nci-cidc-api-modules 1.0.0__py3-none-any.whl → 1.0.1__py3-none-any.whl

cidc_api/shared/auth.py

@@ -1,8 +1,8 @@
 from functools import wraps
-from packaging import version
 from typing import List
 
 import requests
+from packaging import version
 from jose import jwt
 from flask import g, request, current_app as app, Flask
 from werkzeug.exceptions import Unauthorized, BadRequest, PreconditionFailed
@@ -13,6 +13,8 @@ from ..config.logging import get_logger
 
 logger = get_logger(__name__)
 
+TIMEOUT_IN_SECONDS = 20
+
 
 ### Main auth utility functions ###
 def validate_api_auth(app: Flask):
@@ -32,7 +34,7 @@ def validate_api_auth(app: Flask):
     )
 
 
-def requires_auth(resource: str, allowed_roles: list = []):
+def requires_auth(resource: str, allowed_roles: list = None):
     """
     A decorator that adds authentication and basic access to an endpoint.
 
@@ -43,6 +45,9 @@ def requires_auth(resource: str, allowed_roles: list = []):
         Unauthorized if unauthorized
     """
 
+    if allowed_roles is None:
+        allowed_roles = []
+
     def decorator(endpoint):
         # Store metadata on this function stating that it is protected by authentication
         endpoint.is_protected = True
@@ -159,11 +164,11 @@ def _extract_token() -> str:
             assert bearer.lower() == "bearer"
         else:
             id_token = request.json["id_token"]
-    except (AssertionError, AttributeError, KeyError, TypeError, ValueError):
+    except (AssertionError, AttributeError, KeyError, TypeError, ValueError) as exc:
         raise Unauthorized(
             "Either the 'Authorization' header must be set with structure 'Authorization: Bearer <id token>' "
             'or "id_token" must be present in the JSON body of the request.'
-        )
+        ) from exc
 
     return id_token
 
@@ -184,11 +189,11 @@ def _get_issuer_public_key(token: str) -> dict:
     try:
         header = jwt.get_unverified_header(token)
     except jwt.JWTError as e:
-        raise Unauthorized(str(e))
+        raise Unauthorized(str(e)) from e
 
     # Get public keys from our Auth0 domain
     jwks_url = f"https://{AUTH0_DOMAIN}/.well-known/jwks.json"
-    jwks = requests.get(jwks_url).json()
+    jwks = requests.get(jwks_url, timeout=TIMEOUT_IN_SECONDS).json()
 
     # Obtain the public key used to sign this token
     public_key = None
@@ -198,7 +203,7 @@ def _get_issuer_public_key(token: str) -> dict:
 
     # If no matching public key was found, we can't validate the token
     if not public_key:
-        raise Unauthorized("Found no public key with id %s" % header["kid"])
+        raise Unauthorized(f"Found no public key with id {header['kid']}")
 
     return public_key
 
@@ -233,11 +238,11 @@ def _decode_id_token(token: str, public_key: dict) -> dict:
     except jwt.ExpiredSignatureError as e:
         raise Unauthorized(
             f"{e} Token expired. Obtain a new login token from the CIDC Portal, then try logging in again."
-        )
+        ) from e
     except jwt.JWTClaimsError as e:
-        raise Unauthorized(str(e))
+        raise Unauthorized(str(e)) from e
     except jwt.JWTError as e:
-        raise Unauthorized(str(e))
+        raise Unauthorized(str(e)) from e
 
     # Currently, only id_tokens are accepted for authentication.
     # Going forward, we could also accept access tokens that we
@@ -340,9 +345,9 @@ def _enforce_cli_version():
 
     try:
         client, client_version = user_agent.split("/", 1)
-    except ValueError:
-        logger.error(f"Unrecognized user-agent string format: {user_agent}")
-        raise BadRequest("could not parse User-Agent string")
+    except ValueError as exc:
+        logger.error("Unrecognized user-agent string format: %s", user_agent)
+        raise BadRequest("could not parse User-Agent string") from exc
 
     # The CLI sets the User-Agent header to `cidc-cli/{version}`,
     # so we can assess whether the requester needs to update their CLI.

