nci-cidc-api-modules 1.1.11__py3-none-any.whl → 1.1.13__py3-none-any.whl

cidc_api/shared/auth.py

@@ -172,9 +172,7 @@ def _extract_token() -> str:
 
 
 ### Authorization logic ###
-def authorize(
-    user: Users, allowed_roles: List[str], resource: str, method: str
-) -> bool:
+def authorize(user: Users, allowed_roles: List[str], resource: str, method: str) -> bool:
     """Check if the current user is authorized to act on the current request's resource.
     Raises Unauthorized
         - if user is not registered
@@ -220,9 +218,7 @@ def authorize(
 
     # User is approved and registered, so just check their role.
     if allowed_roles and db_user.role not in allowed_roles:
-        raise Unauthorized(
-            f"{db_user.email} is not authorized to access this endpoint."
-        )
+        raise Unauthorized(f"{db_user.email} is not authorized to access this endpoint.")
 
     return True
 
@@ -268,9 +264,7 @@ def _enforce_cli_version():
 
     # The CLI sets the User-Agent header to `cidc-cli/{version}`,
     # so we can assess whether the requester needs to update their CLI.
-    is_old_cli = client == "cidc-cli" and version.parse(client_version) < version.parse(
-        app.config["MIN_CLI_VERSION"]
-    )
+    is_old_cli = client == "cidc-cli" and version.parse(client_version) < version.parse(app.config["MIN_CLI_VERSION"])
 
     if is_old_cli:
         logger.info("cancelling request: detected outdated CLI")

cidc_api/shared/emails.py

@@ -87,18 +87,14 @@ def new_user_registration(email: str) -> dict:
 @sendable
 def new_upload_alert(upload, full_metadata) -> dict:
     """Alert the CIDC administrators that an upload succeeded."""
-    pipeline_configs: Dict[str, Union[bytes, str]] = (
-        generate_analysis_configs_from_upload_patch(
-            full_metadata,
-            upload.metadata_patch,
-            upload.upload_type,
-            GOOGLE_ACL_DATA_BUCKET,
-        )
+    pipeline_configs: Dict[str, Union[bytes, str]] = generate_analysis_configs_from_upload_patch(
+        full_metadata,
+        upload.metadata_patch,
+        upload.upload_type,
+        GOOGLE_ACL_DATA_BUCKET,
     )
 
-    subject = (
-        f"[UPLOAD SUCCESS]({ENV}) {upload.upload_type} uploaded to {upload.trial_id}"
-    )
+    subject = f"[UPLOAD SUCCESS]({ENV}) {upload.upload_type} uploaded to {upload.trial_id}"
 
     html_content = f"""
     <ul>
@@ -119,16 +115,12 @@ def new_upload_alert(upload, full_metadata) -> dict:
 
 
 @sendable
-def intake_metadata(
-    user, trial_id: str, assay_type: str, description: str, xlsx_gcp_url: str
-) -> dict:
+def intake_metadata(user, trial_id: str, assay_type: str, description: str, xlsx_gcp_url: str) -> dict:
     """
     Send an email containing a metadata xlsx file and description of that file to the
     CIDC Admin mailing list.
     """
-    subject = (
-        f"[METADATA SUBMISSION]({ENV}) {user.email} submitted {trial_id}/{assay_type}"
-    )
+    subject = f"[METADATA SUBMISSION]({ENV}) {user.email} submitted {trial_id}/{assay_type}"
     html_content = f"""
     <p><strong>user:</strong> {user.first_n} {user.last_n} ({user.email})</p>
     <p><strong>contact email:</strong> {user.contact_email}</p>

cidc_api/shared/gcloud_client.py

@@ -80,15 +80,11 @@ def _get_storage_client() -> storage.Client:
     if STORAGE_CLIENT is None:
         logger.debug("Getting local client")
         if os.environ.get("DEV_GOOGLE_STORAGE", None):
-            client_options = ClientOptions(
-                api_endpoint=os.environ.get("DEV_GOOGLE_STORAGE")
-            )
+            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"))
             )
-            STORAGE_CLIENT = storage.Client(
-                client_options=client_options, credentials=credentials
-            )
+            STORAGE_CLIENT = storage.Client(client_options=client_options, credentials=credentials)
             logger.debug(f"Local client set to {STORAGE_CLIENT}")
             return STORAGE_CLIENT
 
