From f018ff81256264d66aab2b95c615758e0f6fa382 Mon Sep 17 00:00:00 2001 From: Pauline Ribeyre <4224001+paulineribeyre@users.noreply.github.com> Date: Tue, 17 Dec 2024 09:25:03 -0600 Subject: [PATCH] Remove storage endpoints (#32) --- .secrets.baseline | 6 +- docs/authorization.md | 4 + docs/local_installation.md | 3 + docs/openapi.yaml | 75 +- gen3workflow/auth.py | 13 +- gen3workflow/aws_utils.py | 138 +--- gen3workflow/config-default.yaml | 4 +- gen3workflow/config.py | 17 +- gen3workflow/routes/ga4gh_tes.py | 18 +- gen3workflow/routes/storage.py | 82 +-- poetry.lock | 676 ++++++++++-------- tests/conftest.py | 60 +- tests/migrations/migration_utils.py | 4 +- .../migrations/test_migration_e1886270d9d2.py | 2 +- tests/test_ga4gh_tes.py | 24 +- tests/test_misc.py | 20 + tests/test_storage.py | 208 ------ 17 files changed, 500 insertions(+), 854 deletions(-) delete mode 100644 tests/test_storage.py diff --git a/.secrets.baseline b/.secrets.baseline index 5548e9d..cdbbeee 100644 --- a/.secrets.baseline +++ b/.secrets.baseline @@ -169,7 +169,7 @@ "filename": "gen3workflow/config-default.yaml", "hashed_secret": "afc848c316af1a89d49826c5ae9d00ed769415f3", "is_verified": false, - "line_number": 32 + "line_number": 30 } ], "migrations/versions/e1886270d9d2_create_system_key_table.py": [ @@ -187,7 +187,7 @@ "filename": "tests/conftest.py", "hashed_secret": "0dd78d9147bb410f0cb0199c5037da36594f77d8", "is_verified": false, - "line_number": 222 + "line_number": 226 } ], "tests/migrations/test_migration_e1886270d9d2.py": [ @@ -209,5 +209,5 @@ } ] }, - "generated_at": "2024-12-12T23:42:54Z" + "generated_at": "2024-12-16T22:39:24Z" } diff --git a/docs/authorization.md b/docs/authorization.md index 51b2098..4fcd69e 100644 --- a/docs/authorization.md +++ b/docs/authorization.md @@ -2,6 +2,10 @@ The Gen3 Workflow endpoints are protected by Arborist policies. +Contents: +- [GA4GH TES](#ga4gh-tes) + - [Authorization configuration example](#authorization-configuration-example) + ## GA4GH TES - To create a task, users need `create` access to resource `/services/workflow/gen3-workflow/tasks` on service `gen3-workflow`. diff --git a/docs/local_installation.md b/docs/local_installation.md index e95b622..dc3c9bb 100644 --- a/docs/local_installation.md +++ b/docs/local_installation.md @@ -100,6 +100,9 @@ aws { } workDir = '' ``` + +A Gen3 access token is expected by most endpoints to verify the user's access (see [Authorization](authorization.md) documentation). + > The Gen3Workflow URL should be set to `http://localhost:8080` in this case; this is where the service runs by default when started with `python run.py`. - Run a workflow: diff --git a/docs/openapi.yaml b/docs/openapi.yaml index 0e384f9..9f85173 100644 --- a/docs/openapi.yaml +++ b/docs/openapi.yaml @@ -88,7 +88,9 @@ paths: '200': content: application/json: - schema: {} + schema: + title: Response Service Info Ga4Gh Tes V1 Service Info Get + type: object description: Successful Response summary: Service Info tags: @@ -100,7 +102,9 @@ paths: '200': content: application/json: - schema: {} + schema: + title: Response List Tasks Ga4Gh Tes V1 Tasks Get + type: object description: Successful Response security: - HTTPBearer: [] @@ -113,7 +117,9 @@ paths: '200': content: application/json: - schema: {} + schema: + title: Response Create Task Ga4Gh Tes V1 Tasks Post + type: object description: Successful Response security: - HTTPBearer: [] @@ -134,7 +140,9 @@ paths: '200': content: application/json: - schema: {} + schema: + title: Response Get Task Ga4Gh Tes V1 Tasks Task Id Get + type: object description: Successful Response '422': content: @@ -161,7 +169,9 @@ paths: '200': content: application/json: - schema: {} + schema: + title: Response Cancel Task Ga4Gh Tes V1 Tasks Task Id Cancel Post + type: object description: Successful Response '422': content: @@ -423,57 +433,6 @@ paths: summary: S3 Endpoint tags: - S3 - /storage/credentials: - get: - operationId: get_user_keys - responses: - '200': - content: - application/json: - schema: {} - description: Successful Response - security: - - HTTPBearer: [] - summary: Get User Keys - tags: - - Storage - post: - operationId: generate_user_key - responses: - '201': - content: - application/json: - schema: {} - description: Successful Response - security: - - HTTPBearer: [] - summary: Generate User Key - tags: - - Storage - /storage/credentials/{key_id}: - delete: - operationId: delete_user_key - parameters: - - in: path - name: key_id - required: true - schema: - title: Key Id - type: string - responses: - '204': - description: Successful Response - '422': - content: - application/json: - schema: - $ref: '#/components/schemas/HTTPValidationError' - description: Validation Error - security: - - HTTPBearer: [] - summary: Delete User Key - tags: - - Storage /storage/info: get: operationId: get_storage_info @@ -481,7 +440,9 @@ paths: '200': content: application/json: - schema: {} + schema: + title: Response Get Storage Info Storage Info Get + type: object description: Successful Response security: - HTTPBearer: [] diff --git a/gen3workflow/auth.py b/gen3workflow/auth.py index 09b3965..911991b 100644 --- a/gen3workflow/auth.py +++ b/gen3workflow/auth.py @@ -25,11 +25,11 @@ def __init__( self, api_request: Request, bearer_token: HTTPAuthorizationCredentials = Security(bearer), - ): + ) -> None: self.arborist_client = api_request.app.arborist_client self.bearer_token = bearer_token - def get_access_token(self): + def get_access_token(self) -> str: if config["MOCK_AUTH"]: return "123" @@ -95,7 +95,14 @@ async def authorize( return authorized - async def grant_user_access_to_their_own_tasks(self, username, user_id): + async def grant_user_access_to_their_own_tasks(self, username, user_id) -> None: + """ + Ensure the specified user exists in Arborist and has a policy granting them access to their + own Gen3Workflow tasks ("read" and "delete" access to resource "/users//gen3-workflow/tasks" for service "gen3-workflow"). + Args: + username (str): The user's Gen3 username + user_id (str): The user's unique Gen3 ID + """ logger.info( f"Granting user '{username}' access to their own tasks if they don't already have it" ) diff --git a/gen3workflow/aws_utils.py b/gen3workflow/aws_utils.py index 9b30549..0a9b20a 100644 --- a/gen3workflow/aws_utils.py +++ b/gen3workflow/aws_utils.py @@ -1,11 +1,7 @@ -import json +from typing import Tuple import boto3 -from botocore.exceptions import ClientError -from fastapi import HTTPException -from starlette.status import HTTP_404_NOT_FOUND -from gen3workflow import logger from gen3workflow.config import config @@ -13,7 +9,7 @@ iam_resp_err = "Unexpected response from AWS IAM" -def get_safe_name_from_user_id(user_id): +def get_safe_name_from_user_id(user_id: str) -> str: """ Generate a valid IAM user name or S3 bucket name for the specified user. - IAM user names can contain up to 64 characters. They can only contain alphanumeric characters @@ -36,7 +32,7 @@ def get_safe_name_from_user_id(user_id): return safe_name -def create_user_bucket(user_id): +def create_user_bucket(user_id: str) -> Tuple[str, str, str]: """ Create an S3 bucket for the specified user and return information about the bucket. @@ -46,134 +42,8 @@ def create_user_bucket(user_id): Returns: tuple: (bucket name, prefix where the user stores objects in the bucket, bucket region) """ + # TODO lifetime policy and encryption user_bucket_name = get_safe_name_from_user_id(user_id) s3_client = boto3.client("s3") s3_client.create_bucket(Bucket=user_bucket_name) return user_bucket_name, "ga4gh-tes", config["USER_BUCKETS_REGION"] - - -def create_or_update_policy(policy_name, policy_document, path_prefix, tags): - # attempt to create the policy - try: - response = iam_client.create_policy( - PolicyName=policy_name, - Path=path_prefix, - PolicyDocument=json.dumps(policy_document), - Tags=tags, - ) - assert "Arn" in response.get("Policy", {}), f"{iam_resp_err}: {response}" - return response["Policy"]["Arn"] - except ClientError as e: - if e.response["Error"]["Code"] != "EntityAlreadyExists": - raise - - # policy already exists: update it. - # find the right policy - response = iam_client.list_policies(PathPrefix=path_prefix) - assert "Policies" in response, f"{iam_resp_err}: {response}" - for policy in response["Policies"]: - assert "PolicyName" in policy, f"{iam_resp_err}: {policy}" - assert "Arn" in policy, f"{iam_resp_err}: {policy}" - if policy["PolicyName"] == policy_name: - break - - # there can only be up to 5 versions, so delete old versions of this policy - response = iam_client.list_policy_versions(PolicyArn=policy["Arn"]) - assert "Versions" in response, f"{iam_resp_err}: {response}" - for version in response["Versions"]: - assert "VersionId" in version, f"{iam_resp_err}: {version}" - assert "IsDefaultVersion" in version, f"{iam_resp_err}: {version}" - if version["IsDefaultVersion"]: - continue # do not delete the latest versions - iam_client.delete_policy_version( - PolicyArn=policy["Arn"], VersionId=version["VersionId"] - ) - - # update the policy by creating a new version - iam_client.create_policy_version( - PolicyArn=policy["Arn"], - PolicyDocument=json.dumps(policy_document), - SetAsDefault=True, - ) - return policy["Arn"] - - -def create_iam_user_and_key(user_id): - iam_user_name = get_safe_name_from_user_id(user_id) - escaped_hostname = config["HOSTNAME"].replace(".", "-") - iam_tags = [ - { - "Key": "name", - "Value": f"gen3wf-{escaped_hostname}", - }, - ] - - try: - iam_client.create_user(UserName=iam_user_name, Tags=iam_tags) - except ClientError as e: - # if the user already exists, ignore the error and proceed - if e.response["Error"]["Code"] != "EntityAlreadyExists": - raise - - # grant the IAM user access to the user's s3 bucket - bucket_name, bucket_prefix, _ = create_user_bucket(user_id) - policy_document = { - "Version": "2012-10-17", - "Statement": [ - { - "Sid": "AllowListingBucketFolder", - "Effect": "Allow", - "Action": ["s3:ListBucket"], - "Resource": [f"arn:aws:s3:::{bucket_name}"], - "Condition": {"StringLike": {"s3:prefix": [f"{bucket_prefix}/*"]}}, - }, - { - "Sid": "AllowManagingBucketFolder", - "Effect": "Allow", - "Action": ["s3:GetObject", "s3:PutObject", "s3:DeleteObject"], - "Resource": [f"arn:aws:s3:::{bucket_name}/{bucket_prefix}/*"], - }, - ], - } - path_prefix = f"/{iam_user_name}/" # used later to get existing policies' ARN - policy_arn = create_or_update_policy( - f"{iam_user_name}-policy", policy_document, path_prefix, iam_tags - ) - iam_client.attach_user_policy(PolicyArn=policy_arn, UserName=iam_user_name) - - # create a key for this user - key = iam_client.create_access_key(UserName=iam_user_name) - assert "AccessKeyId" in key.get("AccessKey", {}), f"{iam_resp_err}: {key}" - assert "SecretAccessKey" in key.get("AccessKey", {}), f"{iam_resp_err}: {key}" - - return key["AccessKey"]["AccessKeyId"], key["AccessKey"]["SecretAccessKey"] - - -def list_iam_user_keys(user_id): - iam_user_name = get_safe_name_from_user_id(user_id) - try: - response = iam_client.list_access_keys(UserName=iam_user_name) - except ClientError as e: - if e.response["Error"]["Code"] == "NoSuchEntity": - return [] # user does not exist in IAM, so they have no IAM keys - else: - raise - assert "AccessKeyMetadata" in response, f"{iam_resp_err}: {response}" - for key in response["AccessKeyMetadata"]: - assert "AccessKeyId" in key, f"{iam_resp_err}: {key}" - assert "CreateDate" in key, f"{iam_resp_err}: {key}" - assert "Status" in key, f"{iam_resp_err}: {key}" - return response["AccessKeyMetadata"] - - -def delete_iam_user_key(user_id, key_id): - try: - iam_client.delete_access_key( - UserName=get_safe_name_from_user_id(user_id), - AccessKeyId=key_id, - ) - except ClientError as e: - if e.response["Error"]["Code"] == "NoSuchEntity": - err_msg = f"No such key: '{key_id}'" - logger.error(err_msg) - raise HTTPException(HTTP_404_NOT_FOUND, err_msg) diff --git a/gen3workflow/config-default.yaml b/gen3workflow/config-default.yaml index 53330db..14d318a 100644 --- a/gen3workflow/config-default.yaml +++ b/gen3workflow/config-default.yaml @@ -10,10 +10,8 @@ DOCS_URL_PREFIX: /gen3workflow ARBORIST_URL: # /!\ only use for development! Allows running gen3workflow locally without Arborist interaction -MOCK_AUTH: false # TODO add to config validation. Also add "no unexpected props" to validation. +MOCK_AUTH: false -MAX_IAM_KEYS_PER_USER: 2 # the default AWS AccessKeysPerUser quota is 2 -IAM_KEYS_LIFETIME_DAYS: 30 USER_BUCKETS_REGION: us-east-1 # configure an AWS IAM key to use when making S3 requests on behalf of users. If left empty, it diff --git a/gen3workflow/config.py b/gen3workflow/config.py index 08862b6..d6630d5 100644 --- a/gen3workflow/config.py +++ b/gen3workflow/config.py @@ -36,21 +36,26 @@ def validate(self) -> None: logger.info("Validating configuration") self.validate_top_level_configs() - def validate_top_level_configs(self): + def validate_top_level_configs(self) -> None: schema = { "type": "object", - "additionalProperties": True, + "additionalProperties": False, "properties": { "HOSTNAME": {"type": "string"}, "DEBUG": {"type": "boolean"}, "DOCS_URL_PREFIX": {"type": "string"}, - # aws_utils.list_iam_user_keys should be updated to fetch paginated results if >100 - "MAX_IAM_KEYS_PER_USER": {"type": "integer", "maximum": 100}, - "IAM_KEYS_LIFETIME_DAYS": {"type": "integer"}, + "ARBORIST_URL": {"type": ["string", "null"]}, + "MOCK_AUTH": {"type": "boolean"}, "USER_BUCKETS_REGION": {"type": "string"}, "S3_ENDPOINTS_AWS_ACCESS_KEY_ID": {"type": ["string", "null"]}, "S3_ENDPOINTS_AWS_SECRET_ACCESS_KEY": {"type": ["string", "null"]}, - "ARBORIST_URL": {"type": ["string", "null"]}, + "DB_DRIVER": {"type": "string"}, + "DB_HOST": {"type": "string"}, + "DB_PORT": {"type": "integer"}, + "DB_USER": {"type": "string"}, + "DB_PASSWORD": {"type": "string"}, + "DB_DATABASE": {"type": "string"}, + "DB_CONNECTION_STRING": {"type": "string"}, "TASK_IMAGE_WHITELIST": {"type": "array", "items": {"type": "string"}}, "TES_SERVER_URL": {"type": "string"}, }, diff --git a/gen3workflow/routes/ga4gh_tes.py b/gen3workflow/routes/ga4gh_tes.py index ea1aafe..424d65d 100644 --- a/gen3workflow/routes/ga4gh_tes.py +++ b/gen3workflow/routes/ga4gh_tes.py @@ -31,7 +31,7 @@ async def