cidc_api/shared/gcloud_client.py

@@ -1,23 +1,21 @@
 """Utilities for interacting with the Google Cloud Platform APIs."""
+
+# pylint: disable=logging-fstring-interpolation
+
 import json
 import os
 from os import environ
-
-from cidc_api.config.secrets import get_secrets_manager
-
-os.environ["TZ"] = "UTC"
+import base64
 import datetime
 import warnings
 import hashlib
 from collections import namedtuple
 from concurrent.futures import Future
-from sqlalchemy.orm.session import Session
 from typing import (
     Any,
     BinaryIO,
     Callable,
     Dict,
-    Iterable,
     List,
     Optional,
     Set,
@@ -25,15 +23,18 @@ from typing import (
     Union,
 )
 
-import requests
+from werkzeug.datastructures import FileStorage
+from sqlalchemy.orm.session import Session
 from google.cloud import storage, pubsub, bigquery
 from google.cloud.bigquery.enums import EntityTypes
 from google.oauth2.service_account import Credentials
-from google.auth.credentials import AnonymousCredentials
-from werkzeug.datastructures import FileStorage
-import googleapiclient.discovery
 from google.api_core.iam import Policy
 from google.api_core.client_options import ClientOptions
+import googleapiclient.discovery
+import requests
+
+from cidc_schemas.prism.constants import ASSAY_TO_FILEPATH
+from cidc_api.config.secrets import get_secrets_manager
 
 from ..config.settings import (
     DEV_USE_GCS,
@@ -57,42 +58,43 @@ from ..config.settings import (
 )
 from ..config.logging import get_logger
 
-from cidc_schemas.prism.constants import ASSAY_TO_FILEPATH
-
+os.environ["TZ"] = "UTC"
 logger = get_logger(__name__)
 
-_storage_client = None
-_bigquery_client = None
-_crm_service = None
+TIMEOUT_IN_SECONDS = 20
+
+# these should be initialized here or used as cached values
+STORAGE_CLIENT = None
+BIGQUERY_CLIENT = None
+CRM_SERVICE = None
 
 # The Secret Manager object should only be initiated once and reused.
 # This is due to the fact that every time this object is initiated, a
 # Google Cloud client is also initiated, which is an expensive handshake
 # that significantly adds to the latency of the script.
-if not TESTING:
-    secret_manager = get_secrets_manager()
+SECRET_MANAGER = get_secrets_manager(TESTING)
 
 
 def _get_storage_client() -> storage.Client:
-    global _storage_client
-    if _storage_client is None:
+    global STORAGE_CLIENT
+    if STORAGE_CLIENT is None:
         logger.debug("Getting local client")
         if os.environ.get("DEV_GOOGLE_STORAGE", None):
-            secret_manager = get_secrets_manager()
             client_options = ClientOptions(
                 api_endpoint=os.environ.get("DEV_GOOGLE_STORAGE")
             )
             credentials = Credentials.from_service_account_info(
-                json.loads(secret_manager.get("APP_ENGINE_CREDENTIALS"))
+                json.loads(SECRET_MANAGER.get("APP_ENGINE_CREDENTIALS"))
             )
-            _storage_client = storage.Client(
+            STORAGE_CLIENT = storage.Client(
                 client_options=client_options, credentials=credentials
             )
-            logger.debug(f"Local client set to {_storage_client}")
-            return _storage_client
-        else:
-            return _get_storage_client2()
-    return _storage_client
+            logger.debug(f"Local client set to {STORAGE_CLIENT}")
+            return STORAGE_CLIENT
+
+        return _get_storage_client2()
+
+    return STORAGE_CLIENT
 
 
 def _get_storage_client2() -> storage.Client:
@@ -102,36 +104,36 @@ def _get_storage_client2() -> storage.Client:
 
