wip

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 class="card-body">
-      <h3 class="card-title">Welcome to the new enviPath!</h3>
-    </div>
+  <div>
+  <img src="{% static 'images/bayer-logo.svg' %}">
+
   </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 = {