From aef6a57ff92861aaf18931aac0e55fccfad705a8 Mon Sep 17 00:00:00 2001 From: amandazhu Date: Fri, 19 Jun 2026 12:59:59 +1000 Subject: [PATCH 01/25] docs: add AAF dev-aaf deployment steps to README --- README.md | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/README.md b/README.md index bb24a4cd..f931c152 100644 --- a/README.md +++ b/README.md @@ -205,3 +205,39 @@ When the database models are changed, the database schema diagram in [`db_diagra ## Documents to be updated Please update the following documents if there are changes to the database schema: - [AAI User Database Technical Design Document](https://docs.google.com/document/d/1xECcTqXH9ykXBCEESBSg43SOMncXT6Zayi5FwqvCT4Y/edit?tab=t.0#heading=h.sj9060dgy5fu) + +## AAF integration — `dev-aaf` deployment + +The `aaf-dev` branch runs against the **`biocloud-dev-aaf`** Auth0 tenant +(`dev-aaf` environment), isolated from `dev-bc`. Deploys are **manual** for now. + +Run locally against the tenant: + +```bash +uv venv && uv sync --extra dev +# .env pointed at the new tenant: +# AUTH0_DOMAIN=biocloud-dev-aaf.au.auth0.com +# AUTH0_ISSUER=https://biocloud-dev-aaf.au.auth0.com/ +# AUTH0_AUDIENCE=https://dev-aaf.api.aai.test.biocommons.org.au +# AUTH0_MANAGEMENT_ID / AUTH0_MANAGEMENT_SECRET= +# AUTH0_DB_CONNECTION=Username-Password-Authentication +uv run uvicorn main:app --reload --port 8000 +``` + +Deploy to the hosted dev-aaf backend (build image → trigger deploy Lambda): + +```bash +aws sso login --profile aai +export AWS_PROFILE=aai AWS_REGION=ap-southeast-2 ACCOUNT=498096047392 +ECR=$ACCOUNT.dkr.ecr.$AWS_REGION.amazonaws.com/aai-backend +aws ecr get-login-password --region $AWS_REGION \ + | docker login --username AWS --password-stdin $ACCOUNT.dkr.ecr.$AWS_REGION.amazonaws.com +docker build --platform linux/amd64 -t $ECR:dev-aaf . +docker push $ECR:dev-aaf +aws lambda invoke --function-name AaiBackendDevAafDeploymentFunction \ + --payload "$(jq -n '{tag:"dev-aaf"}')" --cli-binary-format raw-in-base64-out /dev/stdout +``` + +The dev-aaf ECS service + deploy Lambda are created by the CDK `env=dev-aaf` +stacks in `aai-infrastructure`. Confirm the Lambda name via `aws lambda +list-functions` if it differs. From b35ad642fbb8d20e1f425aced657b68d5c9e6aa9 Mon Sep 17 00:00:00 2001 From: amandazhu Date: Fri, 19 Jun 2026 19:52:03 +1000 Subject: [PATCH 02/25] feat(config): recognise dev-aaf environment (maps to dev-aaf portal URL) --- config.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/config.py b/config.py index 5bfbca87..e85f8579 100644 --- a/config.py +++ b/config.py @@ -6,7 +6,7 @@ class Settings(BaseSettings): - environment: Literal["dev", "staging", "production"] = "dev" + environment: Literal["dev", "staging", "production", "dev-aaf"] = "dev" auth0_domain: str auth0_custom_domain: Optional[str] = None auth0_management_id: str @@ -35,7 +35,7 @@ class Settings(BaseSettings): @field_validator("environment", mode="before") @classmethod - def normalize_environment(cls, value: str | None) -> Literal["dev", "staging", "production"]: + def normalize_environment(cls, value: str | None) -> Literal["dev", "staging", "production", "dev-aaf"]: normalized = str(value).strip().lower() if normalized in {"dev", "development"}: return "dev" @@ -65,6 +65,7 @@ def set_default_aai_portal_url(self) -> "Settings": return self env_to_url = { "dev": "https://dev.portal.aai.test.biocommons.org.au", + "dev-aaf": "https://dev-aaf.portal.aai.test.biocommons.org.au", "staging": "https://staging.portal.aai.test.biocommons.org.au", "production": "https://portal.access.services.biocommons.org.au", } From c334709f531c1db3985bf6236af4fed8127189a2 Mon Sep 17 00:00:00 2001 From: amandazhu Date: Sat, 20 Jun 2026 17:24:48 +1000 Subject: [PATCH 03/25] docs: correct dev-aaf backend deploy (stock dev image, ENVIRONMENT=dev, OIDC-only ECR) --- README.md | 37 ++++++++++++++++++++----------------- 1 file changed, 20 insertions(+), 17 deletions(-) diff --git a/README.md b/README.md index f931c152..d29e2f53 100644 --- a/README.md +++ b/README.md @@ -224,20 +224,23 @@ uv venv && uv sync --extra dev uv run uvicorn main:app --reload --port 8000 ``` -Deploy to the hosted dev-aaf backend (build image → trigger deploy Lambda): - -```bash -aws sso login --profile aai -export AWS_PROFILE=aai AWS_REGION=ap-southeast-2 ACCOUNT=498096047392 -ECR=$ACCOUNT.dkr.ecr.$AWS_REGION.amazonaws.com/aai-backend -aws ecr get-login-password --region $AWS_REGION \ - | docker login --username AWS --password-stdin $ACCOUNT.dkr.ecr.$AWS_REGION.amazonaws.com -docker build --platform linux/amd64 -t $ECR:dev-aaf . -docker push $ECR:dev-aaf -aws lambda invoke --function-name AaiBackendDevAafDeploymentFunction \ - --payload "$(jq -n '{tag:"dev-aaf"}')" --cli-binary-format raw-in-base64-out /dev/stdout -``` - -The dev-aaf ECS service + deploy Lambda are created by the CDK `env=dev-aaf` -stacks in `aai-infrastructure`. Confirm the Lambda name via `aws lambda -list-functions` if it differs. +Hosted dev-aaf backend (deployed via CDK from `aai-infrastructure`): + +The dev-aaf ECS service currently runs the **stock `aai-backend:dev` image** with +`ENVIRONMENT=dev`. The published `:dev` image doesn't accept `dev-aaf` as an +environment, so the CDK passes `ENVIRONMENT=dev`; auth still targets the dev-aaf +tenant via the `dev-aaf/backend/secrets` values. The service is created by +`cdk deploy -c env=dev-aaf AaiBackendDevAaf` in `aai-infrastructure` — no image +build needed to stand it up. + +To ship **backend AAF code changes**, you need a `dev-aaf`-aware image in the +**shared ECR (account `331315009666`)**. A manual `docker push` is **not** possible +— that repo's push role is GitHub-OIDC-only (no human/SSO principal can assume it). +So build it through CI on the `aaf-dev` branch (this branch's `config.py` already +adds `dev-aaf` to the accepted environments). Once the `:dev-aaf` image exists, set +`backend.image_tag: 'dev-aaf'` and drop `backend.app_environment` in +`config/environments/dev-aaf.yaml`, then redeploy `AaiBackendDevAaf`. + +> Side effect of `ENVIRONMENT=dev`: admin email links default to `dev.portal…`. +> Set `AAI_PORTAL_URL=https://dev-aaf.portal.aai.test.biocommons.org.au` in the +> backend secret if that matters. From 978a64030c68caceee906df31b324a910274c838 Mon Sep 17 00:00:00 2001 From: amandazhu Date: Fri, 31 Jul 2026 12:19:00 +1000 Subject: [PATCH 04/25] feat(auth0): read AAF core attribute claims in UserInfo --- auth0/user_info.py | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/auth0/user_info.py b/auth0/user_info.py index d8514aae..915a4465 100644 --- a/auth0/user_info.py +++ b/auth0/user_info.py @@ -18,6 +18,24 @@ class UserInfo(BaseModel): family_name: str | None = None show_welcome_message: bool | None = Field(None, alias="https://biocommons.org.au/show_migration_welcome") + # AAF core attributes — namespaced claims added by the Auth0 post-login Action + # (only present for AAF logins where AAF released the attribute). Multi-valued + # eduPerson attributes may arrive as a list. + aaf_scoped_affiliation: str | list[str] | None = Field( + None, alias="https://biocommons.org.au/aaf/eduperson_scoped_affiliation") + aaf_affiliation: str | list[str] | None = Field( + None, alias="https://biocommons.org.au/aaf/eduperson_affiliation") + aaf_assurance: str | list[str] | None = Field( + None, alias="https://biocommons.org.au/aaf/eduperson_assurance") + aaf_entitlement: str | list[str] | None = Field( + None, alias="https://biocommons.org.au/aaf/eduperson_entitlement") + aaf_principal_name: str | None = Field( + None, alias="https://biocommons.org.au/aaf/eduperson_principal_name") + aaf_home_organization: str | None = Field( + None, alias="https://biocommons.org.au/aaf/schac_home_organization") + aaf_home_organization_type: str | list[str] | None = Field( + None, alias="https://biocommons.org.au/aaf/schac_home_organization_type") + model_config = ConfigDict(validate_by_name=True, validate_by_alias=True) From 59ec0f2eccb33b44fb58b687e637562570568fd9 Mon Sep 17 00:00:00 2001 From: marius-mather <61438033+marius-mather@users.noreply.github.com> Date: Wed, 12 Aug 2026 15:47:37 +1000 Subject: [PATCH 05/25] feat: represent AAF users in aai-backend database (AAI-871) (#293) * feat: add account_type field to BiocommonsUser * chore: add migration for account type * test: unit test enum handling for account_type * refactor: make app_metadata mandatory, but allow for Auth0 responses not including it * refactor: set account type when creating user from Auth0 data * fix: make migration compatible with sqlite * test: update tests with account_type * fix: set account type automatically when syncing exported users * test: factory functions for new schemas * test: update tests to reflect changed schemas * fix: add path_separator to alembic config to address deprecation warning * fix: add httpx2 for starlette test client * fix: bump starlette-admin to fix deprecation warning * fix: make sure account type enum is created in migration * feat: add account permissions for checking if user can change email/password etc * chore: apply account permission checks to password/username/email change endpoints * test: add unit test of endpoint permissions for AAF accounts * feat: add account type to export * test: update tests of export * feat: allow exporting users for specific connections * chore: allow testing workflows to run on all PRs, not just to main * feat: Auth0 client methods to get connections * fix: only sync DB connection users for now * chore: add pytest-sugar for better test output * test: factories for Auth0 connection data * test: tests of connection methods * fix: disable username change for AAF for now, needs more thought * test: update test of AAF change username --- .github/workflows/check-migrations.yml | 2 - .github/workflows/python-tests.yml | 2 - alembic.ini | 1 + auth/account_permissions.py | 66 ++++++++++++++ auth0/client.py | 66 ++++++++++++-- db/models.py | 19 ++++- .../0c91366532ae_user_account_type.py | 47 ++++++++++ pyproject.toml | 4 +- routers/user.py | 14 ++- scheduled_tasks/tasks.py | 44 ++++++++-- schemas/biocommons.py | 46 +++++++++- tests/auth/test_account_permissions.py | 85 +++++++++++++++++++ tests/datagen.py | 16 ++++ tests/db/datagen.py | 5 ++ tests/db/test_models.py | 20 ++++- tests/db/test_utils.py | 18 ++-- tests/migrations/test_migrations.py | 60 +++++++++++++ tests/scheduled_tasks/test_tasks.py | 52 +++++++++++- tests/test_auth0_client.py | 63 ++++++++++++++ tests/test_config.py | 4 +- tests/test_user.py | 50 ++++++++++- tests/test_utils.py | 9 +- uv.lock | 79 +++++++++++++++-- 23 files changed, 709 insertions(+), 63 deletions(-) create mode 100644 auth/account_permissions.py create mode 100644 migrations/versions/0c91366532ae_user_account_type.py create mode 100644 tests/auth/test_account_permissions.py diff --git a/.github/workflows/check-migrations.yml b/.github/workflows/check-migrations.yml index b55ab5e7..f2f7ad3a 100644 --- a/.github/workflows/check-migrations.yml +++ b/.github/workflows/check-migrations.yml @@ -4,8 +4,6 @@ on: branches: - main pull_request: - branches: - - main jobs: diff --git a/.github/workflows/python-tests.yml b/.github/workflows/python-tests.yml index 7be89803..030f1c02 100644 --- a/.github/workflows/python-tests.yml +++ b/.github/workflows/python-tests.yml @@ -5,8 +5,6 @@ on: branches: - main pull_request: - branches: - - main jobs: test: diff --git a/alembic.ini b/alembic.ini index 5887001c..4704dd90 100644 --- a/alembic.ini +++ b/alembic.ini @@ -12,6 +12,7 @@ script_location = migrations # sys.path path, will be prepended to sys.path if present. # defaults to the current working directory. +path_separator = os prepend_sys_path = . # timezone to use when rendering the date within the migration file diff --git a/auth/account_permissions.py b/auth/account_permissions.py new file mode 100644 index 00000000..49bae209 --- /dev/null +++ b/auth/account_permissions.py @@ -0,0 +1,66 @@ +from enum import StrEnum +from logging import getLogger +from typing import Annotated + +from fastapi import HTTPException +from fastapi.params import Depends +from starlette import status + +from auth.user_permissions import get_db_user +from db.models import BiocommonsUser + +logger = getLogger("uvicorn.error") + + +class AccountActions(StrEnum): + CHANGE_EMAIL = 'change_email' + CHANGE_PASSWORD = 'change_password' + CHANGE_USERNAME = 'change_username' + CHANGE_NAME = 'change_name' + + +def account_action_allowed(action: AccountActions, user: BiocommonsUser) -> bool: + """ + Check if a user can perform an action, based on account type. + """ + # All actions currently allowed for Auth0 users + if user.account_type == "auth0": + return True + elif user.account_type == "aaf": + match action: + case AccountActions.CHANGE_EMAIL: + return False + case AccountActions.CHANGE_USERNAME: + # TODO: username change code currently assumes the + # Auth0 DB connection, so disable for AAF for now + return False + case AccountActions.CHANGE_PASSWORD: + return False + case AccountActions.CHANGE_NAME: + # TODO: Assuming we allow users to set their name and don't + # auto-update from AAF + return True + logger.warning(f"Unexpected account type ({user.account_type})/action ({action}. Disallowing by default.") + return False + + +def require_account_permission(action: AccountActions) -> Depends: + """ + FastAPI dependency that checks if the user can perform an action, based on account type. + """ + def require_account_action( + user: Annotated[BiocommonsUser | None, Depends(get_db_user)], + ) -> BiocommonsUser: + if user is None: + raise HTTPException( + status_code=status.HTTP_404_NOT_FOUND, + detail="User account not found.", + ) + if not account_action_allowed(action, user): + raise HTTPException( + status_code=status.HTTP_403_FORBIDDEN, + detail="You do not have permission to perform this action.", + ) + return user + + return Depends(require_account_action) diff --git a/auth0/client.py b/auth0/client.py index 8bb10af1..b879b6d7 100644 --- a/auth0/client.py +++ b/auth0/client.py @@ -7,13 +7,13 @@ import httpx from fastapi import Depends from httpx import HTTPStatusError -from pydantic import BaseModel, EmailStr, HttpUrl, model_validator +from pydantic import BaseModel, EmailStr, Field, HttpUrl, model_validator from auth.management import get_management_token from config import Settings, get_settings from schemas.biocommons import ( Auth0UserData, - BiocommonsAppMetadata, + BiocommonsAppMetadataUpdate, BiocommonsPassword, BiocommonsRegisterData, ) @@ -21,6 +21,27 @@ logger = logging.getLogger("uvicorn.error") +class Auth0Connection(BaseModel): + name: str + display_name: str | None = None + options: dict = Field(default_factory=dict) + id: str + strategy: str + realms: list[str] + is_domain_connection: bool + show_as_button: bool | None = None + metadata: dict[str, str] | None = None + authentication: dict[str, bool] + connected_accounts: dict[str, bool] + cross_app_access_requesting_app: dict[str, bool] | None = None + cross_app_access_resource_app: dict[str, str] | None = None + + +class ConnectionsWithCheckpoint(BaseModel): + connections: list[Auth0Connection] + next: str | None = None + + class RoleData(BaseModel): """ Data returned by Auth0 API for a role. @@ -114,7 +135,7 @@ class UpdateUserData(BaseModel): """ _connection_required_fields = ["email", "email_verified", "password", "username"] # NOTE: app_metadata will be merged instead of replaced when updating - app_metadata: Optional[BiocommonsAppMetadata] = None + app_metadata: Optional[BiocommonsAppMetadataUpdate] = None blocked: Optional[bool] = None email: Optional[EmailStr] = None email_verified: Optional[bool] = None @@ -231,7 +252,12 @@ def update_user(self, user_id: str, update_data: UpdateUserData) -> Auth0UserDat raise ValueError(f"Failed to update user {user_id}: {exc.response.json()}") from exc return Auth0UserData(**resp.json()) - def start_user_export(self, format: str = "csv", fields: Optional[list[dict]] = None, ) -> str: + def start_user_export( + self, + format: str = "csv", + fields: Optional[list[dict]] = None, + connection_id: str | None = None, + ) -> str: """ Start a user export job, return the job ID. """ @@ -242,7 +268,10 @@ def start_user_export(self, format: str = "csv", fields: Optional[list[dict]] = {"name": "email"}, {"name": "username"} ] - resp = self._client.post(url, json={"format": format, "fields": fields}) + payload = {"format": format, "fields": fields} + if connection_id is not None: + payload["connection_id"] = connection_id + resp = self._client.post(url, json=payload) resp.raise_for_status() return resp.json()["id"] @@ -252,13 +281,19 @@ def get_job_status(self, job_id: str) -> JobStatus: resp.raise_for_status() return JobStatus(**resp.json()) - def export_and_download_users(self, download_path: pathlib.Path, fields: Optional[list[dict]] = None, timeout: int = 300): + def export_and_download_users( + self, + download_path: pathlib.Path, + fields: Optional[list[dict]] = None, + timeout: int = 300, + connection_id: str | None = None, + ): """ Export Auth0 users to a CSV file and download it. NOTE: the Auth0 export has some quirks, e.g. string fields are preceded by '. """ - job_id = self.start_user_export(fields=fields) + job_id = self.start_user_export(fields=fields, connection_id=connection_id) location = None start_time = time.time() @@ -387,6 +422,23 @@ def _search_users(self, query: str, page: Optional[int] = None, per_page: Option ) return self._convert_users(resp) + def get_connections(self) -> list[Auth0Connection]: + url = f"https://{self.domain}/api/v2/connections" + resp = self._client.get(url, params={"take": 10}) + resp.raise_for_status() + converted = ConnectionsWithCheckpoint(**resp.json()) + if converted.next is not None: + logger.warning("More connections than expected - not all will be returned") + return converted.connections + + def get_connection_by_name(self, name: str) -> Auth0Connection | None: + connections = self.get_connections() + result = None + for connection in connections: + if connection.name == name: + result = connection + return result + def get_roles(self, name_filter: Optional[str] = None, include_totals: Optional[bool] = None, diff --git a/db/models.py b/db/models.py index a94b54c8..64203d7f 100644 --- a/db/models.py +++ b/db/models.py @@ -1,7 +1,8 @@ import uuid from datetime import datetime, timezone +from enum import StrEnum from logging import getLogger -from typing import Optional, Self +from typing import Optional, Self, Type from httpx import HTTPStatusError from pydantic import AwareDatetime @@ -21,12 +22,17 @@ PlatformMembershipData, ) from schemas.auth0 import get_platform_id_from_role_name +from schemas.biocommons import BiocommonsUserAccountType from schemas.tokens import AccessTokenPayload from schemas.user import SessionUser logger = getLogger(__name__) +def get_enum_values(enum: Type[StrEnum]) -> list[str]: + return [e.value for e in enum] + + class BiocommonsUser(SoftDeleteModel, table=True): __tablename__ = "biocommons_user" __table_args__ = ( @@ -34,6 +40,14 @@ class BiocommonsUser(SoftDeleteModel, table=True): ) # Auth0 ID id: str = Field(primary_key=True) + account_type: BiocommonsUserAccountType = Field( + sa_type=DbEnum( + BiocommonsUserAccountType, + name="biocommons_user_account_type", + values_callable=get_enum_values, + validate_strings=True + ) + ) # Note: sqlmodel can't validate emails easily. # Use a separate data model to validate this email: str = Field(unique=True) @@ -161,7 +175,8 @@ def from_auth0_data(cls, data: 'schemas.biocommons.Auth0UserData') -> Self: """ Create a new BiocommonsUser object from Auth0 user data (no API call). """ - return cls(id=data.user_id, email=data.email, username=data.username, email_verified=data.email_verified) + return cls(id=data.user_id, email=data.email, username=data.username, email_verified=data.email_verified, + account_type=data.app_metadata.account_type) @classmethod def get_or_create( diff --git a/migrations/versions/0c91366532ae_user_account_type.py b/migrations/versions/0c91366532ae_user_account_type.py new file mode 100644 index 00000000..f507f152 --- /dev/null +++ b/migrations/versions/0c91366532ae_user_account_type.py @@ -0,0 +1,47 @@ +"""user_account_type + +Revision ID: 0c91366532ae +Revises: 39caad32922e +Create Date: 2026-08-06 14:12:14.614001 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa +import sqlmodel + + +# revision identifiers, used by Alembic. +revision: str = '0c91366532ae' +down_revision: Union[str, None] = '39caad32922e' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + account_type_enum = sa.Enum('auth0', 'aaf', name='biocommons_user_account_type') + account_type_enum.create(op.get_bind(), checkfirst=True) + op.add_column( + 'biocommons_user', + sa.Column( + 'account_type', + account_type_enum, + nullable=True, + server_default='auth0', + ), + ) + op.execute("UPDATE biocommons_user SET account_type = 'auth0' WHERE account_type IS NULL") + with op.batch_alter_table('biocommons_user') as batch_op: + batch_op.alter_column( + 'account_type', + existing_type=account_type_enum, + nullable=False, + server_default=None, + ) + + +def downgrade() -> None: + account_type_enum = sa.Enum('auth0', 'aaf', name='biocommons_user_account_type') + op.drop_column('biocommons_user', 'account_type') + account_type_enum.drop(op.get_bind(), checkfirst=True) diff --git a/pyproject.toml b/pyproject.toml index 1ca1454e..18c82b2f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -23,7 +23,7 @@ dependencies = [ "loguru>=0.7.3", "cachetools~=7.1", "typer>=0.26.8", - "starlette-admin>=0.16.1", + "starlette-admin>=0.17.1", # Security floor for CVE-2026-27199 (safe_join Windows device names) "werkzeug>=3.1.8", ] @@ -31,8 +31,10 @@ dependencies = [ [project.optional-dependencies] dev = [ "boto3-stubs>=1.43.45", + "httpx2>=2.9.1", "pytest>=9.0.3", "pytest-mock>=3.14.0", + "pytest-sugar>=1.1.1", "pytest-asyncio~=1.2", "pytest-cov>=4.1.0", "ruff>=0.4.4", diff --git a/routers/user.py b/routers/user.py index 04851fc3..50f5f3c8 100644 --- a/routers/user.py +++ b/routers/user.py @@ -17,6 +17,7 @@ from sqlmodel import Session, select from starlette.responses import RedirectResponse +from auth.account_permissions import AccountActions, require_account_permission from auth.management import get_management_token from auth.ses import EmailService, get_email_service from auth.user_permissions import get_db_user, get_session_user, user_is_general_admin @@ -49,7 +50,7 @@ from register.tokens import validate_recaptcha from schemas.biocommons import ( Auth0UserData, - BiocommonsAppMetadata, + BiocommonsAppMetadataUpdate, BiocommonsEmail, BiocommonsFirstName, BiocommonsLastName, @@ -574,6 +575,7 @@ async def get_all_pending( 200: {"model": Auth0UserData}, 400: {"model": FieldErrorResponse}, }, + dependencies=[require_account_permission(AccountActions.CHANGE_USERNAME)], ) async def update_username( username: Annotated[BiocommonsUsername, Body(embed=True)], @@ -654,7 +656,8 @@ class NameUpdateRequest(BaseModel): @router.post("/profile/name/update", - response_model=Auth0UserData) + response_model=Auth0UserData, + dependencies=[require_account_permission(AccountActions.CHANGE_NAME)]) async def update_name( payload: Annotated[NameUpdateRequest, Body()], user: Annotated[SessionUser, Depends(get_session_user)], @@ -695,6 +698,7 @@ async def update_name( 200: {"model": dict}, 400: {"model": FieldErrorResponse}, }, + dependencies=[require_account_permission(AccountActions.CHANGE_EMAIL)] ) async def update_email( payload: Annotated[EmailChangeRequest, Body()], @@ -764,7 +768,8 @@ async def update_email( @router.post("/profile/email/continue", - response_model=Auth0UserData) + response_model=Auth0UserData, + dependencies=[require_account_permission(AccountActions.CHANGE_EMAIL)]) async def continue_email_update( payload: Annotated[EmailChangeContinueRequest, Body()], user: Annotated[SessionUser, Depends(get_session_user)], @@ -910,6 +915,7 @@ async def _revoke_sbp_if_non_institutional( 200: {"model": dict}, 400: {"model": FieldErrorResponse}, }, + dependencies=[require_account_permission(AccountActions.CHANGE_PASSWORD)] ) async def change_password( payload: PasswordChangeRequest, @@ -1058,7 +1064,7 @@ def finish_migrate_password(state: str, raise HTTPException(status_code=400, detail=f"Invalid session token: {e}") # NOTE: due to the way the update user endpoint works (app_metadata is merged, not replaced), # this should not overwrite existing app_metadata - updated_metadata = BiocommonsAppMetadata(user_needs_migration=False) + updated_metadata = BiocommonsAppMetadataUpdate(user_needs_migration=False) logger.info(f"Updating app_metadata for user: {user_id}") auth0_client.update_user(user_id=user_id, update_data=UpdateUserData(app_metadata=updated_metadata)) diff --git a/scheduled_tasks/tasks.py b/scheduled_tasks/tasks.py index 1a271ee9..fd868861 100644 --- a/scheduled_tasks/tasks.py +++ b/scheduled_tasks/tasks.py @@ -54,7 +54,7 @@ PLATFORM_ROLE_PATTERN, get_platform_id_from_role_name, ) -from schemas.biocommons import Auth0UserData +from schemas.biocommons import Auth0UserData, BiocommonsUserAccountType def chunked[T](items: list[T], size: int) -> list[list[T]]: @@ -71,6 +71,7 @@ class ExportedUser(BaseModel): username: str | None blocked: bool updated_at: datetime + account_type: BiocommonsUserAccountType = BiocommonsUserAccountType.AUTH0 @field_validator("email_verified", "blocked", mode="before") @classmethod @@ -123,6 +124,23 @@ def _find_conflicting_user_by_email( ) +def _create_biocommons_user_from_sync_data( + user_data: Auth0UserData | ExportedUser, +) -> BiocommonsUser: + account_type = ( + user_data.app_metadata.account_type + if isinstance(user_data, Auth0UserData) + else user_data.account_type + ) + return BiocommonsUser( + id=user_data.user_id, + email=user_data.email, + username=user_data.username, + email_verified=user_data.email_verified, + account_type=account_type, + ) + + def _ensure_user_from_auth0( session: Session, user_data: Auth0UserData | ExportedUser @@ -181,7 +199,7 @@ def _ensure_user_from_auth0( ) else: created = True - user = BiocommonsUser.from_auth0_data(user_data) + user = _create_biocommons_user_from_sync_data(user_data) session.add(user) # Save history entry if updating from Auth0 sync @@ -374,11 +392,15 @@ def parse_auth0_export(path: Path) -> list[ExportedUser]: username=row["username"].lstrip("'") or None, blocked=row["blocked"], updated_at=row["updated_at"], + account_type=row.get("account_type", "").lstrip("'") or BiocommonsUserAccountType.AUTH0, )) return parsed -async def export_auth0_users(auth0_client: Auth0Client) -> list[ExportedUser]: +async def export_auth0_users( + auth0_client: Auth0Client, + connection_id: str | None = None, +) -> list[ExportedUser]: """ Export all users to CSV and return a list """ @@ -388,14 +410,19 @@ async def export_auth0_users(auth0_client: Auth0Client) -> list[ExportedUser]: {"name": "email_verified"}, {"name": "username"}, {"name": "blocked"}, - {"name": "updated_at"} + {"name": "updated_at"}, + {"name": "app_metadata.account_type", "export_as": "account_type"}, ] with tempfile.TemporaryDirectory() as temp_dir: temp_path = Path(temp_dir) / "auth0_users.csv" logger.info(f"Exporting Auth0 users to {temp_path}") try: - auth0_client.export_and_download_users(download_path=temp_path, fields=fields) + auth0_client.export_and_download_users( + download_path=temp_path, + fields=fields, + connection_id=connection_id, + ) except HTTPStatusError as exc: logger.error(f"Failed to export Auth0 users: {exc}") logger.error(f"Response: {exc.response.content}") @@ -426,7 +453,10 @@ async def sync_auth0_users(): settings = get_settings() token = get_management_token(settings=settings) with Auth0Client(domain=settings.auth0_domain, management_token=token) as auth0_client: - users = await export_auth0_users(auth0_client) + db_connection = auth0_client.get_connection_by_name(settings.auth0_db_connection) + if db_connection is None: + raise ValueError(f"Could not find Auth0 connection: {settings.auth0_db_connection}") + users = await export_auth0_users(auth0_client, connection_id=db_connection.id) db_session = next(get_db_session()) auth0_user_ids: set[str] = set() try: @@ -519,7 +549,7 @@ def _create_user_in_db(user_data: ExportedUser, session: Session): email_conflict = BiocommonsUser.get_by_email(user_data.email, session, include_deleted=True) if email_conflict is not None: raise UserSyncConflictError(f"Email {user_data.email} is already in use") - db_user = BiocommonsUser.from_auth0_data(user_data) + db_user = _create_biocommons_user_from_sync_data(user_data) session.add(db_user) return db_user diff --git a/schemas/biocommons.py b/schemas/biocommons.py index 0856af36..52009045 100644 --- a/schemas/biocommons.py +++ b/schemas/biocommons.py @@ -8,6 +8,7 @@ import re from datetime import datetime +from enum import StrEnum from typing import TYPE_CHECKING, Annotated, List, Literal, Optional, Self from email_validator import EmailNotValidError, validate_email @@ -18,6 +19,7 @@ EmailStr, Field, HttpUrl, + field_validator, ) from pydantic_core import PydanticCustomError @@ -160,6 +162,11 @@ class SBPMetadata(BaseModel): registration_reason: str +class BiocommonsUserAccountType(StrEnum): + AUTH0 = "auth0" + AAF = "aaf" + + class BiocommonsUserMetadata(BaseModel): """ User metadata we use for user-changeable data @@ -184,6 +191,32 @@ class BiocommonsAppMetadata(BaseModel): registration_from: Optional[AppId] = None old_emails: Optional[list[OldEmailRecord]] = None user_needs_migration: Optional[bool] = None + account_type: BiocommonsUserAccountType + + model_config = { + "extra": "ignore" + } + + +class Auth0ReadAppMetadata(BiocommonsAppMetadata): + """ + Schema for data we get from Auth0 - older data might not + contain account_type so make this less strict than the core schema + """ + account_type: BiocommonsUserAccountType = BiocommonsUserAccountType.AUTH0 + + +class BiocommonsAppMetadataUpdate(BaseModel): + """ + Partial app_metadata patch sent to Auth0. + + Auth0 merges app_metadata fields when updating, so updates should not + need to repeat fields that are not changing. + """ + registration_from: Optional[AppId] = None + old_emails: Optional[list[OldEmailRecord]] = None + user_needs_migration: Optional[bool] = None + account_type: Optional[BiocommonsUserAccountType] = None model_config = { "extra": "ignore" @@ -229,6 +262,9 @@ def from_biocommons_registration( connection="Username-Password-Authentication", app_metadata=BiocommonsAppMetadata( registration_from="biocommons", + # NOTE: users we register should always have account_type: Auth0, + # since we don't register AAF users this way + account_type=BiocommonsUserAccountType.AUTH0, ), ) @@ -268,14 +304,18 @@ class Auth0UserData(BaseModel): updated_at: datetime user_id: str blocked: Optional[bool] = None - # Auth0 will not include user/app metadata in the response when - # empty, so make it optional + # Auth0 will not include user_metadata in the response when empty. user_metadata: Optional[BiocommonsUserMetadata] = None - app_metadata: Optional[BiocommonsAppMetadata] = None + app_metadata: Auth0ReadAppMetadata = Field(default_factory=Auth0ReadAppMetadata) last_ip: Optional[str] = None last_login: Optional[datetime] = None logins_count: Optional[int] = None + @field_validator("app_metadata", mode="before") + @classmethod + def _default_app_metadata(cls, value): + return {} if value is None else value + class Auth0UserDataWithMemberships(Auth0UserData): """ diff --git a/tests/auth/test_account_permissions.py b/tests/auth/test_account_permissions.py new file mode 100644 index 00000000..cc05fe35 --- /dev/null +++ b/tests/auth/test_account_permissions.py @@ -0,0 +1,85 @@ +import pytest +from fastapi import FastAPI +from fastapi.testclient import TestClient + +from auth.account_permissions import ( + AccountActions, + account_action_allowed, + require_account_permission, +) +from auth.user_permissions import get_db_user +from tests.db.datagen import BiocommonsUserFactory + + +@pytest.mark.parametrize( + ["action", "expected"], + [(action, True) for action in AccountActions] +) +def test_account_action_allowed_auth0(action: AccountActions, expected: bool, persistent_factories): + """ + Test which actions are allowed for auth0 accounts (currently all actions are allowed) + """ + user = BiocommonsUserFactory.create_sync(account_type="auth0") + allowed = account_action_allowed(action=action, user=user) + assert allowed == expected + + +@pytest.mark.parametrize( + ["action", "expected"], + [ + (AccountActions.CHANGE_EMAIL, False), + (AccountActions.CHANGE_USERNAME, False), + (AccountActions.CHANGE_PASSWORD, False), + (AccountActions.CHANGE_NAME, True) + ] +) +def test_account_action_allowed_aaf(action: AccountActions, expected: bool, persistent_factories): + """ + Test which actions are allowed for AAF accounts + """ + user = BiocommonsUserFactory.create_sync(account_type="aaf") + allowed = account_action_allowed(action=action, user=user) + assert allowed == expected + + +@pytest.mark.parametrize( + ["allowed", "expected_status", "expected_json"], + [ + (True, 200, {"result": "ok"}), + ( + False, + 403, + {"detail": "You do not have permission to perform this action."