[Feature] Path prefixes (#369)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#369

.env.prod.example

@@ -3,10 +3,20 @@ EP_DATA_DIR=
 ALLOWED_HOSTS=
 DEBUG=
 LOG_LEVEL=
+MODEL_BUILDING_ENABLED=
+APPLICABILITY_DOMAIN_ENABLED=
 ENVIFORMER_PRESENT=
-FLAG_CELERY_PRESENT=
+ENVIFORMER_DEVICE=
-SERVER_URL=
 PLUGINS_ENABLED=
+SERVER_URL=
+SERVER_PATH=
+ADMIN_APPROVAL_REQUIRED=
+REGISTRATION_MANDATORY=
+LOG_DIR=
+# Celery
+FLAG_CELERY_PRESENT=
+CELERY_BROKER_URL=
+CELERY_RESULT_BACKEND=
 # DB
 POSTGRES_SERVICE_NAME=
 POSTGRES_DB=
@@ -16,5 +26,30 @@ POSTGRES_PORT=
 # MAIL
 EMAIL_HOST_USER=
 EMAIL_HOST_PASSWORD=
-# MATOMO
+DEFAULT_FROM_EMAIL=
-MATOMO_SITE_ID
+SERVER_EMAIL=
+# SENTRY
+SENTRY_ENABLED=
+SENTRY_DSN=
+SENTRY_ENVIRONMENT=
+# MS ENTRA
+MS_ENTRA_ENABLED=
+MS_CLIENT_ID=
+MS_CLIENT_SECRET=
+MS_TENANT_ID=
+MS_REDIRECT_URI=
+MS_SCOPES=
+# Tenant
+TENANT=
+EPDB_PACKAGE_MODEL=
+# Captcha
+CAP_ENABLED=
+CAP_API_BASE=
+CAP_SITE_KEY=
+CAP_SECRET_KEY=
+# QUARKUS (JAVA)
+ENVIRULE_ENABLED=
+FINGERPRINT_URL=
+# Biotransformer
+BIOTRANSFORMER_ENABLED=
+BIOTRANSFORMER_URL=

Dockerfile

@@ -71,6 +71,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     libxrender1 \
     libxext6 \
     libfontconfig1 \
+    nano \
     && rm -rf /var/lib/apt/lists/*
 
 RUN useradd -ms /bin/bash django

envipath/settings.py

@@ -191,11 +191,21 @@ ADMIN_APPROVAL_REQUIRED = os.environ.get("ADMIN_APPROVAL_REQUIRED", "False") ==
 # SESAME_MAX_AGE = 300
 # # TODO set to "home"
 # LOGIN_REDIRECT_URL = "/"
+
+
+SERVER_HOST = os.environ.get("SERVER_URL", "http://localhost:8000")
+SERVER_PATH = os.environ.get("SERVER_PATH", "")
+
+SERVER_URL = SERVER_HOST
+if SERVER_PATH:
+    SERVER_URL = os.path.join(SERVER_HOST, SERVER_PATH)
+
+
 LOGIN_URL = "/login/"
+if SERVER_PATH:
+    LOGIN_URL = f"/{SERVER_PATH}/login/"
 
-SERVER_URL = os.environ.get("SERVER_URL", "http://localhost:8000")
+CSRF_TRUSTED_ORIGINS = [SERVER_HOST]
-
-CSRF_TRUSTED_ORIGINS = [SERVER_URL]
 
 AMBIT_URL = "http://localhost:9001"
 DEFAULT_VALUES = {"description": "no description"}
@@ -229,6 +239,8 @@ PAGINATION_MAX_PER_PAGE_SIZE = int(
 STATIC_ROOT = STATIC_DIR
 
 STATIC_URL = "/static/"
+if SERVER_PATH:
+    STATIC_URL = f"/{SERVER_PATH}/static/"
 
