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This commit is contained in:
Tim Lorsbach
2026-04-17 19:39:54 +02:00
parent ca0508d96a
commit d1a00f71b4
19 changed files with 412 additions and 115 deletions
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16
bayer/admin.py
View File

@ -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)

16
bayer/epdb_hooks.py
View File

@ -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",
)

35
bayer/migrations/0004_pescompound_pesstructure.py Normal file
View File

@ -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',),
),
]

19
bayer/migrations/0005_pesstructure_pes_link.py Normal file
View File

@ -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,
),
]

74
bayer/models.py
View File

@ -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,
@ -96,3 +100,69 @@ class Package(EnviPathModel):
class Meta:
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)}"
}

0
bayer/templates/actions/objects/compound.html
View File

5
bayer/templates/modals/collections/new_pes_modal.html
View File

@ -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>

12
bayer/templates/objects/compound_structure_viz.html Normal file
View File

@ -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 %}

12
bayer/templates/objects/compound_viz.html Normal file
View File

@ -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 %}

12
bayer/templates/objects/node_viz.html Normal file
View File

@ -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 %}

6
bayer/urls.py
View File

@ -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",
),
]

85
bayer/views.py
View File

@ -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")

101
epdb/legacy_api.py
View File

@ -1,17 +1,22 @@
import hashlib
from collections import defaultdict
from typing import Any, Dict, List, Optional
import jwt
import requests
import nh3
from django.conf import settings as s
from django.contrib.auth import get_user_model
from django.http import HttpResponse, JsonResponse
from django.shortcuts import redirect
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
from .logic import (
EPDBURLParser,
GroupManager,
@ -59,7 +64,46 @@ def _anonymous_or_real(request):
return get_user_model().objects.get(username="anonymous")
router = Router(auth=SessionAuth(csrf=False))
def validate_token(token: str) -> dict:
TENANT_ID = s.MS_ENTRA_TENANT_ID
CLIENT_ID = s.MS_ENTRA_CLIENT_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)
public_key = jwt.algorithms.RSAAlgorithm.from_jwk(
next(k for k in jwks["keys"] if k["kid"] == header["kid"])
)
claims = jwt.decode(
token,
public_key,
algorithms=["RS256"],
audience=[CLIENT_ID, f"api://{CLIENT_ID}"],
issuer=f"https://sts.windows.net/{TENANT_ID}/",
)
return claims
class MSBearerTokenAuth(HttpBearer):
def authenticate(self, request, token):
if token is None:
return None
claims = validate_token(token)
if not User.objects.filter(uuid=claims['oid']).exists():
return None
request.user = User.objects.get(uuid=claims['oid'])
return request.user
router = Router(auth=MSBearerTokenAuth())
class Error(Schema):
@ -153,59 +197,6 @@ class SimpleModel(SimpleObject):
identifier: str = "relative-reasoning"
################
# Login/Logout #
################
@router.post("/", response={200: SimpleUser, 403: Error}, auth=None)
def login(request, loginusername: Form[str], loginpassword: Form[str]):
from django.contrib.auth import authenticate, login
if request.headers.get("Authorization"):
import jwt
import requests
TENANT_ID = s.MS_ENTRA_TENANT_ID
CLIENT_ID = s.MS_ENTRA_CLIENT_ID
def validate_token(token: str) -> dict:
# 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)
public_key = jwt.algorithms.RSAAlgorithm.from_jwk(
next(k for k in jwks["keys"] if k["kid"] == header["kid"])
)
claims = jwt.decode(
token,
public_key,
algorithms=["RS256"],
audience=[CLIENT_ID, f"api://{CLIENT_ID}"],
issuer=f"https://sts.windows.net/{TENANT_ID}/",
)
return claims
token = request.headers.get("Authorization").split(" ")[1]
claims = validate_token(token)
if not User.objects.filter(uuid=claims['oid']).exists():
user = None
else:
user = User.objects.get(uuid=claims['oid'])
else:
email = User.objects.get(username=loginusername).email
user = authenticate(username=email, password=loginpassword)
if user:
login(request, user)
return user
else:
return 403, {"message": "Invalid username and/or password"}
########
# User #

31
epdb/logic.py
View File

@ -627,6 +627,25 @@ class PackageManager(object):
else:
pack.reviewed = False
# EDIT START
if data.get("classification"):
if data["classification"] == "INTERNAL":
pack.classification = Package.Classification.RESTRICTED
elif data["classification"] == "RESTRICTED":
pack.classification = Package.Classification.RESTRICTED
elif data["classification"] == "SECRET":
pack.classification = Package.Classification.SECRET
if not "datapool" in data:
raise ValueError("Missing datapool in package")
g = Group.objects.get(uuid=data["datapool"].split('/')[-1])
pack.data_pool = g
else:
raise ValueError(f"Invalid classification {data['classification']}")
# EDIT END
pack.description = data["description"]
pack.save()
@ -712,7 +731,13 @@ class PackageManager(object):
default_structure = None
for structure in compound["structures"]:
struc = CompoundStructure()
if structure.get("pesLink"):
from bayer.models import PESStructure
struc = PESStructure()
struc.pes_link = structure["pesLink"]
else:
struc = CompoundStructure()
# struc.object_url = Command.get_id(structure, keep_ids)
struc.compound = comp
struc.uuid = UUID(structure["id"].split("/")[-1]) if keep_ids else uuid4()
@ -720,6 +745,10 @@ class PackageManager(object):
struc.description = structure["description"]
struc.aliases = structure.get("aliases", [])
struc.smiles = structure["smiles"]
if structure.get("molfile"):
struc.molfile = structure["molfile"]
struc.save()
for scen in structure["scenarios"]:

12
epdb/models.py
View File

@ -1113,6 +1113,7 @@ class CompoundStructure(
canonical_smiles = models.TextField(blank=False, null=False, verbose_name="Canonical SMILES")
inchikey = models.TextField(max_length=27, blank=False, null=False, verbose_name="InChIKey")
normalized_structure = models.BooleanField(null=False, blank=False, default=False)
molfile = models.TextField(blank=True, null=True, verbose_name="Molfile")
external_identifiers = GenericRelation("ExternalIdentifier")
@ -1209,6 +1210,9 @@ class CompoundStructure(
return dict(hls)
def d3_json(self):
return {}
class EnzymeLink(EnviPathModel, KEGGIdentifierMixin):
rule = models.ForeignKey("Rule", on_delete=models.CASCADE, db_index=True)
@ -2215,7 +2219,9 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
if isinstance(ai.get(), PropertyPrediction):
predicted_properties[ai.get().__class__.__name__].append(ai.data)
return {
extra_structure_data = self.default_node_label.d3_json()
res = {
"depth": self.depth,
"stereo_removed": self.stereo_removed,
"url": self.url,
@ -2224,6 +2230,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
"image_svg": IndigoUtils.mol_to_svg(
self.default_node_label.smiles, width=40, height=40
),
"name": self.get_name(),
"smiles": self.default_node_label.smiles,
"scenarios": [{"name": s.get_name(), "url": s.url} for s in self.scenarios.all()],
@ -2238,6 +2245,9 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
"timeseries": self.get_timeseries_data(),
}
res.update(**extra_structure_data)
return res
@staticmethod
@transaction.atomic
def create(

68
static/js/pw.js
View File

@ -637,44 +637,54 @@ function draw(pathway, elem) {
node.filter(d => !d.pseudo).each(function (d, i) {
const g = d3.select(this);
// Parse the SVG string
const parser = new DOMParser();
const svgDoc = parser.parseFromString(d.image_svg, "image/svg+xml");
const svgElem = svgDoc.documentElement;
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");
const svgElem = svgDoc.documentElement;
// Create a unique prefix per node
const prefix = `node-${i}-`;
// Create a unique prefix per node
const prefix = `node-${i}-`;
// Rename all IDs and fix <use> references
svgElem.querySelectorAll('[id]').forEach(el => {
const oldId = el.id;
const newId = prefix + oldId;
el.id = newId;
// Rename all IDs and fix <use> references
svgElem.querySelectorAll("[id]").forEach(el => {
const oldId = el.id;
const newId = prefix + oldId;
el.id = newId;
const XLINK_NS = "http://www.w3.org/1999/xlink";
// Update <use> elements that reference this old ID
const uses = Array.from(svgElem.querySelectorAll('use')).filter(
u => u.getAttributeNS(XLINK_NS, 'href') === `#${oldId}`
);
const XLINK_NS = "http://www.w3.org/1999/xlink";
// Update <use> elements that reference this old ID
const uses = Array.from(svgElem.querySelectorAll("use")).filter(
u => u.getAttributeNS(XLINK_NS, "href") === `#${oldId}`
);
uses.forEach(u => {
u.setAttributeNS(XLINK_NS, 'href', `#${newId}`);
uses.forEach(u => {
u.setAttributeNS(XLINK_NS, "href", `#${newId}`);
});
});
});
g.node().appendChild(svgElem);
g.node().appendChild(svgElem);
const vb = svgElem.viewBox.baseVal;
const svgWidth = vb.width || 40;
const svgHeight = vb.height || 40;
const vb = svgElem.viewBox.baseVal;
const svgWidth = vb.width || 40;
const svgHeight = vb.height || 40;
const scale = (nodeRadius * 2) / Math.max(svgWidth, svgHeight);
const scale = (nodeRadius * 2) / Math.max(svgWidth, svgHeight);
g.select("svg")
.attr("width", svgWidth * scale)
.attr("height", svgHeight * scale)
.attr("x", -svgWidth * scale / 2)
.attr("y", -svgHeight * scale / 2);
}
g.select("svg")
.attr("width", svgWidth * scale)
.attr("height", svgHeight * scale)
.attr("x", -svgWidth * scale / 2)
.attr("y", -svgHeight * scale / 2);
});
// add element to nodes array

7
templates/objects/compound.html
View File

@ -1,4 +1,5 @@
{% extends "framework_modern.html" %}
{% load envipytags %}
{% block content %}
@ -82,6 +83,12 @@
<div class="collapse-content">{{ compound.description }}</div>
</div>
{% epdb_slot_templates "epdb.objects.compound.viz" as viz_templates %}
{% for tpl in viz_templates %}
{% include tpl %}
{% endfor %}
<!-- Image Representation -->
<div class="collapse-arrow bg-base-200 collapse">
<input type="checkbox" checked />

7
templates/objects/compound_structure.html
View File

@ -1,4 +1,5 @@
{% extends "framework_modern.html" %}
{% load envipytags %}
{% block content %}
@ -50,6 +51,12 @@
</div>
</div>
{% epdb_slot_templates "epdb.objects.compound_structure.viz" as viz_templates %}
{% for tpl in viz_templates %}
{% include tpl %}
{% endfor %}
<!-- Image Representation -->
<div class="collapse-arrow bg-base-200 collapse">
<input type="checkbox" checked />

7
templates/objects/node.html
View File

@ -1,4 +1,5 @@
{% extends "framework_modern.html" %}
{% load envipytags %}
{% block content %}
@ -54,6 +55,12 @@
</div>
</div>
{% epdb_slot_templates "epdb.objects.node.viz" as viz_templates %}
{% for tpl in viz_templates %}
{% include tpl %}
{% endfor %}
<!-- Image Representation -->
<div class="collapse-arrow bg-base-200 collapse">
<input type="checkbox" checked />