@@ -124,9 +120,7 @@ def _get_crm_service() -> googleapiclient.discovery.Resource:
         credentials = Credentials.from_service_account_info(
             json.loads(SECRET_MANAGER.get(environ.get("APP_ENGINE_CREDENTIALS_ID")))
         )
-        CRM_SERVICE = googleapiclient.discovery.build(
-            "cloudresourcemanager", "v1", credentials=credentials
-        )
+        CRM_SERVICE = googleapiclient.discovery.build("cloudresourcemanager", "v1", credentials=credentials)
     return CRM_SERVICE
 
 
@@ -176,14 +170,10 @@ def _get_bigquery_dataset(dataset_id: str) -> bigquery.Dataset:
     return dataset
 
 
-XLSX_GCS_URI_FORMAT = (
-    "{trial_id}/xlsx/{template_category}/{template_type}/{upload_moment}.xlsx"
-)
+XLSX_GCS_URI_FORMAT = "{trial_id}/xlsx/{template_category}/{template_type}/{upload_moment}.xlsx"
 
 
-PseudoBblob = namedtuple(
-    "_pseudo_blob", ["name", "size", "md5_hash", "crc32c", "time_created"]
-)
+PseudoBblob = namedtuple("_pseudo_blob", ["name", "size", "md5_hash", "crc32c", "time_created"])
 
 
 def upload_xlsx_to_gcs(
@@ -210,12 +200,8 @@ def upload_xlsx_to_gcs(
     )
 
     if ENV == "dev" and not DEV_USE_GCS:
-        logger.info(
-            f"Would've saved {blob_name} to {GOOGLE_UPLOAD_BUCKET} and {GOOGLE_ACL_DATA_BUCKET}"
-        )
-        return PseudoBblob(
-            blob_name, 0, "_pseudo_md5_hash", "_pseudo_crc32c", upload_moment
-        )
+        logger.info(f"Would've saved {blob_name} to {GOOGLE_UPLOAD_BUCKET} and {GOOGLE_ACL_DATA_BUCKET}")
+        return PseudoBblob(blob_name, 0, "_pseudo_md5_hash", "_pseudo_crc32c", upload_moment)
 
     upload_bucket: storage.Bucket = _get_bucket(GOOGLE_UPLOAD_BUCKET)
     blob = upload_bucket.blob(blob_name)
@@ -348,9 +334,7 @@ def revoke_intake_access(user_email: str) -> None:
         revoke_storage_iam_access(bucket, GOOGLE_INTAKE_ROLE, user_email)
 
 
-def upload_xlsx_to_intake_bucket(
-    user_email: str, trial_id: str, upload_type: str, xlsx: FileStorage
-) -> str:
+def upload_xlsx_to_intake_bucket(user_email: str, trial_id: str, upload_type: str, xlsx: FileStorage) -> str:
     """
     Upload a metadata spreadsheet file to the GCS intake bucket,
     returning the URL to the bucket in the GCP console.
@@ -401,17 +385,13 @@ def get_blob_names(
     session: Optional[Session] = None,
 ) -> Set[str]:
     """session only needed if trial_id is None"""
-    prefixes: Set[str] = _build_trial_upload_prefixes(
-        trial_id, upload_type, session=session
-    )
+    prefixes: Set[str] = _build_trial_upload_prefixes(trial_id, upload_type, session=session)
 
     # https://googleapis.dev/python/storage/latest/client.html#google.cloud.storage.client.Client.list_blobs
     blob_list = []
     storage_client = _get_storage_client()
     for prefix in prefixes:
-        blob_list.extend(
-            storage_client.list_blobs(GOOGLE_ACL_DATA_BUCKET, prefix=prefix)
-        )
+        blob_list.extend(storage_client.list_blobs(GOOGLE_ACL_DATA_BUCKET, prefix=prefix))
     return {blob.name for blob in blob_list}
 
 
@@ -450,13 +430,9 @@ def grant_download_access(
     If the user already has download access for this trial and upload type, idempotent.
     Download access is controlled by IAM on production and ACL elsewhere.
     """
-    user_email_list = (
-        [user_email_list] if isinstance(user_email_list, str) else user_email_list
-    )
+    user_email_list = [user_email_list] if isinstance(user_email_list, str) else user_email_list
 
-    logger.info(
-        f"Granting download access on trial {trial_id} upload {upload_type} to {user_email_list}"
-    )
+    logger.info(f"Granting download access on trial {trial_id} upload {upload_type} to {user_email_list}")
 
     # ---- Handle through main grant permissions topic ----
     # would time out in CFn
@@ -510,12 +486,8 @@ def revoke_download_access(
     Download access is controlled by ACL.
     """
 