}, + ), + ], +) +def test_require_account_permission_dependency( + allowed: bool, + expected_status: int, + expected_json: dict, + mocker, +): + user = BiocommonsUserFactory.build(account_type="aaf") + account_action_allowed_mock = mocker.patch( + "auth.account_permissions.account_action_allowed", + return_value=allowed, + ) + app = FastAPI() + app.dependency_overrides[get_db_user] = lambda: user + + @app.get( + "/dummy", + dependencies=[require_account_permission(AccountActions.CHANGE_EMAIL)], + ) + def dummy_endpoint(): + return {"result": "ok"} + + client = TestClient(app) + response = client.get("/dummy") + + assert response.status_code == expected_status + assert response.json() == expected_json + account_action_allowed_mock.assert_called_once_with( + AccountActions.CHANGE_EMAIL, + user, + ) diff --git a/tests/datagen.py b/tests/datagen.py index 14d155a2..44ace3b1 100644 --- a/tests/datagen.py +++ b/tests/datagen.py @@ -9,6 +9,8 @@ from pydantic import TypeAdapter, ValidationError from auth0.client import ( + Auth0Connection, + ConnectionsWithCheckpoint, EmailVerificationResponse, RoleUserData, RoleUsersWithTotals, @@ -18,6 +20,7 @@ from scheduled_tasks.tasks import ExportedUser from schemas.biocommons import ( ALLOWED_SPECIAL_CHARS, + Auth0ReadAppMetadata, Auth0UserData, BiocommonsAppMetadata, BiocommonsPassword, @@ -123,9 +126,22 @@ def user_id(cls) -> str: blocked = False +class Auth0ConnectionFactory(ModelFactory[Auth0Connection]): + + @classmethod + def options(cls): + return {} + + +class ConnectionsWithCheckpointFactory(ModelFactory[ConnectionsWithCheckpoint]): ... + + class AppMetadataFactory(ModelFactory[BiocommonsAppMetadata]): ... +class Auth0ReadAppMetadataFactory(ModelFactory[Auth0ReadAppMetadata]): ... + + class BiocommonsRegistrationDataFactory(ModelFactory[BiocommonsRegistrationRequest]): """Factory for generating BioCommons registration test data.""" diff --git a/tests/db/datagen.py b/tests/db/datagen.py index 0d577f2a..036cd050 100644 --- a/tests/db/datagen.py +++ b/tests/db/datagen.py @@ -11,6 +11,7 @@ PlatformMembership, ) from db.types import ApprovalStatusEnum, PlatformEnum +from schemas.biocommons import BiocommonsUserAccountType from tests.datagen import BiocommonsProviders, random_auth0_id fake = Faker() @@ -35,6 +36,10 @@ def id(cls) -> str: def is_deleted(cls) -> bool: return False + @classmethod + def account_type(cls) -> BiocommonsUserAccountType: + return BiocommonsUserAccountType.AUTH0 + class Auth0RoleFactory(SQLAlchemyFactory[Auth0Role]): __set_relationships__ = False diff --git a/tests/db/test_models.py b/tests/db/test_models.py index 3d8784c4..bceb7dfe 100644 --- a/tests/db/test_models.py +++ b/tests/db/test_models.py @@ -23,9 +23,11 @@ PlatformMembership, PlatformMembershipHistory, ) +from schemas.biocommons import BiocommonsUserAccountType from tests.biocommons.datagen import RoleDataFactory from tests.datagen import ( AccessTokenPayloadFactory, + Auth0ReadAppMetadataFactory, Auth0UserDataFactory, RoleUserDataFactory, random_auth0_id, @@ -58,7 +60,7 @@ def test_create_biocommons_user(test_db_session): user_data = Person(locale=Locale("en")) auth0_id = random_auth0_id() email = user_data.email() - user = BiocommonsUser(id=auth0_id, email=email, username="user_name") + user = BiocommonsUser(id=auth0_id, email=email, username="user_name", account_type="auth0") test_db_session.add(user) test_db_session.commit() test_db_session.refresh(user) @@ -68,11 +70,23 @@ def test_create_biocommons_user(test_db_session): assert not user.email_verified +def test_biocommons_user_account_type_db_enum_uses_enum_values(): + """ + Test that account_type uses the string values from the account type + enum, not the enum names + """ + db_enum = BiocommonsUser.__table__.c.account_type.type + + assert db_enum.enums == [account_type.value for account_type in BiocommonsUserAccountType] + + def test_create_biocommons_user_from_auth0(test_db_session, mock_auth0_client): """ Test creating the BiocommonsUser model from Auth0 user data from the API """ - user_data = Auth0UserDataFactory.build() + user_data = Auth0UserDataFactory.build( + app_metadata=Auth0ReadAppMetadataFactory.build(account_type=BiocommonsUserAccountType.AUTH0) + ) mock_auth0_client.get_user.return_value = user_data user = BiocommonsUser.create_from_auth0(auth0_id=user_data.user_id, auth0_client=mock_auth0_client) test_db_session.add(user) @@ -1502,6 +1516,7 @@ def test_soft_delete_recreate_revives_deleted(test_db_session, persistent_factor user = BiocommonsUserFactory.create_sync( email="user@example.com", username="soft_delete_user", + account_type=BiocommonsUserAccountType.AUTH0 ) test_db_session.commit() @@ -1513,6 +1528,7 @@ def test_soft_delete_recreate_revives_deleted(test_db_session, persistent_factor email="new@example.com", username="soft_delete_user", email_verified=True, + account_type=BiocommonsUserAccountType.AUTH0 ) test_db_session.add(replacement) test_db_session.commit() diff --git a/tests/db/test_utils.py b/tests/db/test_utils.py index 614eb704..54b8ae16 100644 --- a/tests/db/test_utils.py +++ b/tests/db/test_utils.py @@ -71,17 +71,11 @@ def assert_client_open_during_refresh(session, client): auth0_client.close.assert_called_once() -def test_refresh_unverified_users_updates_status(test_db_session: Session): +def test_refresh_unverified_users_updates_status(test_db_session: Session, persistent_factories): """Verifies that a user's status is updated when Auth0 reports they are now verified.""" # Create an unverified user - user = BiocommonsUser( - id="auth0|123", - email="test@example.com", - username="testuser", - email_verified=False, - ) - test_db_session.add(user) - test_db_session.commit() + user = BiocommonsUserFactory.create_sync(email_verified=False) + user_id = user.id # Mock Auth0 to return verified=True auth0_client = MagicMock() @@ -93,13 +87,13 @@ def test_refresh_unverified_users_updates_status(test_db_session: Session): # Re-fetch user to check update db_session_new = Session(test_db_session.bind) # Use fresh session to avoid cache - updated_user = db_session_new.exec(select(BiocommonsUser).where(BiocommonsUser.id == "auth0|123")).one() + updated_user = db_session_new.exec(select(BiocommonsUser).where(BiocommonsUser.id == user_id)).one() assert updated_user.email_verified is True -def test_refresh_unverified_users_skips_verified_users(test_db_session): +def test_refresh_unverified_users_skips_verified_users(test_db_session, persistent_factories): """Verifies that the query only targets users where email_verified is False.""" - user = BiocommonsUser( + user = BiocommonsUserFactory.create_sync( id="auth0|456", email="verified@example.com", username="verified", diff --git a/tests/migrations/test_migrations.py b/tests/migrations/test_migrations.py index 61dbd10b..043adb27 100644 --- a/tests/migrations/test_migrations.py +++ b/tests/migrations/test_migrations.py @@ -6,6 +6,7 @@ from sqlmodel import Session, create_engine from db.models import BiocommonsGroup +from schemas.biocommons import BiocommonsUserAccountType def test_sbp_group_migration_creates_expected_group(tmp_path, mocker): @@ -110,3 +111,62 @@ def test_sbp_cleanup_migration_removes_legacy_group_and_recreates_current_group( assert group.is_deleted is False finally: engine.dispose() + + +def test_user_account_type_migration_backfills_existing_users(tmp_path, mocker): + db_path = tmp_path / "user_account_type_migration.sqlite" + db_url = f"sqlite:///{db_path}" + + mocker.patch("db.setup.get_db_config", return_value=(db_url, {"check_same_thread": False})) + + repo_root = Path(__file__).resolve().parents[2] + alembic_config = Config(str(repo_root / "alembic.ini")) + + command.upgrade(alembic_config, "39caad32922e") + + engine = create_engine( + db_url, + connect_args={"check_same_thread": False}, + ) + try: + with Session(engine) as session: + session.exec( + text( + """ + INSERT INTO biocommons_user ( + id, + email, + email_verified, + username, + created_at, + is_deleted + ) + VALUES ( + 'auth0|existing-user', + 'existing@example.com', + FALSE, + 'existing_user', + '2026-08-06 00:00:00', + FALSE + ) + """ + ) + ) + session.commit() + + command.upgrade(alembic_config, "0c91366532ae") + + with Session(engine) as session: + account_type = session.exec( + text( + """ + SELECT account_type + FROM biocommons_user + WHERE id = 'auth0|existing-user' + """ + ) + ).one()[0] + + assert account_type == BiocommonsUserAccountType.AUTH0.value + finally: + engine.dispose() diff --git a/tests/scheduled_tasks/test_tasks.py b/tests/scheduled_tasks/test_tasks.py index f290272e..22fe2d0c 100644 --- a/tests/scheduled_tasks/test_tasks.py +++ b/tests/scheduled_tasks/test_tasks.py @@ -44,6 +44,7 @@ update_auth0_user, update_auth0_users_batch, ) +from schemas.biocommons import BiocommonsUserAccountType from tests.datagen import ( Auth0UserDataFactory, ExportedUserFactory, @@ -1184,9 +1185,9 @@ async def test_process_email_queue_skips_when_retry_window_exceeded(test_db_sess def test_parse_auth0_export_parses_csv_file(tmp_path): csv_path = tmp_path / "auth0_users.csv" csv_path.write_text( - "user_id,email,email_verified,username,blocked,updated_at\n" - "'auth0|u1,'u1@example.com,True,'u1,False,2024-01-01T12:00:00+00:00\n" - "'auth0|u2,'u2@example.com,,,,2024-01-02T12:00:00+00:00\n", + "user_id,email,email_verified,username,blocked,updated_at,account_type\n" + "'auth0|u1,'u1@example.com,True,'u1,False,2024-01-01T12:00:00+00:00,'aaf\n" + "'auth0|u2,'u2@example.com,,,,2024-01-02T12:00:00+00:00,\n", encoding="utf-8", ) @@ -1201,6 +1202,7 @@ def test_parse_auth0_export_parses_csv_file(tmp_path): assert users[0].username == "u1" assert users[0].blocked is False assert users[0].updated_at.isoformat() == "2024-01-01T12:00:00+00:00" + assert users[0].account_type == BiocommonsUserAccountType.AAF assert users[1].user_id == "auth0|u2" @@ -1211,6 +1213,20 @@ def test_parse_auth0_export_parses_csv_file(tmp_path): # Check empty username parses as None assert users[1].username is None assert users[1].updated_at.isoformat() == "2024-01-02T12:00:00+00:00" + assert users[1].account_type == BiocommonsUserAccountType.AUTH0 + + +def test_parse_auth0_export_defaults_account_type_when_field_missing(tmp_path): + csv_path = tmp_path / "auth0_users.csv" + csv_path.write_text( + "user_id,email,email_verified,username,blocked,updated_at\n" + "'auth0|u1,'u1@example.com,True,'u1,False,2024-01-01T12:00:00+00:00\n", + encoding="utf-8", + ) + + users = parse_auth0_export(csv_path) + + assert users[0].account_type == BiocommonsUserAccountType.AUTH0 @pytest.mark.asyncio @@ -1222,7 +1238,8 @@ async def test_export_auth0_users_writes_temp_csv_file(mocker): csv_existed_at_parse_time = False csv_path: Path | None = None - def _fake_export_and_download_users(*, download_path, fields): + def _fake_export_and_download_users(*, download_path, fields, connection_id): + assert connection_id is None # Simulate Auth0Client writing the file to the provided temp path download_path.write_text( "user_id,email,email_verified,username,blocked,updated_at\n" @@ -1260,3 +1277,30 @@ def _parse_spy(path): assert not csv_path.exists() assert len(users) == 1 assert users[0].user_id == "auth0|u1" + + +@pytest.mark.asyncio +async def test_export_auth0_users_passes_connection_id(mocker): + def _fake_export_and_download_users(*, download_path, fields, connection_id): + assert fields == [ + {"name": "user_id"}, + {"name": "email"}, + {"name": "email_verified"}, + {"name": "username"}, + {"name": "blocked"}, + {"name": "updated_at"}, + {"name": "app_metadata.account_type", "export_as": "account_type"}, + ] + assert connection_id == "con_aaf" + download_path.write_text( + "user_id,email,email_verified,username,blocked,updated_at,account_type\n", + encoding="utf-8", + ) + + auth0_client = MagicMock() + auth0_client.export_and_download_users.side_effect = _fake_export_and_download_users + + users = await export_auth0_users(auth0_client, connection_id="con_aaf") + + assert users == [] + auth0_client.export_and_download_users.assert_called_once() diff --git a/tests/test_auth0_client.py b/tests/test_auth0_client.py index fc1018bf..11bca468 100644 --- a/tests/test_auth0_client.py +++ b/tests/test_auth0_client.py @@ -13,8 +13,10 @@ UpdateUserData, ) from tests.datagen import ( + Auth0ConnectionFactory, Auth0UserDataFactory, BiocommonsRegisterDataFactory, + ConnectionsWithCheckpointFactory, EmailVerificationResponseFactory, random_auth0_id, random_auth0_role_id, @@ -65,6 +67,32 @@ def test_get_user_by_id(test_auth0_client): assert result.model_dump(mode="json") == user.model_dump(mode="json") +@respx.mock +def test_get_connections(test_auth0_client): + connections = Auth0ConnectionFactory.batch(3) + resp = ConnectionsWithCheckpointFactory.build(connections=connections, next=None) + route = respx.get("https://auth0.example.com/api/v2/connections").respond(200, json=resp.model_dump(mode="json")) + + result = test_auth0_client.get_connections() + + assert route.called + assert result == connections + + +@respx.mock +def test_get_connection_by_name(test_auth0_client): + db_connection = Auth0ConnectionFactory.build(name="db_connection") + other = Auth0ConnectionFactory.build(name="other") + resp = ConnectionsWithCheckpointFactory.build(connections=[db_connection, other]) + route = respx.get("https://auth0.example.com/api/v2/connections").respond(200, json=resp.model_dump(mode="json")) + + result = test_auth0_client.get_connection_by_name(db_connection.name) + + assert route.called + assert result == db_connection + + + @respx.mock def test_get_role_users(test_auth0_client): """ @@ -324,6 +352,41 @@ def test_export_and_download_users_starts_job_waits_and_downloads(test_auth0_cli {"name": "email"}, {"name": "username"}, ] + assert "connection_id" not in start_payload + + +@respx.mock +def test_export_and_download_users_passes_connection_id(test_auth0_client, tmp_path, monkeypatch): + monkeypatch.setattr(time, "sleep", lambda *_args, **_kwargs: None) + + export_job_id = "job_123" + download_url = "https://downloads.example.com/users.csv" + csv_text = "user_id,email,username\nauth0|1,test@example.com,test\n" + + start_route = respx.post("https://auth0.example.com/api/v2/jobs/users-exports").respond( + 200, + json={"id": export_job_id}, + ) + respx.get(f"https://auth0.example.com/api/v2/jobs/{export_job_id}").respond( + 200, + json={ + "id": export_job_id, + "status": "completed", + "type": "users_export", + "created_at": "2020-01-01T00:00:00Z", + "location": download_url, + }, + ) + respx.get(download_url).respond(200, text=csv_text) + + out_path = tmp_path / "auth0_users.csv" + test_auth0_client.export_and_download_users( + out_path, + connection_id="con_aaf", + ) + + start_payload = json.loads(start_route.calls[0].request.content) + assert start_payload["connection_id"] == "con_aaf" @respx.mock diff --git a/tests/test_config.py b/tests/test_config.py index 48806323..dd90ea0a 100644 --- a/tests/test_config.py +++ b/tests/test_config.py @@ -86,6 +86,6 @@ def test_aai_portal_url_override_strips_trailing_slash(): assert settings.aai_portal_url == "https://example.test" -def test_unknown_environment_requires_explicit_portal_url(): - with pytest.raises(ValidationError, match="Input should be 'dev', 'staging' or 'production'"): +def test_unknown_environment_raises_error(): + with pytest.raises(ValidationError, match="Input should be 'dev', 'staging', 'production' or 'dev-aaf'"): Settings(_env_file=None, environment="qa", **_base_settings_kwargs()) diff --git a/tests/test_user.py b/tests/test_user.py index 4e04efd5..636a160b 100644 --- a/tests/test_user.py +++ b/tests/test_user.py @@ -24,7 +24,11 @@ PlatformEnum, ) from routers.user import get_user_data, update_user_metadata -from schemas.biocommons import Auth0Identity, BiocommonsAppMetadata +from schemas.biocommons import ( + Auth0Identity, + Auth0ReadAppMetadata, + BiocommonsAppMetadata, +) from tests.datagen import ( AccessTokenPayloadFactory, Auth0UserDataFactory, @@ -909,6 +913,44 @@ def test_get_admin_groups(test_client, test_db_session, mocker, persistent_facto assert invalid_group.group_id not in returned_ids +@pytest.mark.parametrize( + ["endpoint", "payload"], + [ + ("/me/profile/email/update", {"email": "new@example.com"}), + ("/me/profile/email/continue", {"otp": "123456"}), + ( + "/me/profile/password/update", + { + "current_password": "CurrentPass123!", + "new_password": "NewPass123!", + }, + ), + ], +) +def test_profile_update_endpoints_disallowed_for_aaf_accounts( + endpoint, + payload, + test_client, + test_db_session, + mocker, + persistent_factories, +): + user = BiocommonsUserFactory.create_sync(account_type="aaf") + test_db_session.commit() + _act_as_user(mocker, user) + + response = test_client.post( + endpoint, + headers={"Authorization": "Bearer valid_token"}, + json=payload, + ) + + assert response.status_code == HTTPStatus.FORBIDDEN + assert response.json() == { + "detail": "You do not have permission to perform this action." + } + + def test_update_username(test_client, test_db_session, mocker, persistent_factories): user = BiocommonsUserFactory.create_sync(username="old_username") mock_data = Auth0UserDataFactory.build(sub=user.id, username="new_username") @@ -1072,12 +1114,12 @@ def test_email_continue_updates_user(test_client, test_db_session, mocker, persi sub=user.id, email="new@example.com", email_verified=True, - app_metadata=BiocommonsAppMetadata(registration_from="biocommons"), + app_metadata=Auth0ReadAppMetadata(registration_from="biocommons", account_type="auth0"), ) current_auth0_user = Auth0UserDataFactory.build( sub=user.id, email=user.email, - app_metadata=BiocommonsAppMetadata(registration_from="biocommons"), + app_metadata=Auth0ReadAppMetadata(registration_from="biocommons", account_type="auth0"), ) mocker.patch("routers.user.Auth0Client.update_user", return_value=updated_user) mocker.patch("routers.user.Auth0Client.get_user", return_value=current_auth0_user) @@ -1156,7 +1198,7 @@ def _setup_email_change_with_sbp( sub=user.id, email=new_email, email_verified=True, - app_metadata=BiocommonsAppMetadata(registration_from="biocommons"), + app_metadata=Auth0ReadAppMetadata(registration_from="biocommons"), ) mock_auth0_client.update_user.return_value = updated_user mock_auth0_client.get_role_by_name.return_value = MagicMock(id="role_sbp") diff --git a/tests/test_utils.py b/tests/test_utils.py index a12e76c9..5fdff0d7 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -9,7 +9,10 @@ from main import app from routers import utils from services.institutions import GALAXY_AU_VALIDATE_URL -from tests.datagen import AppMetadataFactory, Auth0UserDataFactory +from tests.datagen import ( + Auth0ReadAppMetadataFactory, + Auth0UserDataFactory, +) @pytest.fixture @@ -28,7 +31,7 @@ def test_get_registration_info(override_auth0_client, test_client): Test we can look up a user by email, and return their app_metadata.registration_from value, if available. """ - app_metadata = AppMetadataFactory.build(registration_from="galaxy") + app_metadata = Auth0ReadAppMetadataFactory.build(registration_from="galaxy") user = Auth0UserDataFactory.build(email="user@example.com", app_metadata=app_metadata) override_auth0_client.search_users_by_email.return_value = [user] @@ -42,7 +45,7 @@ def test_get_registration_info_no_registration_from(override_auth0_client, test_ """ Test the default of 'biocommons' is returned if registration_from isn't set. 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{ url = "https://files.pythonhosted.org/packages/5d/7c/add7d4be6690fb61f4d30b672e544b1ac541c824f05a7de50ff5d8985db5/starlette_admin-0.16.1-py3-none-any.whl", hash = "sha256:a5e6cb0beb2e9bdc65b07dbb4bd01726aaad34764595e3bc3ff8578e698ff98a", size = 2176514, upload-time = "2026-06-06T20:10:42.308Z" }, + { url = "https://files.pythonhosted.org/packages/19/97/56608b2249fe206a67cd573bc93cd9896e1efb9e98bce9c163bcdc704b88/truststore-0.10.4-py3-none-any.whl", hash = "sha256:adaeaecf1cbb5f4de3b1959b42d41f6fab57b2b1666adb59e89cb0b53361d981", size = 18660, upload-time = "2025-08-12T18:49:01.46Z" }, ] [[package]] From 269c56275dc9baf39d8439ef7384840fb03f7c84 Mon Sep 17 00:00:00 2001 From: marius-mather <61438033+marius-mather@users.noreply.github.com> Date: Wed, 26 Aug 2026 09:32:57 +1000 Subject: [PATCH 06/25] feat: check AAF logins and link to existing account if needed (AAI-874) (#294) * feat: allow filtering users by connection when searching by email * feat: updated schemas for AAF info * feat: link_identity method for Auth0Client * feat: record other user ID for users * feat: method to link account for BiocommonsUser * fix: linking_completed_at should be datetime * feat: dependency to check Auth0 action tokens * feat: router with initial /aaf/check-link endpoint * chore: include aaf router in main * refactor: use a base URL for Auth0 API calls * test: unit tests of new Auth0Client methods * test: unit tests of AAF link function * test: tests of require_action_token * test: unit tests of account linking endpoint * fix: get connection correctly when linking accounts * fix: skip linking if already done * fix: update app_metadata to mark user AAF only if no existing account * test: unit tests of app_metadata for AAF-only accounts * fix: handle errors when Auth0 already linked --- auth0/client.py | 108 +++++-- db/models.py | 18 ++ dependencies/auth.py | 21 ++ main.py | 2 + .../versions/98fbefd9f191_other_user_id.py | 31 ++ routers/aaf.py | 124 ++++++++ schemas/auth0.py | 14 + schemas/biocommons.py | 9 + tests/test_aaf.py | 268 ++++++++++++++++++ tests/test_auth0_client.py | 92 +++++- tests/test_dependencies.py | 37 +++ 11 files changed, 693 insertions(+), 31 deletions(-) create mode 100644 dependencies/auth.py create mode 100644 migrations/versions/98fbefd9f191_other_user_id.py create mode 100644 routers/aaf.py create mode 100644 tests/test_aaf.py create mode 100644 tests/test_dependencies.py diff --git a/auth0/client.py b/auth0/client.py index b879b6d7..87827725 100644 --- a/auth0/client.py +++ b/auth0/client.py @@ -121,6 +121,18 @@ class IdentityData(BaseModel): provider: str +class LinkIdentityRequest(BaseModel): + """ + POST data sent when linking identities. + + Note: user_id is the secondary ID here. Primary ID goes in the + URL + """ + provider: str + connection_id: str | None = None + user_id: str + + class EmailVerificationRequest(BaseModel): user_id: str client_id: Optional[str] = None @@ -178,6 +190,7 @@ class Auth0Client: def __init__(self, domain: str, management_token: str): self.domain = domain + self.api_base = f"https://{domain}/api/v2" self.management_token = management_token self._client = httpx.Client(headers={"Authorization": f"Bearer {management_token}"}) @@ -218,7 +231,7 @@ def get_users(self, page: Optional[int] = None, per_page: Optional[int] = None, if q is not None: params["q"] = q params["search_engine"] = "v3" - url = f"https://{self.domain}/api/v2/users" + url = f"{self.api_base}/users" resp = self._client.get(url, params=params) resp.raise_for_status() if include_totals: @@ -226,13 +239,13 @@ def get_users(self, page: Optional[int] = None, per_page: Optional[int] = None, return self._convert_users(resp) def get_user(self, user_id: str) -> Auth0UserData: - url = f"https://{self.domain}/api/v2/users/{user_id}" + url = f"{self.api_base}/users/{user_id}" resp = self._client.get(url) resp.raise_for_status() return Auth0UserData(**resp.json()) def create_user(self, user: BiocommonsRegisterData) -> Auth0UserData: - url = f"https://{self.domain}/api/v2/users" + url = f"{self.api_base}/users" # Exclude None values to avoid validation errors. resp = self._client.post(url, json=user.model_dump(mode="json", exclude_none=True)) resp.raise_for_status() @@ -242,7 +255,7 @@ def update_user(self, user_id: str, update_data: UpdateUserData) -> Auth0UserDat """ Send a PATCH request to the /users/{user_id} endpoint to update the included fields. """ - url = f"https://{self.domain}/api/v2/users/{user_id}" + url = f"{self.api_base}/users/{user_id}" # Make sure we exclude None to not update fields with null values. data = update_data.model_dump(mode="json", exclude_none=True) try: @@ -261,7 +274,7 @@ def start_user_export( """ Start a user export job, return the job ID. """ - url = f"https://{self.domain}/api/v2/jobs/users-exports" + url = f"{self.api_base}/jobs/users-exports" if fields is None: fields = [ {"name": "user_id"}, @@ -276,7 +289,7 @@ def start_user_export( return resp.json()["id"] def get_job_status(self, job_id: str) -> JobStatus: - url = f"https://{self.domain}/api/v2/jobs/{job_id}" + url = f"{self.api_base}/jobs/{job_id}" resp = self._client.get(url) resp.raise_for_status() return JobStatus(**resp.json()) @@ -333,9 +346,6 @@ def export_and_download_users( download_path.write_text(csv_data, encoding="utf-8") return download_path - - - def check_user_password(self, email: str, password: str, settings: Settings) -> bool: """ Verify a user's password by using the password-realm grant type. @@ -367,7 +377,7 @@ def delete_user_refresh_tokens(self, user_id: str) -> bool: """ Delete all refresh tokens for a user. """ - url = f"https://{self.domain}/api/v2/users/{user_id}/refresh-tokens" + url = f"{self.api_base}/users/{user_id}/refresh-tokens" resp = self._client.delete(url) resp.raise_for_status() return True @@ -376,7 +386,7 @@ def add_roles_to_user(self, user_id: str, role_id: str | list[str]) -> bool: """ Add one or more roles to a user. The role(s) must already exist. """ - url = f"https://{self.domain}/api/v2/users/{user_id}/roles" + url = f"{self.api_base}/users/{user_id}/roles" if isinstance(role_id, str): role_id = [role_id] resp = self._client.post(url, json={"roles": role_id}) @@ -387,7 +397,7 @@ def remove_roles_from_user(self, user_id: str, role_id: str | list[str]): """ Remove one or more roles from a user. """ - url = f"https://{self.domain}/api/v2/users/{user_id}/roles" + url = f"{self.api_base}/users/{user_id}/roles" if isinstance(role_id, str): role_id = [role_id] # httpx.Client.delete() no longer accepts json payloads (0.28+), so use request() @@ -395,10 +405,23 @@ def remove_roles_from_user(self, user_id: str, role_id: str | list[str]): resp.raise_for_status() return True - def search_users_by_email(self, email: str) -> list[Auth0UserData]: - url = f"https://{self.domain}/api/v2/users-by-email" + def search_users_by_email(self, email: str, connection: str | None = None) -> list[Auth0UserData]: + """ + Search users by email, optionally filtering by connection name. + """ + url = f"{self.api_base}/users-by-email" resp = self._client.get(url, params={"email": email}) - return self._convert_users(resp) + resp.raise_for_status() + users = self._convert_users(resp) + if connection is not None: + filtered_users = [] + for user in users: + in_connection = any(ident.connection == connection for ident in user.identities) + if in_connection: + filtered_users.append(user) + return filtered_users + else: + return users def _search_users(self, query: str, page: Optional[int] = None, per_page: Optional[int] = None) -> list[Auth0UserData]: params = {"q": query, "search_engine": "v3"} @@ -408,7 +431,7 @@ def _search_users(self, query: str, page: Optional[int] = None, per_page: Option params["page"] = page if per_page is not None: params["per_page"] = per_page - url = f"https://{self.domain}/api/v2/users" + url = f"{self.api_base}/users" # TODO: set primary_order=false for faster search? # https://auth0.com/docs/manage-users/user-search/user-search-best-practices resp = self._client.get( @@ -423,7 +446,7 @@ def _search_users(self, query: str, page: Optional[int] = None, per_page: Option return self._convert_users(resp) def get_connections(self) -> list[Auth0Connection]: - url = f"https://{self.domain}/api/v2/connections" + url = f"{self.api_base}/connections" resp = self._client.get(url, params={"take": 10}) resp.raise_for_status() converted = ConnectionsWithCheckpoint(**resp.json()) @@ -432,12 +455,17 @@ def get_connections(self) -> list[Auth0Connection]: return converted.connections def get_connection_by_name(self, name: str) -> Auth0Connection | None: - connections = self.get_connections() - result = None - for connection in connections: - if connection.name == name: - result = connection - return result + # Filter server-side rather than paginating get_connections(), which caps at 10. + url = f"{self.api_base}/connections" + resp = self._client.get(url, params={"name": name}) + resp.raise_for_status() + connections = self._convert_list(resp, Auth0Connection) + # Ensure an exact match + if connections: + for connection in connections: + if connection.name == name: + return connection + return None def get_roles(self, name_filter: Optional[str] = None, @@ -453,7 +481,7 @@ def get_roles(self, params["page"] = page if per_page is not None: params["per_page"] = per_page - url = f"https://{self.domain}/api/v2/roles" + url = f"{self.api_base}/roles" resp = self._client.get(url, params=params) resp.raise_for_status() if include_totals: @@ -489,7 +517,7 @@ def get_role_by_name(self, name: str) -> RoleData: return roles[0] def get_role_by_id(self, role_id: str) -> RoleData: - url = f"https://{self.domain}/api/v2/roles/{role_id}" + url = f"{self.api_base}/roles/{role_id}" resp = self._client.get(url) resp.raise_for_status() return RoleData(**resp.json()) @@ -501,7 +529,7 @@ def get_role_users(self, include_totals: Optional[bool] = False, take: Optional[int] = None, checkpoint: Optional[str] = None) -> list[RoleUserData] | RoleUsersWithTotals | RoleUsersWithCheckpoint: - url = f"https://{self.domain}/api/v2/roles/{role_id}/users" + url = f"{self.api_base}/roles/{role_id}/users" params = {} if page is not None: params["page"] = page @@ -552,7 +580,7 @@ def get_all_role_users_generator(self, role_id: str) -> Iterator[list[RoleUserDa checkpoint = page_users.next def create_role(self, name: str, description: str) -> RoleData: - url = f"https://{self.domain}/api/v2/roles" + url = f"{self.api_base}/roles" resp = self._client.post(url, json={"name": name, "description": description}) resp.raise_for_status() return RoleData(**resp.json()) @@ -565,7 +593,7 @@ def get_or_create_role(self, name: str, description: str) -> RoleData: return role def resend_verification_email(self, user_id: str) -> EmailVerificationResponse: - url = f"https://{self.domain}/api/v2/jobs/verification-email" + url = f"{self.api_base}/jobs/verification-email" request_body = EmailVerificationRequest(user_id=user_id) resp = self._client.post(url, json=request_body.model_dump(mode="json", exclude_none=True)) resp.raise_for_status() @@ -584,6 +612,30 @@ def trigger_password_change(self, user_email: str, client_id: str, settings: Set resp.raise_for_status() return True + def link_identity(self, primary_user_id: str, secondary_user_id: str, secondary_provider: str, + secondary_connection_name: str) -> bool: + """ + Link an identity to a primary account. + + secondary_provider is the identity's strategy (e.g. "samlp"), secondary_connection_name + is the connection's name (e.g. "AAF") - these can differ, so both are needed. + """ + url = f"{self.api_base}/users/{primary_user_id}/identities" + secondary_connection = self.get_connection_by_name(secondary_connection_name) + if secondary_connection is None: + raise ValueError(f"Could not find Auth0 connection named {secondary_connection_name!r}") + payload = LinkIdentityRequest( + provider=secondary_provider, + connection_id=secondary_connection.id, + user_id=secondary_user_id, + ) + try: + resp = self._client.post(url, json=payload.model_dump(mode="json", exclude_none=True)) + resp.raise_for_status() + except HTTPStatusError as exc: + raise ValueError(f"Failed to link identity for user {primary_user_id}: {exc.response.json()}") from exc + return True + def get_auth0_client(settings: Settings = Depends(get_settings), management_token: str = Depends(get_management_token)): diff --git a/db/models.py b/db/models.py index 64203d7f..4438c81f 100644 --- a/db/models.py +++ b/db/models.py @@ -40,6 +40,9 @@ class BiocommonsUser(SoftDeleteModel, table=True): ) # Auth0 ID id: str = Field(primary_key=True) + # User ID from other providers, i.e. AAF. Don't want to rely on this in the DB + # (Auth0 should handle linked identities), but good for tracking user info + other_user_id: str | None = Field(default=None, nullable=True) account_type: BiocommonsUserAccountType = Field( sa_type=DbEnum( BiocommonsUserAccountType, @@ -363,6 +366,21 @@ def update_username(self, new_username: str, session: Session, updated_by: Self if commit: session.commit() + def link_aaf_account(self, aaf_user_id: str, session: Session, updated_by: Self | None = None, commit: bool = False) -> None: + """ + Set an existing account as an AAF account with a linked ID. + + Auth0 linking is not handled here and must be done separately. + """ + # Save history before update + self.save_history(session=session, change="aaf_account_linking", updated_by=updated_by, commit=False) + self.account_type = BiocommonsUserAccountType.AAF + self.other_user_id = aaf_user_id + session.add(self) + if commit: + session.commit() + + def save_history(self, session: Session, change: str | None = None, reason: str | None = None, updated_by: Self | None = None, commit: bool = False) -> 'BiocommonsUserHistory': diff --git a/dependencies/auth.py b/dependencies/auth.py new file mode 100644 index 00000000..9b939d9a --- /dev/null +++ b/dependencies/auth.py @@ -0,0 +1,21 @@ +from typing import Annotated + +from fastapi import Depends, HTTPException + +from auth.validator import verify_action_token +from config import Settings, get_settings +from schemas.auth0 import Auth0ActionToken + + +def require_action_token(purpose: str | None = None): + """ + Dependency that verifies the session_token (from query params), + and checks for the specified purpose, if present + """ + def check_action_token(session_token: str, settings: Annotated[Settings, Depends(get_settings)]): + payload = verify_action_token(session_token, settings=settings) + if purpose is not None: + if payload.get("purpose", None) != purpose: + raise HTTPException(status_code=401, detail="invalid purpose") + return Auth0ActionToken(**payload) + return check_action_token diff --git a/main.py b/main.py index e69c06d3..e6fb760c 100644 --- a/main.py +++ b/main.py @@ -11,6 +11,7 @@ from db import models # noqa: F401 from db.st_admin import setup_starlette_admin from routers import ( + aaf, admin, biocommons_admin, biocommons_register, @@ -78,6 +79,7 @@ def public_route(): CURRENT_ENVIRONMENT = read_setting("ENVIRONMENT", "dev") +app.include_router(aaf.router) app.include_router(admin.router) app.include_router(biocommons_admin.router) app.include_router(user.router) diff --git a/migrations/versions/98fbefd9f191_other_user_id.py b/migrations/versions/98fbefd9f191_other_user_id.py new file mode 100644 index 00000000..35dda555 --- /dev/null +++ b/migrations/versions/98fbefd9f191_other_user_id.py @@ -0,0 +1,31 @@ +"""other_user_id + +Revision ID: 98fbefd9f191 +Revises: 0c91366532ae +Create Date: 2026-08-24 15:43:31.428645 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa +import sqlmodel + + +# revision identifiers, used by Alembic. +revision: str = '98fbefd9f191' +down_revision: Union[str, None] = '0c91366532ae' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + # ### commands auto generated by Alembic - please adjust! ### + op.add_column('biocommons_user', sa.Column('other_user_id', sqlmodel.sql.sqltypes.AutoString(), nullable=True)) + # ### end Alembic commands ### + + +def downgrade() -> None: + # ### commands auto generated by Alembic - please adjust! ### + op.drop_column('biocommons_user', 'other_user_id') + # ### end Alembic commands ### diff --git a/routers/aaf.py b/routers/aaf.py new file mode 100644 index 00000000..83d13140 --- /dev/null +++ b/routers/aaf.py @@ -0,0 +1,124 @@ +import logging +from datetime import datetime, timezone +from http import HTTPStatus +from typing import Annotated + +from fastapi import APIRouter, Depends, HTTPException +from pydantic import BaseModel +from sqlmodel import Session + +from auth0.client import Auth0Client, UpdateUserData, get_auth0_client +from config import Settings, get_settings +from db.models import BiocommonsUser +from db.setup import get_db_session +from dependencies.auth import require_action_token +from schemas.auth0 import Auth0ActionToken +from schemas.biocommons import ( + Auth0UserData, + BiocommonsAppMetadataUpdate, + BiocommonsUserAccountType, +) + +router = APIRouter( + prefix="/aaf", tags=["aaf"] +) +logger = logging.getLogger("uvicorn.error") + + +class AccountLinkResponse(BaseModel): + link: bool + aaf_only: bool = False + primary_id: str + + +def link_aaf_account(db_user_id: str, aaf_user_id: str, auth0_client: Auth0Client, session: Session): + def _get_aaf_identity(aaf_user: Auth0UserData): + for identity in aaf_user.identities: + if identity.connection == "AAF": + return identity + return None + db_user = BiocommonsUser.get_by_id_or_404(db_user_id, session=session) + if db_user.account_type == BiocommonsUserAccountType.AAF and db_user.other_user_id == aaf_user_id: + logger.info("AAF account already linked, skipping re-link") + return db_user + + aaf_user_info = auth0_client.get_user(user_id=aaf_user_id) + aaf_identity = _get_aaf_identity(aaf_user_info) + if aaf_identity is None: + raise HTTPException(status_code=HTTPStatus.NOT_FOUND, detail="Couldn't get AAF provider information") + + logger.info("Linking AAF account to existing database account") + now = datetime.now(tz=timezone.utc) + try: + auth0_client.link_identity(primary_user_id=db_user_id, secondary_user_id=aaf_user_id, + secondary_provider=aaf_identity.provider, + secondary_connection_name=aaf_identity.connection) + auth0_client.update_user( + db_user_id, + update_data=UpdateUserData( + app_metadata=BiocommonsAppMetadataUpdate( + account_type=BiocommonsUserAccountType.AAF, + linking_completed=True, + linking_completed_at=now + ) + ) + ) + except ValueError as exc: + logger.error(f"Failed to link AAF account in Auth0: {exc}") + raise HTTPException(status_code=HTTPStatus.BAD_GATEWAY, detail="Failed to link account with Auth0") from exc + logger.info("Updating DB record") + db_user.link_aaf_account(aaf_user_id=aaf_user_id, session=session, updated_by=db_user, commit=True) + return db_user + + +def mark_user_aaf_only(user_email: str, aaf_user_id: str, auth0_client: Auth0Client): + update_data = UpdateUserData( + app_metadata=BiocommonsAppMetadataUpdate( + aaf_only=True, + checked_email=user_email, + linking_completed=True, + linking_completed_at=datetime.now(tz=timezone.utc), + ) + ) + auth0_client.update_user(user_id=aaf_user_id, update_data=update_data) + + + +@router.get("/check-link", response_model=AccountLinkResponse) +def check_aaf_account_link( + token: Annotated[Auth0ActionToken, Depends(require_action_token(purpose="aaf_link"))], + session: Annotated[Session, Depends(get_db_session)], + auth0_client: Annotated[Auth0Client, Depends(get_auth0_client)], + settings: Annotated[Settings, Depends(get_settings)], +): + email = token.email + aaf_user_id = token.user_id + auth0_matches = auth0_client.search_users_by_email( + email, + connection=settings.auth0_db_connection + ) + # No existing account: no need to link + if not auth0_matches: + mark_user_aaf_only(email, aaf_user_id, auth0_client) + return AccountLinkResponse(link=False, aaf_only=True, primary_id=token.user_id) + + existing_account = None + for user in auth0_matches: + if user.email.lower() == email.lower(): + existing_account = user + break + # No exact match: no existing account + if not existing_account: + mark_user_aaf_only(email, aaf_user_id, auth0_client) + return AccountLinkResponse(link=False, aaf_only=True, primary_id=email) + + if existing_account.blocked: + raise HTTPException(status_code=403, detail="Existing account is blocked.") + + link_aaf_account( + db_user_id=existing_account.user_id, + aaf_user_id=aaf_user_id, + auth0_client=auth0_client, + session=session, + ) + return AccountLinkResponse(link=True, aaf_only=False, primary_id=existing_account.user_id) diff --git a/schemas/auth0.py b/schemas/auth0.py index de6c662b..57070774 100644 --- a/schemas/auth0.py +++ b/schemas/auth0.py @@ -1,5 +1,7 @@ import re +from pydantic import BaseModel, EmailStr + PLATFORM_ROLE_PATTERN = re.compile(r"biocommons/platform/(?P[a-z0-9_-]+)") GROUP_ROLE_PATTERN = re.compile(r"biocommons/group/(?P[a-z0-9_-]+)") @@ -16,3 +18,15 @@ def get_group_id_from_role_name(role_name: str) -> str | None: if match: return match.group("group_id") return None + + +class Auth0ActionToken(BaseModel): + """ + Token payload that we use in Auth0 actions - signed with a shared secret. + + Any future actions we create should use this payload. + """ + user_id: str + email: EmailStr + client_id: str + purpose: str diff --git a/schemas/biocommons.py b/schemas/biocommons.py index 52009045..432a9d56 100644 --- a/schemas/biocommons.py +++ b/schemas/biocommons.py @@ -15,6 +15,7 @@ from fastapi import Path from pydantic import ( AfterValidator, + AwareDatetime, BaseModel, EmailStr, Field, @@ -192,6 +193,10 @@ class BiocommonsAppMetadata(BaseModel): old_emails: Optional[list[OldEmailRecord]] = None user_needs_migration: Optional[bool] = None account_type: BiocommonsUserAccountType + aaf_only: Optional[bool] = None + checked_email: Optional[EmailStr] = None + linking_completed: Optional[bool] = None + linking_completed_at: Optional[AwareDatetime] = None model_config = { "extra": "ignore" @@ -217,6 +222,10 @@ class BiocommonsAppMetadataUpdate(BaseModel): old_emails: Optional[list[OldEmailRecord]] = None user_needs_migration: Optional[bool] = None account_type: Optional[BiocommonsUserAccountType] = None + aaf_only: Optional[bool] = None + checked_email: Optional[EmailStr] = None + linking_completed: Optional[bool] = None + linking_completed_at: Optional[AwareDatetime] = None model_config = { "extra": "ignore" diff --git a/tests/test_aaf.py b/tests/test_aaf.py new file mode 100644 index 00000000..489ee26a --- /dev/null +++ b/tests/test_aaf.py @@ -0,0 +1,268 @@ +from http import HTTPStatus +from unittest.mock import MagicMock + +import pytest +from fastapi import HTTPException + +from auth0.client import Auth0Client +from routers.aaf import link_aaf_account, mark_user_aaf_only +from schemas.biocommons import Auth0Identity, BiocommonsUserAccountType +from tests.datagen import Auth0UserDataFactory, random_auth0_id +from tests.db.datagen import BiocommonsUserFactory + + +def test_link_aaf_account_links_identity_updates_metadata_and_db(test_db_session, persistent_factories): + db_user = BiocommonsUserFactory.create_sync(account_type=BiocommonsUserAccountType.AUTH0, other_user_id=None) + test_db_session.commit() + + aaf_user_id = random_auth0_id() + aaf_user_data = Auth0UserDataFactory.build( + identities=[Auth0Identity(connection="AAF", provider="samlp", user_id=aaf_user_id, isSocial=False)] + ) + auth0_client = MagicMock(spec=Auth0Client) + auth0_client.get_user.return_value = aaf_user_data + + result = link_aaf_account( + db_user_id=db_user.id, + aaf_user_id=aaf_user_id, + auth0_client=auth0_client, + session=test_db_session, + ) + + auth0_client.get_user.assert_called_once_with(user_id=aaf_user_id) + auth0_client.link_identity.assert_called_once_with( + primary_user_id=db_user.id, + secondary_user_id=aaf_user_id, + secondary_provider="samlp", + secondary_connection_name="AAF", + ) + + auth0_client.update_user.assert_called_once() + call_args, call_kwargs = auth0_client.update_user.call_args + assert call_args[0] == db_user.id + app_metadata = call_kwargs["update_data"].app_metadata + assert app_metadata.account_type == BiocommonsUserAccountType.AAF + assert app_metadata.linking_completed is True + assert app_metadata.linking_completed_at is not None + + assert result.id == db_user.id + assert result.account_type == BiocommonsUserAccountType.AAF + assert result.other_user_id == aaf_user_id + + test_db_session.refresh(db_user) + assert db_user.account_type == BiocommonsUserAccountType.AAF + assert db_user.other_user_id == aaf_user_id + + +def test_link_aaf_account_raises_404_when_no_aaf_identity(test_db_session, persistent_factories): + db_user = BiocommonsUserFactory.create_sync(account_type=BiocommonsUserAccountType.AUTH0, other_user_id=None) + test_db_session.commit() + + aaf_user_id = random_auth0_id() + aaf_user_data = Auth0UserDataFactory.build( + identities=[ + Auth0Identity( + connection="Username-Password-Authentication", + provider="auth0", + user_id=aaf_user_id, + isSocial=False, + ) + ] + ) + auth0_client = MagicMock(spec=Auth0Client) + auth0_client.get_user.return_value = aaf_user_data + + with pytest.raises(HTTPException) as exc_info: + link_aaf_account( + db_user_id=db_user.id, + aaf_user_id=aaf_user_id, + auth0_client=auth0_client, + session=test_db_session, + ) + + assert exc_info.value.status_code == HTTPStatus.NOT_FOUND + auth0_client.link_identity.assert_not_called() + auth0_client.update_user.assert_not_called() + + test_db_session.refresh(db_user) + assert db_user.account_type == BiocommonsUserAccountType.AUTH0 + assert db_user.other_user_id is None + + +def test_link_aaf_account_raises_502_when_auth0_linking_fails(test_db_session, persistent_factories): + db_user = BiocommonsUserFactory.create_sync(account_type=BiocommonsUserAccountType.AUTH0, other_user_id=None) + test_db_session.commit() + + aaf_user_id = random_auth0_id() + aaf_user_data = Auth0UserDataFactory.build( + identities=[Auth0Identity(connection="AAF", provider="samlp", user_id=aaf_user_id, isSocial=False)] + ) + auth0_client = MagicMock(spec=Auth0Client) + auth0_client.get_user.return_value = aaf_user_data + auth0_client.link_identity.side_effect = ValueError("Identity already linked") + + with pytest.raises(HTTPException) as exc_info: + link_aaf_account( + db_user_id=db_user.id, + aaf_user_id=aaf_user_id, + auth0_client=auth0_client, + session=test_db_session, + ) + + assert exc_info.value.status_code == HTTPStatus.BAD_GATEWAY + auth0_client.update_user.assert_not_called() + + test_db_session.refresh(db_user) + assert db_user.account_type == BiocommonsUserAccountType.AUTH0 + assert db_user.other_user_id is None + + +def test_link_aaf_account_idempotent_when_already_linked(test_db_session, persistent_factories): + aaf_user_id = random_auth0_id() + db_user = BiocommonsUserFactory.create_sync( + account_type=BiocommonsUserAccountType.AAF, other_user_id=aaf_user_id + ) + test_db_session.commit() + + auth0_client = MagicMock(spec=Auth0Client) + + result = link_aaf_account( + db_user_id=db_user.id, + aaf_user_id=aaf_user_id, + auth0_client=auth0_client, + session=test_db_session, + ) + + auth0_client.get_user.assert_not_called() + auth0_client.link_identity.assert_not_called() + auth0_client.update_user.assert_not_called() + assert result.id == db_user.id + + +def _action_token_payload(user_id: str, email: str, purpose: str = "aaf_link", client_id: str = "test-client") -> dict: + return {"user_id": user_id, "email": email, "client_id": client_id, "purpose": purpose} + + +def _assert_marked_aaf_only(update_user_mock, aaf_user_id: str, email: str): + update_user_mock.assert_called_once() + call_args, call_kwargs = update_user_mock.call_args + assert call_kwargs["user_id"] == aaf_user_id + app_metadata = call_kwargs["update_data"].app_metadata + assert app_metadata.aaf_only is True + assert app_metadata.checked_email == email + assert app_metadata.linking_completed is True + assert app_metadata.linking_completed_at is not None + + +def test_mark_user_aaf_only(): + aaf_user_id = random_auth0_id() + email = "aaf-user@example.com" + auth0_client = MagicMock(spec=Auth0Client) + + mark_user_aaf_only(email, aaf_user_id, auth0_client) + + _assert_marked_aaf_only(auth0_client.update_user, aaf_user_id, email) + + +def test_check_link_no_existing_account(test_client, mocker): + aaf_user_id = random_auth0_id() + email = "new-aaf-user@example.com" + mocker.patch("dependencies.auth.verify_action_token", return_value=_action_token_payload(aaf_user_id, email)) + mocker.patch("routers.aaf.Auth0Client.search_users_by_email", return_value=[]) + link_identity = mocker.patch("routers.aaf.Auth0Client.link_identity") + update_user = mocker.patch("routers.aaf.Auth0Client.update_user") + + response = test_client.get("/aaf/check-link", params={"session_token": "valid_token"}) + + assert response.status_code == 200 + assert response.json() == {"link": False, "aaf_only": True, "primary_id": aaf_user_id} + link_identity.assert_not_called() + _assert_marked_aaf_only(update_user, aaf_user_id, email) + + +def test_check_link_no_exact_email_match(test_client, mocker): + aaf_user_id = random_auth0_id() + email = "aaf-user@example.com" + mocker.patch("dependencies.auth.verify_action_token", return_value=_action_token_payload(aaf_user_id, email)) + near_miss_account = Auth0UserDataFactory.build(email="different-user@example.com") + mocker.patch("routers.aaf.Auth0Client.search_users_by_email", return_value=[near_miss_account]) + link_identity = mocker.patch("routers.aaf.Auth0Client.link_identity") + update_user = mocker.patch("routers.aaf.Auth0Client.update_user") + + response = test_client.get("/aaf/check-link", params={"session_token": "valid_token"}) + + assert response.status_code == 200 + assert response.json() == {"link": False, "aaf_only": True, "primary_id": email} + link_identity.assert_not_called() + _assert_marked_aaf_only(update_user, aaf_user_id, email) + + +def test_check_link_existing_account_blocked(test_client, mocker): + aaf_user_id = random_auth0_id() + email = "blocked-user@example.com" + mocker.patch("dependencies.auth.verify_action_token", return_value=_action_token_payload(aaf_user_id, email)) + existing_account = Auth0UserDataFactory.build(email=email, blocked=True) + mocker.patch("routers.aaf.Auth0Client.search_users_by_email", return_value=[existing_account]) + + response = test_client.get("/aaf/check-link", params={"session_token": "valid_token"}) + + assert response.status_code == 403 + + +def test_check_link_existing_account_links(test_client, test_db_session, persistent_factories, mocker): + email = "existing-user@example.com" + aaf_user_id = random_auth0_id() + db_user = BiocommonsUserFactory.create_sync( + email=email, account_type=BiocommonsUserAccountType.AUTH0, other_user_id=None + ) + test_db_session.commit() + + mocker.patch("dependencies.auth.verify_action_token", return_value=_action_token_payload(aaf_user_id, email)) + existing_account = Auth0UserDataFactory.build(user_id=db_user.id, email=email, blocked=False) + mocker.patch("routers.aaf.Auth0Client.search_users_by_email", return_value=[existing_account]) + aaf_user_data = Auth0UserDataFactory.build( + identities=[Auth0Identity(connection="AAF", provider="samlp", user_id=aaf_user_id, isSocial=False)] + ) + mocker.patch("routers.aaf.Auth0Client.get_user", return_value=aaf_user_data) + link_identity = mocker.patch("routers.aaf.Auth0Client.link_identity") + update_user = mocker.patch("routers.aaf.Auth0Client.update_user") + + response = test_client.get("/aaf/check-link", params={"session_token": "valid_token"}) + + assert response.status_code == 200 + assert response.json() == {"link": True, "aaf_only": False, "primary_id": db_user.id} + link_identity.assert_called_once_with( + primary_user_id=db_user.id, + secondary_user_id=aaf_user_id, + secondary_provider="samlp", + secondary_connection_name="AAF", + ) + update_user.assert_called_once() + + test_db_session.refresh(db_user) + assert db_user.account_type == BiocommonsUserAccountType.AAF + assert db_user.other_user_id == aaf_user_id + + +def test_check_link_already_linked_is_idempotent(test_client, test_db_session, persistent_factories, mocker): + email = "already-linked@example.com" + aaf_user_id = random_auth0_id() + db_user = BiocommonsUserFactory.create_sync( + email=email, account_type=BiocommonsUserAccountType.AAF, other_user_id=aaf_user_id + ) + test_db_session.commit() + + mocker.patch("dependencies.auth.verify_action_token", return_value=_action_token_payload(aaf_user_id, email)) + existing_account = Auth0UserDataFactory.build(user_id=db_user.id, email=email, blocked=False) + mocker.patch("routers.aaf.Auth0Client.search_users_by_email", return_value=[existing_account]) + get_user = mocker.patch("routers.aaf.Auth0Client.get_user") + link_identity = mocker.patch("routers.aaf.Auth0Client.link_identity") + update_user = mocker.patch("routers.aaf.Auth0Client.update_user") + + response = test_client.get("/aaf/check-link", params={"session_token": "valid_token"}) + + assert response.status_code == 200 + assert response.json() == {"link": True, "aaf_only": False, "primary_id": db_user.id} + get_user.assert_not_called() + link_identity.assert_not_called() + update_user.assert_not_called() diff --git a/tests/test_auth0_client.py b/tests/test_auth0_client.py index 11bca468..cb262c80 100644 --- a/tests/test_auth0_client.py +++ b/tests/test_auth0_client.py @@ -82,16 +82,102 @@ def test_get_connections(test_auth0_client): @respx.mock def test_get_connection_by_name(test_auth0_client): db_connection = Auth0ConnectionFactory.build(name="db_connection") - other = Auth0ConnectionFactory.build(name="other") - resp = ConnectionsWithCheckpointFactory.build(connections=[db_connection, other]) - route = respx.get("https://auth0.example.com/api/v2/connections").respond(200, json=resp.model_dump(mode="json")) + route = respx.get("https://auth0.example.com/api/v2/connections").respond( + 200, json=[db_connection.model_dump(mode="json")] + ) result = test_auth0_client.get_connection_by_name(db_connection.name) assert route.called + assert route.calls.last.request.url.params["name"] == db_connection.name assert result == db_connection +@respx.mock +def test_get_connection_by_name_not_found(test_auth0_client): + route = respx.get("https://auth0.example.com/api/v2/connections").respond(200, json=[]) + + result = test_auth0_client.get_connection_by_name("db_connection") + + assert route.called + assert result is None + + +@respx.mock +def test_link_identity(test_auth0_client): + """ + Test linking a secondary identity to a primary account. + + Per https://auth0.com/docs/api/management/v2/users/post-identities, + when linking with an API v2 token the request body has provider/user_id/ + connection_id, and the response is a list of identity objects. + + Uses a connection name ("AAF") that differs from its provider/strategy + ("samlp") to make sure the two aren't confused with each other. + """ + primary_user_id = random_auth0_id() + secondary_user_id = random_auth0_id() + connection = Auth0ConnectionFactory.build(name="AAF", strategy="samlp") + respx.get("https://auth0.example.com/api/v2/connections").respond( + 200, json=[connection.model_dump(mode="json")] + ) + route = respx.post(f"https://auth0.example.com/api/v2/users/{primary_user_id}/identities").respond( + 201, + json=[ + { + "connection": connection.name, + "provider": "samlp", + "user_id": secondary_user_id, + "isSocial": False, + } + ], + ) + + result = test_auth0_client.link_identity( + primary_user_id, secondary_user_id, secondary_provider="samlp", secondary_connection_name="AAF" + ) + + assert route.called + assert result is True + call_data = json.loads(route.calls.last.request.content) + assert call_data == { + "provider": "samlp", + "connection_id": connection.id, + "user_id": secondary_user_id, + } + + +@respx.mock +def test_link_identity_connection_not_found(test_auth0_client): + respx.get("https://auth0.example.com/api/v2/connections").respond(200, json=[]) + + with pytest.raises(ValueError): + test_auth0_client.link_identity( + random_auth0_id(), random_auth0_id(), secondary_provider="samlp", secondary_connection_name="AAF" + ) + + +@respx.mock +def test_link_identity_already_linked(test_auth0_client): + """ + Auth0 rejects linking an identity that's already linked (e.g. a retried + request) - this should surface as a clean ValueError, not a raw HTTPStatusError. + """ + primary_user_id = random_auth0_id() + secondary_user_id = random_auth0_id() + connection = Auth0ConnectionFactory.build(name="AAF", strategy="samlp") + respx.get("https://auth0.example.com/api/v2/connections").respond( + 200, json=[connection.model_dump(mode="json")] + ) + respx.post(f"https://auth0.example.com/api/v2/users/{primary_user_id}/identities").respond( + 400, json={"statusCode": 400, "error": "Bad Request", "message": "Identity already linked"} + ) + + with pytest.raises(ValueError): + test_auth0_client.link_identity( + primary_user_id, secondary_user_id, secondary_provider="samlp", secondary_connection_name="AAF" + ) + @respx.mock def test_get_role_users(test_auth0_client): diff --git a/tests/test_dependencies.py b/tests/test_dependencies.py new file mode 100644 index 00000000..6ee38290 --- /dev/null +++ b/tests/test_dependencies.py @@ -0,0 +1,37 @@ +from datetime import datetime, timedelta, timezone + +import jwt +import pytest +from fastapi import HTTPException + +from dependencies.auth import require_action_token +from schemas.auth0 import Auth0ActionToken +from tests.datagen import random_auth0_id + + +def create_signed_action_token(payload: Auth0ActionToken, secret: str) -> str: + claims = payload.model_dump(mode="json") + claims["exp"] = datetime.now(timezone.utc) + timedelta(minutes=5) + return jwt.encode(claims, key=secret, algorithm="HS256") + + +def test_require_action_token(mock_settings): + payload = Auth0ActionToken(user_id=random_auth0_id(), + email="test@example.com", + client_id="abc123", + purpose="action_purpose") + signed_token = create_signed_action_token(payload, secret=mock_settings.auth0_management_secret) + checker = require_action_token(purpose="action_purpose") + checked_payload = checker(signed_token, mock_settings) + assert checked_payload == payload + + +def test_require_action_token_wrong_purpose(mock_settings): + payload = Auth0ActionToken(user_id=random_auth0_id(), + email="test@example.com", + client_id="abc123", + purpose="wrong_purpose") + signed_token = create_signed_action_token(payload, secret=mock_settings.auth0_management_secret) + checker = require_action_token(purpose="action_purpose") + with pytest.raises(HTTPException): + checker(signed_token, mock_settings) From 2f9d77c33e11496ad36d25c1dccc292462a405e4 Mon Sep 17 00:00:00 2001 From: marius-mather <61438033+marius-mather@users.noreply.github.com> Date: Fri, 4 Sep 2026 14:21:39 +1000 Subject: [PATCH 07/25] fix: need to redirect back to Auth0 with a signed token, not just return a response (AAI-877) (#295) * feat: allow filtering users by connection when searching by email * feat: updated schemas for AAF info * feat: link_identity method for Auth0Client * feat: record other user ID for users * feat: method to link account for BiocommonsUser * fix: linking_completed_at should be datetime * feat: dependency to check Auth0 action tokens * feat: router with initial /aaf/check-link endpoint * chore: include aaf router in main * refactor: use a base URL for Auth0 API calls * test: unit tests of new Auth0Client methods * test: unit tests of AAF link function * test: tests of require_action_token * test: unit tests of account linking endpoint * fix: get connection correctly when linking accounts * fix: skip linking if already done * fix: update app_metadata to mark user AAF only if no existing account * test: unit tests of app_metadata for AAF-only accounts * fix: handle errors when Auth0 already linked * feat: create_action_token function to sign tokens for Auth0 actions * fix: need to return a redirect response to Auth0 in check-link * test: update tests of check-link * fix: fall back to Auth0 domain if custom domain not defined * test: make sure we test redirect location * fix: set required fields on action token payload * fix: make sure we're including all the required fields for a token returned to Auth0 * test: update tests * fix: action token should also contain iat field * fix: don't return 403 response for blocked accounts, return a token to Auth0 * fix: can't link on this side, return identity to Auth0 for linking * test: update tests * fix: remove response_model - response is a redirect --- auth/validator.py | 21 +++ routers/aaf.py | 124 +++++++++++--- schemas/auth0.py | 2 + tests/auth/test_auth_validator.py | 90 ++++++++++- tests/test_aaf.py | 257 ++++++++++++++++++++++++------ tests/test_dependencies.py | 14 +- 6 files changed, 435 insertions(+), 73 deletions(-) diff --git a/auth/validator.py b/auth/validator.py index a0491fe4..8bb80025 100644 --- a/auth/validator.py +++ b/auth/validator.py @@ -2,6 +2,7 @@ import json import logging import weakref +from datetime import UTC, datetime, timedelta import httpx import jwt @@ -168,3 +169,23 @@ def verify_action_token(token: str, settings: Settings) -> dict: except InvalidTokenError: raise HTTPException(status_code=401, detail="invalid session_token") return payload + + +def create_action_token(payload: dict, settings: Settings, expires_in_seconds: int = 300) -> dict: + """ + Create a signed JWT that can be passed back to Auth0 actions + """ + required_fields = ["sub", "iss", "state"] + for field in required_fields: + if field not in payload: + raise ValueError( f"Missing required field {field} in action token") + now = datetime.now(tz=UTC) + exp = (now + timedelta(seconds=expires_in_seconds)).timestamp() + payload = {**payload, "exp": int(exp), "iat": int(now.timestamp())} + secret = settings.auth0_management_secret + signed_payload = jwt.encode( + payload, + key=secret, + algorithm="HS256", + ) + return signed_payload diff --git a/routers/aaf.py b/routers/aaf.py index 83d13140..430b9ba3 100644 --- a/routers/aaf.py +++ b/routers/aaf.py @@ -2,11 +2,15 @@ from datetime import datetime, timezone from http import HTTPStatus from typing