 # Where the sources are stored...
 STATICFILES_DIRS = (BASE_DIR / "static",)
@@ -331,10 +343,11 @@ DEFAULT_MODEL_THRESHOLD = 0.25
 
 # Loading Plugins
 PLUGINS_ENABLED = os.environ.get("PLUGINS_ENABLED", "False") == "True"
-BASE_PLUGINS = [
+BASE_PLUGINS = os.environ.get("BASE_PLUGINS", None)
-    "pepper.PEPPER",
+if BASE_PLUGINS:
-    "biotransformer.Biotransformer",
+    BASE_PLUGINS = BASE_PLUGINS.split(",")
-]
+else:
+    BASE_PLUGINS = []
 
 CLASSIFIER_PLUGINS = {}
 PROPERTY_PLUGINS = {}
@@ -387,7 +400,6 @@ LOGIN_EXEMPT_URLS = [
     "/o/userinfo/",
     "/password_reset/",
     "/reset/",
-    "/microsoft/",
     "/terms",
     "/privacy",
     "/cookie-policy",
@@ -396,8 +408,13 @@ LOGIN_EXEMPT_URLS = [
     "/careers",
     "/cite",
     "/legal",
+    "/entra/",
+    "/auth/",
 ]
 
+if SERVER_PATH:
+    LOGIN_EXEMPT_URLS = [f"/{SERVER_PATH}{x}" for x in LOGIN_EXEMPT_URLS]
+
 # MS AD/Entra
 MS_ENTRA_ENABLED = os.environ.get("MS_ENTRA_ENABLED", "False") == "True"
 if MS_ENTRA_ENABLED:
@@ -424,5 +441,4 @@ CAP_SECRET_KEY = os.environ.get("CAP_SECRET_KEY", None)
 BIOTRANSFORMER_ENABLED = os.environ.get("BIOTRANSFORMER_ENABLED", "False") == "True"
 FLAGS["BIOTRANSFORMER"] = BIOTRANSFORMER_ENABLED
 if BIOTRANSFORMER_ENABLED:
-    INSTALLED_APPS.append("biotransformer")
     BIOTRANSFORMER_URL = os.environ.get("BIOTRANSFORMER_URL", None)

envipath/urls.py

@@ -21,19 +21,24 @@ from django.urls import include, path
 
 from .api import api_v1, api_legacy
 
+PATH_PREFIX = s.SERVER_PATH
+if PATH_PREFIX and not PATH_PREFIX.endswith("/"):
+    PATH_PREFIX += "/"
+
+
 urlpatterns = [
-    path("", include("epdb.urls")),
+    path(f"{PATH_PREFIX}", include("epdb.urls")),
-    path("admin/", admin.site.urls),
+    path(f"{PATH_PREFIX}admin/", admin.site.urls),
-    path("api/v1/", api_v1.urls),
+    path(f"{PATH_PREFIX}api/v1/", api_v1.urls),
-    path("api/legacy/", api_legacy.urls),
+    path(f"{PATH_PREFIX}api/legacy/", api_legacy.urls),
-    path("o/", include("oauth2_provider.urls", namespace="oauth2_provider")),
+    path(f"{PATH_PREFIX}o/", include("oauth2_provider.urls", namespace="oauth2_provider")),
 ]
 
 if "migration" in s.INSTALLED_APPS:
-    urlpatterns.append(path("", include("migration.urls")))
+    urlpatterns.append(path(f"{PATH_PREFIX}", include("migration.urls")))
 
 if s.MS_ENTRA_ENABLED:
-    urlpatterns.append(path("", include("epauth.urls")))
+    urlpatterns.append(path(f"{PATH_PREFIX}", include("epauth.urls")))
 
