From 1eb731308fa351905d2ef6928380e7ff0467f3ad Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Thu, 19 Oct 2023 16:05:36 -0400 Subject: [PATCH 1/7] feat!: switch to new authz api --- chord_drs/routes.py | 90 +++++++---------------- poetry.lock | 169 +++++++++++++++++++++++++++++++++++++++---- pyproject.toml | 2 +- tests/test_routes.py | 36 ++++----- 4 files changed, 197 insertions(+), 100 deletions(-) diff --git a/chord_drs/routes.py b/chord_drs/routes.py index 6c1bdce..0ce7d56 100644 --- a/chord_drs/routes.py +++ b/chord_drs/routes.py @@ -4,6 +4,7 @@ import subprocess import tempfile +from bento_lib.auth.resources import RESOURCE_EVERYTHING, build_resource from flask import ( Blueprint, Request, @@ -44,56 +45,33 @@ def forbidden() -> Forbidden: return Forbidden() -def check_everything_permission(permission: str) -> bool: - if not current_app.config["AUTHZ_ENABLED"]: - return True - - res = authz_middleware.authz_post(request, "/policy/evaluate", body={ - "requested_resource": {"everything": True}, - "required_permissions": [permission], - })["result"] - - assert isinstance(res, bool) # otherwise, bad response - or bad test mock more likely - return res +def authz_enabled() -> bool: + return current_app.config["AUTHZ_ENABLED"] -def get_requested_resource_from_params(project_id: str | None, dataset_id: str | None, data_type: str | None) -> dict: - if project_id is not None: - return { - "project": project_id, - **({"dataset": dataset_id} if dataset_id is not None else {}), - **({"data_type": data_type} if data_type is not None else {}), - } - else: # Either truly some kind of global object or just bad fields, in either case resort to {everything} - return {"everything": True} +def check_everything_permission(permission: str) -> bool: + return authz_middleware.evaluate_one(request, RESOURCE_EVERYTHING, permission) if authz_enabled() else True -def check_objects_permission(drs_objs: list[DrsBlob | DrsBundle], permission: str) -> tuple[bool, ...]: - if not current_app.config["AUTHZ_ENABLED"]: +def check_objects_permission( + drs_objs: list[DrsBlob | DrsBundle], permission: str, mark_authz_done: bool = False +) -> tuple[bool, ...]: + if not authz_enabled(): return tuple([True] * len(drs_objs)) # Assume we have permission for everything if authz disabled def _post_headers_getter(r: Request) -> dict[str, str]: token = r.form.get("token") return {"Authorization": f"Bearer {token}"} if token else {} - headers_getter = _post_headers_getter if request.method == "POST" else None - - return authz_middleware.authz_post( - request, - "/policy/evaluate", - body={ - "requested_resource": [ - get_requested_resource_from_params( - drs_obj.project_id, - drs_obj.dataset_id, - drs_obj.data_type, - ) - for drs_obj in drs_objs - ], - "required_permissions": [permission], - }, - headers_getter=headers_getter, - )["result"] + return tuple(r[0] for r in ( + authz_middleware.evaluate( + request, + [build_resource(drs_obj.project_id, drs_obj.dataset_id, drs_obj.data_type) for drs_obj in drs_objs], + [permission], + headers_getter=_post_headers_getter if request.method == "POST" else None, + mark_authz_done=mark_authz_done, + ) # gets us a matrix of len(drs_objs) rows, 1 column with the permission evaluation result + )) # now a tuple of length len(drs_objs) of whether we have the permission for each object def fetch_and_check_object_permissions(object_id: str, permission: str) -> tuple[DrsBlob | DrsBundle, bool]: @@ -103,7 +81,7 @@ def fetch_and_check_object_permissions(object_id: str, permission: str) -> tuple if not drs_object: authz_middleware.mark_authz_done(request) - if current_app.config["AUTHZ_ENABLED"] and not view_data_everything: # Don't leak if this object exists + if authz_enabled() and not view_data_everything: # Don't leak if this object exists raise forbidden() raise NotFound("No object found for this ID") @@ -112,9 +90,8 @@ def fetch_and_check_object_permissions(object_id: str, permission: str) -> tuple # Good to go already! authz_middleware.mark_authz_done(request) else: - p = check_objects_permission([drs_object], permission) - authz_middleware.mark_authz_done(request) - if not (p and p[0]): + p = check_objects_permission([drs_object], permission, mark_authz_done=True) + if not p[0]: raise forbidden() # ------------------------------------------------------------------- @@ -365,11 +342,7 @@ def object_download(object_id: str): if range_header is None: # Early return, no range header so send the whole thing - return send_file( - drs_object.location, - mimetype=MIME_OCTET_STREAM, - download_name=drs_object.name, - ) + return send_file(drs_object.location, mimetype=MIME_OCTET_STREAM, download_name=drs_object.name) logger.debug(f"Found Range header: {range_header}") range_err = f"Malformatted range header: expected bytes=X-Y or bytes=X-, got {range_header}" @@ -448,20 +421,13 @@ def object_ingest(): data_type: str | None = data.get("data_type") file = request.files.get("file") - has_permission: bool - if current_app.config["AUTHZ_ENABLED"]: - has_permission = authz_middleware.authz_post(request, "/policy/evaluate", body={ - "requested_resource": get_requested_resource_from_params( - project_id, - dataset_id, - data_type, - ), - "required_permissions": [PERMISSION_INGEST_DATA], - })["result"] - else: - has_permission = True + has_permission: bool = authz_middleware.evaluate_one( + request, + build_resource(project_id, dataset_id, data_type), + PERMISSION_INGEST_DATA, + mark_authz_done=True, # This determines everything, and we check if we have permission right afterward. + ) if authz_enabled() else True - authz_middleware.mark_authz_done(request) if not has_permission: raise Forbidden("Forbidden") diff --git a/poetry.lock b/poetry.lock index 4e24e9e..623e4c0 100644 --- a/poetry.lock +++ b/poetry.lock @@ -141,6 +141,17 @@ typing-extensions = ">=4" [package.extras] tz = ["python-dateutil"] +[[package]] +name = "annotated-types" +version = "0.6.0" +description = "Reusable constraint types to use with typing.Annotated" +optional = false +python-versions = ">=3.8" +files = [ + {file = "annotated_types-0.6.0-py3-none-any.whl", hash = "sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43"}, + {file = "annotated_types-0.6.0.tar.gz", hash = "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d"}, +] + [[package]] name = "async-timeout" version = "4.0.3" @@ -172,13 +183,13 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte [[package]] name = "bento-lib" -version = "7.2.2" +version = "9.0.0a1" description = "A set of common utilities and helpers for Bento platform services." optional = false python-versions = ">=3.10.0" files = [ - {file = "bento_lib-7.2.2-py3-none-any.whl", hash = "sha256:195f09e0aaf5101f51e381f7d713f48a351e30fd3f5cca04b352ba9bbf66fa88"}, - {file = "bento_lib-7.2.2.tar.gz", hash = "sha256:8bdb30b0befb1cfe49206a3bf884eeb2821a1a54181eac9a80e33398e9c66edc"}, + {file = 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a/tests/test_routes.py +++ b/tests/test_routes.py @@ -52,51 +52,43 @@ def test_service_info(client): def authz_everything_true(count=1): - responses.post(f"{AUTHZ_URL}/policy/evaluate", json={"result": [True] * count}) - - -def authz_everything_true_scalar(): - responses.post(f"{AUTHZ_URL}/policy/evaluate", json={"result": True}) + responses.post(f"{AUTHZ_URL}/policy/evaluate", json={"result": [[True] for _ in range(count)]}) def authz_everything_false(count=1): - responses.post(f"{AUTHZ_URL}/policy/evaluate", json={"result": [False] * count}) + responses.post(f"{AUTHZ_URL}/policy/evaluate", json={"result": [[False] for _ in range(count)]}) def authz_drs_specific_obj(iters=1): for _ in range(iters): - authz_everything_false_scalar() + authz_everything_false() authz_everything_true() -def authz_everything_false_scalar(): - responses.post(f"{AUTHZ_URL}/policy/evaluate", json={"result": False}) - - @responses.activate def