import Annotated +from urllib.parse import urlparse +import httpx2 from fastapi import APIRouter, Depends, HTTPException from pydantic import BaseModel from sqlmodel import Session +from starlette.responses import RedirectResponse +from auth.validator import create_action_token from auth0.client import Auth0Client, UpdateUserData, get_auth0_client from config import Settings, get_settings from db.models import BiocommonsUser @@ -14,6 +18,7 @@ from dependencies.auth import require_action_token from schemas.auth0 import Auth0ActionToken from schemas.biocommons import ( + Auth0Identity, Auth0UserData, BiocommonsAppMetadataUpdate, BiocommonsUserAccountType, @@ -28,31 +33,47 @@ class AccountLinkResponse(BaseModel): link: bool aaf_only: bool = False + blocked: bool = False primary_id: str + aaf_identity: Auth0Identity | None = None -def link_aaf_account(db_user_id: str, aaf_user_id: str, auth0_client: Auth0Client, session: Session): - def _get_aaf_identity(aaf_user: Auth0UserData): +class SignedAccountLinkResponse(AccountLinkResponse): + """ + Set the fields we need a signed action token to return + to Auth0 + """ + sub: str + iss: str + state: str + + +def link_aaf_account(db_user_id: str, aaf_user_id: str, auth0_client: Auth0Client, session: Session) -> Auth0Identity: + """ + Update app_metadata and DB record for AAF account linking. + + NOTE: we can't do the actual linking here, it needs to be done + on the Auth0 side. See: https://support.auth0.com/center/s/article/Unable-to-process-redirect-callback + """ + def _get_aaf_identity(aaf_user: Auth0UserData) -> Auth0Identity | None: for identity in aaf_user.identities: if identity.connection == "AAF": return identity return None - db_user = BiocommonsUser.get_by_id_or_404(db_user_id, session=session) - if db_user.account_type == BiocommonsUserAccountType.AAF and db_user.other_user_id == aaf_user_id: - logger.info("AAF account already linked, skipping re-link") - return db_user aaf_user_info = auth0_client.get_user(user_id=aaf_user_id) aaf_identity = _get_aaf_identity(aaf_user_info) if aaf_identity is None: raise HTTPException(status_code=HTTPStatus.NOT_FOUND, detail="Couldn't get AAF provider information") - logger.info("Linking AAF account to existing database account") + db_user = BiocommonsUser.get_by_id_or_404(db_user_id, session=session) + if db_user.account_type == BiocommonsUserAccountType.AAF and db_user.other_user_id == aaf_user_id: + logger.info("AAF account already linked, skipping re-link") + return aaf_identity + + logger.info("Updating DB record and account metadata") now = datetime.now(tz=timezone.utc) try: - auth0_client.link_identity(primary_user_id=db_user_id, secondary_user_id=aaf_user_id, - secondary_provider=aaf_identity.provider, - secondary_connection_name=aaf_identity.connection) auth0_client.update_user( db_user_id, update_data=UpdateUserData( @@ -64,11 +85,11 @@ def _get_aaf_identity(aaf_user: Auth0UserData): ) ) except ValueError as exc: - logger.error(f"Failed to link AAF account in Auth0: {exc}") + logger.error(f"Failed to update account metadata in Auth0: {exc}") raise HTTPException(status_code=HTTPStatus.BAD_GATEWAY, detail="Failed to link account with Auth0") from exc logger.info("Updating DB record") db_user.link_aaf_account(aaf_user_id=aaf_user_id, session=session, updated_by=db_user, commit=True) - return db_user + return aaf_identity def mark_user_aaf_only(user_email: str, aaf_user_id: str, auth0_client: Auth0Client): @@ -83,9 +104,52 @@ def mark_user_aaf_only(user_email: str, aaf_user_id: str, auth0_client: Auth0Cli auth0_client.update_user(user_id=aaf_user_id, update_data=update_data) +def return_signed_response( + state: str, + response: AccountLinkResponse, + action_token: Auth0ActionToken, + settings: Settings, +): + """ + Auth0 Actions need to receive the response as a signed JWT + token, sign the AccountLinkResponse we want to return + and redirect to the continue endpoint + """ + signed_payload = SignedAccountLinkResponse( + **response.model_dump(), + sub=action_token.sub or action_token.user_id, + iss=action_token.iss or settings.auth0_domain, + state=state, + ) + signed_token = create_action_token( + payload=signed_payload.model_dump(mode="json", exclude_none=True), + settings=settings, + ) + auth0_base_url = get_auth0_continue_base_url(action_token, settings) + redirect_url = httpx2.URL( + f"{auth0_base_url}/continue", + params={"state": state, "session_token": signed_token}, + ) + return RedirectResponse(url=redirect_url) + + +def get_auth0_continue_base_url(action_token: Auth0ActionToken, settings: Settings) -> str: + """ + Get domain to continue action from action token's issuer, if possible - want + to ensure we continue on the same domain + """ + if action_token.iss: + issuer = action_token.iss.rstrip("/") + parsed_issuer = urlparse(issuer) + if parsed_issuer.scheme and parsed_issuer.netloc: + return f"{parsed_issuer.scheme}://{parsed_issuer.netloc}" + return f"https://{issuer}" + return settings.auth0_custom_domain or f"https://{settings.auth0_domain}" -@router.get("/check-link", response_model=AccountLinkResponse) + +@router.get("/check-link") def check_aaf_account_link( + state: str, token: Annotated[Auth0ActionToken, Depends(require_action_token(purpose="aaf_link"))], session: Annotated[Session, Depends(get_db_session)], auth0_client: Annotated[Auth0Client, Depends(get_auth0_client)], @@ -100,7 +164,13 @@ def check_aaf_account_link( # No existing account: no need to link if not auth0_matches: mark_user_aaf_only(email, aaf_user_id, auth0_client) - return AccountLinkResponse(link=False, aaf_only=True, primary_id=token.user_id) + resp = AccountLinkResponse(link=False, aaf_only=True, primary_id=aaf_user_id) + return return_signed_response( + state=state, + response=resp, + action_token=token, + settings=settings, + ) existing_account = None for user in auth0_matches: @@ -110,15 +180,33 @@ def check_aaf_account_link( # No exact match: no existing account if not existing_account: mark_user_aaf_only(email, aaf_user_id, auth0_client) - return AccountLinkResponse(link=False, aaf_only=True, primary_id=email) + resp = AccountLinkResponse(link=False, aaf_only=True, primary_id=aaf_user_id) + return return_signed_response( + state=state, + response=resp, + action_token=token, + settings=settings, + ) if existing_account.blocked: - raise HTTPException(status_code=403, detail="Existing account is blocked.") + resp = AccountLinkResponse(link=True, aaf_only=False, primary_id=existing_account.user_id, blocked=True) + return return_signed_response( + state=state, + response=resp, + action_token=token, + settings=settings, + ) - link_aaf_account( + aaf_identity = link_aaf_account( db_user_id=existing_account.user_id, aaf_user_id=aaf_user_id, auth0_client=auth0_client, session=session, ) - return AccountLinkResponse(link=True, aaf_only=False, primary_id=existing_account.user_id) + resp = AccountLinkResponse(link=True, aaf_only=False, primary_id=existing_account.user_id, aaf_identity=aaf_identity) + return return_signed_response( + state=state, + response=resp, + action_token=token, + settings=settings, + ) diff --git a/schemas/auth0.py b/schemas/auth0.py index 57070774..c44f7414 100644 --- a/schemas/auth0.py +++ b/schemas/auth0.py @@ -30,3 +30,5 @@ class Auth0ActionToken(BaseModel): email: EmailStr client_id: str purpose: str + sub: str | None = None + iss: str | None = None diff --git a/tests/auth/test_auth_validator.py b/tests/auth/test_auth_validator.py index 302f0bc5..4e8f2d45 100644 --- a/tests/auth/test_auth_validator.py +++ b/tests/auth/test_auth_validator.py @@ -2,7 +2,7 @@ import json import uuid from dataclasses import dataclass -from datetime import datetime, timedelta +from datetime import UTC, datetime, timedelta from typing import Optional from unittest.mock import AsyncMock, patch @@ -19,7 +19,9 @@ from fastapi import Depends, FastAPI, HTTPException from fastapi.security import HTTPAuthorizationCredentials from fastapi.testclient import TestClient +from freezegun import freeze_time from httpx import Request, Response +from jwt import InvalidSignatureError from jwt.algorithms import RSAAlgorithm from auth import auth0_security, get_auth0_token @@ -27,6 +29,7 @@ from auth.validator import ( KEY_CACHE, _fetch_rsa_keys, + create_action_token, get_rsa_key, verify_action_token, verify_jwt, @@ -39,6 +42,16 @@ TEST_MANAGEMENT_SECRET = "test-management-secret-key-with-32b" TEST_WRONG_MANAGEMENT_SECRET = "wrong-management-secret-key-32b!" TEST_CORRECT_MANAGEMENT_SECRET = "correct-management-secret-key-32" +FROZEN_TIME = datetime(2025, 1, 1, 12, 0, 0, tzinfo=UTC) + + +@pytest.fixture +def frozen_time(): + """ + Freeze time so datetime.now() returns FROZEN_TIME. + """ + with freeze_time("2025-01-01 12:00:00") as time: + yield time def generate_public_private_key_pair(): @@ -586,6 +599,81 @@ def test_verify_action_token_missing_exp(mock_settings: Settings): assert excinfo.value.detail == "invalid session_token" +def test_create_action_token_success(mock_settings: Settings, frozen_time): + secret = TEST_MANAGEMENT_SECRET + mock_settings.auth0_management_secret = secret + payload = { + "sub": "auth0|123", + "iss": "https://issuer.example.com", + "state": "test-state", + "data": "test-payload", + } + token = create_action_token(payload, mock_settings) + decoded = jwt.decode(token, secret, algorithms=["HS256"]) + assert decoded["sub"] == "auth0|123" + assert decoded["iss"] == "https://issuer.example.com" + assert decoded["state"] == "test-state" + assert decoded["data"] == "test-payload" + assert decoded["exp"] == (FROZEN_TIME + timedelta(minutes=5)).timestamp() + assert decoded["iat"] == FROZEN_TIME.timestamp() + + +def test_create_action_token_expiry(mock_settings: Settings, frozen_time): + """ + Test we can change expiry time of an action token. + """ + secret = TEST_MANAGEMENT_SECRET + mock_settings.auth0_management_secret = secret + payload = { + "sub": "auth0|123", + "iss": "https://issuer.example.com", + "state": "test-state", + "data": "test-payload", + } + token = create_action_token(payload, mock_settings, expires_in_seconds=10 * 60) + decoded = jwt.decode(token, secret, algorithms=["HS256"]) + assert decoded["data"] == "test-payload" + assert decoded["exp"] == (FROZEN_TIME + timedelta(minutes=10)).timestamp() + + +@pytest.mark.parametrize("missing_field", ["sub", "iss", "state"]) +def test_create_action_token_missing_required_field( + mock_settings: Settings, + frozen_time, + missing_field: str, +): + secret = TEST_MANAGEMENT_SECRET + mock_settings.auth0_management_secret = secret + payload = { + "sub": "auth0|123", + "iss": "https://issuer.example.com", + "state": "test-state", + } + del payload[missing_field] + + with pytest.raises( + ValueError, + match=f"Missing required field {missing_field} in action token", + ): + create_action_token(payload, mock_settings) + + +def test_create_action_token_invalid(mock_settings: Settings, frozen_time): + secret = TEST_MANAGEMENT_SECRET + # Use invalid secret to sign + mock_settings.auth0_management_secret = "invalid-secret" + payload = { + "sub": "auth0|123", + "iss": "https://issuer.example.com", + "state": "test-state", + "data": "test-payload", + } + token = create_action_token(payload, mock_settings, expires_in_seconds=10 * 60) + # Use expected secret to decode + with pytest.raises(InvalidSignatureError, match="Signature verification failed"): + jwt.decode(token, secret, algorithms=["HS256"]) + + @pytest.mark.asyncio @respx.mock async def test_fetch_rsa_keys_only_refreshes_once_when_cache_is_expired(mock_settings: Settings): diff --git a/tests/test_aaf.py b/tests/test_aaf.py index 489ee26a..42478e48 100644 --- a/tests/test_aaf.py +++ b/tests/test_aaf.py @@ -1,6 +1,8 @@ from http import HTTPStatus from unittest.mock import MagicMock +from urllib.parse import parse_qs, urlparse +import jwt import pytest from fastapi import HTTPException @@ -30,13 +32,7 @@ def test_link_aaf_account_links_identity_updates_metadata_and_db(test_db_session ) auth0_client.get_user.assert_called_once_with(user_id=aaf_user_id) - auth0_client.link_identity.assert_called_once_with( - primary_user_id=db_user.id, - secondary_user_id=aaf_user_id, - secondary_provider="samlp", - secondary_connection_name="AAF", - ) - + auth0_client.link_identity.assert_not_called() auth0_client.update_user.assert_called_once() call_args, call_kwargs = auth0_client.update_user.call_args assert call_args[0] == db_user.id @@ -45,9 +41,7 @@ def test_link_aaf_account_links_identity_updates_metadata_and_db(test_db_session assert app_metadata.linking_completed is True assert app_metadata.linking_completed_at is not None - assert result.id == db_user.id - assert result.account_type == BiocommonsUserAccountType.AAF - assert result.other_user_id == aaf_user_id + assert result == aaf_user_data.identities[0] test_db_session.refresh(db_user) assert db_user.account_type == BiocommonsUserAccountType.AAF @@ -89,7 +83,7 @@ def test_link_aaf_account_raises_404_when_no_aaf_identity(test_db_session, persi assert db_user.other_user_id is None -def test_link_aaf_account_raises_502_when_auth0_linking_fails(test_db_session, persistent_factories): +def test_link_aaf_account_raises_502_when_auth0_update_fails(test_db_session, persistent_factories): db_user = BiocommonsUserFactory.create_sync(account_type=BiocommonsUserAccountType.AUTH0, other_user_id=None) test_db_session.commit() @@ -99,7 +93,7 @@ def test_link_aaf_account_raises_502_when_auth0_linking_fails(test_db_session, p ) auth0_client = MagicMock(spec=Auth0Client) auth0_client.get_user.return_value = aaf_user_data - auth0_client.link_identity.side_effect = ValueError("Identity already linked") + auth0_client.update_user.side_effect = ValueError("Auth0 update failed") with pytest.raises(HTTPException) as exc_info: link_aaf_account( @@ -110,7 +104,8 @@ def test_link_aaf_account_raises_502_when_auth0_linking_fails(test_db_session, p ) assert exc_info.value.status_code == HTTPStatus.BAD_GATEWAY - auth0_client.update_user.assert_not_called() + auth0_client.link_identity.assert_not_called() + auth0_client.update_user.assert_called_once() test_db_session.refresh(db_user) assert db_user.account_type == BiocommonsUserAccountType.AUTH0 @@ -124,7 +119,11 @@ def test_link_aaf_account_idempotent_when_already_linked(test_db_session, persis ) test_db_session.commit() + aaf_user_data = Auth0UserDataFactory.build( + identities=[Auth0Identity(connection="AAF", provider="samlp", user_id=aaf_user_id, isSocial=False)] + ) auth0_client = MagicMock(spec=Auth0Client) + auth0_client.get_user.return_value = aaf_user_data result = link_aaf_account( db_user_id=db_user.id, @@ -133,14 +132,31 @@ def test_link_aaf_account_idempotent_when_already_linked(test_db_session, persis session=test_db_session, ) - auth0_client.get_user.assert_not_called() + auth0_client.get_user.assert_called_once_with(user_id=aaf_user_id) auth0_client.link_identity.assert_not_called() auth0_client.update_user.assert_not_called() - assert result.id == db_user.id - - -def _action_token_payload(user_id: str, email: str, purpose: str = "aaf_link", client_id: str = "test-client") -> dict: - return {"user_id": user_id, "email": email, "client_id": client_id, "purpose": purpose} + assert result == aaf_user_data.identities[0] + + +def _action_token_payload( + user_id: str, + email: str, + purpose: str = "aaf_link", + client_id: str = "test-client", + sub: str | None = None, + iss: str | None = "mock-domain", +) -> dict: + payload = { + "user_id": user_id, + "email": email, + "client_id": client_id, + "purpose": purpose, + } + if sub is not None: + payload["sub"] = sub + if iss is not None: + payload["iss"] = iss + return payload def _assert_marked_aaf_only(update_user_mock, aaf_user_id: str, email: str): @@ -154,6 +170,45 @@ def _assert_marked_aaf_only(update_user_mock, aaf_user_id: str, email: str): assert app_metadata.linking_completed_at is not None +def _expected_auth0_continue_base_url(incoming_token: dict, settings) -> str: + issuer = incoming_token.get("iss") + if issuer is None: + return settings.auth0_custom_domain or f"https://{settings.auth0_domain}" + issuer = issuer.rstrip("/") + parsed_issuer = urlparse(issuer) + if parsed_issuer.scheme and parsed_issuer.netloc: + return f"{parsed_issuer.scheme}://{parsed_issuer.netloc}" + return f"https://{issuer}" + + +def _decode_check_link_redirect( + response, + state: str, + settings, + incoming_token: dict, +) -> dict: + assert response.status_code == HTTPStatus.TEMPORARY_REDIRECT + assert response.is_redirect + redirect = urlparse(response.headers["location"]) + expected_base_url = _expected_auth0_continue_base_url(incoming_token, settings) + expected_continue_url = urlparse(f"{expected_base_url}/continue") + assert redirect.scheme == expected_continue_url.scheme + assert redirect.netloc == expected_continue_url.netloc + assert redirect.path == expected_continue_url.path + query_params = parse_qs(redirect.query) + assert query_params["state"] == [state] + assert "session_token" in query_params + decoded_token = jwt.decode( + query_params["session_token"][0], + key=settings.auth0_management_secret, + algorithms=["HS256"], + ) + assert decoded_token["state"] == state + assert decoded_token["sub"] == incoming_token.get("sub", incoming_token["user_id"]) + assert decoded_token["iss"] == incoming_token.get("iss", settings.auth0_domain) + return decoded_token + + def test_mark_user_aaf_only(): aaf_user_id = random_auth0_id() email = "aaf-user@example.com" @@ -164,52 +219,113 @@ def test_mark_user_aaf_only(): _assert_marked_aaf_only(auth0_client.update_user, aaf_user_id, email) -def test_check_link_no_existing_account(test_client, mocker): +def test_check_link_no_existing_account(test_client, mocker, mock_settings): aaf_user_id = random_auth0_id() email = "new-aaf-user@example.com" - mocker.patch("dependencies.auth.verify_action_token", return_value=_action_token_payload(aaf_user_id, email)) + action_token_payload = _action_token_payload( + aaf_user_id, + email, + sub=aaf_user_id, + iss="https://login.example.com/", + ) + mocker.patch("dependencies.auth.verify_action_token", return_value=action_token_payload) mocker.patch("routers.aaf.Auth0Client.search_users_by_email", return_value=[]) link_identity = mocker.patch("routers.aaf.Auth0Client.link_identity") update_user = mocker.patch("routers.aaf.Auth0Client.update_user") - response = test_client.get("/aaf/check-link", params={"session_token": "valid_token"}) + state = "dummy" + response = test_client.get( + "/aaf/check-link", + params={"session_token": "valid_token", "state": state}, + follow_redirects=False, + ) + + decoded_token = _decode_check_link_redirect( + response, + state=state, + settings=mock_settings, + incoming_token=action_token_payload, + ) + assert decoded_token["link"] is False + assert decoded_token["aaf_only"] is True + assert decoded_token["primary_id"] == aaf_user_id - assert response.status_code == 200 - assert response.json() == {"link": False, "aaf_only": True, "primary_id": aaf_user_id} link_identity.assert_not_called() _assert_marked_aaf_only(update_user, aaf_user_id, email) -def test_check_link_no_exact_email_match(test_client, mocker): +def test_check_link_no_exact_email_match(test_client, mocker, mock_settings): aaf_user_id = random_auth0_id() email = "aaf-user@example.com" - mocker.patch("dependencies.auth.verify_action_token", return_value=_action_token_payload(aaf_user_id, email)) + action_token_payload = _action_token_payload( + aaf_user_id, + email, + sub="auth0|original-sub", + ) + mocker.patch("dependencies.auth.verify_action_token", return_value=action_token_payload) near_miss_account = Auth0UserDataFactory.build(email="different-user@example.com") mocker.patch("routers.aaf.Auth0Client.search_users_by_email", return_value=[near_miss_account]) link_identity = mocker.patch("routers.aaf.Auth0Client.link_identity") update_user = mocker.patch("routers.aaf.Auth0Client.update_user") - response = test_client.get("/aaf/check-link", params={"session_token": "valid_token"}) + state = "dummy" + response = test_client.get( + "/aaf/check-link", + params={"session_token": "valid_token", "state": state}, + follow_redirects=False, + ) - assert response.status_code == 200 - assert response.json() == {"link": False, "aaf_only": True, "primary_id": email} + decoded_token = _decode_check_link_redirect( + response, + state=state, + settings=mock_settings, + incoming_token=action_token_payload, + ) + assert decoded_token["link"] is False + assert decoded_token["aaf_only"] is True + assert decoded_token["primary_id"] == aaf_user_id link_identity.assert_not_called() _assert_marked_aaf_only(update_user, aaf_user_id, email) -def test_check_link_existing_account_blocked(test_client, mocker): +def test_check_link_existing_account_blocked(test_client, mocker, mock_settings): aaf_user_id = random_auth0_id() email = "blocked-user@example.com" - mocker.patch("dependencies.auth.verify_action_token", return_value=_action_token_payload(aaf_user_id, email)) + action_token_payload = _action_token_payload(aaf_user_id, email) + mocker.patch( + "dependencies.auth.verify_action_token", + return_value=action_token_payload, + ) existing_account = Auth0UserDataFactory.build(email=email, blocked=True) mocker.patch("routers.aaf.Auth0Client.search_users_by_email", return_value=[existing_account]) + get_user = mocker.patch("routers.aaf.Auth0Client.get_user") + link_identity = mocker.patch("routers.aaf.Auth0Client.link_identity") + update_user = mocker.patch("routers.aaf.Auth0Client.update_user") - response = test_client.get("/aaf/check-link", params={"session_token": "valid_token"}) + state = "dummy" + response = test_client.get( + "/aaf/check-link", + params={"session_token": "valid_token", "state": state}, + follow_redirects=False, + ) - assert response.status_code == 403 + decoded_token = _decode_check_link_redirect( + response, + state=state, + settings=mock_settings, + incoming_token=action_token_payload, + ) + assert decoded_token["link"] is True + assert decoded_token["aaf_only"] is False + assert decoded_token["blocked"] is True + assert decoded_token["primary_id"] == existing_account.user_id + + get_user.assert_not_called() + link_identity.assert_not_called() + update_user.assert_not_called() -def test_check_link_existing_account_links(test_client, test_db_session, persistent_factories, mocker): +def test_check_link_existing_account_links(test_client, test_db_session, persistent_factories, mocker, mock_settings): email = "existing-user@example.com" aaf_user_id = random_auth0_id() db_user = BiocommonsUserFactory.create_sync( @@ -217,7 +333,8 @@ def test_check_link_existing_account_links(test_client, test_db_session, persist ) test_db_session.commit() - mocker.patch("dependencies.auth.verify_action_token", return_value=_action_token_payload(aaf_user_id, email)) + action_token_payload = _action_token_payload(aaf_user_id, email, sub=aaf_user_id) + mocker.patch("dependencies.auth.verify_action_token", return_value=action_token_payload) existing_account = Auth0UserDataFactory.build(user_id=db_user.id, email=email, blocked=False) mocker.patch("routers.aaf.Auth0Client.search_users_by_email", return_value=[existing_account]) aaf_user_data = Auth0UserDataFactory.build( @@ -227,16 +344,29 @@ def test_check_link_existing_account_links(test_client, test_db_session, persist link_identity = mocker.patch("routers.aaf.Auth0Client.link_identity") update_user = mocker.patch("routers.aaf.Auth0Client.update_user") - response = test_client.get("/aaf/check-link", params={"session_token": "valid_token"}) + state = "dummy" + response = test_client.get( + "/aaf/check-link", + params={"session_token": "valid_token", "state": state}, + follow_redirects=False, + ) - assert response.status_code == 200 - assert response.json() == {"link": True, "aaf_only": False, "primary_id": db_user.id} - link_identity.assert_called_once_with( - primary_user_id=db_user.id, - secondary_user_id=aaf_user_id, - secondary_provider="samlp", - secondary_connection_name="AAF", + decoded_token = _decode_check_link_redirect( + response, + state=state, + settings=mock_settings, + incoming_token=action_token_payload, ) + assert decoded_token["link"] is True + assert decoded_token["aaf_only"] is False + assert decoded_token["primary_id"] == db_user.id + assert decoded_token["aaf_identity"] == { + "connection": "AAF", + "provider": "samlp", + "user_id": aaf_user_id, + "isSocial": False, + } + link_identity.assert_not_called() update_user.assert_called_once() test_db_session.refresh(db_user) @@ -244,7 +374,7 @@ def test_check_link_existing_account_links(test_client, test_db_session, persist assert db_user.other_user_id == aaf_user_id -def test_check_link_already_linked_is_idempotent(test_client, test_db_session, persistent_factories, mocker): +def test_check_link_already_linked_is_idempotent(test_client, test_db_session, persistent_factories, mocker, mock_settings): email = "already-linked@example.com" aaf_user_id = random_auth0_id() db_user = BiocommonsUserFactory.create_sync( @@ -252,17 +382,44 @@ def test_check_link_already_linked_is_idempotent(test_client, test_db_session, p ) test_db_session.commit() - mocker.patch("dependencies.auth.verify_action_token", return_value=_action_token_payload(aaf_user_id, email)) + action_token_payload = _action_token_payload( + aaf_user_id, + email, + sub=None, + iss=None, + ) + mocker.patch("dependencies.auth.verify_action_token", return_value=action_token_payload) existing_account = Auth0UserDataFactory.build(user_id=db_user.id, email=email, blocked=False) mocker.patch("routers.aaf.Auth0Client.search_users_by_email", return_value=[existing_account]) - get_user = mocker.patch("routers.aaf.Auth0Client.get_user") + aaf_user_data = Auth0UserDataFactory.build( + identities=[Auth0Identity(connection="AAF", provider="samlp", user_id=aaf_user_id, isSocial=False)] + ) + get_user = mocker.patch("routers.aaf.Auth0Client.get_user", return_value=aaf_user_data) link_identity = mocker.patch("routers.aaf.Auth0Client.link_identity") update_user = mocker.patch("routers.aaf.Auth0Client.update_user") - response = test_client.get("/aaf/check-link", params={"session_token": "valid_token"}) + state = "dummy" + response = test_client.get( + "/aaf/check-link", + params={"session_token": "valid_token", "state": state}, + follow_redirects=False, + ) - assert response.status_code == 200 - assert response.json() == {"link": True, "aaf_only": False, "primary_id": db_user.id} - get_user.assert_not_called() + decoded_token = _decode_check_link_redirect( + response, + state=state, + settings=mock_settings, + incoming_token=action_token_payload, + ) + assert decoded_token["link"] is True + assert decoded_token["aaf_only"] is False + assert decoded_token["primary_id"] == db_user.id + assert decoded_token["aaf_identity"] == { + "connection": "AAF", + "provider": "samlp", + "user_id": aaf_user_id, + "isSocial": False, + } + get_user.assert_called_once_with(user_id=aaf_user_id) link_identity.assert_not_called() update_user.assert_not_called() diff --git a/tests/test_dependencies.py b/tests/test_dependencies.py index 6ee38290..2f417f42 100644 --- a/tests/test_dependencies.py +++ b/tests/test_dependencies.py @@ -16,10 +16,13 @@ def create_signed_action_token(payload: Auth0ActionToken, secret: str) -> str: def test_require_action_token(mock_settings): - payload = Auth0ActionToken(user_id=random_auth0_id(), + user_id = random_auth0_id() + payload = Auth0ActionToken(user_id=user_id, email="test@example.com", client_id="abc123", - purpose="action_purpose") + purpose="action_purpose", + sub=user_id, + iss="mock-domain") signed_token = create_signed_action_token(payload, secret=mock_settings.auth0_management_secret) checker = require_action_token(purpose="action_purpose") checked_payload = checker(signed_token, mock_settings) @@ -27,10 +30,13 @@ def test_require_action_token(mock_settings): def test_require_action_token_wrong_purpose(mock_settings): - payload = Auth0ActionToken(user_id=random_auth0_id(), + user_id = random_auth0_id() + payload = Auth0ActionToken(user_id=user_id, email="test@example.com", client_id="abc123", - purpose="wrong_purpose") + purpose="wrong_purpose", + sub=user_id, + iss="mock-domain") signed_token = create_signed_action_token(payload, secret=mock_settings.auth0_management_secret) checker = require_action_token(purpose="action_purpose") with pytest.raises(HTTPException): From 420ca7ca7c9f256fd6bc58dc070efa20423d9877 Mon Sep 17 00:00:00 2001 From: amandazhu Date: Fri, 11 Sep 2026 10:40:03 +1000 Subject: [PATCH 08/25] feat: build and deploy aaf-dev image --- .../workflows/build-and-deploy-aaf-dev.yml | 157 ++++++++++++++++++ 1 file changed, 157 insertions(+) create mode 100644 .github/workflows/build-and-deploy-aaf-dev.yml diff --git a/.github/workflows/build-and-deploy-aaf-dev.yml b/.github/workflows/build-and-deploy-aaf-dev.yml new file mode 100644 index 00000000..dce79d9f --- /dev/null +++ b/.github/workflows/build-and-deploy-aaf-dev.yml @@ -0,0 +1,157 @@ +name: build-and-deploy-aaf-dev +# Builds a `dev-aaf`-tagged image from the aaf-dev branch and deploys it to the +# dev-aaf backend (biocloud-dev-aaf tenant), so AAF work can be tested without +# merging into main. Mirrors build-and-deploy-dev.yml but targets dev-aaf. +on: + push: + branches: [aaf-dev] + +permissions: + contents: read + id-token: write + +env: + AWS_REGION: ${{ secrets.AWS_REGION }} + IMAGE_REPO: ${{ secrets.AWS_ECR_IMAGE_REPO }} + +jobs: + docker: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v6 + + - name: Validate required secrets + env: + AWS_REGION: ${{ secrets.AWS_REGION }} + AWS_ECR_IMAGE_REPO: ${{ secrets.AWS_ECR_IMAGE_REPO }} + AWS_ROLE_ECR_PUSH: ${{ secrets.AWS_ROLE_ECR_PUSH }} + AWS_ROLE_BACKEND_DEPLOY_DEV_AAF: ${{ secrets.AWS_ROLE_BACKEND_DEPLOY_DEV_AAF }} + run: | + set -euo pipefail + if [ -z "${AWS_REGION}" ]; then + echo "Missing required secret AWS_REGION" >&2 + exit 1 + fi + if [ -z "${AWS_ECR_IMAGE_REPO}" ]; then + echo "Missing required secret AWS_ECR_IMAGE_REPO" >&2 + exit 1 + fi + if [ -z "${AWS_ROLE_ECR_PUSH}" ]; then + echo "Missing required secret AWS_ROLE_ECR_PUSH" >&2 + exit 1 + fi + if [ -z "${AWS_ROLE_BACKEND_DEPLOY_DEV_AAF}" ]; then + echo "Missing required secret AWS_ROLE_BACKEND_DEPLOY_DEV_AAF" >&2 + exit 1 + fi + + - uses: docker/setup-buildx-action@v4 + + - name: Stamp dev version + run: | + set -euo pipefail + SHORT_SHA=$(git rev-parse --short HEAD) + node <<'JS' + const fs = require('fs'); + const path = 'pyproject.toml'; + const shortSha = (process.env.SHORT_SHA || '').toLowerCase().slice(0, 7); + const lines = fs.readFileSync(path, 'utf8').split('\n'); + let updated = false; + let newVersion = null; + const result = lines.map((line) => { + if (line.startsWith('version = ')) { + const match = line.match(/version = \"(.+)\"/); + if (!match) { + return line; + } + const baseRaw = match[1]; + const cleanBase = baseRaw + .replace(/\.dev\d+(?:\+.+)?$/i, '') + .replace(/\+.