get_request_body(request: Request): @router.get("/service-info", status_code=HTTP_200_OK) -async def service_info(request: Request): +async def service_info(request: Request) -> dict: url = f"{config['TES_SERVER_URL']}/service-info" res = await request.app.async_client.get(url) if res.status_code != HTTP_200_OK: @@ -72,7 +72,7 @@ def get_non_allowed_images(images: set, username: str) -> set: @router.post("/tasks", status_code=HTTP_200_OK) -async def create_task(request: Request, auth=Depends(Auth)): +async def create_task(request: Request, auth=Depends(Auth)) -> dict: await auth.authorize("create", ["/services/workflow/gen3-workflow/tasks"]) body = await get_request_body(request) @@ -124,11 +124,17 @@ async def create_task(request: Request, auth=Depends(Auth)): return res.json() -def apply_view_to_task(view, task) -> dict: +def apply_view_to_task(view: str, task: dict) -> dict: """ We always set the view to "FULL" when making get/list requests to the TES server, because we need to get the AUTHZ tag in order to check whether users have access. This function applies the view that was originally requested by removing fields according to the TES spec. + + Args: + view (str): view to apply (FULL, MINIMAL or BASIC). If None, MINIMAL is applied. + task (dict): TES task + Returns: + dict: TES task with applied view """ if view == "FULL": return task @@ -149,7 +155,7 @@ def apply_view_to_task(view, task) -> dict: @router.get("/tasks", status_code=HTTP_200_OK) -async def list_tasks(request: Request, auth=Depends(Auth)): +async def list_tasks(request: Request, auth=Depends(Auth)) -> dict: supported_params = { "name_prefix", "state", @@ -209,7 +215,7 @@ async def list_tasks(request: Request, auth=Depends(Auth)): @router.get("/tasks/{task_id}", status_code=HTTP_200_OK) -async def get_task(request: Request, task_id: str, auth=Depends(Auth)): +async def get_task(request: Request, task_id: str, auth=Depends(Auth)) -> dict: supported_params = {"view"} query_params = { k: v for k, v in dict(request.query_params).items() if k in supported_params @@ -239,7 +245,7 @@ async def get_task(request: Request, task_id: str, auth=Depends(Auth)): @router.post("/tasks/{task_id}:cancel", status_code=HTTP_200_OK) -async def cancel_task(request: Request, task_id: str, auth=Depends(Auth)): +async def cancel_task(request: Request, task_id: str, auth=Depends(Auth)) -> dict: # check if this user has access to delete this task url = f"{config['TES_SERVER_URL']}/tasks/{task_id}?view=FULL" res = await request.app.async_client.get(url) diff --git a/gen3workflow/routes/storage.py b/gen3workflow/routes/storage.py index a7d354c..c271a15 100644 --- a/gen3workflow/routes/storage.py +++ b/gen3workflow/routes/storage.py @@ -1,23 +1,15 @@ -from datetime import datetime, timedelta, timezone +from fastapi import APIRouter, Depends, Request +from starlette.status import HTTP_200_OK -from fastapi import APIRouter, Depends, HTTPException, Request -from starlette.status import ( - HTTP_200_OK, - HTTP_201_CREATED, - HTTP_204_NO_CONTENT, - HTTP_400_BAD_REQUEST, -) - -from gen3workflow import aws_utils, logger +from gen3workflow import aws_utils from gen3workflow.auth import Auth -from gen3workflow.config import config router = APIRouter(prefix="/storage") @router.get("/info", status_code=HTTP_200_OK) -async def get_storage_info(request: Request, auth=Depends(Auth)): +async def get_storage_info(request: Request, auth=Depends(Auth)) -> dict: token_claims = await auth.get_token_claims() user_id = token_claims.get("sub") bucket_name, bucket_prefix, bucket_region = aws_utils.create_user_bucket(user_id) @@ -26,69 +18,3 @@ async def get_storage_info(request: Request, auth=Depends(Auth)): "workdir": f"s3://{bucket_name}/{bucket_prefix}", "region": bucket_region, } - - -@router.post("/credentials", status_code=HTTP_201_CREATED) -async def generate_user_key(request: Request, auth=Depends(Auth)): - token_claims = await auth.get_token_claims() - user_id = token_claims.get("sub") - - existing_keys = aws_utils.list_iam_user_keys(user_id) - if len(existing_keys) >= config["MAX_IAM_KEYS_PER_USER"]: - err_msg = f"Too many existing keys: only {config['MAX_IAM_KEYS_PER_USER']} are allowed per user. Delete an existing key before creating a new one" - logger.error(err_msg) - raise HTTPException(HTTP_400_BAD_REQUEST, err_msg) - - key_id, key_secret = aws_utils.create_iam_user_and_key(user_id) - return { - "aws_key_id": key_id, - "aws_key_secret": key_secret, - } - - -def seconds_to_human_time(seconds): - if seconds < 0: - return None - m, s = divmod(seconds, 60) - h, m = divmod(m, 60) - d, h = divmod(h, 24) - if d: - return "{} days".format(int(d)) - if h: - return "{} hours".format(int(h)) - if m: - return "{} minutes".format(int(h)) - return "{} seconds".format(int(s)) - - -@router.get("/credentials", status_code=HTTP_200_OK) -async def get_user_keys(request: Request, auth=Depends(Auth)): - token_claims = await auth.get_token_claims() - user_id = token_claims.get("sub") - now = datetime.now(timezone.utc) - - def get_key_expiration(key_status, key_creation_date): - if ( - key_status == "Inactive" - or (now - key_creation_date).days > config["IAM_KEYS_LIFETIME_DAYS"] - ): - return "expired" - expires_in = ( - key_creation_date + timedelta(days=config["IAM_KEYS_LIFETIME_DAYS"]) - now - ) - return f"expires in {seconds_to_human_time(expires_in.total_seconds())}" - - return [ - { - "aws_key_id": key["AccessKeyId"], - "status": get_key_expiration(key["Status"], key["CreateDate"]), - } - for key in aws_utils.list_iam_user_keys(user_id) - ] - - -@router.delete("/credentials/{key_id}", status_code=HTTP_204_NO_CONTENT) -async def delete_user_key(request: Request, key_id: str, auth=Depends(Auth)): - token_claims = await auth.get_token_claims() - user_id = token_claims.get("sub") - aws_utils.delete_iam_user_key(user_id, key_id) diff --git a/poetry.lock b/poetry.lock index c4b36bf..b031427 100644 --- a/poetry.lock +++ b/poetry.lock @@ -32,24 +32,24 @@ files = [ [[package]] name = "anyio" -version = "4.6.2.post1" +version = "4.7.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" optional = false python-versions = ">=3.9" 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a/tests/conftest.py +++ b/tests/conftest.py @@ -2,7 +2,6 @@ See https://github.com/uc-cdis/gen3-user-data-library/blob/main/tests/conftest.py#L1 """ -import asyncio from datetime import datetime from dateutil.tz import tzutc import json @@ -19,15 +18,17 @@ from threading import Thread import uvicorn -# Set GEN3WORKFLOW_CONFIG_PATH *before* loading the app, which loads the configuration +# Set up the config *before* loading the app, which loads the configuration CURRENT_DIR = os.path.dirname(os.path.realpath(__file__)) environ["GEN3WORKFLOW_CONFIG_PATH"] = os.path.join( CURRENT_DIR, "test-gen3workflow-config.yaml" ) +from gen3workflow.config import config + +config.validate() from gen3workflow.app import get_app -from gen3workflow.config import config -from gen3workflow.models import Base +from tests.migrations.migration_utils import MigrationRunner TEST_USER_ID = "64" @@ -64,44 +65,47 @@ } -@pytest_asyncio.fixture(scope="function") -async def engine(): +@pytest_asyncio.fixture(scope="session", autouse=True) +async def migrate_database_to_the_latest(): """ - Non-session scoped engine which recreates the database, yields, then drops the tables + Migrate the database to the latest version before running the tests. """ - engine = create_async_engine( - config["DB_CONNECTION_STRING"], echo=False, future=True - ) + migration_runner = MigrationRunner() + await migration_runner.upgrade("head") - async with engine.begin() as conn: - await conn.run_sync(Base.metadata.drop_all) - await conn.run_sync(Base.metadata.create_all) - yield engine +@pytest_asyncio.fixture(scope="function") +async def reset_database(): + """ + Most tests do not store data in the database, so for performance this fixture does not + autorun. To be used in tests that interact with the database. + """ + migration_runner = MigrationRunner() + await migration_runner.downgrade("base") + await migration_runner.upgrade("head") - async with engine.begin() as conn: - await conn.run_sync(Base.metadata.drop_all) + yield - await engine.dispose() + await migration_runner.downgrade("base") + await migration_runner.upgrade("head") -@pytest_asyncio.fixture() -async def session(engine): +@pytest_asyncio.fixture(scope="function") +async def session(): """ - Database session which utilizes the above engine and event loop and sets up a nested transaction before yielding. - It rolls back the nested transaction after yield. + Database session """ - event_loop = asyncio.get_running_loop() + engine = create_async_engine( + config["DB_CONNECTION_STRING"], echo=False, future=True + ) session_maker = async_sessionmaker( engine, expire_on_commit=False, autocommit=False, autoflush=False ) - async with engine.connect() as conn: - tsx = await conn.begin() - async with session_maker(bind=conn) as session: - yield session + async with session_maker() as session: + yield session - await tsx.rollback() + await engine.dispose() @pytest.fixture(scope="function") @@ -352,7 +356,7 @@ def run_uvicorn(): else: # the tests use a real httpx client that forwards requests to the app async with httpx.AsyncClient( - app=app, base_url="http://test-gen3-wf" + transport=httpx.ASGITransport(app=app), base_url="http://test-gen3-wf" ) as real_httpx_client: # for easier access to the param in the tests real_httpx_client.tes_resp_code = tes_resp_code