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[Feature] Changes required for non public tenants (#370)

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Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#370
This commit is contained in:
jebus
2026-04-22 06:08:39 +12:00
parent b508511cd6
commit 8498e59fa1
13 changed files with 249 additions and 88 deletions
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2
Dockerfile
View File

@ -36,11 +36,13 @@ RUN --mount=type=ssh \
# Now copy source and do a final sync to install the project itself
# Ensure .dockerignore is reasonable
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

3
envipath/urls.py
View File

@ -40,6 +40,9 @@ if "migration" in s.INSTALLED_APPS:
if s.MS_ENTRA_ENABLED:
urlpatterns.append(path(f"{PATH_PREFIX}", include("epauth.urls")))
if s.TENANT != "public":
urlpatterns.append(path(f"{PATH_PREFIX}", include(f"{s.TENANT}.urls")))
# Custom error handlers
handler400 = "epdb.views.handler400"
handler403 = "epdb.views.handler403"

90
epauth/views.py
View File

@ -1,12 +1,32 @@
import msal
from django.conf import settings as s
from django.contrib.auth import get_user_model
from django.contrib.auth import login
from django.shortcuts import redirect
from django.contrib.auth import get_user_model
from epdb.logic import UserManager
def get_msal_app_with_cache(request):
"""
Create MSAL app with session-based token cache.
"""
cache = msal.SerializableTokenCache()
# Load cache from session if it exists
if request.session.get("msal_token_cache"):
cache.deserialize(request.session["msal_token_cache"])
msal_app = msal.ConfidentialClientApplication(
client_id=s.MS_ENTRA_CLIENT_ID,
client_credential=s.MS_ENTRA_CLIENT_SECRET,
authority=s.MS_ENTRA_AUTHORITY,
token_cache=cache,
)
return msal_app, cache
def entra_login(request):
msal_app = msal.ConfidentialClientApplication(
client_id=s.MS_ENTRA_CLIENT_ID,
@ -23,11 +43,7 @@ def entra_login(request):
def entra_callback(request):
msal_app = msal.ConfidentialClientApplication(
client_id=s.MS_ENTRA_CLIENT_ID,
client_credential=s.MS_ENTRA_CLIENT_SECRET,
authority=s.MS_ENTRA_AUTHORITY,
)
msal_app, cache = get_msal_app_with_cache(request)
flow = request.session.pop("msal_auth_flow", None)
if not flow:
@ -36,11 +52,18 @@ def entra_callback(request):
# Acquire token using the flow and callback request
result = msal_app.acquire_token_by_auth_code_flow(flow, request.GET)
# Save the token cache to session
if cache.has_state_changed:
request.session["msal_token_cache"] = cache.serialize()
claims = result["id_token_claims"]
user_name = claims["name"]
user_email = claims["emailaddress"]
user_oid = claims["oid"]
user_name = claims.get("name")
user_email = claims.get("emailaddress", claims.get("email"))
user_oid = claims.get("oid")
if not all([user_name, user_email, user_oid]):
raise ValueError("Missing required claims in ID token")
# Get implementing class
User = get_user_model()
@ -57,4 +80,51 @@ def entra_callback(request):
login(request, u)
return redirect("/") # Handle errors
return redirect(s.SERVER_URL) # Handle errors
def get_access_token_from_request(request, scopes=None):
"""
Get an access token from the request using MSAL token cache.
"""
if scopes is None:
scopes = s.MS_ENTRA_SCOPES
# Get user from request (must be authenticated)
if not request.user.is_authenticated:
return None
# Create MSAL app with persistent cache
msal_app, cache = get_msal_app_with_cache(request)
# Try to get accounts from cache
accounts = msal_app.get_accounts()
if not accounts:
return None
# Find the account that matches the current user
user_account = None
for account in accounts:
if account.get("local_account_id") == str(request.user.uuid):
user_account = account
break
# If no matching account found, use the first available account
if not user_account and accounts:
user_account = accounts[0]
if not user_account:
return None
# Try to acquire token silently from cache
result = msal_app.acquire_token_silent(scopes=scopes, account=user_account)
# Save cache changes back to session
if cache.has_state_changed:
request.session["msal_token_cache"] = cache.serialize()
if result and "access_token" in result:
return result
return None

2
epdb/legacy_api.py
View File

@ -1969,7 +1969,7 @@ 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}")