-    user_email_list = (
-        [user_email_list] if isinstance(user_email_list, str) else user_email_list
-    )
-    logger.info(
-        f"Revoking download access on trial {trial_id} upload {upload_type} from {user_email_list}"
-    )
+    user_email_list = [user_email_list] if isinstance(user_email_list, str) else user_email_list
+    logger.info(f"Revoking download access on trial {trial_id} upload {upload_type} from {user_email_list}")
 
     # ---- Handle through main grant permissions topic ----
     # would timeout in cloud function
@@ -554,20 +526,13 @@ def _build_trial_upload_prefixes(
     if not trial_id:
         from ..models.models import TrialMetadata
 
-        trial_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])
 
     if not upload_type or None in upload_type:
-        upload_set = {
-            upload_name
-            for upload_name in ASSAY_TO_FILEPATH.keys()
-            if upload_name != "clinical_data"
-        }
+        upload_set = {upload_name for upload_name in ASSAY_TO_FILEPATH.keys() if upload_name != "clinical_data"}
     else:
         upload_set = set(upload_type)
 
@@ -613,9 +578,7 @@ def grant_storage_iam_access(
         # special value -1 for non-expiring
         binding = _build_storage_iam_binding(bucket.name, role, user_email, ttl_days=-1)
     else:
-        binding = _build_storage_iam_binding(
-            bucket.name, role, user_email
-        )  # use default
+        binding = _build_storage_iam_binding(bucket.name, role, user_email)  # use default
     # insert the binding into the policy
     policy.bindings.append(binding)
 
@@ -634,20 +597,14 @@ def grant_bigquery_iam_access(policy: Policy, user_emails: List[str]) -> None:
     """
     roles = [b["role"] for b in policy["bindings"]]
 
-    if (
-        GOOGLE_BIGQUERY_USER_ROLE in roles
-    ):  # if the role is already in the policy, add the users
-        binding = next(
-            b for b in policy["bindings"] if b["role"] == GOOGLE_BIGQUERY_USER_ROLE
-        )
+    if GOOGLE_BIGQUERY_USER_ROLE in roles:  # if the role is already in the policy, add the users
+        binding = next(b for b in policy["bindings"] if b["role"] == GOOGLE_BIGQUERY_USER_ROLE)
         for user_email in user_emails:
             binding["members"].append(user_member(user_email))
     else:  # otherwise create the role and add to policy
         binding = {
             "role": GOOGLE_BIGQUERY_USER_ROLE,
-            "members": [
-                user_member(user_email) for user_email in user_emails
-            ],  # convert format
+            "members": [user_member(user_email) for user_email in user_emails],  # convert format
         }
         policy["bindings"].append(binding)
 
@@ -683,9 +640,7 @@ def grant_bigquery_iam_access(policy: Policy, user_emails: List[str]) -> None:
 MAX_REVOKE_ALL_ITERATIONS = 250
 
 
-def revoke_storage_iam_access(
-    bucket: storage.Bucket, role: str, user_email: str
-) -> None:
+def revoke_storage_iam_access(bucket: storage.Bucket, role: str, user_email: str) -> None:
     """Revoke a bucket IAM policy made by calling `grant_storage_iam_access`."""
     # see https://cloud.google.com/storage/docs/access-control/using-iam-permissions#code-samples_3
     policy = bucket.get_iam_policy(requested_policy_version=3)
@@ -696,9 +651,7 @@ def revoke_storage_iam_access(
         removed_binding = _find_and_pop_storage_iam_binding(policy, role, user_email)
         if removed_binding is None:
             if i == 0:
-                warnings.warn(
-                    f"Tried to revoke a non-existent download IAM permission for {user_email}"
-                )
+                warnings.warn(f"Tried to revoke a non-existent download IAM permission for {user_email}")
             break
 
     try:
@@ -715,13 +668,9 @@ def revoke_bigquery_iam_access(policy: Policy, user_email: str) -> None:
     revoked from the public bigquery dataset in prod.
     """
     # find and remove user on binding
-    binding = next(
-        (b for b in policy["bindings"] if b["role"] == GOOGLE_BIGQUERY_USER_ROLE), None
-    )
+    binding = next((b for b in policy["bindings"] if b["role"] == GOOGLE_BIGQUERY_USER_ROLE), None)
     if not binding:
-        logger.warning(
-            "Expected at least 1 user to have a bigquery jobUser role, but 0 found."
-        )
+        logger.warning("Expected at least 1 user to have a bigquery jobUser role, but 0 found.")
         return
 
     if "members" in binding and user_member(user_email) in binding["members"]:
@@ -748,9 +697,7 @@ def revoke_bigquery_iam_access(policy: Policy, user_email: str) -> None:
     dataset = _get_bigquery_dataset(dataset_id)
     entries = list(dataset.access_entries)
 