diff --git a/tests/migrations/migration_utils.py b/tests/migrations/migration_utils.py index 19852e7..3562070 100644 --- a/tests/migrations/migration_utils.py +++ b/tests/migrations/migration_utils.py @@ -41,6 +41,6 @@ def _run_command(connection): else: raise Exception(f"Unknown MigrationRunner action '{self.action}'") - async_engine = create_async_engine(config["DB_CONNECTION_STRING"], echo=True) - async with async_engine.begin() as conn: + engine = create_async_engine(config["DB_CONNECTION_STRING"], echo=True) + async with engine.begin() as conn: await conn.run_sync(_run_command) diff --git a/tests/migrations/test_migration_e1886270d9d2.py b/tests/migrations/test_migration_e1886270d9d2.py index 671a8d6..64d406a 100644 --- a/tests/migrations/test_migration_e1886270d9d2.py +++ b/tests/migrations/test_migration_e1886270d9d2.py @@ -7,7 +7,7 @@ @pytest.mark.asyncio -async def test_e1886270d9d2_upgrade(session): +async def test_e1886270d9d2_upgrade(reset_database, session): # state before the migration migration_runner = MigrationRunner() await migration_runner.downgrade("base") diff --git a/tests/test_ga4gh_tes.py b/tests/test_ga4gh_tes.py index 8a29fda..6652692 100644 --- a/tests/test_ga4gh_tes.py +++ b/tests/test_ga4gh_tes.py @@ -95,7 +95,7 @@ async def test_get_task(client, access_token_patcher, view): mock_arborist_request.assert_called_with( method="POST", path=f"/auth/request", - body=f'{{"requests": [{{"resource": "/users/{TEST_USER_ID}/gen3-workflow/tasks/123", "action": {{"service": "gen3-workflow", "method": "read"}}}}], "user": {{"token": "123"}}}}', + body=f'{{"requests":[{{"resource":"/users/{TEST_USER_ID}/gen3-workflow/tasks/123","action":{{"service":"gen3-workflow","method":"read"}}}}],"user":{{"token":"123"}}}}', authorized=client.authorized, ) @@ -129,7 +129,7 @@ async def test_create_task(client, access_token_patcher): method="POST", path="/tasks", query_params={}, - body=f'{{"name": "test-task", "tags": {{"AUTHZ": "/users/{TEST_USER_ID}/gen3-workflow/tasks/TASK_ID_PLACEHOLDER"}}}}', + body=f'{{"name":"test-task","tags":{{"AUTHZ":"/users/{TEST_USER_ID}/gen3-workflow/tasks/TASK_ID_PLACEHOLDER"}}}}', status_code=client.tes_resp_code, ) @@ -137,14 +137,14 @@ async def test_create_task(client, access_token_patcher): mock_arborist_request.assert_any_call( method="POST", path=f"/auth/request", - body=f'{{"requests": [{{"resource": "/services/workflow/gen3-workflow/tasks", "action": {{"service": "gen3-workflow", "method": "create"}}}}], "user": {{"token": "123"}}}}', + body=f'{{"requests":[{{"resource":"/services/workflow/gen3-workflow/tasks","action":{{"service":"gen3-workflow","method":"create"}}}}],"user":{{"token":"123"}}}}', authorized=client.authorized, ) if client.authorized and client.tes_resp_code != 500: mock_arborist_request.assert_any_call( method="POST", path=f"/auth/request", - body=f'{{"requests": [{{"resource": "/users/{TEST_USER_ID}/gen3-workflow/tasks", "action": {{"service": "gen3-workflow", "method": "read"}}}}], "user": {{"token": "123"}}}}', + body=f'{{"requests":[{{"resource":"/users/{TEST_USER_ID}/gen3-workflow/tasks","action":{{"service":"gen3-workflow","method":"read"}}}}],"user":{{"token":"123"}}}}', authorized=client.authorized, ) @@ -169,7 +169,7 @@ async def test_create_task_new_user(client, access_token_patcher): method="POST", path="/tasks", query_params={}, - body=f'{{"name": "test-task", "tags": {{"AUTHZ": "/users/{NEW_TEST_USER_ID}/gen3-workflow/tasks/TASK_ID_PLACEHOLDER"}}}}', + body=f'{{"name":"test-task","tags":{{"AUTHZ":"/users/{NEW_TEST_USER_ID}/gen3-workflow/tasks/TASK_ID_PLACEHOLDER"}}}}', status_code=200, ) @@ -177,31 +177,31 @@ async def test_create_task_new_user(client, access_token_patcher): mock_arborist_request.assert_any_call( method="POST", path=f"/resource/users/{NEW_TEST_USER_ID}/gen3-workflow", - body=f'{{"name": "tasks", "description": "Represents workflow tasks owned by user \'test-username-{NEW_TEST_USER_ID}\'"}}', + body=f'{{"name":"tasks","description":"Represents workflow tasks owned by user \'test-username-{NEW_TEST_USER_ID}\'"}}', authorized=True, ) mock_arborist_request.assert_any_call( method="POST", path="/role", - body='{"id": "gen3-workflow_task_owner", "permissions": [{"id": "gen3-workflow-reader", "action": {"service": "gen3-workflow", "method": "read"}}, {"id": "gen3-workflow-deleter", "action": {"service": "gen3-workflow", "method": "delete"}}]}', + body='{"id":"gen3-workflow_task_owner","permissions":[{"id":"gen3-workflow-reader","action":{"service":"gen3-workflow","method":"read"}},{"id":"gen3-workflow-deleter","action":{"service":"gen3-workflow","method":"delete"}}]}', authorized=True, ) mock_arborist_request.assert_any_call( method="POST", path="/policy", - body=f'{{"id": "gen3-workflow_task_owner_sub-{NEW_TEST_USER_ID}", "description": "policy