61
epdb/logic.py
View File

@ -264,8 +264,12 @@ class GroupManager(object):
return bool(re.findall(GroupManager.group_pattern, url))
@staticmethod
def create_group(current_user, name, description):
def create_group(current_user, name, description, *args, **kwargs):
g = Group()
if "uuid" in kwargs:
g.uuid = kwargs["uuid"]
# Clean for potential XSS
g.name = nh3.clean(name, tags=s.ALLOWED_HTML_TAGS).strip()
g.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
@ -341,52 +345,17 @@ class PackageManager(object):
@staticmethod
def readable(user, package):
if (
UserPackagePermission.objects.filter(package=package, user=user).exists()
or GroupPackagePermission.objects.filter(
package=package, group__in=GroupManager.get_groups(user)
return (
PackageManager.has_package_permission(user, package, "read") | package.reviewed is True
)
or package.reviewed is True
or user.is_superuser
):
return True
return False
@staticmethod
def writable(user, package):
if (
UserPackagePermission.objects.filter(
package=package, user=user, permission=Permission.WRITE[0]
).exists()
or GroupPackagePermission.objects.filter(
package=package,
group__in=GroupManager.get_groups(user),
permission=Permission.WRITE[0],
).exists()
or UserPackagePermission.objects.filter(
package=package, user=user, permission=Permission.ALL[0]
).exists()
or user.is_superuser
):
return True
return False
return PackageManager.has_package_permission(user, package, "write")
@staticmethod
def administrable(user, package):
if (
UserPackagePermission.objects.filter(
package=package, user=user, permission=Permission.ALL[0]
).exists()
or GroupPackagePermission.objects.filter(
package=package,
group__in=GroupManager.get_groups(user),
permission=Permission.ALL[0],
).exists()
or user.is_superuser
):
return True
return False
return PackageManager.has_package_permission(user, package, "all")
@staticmethod
def has_package_permission(user: "User", package: Union[str, UUID, "Package"], permission: str):
@ -470,7 +439,9 @@ 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()
return qs
@staticmethod
def get_all_writeable_packages(user):
@ -514,7 +485,9 @@ class PackageManager(object):
qs = qs.filter(reviewed=False)
return qs.distinct()
qs = qs.distinct()
return qs
@staticmethod
def get_packages():
@ -716,6 +689,10 @@ 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"]:

49
epdb/migrations/0023_alter_compoundstructure_options_and_more.py Normal file
View File

@ -0,0 +1,49 @@
# Generated by Django 6.0.3 on 2026-04-21 11:43
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
("epdb", "0022_alter_classifierpluginmodel_data_packages_and_more"),
]
operations = [
migrations.AlterModelOptions(
name="compoundstructure",
options={},
),
migrations.AlterModelOptions(
name="epmodel",
options={},
),
migrations.AlterModelOptions(
name="parallelrule",
options={},
),
migrations.AlterModelOptions(
name="rule",
options={},
),
migrations.AlterModelOptions(
name="sequentialrule",
options={},
),
migrations.AlterModelOptions(
name="simpleambitrule",
options={},
),
migrations.AlterModelOptions(
name="simplerdkitrule",
options={},
),
migrations.AlterModelOptions(
name="simplerule",
options={},
),
migrations.AddField(
model_name="compoundstructure",
name="molfile",
field=models.TextField(blank=True, null=True, verbose_name="Molfile"),
),
]

14
epdb/models.py
View File

@ -1112,6 +1112,7 @@ 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")
@ -1208,6 +1209,9 @@ 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)
@ -2214,7 +2218,11 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
if isinstance(ai.get(), PropertyPrediction):
predicted_properties[ai.get().__class__.__name__].append(ai.data)
return {
# If we have Subclasses of a CompoundStructure we can overwrite keys (e.g. images)
# by overwriting keys
structure_data = self.default_node_label.d3_json()
res = {
"depth": self.depth,
"stereo_removed": self.stereo_removed,
"url": self.url,
@ -2223,6 +2231,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
"image_svg": IndigoUtils.mol_to_svg(
self.default_node_label.smiles, width=40, height=40
),
"image_type": "svg",
"name": self.get_name(),
"smiles": self.default_node_label.smiles,
"scenarios": [{"name": s.get_name(), "url": s.url} for s in self.scenarios.all()],
@ -2235,8 +2244,11 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
"predicted_properties": predicted_properties,
"is_engineered_intermediate": self.kv.get("is_engineered_intermediate", False),
"timeseries": self.get_timeseries_data(),
**structure_data,
}
return res
@staticmethod
@transaction.atomic
def create(