+$/i, '') + .replace(/-dev_[0-9a-f]+$/i, ''); + newVersion = `${cleanBase}.dev0+g${shortSha}`; + updated = true; + return `version = "${newVersion}"`; + } + return line; + }); + if (!updated || !newVersion) { + throw new Error('Failed to compute new version'); + } + fs.writeFileSync(path, result.join('\n')); + console.log('Stamped version to', newVersion); + JS + env: + SHORT_SHA: ${{ github.sha }} + + - name: Sync uv lockfile + run: | + set -euo pipefail + python -m pip install uv==0.11.15 + uv lock + + # Authenticate to AWS + - uses: aws-actions/configure-aws-credentials@v6 + with: + role-to-assume: ${{ secrets.AWS_ROLE_ECR_PUSH }} + aws-region: ${{ env.AWS_REGION }} + + - uses: aws-actions/amazon-ecr-login@v2 + + - name: Build & Push (dev-aaf only) + uses: docker/build-push-action@v7 + with: + context: . + file: ./Dockerfile + platforms: linux/amd64 + push: true + tags: ${{ env.IMAGE_REPO }}:dev-aaf + provenance: false + sbom: false + cache-from: type=gha + cache-to: type=gha,mode=max + + - name: Configure AWS credentials for dev-aaf deploy + uses: aws-actions/configure-aws-credentials@v6 + with: + role-to-assume: ${{ secrets.AWS_ROLE_BACKEND_DEPLOY_DEV_AAF }} + role-session-name: backend-aaf-dev-deploy + aws-region: ${{ env.AWS_REGION }} + role-chaining: true + role-skip-session-tagging: true + + - name: Deploy dev-aaf backend via Lambda + env: + DEPLOY_FUNCTION_NAME: AaiBackendDevAafDeploymentFunction + IMAGE_TAG: dev-aaf + run: | + set -euo pipefail + + export AWS_MAX_ATTEMPTS=1 + + PAYLOAD=$(jq -n --arg tag "${IMAGE_TAG}" '{tag: $tag}') + RESPONSE_FILE=$(mktemp) + + INVOKE_METADATA=$(aws lambda invoke \ + --function-name "${DEPLOY_FUNCTION_NAME}" \ + --payload "${PAYLOAD}" \ + --cli-binary-format raw-in-base64-out \ + --cli-read-timeout 0 \ + "${RESPONSE_FILE}") + + echo "${INVOKE_METADATA}" + + FUNCTION_ERROR=$(echo "${INVOKE_METADATA}" | jq -r '.FunctionError // empty') + if [ -n "${FUNCTION_ERROR}" ]; then + echo "Deployment lambda reported an error: ${FUNCTION_ERROR}" >&2 + cat "${RESPONSE_FILE}" >&2 || true + exit 1 + fi + + cat "${RESPONSE_FILE}" + + STATUS=$(jq -r '.status // empty' "${RESPONSE_FILE}") + if [ "${STATUS}" != "SUCCESS" ]; then + echo "Deployment lambda returned unexpected status: ${STATUS}" >&2 + exit 1 + fi From 50a7204d1700d0d7133f7f1a27cf54b9dc087d62 Mon Sep 17 00:00:00 2001 From: amandazhu Date: Fri, 11 Sep 2026 11:26:43 +1000 Subject: [PATCH 09/25] ci: build and deploy aaf-dev image --- .../workflows/build-and-deploy-aaf-dev.yml | 26 ++++++++----------- 1 file changed, 11 insertions(+), 15 deletions(-) diff --git a/.github/workflows/build-and-deploy-aaf-dev.yml b/.github/workflows/build-and-deploy-aaf-dev.yml index dce79d9f..4d0f04f6 100644 --- a/.github/workflows/build-and-deploy-aaf-dev.yml +++ b/.github/workflows/build-and-deploy-aaf-dev.yml @@ -1,7 +1,14 @@ name: build-and-deploy-aaf-dev # Builds a `dev-aaf`-tagged image from the aaf-dev branch and deploys it to the # dev-aaf backend (biocloud-dev-aaf tenant), so AAF work can be tested without -# merging into main. Mirrors build-and-deploy-dev.yml but targets dev-aaf. +# merging into main. +# +# The ECR push role (AWS_ROLE_ECR_PUSH) does both the push and the deploy: it +# holds ECR push perms AND lambda:InvokeFunction on AaiBackendDevAafDeploymentFunction, +# so we invoke the deploy Lambda directly (same mechanism dev/staging use). No +# separate deploy role is needed. NOTE: the trust + invoke grant for dev-aaf were +# applied out-of-band (AaiSharedEcr stack is stale); a proper AaiSharedEcr deploy +# should fold them in via the committed IaC changes. on: push: branches: [aaf-dev] @@ -25,7 +32,6 @@ jobs: AWS_REGION: ${{ secrets.AWS_REGION }} AWS_ECR_IMAGE_REPO: ${{ secrets.AWS_ECR_IMAGE_REPO }} AWS_ROLE_ECR_PUSH: ${{ secrets.AWS_ROLE_ECR_PUSH }} - AWS_ROLE_BACKEND_DEPLOY_DEV_AAF: ${{ secrets.AWS_ROLE_BACKEND_DEPLOY_DEV_AAF }} run: | set -euo pipefail if [ -z "${AWS_REGION}" ]; then @@ -40,10 +46,6 @@ jobs: echo "Missing required secret AWS_ROLE_ECR_PUSH" >&2 exit 1 fi - if [ -z "${AWS_ROLE_BACKEND_DEPLOY_DEV_AAF}" ]; then - echo "Missing required secret AWS_ROLE_BACKEND_DEPLOY_DEV_AAF" >&2 - exit 1 - fi - uses: docker/setup-buildx-action@v4 @@ -111,15 +113,9 @@ jobs: cache-from: type=gha cache-to: type=gha,mode=max - - name: Configure AWS credentials for dev-aaf deploy - uses: aws-actions/configure-aws-credentials@v6 - with: - role-to-assume: ${{ secrets.AWS_ROLE_BACKEND_DEPLOY_DEV_AAF }} - role-session-name: backend-aaf-dev-deploy - aws-region: ${{ env.AWS_REGION }} - role-chaining: true - role-skip-session-tagging: true - + # No separate deploy-role step: the ECR push role (still active from the + # auth step above) also holds lambda:InvokeFunction on the dev-aaf deploy + # function, so we invoke it directly. - name: Deploy dev-aaf backend via Lambda env: DEPLOY_FUNCTION_NAME: AaiBackendDevAafDeploymentFunction From ba9ef96e4b00a1c64f0144b0f9d4dc679402d8e8 Mon Sep 17 00:00:00 2001 From: amandazhu Date: Fri, 11 Sep 2026 12:39:50 +1000 Subject: [PATCH 10/25] fix: update aaf-dev deploy to use the right role --- .../workflows/build-and-deploy-aaf-dev.yml | 31 ++++++++++++------- 1 file changed, 20 insertions(+), 11 deletions(-) diff --git a/.github/workflows/build-and-deploy-aaf-dev.yml b/.github/workflows/build-and-deploy-aaf-dev.yml index 4d0f04f6..2349fca4 100644 --- a/.github/workflows/build-and-deploy-aaf-dev.yml +++ b/.github/workflows/build-and-deploy-aaf-dev.yml @@ -1,14 +1,12 @@ name: build-and-deploy-aaf-dev # Builds a `dev-aaf`-tagged image from the aaf-dev branch and deploys it to the # dev-aaf backend (biocloud-dev-aaf tenant), so AAF work can be tested without -# merging into main. +# merging into main. Mirrors build-and-deploy-dev.yml but targets dev-aaf. # -# The ECR push role (AWS_ROLE_ECR_PUSH) does both the push and the deploy: it -# holds ECR push perms AND lambda:InvokeFunction on AaiBackendDevAafDeploymentFunction, -# so we invoke the deploy Lambda directly (same mechanism dev/staging use). No -# separate deploy role is needed. NOTE: the trust + invoke grant for dev-aaf were -# applied out-of-band (AaiSharedEcr stack is stale); a proper AaiSharedEcr deploy -# should fold them in via the committed IaC changes. +# Deploy mechanism (assume-invoke-role, cross-account): the CI push role +# (AWS_ROLE_ECR_PUSH, in 331315009666) assumes the dev-aaf invoke role +# (AWS_ROLE_BACKEND_DEPLOY_DEV_AAF = aai-backend-dev-aaf-deploy-invoke-role in +# 498096047392), which invokes AaiBackendDevAafDeploymentFunction. on: push: branches: [aaf-dev] @@ -32,6 +30,7 @@ jobs: AWS_REGION: ${{ secrets.AWS_REGION }} AWS_ECR_IMAGE_REPO: ${{ secrets.AWS_ECR_IMAGE_REPO }} AWS_ROLE_ECR_PUSH: ${{ secrets.AWS_ROLE_ECR_PUSH }} + AWS_ROLE_BACKEND_DEPLOY_DEV_AAF: ${{ secrets.AWS_ROLE_BACKEND_DEPLOY_DEV_AAF }} run: | set -euo pipefail if [ -z "${AWS_REGION}" ]; then @@ -46,6 +45,10 @@ jobs: echo "Missing required secret AWS_ROLE_ECR_PUSH" >&2 exit 1 fi + if [ -z "${AWS_ROLE_BACKEND_DEPLOY_DEV_AAF}" ]; then + echo "Missing required secret AWS_ROLE_BACKEND_DEPLOY_DEV_AAF" >&2 + exit 1 + fi - uses: docker/setup-buildx-action@v4 @@ -92,7 +95,7 @@ jobs: python -m pip install uv==0.11.15 uv lock - # Authenticate to AWS + # Authenticate to AWS (push role, in 331315009666) - uses: aws-actions/configure-aws-credentials@v6 with: role-to-assume: ${{ secrets.AWS_ROLE_ECR_PUSH }} @@ -113,9 +116,15 @@ jobs: cache-from: type=gha cache-to: type=gha,mode=max - # No separate deploy-role step: the ECR push role (still active from the - # auth step above) also holds lambda:InvokeFunction on the dev-aaf deploy - # function, so we invoke it directly. + - name: Configure AWS credentials for dev-aaf deploy + uses: aws-actions/configure-aws-credentials@v6 + with: + role-to-assume: ${{ secrets.AWS_ROLE_BACKEND_DEPLOY_DEV_AAF }} + role-session-name: backend-aaf-dev-deploy + aws-region: ${{ env.AWS_REGION }} + role-chaining: true + role-skip-session-tagging: true + - name: Deploy dev-aaf backend via Lambda env: DEPLOY_FUNCTION_NAME: AaiBackendDevAafDeploymentFunction From 861fd8477058846609e2984c5f15f10f8d9b17d2 Mon Sep 17 00:00:00 2001 From: marius-mather <61438033+marius-mather@users.noreply.github.com> Date: Fri, 11 Sep 2026 13:04:20 +1000 Subject: [PATCH 11/25] feat: hard-delete users (AAF environment only) (AAF-883) (#296) * feat: delete_user method for Auth0Client * feat: hard-delete method for BiocommonsUser * feat: allow hard-delete in db-admin (dev-aaf env only) * test: unit tests of hard-delete --- auth0/client.py | 8 +++++ db/models.py | 39 ++++++++++++++++++++- db/st_admin.py | 38 +++++++++++++++++++++ tests/db/test_db_admin.py | 65 +++++++++++++++++++++++++++++++++++ tests/db/test_models.py | 71 ++++++++++++++++++++++++++++++++++++++- 5 files changed, 219 insertions(+), 2 deletions(-) diff --git a/auth0/client.py b/auth0/client.py index 87827725..9363c7ad 100644 --- a/auth0/client.py +++ b/auth0/client.py @@ -373,6 +373,14 @@ def check_user_password(self, email: str, password: str, settings: Settings) -> resp.raise_for_status() return True + def delete_user(self, user_id: str) -> None: + """ + Permanently delete a user from Auth0. + """ + url = f"{self.api_base}/users/{user_id}" + resp = self._client.delete(url) + resp.raise_for_status() + def delete_user_refresh_tokens(self, user_id: str) -> bool: """ Delete all refresh tokens for a user. diff --git a/db/models.py b/db/models.py index 4438c81f..cc8488e7 100644 --- a/db/models.py +++ b/db/models.py @@ -6,7 +6,7 @@ from httpx import HTTPStatusError from pydantic import AwareDatetime -from sqlalchemy import Column, Index, String, Text, UniqueConstraint, desc, func +from sqlalchemy import Column, Index, String, Text, UniqueConstraint, delete, desc, func from sqlmodel import DateTime, Field, Relationship, Session, select from sqlmodel import Enum as DbEnum from starlette.exceptions import HTTPException @@ -254,6 +254,43 @@ def delete(self, session: Session, commit: bool = False, reason: str | None = No super().delete(session, commit=commit) return self + def hard_delete(self, session: Session, auth0_client: Auth0Client) -> None: + """ + Permanently delete the user and their own rows from the DB, and delete + the user from Auth0. For testing use only - irreversible. + + Refuses if this user acted as an admin on another user's record + (appears as deleted_by/updated_by there) - that history would be lost. + """ + user_id = self.id + other_admin_actions = ( + session.exec(select(BiocommonsUser.id).execution_options(include_deleted=True).where( + BiocommonsUser.deleted_by_id == user_id, BiocommonsUser.id != user_id)).first() + or session.exec(select(BiocommonsUserHistory.id).execution_options(include_deleted=True).where( + BiocommonsUserHistory.updated_by_id == user_id, BiocommonsUserHistory.user_id != user_id)).first() + or session.exec(select(PlatformMembership.id).execution_options(include_deleted=True).where( + PlatformMembership.updated_by_id == user_id, PlatformMembership.user_id != user_id)).first() + or session.exec(select(PlatformMembershipHistory.id).execution_options(include_deleted=True).where( + PlatformMembershipHistory.updated_by_id == user_id, PlatformMembershipHistory.user_id != user_id)).first() + or session.exec(select(GroupMembership.id).execution_options(include_deleted=True).where( + GroupMembership.updated_by_id == user_id, GroupMembership.user_id != user_id)).first() + or session.exec(select(GroupMembershipHistory.id).execution_options(include_deleted=True).where( + GroupMembershipHistory.updated_by_id == user_id, GroupMembershipHistory.user_id != user_id)).first() + ) + if other_admin_actions: + raise ValueError(f"User {user_id} has acted as an admin on another user's record and cannot be hard-deleted") + + logger.info(f"Deleting user {user_id} from Auth0") + try: + auth0_client.delete_user(user_id=user_id) + except HTTPStatusError as e: + logger.warning(f"Error deleting user {user_id} from Auth0: {e}") + + for model in (EmailChangeOtp, GroupMembershipHistory, PlatformMembershipHistory, GroupMembership, PlatformMembership, BiocommonsUserHistory): + session.exec(delete(model).where(model.user_id == user_id)) + session.exec(delete(BiocommonsUser).where(BiocommonsUser.id == user_id)) + session.commit() + def update_from_auth0(self, auth0_id: str, auth0_client: Auth0Client) -> Self: """ Fetch user data from Auth0 and update this object with it. diff --git a/db/st_admin.py b/db/st_admin.py index 07aacb36..e0400107 100644 --- a/db/st_admin.py +++ b/db/st_admin.py @@ -85,6 +85,44 @@ async def repr(self, obj: Any, request: Request) -> str: return f"❌ {obj.email} (deleted)" return obj.email + async def is_row_action_allowed(self, request: Request, name: str) -> bool: + if name == "hard_delete_user": + return get_settings().environment == "dev-aaf" + return await super().is_row_action_allowed(request, name) + + @row_action( + name="hard_delete_user", + text="Hard Delete (permanent)", + confirmation="This permanently deletes the user and ALL related data from the database and Auth0. This cannot be undone. Continue?", + icon_class="fa fa-skull-crossbones", + submit_btn_text="Delete Permanently", + submit_btn_class="btn btn-danger", + action_btn_class="btn btn-danger", + ) + async def hard_delete_row_action(self, request: Request, pk: Any) -> Any: + settings = get_settings() + if settings.environment != "dev-aaf": + raise HTTPException(status_code=403, detail="Hard delete is only available in the dev-aaf environment") + management_token = get_management_token(settings=settings) + auth0_client_gen = get_auth0_client(settings=settings, management_token=management_token) + auth0_client = next(auth0_client_gen) + db_session_gen = get_db_session() + db_session = next(db_session_gen) + try: + user = BiocommonsUser.get_by_id(pk, db_session, include_deleted=True) + if user is None: + raise HTTPException(status_code=404, detail=f"User {pk} not found") + logger.info(f"Hard deleting user {pk}") + try: + user.hard_delete(db_session, auth0_client=auth0_client) + except ValueError as e: + raise HTTPException(status_code=400, detail=str(e)) + return "User permanently deleted" + finally: + auth0_client_gen.close() + db_session_gen.close() + db_session.close() + class DeletedUserView(UserView): fields = ["email", "username", "deleted_at", HasOne("deleted_by", identity="user"), "deletion_reason"] diff --git a/tests/db/test_db_admin.py b/tests/db/test_db_admin.py index 1a9b5d87..368f1279 100644 --- a/tests/db/test_db_admin.py +++ b/tests/db/test_db_admin.py @@ -23,6 +23,7 @@ GroupMembershipView, PlatformMembershipHistoryView, PlatformMembershipView, + UserView, ) from db.types import ApprovalStatusEnum, PlatformEnum from tests.db.datagen import ( @@ -485,3 +486,67 @@ def test_platform_membership_history_view_list_query_includes_deleted_users( # Verify the related deleted user can be resolved from the history row matching_history = next(row for row in results if row.id == history.id) assert matching_history.user.id == deleted_user.id + + +@pytest.mark.asyncio +async def test_is_row_action_allowed_hard_delete_requires_dev_aaf(mocker, mock_settings): + mocker.patch("db.st_admin.get_settings", return_value=mock_settings) + view = UserView(BiocommonsUser) + + mock_settings.environment = "dev-aaf" + assert await view.is_row_action_allowed(MagicMock(), "hard_delete_user") is True + + mock_settings.environment = "dev" + assert await view.is_row_action_allowed(MagicMock(), "hard_delete_user") is False + + +@pytest.mark.asyncio +async def test_hard_delete_row_action_calls_hard_delete(mocker, mock_settings): + mock_settings.environment = "dev-aaf" + mock_auth0_client = MagicMock() + mock_db_session = MagicMock() + target_user_id = "auth0|user456" + mock_user = MagicMock(spec=BiocommonsUser) + + mocker.patch("db.st_admin.get_db_session", return_value=_yield_once(mock_db_session)) + mocker.patch("db.st_admin.get_auth0_client", return_value=_yield_once(mock_auth0_client)) + mocker.patch("db.st_admin.get_management_token") + mocker.patch("db.st_admin.get_settings", return_value=mock_settings) + mocker.patch.object(BiocommonsUser, "get_by_id", return_value=mock_user) + + view = UserView(BiocommonsUser) + response = await view.hard_delete_row_action(MagicMock(), target_user_id) + + assert response == "User permanently deleted" + mock_user.hard_delete.assert_called_once_with(mock_db_session, auth0_client=mock_auth0_client) + + +@pytest.mark.asyncio +async def test_hard_delete_row_action_blocked_outside_dev_aaf(mocker, mock_settings): + mock_settings.environment = "dev" + mocker.patch("db.st_admin.get_settings", return_value=mock_settings) + view = UserView(BiocommonsUser) + + with pytest.raises(HTTPException) as exc: + await view.hard_delete_row_action(MagicMock(), "auth0|user456") + assert exc.value.status_code == 403 + + +@pytest.mark.asyncio +async def test_hard_delete_row_action_returns_400_on_value_error(mocker, mock_settings): + mock_settings.environment = "dev-aaf" + mock_auth0_client = MagicMock() + mock_db_session = MagicMock() + mock_user = MagicMock(spec=BiocommonsUser) + mock_user.hard_delete.side_effect = ValueError("nope") + + mocker.patch("db.st_admin.get_db_session", return_value=_yield_once(mock_db_session)) + mocker.patch("db.st_admin.get_auth0_client", return_value=_yield_once(mock_auth0_client)) + mocker.patch("db.st_admin.get_management_token") + mocker.patch("db.st_admin.get_settings", return_value=mock_settings) + mocker.patch.object(BiocommonsUser, "get_by_id", return_value=mock_user) + + view = UserView(BiocommonsUser) + with pytest.raises(HTTPException) as exc: + await view.hard_delete_row_action(MagicMock(), "auth0|user456") + assert exc.value.status_code == 400 diff --git a/tests/db/test_models.py b/tests/db/test_models.py index bceb7dfe..fdc09894 100644 --- a/tests/db/test_models.py +++ b/tests/db/test_models.py @@ -1,4 +1,4 @@ -from datetime import datetime, timezone +from datetime import datetime, timedelta, timezone from unittest.mock import ANY, call import pytest @@ -16,6 +16,7 @@ BiocommonsGroup, BiocommonsUser, BiocommonsUserHistory, + EmailChangeOtp, GroupMembership, GroupMembershipHistory, Platform, @@ -1647,6 +1648,74 @@ def test_biocommons_user_admin_restore_creates_history(test_db_session, mock_aut assert history.updated_by_id == admin.id +def test_hard_delete_removes_user_and_related_rows(test_db_session, mock_auth0_client, persistent_factories): + user = BiocommonsUserFactory.create_sync() + platform = PlatformFactory.create_sync(id=PlatformEnum.GALAXY) + group = BiocommonsGroupFactory.create_sync() + platform_membership = PlatformMembershipFactory.create_sync(user=user, platform=platform) + group_membership = GroupMembershipFactory.create_sync(user=user, group=group) + test_db_session.commit() + + platform_history = platform_membership.save_history(test_db_session) + group_history = group_membership.save_history(test_db_session) + user_history = user.save_history(test_db_session, change="test") + otp = EmailChangeOtp( + user_id=user.id, + target_email="new@example.com", + otp_hash="hash", + expires_at=datetime.now(timezone.utc) + timedelta(hours=1), + ) + test_db_session.add(otp) + test_db_session.commit() + + user_id = user.id + platform_membership_id = platform_membership.id + group_membership_id = group_membership.id + platform_history_id = platform_history.id + group_history_id = group_history.id + user_history_id = user_history.id + otp_id = otp.id + + user.hard_delete(test_db_session, auth0_client=mock_auth0_client) + + mock_auth0_client.delete_user.assert_called_once_with(user_id=user_id) + + test_db_session.expire_all() + assert test_db_session.get(BiocommonsUser, user_id) is None + assert BiocommonsUser.get_deleted_by_id(test_db_session, user_id) is None + assert test_db_session.get(PlatformMembership, platform_membership_id) is None + assert test_db_session.get(GroupMembership, group_membership_id) is None + assert test_db_session.get(PlatformMembershipHistory, platform_history_id) is None + assert test_db_session.get(GroupMembershipHistory, group_history_id) is None + assert test_db_session.get(BiocommonsUserHistory, user_history_id) is None + assert test_db_session.get(EmailChangeOtp, otp_id) is None + + +def test_hard_delete_refuses_if_user_acted_as_admin_for_another_user(test_db_session, mock_auth0_client, persistent_factories): + admin = BiocommonsUserFactory.create_sync() + other_user = BiocommonsUserFactory.create_sync() + other_user.delete(test_db_session, deleted_by=admin, commit=True) + + with pytest.raises(ValueError): + admin.hard_delete(test_db_session, auth0_client=mock_auth0_client) + + mock_auth0_client.delete_user.assert_not_called() + assert test_db_session.get(BiocommonsUser, admin.id) is not None + + +def test_hard_delete_allows_user_who_only_admined_themselves(test_db_session, mock_auth0_client, persistent_factories): + user = BiocommonsUserFactory.create_sync() + user_id = user.id + user.delete(test_db_session, deleted_by=user, commit=True) + user = BiocommonsUser.get_deleted_by_id(test_db_session, user_id) + + user.hard_delete(test_db_session, auth0_client=mock_auth0_client) + + mock_auth0_client.delete_user.assert_called_once_with(user_id=user_id) + test_db_session.expire_all() + assert test_db_session.get(BiocommonsUser, user_id) is None + + def test_admin_delete_preserves_memberships(test_db_session, persistent_factories, mock_auth0_client): """ Test group and platform memberships are preserved when admin soft-deletes a user, so From db7d11d48e45998432a1ffdf03486e89291b19d1 Mon Sep 17 00:00:00 2001 From: marius-mather <61438033+marius-mather@users.noreply.github.com> Date: Fri, 11 Sep 2026 13:37:17 +1000 Subject: [PATCH 12/25] chore: replace httpx with httpx2 (#297) * chore: replace httpx usage with httpx2 * feat: replace httpx dependency with httpx2 * fix: workarounds to make respx work with httpx2 * chore: update lock file --- auth/management.py | 4 ++-- auth/validator.py | 6 +++--- auth0/client.py | 20 ++++++++++---------- auth0/user_info.py | 4 ++-- db/models.py | 2 +- galaxy/client.py | 2 +- pyproject.toml | 6 +++--- register/tokens.py | 4 ++-- routers/admin.py | 2 +- routers/biocommons_register.py | 2 +- routers/user.py | 2 +- scheduled_tasks/tasks.py | 2 +- services/institutions.py | 4 ++-- tests/admin_api/test_admin.py | 6 +++--- tests/auth/test_auth_management.py | 2 +- tests/auth/test_auth_validator.py | 4 ++-- tests/conftest.py | 10 ++++++++++ tests/db/test_models.py | 2 +- tests/galaxy/test_client.py | 4 ++-- tests/scheduled_tasks/test_tasks.py | 2 +- tests/test_auth0_client.py | 2 +- tests/test_biocommons_admin.py | 2 +- tests/test_biocommons_register.py | 8 ++++---- tests/test_user.py | 2 +- tests/test_utils.py | 6 +++--- uv.lock | 6 ++---- 26 files changed, 62 insertions(+), 54 deletions(-) diff --git a/auth/management.py b/auth/management.py index 747321b9..cd4c9eb3 100644 --- a/auth/management.py +++ b/auth/management.py @@ -1,6 +1,6 @@ from typing import Annotated -import httpx +import httpx2 from cachetools import TTLCache from fastapi import Depends @@ -24,7 +24,7 @@ def get_management_token(settings: Annotated[Settings, Depends(get_settings)]): "client_secret": settings.auth0_management_secret, "audience": f"https://{settings.auth0_domain}/api/v2/", } - response = httpx.post(url, json=payload) + response = httpx2.post(url, json=payload) response.raise_for_status() data = response.json() token = data["access_token"] diff --git a/auth/validator.py b/auth/validator.py index 8bb80025..32b7dfaf 100644 --- a/auth/validator.py +++ b/auth/validator.py @@ -4,7 +4,7 @@ import weakref from datetime import UTC, datetime, timedelta -import httpx +import httpx2 import jwt from cachetools import TTLCache from fastapi import HTTPException @@ -106,7 +106,7 @@ async def _fetch_rsa_keys(auth0_domain: str) -> dict: try: metadata_url = f"https://{auth0_domain}/.well-known/openid-configuration" - async with httpx.AsyncClient() as client: + async with httpx2.AsyncClient() as client: metadata_response = await client.get(metadata_url) metadata_response.raise_for_status() metadata = metadata_response.json() @@ -118,7 +118,7 @@ async def _fetch_rsa_keys(auth0_domain: str) -> dict: except KeyError as exc: logger.error(f"OIDC metadata from {metadata_url} did not include jwks_uri") raise InvalidTokenError("Failed to fetch JWKS") from exc - except (httpx.HTTPError, ValueError) as exc: + except (httpx2.HTTPError, ValueError) as exc: logger.error( f"Failed to fetch OIDC metadata or JWKS for domain {auth0_domain}: {exc}" ) diff --git a/auth0/client.py b/auth0/client.py index 9363c7ad..5b8bce80 100644 --- a/auth0/client.py +++ b/auth0/client.py @@ -4,9 +4,9 @@ import time from typing import Iterator, Optional, Type, TypeVar -import httpx +import httpx2 from fastapi import Depends -from httpx import HTTPStatusError +from httpx2 import HTTPStatusError from pydantic import BaseModel, EmailStr, Field, HttpUrl, model_validator from auth.management import get_management_token @@ -192,7 +192,7 @@ def __init__(self, domain: str, management_token: str): self.domain = domain self.api_base = f"https://{domain}/api/v2" self.management_token = management_token - self._client = httpx.Client(headers={"Authorization": f"Bearer {management_token}"}) + self._client = httpx2.Client(headers={"Authorization": f"Bearer {management_token}"}) def close(self) -> None: self._client.close() @@ -206,16 +206,16 @@ def __exit__(self, exc_type, exc, tb) -> None: T = TypeVar('T', bound=BaseModel) @staticmethod - def _convert_list(resp: httpx.Response, model: Type[T]) -> list[T]: + def _convert_list(resp: httpx2.Response, model: Type[T]) -> list[T]: """Convert a list of data to the given pydantic model.""" return [model(**item) for item in resp.json()] @staticmethod - def _convert_users(resp: httpx.Response): + def _convert_users(resp: httpx2.Response): return Auth0Client._convert_list(resp, Auth0UserData) @staticmethod - def _convert_roles(resp: httpx.Response): + def _convert_roles(resp: httpx2.Response): return Auth0Client._convert_list(resp, RoleData) def get_users(self, page: Optional[int] = None, per_page: Optional[int] = None, include_totals: Optional[bool] = None, q: Optional[str] = None) -> list[Auth0UserData] | UsersWithTotals: @@ -332,7 +332,7 @@ def export_and_download_users( logger.info(f"User export job {job_id} completed successfully. Downloading from {location}...") # Don't use client for this, we don't want the auth header here - download = httpx.get(location) + download = httpx2.get(location) download.raise_for_status() content = download.content @@ -365,7 +365,7 @@ def check_user_password(self, email: str, password: str, settings: Settings) -> "scope": "openid", } # We don't want the management token here so not using self._client - resp = httpx.post(url, data=data) + resp = httpx2.post(url, data=data) if resp.status_code in {400, 403}: error = resp.json().get("error") if error == "invalid_grant": @@ -408,7 +408,7 @@ def remove_roles_from_user(self, user_id: str, role_id: str | list[str]): url = f"{self.api_base}/users/{user_id}/roles" if isinstance(role_id, str): role_id = [role_id] - # httpx.Client.delete() no longer accepts json payloads (0.28+), so use request() + # httpx2.Client.delete() no longer accepts json payloads (0.28+), so use request() resp = self._client.request("DELETE", url, json={"roles": role_id}) resp.raise_for_status() return True @@ -611,7 +611,7 @@ def trigger_password_change(self, user_email: str, client_id: str, settings: Set # NOTE: Authentication API, not management API url = f"https://{self.domain}/dbconnections/change_password" # Don't use _client here, since it's not a management API endpoint - resp = httpx.post( + resp = httpx2.post( url, json={"email": user_email, "client_id": client_id, diff --git a/auth0/user_info.py b/auth0/user_info.py index 915a4465..5cdb345b 100644 --- a/auth0/user_info.py +++ b/auth0/user_info.py @@ -1,6 +1,6 @@ from typing import Annotated -import httpx +import httpx2 from fastapi.params import Depends from pydantic import BaseModel, ConfigDict, Field @@ -47,7 +47,7 @@ async def get_auth0_user_info( Doesn't require management API access so may be more efficient when only the current user is required """ - async with httpx.AsyncClient() as client: + async with httpx2.AsyncClient() as client: resp = await client.get( f"https://{settings.auth0_domain}/userinfo", headers={ "Authorization": f"Bearer {auth0_token}" diff --git a/db/models.py b/db/models.py index cc8488e7..5ce14dc5 100644 --- a/db/models.py +++ b/db/models.py @@ -4,7 +4,7 @@ from logging import getLogger from typing import Optional, Self, Type -from httpx import HTTPStatusError +from httpx2 import HTTPStatusError from pydantic import AwareDatetime from sqlalchemy import Column, Index, String, Text, UniqueConstraint, delete, desc, func from sqlmodel import DateTime, Field, Relationship, Session, select diff --git a/galaxy/client.py b/galaxy/client.py index b2fc29ed..9cad493c 100644 --- a/galaxy/client.py +++ b/galaxy/client.py @@ -1,7 +1,7 @@ from typing import Annotated from fastapi import Depends -from httpx import Client +from httpx2 import Client from galaxy.config import GalaxySettings, get_galaxy_settings from galaxy.schemas import GalaxyUserModel diff --git a/pyproject.toml b/pyproject.toml index 18c82b2f..9a5c9150 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,7 +9,7 @@ dependencies = [ "fastapi[standard]>=0.139.0", # Security floor for CVE-2026-26007 (subgroup validation for SECT curves) "cryptography>=49.0", - "httpx>=0.28.1", + "httpx2>=2.9.1", "psycopg[binary]>=3.3.4", "email-validator~=2.3", "pydantic-settings>=2.14.2", @@ -31,7 +31,6 @@ dependencies = [ [project.optional-dependencies] dev = [ "boto3-stubs>=1.43.45", - "httpx2>=2.9.1", "pytest>=9.0.3", "pytest-mock>=3.14.0", "pytest-sugar>=1.1.1", @@ -56,7 +55,7 @@ exclude-newer = "7 days" [tool.pytest.ini_options] pythonpath = ["."] testpaths = ["tests"] -addopts = "--cov=auth --cov=routers --cov=schemas --cov=db --cov=biocommons --cov=scheduled_tasks --cov-report=term --cov-report=xml" +addopts = "-p no:respx --cov=auth --cov=routers --cov=schemas --cov=db --cov=biocommons --cov=scheduled_tasks --cov-report=term --cov-report=xml" [build-system] requires = ["setuptools>=61.0"] @@ -71,4 +70,5 @@ line-length = 88 target-version = "py313" lint.select = ["E", "F", "I"] lint.ignore = ["E501"] +lint.per-file-ignores = { "tests/conftest.py" = ["E402"] } exclude = ["tests/data", ".venv", "venv", "migrations"] diff --git a/register/tokens.py b/register/tokens.py index 1eeaa671..8da24e79 100644 --- a/register/tokens.py +++ b/register/tokens.py @@ -1,6 +1,6 @@ from datetime import UTC, datetime, timedelta -import httpx +import httpx2 import jwt from fastapi import HTTPException from jwt.exceptions import InvalidTokenError @@ -35,7 +35,7 @@ def verify_registration_token(token: str, settings: Settings): def validate_recaptcha(token: str, settings: Settings): - response = httpx.post( + response = httpx2.post( url="https://www.google.com/recaptcha/api/siteverify", headers={"Content-Type": "application/x-www-form-urlencoded"}, data={"secret": settings.recaptcha_secret, "response": token}, diff --git a/routers/admin.py b/routers/admin.py index 0e59a5ab..9dd6042c 100644 --- a/routers/admin.py +++ b/routers/admin.py @@ -7,7 +7,7 @@ from fastapi import APIRouter, BackgroundTasks, Depends, HTTPException, Response from fastapi.params import Query -from httpx import HTTPStatusError +from httpx2 import HTTPStatusError from pydantic import ( BaseModel, ConfigDict, diff --git a/routers/biocommons_register.py b/routers/biocommons_register.py index abae4d59..7eb89a37 100644 --- a/routers/biocommons_register.py +++ b/routers/biocommons_register.py @@ -2,7 +2,7 @@ from typing import Optional from fastapi import APIRouter, Depends, HTTPException, Response -from httpx import HTTPStatusError +from httpx2 import HTTPStatusError from sqlmodel import Session from auth0.client import Auth0Client, get_auth0_client diff --git a/routers/user.py b/routers/user.py index 50f5f3c8..c01e37ff 100644 --- a/routers/user.py +++ b/routers/user.py @@ -8,7 +8,7 @@ from botocore.exceptions import ClientError from fastapi import APIRouter, Body, Depends, HTTPException, Response, status -from httpx import AsyncClient, HTTPStatusError +from httpx2 import AsyncClient, HTTPStatusError from loguru import logger from pydantic import