created by gen3-workflow for user \'test-username-{NEW_TEST_USER_ID}\'", "role_ids": ["gen3-workflow_task_owner"], "resource_paths": ["/users/{NEW_TEST_USER_ID}/gen3-workflow/tasks"]}}', + body=f'{{"id":"gen3-workflow_task_owner_sub-{NEW_TEST_USER_ID}","description":"policy created by gen3-workflow for user \'test-username-{NEW_TEST_USER_ID}\'","role_ids":["gen3-workflow_task_owner"],"resource_paths":["/users/{NEW_TEST_USER_ID}/gen3-workflow/tasks"]}}', authorized=True, ) mock_arborist_request.assert_any_call( method="POST", path="/user", - body=f'{{"name": "test-username-{NEW_TEST_USER_ID}"}}', + body=f'{{"name":"test-username-{NEW_TEST_USER_ID}"}}', authorized=True, ) mock_arborist_request.assert_any_call( method="POST", path=f"/user/test-username-{NEW_TEST_USER_ID}/policy", - body=f'{{"policy": "gen3-workflow_task_owner_sub-{NEW_TEST_USER_ID}"}}', + body=f'{{"policy":"gen3-workflow_task_owner_sub-{NEW_TEST_USER_ID}"}}', authorized=True, ) @@ -357,7 +357,7 @@ async def test_create_task_with_whitelist_images( method="POST", path="/tasks", query_params={}, - body=json.dumps(result_body), + body=json.dumps(result_body, separators=(",", ":")), status_code=200, ) @@ -481,6 +481,6 @@ async def test_delete_task(client, access_token_patcher): mock_arborist_request.assert_called_with( method="POST", path=f"/auth/request", - body=f'{{"requests": [{{"resource": "/users/{TEST_USER_ID}/gen3-workflow/tasks/123", "action": {{"service": "gen3-workflow", "method": "delete"}}}}], "user": {{"token": "123"}}}}', + body=f'{{"requests":[{{"resource":"/users/{TEST_USER_ID}/gen3-workflow/tasks/123","action":{{"service":"gen3-workflow","method":"delete"}}}}],"user":{{"token":"123"}}}}', authorized=client.authorized, ) diff --git a/tests/test_misc.py b/tests/test_misc.py index 83e292f..90aaf84 100644 --- a/tests/test_misc.py +++ b/tests/test_misc.py @@ -1,5 +1,9 @@ +import boto3 +from moto import mock_aws import pytest +from conftest import TEST_USER_ID +from gen3workflow import aws_utils from gen3workflow.aws_utils import get_safe_name_from_user_id from gen3workflow.config import config @@ -29,3 +33,19 @@ def test_get_safe_name_from_user_id(reset_config_hostname): safe_name = get_safe_name_from_user_id(user_id) assert len(safe_name) == 63 assert safe_name == f"gen3wf-{escaped_shortened_hostname}-{user_id}" + + +@pytest.mark.asyncio +async def test_storage_info(client, access_token_patcher): + with mock_aws(): + aws_utils.iam_client = boto3.client("iam") + expected_bucket_name = f"gen3wf-{config['HOSTNAME']}-{TEST_USER_ID}" + + res = await client.get("/storage/info", headers={"Authorization": "bearer 123"}) + assert res.status_code == 200, res.text + storage_info = res.json() + assert storage_info == { + "bucket": expected_bucket_name, + "workdir": f"s3://{expected_bucket_name}/ga4gh-tes", + "region": config["USER_BUCKETS_REGION"], + } diff --git a/tests/test_storage.py b/tests/test_storage.py deleted file mode 100644 index 2f503cf..0000000 --- a/tests/test_storage.py +++ /dev/null @@ -1,208 +0,0 @@ -import boto3 -from freezegun import freeze_time -from moto import mock_aws -import pytest - -from conftest import TEST_USER_ID -from gen3workflow import aws_utils -from gen3workflow.config import config -from gen3workflow.aws_utils import get_safe_name_from_user_id - - -@pytest.mark.asyncio -async def test_create_and_list_user_keys(client, access_token_patcher): - """ - Create and delete keys, and check that the listing endpoint returns active keys. - """ - with mock_aws(): - aws_utils.iam_client = boto3.client("iam") - - # the user does not have keys yet - res = await client.get( - "/storage/credentials", headers={"Authorization": "bearer 123"} - ) - assert res.status_code == 200, res.text - assert res.json() == [] - - # create 2 keys - keys = [] - for _ in range(2): - res = await client.post( - "/storage/credentials", headers={"Authorization": "bearer 123"} - ) - assert res.status_code == 201, res.text - key_data = res.json() - assert "aws_key_id" in key_data and "aws_key_secret" in key_data - keys.append(key_data) - - # both keys should be listed in the user's keys - res = await client.get( - "/storage/credentials", headers={"Authorization": "bearer 123"} - ) - assert res.status_code == 200, res.text - assert res.json() == [ - { - "aws_key_id": keys[0]["aws_key_id"], - "status": f"expires in {config['IAM_KEYS_LIFETIME_DAYS'] - 1} days", - }, - { - "aws_key_id": keys[1]["aws_key_id"], - "status": f"expires in {config['IAM_KEYS_LIFETIME_DAYS'] - 1} days", - }, - ] - - # delete the 1st key - res = await client.delete( - f"/storage/credentials/{keys[0]['aws_key_id']}", - headers={"Authorization": "bearer 123"}, - ) - assert res.status_code == 204, res.text - - # only the 2nd key should now be listed in the user's keys - res = await client.get( - "/storage/credentials", headers={"Authorization": "bearer 123"} - ) - assert res.status_code == 200, res.text - assert res.json() == [ - { - "aws_key_id": keys[1]["aws_key_id"], - "status": f"expires in {config['IAM_KEYS_LIFETIME_DAYS'] - 1} days", - } - ] - - -@pytest.mark.asyncio -async def test_list_user_keys_status(client, access_token_patcher): - """ - Keys that are deactivated or past the expiration date should be listed as "expired" when listing a user's keys. - """ - with mock_aws(): - aws_utils.iam_client = boto3.client("iam") - - # create 2 keys. The 1st one has a mocked creation date of more than IAM_KEYS_LIFETIME_DAYS - # days ago, so it should be expired. - keys = [] - import datetime - - for i in range(2): - if i == 0: - with freeze_time( - datetime.date.today() - - datetime.timedelta(days=config["IAM_KEYS_LIFETIME_DAYS"] + 1) - ): - res = await client.post( - "/storage/credentials", headers={"Authorization": "bearer 123"} - ) - else: - res = await client.post( - "/storage/credentials", headers={"Authorization": "bearer 123"} - ) - assert res.status_code == 201, res.text - key_data = res.json() - assert "aws_key_id" in key_data and "aws_key_secret" in key_data - keys.append(key_data) - - # list the user's keys; the 1st key should show as expired - res = await client.get( - "/storage/credentials", headers={"Authorization": "bearer 123"} - ) - assert res.status_code == 200, res.text - assert res.json() == [ - {"aws_key_id": keys[0]["aws_key_id"], "status": f"expired"}, - { - "aws_key_id": keys[1]["aws_key_id"], - "status": f"expires in {config['IAM_KEYS_LIFETIME_DAYS'] - 1} days", - }, - ] - - # deactivate the 2nd key - access_key = boto3.resource("iam").AccessKey( - user_name=get_safe_name_from_user_id(TEST_USER_ID), - id=keys[1]["aws_key_id"], - ) - access_key.deactivate() - - # list the user's keys; both keys should now show as expired - res = await client.get( - "/storage/credentials", headers={"Authorization": "bearer 123"} - ) - assert res.status_code == 200, res.text - assert res.json() == [ - {"aws_key_id": keys[0]["aws_key_id"], "status": "expired"}, - {"aws_key_id": keys[1]["aws_key_id"], "status": "expired"}, - ] - - -@pytest.mark.asyncio -async def test_too_many_user_keys(client, access_token_patcher): - """ - Users should not be able to create new keys after reaching MAX_IAM_KEYS_PER_USER. - """ - with mock_aws(): - aws_utils.iam_client = boto3.client("iam") - - # create the max number of keys - for _ in range(config["MAX_IAM_KEYS_PER_USER"]): - res = await client.post( - "/storage/credentials", headers={"Authorization": "bearer 123"} - ) - assert res.status_code == 201, res.text - key_data = res.json() - assert "aws_key_id" in key_data and "aws_key_secret" in key_data - - # attempt to create another key; this should fail since `MAX_IAM_KEYS_PER_USER` is reached - res = await client.post( - "/storage/credentials", headers={"Authorization": "bearer 123"} - ) - assert res.status_code == 400, res.text - assert res.json() == { - "detail": "Too many existing keys: only 2 are allowed per user. Delete an existing key before creating a new one" - } - - # delete one of the keys - res = await client.delete( - f"/storage/credentials/{key_data['aws_key_id']}", - headers={"Authorization": "bearer 123"}, - ) - assert res.status_code == 204, res.text - - # attempt to create another key; now it should succeed - res = await client.post( - "/storage/credentials", headers={"Authorization": "bearer 123"} - ) - assert res.status_code == 201, res.text - key_data = res.json() - assert "aws_key_id" in key_data and "aws_key_secret" in key_data - - -@pytest.mark.asyncio -async def test_delete_non_existent_key(client, access_token_patcher): - """ - Attempting to delete a key that does not exist should result in a 404 error. - """ - with mock_aws(): - aws_utils.iam_client = boto3.client("iam") - - key_id = "thiskeydoesnotexist" - res = await client.delete( - f"/storage/credentials/{key_id}", - headers={"Authorization": "bearer 123"}, - ) - assert res.status_code == 404, res.text - assert res.json() == {"detail": f"No such key: '{key_id}'"} - - -@pytest.mark.asyncio -async def test_storage_info(client, access_token_patcher): - with mock_aws(): - aws_utils.iam_client = boto3.client("iam") - expected_bucket_name = f"gen3wf-{config['HOSTNAME']}-{TEST_USER_ID}" - - res = await client.get("/storage/info", headers={"Authorization": "bearer 123"}) - assert res.status_code == 200, res.text - storage_info = res.json() - assert storage_info == { - "bucket": expected_bucket_name, - "workdir": f"s3://{expected_bucket_name}/ga4gh-tes", - "region": config["USER_BUCKETS_REGION"], - }