test_object_fail(client): - authz_everything_true_scalar() + authz_everything_true() res = client.get(f"/objects/{NON_EXISTENT_ID}") assert res.status_code == 404 @responses.activate def test_object_fail_forbidden(client): - authz_everything_false_scalar() + authz_everything_false() res = client.get(f"/objects/{NON_EXISTENT_ID}") # can't know if this exists since we don't have access assert res.status_code == 403 @responses.activate def test_object_download_fail(client): - authz_everything_true_scalar() + authz_everything_true() res = client.get(f"/objects/{NON_EXISTENT_ID}/download") assert res.status_code == 404 @responses.activate def test_object_access_fail(client): - authz_everything_true_scalar() + authz_everything_true() res = client.get(f"/objects/{NON_EXISTENT_ID}/access/no_access") assert res.status_code == 404 @@ -176,7 +168,7 @@ def _test_object_and_download(client, obj, test_range=False): @responses.activate def test_object_and_download_minio(client_minio, drs_object_minio): - authz_everything_true_scalar() + authz_everything_true() _test_object_and_download(client_minio, drs_object_minio) @@ -189,7 +181,7 @@ def test_object_and_download_minio_specific_perms(client_minio, drs_object_minio @responses.activate def test_object_and_download(client, drs_object): - authz_everything_true_scalar() + authz_everything_true() _test_object_and_download(client, drs_object) @@ -202,14 +194,14 @@ def test_object_and_download_specific_perms(client, drs_object): @responses.activate def test_object_and_download_with_ranges(client_local, drs_object): - authz_everything_true_scalar() + authz_everything_true() # Only local backend supports ranges for now _test_object_and_download(client_local, drs_object, test_range=True) @responses.activate def test_object_with_internal_path(client, drs_object): - authz_everything_true_scalar() + authz_everything_true() res = client.get(f"/objects/{drs_object.id}?internal_path=1") data = res.get_json() @@ -220,7 +212,7 @@ def test_object_with_internal_path(client, drs_object): @responses.activate def test_object_with_disabled_internal_path(client, drs_object): - authz_everything_true_scalar() + authz_everything_true() res = client.get(f"/objects/{drs_object.id}?internal_path=0") data = res.get_json() @@ -231,7 +223,7 @@ def test_object_with_disabled_internal_path(client, drs_object): @responses.activate def test_bundle_and_download(client, drs_bundle): - authz_everything_true_scalar() + authz_everything_true() res = client.get(f"/objects/{drs_bundle.id}") data = res.get_json() @@ -391,7 +383,7 @@ def test_object_ingest_bad_req(client): @responses.activate def test_object_ingest_forbidden(client): - authz_everything_false_scalar() + authz_everything_false() res = client.post("/ingest", data={}) # invalid body shouldn't be caught until after assert res.status_code == 403 From 68165b12a4f10a97d95962488da266b3cafec1bb Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Thu, 19 Oct 2023 16:06:21 -0400 Subject: [PATCH 2/7] chore: bump version to 0.14.0 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 0c38857..9c6c77f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "chord-drs" -version = "0.13.0" +version = "0.14.0" description = "An implementation of a data repository system (as per GA4GH's specs) for the Bento platform." authors = ["David Lougheed "] license = "LGPL-3.0" From c0b30609779d9a4418104379378a0e2152110706 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Thu, 19 Oct 2023 16:12:14 -0400 Subject: [PATCH 3/7] refact: use permissions defs from bento_lib --- chord_drs/authz.py | 7 ------- chord_drs/routes.py | 22 ++++++++++++---------- 2 files changed, 12 insertions(+), 17 deletions(-) diff --git a/chord_drs/authz.py b/chord_drs/authz.py index 0cd9310..cdf1d45 100644 --- a/chord_drs/authz.py +++ b/chord_drs/authz.py @@ -3,9 +3,6 @@ __all__ = [ "authz_middleware", - "PERMISSION_INGEST_DATA", - "PERMISSION_QUERY_DATA", - "PERMISSION_DOWNLOAD_DATA", ] authz_middleware = FlaskAuthMiddleware( @@ -13,7 +10,3 @@ debug_mode=Config.BENTO_DEBUG, enabled=Config.AUTHZ_ENABLED, ) - -PERMISSION_INGEST_DATA = "ingest:data" -PERMISSION_QUERY_DATA = "query:data" -PERMISSION_DOWNLOAD_DATA = "download:data" diff --git a/chord_drs/routes.py b/chord_drs/routes.py index 0ce7d56..cbc849b 100644 --- a/chord_drs/routes.py +++ b/chord_drs/routes.py @@ -4,6 +4,7 @@ import subprocess import tempfile +from bento_lib.auth.permissions import Permission, P_INGEST_DATA, P_QUERY_DATA, P_DOWNLOAD_DATA from bento_lib.auth.resources import RESOURCE_EVERYTHING, build_resource from flask import ( Blueprint, @@ -20,7 +21,7 @@ from werkzeug.exceptions import BadRequest, Forbidden, NotFound, InternalServerError from . import __version__ -from .authz import authz_middleware, PERMISSION_INGEST_DATA, PERMISSION_QUERY_DATA, PERMISSION_DOWNLOAD_DATA +from .authz import authz_middleware from .constants import BENTO_SERVICE_KIND, SERVICE_NAME, SERVICE_TYPE from .data_sources import DATA_SOURCE_LOCAL, DATA_SOURCE_MINIO from .db import db @@ -49,12 +50,12 @@ def authz_enabled() -> bool: return current_app.config["AUTHZ_ENABLED"] -def check_everything_permission(permission: str) -> bool: +def check_everything_permission(permission: Permission) -> bool: return authz_middleware.evaluate_one(request, RESOURCE_EVERYTHING, permission) if authz_enabled() else True def check_objects_permission( - drs_objs: list[DrsBlob | DrsBundle], permission: str, mark_authz_done: bool = False + drs_objs: list[DrsBlob | DrsBundle], permission: Permission, mark_authz_done: bool = False ) -> tuple[bool, ...]: if not authz_enabled(): return tuple([True] * len(drs_objs)) # Assume we have permission for everything if authz disabled @@ -74,7 +75,7 @@ def _post_headers_getter(r: Request) -> dict[str, str]: )) # now a tuple of length len(drs_objs) of whether we have the permission for each object -def fetch_and_check_object_permissions(object_id: str, permission: str) -> tuple[DrsBlob | DrsBundle, bool]: +def fetch_and_check_object_permissions(object_id: str, permission: Permission) -> tuple[DrsBlob | DrsBundle, bool]: view_data_everything = check_everything_permission(permission) drs_object, is_bundle = get_drs_object(object_id) @@ -264,7 +265,7 @@ def get_drs_object(object_id: str) -> tuple[DrsBlob | DrsBundle | None, bool]: @drs_service.route("/objects/", methods=["GET"]) @drs_service.route("/ga4gh/drs/v1/objects/", methods=["GET"]) def object_info(object_id: str): - drs_object, is_bundle = fetch_and_check_object_permissions(object_id, PERMISSION_QUERY_DATA) + drs_object, is_bundle = fetch_and_check_object_permissions(object_id, P_QUERY_DATA) if is_bundle: expand: bool = str_to_bool(request.args.get("expand", "")) @@ -278,7 +279,7 @@ def object_info(object_id: str): @drs_service.route("/objects//access/", methods=["GET"]) @drs_service.route("/ga4gh/drs/v1/objects//access/", methods=["GET"]) def object_access(object_id: str, access_id: str): - fetch_and_check_object_permissions(object_id, PERMISSION_QUERY_DATA) + fetch_and_check_object_permissions(object_id, P_QUERY_DATA) # We explicitly do not support access_id-based accesses; all of them will be 'not found' # since we don't provide access IDs @@ -315,7 +316,7 @@ def object_search(): raise BadRequest("Missing GET search terms (name | fuzzy_name | q)") # TODO: map objects to resources to avoid duplicate calls to same resource in check_objects_permission - for obj, p in zip(objects, check_objects_permission(list(objects), PERMISSION_QUERY_DATA)): + for obj, p in zip(objects, check_objects_permission(list(objects), P_QUERY_DATA)): if p: # Only include the blob in the search results if we have permissions to view it. response.append(build_blob_json(obj, internal_path)) @@ -329,7 +330,7 @@ def object_download(object_id: str): # TODO: Bundle download - drs_object, is_bundle = fetch_and_check_object_permissions(object_id, PERMISSION_DOWNLOAD_DATA) + drs_object, is_bundle = fetch_and_check_object_permissions(object_id, P_DOWNLOAD_DATA) if is_bundle: raise BadRequest("Bundle download is currently unsupported") @@ -421,11 +422,12 @@ def object_ingest(): data_type: str | None = data.get("data_type") file = request.files.get("file") + # This authz call determines everything, so we can mark authz as done when the call completes: has_permission: bool = authz_middleware.evaluate_one( request, build_resource(project_id, dataset_id, data_type), - PERMISSION_INGEST_DATA, - mark_authz_done=True, # This determines everything, and we check if we have permission right afterward. + P_INGEST_DATA, + mark_authz_done=True, ) if authz_enabled() else True if not has_permission: From 692e9685c70a0f83845f9a8429f92d6790039695 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Mon, 23 Oct 2023 14:28:26 -0400 Subject: [PATCH 4/7] chore: update bento_lib --- poetry.lock | 10 +++++----- pyproject.toml | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/poetry.lock b/poetry.lock index 623e4c0..cdf6944 100644 --- a/poetry.lock +++ b/poetry.lock @@ -183,13 +183,13 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte [[package]] name = "bento-lib" -version = "9.0.0a1" +version = "9.0.0a4" description = "A set of common utilities and helpers for Bento platform services." optional = false python-versions = ">=3.10.0" files = [ - {file = "bento_lib-9.0.0a1-py3-none-any.whl", hash = "sha256:16eed662dafad50ca20f87ed560bc09944e3af6048f9ab86d7fbbf5cbe3b634c"}, - {file = "bento_lib-9.0.0a1.tar.gz", hash = "sha256:9d6f23dc299163294cc5be96deab5c0789e8031a4b62f1e835a8abde5ec94e40"}, + {file = "bento_lib-9.0.0a4-py3-none-any.whl", hash = "sha256:26b1ff7d868ec968a4746cb1aa4e2d0dd3d6b80985f99ecb2a7f73a127923087"}, + {file = "bento_lib-9.0.0a4.tar.gz", hash = "sha256:299e24f9cddd5f41af27265febd37a344f382ec69e1cb343dd37f3cafc185cce"}, ] [package.dependencies] @@ -204,7 +204,7 @@ Werkzeug = ">=2.2.3,<3" [package.extras] django = ["Django (>=4.2.1,<5)", "djangorestframework (>=3.14.0,<3.15)"] -fastapi = ["fastapi (>=0.100,<0.104)"] +fastapi = ["fastapi (>=0.100,<0.105)"] flask = ["Flask (>=2.2.5,<3)"] [[package]] @@ -2091,4 +2091,4 @@ multidict = ">=4.0" [metadata] lock-version = "2.0" python-versions = "^3.10" -content-hash = "fe9290f606121b67774a2f741d8934334e0897e5758bcd8dd882d9138c5b5469" +content-hash = "c46773f51d67e50b97caa498db203945a02aab09695ac934ae0482ec13e406e3" diff --git a/pyproject.toml b/pyproject.toml index 9c6c77f..9656313 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -14,7 +14,7 @@ include = [ [tool.poetry.dependencies] python = "^3.10" boto3 = ">=1.18.34,<1.19" -bento-lib = {version = "9.0.0a1", extras = ["flask"]} +bento-lib = {version = "9.0.0a4", extras = ["flask"]} flask = ">=2.2.3,<2.3" flask-sqlalchemy = ">=2.5.1,<2.6" flask-migrate = ">=3.1.0,<3.2" From 45720e6ddb63302502468e75d9d17a0817c44efa Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Mon, 23 Oct 2023 15:52:44 -0400 Subject: [PATCH 5/7] chore: revert version to 0.13.0 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 9656313..4c31191 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "chord-drs" -version = "0.14.0" +version = "0.13.0" description = "An implementation of a data repository system (as per GA4GH's specs) for the Bento platform." authors = ["David Lougheed "] license = "LGPL-3.0" From 5ad1774e74c4273659aeeeb631ad9ed7d54a1a73 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Mon, 13 Nov 2023 12:12:01 -0500 Subject: [PATCH 6/7] chore: use prod bento_lib 9.1 + update lockfile deps --- poetry.lock | 529 ++++++++++++++++++++++++------------------------- pyproject.toml | 2 +- 2 files changed, 259 insertions(+), 272 deletions(-) diff --git a/poetry.lock b/poetry.lock index 617936c..e0d3bb4 100644 --- a/poetry.lock +++ b/poetry.lock @@ -124,13 +124,13 @@ frozenlist = ">=1.1.0" 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