     directly providing service account credentials for signing in get_signed_url() below
     """
-    global _storage_client
-    if _storage_client is None:
+    global STORAGE_CLIENT
+    if STORAGE_CLIENT is None:
         credentials = Credentials.from_service_account_info(
-            json.loads(secret_manager.get(environ.get("APP_ENGINE_CREDENTIALS_ID")))
+            json.loads(SECRET_MANAGER.get(environ.get("APP_ENGINE_CREDENTIALS_ID")))
         )
         # client_options = ClientOptions(api_endpoint=os.environ.get("DEV_GOOGLE_STORAGE"))
-        # _storage_client = storage.Client(client_options=client_options, credentials=credentials)
-        _storage_client = storage.Client(credentials=credentials)
-    return _storage_client
+        # STORAGE_CLIENT = storage.Client(client_options=client_options, credentials=credentials)
+        STORAGE_CLIENT = storage.Client(credentials=credentials)
+    return STORAGE_CLIENT
 
 
 def _get_crm_service() -> googleapiclient.discovery.Resource:
     """
     Initializes a Cloud Resource Manager service.
     """
-    global _crm_service
-    if _crm_service is None:
+    global CRM_SERVICE
+    if CRM_SERVICE is None:
         credentials = Credentials.from_service_account_info(
-            json.loads(secret_manager.get(environ.get("APP_ENGINE_CREDENTIALS_ID")))
+            json.loads(SECRET_MANAGER.get(environ.get("APP_ENGINE_CREDENTIALS_ID")))
         )
-        _crm_service = googleapiclient.discovery.build(
+        CRM_SERVICE = googleapiclient.discovery.build(
             "cloudresourcemanager", "v1", credentials=credentials
         )
-    return _crm_service
+    return CRM_SERVICE
 
 
 def _get_bucket(bucket_name: str) -> storage.Bucket:
     """
     Get the bucket with name `bucket_name` from GCS.
-    This does not make an HTTP request; it simply instantiates a bucket object owned by _storage_client.
+    This does not make an HTTP request; it simply instantiates a bucket object owned by STORAGE_CLIENT.
     see: https://googleapis.dev/python/storage/latest/client.html#google.cloud.storage.client.Client.bucket
     """
     storage_client = _get_storage_client()
@@ -160,26 +162,26 @@ def _get_bigquery_dataset(dataset_id: str) -> bigquery.Dataset:
     Get the bigquery dataset with the id 'dataset_id'.
     makes an API request to pull this with the bigquery client
     """
-    global _bigquery_client
-    if _bigquery_client is None:
+    global BIGQUERY_CLIENT
+    if BIGQUERY_CLIENT is None:
         credentials = Credentials.from_service_account_info(
-            json.loads(secret_manager.get(environ.get("APP_ENGINE_CREDENTIALS_ID")))
+            json.loads(SECRET_MANAGER.get(environ.get("APP_ENGINE_CREDENTIALS_ID")))
         )
         # client_options = ClientOptions(api_endpoint=os.environ.get("DEV_GOOGLE_BIGQUERY"))
-        # _bigquery_client = bigquery.Client(client_options=client_options, credentials=credentials)
-        _bigquery_client = bigquery.Client(credentials=credentials)
+        # BIGQUERY_CLIENT = bigquery.Client(client_options=client_options, credentials=credentials)
+        BIGQUERY_CLIENT = bigquery.Client(credentials=credentials)
 
-    dataset = _bigquery_client.get_dataset(dataset_id)  # Make an API request.
+    dataset = BIGQUERY_CLIENT.get_dataset(dataset_id)  # Make an API request.
 
     return dataset
 
 
-_xlsx_gcs_uri_format = (
+XLSX_GCS_URI_FORMAT = (
     "{trial_id}/xlsx/{template_category}/{template_type}/{upload_moment}.xlsx"
 )
 
 
-_pseudo_blob = namedtuple(
+PseudoBblob = namedtuple(
     "_pseudo_blob", ["name", "size", "md5_hash", "crc32c", "time_created"]
 )
 
@@ -200,7 +202,7 @@ def upload_xlsx_to_gcs(
     Returns:
         arg1: GCS blob object
     """
-    blob_name = _xlsx_gcs_uri_format.format(
+    blob_name = XLSX_GCS_URI_FORMAT.format(
         trial_id=trial_id,
         template_category=template_category,
         template_type=template_type,
@@ -211,7 +213,7 @@ def upload_xlsx_to_gcs(
         logger.info(
             f"Would've saved {blob_name} to {GOOGLE_UPLOAD_BUCKET} and {GOOGLE_ACL_DATA_BUCKET}"
         )
-        return _pseudo_blob(
+        return PseudoBblob(
             blob_name, 0, "_pseudo_md5_hash", "_pseudo_crc32c", upload_moment
         )
 
