+        # EDIT START
+        qs = PackageManager.check_package_classifications(user, qs)
+        # EDIT END
+
+        return qs
 
     @staticmethod
     def get_all_writeable_packages(user):
@@ -518,11 +528,13 @@ class PackageManager(object):
 
         qs = qs.filter(reviewed=False)
 
-        return qs.distinct()
+        qs = qs.distinct()
 
-    @staticmethod
+        # EDIT START
-    def get_packages():
+        qs = PackageManager.check_package_classifications(user, qs)
-        return Package.objects.all()
+        # EDIT END
+
+        return qs
 
     @staticmethod
     @transaction.atomic
@@ -548,7 +560,7 @@ class PackageManager(object):
     @staticmethod
     @transaction.atomic
     def update_permissions(
-        caller: User, package: Package, grantee: Union[User, Group], new_perm: Optional[str]
+            caller: User, package: Package, grantee: Union[User, Group], new_perm: Optional[str]
     ):
         caller_perm = None
         if not caller.is_superuser:
@@ -591,7 +603,7 @@ class PackageManager(object):
     @staticmethod
     @transaction.atomic
     def import_legacy_package(
-        data: dict, owner: User, keep_ids=False, add_import_timestamp=True, trust_reviewed=False
+            data: dict, owner: User, keep_ids=False, add_import_timestamp=True, trust_reviewed=False
     ):
         from collections import defaultdict
         from datetime import datetime
@@ -671,7 +683,7 @@ class PackageManager(object):
             # Check if parent exists and park this Scenario to convert it later into an
             # AdditionalInformation object
             for ex in scenario.get("additionalInformationCollection", {}).get(
-                "additionalInformation", []
+                    "additionalInformation", []
             ):
                 if ex["name"] == "referringscenario":
                     postponed_scens[ex["data"]].append(scenario)
@@ -694,7 +706,7 @@ class PackageManager(object):
             mapping[scenario["id"]] = scen.uuid
 
             for ex in scenario.get("additionalInformationCollection", {}).get(
-                "additionalInformation", []
+                    "additionalInformation", []
             ):
                 name = ex["name"]
                 addinf_data = ex["data"]
@@ -963,7 +975,7 @@ class PackageManager(object):
         for parent, children in postponed_scens.items():
             for child in children:
                 for ex in child.get("additionalInformationCollection", {}).get(
-                    "additionalInformation", []
+                        "additionalInformation", []
                 ):
                     child_id = child["id"]
                     name = ex["name"]
@@ -1104,11 +1116,11 @@ class PackageManager(object):
     @staticmethod
     @transaction.atomic
     def import_package(
-        data: Dict[str, Any],
+            data: Dict[str, Any],
-        owner: User,
+            owner: User,
-        preserve_uuids=False,
+            preserve_uuids=False,
-        add_import_timestamp=True,
+            add_import_timestamp=True,
-        trust_reviewed=False,
+            trust_reviewed=False,
     ) -> Package:
         importer = PackageImporter(data, preserve_uuids, add_import_timestamp, trust_reviewed)
         imported_package = importer.do_import()
@@ -1123,7 +1135,7 @@ class PackageManager(object):
 
     @staticmethod
     def export_package(
-        package: Package, include_models: bool = False, include_external_identifiers: bool = True
+            package: Package, include_models: bool = False, include_external_identifiers: bool = True
     ) -> Dict[str, Any]:
         return PackageExporter(package).do_export()
 
@@ -1150,10 +1162,10 @@ class SettingManager(object):
         s = Setting.objects.get(uuid=setting_id)
 
         if (
-            s.global_default
+                s.global_default
-            or s.public
+                or s.public
-            or user.is_superuser
+                or user.is_superuser
-            or UserSettingPermission.objects.filter(user=user, setting=s).exists()
+                or UserSettingPermission.objects.filter(user=user, setting=s).exists()
         ):
             return s
 
@@ -1163,24 +1175,24 @@ class SettingManager(object):
     def get_all_settings(user):
         sp = UserSettingPermission.objects.filter(user=user).values("setting")
         return (
-            Setting.objects.filter(id__in=sp)
+                Setting.objects.filter(id__in=sp)
-            | Setting.objects.filter(public=True)
+                | Setting.objects.filter(public=True)
-            | Setting.objects.filter(global_default=True)
+                | Setting.objects.filter(global_default=True)
         ).distinct()
 