 # Custom error handlers
 handler400 = "epdb.views.handler400"

epauth/urls.py

@@ -3,6 +3,6 @@ from django.urls import path
 from . import views
 
 urlpatterns = [
-    path("microsoft/login/", views.microsoft_login, name="microsoft_login"),
+    path("entra/login/", views.entra_login, name="entra_login"),
-    path("microsoft/callback/", views.microsoft_callback, name="microsoft_callback"),
+    path("auth/redirect/", views.entra_callback, name="entra_callback"),
 ]

epauth/views.py

@@ -7,27 +7,26 @@ from django.contrib.auth import get_user_model
 from epdb.logic import UserManager
 
 
-def microsoft_login(request):
+def entra_login(request):
     msal_app = msal.ConfidentialClientApplication(
         client_id=s.MS_ENTRA_CLIENT_ID,
         client_credential=s.MS_ENTRA_CLIENT_SECRET,
-        authority=s.MS_ENTRA_AUTHORITY
+        authority=s.MS_ENTRA_AUTHORITY,
     )
 
     flow = msal_app.initiate_auth_code_flow(
-        scopes=s.MS_ENTRA_SCOPES,
+        scopes=s.MS_ENTRA_SCOPES, redirect_uri=s.MS_ENTRA_REDIRECT_URI
-        redirect_uri=s.MS_ENTRA_REDIRECT_URI
     )
 
     request.session["msal_auth_flow"] = flow
     return redirect(flow["auth_uri"])
 
 
-def microsoft_callback(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
+        authority=s.MS_ENTRA_AUTHORITY,
     )
 
     flow = request.session.pop("msal_auth_flow", None)
@@ -37,30 +36,25 @@ def microsoft_callback(request):
     # Acquire token using the flow and callback request
     result = msal_app.acquire_token_by_auth_code_flow(flow, request.GET)
 
-    if "access_token" in result:
+    claims = result["id_token_claims"]
-        # Optional: Fetch user info from Microsoft Graph
-        import requests
-        resp = requests.get(
-            "https://graph.microsoft.com/v1.0/me",
-            headers={"Authorization": f"Bearer {result['access_token']}"}
-        )
-        user_info = resp.json()
 
-        user_name = user_info["displayName"]
+    user_name = claims["name"]
-        user_email = user_info["mail"]
+    user_email = claims["emailaddress"]
-        user_oid = user_info["id"]
+    user_oid = claims["oid"]
 
     # Get implementing class
     User = get_user_model()
 
     if User.objects.filter(uuid=user_oid).exists():
-            login(request, User.objects.get(uuid=user_oid))
+        u = User.objects.get(uuid=user_oid)
+
+        if u.username != user_name:
+            u.username = user_name
+            u.save()
+
     else:
         u = UserManager.create_user(user_name, user_email, None, uuid=user_oid, is_active=True)
+
     login(request, u)
 
-        # TODO Group Sync
-
-        return redirect("/")
-
     return redirect("/")  # Handle errors

epdb/views.py

@@ -556,7 +556,7 @@ def packages(request):
 
         # Context for paginated template
         context["entity_type"] = "package"
-        context["api_endpoint"] = "/api/v1/packages/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/packages/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "packages"
 
@@ -614,7 +614,7 @@ def compounds(request):
 
         # Context for paginated template
         context["entity_type"] = "compound"
-        context["api_endpoint"] = "/api/v1/compounds/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/compounds/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_mode"] = "tabbed"
         context["list_title"] = "compounds"
@@ -643,7 +643,7 @@ def rules(request):
 
         # Context for paginated template
         context["entity_type"] = "rule"
-        context["api_endpoint"] = "/api/v1/rules/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/rules/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "rules"
 
@@ -671,7 +671,7 @@ def reactions(request):
 
         # Context for paginated template
         context["entity_type"] = "reaction"
-        context["api_endpoint"] = "/api/v1/reactions/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/reactions/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "reactions"
 
@@ -699,7 +699,7 @@ def pathways(request):
 
         # Context for paginated template
         context["entity_type"] = "pathway"
-        context["api_endpoint"] = "/api/v1/pathways/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/pathways/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "pathways"
 