20
static/js/pw.js
View File

@ -637,6 +637,7 @@ function draw(pathway, elem) {
node.filter(d => !d.pseudo).each(function (d, i) {
const g = d3.select(this);
if (d.image_type === "svg") {
// Parse the SVG string
const parser = new DOMParser();
const svgDoc = parser.parseFromString(d.image_svg, "image/svg+xml");
@ -646,19 +647,19 @@ function draw(pathway, elem) {
const prefix = `node-${i}-`;
// Rename all IDs and fix <use> references
svgElem.querySelectorAll('[id]').forEach(el => {
svgElem.querySelectorAll("[id]").forEach(el => {
const oldId = el.id;
const newId = prefix + oldId;
el.id = newId;
const XLINK_NS = "http://www.w3.org/1999/xlink";
// Update <use> elements that reference this old ID
const uses = Array.from(svgElem.querySelectorAll('use')).filter(
u => u.getAttributeNS(XLINK_NS, 'href') === `#${oldId}`
const uses = Array.from(svgElem.querySelectorAll("use")).filter(
u => u.getAttributeNS(XLINK_NS, "href") === `#${oldId}`
);
uses.forEach(u => {
u.setAttributeNS(XLINK_NS, 'href', `#${newId}`);
u.setAttributeNS(XLINK_NS, "href", `#${newId}`);
});
});
@ -675,6 +676,17 @@ function draw(pathway, elem) {
.attr("height", svgHeight * scale)
.attr("x", -svgWidth * scale / 2)
.attr("y", -svgHeight * scale / 2);
} else {
// We have a image type different than svg
// include it via img url
g.append("svg:image")
.attr("xlink:href", d.image)
.attr("width", 40)
.attr("height", 40)
.attr("x", -20)
.attr("y", -20);
}
});
// add element to nodes array

7
templates/actions/objects/pathway.html
View File

@ -1,3 +1,5 @@
{% load envipytags %}
{% if meta.can_edit %}
<li>
<a
@ -15,6 +17,11 @@
<i class="glyphicon glyphicon-plus"></i> Add Reaction</a
>
</li>
{% epdb_slot_templates "epdb.actions.objects.pathway.add" as action_button_templates %}
{% for tpl in action_button_templates %}
{% include tpl %}
{% endfor %}
<li role="separator" class="divider"></li>
{% endif %}
<li>

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>
<!-- Extension Slot for Viz -->
{% 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>
<!-- Extension Slot for Viz -->
{% 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 />

6
templates/objects/pathway.html
View File

@ -1,5 +1,7 @@
{% extends "framework_modern.html" %}
{% load static %}
{% load envipytags %}
{% block content %}
<script src="https://d3js.org/d3.v7.min.js"></script>
<style>
@ -76,6 +78,10 @@
{% block action_modals %}
{% include "modals/objects/add_pathway_node_modal.html" %}
{% include "modals/objects/add_pathway_edge_modal.html" %}
{% epdb_slot_templates "epdb.modals.objects.pathway.add" as add_templates %}
{% for tpl in add_templates %}
{% include tpl %}
{% endfor %}
{% include "modals/objects/download_pathway_csv_modal.html" %}
{% include "modals/objects/download_pathway_image_modal.html" %}
{% include "modals/objects/identify_missing_rules_modal.html" %}

17
utilities/chem.py
View File

@ -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)
@ -171,12 +175,17 @@ class FormatConverter(object):
try:
Chem.Kekulize(mol)
except Exception:
mc = Chem.Mol(mol.ToBinary())
mol = Chem.Mol(mol.ToBinary())
if not mc.GetNumConformers():
Chem.rdDepictor.Compute2DCoords(mc)
if not mol.GetNumConformers():
Chem.rdDepictor.Compute2DCoords(mol)
pass
drawer = rdMolDraw2D.MolDraw2DCairo(*mol_size)
opts = drawer.drawOptions()
opts.clearBackground = False
drawer.DrawMolecule(mol)
drawer.FinishDrawing()
return drawer.GetDrawingText()
@staticmethod
def normalize(smiles):