     @staticmethod
     @transaction.atomic
     def create_setting(
-        user: User,
+            user: User,
-        name: str = None,
+            name: str = None,
-        description: str = None,
+            description: str = None,
-        max_nodes: int = None,
+            max_nodes: int = None,
-        max_depth: int = None,
+            max_depth: int = None,
-        rule_packages: List[Package] | None = None,
+            rule_packages: List[Package] | None = None,
-        model: EPModel = None,
+            model: EPModel = None,
-        model_threshold: float = None,
+            model_threshold: float = None,
-        expansion_scheme: ExpansionSchemeChoice = ExpansionSchemeChoice.BFS,
+            expansion_scheme: ExpansionSchemeChoice = ExpansionSchemeChoice.BFS,
-        property_models: List["PropertyPluginModel"] | None = None,
+            property_models: List["PropertyPluginModel"] | None = None,
     ):
         new_s = Setting()
 
@@ -1259,8 +1271,8 @@ class SearchManager(object):
         pathway_qs = Pathway.objects.filter(
             Q(package__in=packages)
             & (
-                Q(edge__edge_label__educts__inchikey=searchterm)
+                    Q(edge__edge_label__educts__inchikey=searchterm)
-                | Q(edge__edge_label__products__inchikey=searchterm)
+                    | Q(edge__edge_label__products__inchikey=searchterm)
             )
         ).distinct()
 
@@ -1298,8 +1310,8 @@ class SearchManager(object):
         pathway_qs = Pathway.objects.filter(
             Q(package__in=packages)
             & (
-                Q(edge__edge_label__educts__smiles=searchterm)
+                    Q(edge__edge_label__educts__smiles=searchterm)
-                | Q(edge__edge_label__products__smiles=searchterm)
+                    | Q(edge__edge_label__products__smiles=searchterm)
             )
         ).distinct()
 
@@ -1335,15 +1347,15 @@ class SearchManager(object):
         reactions_qs = Reaction.objects.filter(
             Q(package__in=packages)
             & (
-                Q(educts__inchikey__startswith=inchi_front)
+                    Q(educts__inchikey__startswith=inchi_front)
-                | Q(products__inchikey__startswith=inchi_front)
+                    | Q(products__inchikey__startswith=inchi_front)
             )
         ).distinct()
         pathway_qs = Pathway.objects.filter(
             Q(package__in=packages)
             & (
-                Q(edge__edge_label__educts__inchikey__startswith=inchi_front)
+                    Q(edge__edge_label__educts__inchikey__startswith=inchi_front)
-                | Q(edge__edge_label__products__inchikey__startswith=inchi_front)
+                    | Q(edge__edge_label__products__inchikey__startswith=inchi_front)
             )
         ).distinct()
 
@@ -1381,8 +1393,8 @@ class SearchManager(object):
         pathway_qs = Pathway.objects.filter(
             Q(package__in=packages)
             & (
-                Q(edge__edge_label__educts__canonical_smiles=searchterm)
+                    Q(edge__edge_label__educts__canonical_smiles=searchterm)
-                | Q(edge__edge_label__products__canonical_smiles=searchterm)
+                    | Q(edge__edge_label__products__canonical_smiles=searchterm)
             )
         ).distinct()
 
@@ -1457,11 +1469,11 @@ class SNode(object):
 
 class SEdge(object):
     def __init__(
-        self,
+            self,
-        educts: Union[SNode, List[SNode]],
+            educts: Union[SNode, List[SNode]],
-        products: Union[SNode | List[SNode]],
+            products: Union[SNode | List[SNode]],
-        rule: Optional["Rule"] = None,
+            rule: Optional["Rule"] = None,
-        probability: Optional[float] = None,
+            probability: Optional[float] = None,
     ):
         if not isinstance(educts, list):
             educts = [educts]
@@ -1493,11 +1505,11 @@ class SEdge(object):
             return False
 
         if (
-            self.rule is not None
+                self.rule is not None
-            and other.rule is None
+                and other.rule is None
-            or self.rule is None
+                or self.rule is None
-            and other.rule is not None
+                and other.rule is not None
-            or self.rule != other.rule
+                or self.rule != other.rule
         ):
             return False
 
