jebus/enviPy-bayer
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develop-bayer #1

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jebus wants to merge 5 commits from develop-bayer into develop
pull from: develop-bayer
merge into: jebus:develop
Conversation 0 Commits 5 Files Changed 79 +2928 -2893
73 changed files with 2928 additions and 2893 deletions
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3
Dockerfile
View File

@ -30,12 +30,13 @@ RUN mkdir -p -m 0700 /root/.ssh \
&& ssh-keyscan git.envipath.com >> /root/.ssh/known_hosts
# We'll need access to private repos, let docker make use of host ssh agent and use it like:
# docker build --ssh default -t envipath/envipy:1.0 .
# docker build --ssh default -t envipath/envipy-bayer:1.0 .
RUN --mount=type=ssh \
uv sync --locked --extra ms-login --extra pepper-plugin
# Now copy source and do a final sync to install the project itself
# Ensure .dockerignore is reasonable
COPY bb4g bb4g
COPY biotransformer biotransformer
COPY bayer bayer
COPY bridge bridge

11
bayer/views.py
View File

@ -103,20 +103,15 @@ def create_pes_node(request, package_uuid, pathway_uuid):
def fetch_pes(request, pes_url) -> dict:
proxies = {
"http": "http://10.185.190.100:8080",
"https": "http://10.185.190.100:8080",
}
from epauth.views import get_access_token_from_request
token = get_access_token_from_request(request)
if token or True:
if token:
for k, v in s.PES_API_MAPPING.items():
if pes_url.startswith(k):
pes_id = pes_url.split('/')[-1]
if pes_id == 'dummy' or True:
if pes_id == 'dummy':
import json
res_data = json.load(open(s.BASE_DIR / "fixtures/pes.json"))
res_data["pes_url"] = pes_url
@ -125,7 +120,7 @@ def fetch_pes(request, pes_url) -> dict:
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)
res = requests.get(v, headers=headers, params=params, proxies=s.PROXIES or None)
try:
res.raise_for_status()

44
bb4g/__init__.py
View File

@ -2,9 +2,11 @@ import json
import math
from datetime import datetime
from typing import List
import enum
import requests
from django.conf import settings as s
from envipy_additional_information import EnviPyModel, UIConfig, WidgetType
from envipy_additional_information import register
from bridge.contracts import Classifier # noqa: I001
from bridge.dto import (
@ -15,12 +17,36 @@ from bridge.dto import (
TransformationProductPrediction,
) # noqa: I001
class SamplingAlgorithm(enum.Enum):
EXACT = "exact"
@register("bb4gconfig")
class BB4GConfig(EnviPyModel):
sampling_algorithm: SamplingAlgorithm = SamplingAlgorithm.EXACT
cutoff: int = -5
class UI:
title = "BB4G Configuration"
sampling_algorithm = UIConfig(
widget=WidgetType.SELECT,
label="BB4G Sampling Algorithm",
order=1,
placeholder="If unset defaults to 'exact'"
)
cutoff = UIConfig(
widget=WidgetType.NUMBER,
label="BB4G Cutoff",
order=2,
placeholder="If unset defaults to -5"
)
# Once stable these will be exposed by enviPy-plugins lib
class BB4G(Classifier):
Config = None
Config = BB4GConfig
def __init__(self, config=None):
def __init__(self, config: BB4GConfig | None = None):
super().__init__(config)
self.url = f"{s.BB4G_URL}"
@ -29,10 +55,6 @@ class BB4G(Classifier):
"Authorization": f"Bearer {self.token}",
"Content-Type": "application/json",
}
self.proxies = {
"http": s.HTTP_PROXY,
"https": s.HTTPS_PROXY,
}
def acquire_token(self):
BB4G_TENANT_ID = s.BB4G_TENANT_ID
@ -65,7 +87,7 @@ class BB4G(Classifier):
started = False
retries = 0
while not started and retries < 5:
res = requests.post(f"{self.url}/start", headers=header, data={}, proxies=self.proxies)
res = requests.post(f"{self.url}/start", headers=header, data={}, proxies=s.PROXIES or None)
if res.status_code == 200:
started = True
@ -140,11 +162,11 @@ class BB4G(Classifier):
for smi in smiles:
data = {
"smiles": smi,
"sampling_alg": "exact",
"cutoff": -5,
"sampling_alg": self.config.sampling_algorithm.value,
"cutoff": self.config.cutoff,
}
resp = requests.post(f"{self.url}/compute", headers=header, data=json.dumps(data), proxies=self.proxies)
resp = requests.post(f"{self.url}/compute", headers=header, data=json.dumps(data), proxies=s.PROXIES or None)
resp.raise_for_status()