@@ -410,7 +412,7 @@ def get_blob_names(
         blob_list.extend(
             storage_client.list_blobs(GOOGLE_ACL_DATA_BUCKET, prefix=prefix)
         )
-    return set([blob.name for blob in blob_list])
+    return {blob.name for blob in blob_list}
 
 
 def grant_download_access_to_blob_names(
@@ -552,14 +554,11 @@ def _build_trial_upload_prefixes(
     if not trial_id:
         from ..models.models import TrialMetadata
 
-        trial_set = set(
-            [
-                str(t.trial_id)
-                for t in session.query(TrialMetadata).add_columns(
-                    TrialMetadata.trial_id
-                )
-            ]
-        )
+        trial_set = {
+            str(t.trial_id)
+            for t in session.query(TrialMetadata).add_columns(TrialMetadata.trial_id)
+        }
+
     else:
         trial_set = set([trial_id])
 
@@ -654,7 +653,7 @@ def grant_bigquery_iam_access(policy: Policy, user_emails: List[str]) -> None:
 
     # try to set the new policy with edits
     try:
-        _crm_service.projects().setIamPolicy(
+        CRM_SERVICE.projects().setIamPolicy(
             resource=GOOGLE_CLOUD_PROJECT,
             body={
                 "policy": policy,
@@ -677,7 +676,7 @@ def grant_bigquery_iam_access(policy: Policy, user_emails: List[str]) -> None:
             )
         )
     dataset.access_entries = entries
-    _bigquery_client.update_dataset(dataset, ["access_entries"])  # Make an API request.
+    BIGQUERY_CLIENT.update_dataset(dataset, ["access_entries"])  # Make an API request.
 
 
 # Arbitrary upper bound on the number of GCS IAM bindings we expect a user to have for uploads
@@ -731,7 +730,7 @@ def revoke_bigquery_iam_access(policy: Policy, user_email: str) -> None:
     # try update of the policy
     try:
         policy = (
-            _crm_service.projects()
+            CRM_SERVICE.projects()
             .setIamPolicy(
                 resource=GOOGLE_CLOUD_PROJECT,
                 body={
@@ -753,14 +752,15 @@ def revoke_bigquery_iam_access(policy: Policy, user_email: str) -> None:
         entry for entry in entries if entry.entity_id != user_email
     ]
 
-    dataset = _bigquery_client.update_dataset(
+    dataset = BIGQUERY_CLIENT.update_dataset(
         dataset,
         # Update just the `access_entries` property of the dataset.
         ["access_entries"],
     )  # Make an API request.
 
 
-user_member = lambda email: f"user:{email}"
+def user_member(email):
+    return f"user:{email}"
 
 
 def _build_storage_iam_binding(
@@ -897,26 +897,28 @@ def _encode_and_publish(content: str, topic: str) -> Future:
             logger.info(
                 f"Publishing message {content!r} to topic {DEV_CFUNCTIONS_SERVER}/{topic}"
             )
-            import base64
 
             bdata = base64.b64encode(content.encode("utf-8"))
             try:
                 res = requests.post(
-                    f"{DEV_CFUNCTIONS_SERVER}/{topic}", data={"data": bdata}
+                    f"{DEV_CFUNCTIONS_SERVER}/{topic}",
+                    data={"data": bdata},
+                    timeout=TIMEOUT_IN_SECONDS,
                 )
             except Exception as e:
                 raise Exception(
                     f"Couldn't publish message {content!r} to topic {DEV_CFUNCTIONS_SERVER}/{topic}"
                 ) from e
-            else:
-                logger.info(f"Got {res}")
-                if res.status_code != 200:
-                    raise Exception(
-                        f"Couldn't publish message {content!r} to {DEV_CFUNCTIONS_SERVER}/{topic}: {res!r}"
-                    )
+
+            logger.info(f"Got {res}")
+            if res.status_code != 200:
+                raise Exception(
+                    f"Couldn't publish message {content!r} to {DEV_CFUNCTIONS_SERVER}/{topic}: {res!r}"
+                )
+
         else:
             logger.info(f"Would've published message {content} to topic {topic}")
-        return
+        return None
 