-    dataset.access_entries = [
-        entry for entry in entries if entry.entity_id != user_email
-    ]
+    dataset.access_entries = [entry for entry in entries if entry.entity_id != user_email]
 
     dataset = BIGQUERY_CLIENT.update_dataset(
         dataset,
@@ -837,11 +784,7 @@ def _find_and_pop_storage_iam_binding(
                 )
             user_binding_index = i
 
-    binding = (
-        policy.bindings.pop(user_binding_index)
-        if user_binding_index is not None
-        else None
-    )
+    binding = policy.bindings.pop(user_binding_index) if user_binding_index is not None else None
 
     return binding
 
@@ -870,9 +813,9 @@ def get_signed_url(
     full_filename = object_name.replace("/", "_").replace('"', "_").replace(" ", "_")
     other_kwargs = {}
     if os.environ.get("DEV_GOOGLE_STORAGE", None):
-        other_kwargs["api_access_endpoint"] = (
-            os.environ.get("DEV_GOOGLE_STORAGE") or ""
-        ) + (os.environ.get("DEV_GOOGLE_STORAGE_PATH") or "")
+        other_kwargs["api_access_endpoint"] = (os.environ.get("DEV_GOOGLE_STORAGE") or "") + (
+            os.environ.get("DEV_GOOGLE_STORAGE_PATH") or ""
+        )
     url = blob.generate_signed_url(
         version="v2",
         expiration=expiration,
@@ -894,9 +837,7 @@ def _encode_and_publish(content: str, topic: str) -> Future:
     # Don't actually publish to Pub/Sub if running locally
     if ENV == "dev":
         if DEV_CFUNCTIONS_SERVER:
-            logger.info(
-                f"Publishing message {content!r} to topic {DEV_CFUNCTIONS_SERVER}/{topic}"
-            )
+            logger.info(f"Publishing message {content!r} to topic {DEV_CFUNCTIONS_SERVER}/{topic}")
 
             bdata = base64.b64encode(content.encode("utf-8"))
             try:
@@ -906,15 +847,11 @@ def _encode_and_publish(content: str, topic: str) -> Future:
                     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
+                raise Exception(f"Couldn't publish message {content!r} to topic {DEV_CFUNCTIONS_SERVER}/{topic}") from e
 
             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}"
-                )
+                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}")
@@ -966,9 +903,7 @@ def send_email(to_emails: List[str], subject: str, html_content: str, **kw) -> N
         return
 
     logger.info(f"({ENV}) Sending email to {to_emails} with subject {subject}")
-    email_json = json.dumps(
-        {"to_emails": to_emails, "subject": subject, "html_content": html_content, **kw}
-    )
+    email_json = json.dumps({"to_emails": to_emails, "subject": subject, "html_content": html_content, **kw})
 
     report = _encode_and_publish(email_json, GOOGLE_EMAILS_TOPIC)
 

cidc_api/shared/jose.py

@@ -17,9 +17,7 @@ PUBLIC_KEYS_CACHE = TTLCache(maxsize=3600, ttl=1024)  # 1 hour, 1 MB
 @cached(cache=PUBLIC_KEYS_CACHE)
 def get_jwks() -> list:
     # get jwks from our Auth0 domain
-    return requests.get(
-        f"https://{AUTH0_DOMAIN}/.well-known/jwks.json", timeout=TIMEOUT_IN_SECONDS
-    ).json()
+    return requests.get(f"https://{AUTH0_DOMAIN}/.well-known/jwks.json", timeout=TIMEOUT_IN_SECONDS).json()
 
 
 def decode_id_token(token: str) -> dict:

cidc_api/shared/rest_utils.py

@@ -149,9 +149,7 @@ def lookup(
 
     if check_etag:
         if etag != record._etag:
-            raise PreconditionFailed(
-                "provided ETag does not match the stored ETag for this record"
-            )
+            raise PreconditionFailed("provided ETag does not match the stored ETag for this record")
 
     return record
 
@@ -177,9 +175,7 @@ def use_args_with_pagination(argmap: dict, model_schema: BaseSchema):
 
     # Ensure there are no collisions between argmaps
     for arg in argmap.keys():
-        assert (
-            arg not in pagination_argmap
-        ), f"Provided arg `{arg}` collides with pagination args"
+        assert arg not in pagination_argmap, f"Provided arg `{arg}` collides with pagination args"
 
     full_argmap = {**pagination_argmap, **argmap}
 

{nci_cidc_api_modules-1.1.11.dist-info → nci_cidc_api_modules-1.1.13.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nci_cidc_api_modules
-Version: 1.1.11
+Version: 1.1.13
 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-1.1.13.dist-info/RECORD

