wip

bayer/admin.py

@@ -1,3 +1,19 @@
 from django.contrib import admin
 
 # Register your models here.
+from .models import (
+    PESCompound,
+    PESStructure
+)
+
+
+class PESCompoundAdmin(admin.ModelAdmin):
+    pass
+
+
+class PESStructureAdmin(admin.ModelAdmin):
+    pass
+
+
+admin.site.register(PESCompound, PESCompoundAdmin)
+admin.site.register(PESStructure, PESStructureAdmin)

bayer/epdb_hooks.py

@@ -4,6 +4,7 @@ from epdb.template_registry import register_template
 
 logger = logging.getLogger(__name__)
 
+# PES Create
 register_template(
     "epdb.actions.collections.compound",
     "actions/collections/new_pes.html",
@@ -13,3 +14,18 @@ register_template(
     "modals/collections/new_pes_modal.html",
 )
 
+# PES Viz
+register_template(
+    "epdb.objects.compound.viz",
+    "objects/compound_viz.html",
+)
+
+register_template(
+    "epdb.objects.compound_structure.viz",
+    "objects/compound_structure_viz.html",
+)
+
+register_template(
+    "epdb.objects.node.viz",
+    "objects/node_viz.html",
+)

bayer/migrations/0004_pescompound_pesstructure.py

@@ -0,0 +1,35 @@
+# Generated by Django 6.0.3 on 2026-04-15 20:03
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('bayer', '0003_package_data_pool'),
+        ('epdb', '0023_alter_compoundstructure_options_and_more'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='PESCompound',
+            fields=[
+                ('compound_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='epdb.compound')),
+            ],
+            options={
+                'abstract': False,
+            },
+            bases=('epdb.compound',),
+        ),
+        migrations.CreateModel(
+            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')),
+            ],
+            options={
+                'abstract': False,
+            },
+            bases=('epdb.compoundstructure',),
+        ),
+    ]

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

@@ -1,11 +1,15 @@
 from typing import List
-
+import urllib.parse
+import nh3
 from django.conf import settings as s
-from django.db import models
+from django.db import models, transaction
 from django.db.models import QuerySet
+from django.urls import reverse
 
 from epdb.models import (
     EnviPathModel,
+    Compound,
+    CompoundStructure,
     ParallelRule,
     SequentialRule,
     SimpleAmbitRule,
@@ -95,4 +99,70 @@ class Package(EnviPathModel):
         return rules
 
     class Meta:
-        db_table = "epdb_package"
+        db_table = "epdb_package"
+
+
+class PESCompound(Compound):
+
+    @staticmethod
+    @transaction.atomic
+    def create(
+        package: "Package", pes_data: dict, name: str = None, description: str = None, *args, **kwargs
+    ) -> "Compound":
+
+        pes_url = pes_data["pes_url"]
+
+        # 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
+
+        # Generate Compound
+        c = PESCompound()
+        c.package = package
+
+        if name is not None:
+            # Clean for potential XSS
+            name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
+
+        if name is None or name == "":
+            name = f"Compound {Compound.objects.filter(package=package).count() + 1}"
+
+        c.name = name
+
+        # We have a default here only set the value if it carries some payload
+        if description is not None and description.strip() != "":
+            c.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
+
+        c.save()
+
+        is_standardized = standardized_smiles == smiles
+
+        if not is_standardized:
+            _ = CompoundStructure.create(
+                c,
+                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
+        )
+
+        c.default_structure = cs
+        c.save()
+
+        return c
+
+
+class PESStructure(CompoundStructure):
+    pes_link = models.URLField(blank=False, null=False, verbose_name="PES Link")
+
+    def d3_json(self):
+        return {
+            "is_pes": True,
+            "pes_link": self.pes_link,
+            # Will overwrite image from Node
+            "image": f"{reverse("depict_pes")}?pesLink={urllib.parse.quote(self.pes_link)}"
+        }

bayer/templates/modals/collections/new_pes_modal.html

@@ -90,7 +90,7 @@
       <form
         id="new-pes-modal-form"
         accept-charset="UTF-8"
-        action="{% url 'package compound list' meta.current_package.uuid %}"
+        action="{% url 'create pes' meta.current_package.uuid %}"
         method="post"
       >
         {% csrf_token %}
@@ -129,9 +129,10 @@
             name="pes-link"
             type="text"
             class="input input-bordered w-full"
-            placeholder="Link to PES"
+            placeholder="Link to PES e.g. https://pesregapp-test.cropkey-np.ag/entities/PES-000126"
             x-model="pesLink"
             @input="updatePesViz()"
+            required
           />
         </div>
 

bayer/templates/objects/compound_structure_viz.html

@@ -0,0 +1,12 @@
+{% if compound_structure.pes_link %}
+  <!-- Image Representation -->
+  <div class="collapse-arrow bg-base-200 collapse">
+    <input type="checkbox" checked />
+    <div class="collapse-title text-xl font-medium">PES Image Representation</div>
+    <div class="collapse-content">
+      <div class="flex justify-center">
+        <img src='{% url 'depict_pes' %}?pesLink={{ compound_structure.pes_link|urlencode }}'/>
+      </div>
+    </div>
+  </div>
+{% endif %}