     # The Pub/Sub publisher client returns a concurrent.futures.Future
     # containing info about whether the publishing was successful.
@@ -965,7 +967,7 @@ def send_email(to_emails: List[str], subject: str, html_content: str, **kw) -> N
 
     logger.info(f"({ENV}) Sending email to {to_emails} with subject {subject}")
     email_json = json.dumps(
-        dict(to_emails=to_emails, subject=subject, html_content=html_content, **kw)
+        {"to_emails": to_emails, "subject": subject, "html_content": html_content, **kw}
     )
 
     report = _encode_and_publish(email_json, GOOGLE_EMAILS_TOPIC)

cidc_api/shared/rest_utils.py

@@ -1,4 +1,5 @@
 """Shared utility functions for building CIDC API resource endpoints."""
+
 from functools import wraps
 from typing import Optional, Callable, Union
 
@@ -6,6 +7,7 @@ from flask import request, jsonify
 from webargs import fields
 from webargs.flaskparser import use_args
 from marshmallow import validate
+from marshmallow.exceptions import ValidationError
 from werkzeug.exceptions import (
     PreconditionRequired,
     PreconditionFailed,
@@ -13,7 +15,6 @@ from werkzeug.exceptions import (
     BadRequest,
     UnprocessableEntity,
 )
-from marshmallow.exceptions import ValidationError
 
 from ..models import BaseModel, BaseSchema, ValidationMultiError
 
@@ -48,11 +49,11 @@ def unmarshal_request(schema: BaseSchema, kwarg_name: str, load_sqla: bool = Tru
                 loaded_instance.validate()
             # The many ways that validation errors might get raised...
             except ValueError as e:
-                raise UnprocessableEntity(str(e))
+                raise UnprocessableEntity(str(e)) from e
             except ValidationError as e:
-                raise UnprocessableEntity(e.messages)
+                raise UnprocessableEntity(e.messages) from e
             except ValidationMultiError as e:
-                raise UnprocessableEntity({"errors": e.args[0]})
+                raise UnprocessableEntity({"errors": e.args[0]}) from e
 
             kwargs[kwarg_name] = body
 
@@ -186,7 +187,7 @@ def use_args_with_pagination(argmap: dict, model_schema: BaseSchema):
         return {k: v for k, v in args.items() if k in argmap.keys()}
 
     def get_pagination_args(args: dict):
-        return {k: v for k, v in args.items() if k in pagination_argmap.keys()}
+        return {k: v for k, v in args.items() if k in pagination_argmap}
 
     def decorator(endpoint):
         @wraps(endpoint)

{nci_cidc_api_modules-1.0.0.dist-info → nci_cidc_api_modules-1.0.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nci_cidc_api_modules
-Version: 1.0.0
+Version: 1.0.1
 Summary: SQLAlchemy data models and configuration tools used in the NCI CIDC API
 Home-page: https://github.com/NCI-CIDC/cidc-api-gae
 License: MIT license