@@ -0,0 +1,26 @@
+cidc_api/config/__init__.py,sha256=5mX8GAPxUKV84iS-aGOoE-4m68LsOCGCDptXNdlgvj0,148
+cidc_api/config/db.py,sha256=cyWhWtmXha4OsrwUf6ez8aKSfm7tPSmPDE9JVSBx3Fk,1935
+cidc_api/config/logging.py,sha256=E-SdjOYTpfsml-YaBL7Mj2mUT60OTAHH2X6TdeJWasU,1038
+cidc_api/config/secrets.py,sha256=jRFj7W43pWuPf9DZQLCKF7WPXf5cUv-BAaS3ASqhV_Q,1481
+cidc_api/config/settings.py,sha256=p3YuGCH64S8pkdi_b5sDleVqXO6m7tZcDTd5EJnHlbE,4090
+cidc_api/csms/__init__.py,sha256=eJkY6rWNOAUBmSd4G1_U6h7i472druKEtBdVmgFZVPg,20
+cidc_api/csms/auth.py,sha256=VTfHlCym_hqVrHXv41Ku9RMAGN9BiNe7ui0o9KZCKtY,3185
+cidc_api/models/__init__.py,sha256=bl445G8Zic9YbhZ8ZBni07wtBMhLJRMBA-JqjLxx2bw,66
+cidc_api/models/csms_api.py,sha256=ovi_jZXZBg6XYEvIupbf5c0WyMbPi4V07OywbleKGqs,30737
+cidc_api/models/migrations.py,sha256=gp9vtkYbA9FFy2s-7woelAmsvQbJ41LO2_DY-YkFIrQ,11464
+cidc_api/models/models.py,sha256=tKLyBrVH_7fL2smGzApypBTyL-nuuXQHxI-TJsUAIMg,129200
+cidc_api/models/schemas.py,sha256=7tDYtmULuzTt2kg7RorWhte06ffalgpQKrFiDRGcPEQ,2711
+cidc_api/models/files/__init__.py,sha256=8BMTnUSHzUbz0lBeEQY6NvApxDD3GMWMduoVMos2g4Y,213
+cidc_api/models/files/details.py,sha256=v4v_BetAOBiEq-FVcxho8lamZCRGb48oAvKk9yq4ZOI,62204
+cidc_api/models/files/facets.py,sha256=803siMWziH5UVaF2tj49a_kJYb6CmSWHsGQJweXwyJY,28705
+cidc_api/shared/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+cidc_api/shared/auth.py,sha256=PHqmVGkqDjbmUofytVFwD_9ssgUomESl3fFtFHPwZYQ,9062
+cidc_api/shared/emails.py,sha256=MG2csNhMaw3WtbUEqjMxhzV3X1pMzC8RGYBfNy_X0nc,4334
+cidc_api/shared/gcloud_client.py,sha256=spgH0fapO713X82eV23uLXtq4aVWJHwEDK-XDxaehJc,33088
+cidc_api/shared/jose.py,sha256=-qzGzEDAlokEp9E7WtBtQkXyyfPWTYXlwYpCqVJWmqM,1830
+cidc_api/shared/rest_utils.py,sha256=RwR30WOUAYCxL7V-i2totEyeriG30GbBDvBcpLXhM9w,6594
+nci_cidc_api_modules-1.1.13.dist-info/licenses/LICENSE,sha256=pNYWVTHaYonnmJyplmeAp7tQAjosmDpAWjb34jjv7Xs,1102
+nci_cidc_api_modules-1.1.13.dist-info/METADATA,sha256=yk1QTeCl_Oal9mBirw9EvWHlLle0hmVOFzKxGnLw4Jk,41284
+nci_cidc_api_modules-1.1.13.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
+nci_cidc_api_modules-1.1.13.dist-info/top_level.txt,sha256=rNiRzL0lJGi5Q9tY9uSoMdTbJ-7u5c_D2E86KA94yRA,9
+nci_cidc_api_modules-1.1.13.dist-info/RECORD,,

nci_cidc_api_modules-1.1.11.dist-info/RECORD

@@ -1,26 +0,0 @@
-cidc_api/config/__init__.py,sha256=5mX8GAPxUKV84iS-aGOoE-4m68LsOCGCDptXNdlgvj0,148
-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=2VHOVWdN4yUCNYMob2gaWgH2-1_4sbuo46JEIVT_PCY,4021
-cidc_api/csms/__init__.py,sha256=eJkY6rWNOAUBmSd4G1_U6h7i472druKEtBdVmgFZVPg,20
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