10
bridge/contracts.py
View File

@ -254,7 +254,15 @@ class Classifier(Plugin):
def parse_config(cls, data: dict | None = None) -> EnviPyModel | None:
if cls.Config is None:
return None
return cls.Config(**(data or {}))
# remove empty strings a.k.a unset params to not overwrite defaults
cpy = {}
if data is not None:
for k, v in data.items():
if v != "":
cpy[k] = v
return cls.Config(**cpy)
@classmethod
def create(cls, data: dict | None = None):

17
envipath/settings.py
View File

@ -143,6 +143,12 @@ if os.environ.get("USE_TEMPLATE_DB", False) == "True":
"TEMPLATE": os.environ["TEMPLATE_DB"],
}
CACHES = {
"default": {
"BACKEND": "django.core.cache.backends.locmem.LocMemCache",
"LOCATION": "unique-snowflake",
}
}
# Password validation
# https://docs.djangoproject.com/en/4.2/ref/settings/#auth-password-validators
@ -474,3 +480,14 @@ if DATA_POOL_MAPPING:
else:
DATA_POOL_MAPPING = {}
PROXIES = {}
if os.environ.get("HTTP_PROXY"):
PROXIES["http"] = os.environ.get("HTTP_PROXY")
PROXIES["https"] = os.environ.get("HTTPS_PROXY")
# BB4g
BB4G_URL = os.environ.get("BB4G_URL")
BB4G_TENANT_ID = os.environ.get("BB4G_TENANT_ID")
BB4G_CLIENT_ID = os.environ.get("BB4G_CLIENT_ID")
BB4G_CLIENT_SECRET = os.environ.get("BB4G_CLIENT_SECRET")
BB4G_SCOPE = os.environ.get("BB4G_SCOPE")

1
epauth/urls.py
View File

@ -5,4 +5,5 @@ from . import views
urlpatterns = [
path("entra/login/", views.entra_login, name="entra_login"),
path("auth/redirect/", views.entra_callback, name="entra_callback"),
path("auth/token/", views.get_token, name="get_token"),
]

17
epauth/views.py
View File

@ -2,9 +2,11 @@ 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.http import HttpResponse
from django.shortcuts import redirect
from epdb.logic import UserManager
from epdb.logic import UserManager, GroupManager
from epdb.models import Group
def get_msal_app_with_cache(request):
@ -81,10 +83,12 @@ def entra_callback(request):
login(request, u)
# EDIT START
# 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
@ -93,7 +97,8 @@ 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)
@ -152,3 +157,9 @@ def get_access_token_from_request(request, scopes=None):
return result
return None
def get_token(request):
token = get_access_token_from_request(request)
msg = f"{token}"
return HttpResponse(msg, content_type='text/plain')

54
epdb/legacy_api.py
View File

@ -1,19 +1,17 @@
import hashlib
from collections import defaultdict
from typing import Any, Dict, List, Optional
import jwt
import requests
import nh3
import requests
from django.conf import settings as s
from django.contrib.auth import get_user_model
from django.core.cache import cache
from django.http import HttpResponse, JsonResponse
from django.shortcuts import redirect
from jwt import InvalidIssuerError
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
@ -51,6 +49,26 @@ from .models import (
Package = s.GET_PACKAGE_MODEL()
def get_cached_jwks(tenant_id: str, force=False) -> Dict:
"""Get JWKS using Django cache"""
cache_key = f"jwks_{tenant_id}"
jwks = cache.get(cache_key)
if jwks is None or force:
# Cache miss, fetch new keys
jwks_uri = f"https://login.microsoftonline.com/{tenant_id}/discovery/v2.0/keys"
response = requests.get(jwks_uri)
response.raise_for_status()
jwks = response.json()
# Cache for 1 hour (3600 seconds)
cache.set(cache_key, jwks, 3600)
return jwks
def get_package_for_write(user, package_uuid):
p = PackageManager.get_package_by_id(user, package_uuid)
if not PackageManager.writable(user, p):
@ -68,9 +86,7 @@ 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()
jwks = get_cached_jwks(TENANT_ID)
header = jwt.get_unverified_header(token)
@ -78,13 +94,21 @@ def validate_token(token: str) -> dict:
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}/",
)
# Handle V1 and V2 tokens
try:
claims = jwt.decode(
token,
public_key,
algorithms=["RS256"],
audience=[CLIENT_ID, f"api://{CLIENT_ID}"],
issuer=[
f"https://sts.windows.net/{TENANT_ID}/",
f"https://login.microsoftonline.com/{TENANT_ID}/v2.0"
]
)
except Exception as e:
raise ValueError(f"Token verification failed! - {e}")
return claims