nci_cidc_api_modules-1.0.1.dist-info/RECORD

@@ -0,0 +1,25 @@
+cidc_api/config/__init__.py,sha256=5kcMGor07TrBm6e_UW6CCVnJu5wJ-8QX8X9ZRmeuPKA,147
+cidc_api/config/db.py,sha256=ayeeNV-sV20hGoFyMMTMncI2V-FI9lVN3JV-Lmpr3xI,1981
+cidc_api/config/logging.py,sha256=gJ2TGgQVREng4Hv0phlCCkQai7HhumKYjJxubpxS6Q0,1090
+cidc_api/config/secrets.py,sha256=2DXeew1Pm0lnf2SLuo8wW5c5kOJp2WrhjflxZGsY_Ng,1505
+cidc_api/config/settings.py,sha256=Ua6UpiQu9l1ZD-YlmpaWuQOv9tPyYLxWFLC2DEJdAyQ,4044
+cidc_api/csms/__init__.py,sha256=eJkY6rWNOAUBmSd4G1_U6h7i472druKEtBdVmgFZVPg,20
+cidc_api/csms/auth.py,sha256=25Yma2Kz3KLENAPSeBYacFuSZXng-EDgmgInKBsRyP0,3191
+cidc_api/models/__init__.py,sha256=bl445G8Zic9YbhZ8ZBni07wtBMhLJRMBA-JqjLxx2bw,66
+cidc_api/models/csms_api.py,sha256=Wp4b53vwOqSlOIaoAYGlI1p8ZfXRXmVJ6MLcsvzq0LA,31664
+cidc_api/models/migrations.py,sha256=gp9vtkYbA9FFy2s-7woelAmsvQbJ41LO2_DY-YkFIrQ,11464
+cidc_api/models/models.py,sha256=AYt0rIzaeQ0HHlTSeerbTpYwMJwqt93aadOuFLLEqBA,120820
+cidc_api/models/schemas.py,sha256=7tDYtmULuzTt2kg7RorWhte06ffalgpQKrFiDRGcPEQ,2711
+cidc_api/models/files/__init__.py,sha256=8BMTnUSHzUbz0lBeEQY6NvApxDD3GMWMduoVMos2g4Y,213
+cidc_api/models/files/details.py,sha256=eg1u8uZwtxb0m9mFobcTL_mnPBMq1MPZv3NN3KWMGOI,62309
+cidc_api/models/files/facets.py,sha256=5xI5eM1J0Uc97W0-MvAPSRRN-2Hs2xb_AIupliJRMJU,29172
+cidc_api/shared/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+cidc_api/shared/auth.py,sha256=VMd_3QJE2iG16QxuGzHBV9MzJJItOZNn9gcw0_iUBLI,11647
+cidc_api/shared/emails.py,sha256=AhSp2hxWyuMpe21pERuQwrAEy0yCfy3rvSygDNKtgdc,4820
+cidc_api/shared/gcloud_client.py,sha256=7dDs0crLMJKdIp4IDSfrZBMB3h-zvWNieB81azoeLO4,33746
+cidc_api/shared/rest_utils.py,sha256=LMfBpvJRjkfQjCzVXuhTTe4Foz4wlvaKg6QntyR-Hkc,6648
+nci_cidc_api_modules-1.0.1.dist-info/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
+nci_cidc_api_modules-1.0.1.dist-info/METADATA,sha256=rhlYaotiiwG6djDCZaSq5GT9CcE_2YVlHs_gnSd9tgY,40275
+nci_cidc_api_modules-1.0.1.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+nci_cidc_api_modules-1.0.1.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
+nci_cidc_api_modules-1.0.1.dist-info/RECORD,,

{nci_cidc_api_modules-1.0.0.dist-info → nci_cidc_api_modules-1.0.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.42.0)
+Generator: bdist_wheel (0.43.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

nci_cidc_api_modules-1.0.0.dist-info/RECORD

@@ -1,25 +0,0 @@
-cidc_api/config/__init__.py,sha256=5kcMGor07TrBm6e_UW6CCVnJu5wJ-8QX8X9ZRmeuPKA,147
-cidc_api/config/db.py,sha256=cw0wTfcak_FyAKZE8oKVYLVkph644Lv-_MAbYutGV44,1978
-cidc_api/config/logging.py,sha256=gJ2TGgQVREng4Hv0phlCCkQai7HhumKYjJxubpxS6Q0,1090
-cidc_api/config/secrets.py,sha256=DlloiKiy420WJO250SfKs_-T0wKYPbgdwyPncP5MGLY,1518
-cidc_api/config/settings.py,sha256=GyeGDCj1tt61u4fbhomPIDq_fiamRMIT6dQPY1ufl-w,4076
-cidc_api/csms/__init__.py,sha256=eJkY6rWNOAUBmSd4G1_U6h7i472druKEtBdVmgFZVPg,20
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