bayer/templates/objects/compound_viz.html

@@ -0,0 +1,12 @@
+{% if compound.default_structure.pes_link %}
+  <!-- Image Representation -->
+  <div class="collapse-arrow bg-base-200 collapse">
+    <input type="checkbox" checked />
+    <div class="collapse-title text-xl font-medium">PES Image Representation</div>
+    <div class="collapse-content">
+      <div class="flex justify-center">
+        <img src='{% url 'depict_pes' %}?pesLink={{ compound.default_structure.pes_link|urlencode }}'/>
+      </div>
+    </div>
+  </div>
+{% endif %}

bayer/templates/objects/node_viz.html

@@ -0,0 +1,12 @@
+{% if node.default_node_label.pes_link %}
+  <!-- Image Representation -->
+  <div class="collapse-arrow bg-base-200 collapse">
+    <input type="checkbox" checked />
+    <div class="collapse-title text-xl font-medium">PES Image Representation</div>
+    <div class="collapse-content">
+      <div class="flex justify-center">
+        <img src='{% url 'depict_pes' %}?pesLink={{ node.default_node_label.pes_link|urlencode }}'/>
+      </div>
+    </div>
+  </div>
+{% endif %}

bayer/urls.py

@@ -2,7 +2,13 @@ from django.urls import re_path
 
 from . import views as v
 
+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$", v.visualize_pes, name="depict_pes"),
+    re_path(
+        rf"^package/(?P<package_uuid>{UUID})/compound$",
+        v.create_pes,
+        name="create pes",
+    ),
 ]

bayer/views.py

@@ -1,13 +1,41 @@
+import base64
+
 import requests
 from django.conf import settings as s
+from django.core.exceptions import BadRequest
 from django.http import HttpResponse
-from pydantic import BaseModel
+from django.shortcuts import redirect
 
-from utilities.chem import FormatConverter
+from bayer.models import PESCompound
+from epdb.logic import PackageManager
+from epdb.views import _anonymous_or_real
+from utilities.decorators import package_permission_required
 
 
-class PES(BaseModel):
-    pass
+@package_permission_required()
+def create_pes(request, package_uuid):
+    current_user = _anonymous_or_real(request)
+    current_package = PackageManager.get_package_by_id(current_user, package_uuid)
+
+    if request.method == "POST":
+        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}")
+
+            pes = PESCompound.create(current_package, pes_data, compound_name, compound_description)
+
+            return redirect(pes.url)
+        else:
+            return BadRequest("Please provide a PES link.")
+    else:
+        pass
+
 
 
 def fetch_pes(request, pes_url) -> dict:
@@ -19,28 +47,35 @@ def fetch_pes(request, pes_url) -> dict:
     from epauth.views import get_access_token_from_request
     token = get_access_token_from_request(request)
 
-    if token:
+    if token or True:
         for k, v in s.PES_API_MAPPING.items():
-            if pes_url.startsWith(k):
+            if pes_url.startswith(k):
                 pes_id = pes_url.split('/')[-1]
-                headers = {"Authorization": f"Bearer {token['access_token']}"}
-                params = {"pes_reg_entity_corporate_id": pes_id}
 
-                res = requests.get(v, headers=headers, params=params, proxies=proxies)
-
-                try:
-                    res.raise_for_status()
-                    pes_data = res.json()
-
-                    if len(pes_data) == 0:
-                        raise ValueError(f"PES with id {pes_id} not found")
-
-                    res_data = pes_data[0]
+                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
                     return res_data
+                else:
+                    headers = {"Authorization": f"Bearer {token['access_token']}"}
+                    params = {"pes_reg_entity_corporate_id": pes_id}
 
-                except requests.exceptions.HTTPError as e:
-                    raise ValueError(f"Error fetching PES with id {pes_id}: {e}")
+                    res = requests.get(v, headers=headers, params=params, proxies=proxies)
+
+                    try:
+                        res.raise_for_status()
+                        pes_data = res.json()
+
+                        if len(pes_data) == 0:
+                            raise ValueError(f"PES with id {pes_id} not found")
+
+                        res_data = pes_data[0]
+                        res_data["pes_url"] = pes_url
+                        return res_data
+
+                    except requests.exceptions.HTTPError as e:
+                        raise ValueError(f"Error fetching PES with id {pes_id}: {e}")
         else:
             raise ValueError(f"Unknown URL {pes_url}")
     else:
@@ -52,8 +87,10 @@ def visualize_pes(request):
 
     if pes_link:
         pes_data = fetch_pes(request, pes_link)
-        print(pes_data)
 
-    return HttpResponse(
-        FormatConverter.to_png("c1ccccc1"), content_type="image/png"
-    )
+        representations = pes_data.get('representations')
+
+        for rep in representations:
+            if rep.get('type') == 'color':
+                image_data = base64.b64decode(rep.get('base64').replace("data:image/png;base64,", ""))
+                return HttpResponse(image_data, content_type="image/png")