6
epdb/views.py
View File

@ -937,12 +937,14 @@ def package_models(request, package_uuid):
"requires_rule_packages": True,
"requires_data_packages": True,
},
"EnviFormer": {
}
if s.ENVIFORMER_PRESENT:
context["model_types"]["EnviFormer"] = {
"type": "enviformer",
"requires_rule_packages": False,
"requires_data_packages": True,
},
}
if s.FLAGS.get("PLUGINS", False):
for k, v in s.CLASSIFIER_PLUGINS.items():

2
templates/collections/compounds_paginated.html
View File

@ -5,7 +5,7 @@
{% block action_button %}
<div class="flex items-center gap-2">
{% if meta.can_edit %}
{% if meta.can_edit or not meta.url_contains_package %}
<button
type="button"
class="btn btn-primary btn-sm"

18
templates/collections/models_paginated.html
View File

@ -3,14 +3,16 @@
{% block page_title %}Models{% endblock %}
{% block action_button %}
{% if meta.can_edit and meta.enabled_features.MODEL_BUILDING %}
<button
type="button"
class="btn btn-primary btn-sm"
onclick="document.getElementById('new_model_modal').showModal(); return false;"
>
New Model
</button>
{% if meta.can_edit or not meta.url_contains_package %}
{% if meta.enabled_features.MODEL_BUILDING %}
<button
type="button"
class="btn btn-primary btn-sm"
onclick="document.getElementById('new_model_modal').showModal(); return false;"
>
New Model
</button>
{% endif %}
{% endif %}
{% endblock action_button %}

2
templates/collections/packages_paginated.html
View File

@ -3,7 +3,6 @@
{% block page_title %}Packages{% endblock %}
{% block action_button %}
{% if meta.can_edit %}
<div class="flex items-center gap-2">
<button
type="button"
@ -71,7 +70,6 @@
</ul>
</div>
</div>
{% endif %}
{% endblock action_button %}
{% block action_modals %}

2
templates/collections/pathways_paginated.html
View File

@ -3,7 +3,7 @@
{% block page_title %}Pathways{% endblock %}
{% block action_button %}
{% if meta.can_edit %}
{% if meta.can_edit or not meta.url_contains_package %}
<div class="flex items-center gap-2">
<a
class="btn btn-primary btn-sm"

2
templates/collections/reactions_paginated.html
View File

@ -3,7 +3,7 @@
{% block page_title %}Reactions{% endblock %}
{% block action_button %}
{% if meta.can_edit %}
{% if meta.can_edit or not meta.url_contains_package %}
<button
type="button"
class="btn btn-primary btn-sm"

2
templates/collections/rules_paginated.html
View File

@ -3,7 +3,7 @@
{% block page_title %}Rules{% endblock %}
{% block action_button %}
{% if meta.can_edit %}
{% if meta.can_edit or not meta.url_contains_package %}
<button
type="button"
class="btn btn-primary btn-sm"

2
templates/collections/scenarios_paginated.html
View File

@ -11,7 +11,7 @@
{% endblock action_modals %}
{% block action_button %}
{% if meta.can_edit %}
{% if meta.can_edit or not meta.url_contains_package %}
<button
type="button"
class="btn btn-primary btn-sm"

2
templates/collections/structures_paginated.html
View File

@ -3,7 +3,7 @@
{% block page_title %}{{ page_title|default:"Structures" }}{% endblock %}
{% block action_button %}
{% if meta.can_edit %}
{% if meta.can_edit or not meta.url_contains_package %}
<button
type="button"
class="btn btn-primary btn-sm"