14 Commits

Author SHA1 Message Date
2e24666744 wip
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CI / test (pull_request) Failing after 20s
2026-04-21 22:23:17 +02:00
d9c8c9746d wip 2026-04-21 22:17:20 +02:00
d668315064 More on PES 2026-04-21 22:15:06 +02:00
05a17ecdcf wip 2026-04-21 22:13:37 +02:00
2bdedc39ee Prep configs, added Package Create Modal 2026-04-21 22:10:52 +02:00
c9564a3dca Adjusted View for Package creation 2026-04-21 22:10:52 +02:00
512b51137f Adding secret flags to group, add secret pools to packages 2026-04-21 22:10:49 +02:00
5750257cfb Adjusted Dockerfile for Bayer 2026-04-21 22:08:13 +02:00
0bad0eb087 Adjusted docker compose to bayer specifics 2026-04-21 22:06:57 +02:00
c01ad663b7 Show Pack Classification 2026-04-21 22:06:57 +02:00
f1936eea8f Initial bayer app 2026-04-21 22:06:57 +02:00
624acccb3e adjusted migration 2026-04-21 22:06:57 +02:00
689f7998eb [Dep] Updated enviFormer, additional information lib, aiohttp, fsspec (#371)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#371
2026-04-22 06:38:31 +12:00
8498e59fa1 [Feature] Changes required for non public tenants (#370)
Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#370
2026-04-22 06:08:39 +12:00
13 changed files with 212 additions and 201 deletions

View File

@ -36,8 +36,8 @@ 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 biotransformer biotransformer
COPY bayer bayer
COPY bridge bridge
COPY envipath envipath
COPY epapi epapi

View File

@ -41,9 +41,7 @@ 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"))
)
urlpatterns.append(path(f"{PATH_PREFIX}", include(f"{s.TENANT}.urls")))
# Custom error handlers
handler400 = "epdb.views.handler400"

View File

@ -4,8 +4,7 @@ from django.contrib.auth import get_user_model
from django.contrib.auth import login
from django.shortcuts import redirect
from epdb.logic import UserManager, GroupManager
from epdb.models import Group
from epdb.logic import UserManager
def get_msal_app_with_cache(request):
@ -22,7 +21,7 @@ def get_msal_app_with_cache(request):
client_id=s.MS_ENTRA_CLIENT_ID,
client_credential=s.MS_ENTRA_CLIENT_SECRET,
authority=s.MS_ENTRA_AUTHORITY,
token_cache=cache
token_cache=cache,
)
return msal_app, cache
@ -59,9 +58,12 @@ def entra_callback(request):
claims = result["id_token_claims"]
user_name = claims["name"]
user_email = claims.get("emailaddress", claims["email"])
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()
@ -82,8 +84,7 @@ def entra_callback(request):
# Ensure groups exists in eP
for id, name in s.ENTRA_SECRET_GROUPS.items():
if not Group.objects.filter(uuid=id).exists():
g = GroupManager.create_group(User.objects.get(username="admin"), name, f"Synced Entra Group {name} ",
uuid=id)
g = GroupManager.create_group(User.objects.get(username="admin"), name, f"Synced Entra Group {name} ", uuid=id)
else:
g = Group.objects.get(uuid=id)
# Ensure its secret
@ -92,8 +93,7 @@ def entra_callback(request):
for id, name in s.ENTRA_GROUPS.items():
if not Group.objects.filter(uuid=id).exists():
g = GroupManager.create_group(User.objects.get(username="admin"), name, f"Synced Entra Group {name} ",
uuid=id)
g = GroupManager.create_group(User.objects.get(username="admin"), name, f"Synced Entra Group {name} ", uuid=id)
else:
g = Group.objects.get(uuid=id)
@ -142,10 +142,7 @@ def get_access_token_from_request(request, scopes=None):
return None
# Try to acquire token silently from cache
result = msal_app.acquire_token_silent(
scopes=scopes,
account=user_account
)
result = msal_app.acquire_token_silent(scopes=scopes, account=user_account)
# Save cache changes back to session
if cache.has_state_changed:

View File

@ -95,8 +95,8 @@ class EPDBURLParser:
def contains_package_url(self):
return (
bool(self.MODEL_PATTERNS["epdb.Package"].findall(self.url))
and not self.is_package_url()
bool(self.MODEL_PATTERNS["epdb.Package"].findall(self.url))
and not self.is_package_url()
)
def is_user_url(self) -> bool:
@ -188,7 +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()
@ -346,7 +346,9 @@ class PackageManager(object):
@staticmethod
def readable(user, package):
return PackageManager.has_package_permission(user, package, "read")
return (
PackageManager.has_package_permission(user, package, "read") | package.reviewed is True
)
@staticmethod
def writable(user, package):
@ -376,13 +378,13 @@ class PackageManager(object):
valid_perms = perms.get(permission)
if (
UserPackagePermission.objects.filter(
package=package, user=user, permission__in=valid_perms
).exists()
or GroupPackagePermission.objects.filter(
package=package, group__in=groups, permission__in=valid_perms
).exists()
or user.is_superuser
UserPackagePermission.objects.filter(
package=package, user=user, permission__in=valid_perms
).exists()
or GroupPackagePermission.objects.filter(
package=package, group__in=groups, permission__in=valid_perms
).exists()
or user.is_superuser
):
return True
@ -560,7 +562,7 @@ 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:
@ -603,7 +605,7 @@ 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
@ -683,7 +685,7 @@ 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)
@ -706,7 +708,7 @@ class PackageManager(object):
mapping[scenario["id"]] = scen.uuid
for ex in scenario.get("additionalInformationCollection", {}).get(
"additionalInformation", []
"additionalInformation", []
):
name = ex["name"]
addinf_data = ex["data"]
@ -975,7 +977,7 @@ 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"]
@ -1116,11 +1118,11 @@ class PackageManager(object):
@staticmethod
@transaction.atomic
def import_package(
data: Dict[str, Any],
owner: User,
preserve_uuids=False,
add_import_timestamp=True,
trust_reviewed=False,
data: Dict[str, Any],
owner: User,
preserve_uuids=False,
add_import_timestamp=True,
trust_reviewed=False,
) -> Package:
importer = PackageImporter(data, preserve_uuids, add_import_timestamp, trust_reviewed)
imported_package = importer.do_import()
@ -1135,7 +1137,7 @@ 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()
@ -1162,10 +1164,10 @@ class SettingManager(object):
s = Setting.objects.get(uuid=setting_id)
if (
s.global_default
or s.public
or user.is_superuser
or UserSettingPermission.objects.filter(user=user, setting=s).exists()
s.global_default
or s.public
or user.is_superuser
or UserSettingPermission.objects.filter(user=user, setting=s).exists()
):
return s
@ -1175,24 +1177,24 @@ 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(public=True)
| Setting.objects.filter(global_default=True)
Setting.objects.filter(id__in=sp)
| Setting.objects.filter(public=True)
| Setting.objects.filter(global_default=True)
).distinct()
@staticmethod
@transaction.atomic
def create_setting(
user: User,
name: str = None,
description: str = None,
max_nodes: int = None,
max_depth: int = None,
rule_packages: List[Package] | None = None,
model: EPModel = None,
model_threshold: float = None,
expansion_scheme: ExpansionSchemeChoice = ExpansionSchemeChoice.BFS,
property_models: List["PropertyPluginModel"] | None = None,
user: User,
name: str = None,
description: str = None,
max_nodes: int = None,
max_depth: int = None,
rule_packages: List[Package] | None = None,
model: EPModel = None,
model_threshold: float = None,
expansion_scheme: ExpansionSchemeChoice = ExpansionSchemeChoice.BFS,
property_models: List["PropertyPluginModel"] | None = None,
):
new_s = Setting()
@ -1271,8 +1273,8 @@ class SearchManager(object):