@@ -1505,8 +1517,8 @@ class SEdge(object):
             return False
 
         for n1, n2 in zip(
-            sorted(self.educts, key=lambda x: x.smiles),
+                sorted(self.educts, key=lambda x: x.smiles),
-            sorted(other.educts, key=lambda x: x.smiles),
+                sorted(other.educts, key=lambda x: x.smiles),
         ):
             if n1.smiles != n2.smiles:
                 return False
@@ -1515,8 +1527,8 @@ class SEdge(object):
             return False
 
         for n1, n2 in zip(
-            sorted(self.products, key=lambda x: x.smiles),
+                sorted(self.products, key=lambda x: x.smiles),
-            sorted(other.products, key=lambda x: x.smiles),
+                sorted(other.products, key=lambda x: x.smiles),
         ):
             if n1.smiles != n2.smiles:
                 return False
@@ -1529,10 +1541,10 @@ class SEdge(object):
 
 class SPathway(object):
     def __init__(
-        self,
+            self,
-        root_nodes: Optional[Union[str, SNode, List[str | SNode]]] = None,
+            root_nodes: Optional[Union[str, SNode, List[str | SNode]]] = None,
-        persist: Optional["Pathway"] = None,
+            persist: Optional["Pathway"] = None,
-        prediction_setting: Optional[Setting] = None,
+            prediction_setting: Optional[Setting] = None,
     ):
         self.root_nodes = []
 
@@ -1677,9 +1689,9 @@ class SPathway(object):
             # We don't have any substrate, but technically we have at least one rule that triggered.
             # If our substrate is a root node a.k.a. depth == 0 store that info in SPathway
             if (
-                len(expansion_result["transformations"]) == 0
+                    len(expansion_result["transformations"]) == 0
-                and expansion_result["rule_triggered"]
+                    and expansion_result["rule_triggered"]
-                and sub.depth == 0
+                    and sub.depth == 0
             ):
                 self.empty_due_to_threshold = True
 
@@ -1786,8 +1798,8 @@ class SPathway(object):
                         for prod in edge.products:
                             # Either is a new product or a product and we found a path with a higher prob
                             if (
-                                prod not in node_probs
+                                    prod not in node_probs
-                                or current_prob * edge.probability > node_probs[prod]
+                                    or current_prob * edge.probability > node_probs[prod]
                             ):
                                 node_probs[prod] = current_prob * edge.probability
 

epdb/migrations/0023_alter_compoundstructure_options_and_more.py

@@ -1,4 +1,4 @@
-# Generated by Django 6.0.3 on 2026-04-14 19:07
+# Generated by Django 6.0.3 on 2026-04-17 21:22
 
 from django.db import migrations, models
 
@@ -42,6 +42,11 @@ class Migration(migrations.Migration):
             name='simplerule',
             options={},
         ),
+        migrations.AddField(
+            model_name='compoundstructure',
+            name='molfile',
+            field=models.TextField(blank=True, null=True, verbose_name='Molfile'),
+        ),
         migrations.AddField(
             model_name='group',
             name='secret',

epdb/models.py

@@ -867,18 +867,25 @@ 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 CompoundStructure.objects.filter(smiles=smiles, compound__package=package).exists():
+        if qs.exists():
-            return CompoundStructure.objects.get(smiles=smiles, compound__package=package).compound
+            return qs.first().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 CompoundStructure.objects.filter(
+        if qs.exists():
-            smiles=standardized_smiles, compound__package=package
-        ).exists():
             # TODO should we add a structure?
-            return CompoundStructure.objects.get(
+            return qs.first().compound
-                smiles=standardized_smiles, compound__package=package
-            ).compound
 
         # Generate Compound
         c = Compound()

static/images/bayer-logo.svg

@@ -0,0 +1,30 @@
+<?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>

templates/actions/objects/pathway.html

@@ -7,6 +7,14 @@
       <i class="glyphicon glyphicon-plus"></i> Add Compound</a
     >
   </li>
+  <li>
+    <a
+      class="button"
+      onclick="document.getElementById('add_pathway_pes_node_modal').showModal(); return false;"
+    >
+      <i class="glyphicon glyphicon-plus"></i> Add PES</a
+    >
+  </li>
   <li>
     <a
       class="button"

templates/components/navbar.html

@@ -35,6 +35,7 @@
             <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 %}
@@ -100,6 +101,11 @@
       {% 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/objects/pathway.html

@@ -75,6 +75,7 @@
 
   {% 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" %}
     {% include "modals/objects/download_pathway_csv_modal.html" %}
     {% include "modals/objects/download_pathway_image_modal.html" %}

utilities/chem.py

@@ -88,6 +88,10 @@ 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)