@@ -729,7 +729,7 @@ def scenarios(request):
 
         # Context for paginated template
         context["entity_type"] = "scenario"
-        context["api_endpoint"] = "/api/v1/scenarios/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/scenarios/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "scenarios"
 
@@ -789,7 +789,7 @@ def models(request):
 
         # Context for paginated template
         context["entity_type"] = "model"
-        context["api_endpoint"] = "/api/v1/models/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/models/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "models"
 
@@ -871,7 +871,7 @@ def package_models(request, package_uuid):
         context["object_type"] = "model"
         context["breadcrumbs"] = breadcrumbs(current_package, "model")
         context["entity_type"] = "model"
-        context["api_endpoint"] = f"/api/v1/package/{current_package.uuid}/model/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/package/{current_package.uuid}/model/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "models"
 
@@ -1341,7 +1341,7 @@ def package_compounds(request, package_uuid):
         context["object_type"] = "compound"
         context["breadcrumbs"] = breadcrumbs(current_package, "compound")
         context["entity_type"] = "compound"
-        context["api_endpoint"] = f"/api/v1/package/{current_package.uuid}/compound/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/package/{current_package.uuid}/compound/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_mode"] = "tabbed"
         context["list_title"] = "compounds"
@@ -1494,7 +1494,7 @@ def package_compound_structures(request, package_uuid, compound_uuid):
         context["entity_type"] = "structure"
         context["page_title"] = f"{current_compound.get_name()} - Structures"
         context["api_endpoint"] = (
-            f"/api/v1/package/{current_package.uuid}/compound/{current_compound.uuid}/structure/"
+            f"{s.SERVER_PATH}/api/v1/package/{current_package.uuid}/compound/{current_compound.uuid}/structure/"
         )
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["compound"] = current_compound
@@ -1657,7 +1657,7 @@ def package_rules(request, package_uuid):
         context["object_type"] = "rule"
         context["breadcrumbs"] = breadcrumbs(current_package, "rule")
         context["entity_type"] = "rule"
-        context["api_endpoint"] = f"/api/v1/package/{current_package.uuid}/rule/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/package/{current_package.uuid}/rule/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "rules"
 
@@ -1865,7 +1865,7 @@ def package_reactions(request, package_uuid):
         context["object_type"] = "reaction"
         context["breadcrumbs"] = breadcrumbs(current_package, "reaction")
         context["entity_type"] = "reaction"
-        context["api_endpoint"] = f"/api/v1/package/{current_package.uuid}/reaction/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/package/{current_package.uuid}/reaction/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "reactions"
 
@@ -2015,7 +2015,7 @@ def package_pathways(request, package_uuid):
         context["object_type"] = "pathway"
         context["breadcrumbs"] = breadcrumbs(current_package, "pathway")
         context["entity_type"] = "pathway"
-        context["api_endpoint"] = f"/api/v1/package/{current_package.uuid}/pathway/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/package/{current_package.uuid}/pathway/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "pathways"
 
@@ -2591,7 +2591,7 @@ def package_scenarios(request, package_uuid):
         context["object_type"] = "scenario"
         context["breadcrumbs"] = breadcrumbs(current_package, "scenario")
         context["entity_type"] = "scenario"
-        context["api_endpoint"] = f"/api/v1/package/{current_package.uuid}/scenario/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/package/{current_package.uuid}/scenario/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "scenarios"
 
@@ -2940,7 +2940,7 @@ def settings(request):
 
         # Context for paginated template
         context["entity_type"] = "setting"
-        context["api_endpoint"] = "/api/v1/settings/"
+        context["api_endpoint"] = f"{s.SERVER_PATH}/api/v1/settings/"
         context["per_page"] = s.API_PAGINATION_DEFAULT_PAGE_SIZE
         context["list_title"] = "settings"
         context["list_mode"] = "combined"