pathway_qs = Pathway.objects.filter(
Q(package__in=packages)
& (
Q(edge__edge_label__educts__inchikey=searchterm)
| Q(edge__edge_label__products__inchikey=searchterm)
Q(edge__edge_label__educts__inchikey=searchterm)
| Q(edge__edge_label__products__inchikey=searchterm)
)
).distinct()
@ -1310,8 +1312,8 @@ class SearchManager(object):
pathway_qs = Pathway.objects.filter(
Q(package__in=packages)
& (
Q(edge__edge_label__educts__smiles=searchterm)
| Q(edge__edge_label__products__smiles=searchterm)
Q(edge__edge_label__educts__smiles=searchterm)
| Q(edge__edge_label__products__smiles=searchterm)
)
).distinct()
@ -1347,15 +1349,15 @@ class SearchManager(object):
reactions_qs = Reaction.objects.filter(
Q(package__in=packages)
& (
Q(educts__inchikey__startswith=inchi_front)
| Q(products__inchikey__startswith=inchi_front)
Q(educts__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__products__inchikey__startswith=inchi_front)
Q(edge__edge_label__educts__inchikey__startswith=inchi_front)
| Q(edge__edge_label__products__inchikey__startswith=inchi_front)
)
).distinct()
@ -1393,8 +1395,8 @@ class SearchManager(object):
pathway_qs = Pathway.objects.filter(
Q(package__in=packages)
& (
Q(edge__edge_label__educts__canonical_smiles=searchterm)
| Q(edge__edge_label__products__canonical_smiles=searchterm)
Q(edge__edge_label__educts__canonical_smiles=searchterm)
| Q(edge__edge_label__products__canonical_smiles=searchterm)
)
).distinct()
@ -1469,11 +1471,11 @@ class SNode(object):
class SEdge(object):
def __init__(
self,
educts: Union[SNode, List[SNode]],
products: Union[SNode | List[SNode]],
rule: Optional["Rule"] = None,
probability: Optional[float] = None,
self,
educts: Union[SNode, List[SNode]],
products: Union[SNode | List[SNode]],
rule: Optional["Rule"] = None,
probability: Optional[float] = None,
):
if not isinstance(educts, list):
educts = [educts]
@ -1505,11 +1507,11 @@ class SEdge(object):
return False
if (
self.rule is not None
and other.rule is None
or self.rule is None
and other.rule is not None
or self.rule != other.rule
self.rule is not None
and other.rule is None
or self.rule is None
and other.rule is not None
or self.rule != other.rule
):
return False
@ -1517,8 +1519,8 @@ class SEdge(object):
return False
for n1, n2 in zip(
sorted(self.educts, key=lambda x: x.smiles),
sorted(other.educts, key=lambda x: x.smiles),
sorted(self.educts, key=lambda x: x.smiles),
sorted(other.educts, key=lambda x: x.smiles),
):
if n1.smiles != n2.smiles:
return False
@ -1527,8 +1529,8 @@ class SEdge(object):
return False
for n1, n2 in zip(
sorted(self.products, key=lambda x: x.smiles),
sorted(other.products, key=lambda x: x.smiles),
sorted(self.products, key=lambda x: x.smiles),
sorted(other.products, key=lambda x: x.smiles),
):
if n1.smiles != n2.smiles:
return False
@ -1541,10 +1543,10 @@ class SEdge(object):
class SPathway(object):
def __init__(
self,
root_nodes: Optional[Union[str, SNode, List[str | SNode]]] = None,
persist: Optional["Pathway"] = None,
prediction_setting: Optional[Setting] = None,
self,
root_nodes: Optional[Union[str, SNode, List[str | SNode]]] = None,
persist: Optional["Pathway"] = None,
prediction_setting: Optional[Setting] = None,
):
self.root_nodes = []
@ -1689,9 +1691,9 @@ 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
and expansion_result["rule_triggered"]
and sub.depth == 0
len(expansion_result["transformations"]) == 0
and expansion_result["rule_triggered"]
and sub.depth == 0
):
self.empty_due_to_threshold = True
@ -1798,8 +1800,8 @@ 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
or current_prob * edge.probability > node_probs[prod]
prod not in node_probs
or current_prob * edge.probability > node_probs[prod]
):
node_probs[prod] = current_prob * edge.probability