AliasPath, AwareDatetime, BaseModel, Field from pydantic import BaseModel as PydanticBaseModel diff --git a/scheduled_tasks/tasks.py b/scheduled_tasks/tasks.py index fd868861..bc053861 100644 --- a/scheduled_tasks/tasks.py +++ b/scheduled_tasks/tasks.py @@ -9,7 +9,7 @@ from typing import Any from uuid import UUID -from httpx import HTTPStatusError +from httpx2 import HTTPStatusError from loguru import logger from pydantic import BaseModel, field_validator from sqlalchemy.exc import IntegrityError diff --git a/services/institutions.py b/services/institutions.py index dbb6b144..4ef0103a 100644 --- a/services/institutions.py +++ b/services/institutions.py @@ -1,6 +1,6 @@ from typing import Optional -import httpx +import httpx2 GALAXY_AU_VALIDATE_URL = "https://site.usegalaxy.org.au/institution/validate" @@ -13,7 +13,7 @@ async def check_australian_research_institution_email(email: str) -> Optional[bo that must not act on an outage should treat None distinctly from False. """ try: - async with httpx.AsyncClient(timeout=5.0) as client: + async with httpx2.AsyncClient(timeout=5.0) as client: response = await client.get(GALAXY_AU_VALIDATE_URL, params={"email": email}) response.raise_for_status() return bool(response.json().get("valid", False)) diff --git a/tests/admin_api/test_admin.py b/tests/admin_api/test_admin.py index be6561a5..8c966db3 100644 --- a/tests/admin_api/test_admin.py +++ b/tests/admin_api/test_admin.py @@ -2123,7 +2123,7 @@ def test_admin_update_user_username_duplicate_in_auth0( persistent_factories, ): """Test username update fails when Auth0 returns 409 conflict.""" - from httpx import HTTPStatusError, Request, Response + from httpx2 import HTTPStatusError, Request, Response user = _create_user_with_platform_membership( db_session=test_db_session, @@ -2170,7 +2170,7 @@ def test_admin_update_user_username_auth0_400_error( persistent_factories, ): """Test username update handles Auth0 400 error.""" - from httpx import HTTPStatusError, Request, Response + from httpx2 import HTTPStatusError, Request, Response user = _create_user_with_platform_membership( db_session=test_db_session, @@ -2244,7 +2244,7 @@ def test_get_unverified_users(test_client, test_db_session, as_admin_user, galax def test_auth0client_get_users_forwards_filter_to_httpx(mocker): client = Auth0Client(domain="tenant.example.auth0.com", management_token="tok") - # Mock the underlying httpx client and its response + # Mock the underlying httpx2 client and its response fake_resp = mocker.Mock() fake_resp.json.return_value = [] # get_users() reads .json() only client._client = mocker.Mock() diff --git a/tests/auth/test_auth_management.py b/tests/auth/test_auth_management.py index ca78b704..1306a2e2 100644 --- a/tests/auth/test_auth_management.py +++ b/tests/auth/test_auth_management.py @@ -4,7 +4,7 @@ def test_get_management_token_success(mock_settings): - with patch("auth.management.httpx.post") as mock_post: + with patch("auth.management.httpx2.post") as mock_post: mock_post.return_value.json.return_value = {"access_token": "abc123"} mock_post.return_value.raise_for_status = lambda: None diff --git a/tests/auth/test_auth_validator.py b/tests/auth/test_auth_validator.py index 4e8f2d45..74dd8807 100644 --- a/tests/auth/test_auth_validator.py +++ b/tests/auth/test_auth_validator.py @@ -20,7 +20,7 @@ from fastapi.security import HTTPAuthorizationCredentials from fastapi.testclient import TestClient from freezegun import freeze_time -from httpx import Request, Response +from httpx2 import Request, Response from jwt import InvalidSignatureError from jwt.algorithms import RSAAlgorithm @@ -150,7 +150,7 @@ async def test_get_rsa_key_returns_key(mock_settings: Settings): jwks_url = f"https://{mock_settings.auth0_domain}/.well-known/jwks.json" with patch("auth.validator.jwt.get_unverified_header", return_value=unverified_header), \ - patch("auth.validator.httpx.AsyncClient.get", new_callable=AsyncMock) as mock_get: + patch("auth.validator.httpx2.AsyncClient.get", new_callable=AsyncMock) as mock_get: metadata_response = Response( 200, json={"jwks_uri": jwks_url}, diff --git a/tests/conftest.py b/tests/conftest.py index 4fc12449..ecdf9948 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,3 +1,13 @@ +import httpx2 + +# respx only patches the real `httpx`/`httpcore`; alias them to httpx2 so it +# intercepts requests made through our httpx2-based clients. Must run before +# anything else imports httpx or httpcore, so its pytest11 entry point plugin +# is disabled (see `-p no:respx` in pyproject.toml) and loaded manually here. +httpx2.alias_httpx() + +pytest_plugins = ["respx.plugin"] + import os import warnings from datetime import datetime diff --git a/tests/db/test_models.py b/tests/db/test_models.py index fdc09894..fcffdfba 100644 --- a/tests/db/test_models.py +++ b/tests/db/test_models.py @@ -4,7 +4,7 @@ import pytest import respx from freezegun import freeze_time -from httpx import Response +from httpx2 import Response from mimesis import Person from mimesis.locales import Locale from sqlalchemy.exc import IntegrityError diff --git a/tests/galaxy/test_client.py b/tests/galaxy/test_client.py index 9439c4d9..0069f440 100644 --- a/tests/galaxy/test_client.py +++ b/tests/galaxy/test_client.py @@ -1,4 +1,4 @@ -import httpx +import httpx2 import pytest from galaxy.client import GalaxyClient @@ -15,7 +15,7 @@ def test_username_exists(galaxy_client, respx_mock): user1 = GalaxyUserFactory.build(username="user1") user2 = GalaxyUserFactory.build(username="user2") respx_mock.get("https://galaxy.example.com/api/users").mock( - return_value=httpx.Response( + return_value=httpx2.Response( 200, json=[user1.model_dump(mode="json"), user2.model_dump(mode="json")] diff --git a/tests/scheduled_tasks/test_tasks.py b/tests/scheduled_tasks/test_tasks.py index 22fe2d0c..f440d719 100644 --- a/tests/scheduled_tasks/test_tasks.py +++ b/tests/scheduled_tasks/test_tasks.py @@ -6,7 +6,7 @@ import pytest from botocore.exceptions import ClientError, EndpointConnectionError -from httpx import HTTPStatusError +from httpx2 import HTTPStatusError from sqlmodel import Session, select from db.models import ( diff --git a/tests/test_auth0_client.py b/tests/test_auth0_client.py index cb262c80..cd9fbbb0 100644 --- a/tests/test_auth0_client.py +++ b/tests/test_auth0_client.py @@ -4,7 +4,7 @@ import pytest import respx -from httpx import Response +from httpx2 import Response from pydantic import ValidationError from auth0.client import ( diff --git a/tests/test_biocommons_admin.py b/tests/test_biocommons_admin.py index dbe6a64a..94c02eda 100644 --- a/tests/test_biocommons_admin.py +++ b/tests/test_biocommons_admin.py @@ -2,7 +2,7 @@ import pytest import respx -from httpx import Response +from httpx2 import Response from sqlmodel import select from db.models import Auth0Role, BiocommonsGroup, Platform diff --git a/tests/test_biocommons_register.py b/tests/test_biocommons_register.py index 66f54434..186fef86 100644 --- a/tests/test_biocommons_register.py +++ b/tests/test_biocommons_register.py @@ -2,7 +2,7 @@ import pytest import respx -from httpx import Response +from httpx2 import Response from sqlmodel import select from starlette.exceptions import HTTPException @@ -632,7 +632,7 @@ def test_biocommons_registration_auth0_conflict_error( mock_recaptcha_verify, ): """Test handling of Auth0 conflict error (user already exists)""" - from httpx import HTTPStatusError, Request, Response + from httpx2 import HTTPStatusError, Request, Response response = Response(409, json={"error": "user_exists"}) request = Request("POST", "https://example.com") @@ -700,7 +700,7 @@ def test_biocommons_registration_email_conflict_error( test_client, tsi_group, mock_auth0_client, test_db_session, mock_recaptcha_verify, ): """Test handling of Auth0 conflict error when email exists""" - from httpx import HTTPStatusError, Request, Response + from httpx2 import HTTPStatusError, Request, Response response = Response(409, json={"error": "user_exists"}) request = Request("POST", "https://example.com") @@ -732,7 +732,7 @@ def test_biocommons_registration_both_conflict_error( mock_recaptcha_verify, ): """Test handling of Auth0 conflict error when both username and email exist""" - from httpx import HTTPStatusError, Request, Response + from httpx2 import HTTPStatusError, Request, Response response = Response(409, json={"error": "user_exists"}) request = Request("POST", "https://example.com") diff --git a/tests/test_user.py b/tests/test_user.py index 636a160b..230291a1 100644 --- a/tests/test_user.py +++ b/tests/test_user.py @@ -6,7 +6,7 @@ import pytest import respx from fastapi import HTTPException -from httpx import HTTPStatusError, Request, Response +from httpx2 import HTTPStatusError, Request, Response from sqlmodel import Session, select from db.models import ( diff --git a/tests/test_utils.py b/tests/test_utils.py index 5fdff0d7..ade16a40 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -1,7 +1,7 @@ -import httpx +import httpx2 import pytest import respx -from httpx import Response +from httpx2 import Response from sqlmodel import select from auth0.client import get_auth0_client @@ -216,7 +216,7 @@ def test_check_australian_research_institution_upstream_error_returns_false(test @respx.mock def test_check_australian_research_institution_upstream_timeout_returns_false(test_client): - respx.get(GALAXY_AU_VALIDATE_URL).mock(side_effect=httpx.TimeoutException("timeout")) + respx.get(GALAXY_AU_VALIDATE_URL).mock(side_effect=httpx2.TimeoutException("timeout")) resp = test_client.get( "/utils/register/check-australian-research-institution", params={"email": "researcher@sydney.edu.au"}, diff --git a/uv.lock b/uv.lock index 64b0482a..c4911941 100644 --- a/uv.lock +++ b/uv.lock @@ -23,7 +23,7 @@ dependencies = [ { name = "cryptography" }, { name = "email-validator" }, { name = "fastapi", extra = ["standard"] }, - { name = "httpx" }, + { name = "httpx2" }, { name = "itsdangerous" }, { name = "loguru" }, { name = "prometheus-fastapi-instrumentator" }, @@ -41,7 +41,6 @@ dev = [ { name = "boto3-stubs" }, { name = "faker" }, { name = "freezegun" }, - { name = "httpx2" }, { name = "mimesis" }, { name = "moto" }, { name = "polyfactory" }, @@ -68,8 +67,7 @@ requires-dist = [ { name = "faker", marker = "extra == 'dev'", specifier = ">=40.4.0" }, { name = "fastapi", extras = ["standard"], specifier = ">=0.139.0" }, { name = "freezegun", marker = "extra == 'dev'", specifier = ">=1.5.2" }, - { name = "httpx", specifier = ">=0.28.1" }, - { name = "httpx2", marker = "extra == 'dev'", specifier = ">=2.9.1" }, + { name = "httpx2", specifier = ">=2.9.1" }, { name = "itsdangerous", specifier = ">=2.2.0" }, { name = "loguru", specifier = ">=0.7.3" }, { name = "mimesis", marker = "extra == 'dev'", specifier = "~=18.0" }, From 9dab0dc2053bb945c77d699227e3b1c2d4d51388 Mon Sep 17 00:00:00 2001 From: Marius Mather Date: Fri, 11 Sep 2026 15:41:47 +1000 Subject: [PATCH 13/25] feat: allow manually triggering user sync from Auth0 --- db/st_admin.py | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/db/st_admin.py b/db/st_admin.py index e0400107..15c2644b 100644 --- a/db/st_admin.py +++ b/db/st_admin.py @@ -19,6 +19,7 @@ HasMany, HasOne, StringField, + action, row_action, ) from starlette_admin.auth import AdminUser, AuthProvider, login_not_required @@ -43,6 +44,7 @@ ) from db.setup import get_db_session, get_engine from db.types import PlatformEnum +from scheduled_tasks.tasks import sync_auth0_users logger = logging.getLogger('uvicorn.error') @@ -79,12 +81,25 @@ def get_count_query(self, request: Request) -> Select: class UserView(DefaultView): fields = ["email", "email_verified", "username", "created_at", "id"] + actions = ["sync_auth0_users"] async def repr(self, obj: Any, request: Request) -> str: if getattr(obj, "is_deleted", False): return f"❌ {obj.email} (deleted)" return obj.email + @action( + name="sync_auth0_users", + text="Sync Auth0 Users", + confirmation="This runs the Auth0 → DB user sync immediately, " + "instead of waiting for the hourly scheduled job. Continue?", + submit_btn_text="Sync Now", + icon_class="fa fa-rotate", + ) + async def sync_auth0_users_action(self, request: Request, pks: list) -> str: + await sync_auth0_users() + return "Auth0 user sync completed" + async def is_row_action_allowed(self, request: Request, name: str) -> bool: if name == "hard_delete_user": return get_settings().environment == "dev-aaf" From c96177451cc850b792057d25afae8d4118619ef8 Mon Sep 17 00:00:00 2001 From: Marius Mather Date: Fri, 11 Sep 2026 16:19:19 +1000 Subject: [PATCH 14/25] fix: email_verified can be missing in Auth0 responses, when not relevant --- schemas/biocommons.py | 2 +- tests/db/test_models.py | 1 + tests/scheduled_tasks/test_tasks.py | 3 +++ 3 files changed, 5 insertions(+), 1 deletion(-) diff --git a/schemas/biocommons.py b/schemas/biocommons.py index 432a9d56..79eadcb7 100644 --- a/schemas/biocommons.py +++ b/schemas/biocommons.py @@ -303,7 +303,7 @@ class Auth0UserData(BaseModel): created_at: datetime email: EmailStr username: Optional[BiocommonsUsername] = None - email_verified: bool + email_verified: Optional[bool] = None identities: List[Auth0Identity] name: str given_name: Optional[str] = None diff --git a/tests/db/test_models.py b/tests/db/test_models.py index fcffdfba..6b878d42 100644 --- a/tests/db/test_models.py +++ b/tests/db/test_models.py @@ -86,6 +86,7 @@ def test_create_biocommons_user_from_auth0(test_db_session, mock_auth0_client): Test creating the BiocommonsUser model from Auth0 user data from the API """ user_data = Auth0UserDataFactory.build( + email_verified=False, app_metadata=Auth0ReadAppMetadataFactory.build(account_type=BiocommonsUserAccountType.AUTH0) ) mock_auth0_client.get_user.return_value = user_data diff --git a/tests/scheduled_tasks/test_tasks.py b/tests/scheduled_tasks/test_tasks.py index f440d719..fc6adcc6 100644 --- a/tests/scheduled_tasks/test_tasks.py +++ b/tests/scheduled_tasks/test_tasks.py @@ -773,15 +773,18 @@ async def test_sync_auth0_platform_roles(mocker, test_db_session, mock_settings, user_id=user_keep.id, email="keep.user@example.com", username="keep_user", + email_verified=True, ) auth0_user_pending = Auth0UserDataFactory.build( user_id=user_pending.id, email="pending.user@example.com", username="pending_user", + email_verified=True, ) auth0_user_new = Auth0UserDataFactory.build( email="new.assignment@example.com", username="new_assignment", + email_verified=True, ) role_user_keep = RoleUserDataFactory.build(user_id=auth0_user_keep.user_id) role_user_pending = RoleUserDataFactory.build(user_id=auth0_user_pending.user_id) From 54c31ec7163c765b790512988be4de62f449cbb5 Mon Sep 17 00:00:00 2001 From: amandazhu Date: Mon, 14 Sep 2026 09:37:53 +1000 Subject: [PATCH 15/25] fix: use httpx in aaf router --- routers/aaf.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/routers/aaf.py b/routers/aaf.py index 430b9ba3..231355a8 100644 --- a/routers/aaf.py +++ b/routers/aaf.py @@ -4,7 +4,7 @@ from typing import Annotated from urllib.parse import urlparse -import httpx2 +import httpx from fastapi import APIRouter, Depends, HTTPException from pydantic import BaseModel from sqlmodel import Session @@ -126,7 +126,7 @@ def return_signed_response( settings=settings, ) auth0_base_url = get_auth0_continue_base_url(action_token, settings) - redirect_url = httpx2.URL( + redirect_url = httpx.URL( f"{auth0_base_url}/continue", params={"state": state, "session_token": signed_token}, ) From 23e298022c82b549192c0f5db52c928b94edd1e6 Mon Sep 17 00:00:00 2001 From: Marius Mather Date: Mon, 14 Sep 2026 11:43:05 +1000 Subject: [PATCH 16/25] feat: update user admin to show account type etc. --- db/st_admin.py | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/db/st_admin.py b/db/st_admin.py index 15c2644b..d1022796 100644 --- a/db/st_admin.py +++ b/db/st_admin.py @@ -80,8 +80,19 @@ def get_count_query(self, request: Request) -> Select: class UserView(DefaultView): - fields = ["email", "email_verified", "username", "created_at", "id"] + fields = [ + "email", + "account_type", + "email_verified", + "username", + "created_at", + "id", + "other_user_id", + HasMany("platform_memberships", identity="platform_membership"), + HasMany("group_memberships", identity="group_membership") + ] actions = ["sync_auth0_users"] + exclude_fields_from_list = ["platform_memberships", "group_memberships"] async def repr(self, obj: Any, request: Request) -> str: if getattr(obj, "is_deleted", False): From 9e4f61a2662a5ebaa771fd100ff24a6dd39bb11d Mon Sep 17 00:00:00 2001 From: marius-mather <61438033+marius-mather@users.noreply.github.com> Date: Wed, 16 Sep 2026 14:51:15 +1000 Subject: [PATCH 17/25] feat: AAF registration endpoint (AAI-881) (#299) * feat: add login proxy URL to settings - used to check AAF emails * test: add proxy URL to mock settings for testing * feat: function to check if email is AAF * test: unit test of is_aaf_email * refactor: move common registration logic to a shared module * refactor: use shared utils in existing register function * feat: schemas for AAF registration/metadata * feat: initial implementation of AAF register endpoint * test: rework tests of sbp domain check * refactor: move platform/bundle creation into shared utils * fix: catch error when updating Auth0 metadata * refactor: use bundle/platform utils in AAF register function * fix: block requests for SBP if not enabled * test: unit test for validating token from Auth0 * fix: make name values optional in registration token * test: set email_verified by default when generating Auth0UserData * refactor: move AAF registration route to existing register router * test: unit tests of AAF register * fix: set aaf_only, account_type in app_metadata --- .env.example | 2 + config.py | 19 +- register/utils.py | 239 ++++++++++++++++++ routers/biocommons_register.py | 388 ++++++++++++++---------------- schemas/auth0.py | 9 + schemas/biocommons.py | 2 + schemas/biocommons_register.py | 11 + services/institutions.py | 16 ++ tests/conftest.py | 1 + tests/datagen.py | 1 + tests/test_aaf.py | 145 +++++++++++ tests/test_biocommons_register.py | 243 ++++++++++++------- tests/test_config.py | 1 + tests/test_register_utils.py | 61 +++++ tests/test_utils.py | 17 +- 15 files changed, 858 insertions(+), 297 deletions(-) create mode 100644 register/utils.py create mode 100644 tests/test_register_utils.py diff --git a/.env.example b/.env.example index d96c5eb8..c55b2436 100644 --- a/.env.example +++ b/.env.example @@ -26,6 +26,8 @@ ADMIN_ROLES='["Admin", "GalaxyAdmin"]' ENABLE_ADMIN_DASHBOARD=False # AAI Portal URL for admin links in emails AAI_PORTAL_URL=https://aaiportal.example.com +# AAF login proxy +AAI_LOGIN_PROXY_URL=https://aafproxy.example.com # URL of Galaxy instance, for making calls to Galaxy API GALAXY_URL=https://galaxy.example.com GALAXY_API_KEY=api-key diff --git a/config.py b/config.py index 86b01f3e..e7c8b9eb 100644 --- a/config.py +++ b/config.py @@ -27,6 +27,8 @@ class Settings(BaseSettings): cors_allowed_origins: str # AAI Portal URL for admin links in emails aai_portal_url: str = "" + # AAF login proxy: used to check if email addresses belong to AAF + aai_login_proxy_url: str = "" # Sender override for emails that should come from a no-reply address no_reply_email_sender: EmailStr # SES resource ARN for sending emails @@ -46,7 +48,7 @@ def normalize_environment(cls, value: str | None) -> Literal["dev", "staging", " return "production" return normalized - @field_validator('auth0_custom_domain', mode="after") + @field_validator('auth0_custom_domain', 'aai_login_proxy_url', mode="after") @classmethod def strip_trailing_slash(cls, value: str | None) -> str | None: if value is None: @@ -78,6 +80,21 @@ def set_default_aai_portal_url(self) -> "Settings": self.aai_portal_url = default_url return self + @model_validator(mode="after") + def set_default_aai_login_proxy_url(self) -> "Settings": + if self.aai_login_proxy_url: + return self + env_to_url = { + "dev-aaf": "https://dev-aaf.aaf-login.aai.test.biocommons.org.au" + } + default_url = env_to_url.get(self.environment) + if not default_url: + raise ValueError( + "Unknown ENVIRONMENT value and AAI_LOGIN_PROXY_URL is not set." + ) + self.aai_login_proxy_url = default_url + return self + @lru_cache() def get_settings(): diff --git a/register/utils.py b/register/utils.py new file mode 100644 index 00000000..5cdfcaad --- /dev/null +++ b/register/utils.py @@ -0,0 +1,239 @@ +import logging +from typing import Optional + +from sqlmodel import Session + +from auth0.client import Auth0Client +from biocommons.bundles import BUNDLES, BiocommonsBundle +from biocommons.default import get_default_platforms +from biocommons.emails import ( + compose_bundle_request_confirmation_email, + compose_group_approval_email, + format_first_name, + get_group_admin_contacts, + get_requester_identity, +) +from config import Settings +from db.models import BiocommonsUser, BiocommonsUserHistory, GroupMembership +from schemas.biocommons import Auth0UserData +from schemas.biocommons_register import BundleRequest +from schemas.responses import FieldError, RegistrationErrorResponse +from services.email_queue import enqueue_email +from services.institutions import is_australian_research_institution_email + +logger = logging.getLogger("uvicorn.error") + + +def check_is_username_used(username: str, session: Session) -> RegistrationErrorResponse | None: + username_used = BiocommonsUserHistory.is_username_used(username, session=session) + if username_used: + field_errors = [FieldError(field="username", message="Username is already taken")] + error_response = RegistrationErrorResponse( + message="Username is already taken", + field_errors=field_errors, + ) + return error_response + return None + + +def process_bundle_request_notifications( + bundles: list[BundleRequest], + db_user: BiocommonsUser, + auth0_user_data: Auth0UserData, + auth0_client: Auth0Client, + db_session: Session, + settings: Settings,): + """ + Send any admin/requester notifications that are needed based on requested bundles + Bundles that are auto-approved don't need notifications + """ + for bundle_request in bundles: + bundle = BUNDLES[bundle_request.bundle_id] + if bundle.group_auto_approve: + continue + _notify_bundle_group_admins( + bundle=bundle, + user=db_user, + auth0_client=auth0_client, + db_session=db_session, + settings=settings, + ) + _notify_bundle_requester( + bundle=bundle, + user=db_user, + auth0_user_data=auth0_user_data, + db_session=db_session, + settings=settings, + request_reason=bundle_request.reason, + ) + + +def _notify_bundle_group_admins( + *, + bundle: BiocommonsBundle, + user: BiocommonsUser, + auth0_client: Auth0Client, + db_session: Session, + settings: Settings, +) -> None: + """ + Queue approval emails for bundle group admins when memberships require review. + """ + if bundle.group_auto_approve: + return + + membership = GroupMembership.get_by_user_id_and_group_id( + user_id=user.id, + group_id=bundle.group_id.value, + session=db_session, + ) + if membership is None: + logger.warning( + "Unable to find group membership for user %s and bundle %s", + user.id, + bundle.id, + ) + return + + db_session.refresh(membership, attribute_names=["group", "user"]) + + admin_contacts = get_group_admin_contacts(group=membership.group, auth0_client=auth0_client) + if not admin_contacts: + logger.info("No admins found for group %s; skipping notification", membership.group_id) + return + + try: + requester_email, requester_full_name = get_requester_identity( + auth0_client=auth0_client, + user_id=membership.user_id, + fallback_email=membership.user.email, + ) + except Exception as exc: + logger.warning( + "Failed to fetch Auth0 user data for %s; using fallback values: %s", + membership.user_id, + exc, + ) + requester_email = membership.user.email + requester_full_name = requester_email or "Unknown user" + for email, admin_first_name in admin_contacts: + subject, body_html = compose_group_approval_email( + admin_first_name=admin_first_name, + bundle_name=membership.group.name, + requester_full_name=requester_full_name, + requester_email=requester_email, + request_reason=membership.request_reason, + settings=settings, + ) + enqueue_email( + db_session, + to_address=email, + subject=subject, + body_html=body_html, + settings=settings, + ) + + +def _notify_bundle_requester( + *, + bundle: BiocommonsBundle, + user: BiocommonsUser, + auth0_user_data: Auth0UserData, + db_session: Session, + settings: Settings, + request_reason: Optional[str], +) -> None: + """ + Queue a confirmation email to the user after they request bundle access. + """ + if bundle.group_auto_approve: + return + + membership = GroupMembership.get_by_user_id_and_group_id( + user_id=user.id, + group_id=bundle.group_id.value, + session=db_session, + ) + if membership is None: + logger.warning( + "Unable to find group membership for user %s and bundle %s", + user.id, + bundle.id, + ) + return + + db_session.refresh(membership, attribute_names=["group"]) + + first_name = format_first_name( + full_name=auth0_user_data.name, + given_name=auth0_user_data.given_name, + fallback="there", + ) + subject, body_html = compose_bundle_request_confirmation_email( + first_name=first_name, + bundle_name=membership.group.name, + request_reason=request_reason, + settings=settings, + ) + enqueue_email( + db_session, + to_address=str(auth0_user_data.email), + subject=subject, + body_html=body_html, + settings=settings, + ) + + +async def check_sbp_email_allowed(email: str, bundles: list[BundleRequest] | None) -> RegistrationErrorResponse | None: + """ + If user requests SBP access, check if the email domain is allowed. + + Return a RegistrationErrorResponse if SBP is requested and domain is not allowed, otherwise None. + """ + if bundles is not None: + has_sbp_bundle = any(bundle.bundle_id == "sbp_workflow_execution" for bundle in bundles) + if has_sbp_bundle: + is_institute = await is_australian_research_institution_email(email) + if not is_institute: + return RegistrationErrorResponse( + message="SBP workflow execution requires an Australian institutional email address.", + field_errors=[ + FieldError( + field="email", + message="Please use an Australian institutional email address if applying for SBP workflow execution access.", + ) + ], + ) + else: + return None + return None + + +def create_platform_memberships(db_user: BiocommonsUser, auth0_client: Auth0Client, session: Session, sbp_enabled: bool = True) -> None: + """ + Create default platform memberships (database record and Auth0 role) for a user + """ + for platform in get_default_platforms(sbp_enabled=sbp_enabled): + db_user.add_platform_membership( + platform=platform, + db_session=session, + auth0_client=auth0_client, + auto_approve=True + ) + + +def create_bundle_requests(bundles: list[BundleRequest] | None, db_user: BiocommonsUser, auth0_client: Auth0Client, session: Session) -> None: + """ + Create bundle requests for a user, based on the bundles requested at registration + """ + if bundles is not None: + for bundle_request in bundles: + bundle = BUNDLES[bundle_request.bundle_id] + logger.info(f"Adding group/platform memberships for bundle: {bundle}") + bundle.create_memberships( + user=db_user, + auth0_client=auth0_client, + db_session=session, + commit=False, + request_reason=bundle_request.reason, + ) diff --git a/routers/biocommons_register.py b/routers/biocommons_register.py index 7eb89a37..8c2ab6b3 100644 --- a/routers/biocommons_register.py +++ b/routers/biocommons_register.py @@ -1,35 +1,46 @@ import logging -from typing import Optional +from http import HTTPStatus +from typing import Annotated, Optional -from fastapi import APIRouter, Depends, HTTPException, Response +from fastapi import APIRouter, Depends, HTTPException from httpx2 import HTTPStatusError from sqlmodel import Session +from starlette import status +from starlette.responses import Response -from auth0.client import Auth0Client, get_auth0_client -from biocommons.bundles import BUNDLES, BiocommonsBundle -from biocommons.default import get_default_platforms -from biocommons.emails import ( - compose_bundle_request_confirmation_email, - compose_group_approval_email, - format_first_name, - get_group_admin_contacts, - get_requester_identity, -) +from auth.validator import verify_action_token +from auth0.client import Auth0Client, UpdateUserData, get_auth0_client from config import Settings, get_settings -from db.models import BiocommonsUser, BiocommonsUserHistory, GroupMembership +from db.models import BiocommonsUser from db.setup import get_db_session from register.tokens import validate_recaptcha +from register.utils import ( + check_is_username_used, + check_sbp_email_allowed, + create_bundle_requests, + create_platform_memberships, + process_bundle_request_notifications, +) from routers.errors import RegistrationRoute from routers.utils import check_existing_user -from schemas.biocommons import Auth0UserData, BiocommonsRegisterData -from schemas.biocommons_register import BiocommonsRegistrationRequest, BundleRequest +from schemas.auth0 import AafRegistrationActionToken +from schemas.biocommons import ( + Auth0UserData, + BiocommonsAppMetadataUpdate, + BiocommonsRegisterData, + BiocommonsUserAccountType, +) +from schemas.biocommons_register import ( + AafRegistrationRequest, + BiocommonsRegistrationRequest, + BundleRequest, +) from schemas.responses import ( FieldError, RegistrationErrorResponse, RegistrationResponse, ) -from services.email_queue import enqueue_email -from services.institutions import is_australian_research_institution_email +from services.institutions import is_aaf_email logger = logging.getLogger("uvicorn.error") @@ -50,166 +61,20 @@ def create_user_in_db(user_data: Auth0UserData, db_user = BiocommonsUser.from_auth0_data(data=user_data) session.add(db_user) session.flush() - for platform in get_default_platforms(sbp_enabled=sbp_enabled): - db_user.add_platform_membership( - platform=platform, - db_session=session, - auth0_client=auth0_client, - auto_approve=True - ) - - if bundles is not None: - for bundle_request in bundles: - bundle = BUNDLES[bundle_request.bundle_id] - logger.info(f"Adding group/platform memberships for bundle: {bundle}") - bundle.create_memberships( - user=db_user, - auth0_client=auth0_client, - db_session=session, - commit=False, - request_reason=bundle_request.reason, - ) - + # Add default platform memberships + create_platform_memberships(db_user=db_user, auth0_client=auth0_client, session=session, sbp_enabled=sbp_enabled) + # Create requests for selected bundles (if any) + create_bundle_requests(bundles=bundles, db_user=db_user, session=session, auth0_client=auth0_client) session.flush() if commit: session.commit() return db_user -def _notify_bundle_group_admins( - *, - bundle: BiocommonsBundle, - user: BiocommonsUser, - auth0_client: Auth0Client, - db_session: Session, - settings: Settings, -) -> None: - """ - Queue approval emails for bundle group admins when memberships require review. - """ - if bundle.group_auto_approve: - return - - membership = GroupMembership.get_by_user_id_and_group_id( - user_id=user.id, - group_id=bundle.group_id.value, - session=db_session, - ) - if membership is None: - logger.warning( - "Unable to find group membership for user %s and bundle %s", - user.id, - bundle.id, - ) - return - - db_session.refresh(membership, attribute_names=["group", "user"]) - - admin_contacts = get_group_admin_contacts(group=membership.group, auth0_client=auth0_client) - if not admin_contacts: - logger.info("No admins found for group %s; skipping notification", membership.group_id) - return - - try: - requester_email, requester_full_name = get_requester_identity( - auth0_client=auth0_client, - user_id=membership.user_id, - fallback_email=membership.user.email, - ) - except Exception as exc: - logger.warning( - "Failed to fetch Auth0 user data for %s; using fallback values: %s", - membership.user_id, - exc, - ) - requester_email = membership.user.email - requester_full_name = requester_email or "Unknown user" - for email, admin_first_name in admin_contacts: - subject, body_html = compose_group_approval_email( - admin_first_name=admin_first_name, - bundle_name=membership.group.name, - requester_full_name=requester_full_name, - requester_email=requester_email, - request_reason=membership.request_reason, - settings=settings, - ) - enqueue_email( - db_session, - to_address=email, - subject=subject, - body_html=body_html, - settings=settings, - ) - - -def _notify_bundle_requester( - *, - bundle: BiocommonsBundle, - user: BiocommonsUser, - auth0_user_data: Auth0UserData, - db_session: Session, - settings: Settings, - request_reason: Optional[str], -) -> None: - """ - Queue a confirmation email to the user after they request bundle access. - """ - if bundle.group_auto_approve: - return - - membership = GroupMembership.get_by_user_id_and_group_id( - user_id=user.id, - group_id=bundle.group_id.value, - session=db_session, - ) - if membership is None: - logger.warning( - "Unable to find group membership for user %s and bundle %s", - user.id, - bundle.id, - ) - return - - db_session.refresh(membership, attribute_names=["group"]) - - first_name = format_first_name( - full_name=auth0_user_data.name, - given_name=auth0_user_data.given_name, - fallback="there", - ) - subject, body_html = compose_bundle_request_confirmation_email( - first_name=first_name, - bundle_name=membership.group.name, - request_reason=request_reason, - settings=settings, - ) - enqueue_email( - db_session, - to_address=str(auth0_user_data.email), - subject=subject, - body_html=body_html, - settings=settings, - ) - - -async def check_sbp_email_domain(registration: BiocommonsRegistrationRequest) -> bool: - """ - If user requests SBP access, check if the email domain is allowed. - - Return false if the email domain is not allowed. - """ - if registration.bundles is not None: - has_sbp_bundle = any(bundle.bundle_id == "sbp_workflow_execution" for bundle in registration.bundles) - if has_sbp_bundle: - is_institute = await is_australian_research_institution_email(registration.email) - return is_institute - return True - - -def _requests_sbp_bundle(registration: BiocommonsRegistrationRequest) -> bool: - if registration.bundles is None: +def _requests_sbp_bundle(bundles: list[BundleRequest] | None) -> bool: + if bundles is None: return False - return any(bundle.bundle_id == "sbp_workflow_execution" for bundle in registration.bundles) + return any(bundle.bundle_id == "sbp_workflow_execution" for bundle in bundles) @router.post( "/register", @@ -235,36 +100,23 @@ async def register_biocommons_user( response.status_code = 400 return RegistrationErrorResponse(message="Invalid recaptcha token, please try again") - if _requests_sbp_bundle(registration) and not settings.sbp_enabled: + if _requests_sbp_bundle(registration.bundles) and not settings.sbp_enabled: response.status_code = 400 return RegistrationErrorResponse(message="SBP workflow execution is currently unavailable.") # Pre-registration checks - email_ok = await check_sbp_email_domain(registration) - if not email_ok: + sbp_email_error = await check_sbp_email_allowed(email=registration.email, bundles=registration.bundles) + if sbp_email_error is not None: response.status_code = 400 - return RegistrationErrorResponse( - message="SBP workflow execution requires an Australian institutional email address.", - field_errors=[ - FieldError( - field="email", - message="Please use an Australian institutional email address if applying for SBP workflow execution access." - ) - ] - ) + return sbp_email_error # Create Auth0 user data user_data = BiocommonsRegisterData.from_biocommons_registration(registration) # Check if username has already been used previously - username_used = BiocommonsUserHistory.is_username_used(user_data.username, session=db_session) - if username_used: - field_errors = [FieldError(field="username", message="Username is already taken")] - error_response = RegistrationErrorResponse( - message="Username is already taken", - field_errors=field_errors - ) + duplicate_username_error = check_is_username_used(username=user_data.username, session=db_session) + if duplicate_username_error: response.status_code = 400 - return error_response + return duplicate_username_error try: logger.info("Registering user with Auth0") @@ -280,25 +132,14 @@ async def register_biocommons_user( ) if registration.bundles is not None: - for bundle_request in registration.bundles: - bundle = BUNDLES[bundle_request.bundle_id] - if bundle.group_auto_approve: - continue - _notify_bundle_group_admins( - bundle=bundle, - user=db_user, - auth0_client=auth0_client, - db_session=db_session, - settings=settings, - ) - _notify_bundle_requester( - bundle=bundle, - user=db_user, - auth0_user_data=auth0_user_data, - db_session=db_session, - settings=settings, - request_reason=bundle_request.reason, - ) + process_bundle_request_notifications( + bundles=registration.bundles, + db_user=db_user, + auth0_user_data=auth0_user_data, + auth0_client=auth0_client, + db_session=db_session, + settings=settings, + ) db_session.commit() @@ -344,3 +185,132 @@ async def register_biocommons_user( except Exception as e: logger.error(f"Unexpected error during registration: {e}") raise HTTPException(status_code=500, detail="Internal server error") + + +def create_aaf_user_in_db(register_data: AafRegistrationRequest, + *, + auth0_token: AafRegistrationActionToken, + auth0_client: Auth0Client, + session: Session, + settings: Settings, + commit: bool = False): + db_user = BiocommonsUser( + id=auth0_token.user_id, + email=auth0_token.email, + username=register_data.username, + # AAF users are considered email_verified by default + email_verified=True, + account_type=BiocommonsUserAccountType.AAF.value, + ) + session.add(db_user) + session.flush() + # Add default platform memberships + create_platform_memberships(db_user=db_user, auth0_client=auth0_client, session=session, sbp_enabled=settings.sbp_enabled) + # Create requests for selected bundles (if any) + create_bundle_requests(bundles=register_data.bundles, db_user=db_user, auth0_client=auth0_client, session=session) + session.flush() + if commit: + session.commit() + return db_user + + +def verify_registration_token(token: str, settings: Settings): + """ + Verify the token sent through from the original Auth0 action - we use this to provide + id, name + email so want to make sure it's verified + """ + payload = verify_action_token(token, settings) + if payload.get("purpose", None) != "aaf_registration": + raise HTTPException(status_code=status.HTTP_401_UNAUTHORIZED, detail="Token from Auth0 expired.") + return AafRegistrationActionToken(**payload) + + +@router.post("/register-aaf") +async def register_aaf( + register_data: AafRegistrationRequest, + response: Response, + session: Annotated[Session, Depends(get_db_session)], + auth0_client: Annotated[Auth0Client, Depends(get_auth0_client)], + settings: Annotated[Settings, Depends(get_settings)], +): + """ + Register an AAF user. Because we want to ensure we use the email and name provided by + the AAF, using a signed token passed through from Auth0 + """ + if not register_data.recaptcha_token: + response.status_code = status.HTTP_400_BAD_REQUEST + return RegistrationErrorResponse(message="Recaptcha token is required") + recaptcha_check = validate_recaptcha(register_data.recaptcha_token, settings=settings) + if not recaptcha_check: + response.status_code = status.HTTP_400_BAD_REQUEST + return RegistrationErrorResponse(message="Invalid recaptcha token, please try again") + + validated_token = verify_registration_token(register_data.session_token, settings=settings) + + if _requests_sbp_bundle(register_data.bundles) and not settings.sbp_enabled: + response.status_code = status.HTTP_400_BAD_REQUEST + return RegistrationErrorResponse(message="SBP workflow execution is currently unavailable.") + + is_aaf = is_aaf_email(validated_token.email, settings=settings) + if not is_aaf: + raise HTTPException(status_code=HTTPStatus.UNPROCESSABLE_CONTENT, detail=f"{validated_token.email} is not an AAF-associated email.") + + sbp_email_error = await check_sbp_email_allowed(email=validated_token.email, bundles=register_data.bundles) + if sbp_email_error is not None: + response.status_code = status.HTTP_400_BAD_REQUEST + return sbp_email_error + + duplicate_username_error = check_is_username_used(username=register_data.username, session=session) + if duplicate_username_error: + response.status_code = status.HTTP_400_BAD_REQUEST + return duplicate_username_error + + try: + logger.info("Setting username in app_metadata") + update_data = UpdateUserData( + app_metadata=BiocommonsAppMetadataUpdate( + username=register_data.username, + account_type=BiocommonsUserAccountType.AAF, + aaf_only=True, + ) + ) + try: + auth0_user_data = auth0_client.update_user(user_id=validated_token.user_id, update_data=update_data) + except ValueError as e: + logger.error(f"AAF registration failed: {e}") + response.status_code = status.HTTP_400_BAD_REQUEST + return RegistrationErrorResponse(message=f"AAF registration failed - couldn't update app_metadata: {e}") + logger.info("Adding user to database...") + db_user = create_aaf_user_in_db( + register_data=register_data, + auth0_token=validated_token, + auth0_client=auth0_client, + session=session, + settings=settings, + commit=False, + ) + if register_data.bundles is not None: + process_bundle_request_notifications( + bundles=register_data.bundles, + db_user=db_user, + auth0_user_data=auth0_user_data, + auth0_client=auth0_client, + db_session=session, + settings=settings + ) + + session.commit() + logger.info("Successfully added user to database.") + return { + "message": "User registered successfully", + "user": auth0_user_data + } + except HTTPStatusError as e: + logger.error(f"AAF registration failed: {e}") + # NOTE: don't think the checks of specific Auth0 issues are relevant here as we + # aren't registering in Auth0 + response.status_code = status.HTTP_400_BAD_REQUEST + return RegistrationErrorResponse(message=f"AAF registration failed: {e.response.text}") + except Exception as e: + logger.error(f"Unexpected error during registration: {e}") + raise HTTPException(status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail="Internal server error") diff --git a/schemas/auth0.py b/schemas/auth0.py index c44f7414..638c9dff 100644 --- a/schemas/auth0.py +++ b/schemas/auth0.py @@ -32,3 +32,12 @@ class Auth0ActionToken(BaseModel): purpose: str sub: str | None = None iss: str | None = None + + +class AafRegistrationActionToken(Auth0ActionToken): + """ + Extends Auth0ActionToken with extra fields used during AAF registration. + """ + given_name: str | None = None + family_name: str | None = None + name: str | None = None diff --git a/schemas/biocommons.py b/schemas/biocommons.py index 79eadcb7..9550d7d3 100644 --- a/schemas/biocommons.py +++ b/schemas/biocommons.py @@ -189,6 +189,7 @@ class BiocommonsAppMetadata(BaseModel): Note we expect all app_metadata from Auth0 to match this format (if not empty). """ + username: Optional[str] = None registration_from: Optional[AppId] = None old_emails: Optional[list[OldEmailRecord]] = None user_needs_migration: Optional[bool] = None @@ -218,6 +219,7 @@ class BiocommonsAppMetadataUpdate(BaseModel): Auth0 merges app_metadata fields when updating, so updates should not need to repeat fields that are not changing. """ + username: Optional[str] = None registration_from: Optional[AppId] = None old_emails: Optional[list[OldEmailRecord]] = None user_needs_migration: Optional[bool] = None diff --git a/schemas/biocommons_register.py b/schemas/biocommons_register.py index 1b3c991e..b828299c 100644 --- a/schemas/biocommons_register.py +++ b/schemas/biocommons_register.py @@ -21,3 +21,14 @@ class BiocommonsRegistrationRequest(BaseModel): recaptcha_token: Optional[str] = None model_config = ConfigDict(extra="forbid") + + +class AafRegistrationRequest(BaseModel): + """ + email and name come from AAF and are encoded in the session_token, + which needs to be verified. + """ + session_token: str + username: BiocommonsUsername + bundles: Optional[list[BundleRequest]] = None + recaptcha_token: Optional[str] = None diff --git a/services/institutions.py b/services/institutions.py index 4ef0103a..0a01da5f 100644 --- a/services/institutions.py +++ b/services/institutions.py @@ -1,6 +1,9 @@ from typing import Optional import httpx2 +from pydantic import BaseModel + +from config import Settings GALAXY_AU_VALIDATE_URL = "https://site.usegalaxy.org.au/institution/validate" @@ -28,3 +31,16 @@ async def is_australian_research_institution_email(email: str) -> bool: blocked by an upstream outage. """ return await check_australian_research_institution_email(email) is True + + +class AafCheckEmailResponse(BaseModel): + email: str + is_aaf: bool + + +def is_aaf_email(email: str, settings: Settings) -> bool: + check_email_url = settings.aai_login_proxy_url + "/aaf/email-check" + resp = httpx2.get(check_email_url, params={"email": email}) + resp.raise_for_status() + data = AafCheckEmailResponse.model_validate_json(resp.content) + return data.is_aaf diff --git a/tests/conftest.py b/tests/conftest.py index ecdf9948..330ff01d 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -191,6 +191,7 @@ def mock_settings(): auth0_db_connection="Username-Password-Authentication", jwt_secret_key="mock-secret-key", cors_allowed_origins="https://test", + aai_login_proxy_url="https://mock-proxy-url", admin_roles=["Admin"], auth0_algorithms=["RS256"], recaptcha_secret="mock-secret", diff --git a/tests/datagen.py b/tests/datagen.py index 44ace3b1..1d30f8e0 100644 --- a/tests/datagen.py +++ b/tests/datagen.py @@ -124,6 +124,7 @@ def user_id(cls) -> str: username = BiocommonsProviders.biocommons_username # blocked = False by default blocked = False + email_verified = True class Auth0ConnectionFactory(ModelFactory[Auth0Connection]): diff --git a/tests/test_aaf.py b/tests/test_aaf.py index 42478e48..7f099fe7 100644 --- a/tests/test_aaf.py +++ b/tests/test_aaf.py @@ -1,3 +1,4 @@ +from datetime import datetime, timedelta from http import HTTPStatus from unittest.mock import MagicMock from urllib.parse import parse_qs, urlparse @@ -8,6 +9,7 @@ from auth0.client import Auth0Client from routers.aaf import link_aaf_account, mark_user_aaf_only +from routers.biocommons_register import verify_registration_token from schemas.biocommons import Auth0Identity, BiocommonsUserAccountType from tests.datagen import Auth0UserDataFactory, random_auth0_id from tests.db.datagen import BiocommonsUserFactory @@ -159,6 +161,20 @@ def _action_token_payload( return payload +def _aaf_registration_token_payload( + user_id: str, + email: str, + purpose: str = "aaf_registration", +) -> dict: + return { + **_action_token_payload(user_id=user_id, email=email, purpose=purpose), + "given_name": "AAF", + "family_name": "User", + "name": "AAF User", + "exp": int((datetime.now() + timedelta(minutes=5)).timestamp()), + } + + def _assert_marked_aaf_only(update_user_mock, aaf_user_id: str, email: str): update_user_mock.assert_called_once() call_args, call_kwargs = update_user_mock.call_args @@ -209,6 +225,47 @@ def _decode_check_link_redirect( return decoded_token +def test_verify_registration_token_accepts_token_signed_with_settings_secret(mock_settings): + aaf_user_id = random_auth0_id() + payload = _aaf_registration_token_payload( + user_id=aaf_user_id, + email="aaf-user@example.edu.au", + ) + token = jwt.encode( + payload, + key=mock_settings.auth0_management_secret, + algorithm="HS256", + ) + + result = verify_registration_token(token, settings=mock_settings) + + assert result.user_id == aaf_user_id + assert str(result.email) == "aaf-user@example.edu.au" + assert result.client_id == "test-client" + assert result.purpose == "aaf_registration" + assert result.given_name == "AAF" + assert result.family_name == "User" + assert result.name == "AAF User" + + +def test_verify_registration_token_rejects_wrong_purpose(mock_settings): + token = jwt.encode( + _aaf_registration_token_payload( + user_id=random_auth0_id(), + email="aaf-user@example.edu.au", + purpose="aaf_link", + ), + key=mock_settings.auth0_management_secret, + algorithm="HS256", + ) + + with pytest.raises(HTTPException) as exc_info: + verify_registration_token(token, settings=mock_settings) + + assert exc_info.value.status_code == HTTPStatus.UNAUTHORIZED + assert exc_info.value.detail == "Token from Auth0 expired." + + def test_mark_user_aaf_only(): aaf_user_id = random_auth0_id() email = "aaf-user@example.com" @@ -423,3 +480,91 @@ def test_check_link_already_linked_is_idempotent(test_client, test_db_session, p get_user.assert_called_once_with(user_id=aaf_user_id) link_identity.assert_not_called() update_user.assert_not_called() + + +def test_register_aaf_returns_registration_error_when_auth0_update_fails( + test_client, + test_db_session, + mock_auth0_client, + mocker, +): + aaf_user_id = random_auth0_id() + email = "new-aaf-user@example.edu.au" + action_token_payload = _action_token_payload( + aaf_user_id, + email, + purpose="aaf_registration", + ) + action_token_payload.update( + { + "given_name": "New", + "family_name": "User", + "name": "New User", + } + ) + mocker.patch("routers.biocommons_register.verify_action_token", return_value=action_token_payload) + mocker.patch("routers.biocommons_register.validate_recaptcha", return_value=True) + mocker.patch("routers.biocommons_register.is_aaf_email", return_value=True) + mock_auth0_client.update_user.side_effect = ValueError("Failed to update user auth0|123: {'message': 'bad request'}") + + response = test_client.post( + "/biocommons/register-aaf", + json={ + "session_token": "valid_token", + "username": "new_aaf_user", + "recaptcha_token": "valid_recaptcha", + }, + ) + + assert response.status_code == HTTPStatus.BAD_REQUEST + assert response.json() == { + "message": "AAF registration failed - couldn't update app_metadata: Failed to update user auth0|123: {'message': 'bad request'}", + "field_errors": [], + } + mock_auth0_client.update_user.assert_called_once() + + +def test_register_aaf_sbp_disabled_rejects_before_creating_user( + test_client, + mock_settings, + mock_auth0_client, + mocker, +): + mock_settings.sbp_enabled = False + aaf_user_id = random_auth0_id() + email = "researcher@unimelb.edu.au" + action_token_payload = _action_token_payload( + aaf_user_id, + email, + purpose="aaf_registration", + ) + action_token_payload.update( + { + "given_name": "SBP", + "family_name": "Disabled", + "name": "SBP Disabled", + } + ) + mocker.patch("routers.biocommons_register.verify_action_token", return_value=action_token_payload) + mocker.patch("routers.biocommons_register.validate_recaptcha", return_value=True) + is_aaf_email = mocker.patch("routers.biocommons_register.is_aaf_email", return_value=True) + institution_check = mocker.patch("register.utils.is_australian_research_institution_email") + + response = test_client.post( + "/biocommons/register-aaf", + json={ + "session_token": "valid_token", + "username": "sbp_disabled_user", + "bundles": [{"bundle_id": "sbp_workflow_execution", "reason": "SBP access"}], + "recaptcha_token": "valid_recaptcha", + }, + ) + + assert response.status_code == HTTPStatus.BAD_REQUEST + assert response.json() == { + "message": "SBP workflow execution is currently unavailable.", + "field_errors": [], + } + is_aaf_email.assert_not_called() + institution_check.assert_not_called() + mock_auth0_client.update_user.assert_not_called() diff --git a/tests/test_biocommons_register.py b/tests/test_biocommons_register.py index 186fef86..bf3f142f 100644 --- a/tests/test_biocommons_register.py +++ b/tests/test_biocommons_register.py @@ -10,13 +10,14 @@ from biocommons.default import get_default_platforms from db.models import BiocommonsUser, BiocommonsUserHistory, EmailNotification from db.types import ApprovalStatusEnum, EmailStatusEnum, GroupEnum, PlatformEnum -from routers.biocommons_register import check_sbp_email_domain, create_user_in_db -from schemas.biocommons import BiocommonsRegisterData +from routers.biocommons_register import create_user_in_db +from schemas.biocommons import BiocommonsRegisterData, BiocommonsUserAccountType from schemas.biocommons_register import BiocommonsRegistrationRequest, BundleRequest from tests.datagen import ( Auth0UserDataFactory, BiocommonsRegistrationRequestFactory, RoleUserDataFactory, + random_auth0_id, ) from tests.db.datagen import ( Auth0RoleFactory, @@ -95,6 +96,18 @@ def sbp_group(persistent_factories): ) +def _aaf_registration_token_payload(user_id: str, email: str) -> dict: + return { + "user_id": user_id, + "email": email, + "client_id": "test-client", + "purpose": "aaf_registration", + "given_name": "AAF", + "family_name": "User", + "name": "AAF User", + } + + def test_biocommons_registration_data_excludes_null_user_metadata(): """Test that user_metadata is excluded when None and basic Auth0 data is correct""" req = BiocommonsRegistrationRequest( @@ -174,87 +187,6 @@ def test_biocommons_registration_tsi_bundle(): assert dumped["app_metadata"].get("services", []) == [] -@pytest.mark.asyncio -async def test_check_sbp_email_domain_skips_check_without_bundles(mocker): - institution_check = mocker.patch( - "routers.biocommons_register.is_australian_research_institution_email", - new=AsyncMock(return_value=False), - ) - registration = BiocommonsRegistrationRequest( - first_name="No", - last_name="Bundle", - email="no.bundle@example.com", - username="no_bundle", - password="StrongPass1!", - bundles=None, - ) - - assert await check_sbp_email_domain(registration) is True - institution_check.assert_not_awaited() - - -@pytest.mark.asyncio -async def test_check_sbp_email_domain_skips_check_without_sbp_bundle(mocker): - institution_check = mocker.patch( - "routers.biocommons_register.is_australian_research_institution_email", - new=AsyncMock(return_value=False), - ) - registration = BiocommonsRegistrationRequest( - first_name="TSI", - last_name="User", - email="tsi.user@example.com", - username="tsi_user", - password="StrongPass1!", - bundles=[BundleRequest(bundle_id="tsi", reason="TSI access")], - ) - - assert await check_sbp_email_domain(registration) is True - institution_check.assert_not_awaited() - - -@pytest.mark.asyncio -async def test_check_sbp_email_domain_checks_sbp_bundle(mocker): - institution_check = mocker.patch( - "routers.biocommons_register.is_australian_research_institution_email", - new=AsyncMock(return_value=True), - ) - registration = BiocommonsRegistrationRequest( - first_name="SBP", - last_name="User", - email="sbp.user@unimelb.edu.au", - username="sbp_user", - password="StrongPass1!", - bundles=[BundleRequest(bundle_id="sbp_workflow_execution", reason="SBP access")], - ) - - assert await check_sbp_email_domain(registration) is True - institution_check.assert_awaited_once_with("sbp.user@unimelb.edu.au") - - -@pytest.mark.asyncio -async def test_check_sbp_email_domain_returns_false_when_sbp_domain_check_fails(mocker): - institution_check = mocker.patch( - "routers.biocommons_register.is_australian_research_institution_email", - new=AsyncMock(return_value=False), - ) - registration = BiocommonsRegistrationRequest( - first_name="SBP", - last_name="User", - email="sbp.user@example.com", - username="sbp_user", - password="StrongPass1!", - bundles=[ - BundleRequest(bundle_id="tsi", reason="TSI access"), - BundleRequest(bundle_id="sbp_workflow_execution", reason="SBP access"), - ], - ) - - assert await check_sbp_email_domain(registration) is False - institution_check.assert_awaited_once_with("sbp.user@example.com") - - - - def test_create_biocommons_user_record_tsi_bundle(test_db_session, mock_auth0_client, tsi_group, galaxy_platform, bpa_platform, sbp_platform, persistent_factories): """Test database record creation for tsi bundle""" from db.models import PlatformEnum @@ -435,6 +367,145 @@ def test_successful_biocommons_registration_endpoint( assert user_email.subject == "Your Threatened Species Initiative Service Bundle request has been received" +def test_register_aaf_endpoint_success_no_bundles( + test_client, + mock_settings, + mock_auth0_client, + galaxy_platform, + bpa_platform, + sbp_platform, + test_db_session, + mock_recaptcha_verify, + mocker, +): + """Test successful AAF registration without bundle requests.""" + mock_settings.sbp_enabled = True + aaf_user_id = random_auth0_id() + email = "aaf-user@example.edu.au" + username = "new_aaf_user" + auth0_data = Auth0UserDataFactory.build( + user_id=aaf_user_id, + email=email, + username=username, + name="AAF User", + ) + mock_auth0_client.update_user.return_value = auth0_data + mocker.patch( + "routers.biocommons_register.verify_action_token", + return_value=_aaf_registration_token_payload(aaf_user_id, email), + ) + is_aaf_email = mocker.patch("routers.biocommons_register.is_aaf_email", return_value=True) + + response = test_client.post( + "/biocommons/register-aaf", + json={ + "session_token": "valid_token", + "username": username, + "recaptcha_token": "mock-token", + }, + ) + + assert response.status_code == 200 + assert response.json()["message"] == "User registered successfully" + assert response.json()["user"]["user_id"] == aaf_user_id + assert mock_recaptcha_verify.called + is_aaf_email.assert_called_once_with(email, settings=mock_settings) + mock_auth0_client.update_user.assert_called_once() + update_call = mock_auth0_client.update_user.call_args + assert update_call.kwargs["user_id"] == aaf_user_id + app_metadata = update_call.kwargs["update_data"].app_metadata + assert app_metadata.username == username + assert app_metadata.account_type == BiocommonsUserAccountType.AAF + assert app_metadata.aaf_only is True + + db_user = test_db_session.get(BiocommonsUser, aaf_user_id) + assert db_user is not None + assert db_user.email == email + assert db_user.username == username + assert db_user.email_verified is True + assert db_user.account_type == BiocommonsUserAccountType.AAF + assert db_user.group_memberships == [] + + platform_ids = {membership.platform_id for membership in db_user.platform_memberships} + assert platform_ids == {PlatformEnum.BPA_DATA_PORTAL, PlatformEnum.GALAXY, PlatformEnum.SBP} + assert test_db_session.exec(select(EmailNotification)).all() == [] + + +def test_register_aaf_endpoint_success_with_bundles( + test_client_with_email, + mock_settings, + mock_auth0_client, + tsi_group, + galaxy_platform, + bpa_platform, + sbp_platform, + test_db_session, + mock_recaptcha_verify, + mocker, +): + """Test successful AAF registration with requested bundles.""" + mock_settings.sbp_enabled = True + aaf_user_id = random_auth0_id() + email = "bundle-aaf-user@example.edu.au" + username = "bundle_aaf_user" + auth0_data = Auth0UserDataFactory.build( + user_id=aaf_user_id, + email=email, + username=username, + name="Bundle AAF User", + ) + mock_auth0_client.update_user.return_value = auth0_data + admin_stub = RoleUserDataFactory.build(email="tsi.admin@example.com") + mock_auth0_client.get_all_role_users.return_value = [admin_stub] + mock_auth0_client.get_user.return_value = Auth0UserDataFactory.build( + user_id=admin_stub.user_id, + email=admin_stub.email, + ) + mocker.patch( + "routers.biocommons_register.verify_action_token", + return_value=_aaf_registration_token_payload(aaf_user_id, email), + ) + mocker.patch("routers.biocommons_register.is_aaf_email", return_value=True) + + response = test_client_with_email.post( + "/biocommons/register-aaf", + json={ + "session_token": "valid_token", + "username": username, + "bundles": [{"bundle_id": "tsi", "reason": "Need TSI access"}], + "recaptcha_token": "mock-token", + }, + ) + + assert response.status_code == 200 + assert response.json()["message"] == "User registered successfully" + update_call = mock_auth0_client.update_user.call_args + app_metadata = update_call.kwargs["update_data"].app_metadata + assert app_metadata.username == username + assert app_metadata.account_type == BiocommonsUserAccountType.AAF + assert app_metadata.aaf_only is True + + db_user = test_db_session.get(BiocommonsUser, aaf_user_id) + assert db_user is not None + assert db_user.account_type == BiocommonsUserAccountType.AAF + group_memberships = {membership.group_id: membership for membership in db_user.group_memberships} + assert set(group_memberships) == {GroupEnum.TSI.value} + assert group_memberships[GroupEnum.TSI.value].approval_status == ApprovalStatusEnum.PENDING + assert group_memberships[GroupEnum.TSI.value].request_reason == "Need TSI access" + + platform_ids = {membership.platform_id for membership in db_user.platform_memberships} + assert platform_ids == {PlatformEnum.BPA_DATA_PORTAL, PlatformEnum.GALAXY, PlatformEnum.SBP} + + queued_emails = test_db_session.exec(select(EmailNotification)).all() + assert len(queued_emails) == 2 + emails_by_address = {email_notification.to_address: email_notification for email_notification in queued_emails} + assert emails_by_address[admin_stub.email].subject == "Threatened Species Initiative Service Bundle request" + assert emails_by_address[email].subject == ( + "Your Threatened Species Initiative Service Bundle request has been received" + ) + assert all(email_notification.status == EmailStatusEnum.PENDING for email_notification in queued_emails) + + def test_biocommons_registration_endpoint_multiple_bundles( test_client_with_email, mock_settings, @@ -463,7 +534,7 @@ def test_biocommons_registration_endpoint_multiple_bundles( email=admin_stub.email, ) domain_check = mocker.patch( - "routers.biocommons_register.is_australian_research_institution_email", + "register.utils.is_australian_research_institution_email", new=AsyncMock(return_value=True), ) @@ -511,7 +582,7 @@ def test_biocommons_registration_endpoint_sbp_rejects_non_institutional_email( """Test SBP workflow registration checks the email domain before creating a user.""" mock_settings.sbp_enabled = True domain_check = mocker.patch( - "routers.biocommons_register.is_australian_research_institution_email", + "register.utils.is_australian_research_institution_email", new=AsyncMock(return_value=False), ) @@ -551,7 +622,7 @@ def test_biocommons_registration_endpoint_sbp_disabled_rejects_before_creating_u """Test SBP workflow registration is blocked by the feature flag.""" mock_settings.sbp_enabled = False domain_check = mocker.patch( - "routers.biocommons_register.is_australian_research_institution_email", + "register.utils.is_australian_research_institution_email", new=AsyncMock(return_value=True), ) diff --git a/tests/test_config.py b/tests/test_config.py index dd90ea0a..3d3f5f7c 100644 --- a/tests/test_config.py +++ b/tests/test_config.py @@ -23,6 +23,7 @@ def _base_settings_kwargs(): "recaptcha_secret": "mock-recaptcha", "jwt_secret_key": "mock-secret-key", "cors_allowed_origins": "https://test", + "aai_login_proxy_url": "https://proxy", "no_reply_email_sender": "no-reply@example.com", } diff --git a/tests/test_register_utils.py b/tests/test_register_utils.py new file mode 100644 index 00000000..fbcfe082 --- /dev/null +++ b/tests/test_register_utils.py @@ -0,0 +1,61 @@ +from unittest.mock import AsyncMock + +import pytest + +from register.utils import check_sbp_email_allowed +from schemas.biocommons_register import BundleRequest + + +@pytest.mark.asyncio +async def test_check_sbp_email_allowed_skips_check_without_bundles(mocker): + institution_check = mocker.patch( + "register.utils.is_australian_research_institution_email", + new=AsyncMock(return_value=False), + ) + + assert await check_sbp_email_allowed(email="no.bundle@example.com", bundles=None) is None + institution_check.assert_not_awaited() + + +@pytest.mark.asyncio +async def test_check_sbp_email_allowed_skips_check_without_sbp_bundle(mocker): + institution_check = mocker.patch( + "register.utils.is_australian_research_institution_email", + new=AsyncMock(return_value=False), + ) + bundles = [BundleRequest(bundle_id="tsi", reason="TSI access")] + + assert await check_sbp_email_allowed(email="tsi.user@example.com", bundles=bundles) is None + institution_check.assert_not_awaited() + + +@pytest.mark.asyncio +async def test_check_sbp_email_allowed_checks_sbp_bundle(mocker): + institution_check = mocker.patch( + "register.utils.is_australian_research_institution_email", + new=AsyncMock(return_value=True), + ) + bundles = [BundleRequest(bundle_id="sbp_workflow_execution", reason="SBP access")] + + result = await check_sbp_email_allowed(email="sbp.user@unimelb.edu.au", bundles=bundles) + + assert result is None + institution_check.assert_awaited_once_with("sbp.user@unimelb.edu.au") + + +@pytest.mark.asyncio +async def test_check_sbp_email_allowed_returns_error_when_domain_check_fails(mocker): + institution_check = mocker.patch( + "register.utils.is_australian_research_institution_email", + new=AsyncMock(return_value=False), + ) + bundles = [ + BundleRequest(bundle_id="tsi", reason="TSI access"), + BundleRequest(bundle_id="sbp_workflow_execution", reason="SBP access"), + ] + + result = await check_sbp_email_allowed(email="sbp.user@example.com", bundles=bundles) + + assert result is not None + assert result.message == "SBP workflow execution requires an Australian institutional email address." + institution_check.assert_awaited_once_with("sbp.user@example.com") diff --git a/tests/test_utils.py b/tests/test_utils.py index ade16a40..33f88a81 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -8,7 +8,11 @@ from db.models import EmailNotification from main import app from routers import utils -from services.institutions import GALAXY_AU_VALIDATE_URL +from services.institutions import ( + GALAXY_AU_VALIDATE_URL, + AafCheckEmailResponse, + is_aaf_email, +) from tests.datagen import ( Auth0ReadAppMetadataFactory, Auth0UserDataFactory, @@ -242,3 +246,14 @@ def test_send_welcome_email_suppresses_duplicate(override_auth0_client, test_cli assert resp.json()["message"] == "Welcome email already queued or sent." queued = test_db_session.exec(select(EmailNotification)).all() assert len(queued) == 1 + + +@respx.mock +def test_is_aaf_email(mock_settings): + mock_resp = AafCheckEmailResponse(email="user@example.com", is_aaf=True) + url = f"{mock_settings.aai_login_proxy_url}/aaf/email-check" + route = respx.get(url, params={"email": "user@example.com"}).respond(200, json=mock_resp.model_dump(mode="json")) + + result = is_aaf_email(email="user@example.com", settings=mock_settings) + assert result is True + assert route.called From f132517a761607bd2bdb9f7fc173417b03cd8571 Mon Sep 17 00:00:00 2001 From: Marius Mather Date: Thu, 17 Sep 2026 11:42:39 +1000 Subject: [PATCH 18/25] fix: AAF registration needs to set aaf_registration_complete flag --- routers/biocommons_register.py | 1 + schemas/biocommons.py | 2 ++ 2 files changed, 3 insertions(+) diff --git a/routers/biocommons_register.py b/routers/biocommons_register.py index 8c2ab6b3..c2b8949e 100644 --- a/routers/biocommons_register.py +++ b/routers/biocommons_register.py @@ -272,6 +272,7 @@ async def register_aaf( username=register_data.username, account_type=BiocommonsUserAccountType.AAF, aaf_only=True, + aaf_registration_complete=True, ) ) try: diff --git a/schemas/biocommons.py b/schemas/biocommons.py index 9550d7d3..8a4e84de 100644 --- a/schemas/biocommons.py +++ b/schemas/biocommons.py @@ -195,6 +195,7 @@ class BiocommonsAppMetadata(BaseModel): user_needs_migration: Optional[bool] = None account_type: BiocommonsUserAccountType aaf_only: Optional[bool] = None + aaf_registration_complete: Optional[bool] = None checked_email: Optional[EmailStr] = None linking_completed: Optional[bool] = None linking_completed_at: Optional[AwareDatetime] = None @@ -225,6 +226,7 @@ class BiocommonsAppMetadataUpdate(BaseModel): user_needs_migration: Optional[bool] = None account_type: Optional[BiocommonsUserAccountType] = None aaf_only: Optional[bool] = None + aaf_registration_complete: Optional[bool] = None checked_email: Optional[EmailStr] = None linking_completed: Optional[bool] = None linking_completed_at: Optional[AwareDatetime] = None From aa4b58f66f66965a041df85ceed1078978f06a95 Mon Sep 17 00:00:00 2001 From: Marius Mather Date: Thu, 17 Sep 2026 11:58:29 +1000 Subject: [PATCH 19/25] fix: email_verified is optional in Auth0 user info --- auth0/user_info.py | 5 +++-- schemas/biocommons.py | 2 +- tests/schemas/test_biocommons_schemas.py | 2 +- 3 files changed, 5 insertions(+), 4 deletions(-) diff --git a/auth0/user_info.py b/auth0/user_info.py index 5cdb345b..aaeb18e9 100644 --- a/auth0/user_info.py +++ b/auth0/user_info.py @@ -1,4 +1,4 @@ -from typing import Annotated +from typing import Annotated, Optional import httpx2 from fastapi.params import Depends @@ -13,7 +13,8 @@ class UserInfo(BaseModel): name: str email: str picture: str - email_verified: bool + # email_verified may be missing for external OIDC users (e.g. AAF) + email_verified: Optional[bool] = None given_name: str | None = None family_name: str | None = None show_welcome_message: bool | None = Field(None, alias="https://biocommons.org.au/show_migration_welcome") diff --git a/schemas/biocommons.py b/schemas/biocommons.py index 8a4e84de..55beb6c8 100644 --- a/schemas/biocommons.py +++ b/schemas/biocommons.py @@ -396,7 +396,7 @@ class UserProfileData(BaseModel): user_id: str name: str email: str - email_verified: bool + email_verified: Optional[bool] = None username: BiocommonsUsername picture: str given_name: str | None = None diff --git a/tests/schemas/test_biocommons_schemas.py b/tests/schemas/test_biocommons_schemas.py index ae35082a..7ddeaf36 100644 --- a/tests/schemas/test_biocommons_schemas.py +++ b/tests/schemas/test_biocommons_schemas.py @@ -66,7 +66,7 @@ def test_invalid_password(password: str, expected_error: str): def test_user_profile_data_with_memberships(test_db_session, persistent_factories): - auth0_user = UserInfoFactory.build() + auth0_user = UserInfoFactory.build(email_verified=True) db_user = BiocommonsUserFactory.create_sync( id=auth0_user.sub, email=auth0_user.email, From a24d3d6860d26b1c5db8a89b0282835b6b301dd2 Mon Sep 17 00:00:00 2001 From: Marius Mather Date: Thu, 17 Sep 2026 16:26:37 +1000 Subject: [PATCH 20/25] test: update unit tests to check for aaf_registration_complete --- tests/test_biocommons_register.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/tests/test_biocommons_register.py b/tests/test_biocommons_register.py index bf3f142f..c8dbaf0f 100644 --- a/tests/test_biocommons_register.py +++ b/tests/test_biocommons_register.py @@ -417,6 +417,7 @@ def test_register_aaf_endpoint_success_no_bundles( assert app_metadata.username == username assert app_metadata.account_type == BiocommonsUserAccountType.AAF assert app_metadata.aaf_only is True + assert app_metadata.aaf_registration_complete is True db_user = test_db_session.get(BiocommonsUser, aaf_user_id) assert db_user is not None @@ -484,6 +485,7 @@ def test_register_aaf_endpoint_success_with_bundles( assert app_metadata.username == username assert app_metadata.account_type == BiocommonsUserAccountType.AAF assert app_metadata.aaf_only is True + assert app_metadata.aaf_registration_complete is True db_user = test_db_session.get(BiocommonsUser, aaf_user_id) assert db_user is not None From 23b20e3ba1dd919228009abd70cdb3ee53328cff Mon Sep 17 00:00:00 2001 From: amandazhu Date: Mon, 21 Sep 2026 14:27:45 +1000 Subject: [PATCH 21/25] feat: return /continue redirect_url from register-aaf --- pyproject.toml | 10 +- routers/aaf.py | 4 +- routers/biocommons_register.py | 33 +- schemas/biocommons_register.py | 4 + uv.lock | 1810 +++++++++++++++++++------------- 5 files changed, 1096 insertions(+), 765 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 9a5c9150..2cd30a0a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -23,7 +23,9 @@ dependencies = [ "loguru>=0.7.3", "cachetools~=7.1", "typer>=0.26.8", - "starlette-admin>=0.17.1", + # Pin below 1.0: the 1.x line removed the HasMany(identity=...) API that + # db/st_admin.py relies on. Bump + migrate st_admin.py to move to 1.x. + "starlette-admin>=0.17.1,<1.0", # Security floor for CVE-2026-27199 (safe_join Windows device names) "werkzeug>=3.1.8", ] @@ -46,12 +48,6 @@ dev = [ "faker>=40.4.0", ] -[tool.uv] -# Exclude packages newer than 7 days - may help -# prevent security issues, since hijacked packages are generally -# fixed quickly -exclude-newer = "7 days" - [tool.pytest.ini_options] pythonpath = ["."] testpaths = ["tests"] diff --git a/routers/aaf.py b/routers/aaf.py index 231355a8..430b9ba3 100644 --- a/routers/aaf.py +++ b/routers/aaf.py @@ -4,7 +4,7 @@ from typing import Annotated from urllib.parse import urlparse -import httpx +import httpx2 from fastapi import APIRouter, Depends, HTTPException from pydantic import BaseModel from sqlmodel import Session @@ -126,7 +126,7 @@ def return_signed_response( settings=settings, ) auth0_base_url = get_auth0_continue_base_url(action_token, settings) - redirect_url = httpx.URL( + redirect_url = httpx2.URL( f"{auth0_base_url}/continue", params={"state": state, "session_token": signed_token}, ) diff --git a/routers/biocommons_register.py b/routers/biocommons_register.py index c2b8949e..695bfbcc 100644 --- a/routers/biocommons_register.py +++ b/routers/biocommons_register.py @@ -3,12 +3,13 @@ from typing import Annotated, Optional from fastapi import APIRouter, Depends, HTTPException -from httpx2 import HTTPStatusError +from httpx2 import URL, HTTPStatusError from sqlmodel import Session from starlette import status from starlette.responses import Response -from auth.validator import verify_action_token +from auth.validator import create_action_token, verify_action_token +from routers.aaf import get_auth0_continue_base_url from auth0.client import Auth0Client, UpdateUserData, get_auth0_client from config import Settings, get_settings from db.models import BiocommonsUser @@ -302,10 +303,34 @@ async def register_aaf( session.commit() logger.info("Successfully added user to database.") - return { + result = { "message": "User registered successfully", - "user": auth0_user_data + "user": auth0_user_data, } + # When the Auth0 redirect state is present, sign a registration_complete + # token and return the /continue URL so the aaf-require-registration + # action resumes login instead of denying. + if register_data.state: + signed_token = create_action_token( + payload={ + "registration_complete": True, + "sub": validated_token.sub or validated_token.user_id, + "iss": validated_token.iss or settings.auth0_domain, + "state": register_data.state, + }, + settings=settings, + ) + continue_base_url = get_auth0_continue_base_url(validated_token, settings) + result["redirect_url"] = str( + URL( + f"{continue_base_url}/continue", + params={ + "state": register_data.state, + "session_token": signed_token, + }, + ) + ) + return result except HTTPStatusError as e: logger.error(f"AAF registration failed: {e}") # NOTE: don't think the checks of specific Auth0 issues are relevant here as we diff --git a/schemas/biocommons_register.py b/schemas/biocommons_register.py index b828299c..50e7538b 100644 --- a/schemas/biocommons_register.py +++ b/schemas/biocommons_register.py @@ -29,6 +29,10 @@ class AafRegistrationRequest(BaseModel): which needs to be verified. """ session_token: str + # Auth0 redirect state; when present the endpoint returns a redirect_url that + # resumes the post-login action at Auth0 /continue. Optional so non-redirect + # callers (and existing tests) still work. + state: Optional[str] = None username: BiocommonsUsername bundles: Optional[list[BundleRequest]] = None recaptcha_token: Optional[str] = None diff --git a/uv.lock b/uv.lock index c4911941..39ae3f9b 100644 --- a/uv.lock +++ b/uv.lock @@ -6,10 +6,6 @@ resolution-markers = [ "python_full_version < '3.14'", ] -[options] -exclude-newer = "0001-01-01T00:00:00Z" # This has no effect and is included for backwards compatibility when using relative exclude-newer values. -exclude-newer-span = "P7D" - [[package]] name = "aai-backend" version = "1.4.0" @@ -86,66 +82,76 @@ requires-dist = [ { name = "respx", marker = "extra == 'dev'", specifier = ">=0.22.0" }, { name = "ruff", marker = "extra == 'dev'", specifier = ">=0.4.4" }, { name = "sqlmodel", specifier = ">=0.0.39" }, - { name = "starlette-admin", specifier = ">=0.17.1" }, + { name = "starlette-admin", specifier = ">=0.17.1,<1.0" }, { name = "typer", specifier = ">=0.26.8" 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Tue, 22 Sep 2026 11:05:04 +1000 Subject: [PATCH 22/25] fix: type errors --- routers/biocommons_register.py | 29 +++++++++++ schemas/biocommons.py | 17 ++++++- tests/schemas/test_biocommons_schemas.py | 62 ++++++++++++++++++++++++ tests/test_biocommons_register.py | 25 +++++++--- 4 files changed, 125 insertions(+), 8 deletions(-) diff --git a/routers/biocommons_register.py b/routers/biocommons_register.py index 695bfbcc..5fa36cf0 100644 --- a/routers/biocommons_register.py +++ b/routers/biocommons_register.py @@ -9,12 +9,14 @@ from starlette.responses import Response from auth.validator import create_action_token, verify_action_token +from biocommons.emails import compose_welcome_email, format_first_name from routers.aaf import get_auth0_continue_base_url from auth0.client import Auth0Client, UpdateUserData, get_auth0_client from config import Settings, get_settings from db.models import BiocommonsUser from db.setup import get_db_session from register.tokens import validate_recaptcha +from services.email_queue import enqueue_email from register.utils import ( check_is_username_used, check_sbp_email_allowed, @@ -303,6 +305,33 @@ async def register_aaf( session.commit() logger.info("Successfully added user to database.") + + # AAF users skip Auth0 email verification (their email is asserted by the + # federation), so the welcome email that normally fires after verification + # would never be sent. Enqueue it here instead. Best-effort: a mail failure + # must not fail the registration that already committed above. + try: + first_name = format_first_name( + full_name=validated_token.name, + given_name=validated_token.given_name, + fallback=str(validated_token.email), + ) + subject, body_html = compose_welcome_email( + first_name=first_name, + portal_url=settings.aai_portal_url, + ) + enqueue_email( + session, + to_address=str(validated_token.email), + subject=subject, + body_html=body_html, + settings=settings, + ) + session.commit() + except Exception as e: + logger.error(f"Failed to enqueue AAF welcome email for {validated_token.email}: {e}") + session.rollback() + result = { "message": "User registered successfully", "user": auth0_user_data, diff --git a/schemas/biocommons.py b/schemas/biocommons.py index 55beb6c8..245d6d9d 100644 --- a/schemas/biocommons.py +++ b/schemas/biocommons.py @@ -397,6 +397,9 @@ class UserProfileData(BaseModel): name: str email: str email_verified: Optional[bool] = None + # Account type (AAF vs Auth0) so the portal can lock IdP-managed fields + # (name/password) and treat AAF users as email-verified. + account_type: BiocommonsUserAccountType = BiocommonsUserAccountType.AUTH0 username: BiocommonsUsername picture: str given_name: str | None = None @@ -419,11 +422,23 @@ def from_db_user(cls, user: 'models.BiocommonsUser', auth0_user_info: UserInfo) group_memberships = [UserProfileGroupData.from_group_membership(membership) for membership in user.group_memberships if membership.approval_status != ApprovalStatusEnum.REVOKED] + # AAF detection. The DB account_type is the durable signal, but fall back + # to the login itself: AAF-only users have an enterprise sub of the form + # "oidc|AAF|..." (linked users keep their DB account_type instead). This + # makes the profile resolve correctly even if the DB record predates the + # account_type logic. + is_aaf = ( + user.account_type == BiocommonsUserAccountType.AAF + or "|AAF|" in (auth0_user_info.sub or "") + ) return cls( user_id=user.id, name=auth0_user_info.name, email=user.email, - email_verified=auth0_user_info.email_verified, + # AAF emails are federation-verified; the Auth0/DB flag is unreliable + # for enterprise users (can't be set via Management API), so trust AAF. + email_verified=True if is_aaf else auth0_user_info.email_verified, + account_type=BiocommonsUserAccountType.AAF if is_aaf else user.account_type, username=user.username, picture=auth0_user_info.picture, given_name=auth0_user_info.given_name, diff --git a/tests/schemas/test_biocommons_schemas.py b/tests/schemas/test_biocommons_schemas.py index 7ddeaf36..ff2bc29e 100644 --- a/tests/schemas/test_biocommons_schemas.py +++ b/tests/schemas/test_biocommons_schemas.py @@ -11,6 +11,7 @@ PASSWORD_FORMAT_MESSAGE, BiocommonsEmail, BiocommonsPassword, + BiocommonsUserAccountType, BiocommonsUsername, UserProfileData, ) @@ -141,6 +142,67 @@ def test_user_profile_data_with_memberships(test_db_session, persistent_factorie assert tsi_membership.approval_status == ApprovalStatusEnum.APPROVED +def test_user_profile_data_aaf_by_account_type(test_db_session, persistent_factories): + """A linked AAF user (DB account_type=AAF) is reported AAF and email-verified, + even though the Auth0 flag says unverified.""" + auth0_user = UserInfoFactory.build(sub="auth0|linked-user", email_verified=False) + db_user = BiocommonsUserFactory.create_sync( + id="auth0|linked-user", + email="linked@example.edu.au", + username="linked-user", + account_type=BiocommonsUserAccountType.AAF, + platform_memberships=[], + group_memberships=[], + ) + test_db_session.flush() + test_db_session.refresh(db_user) + + profile = UserProfileData.from_db_user(db_user, auth0_user) + + assert profile.account_type == BiocommonsUserAccountType.AAF + assert profile.email_verified is True + + +def test_user_profile_data_aaf_by_sub_fallback(test_db_session, persistent_factories): + """An AAF-only login (sub 'oidc|AAF|...') resolves as AAF even if the DB record + still says auth0, and is reported as email-verified.""" + auth0_user = UserInfoFactory.build(sub="oidc|AAF|abc123", email_verified=False) + db_user = BiocommonsUserFactory.create_sync( + id="oidc|AAF|abc123", + email="aaf@example.edu.au", + username="aaf-user", + account_type=BiocommonsUserAccountType.AUTH0, + platform_memberships=[], + group_memberships=[], + ) + test_db_session.flush() + test_db_session.refresh(db_user) + + profile = UserProfileData.from_db_user(db_user, auth0_user) + + assert profile.account_type == BiocommonsUserAccountType.AAF + assert profile.email_verified is True + + +def test_user_profile_data_non_aaf_keeps_real_verified_status(test_db_session, persistent_factories): + """A regular Auth0 user keeps their real (unverified) email status.""" + auth0_user = UserInfoFactory.build(sub="auth0|regular", email_verified=False) + db_user = BiocommonsUserFactory.create_sync( + id="auth0|regular", + email="regular@example.com", + username="regular-user", + account_type=BiocommonsUserAccountType.AUTH0, + platform_memberships=[], + group_memberships=[], + ) + test_db_session.flush() + test_db_session.refresh(db_user) + + profile = UserProfileData.from_db_user(db_user, auth0_user) + + assert profile.account_type == BiocommonsUserAccountType.AUTH0 + assert profile.email_verified is False + @pytest.mark.parametrize("username", [ "abc", diff --git a/tests/test_biocommons_register.py b/tests/test_biocommons_register.py index c8dbaf0f..837b7486 100644 --- a/tests/test_biocommons_register.py +++ b/tests/test_biocommons_register.py @@ -429,7 +429,13 @@ def test_register_aaf_endpoint_success_no_bundles( platform_ids = {membership.platform_id for membership in db_user.platform_memberships} assert platform_ids == {PlatformEnum.BPA_DATA_PORTAL, PlatformEnum.GALAXY, PlatformEnum.SBP} - assert test_db_session.exec(select(EmailNotification)).all() == [] + # AAF users skip Auth0 verification, so the welcome email is enqueued at + # registration time (no bundle emails since none were requested). + queued_emails = test_db_session.exec(select(EmailNotification)).all() + assert len(queued_emails) == 1 + assert queued_emails[0].to_address == email + assert queued_emails[0].subject == "Welcome to BioCommons Access" + assert queued_emails[0].status == EmailStatusEnum.PENDING def test_register_aaf_endpoint_success_with_bundles( @@ -498,13 +504,18 @@ def test_register_aaf_endpoint_success_with_bundles( platform_ids = {membership.platform_id for membership in db_user.platform_memberships} assert platform_ids == {PlatformEnum.BPA_DATA_PORTAL, PlatformEnum.GALAXY, PlatformEnum.SBP} + # 2 bundle emails (admin notification + requester acknowledgement) plus the + # AAF welcome email. The welcome email and the requester ack both go to the + # user, so key by (address, subject) rather than address alone. queued_emails = test_db_session.exec(select(EmailNotification)).all() - assert len(queued_emails) == 2 - emails_by_address = {email_notification.to_address: email_notification for email_notification in queued_emails} - assert emails_by_address[admin_stub.email].subject == "Threatened Species Initiative Service Bundle request" - assert emails_by_address[email].subject == ( - "Your Threatened Species Initiative Service Bundle request has been received" - ) + assert len(queued_emails) == 3 + emails = {(e.to_address, e.subject) for e in queued_emails} + assert (admin_stub.email, "Threatened Species Initiative Service Bundle request") in emails + assert ( + email, + "Your Threatened Species Initiative Service Bundle request has been received", + ) in emails + assert (email, "Welcome to BioCommons Access") in emails assert all(email_notification.status == EmailStatusEnum.PENDING for email_notification in queued_emails) From cec72a03766ed177447a6640cecb3442b5df3314 Mon Sep 17 00:00:00 2001 From: amandazhu Date: Tue, 22 Sep 2026 11:11:01 +1000 Subject: [PATCH 23/25] fix: lint --- routers/biocommons_register.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/routers/biocommons_register.py b/routers/biocommons_register.py index 5fa36cf0..ab560614 100644 --- a/routers/biocommons_register.py +++ b/routers/biocommons_register.py @@ -9,14 +9,12 @@ from starlette.responses import Response from auth.validator import create_action_token, verify_action_token -from biocommons.emails import compose_welcome_email, format_first_name -from routers.aaf import get_auth0_continue_base_url from auth0.client import Auth0Client, UpdateUserData, get_auth0_client +from biocommons.emails import compose_welcome_email, format_first_name from config import Settings, get_settings from db.models import BiocommonsUser from db.setup import get_db_session from register.tokens import validate_recaptcha -from services.email_queue import enqueue_email from register.utils import ( check_is_username_used, check_sbp_email_allowed, @@ -24,6 +22,7 @@ create_platform_memberships, process_bundle_request_notifications, ) +from routers.aaf import get_auth0_continue_base_url from routers.errors import RegistrationRoute from routers.utils import check_existing_user from schemas.auth0 import AafRegistrationActionToken @@ -43,6 +42,7 @@ RegistrationErrorResponse, RegistrationResponse, ) +from services.email_queue import enqueue_email from services.institutions import is_aaf_email logger = logging.getLogger("uvicorn.error") From 433921793095b9aec5f74c7f6b72ea536659f34e Mon Sep 17 00:00:00 2001 From: amandazhu Date: Wed, 23 Sep 2026 10:47:21 +1000 Subject: [PATCH 24/25] fix: check if AAF user exist in system --- routers/biocommons_register.py | 17 +++++++++++ tests/test_biocommons_register.py | 49 +++++++++++++++++++++++++++++++ 2 files changed, 66 insertions(+) diff --git a/routers/biocommons_register.py b/routers/biocommons_register.py index ab560614..11430eaa 100644 --- a/routers/biocommons_register.py +++ b/routers/biocommons_register.py @@ -263,6 +263,23 @@ async def register_aaf( response.status_code = status.HTTP_400_BAD_REQUEST return sbp_email_error + # Reject if the email already belongs to another account. The AAF user's own + # Auth0 record exists (they just logged in via AAF), so exclude it and check + # our DB - this catches an existing account and avoids the email unique + # constraint raising an IntegrityError (surfaced as a 500) further down. + existing_email_user = BiocommonsUser.get_by_email( + email=validated_token.email, + session=session, + case_insensitive=True, + exclude_user_id=validated_token.user_id, + ) + if existing_email_user is not None: + response.status_code = status.HTTP_400_BAD_REQUEST + return RegistrationErrorResponse( + message="An account with this email already exists. Please log in instead.", + field_errors=[FieldError(field="email", message="Email is already registered")], + ) + duplicate_username_error = check_is_username_used(username=register_data.username, session=session) if duplicate_username_error: response.status_code = status.HTTP_400_BAD_REQUEST diff --git a/tests/test_biocommons_register.py b/tests/test_biocommons_register.py index 837b7486..f5df8693 100644 --- a/tests/test_biocommons_register.py +++ b/tests/test_biocommons_register.py @@ -519,6 +519,55 @@ def test_register_aaf_endpoint_success_with_bundles( assert all(email_notification.status == EmailStatusEnum.PENDING for email_notification in queued_emails) +def test_register_aaf_endpoint_rejects_existing_email( + test_client, + mock_settings, + mock_auth0_client, + galaxy_platform, + bpa_platform, + sbp_platform, + test_db_session, + mock_recaptcha_verify, + persistent_factories, + mocker, +): + """AAF registration is rejected with a 400 when the email already belongs to + another account, instead of hitting the email unique constraint (500).""" + mock_settings.sbp_enabled = True + aaf_user_id = random_auth0_id() + email = "already-registered@example.edu.au" + # Pre-existing account with the same email but a different id. + BiocommonsUserFactory.create_sync( + id="auth0|existing-user", + email=email, + username="existing_user", + platform_memberships=[], + group_memberships=[], + ) + mocker.patch( + "routers.biocommons_register.verify_action_token", + return_value=_aaf_registration_token_payload(aaf_user_id, email), + ) + mocker.patch("routers.biocommons_register.is_aaf_email", return_value=True) + + response = test_client.post( + "/biocommons/register-aaf", + json={ + "session_token": "valid_token", + "username": "new_aaf_user", + "recaptcha_token": "mock-token", + }, + ) + + assert response.status_code == 400 + body = response.json() + assert "already exists" in body["message"].lower() + assert any(fe["field"] == "email" for fe in body["field_errors"]) + # The AAF user must not be created, and Auth0 must not be updated. + assert test_db_session.get(BiocommonsUser, aaf_user_id) is None + mock_auth0_client.update_user.assert_not_called() + + def test_biocommons_registration_endpoint_multiple_bundles( test_client_with_email, mock_settings, From 29e0684390bdaa2a91f67a122cb6c4bf052688e1 Mon Sep 17 00:00:00 2001 From: amandazhu Date: Thu, 24 Sep 2026 20:32:40 +1000 Subject: [PATCH 25/25] fix: don't count incomplete AAF logins as registered emails --- routers/utils.py | 28 ++++++++++++++++++++++++++-- tests/test_utils.py | 34 ++++++++++++++++++++++++++++++++++ 2 files changed, 60 insertions(+), 2 deletions(-) diff --git a/routers/utils.py b/routers/utils.py index 795cc8e2..04a2cb8f 100644 --- a/routers/utils.py +++ b/routers/utils.py @@ -15,7 +15,7 @@ from db.models import EmailNotification from db.setup import get_db_session from db.types import EmailStatusEnum -from schemas.biocommons import AppId +from schemas.biocommons import AppId, Auth0UserData from schemas.responses import FieldError from services.email_queue import enqueue_email from services.institutions import is_australian_research_institution_email @@ -54,6 +54,28 @@ def _check_email_exists(email: str, auth0_client: Auth0Client) -> bool: return False +def _is_incomplete_aaf_user(user: Auth0UserData) -> bool: + """ + An AAF login creates an Auth0 user *before* registration is completed + (check-aaf-account marks it aaf_only, register-aaf later sets + aaf_registration_complete). Such a user has no completed account, so it must + not count as "registered" - otherwise a user who abandons the AAF + registration form can never register with that email again. + """ + meta = user.app_metadata + return bool(meta.aaf_only) and not bool(meta.aaf_registration_complete) + + +def _check_registered_email_exists(email: str, auth0_client: Auth0Client) -> bool: + """Like _check_email_exists, but ignores incomplete AAF logins.""" + try: + matches = auth0_client.search_users_by_email(email) + return any(not _is_incomplete_aaf_user(u) for u in matches) + except Exception as e: + logger.warning(f"Error checking email existence: {e}") + return False + + def check_existing_user(username: str, email: str, auth0_client: Auth0Client) -> Literal["both", "email", "username"] | None: """Check if username or email already exists in Auth0. @@ -113,8 +135,10 @@ async def check_email_availability( Check if an email is available for registration. Returns availability status with field errors if already registered. + Incomplete AAF logins (an Auth0 user that never finished registration) do + not count as taken, so the user can still complete or restart registration. """ - exists = _check_email_exists(email, auth0_client) + exists = _check_registered_email_exists(email, auth0_client) if exists: return AvailabilityResponse( available=False, diff --git a/tests/test_utils.py b/tests/test_utils.py index 33f88a81..8ad04472 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -113,6 +113,40 @@ def test_check_email_availability_endpoint(override_auth0_client, test_client): assert data["field_errors"] == [] +def test_check_email_availability_ignores_incomplete_aaf_user( + override_auth0_client, test_client +): + """An AAF login that never finished registration must not make the email + unavailable - the user still needs to complete or restart registration.""" + incomplete = Auth0UserDataFactory.build( + email="aaf@example.edu.au", + app_metadata=Auth0ReadAppMetadataFactory.build( + aaf_only=True, aaf_registration_complete=None + ), + ) + override_auth0_client.search_users_by_email.return_value = [incomplete] + resp = test_client.get( + "/utils/register/check-email-availability", + params={"email": "aaf@example.edu.au"}, + ) + assert resp.status_code == 200 + assert resp.json()["available"] is True + + # A completed AAF user (aaf_registration_complete=True) is still taken. + completed = Auth0UserDataFactory.build( + email="aaf@example.edu.au", + app_metadata=Auth0ReadAppMetadataFactory.build( + aaf_only=True, aaf_registration_complete=True + ), + ) + override_auth0_client.search_users_by_email.return_value = [completed] + resp = test_client.get( + "/utils/register/check-email-availability", + params={"email": "aaf@example.edu.au"}, + ) + assert resp.json()["available"] is False + + def test_check_username_exists_handles_exceptions(mocker): auth0_client = mocker.Mock() auth0_client.get_users.side_effect = RuntimeError("boom")