Source code for airflow.providers.google.cloud.hooks.life_sciences
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"""Hook for Google Cloud Life Sciences service."""
from __future__ import annotations
import time
from typing import Sequence
import google.api_core.path_template
from deprecated import deprecated
from googleapiclient.discovery import build
from airflow.exceptions import AirflowException, AirflowProviderDeprecationWarning
from airflow.providers.google.common.hooks.base_google import GoogleBaseHook
# Time to sleep between active checks of the operation results
[docs]TIME_TO_SLEEP_IN_SECONDS = 5
@deprecated(
reason=(
"This hook is deprecated. Consider using "
"Google Cloud Batch Operators' hook instead. "
"The Life Sciences API (beta) will be discontinued "
"on July 8, 2025 in favor of Google Cloud Batch."
),
category=AirflowProviderDeprecationWarning,
)
[docs]class LifeSciencesHook(GoogleBaseHook):
"""
Hook for the Google Cloud Life Sciences APIs.
.. warning::
This hook is deprecated. Consider using Google Cloud Batch Operators' hook instead.
The Life Sciences API (beta) will be discontinued on July 8, 2025 in favor
of Google Cloud Batch.
All the methods in the hook where project_id is used must be called with
keyword arguments rather than positional.
:param api_version: API version used (for example v1 or v1beta1).
:param gcp_conn_id: The connection ID to use when fetching connection info.
:param impersonation_chain: Optional service account to impersonate using short-term
credentials, or chained list of accounts required to get the access_token
of the last account in the list, which will be impersonated in the request.
If set as a string, the account must grant the originating account
the Service Account Token Creator IAM role.
If set as a sequence, the identities from the list must grant
Service Account Token Creator IAM role to the directly preceding identity, with first
account from the list granting this role to the originating account.
"""
_conn: build | None = None
def __init__(
self,
api_version: str = "v2beta",
gcp_conn_id: str = "google_cloud_default",
impersonation_chain: str | Sequence[str] | None = None,
**kwargs,
) -> None:
if kwargs.get("delegate_to") is not None:
raise RuntimeError(
"The `delegate_to` parameter has been deprecated before and finally removed in this version"
" of Google Provider. You MUST convert it to `impersonate_chain`"
)
super().__init__(
gcp_conn_id=gcp_conn_id,
impersonation_chain=impersonation_chain,
)
self.api_version = api_version
[docs] def get_conn(self) -> build:
"""
Retrieve the connection to Cloud Life Sciences.
:return: Google Cloud Life Sciences service object.
"""
if not self._conn:
http_authorized = self._authorize()
self._conn = build("lifesciences", self.api_version, http=http_authorized, cache_discovery=False)
return self._conn
@GoogleBaseHook.fallback_to_default_project_id
[docs] def run_pipeline(self, body: dict, location: str, project_id: str) -> dict:
"""
Run a pipeline.
:param body: The request body.
:param location: The location of the project. For example: "us-east1".
:param project_id: Optional, Google Cloud Project project_id where the function belongs.
If set to None or missing, the default project_id from the Google Cloud connection is used.
"""
parent = self._location_path(project_id=project_id, location=location)
service = self.get_conn()
request = service.projects().locations().pipelines().run(parent=parent, body=body)
response = request.execute(num_retries=self.num_retries)
# wait
operation_name = response["name"]
self._wait_for_operation_to_complete(operation_name)
return response
@GoogleBaseHook.fallback_to_default_project_id
def _location_path(self, project_id: str, location: str) -> str:
"""
Return a location string.
:param project_id: Optional, Google Cloud Project project_id where the
function belongs. If set to None or missing, the default project_id
from the Google Cloud connection is used.
:param location: The location of the project. For example: "us-east1".
"""
return google.api_core.path_template.expand(
"projects/{project}/locations/{location}",
project=project_id,
location=location,
)
def _wait_for_operation_to_complete(self, operation_name: str) -> None:
"""
Wait for the named operation to complete - checks status of the asynchronous call.
:param operation_name: The name of the operation.
:return: The response returned by the operation.
:exception: AirflowException in case error is returned.
"""
service = self.get_conn()
while True:
operation_response = (
service.projects()
.locations()
.operations()
.get(name=operation_name)
.execute(num_retries=self.num_retries)
)
self.log.info("Waiting for pipeline operation to complete")
if operation_response.get("done"):
response = operation_response.get("response")
error = operation_response.get("error")
# Note, according to documentation always either response or error is
# set when "done" == True
if error:
raise AirflowException(str(error))
return response
time.sleep(TIME_TO_SLEEP_IN_SECONDS)