View File

@ -1,55 +1,54 @@
# Generated by Django 6.0.3 on 2026-04-17 21:22
# 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'),
("epdb", "0022_alter_classifierpluginmodel_data_packages_and_more"),
]
operations = [
migrations.AlterModelOptions(
name='compoundstructure',
name="compoundstructure",
options={},
),
migrations.AlterModelOptions(
name='epmodel',
name="epmodel",
options={},
),
migrations.AlterModelOptions(
name='parallelrule',
name="parallelrule",
options={},
),
migrations.AlterModelOptions(
name='rule',
name="rule",
options={},
),
migrations.AlterModelOptions(
name='sequentialrule',
name="sequentialrule",
options={},
),
migrations.AlterModelOptions(
name='simpleambitrule',
name="simpleambitrule",
options={},
),
migrations.AlterModelOptions(
name='simplerdkitrule',
name="simplerdkitrule",
options={},
),
migrations.AlterModelOptions(
name='simplerule',
name="simplerule",
options={},
),
migrations.AddField(
model_name='compoundstructure',
name='molfile',
field=models.TextField(blank=True, null=True, verbose_name='Molfile'),
model_name="compoundstructure",
name="molfile",
field=models.TextField(blank=True, null=True, verbose_name="Molfile"),
),
migrations.AddField(
model_name='group',
name='secret',
field=models.BooleanField(default=False, verbose_name='Secret Group'),
model_name="group",
name="secret",
field=models.BooleanField(default=False, verbose_name="Secret Group"),
),
]

View File

@ -2226,7 +2226,9 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin)
if isinstance(ai.get(), PropertyPrediction):
predicted_properties[ai.get().__class__.__name__].append(ai.data)
extra_structure_data = self.default_node_label.d3_json()
# 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,
@ -2237,7 +2239,7 @@ 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()],
@ -2250,9 +2252,9 @@ 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,
}
res.update(**extra_structure_data)
return res
@staticmethod

View File

@ -637,14 +637,7 @@ function draw(pathway, elem) {
node.filter(d => !d.pseudo).each(function (d, i) {
const g = d3.select(this);
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 {
if (d.image_type === "svg") {
// Parse the SVG string
const parser = new DOMParser();
const svgDoc = parser.parseFromString(d.image_svg, "image/svg+xml");
@ -662,7 +655,7 @@ function draw(pathway, elem) {
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") === `#${oldId}`
u => u.getAttributeNS(XLINK_NS, "href") === `#${oldId}`
);
uses.forEach(u => {
@ -679,10 +672,19 @@ function draw(pathway, elem) {
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);
.attr("width", svgWidth * scale)
.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);
}
});

View File

@ -1,3 +1,5 @@
{% load envipytags %}
{% if meta.can_edit %}
<li>
<a
@ -23,6 +25,11 @@
<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>

View File

@ -83,8 +83,8 @@
<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 %}

View File

@ -51,8 +51,8 @@
</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 %}

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>
@ -77,6 +79,10 @@
{% 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" %}
{% 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" %}

View File

@ -182,11 +182,9 @@ class FormatConverter(object):
drawer = rdMolDraw2D.MolDraw2DCairo(*mol_size)
opts = drawer.drawOptions()
opts.clearBackground = False
drawer.DrawMolecule(mol)
drawer.FinishDrawing()
return drawer.GetDrawingText()
@staticmethod

148
uv.lock generated
View File

@ -17,7 +17,7 @@ wheels = [
[[package]]
name = "aiohttp"
version = "3.13.3"
version = "3.13.5"
source = { registry = "https://pypi.org/simple" }
dependencies = [
{ name = "aiohappyeyeballs" },
@ -28,76 +28,76 @@ dependencies = [
{ name = "propcache" },
{ name = "yarl" },
]
sdist = { url = "https://files.pythonhosted.org/packages/50/42/32cf8e7704ceb4481406eb87161349abb46a57fee3f008ba9cb610968646/aiohttp-3.13.3.tar.gz", hash = "sha256:a949eee43d3782f2daae4f4a2819b2cb9b0c5d3b7f7a927067cc84dafdbb9f88", size = 7844556, upload-time = "2026-01-03T17:33:05.204Z" }
sdist = { url = "https://files.pythonhosted.org/packages/77/9a/152096d4808df8e4268befa55fba462f440f14beab85e8ad9bf990516918/aiohttp-3.13.5.tar.gz", hash = "sha256:9d98cc980ecc96be6eb4c1994ce35d28d8b1f5e5208a23b421187d1209dbb7d1", size = 7858271, upload-time = "2026-03-31T22:01:03.343Z" }
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