Source code for tests.system.providers.google.cloud.life_sciences.example_life_sciences

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from __future__ import annotations

import os
from datetime import datetime
from pathlib import Path

from airflow.models.baseoperator import chain
from airflow.models.dag import DAG
from airflow.providers.google.cloud.operators.gcs import GCSCreateBucketOperator, GCSDeleteBucketOperator
from airflow.providers.google.cloud.operators.life_sciences import LifeSciencesRunPipelineOperator
from airflow.providers.google.cloud.transfers.local_to_gcs import LocalFilesystemToGCSOperator
from airflow.utils.trigger_rule import TriggerRule
from tests.system.providers.google import DEFAULT_GCP_SYSTEM_TEST_PROJECT_ID

[docs]ENV_ID = os.environ.get("SYSTEM_TESTS_ENV_ID")
[docs]PROJECT_ID = os.environ.get("SYSTEM_TESTS_GCP_PROJECT") or DEFAULT_GCP_SYSTEM_TEST_PROJECT_ID
[docs]DAG_ID = "example_life_sciences"
[docs]BUCKET_NAME = f"bucket_{DAG_ID}-{ENV_ID}"
[docs]FILE_NAME = "file"
[docs]LOCATION = "us-central1"
[docs]CURRENT_FOLDER = Path(__file__).parent
[docs]FILE_LOCAL_PATH = str(Path(CURRENT_FOLDER) / "resources" / FILE_NAME)
# [START howto_configure_simple_action_pipeline]
[docs]SIMPLE_ACTION_PIPELINE = { "pipeline": { "actions": [ {"imageUri": "bash", "commands": ["-c", "echo Hello, world"]}, ], "resources": { "regions": [f"{LOCATION}"], "virtualMachine": { "machineType": "n1-standard-1", }, }, }, }
# [END howto_configure_simple_action_pipeline] # [START howto_configure_multiple_action_pipeline]
[docs]MULTI_ACTION_PIPELINE = { "pipeline": { "actions": [ { "imageUri": "google/cloud-sdk", "commands": ["gsutil", "cp", f"gs://{BUCKET_NAME}/{FILE_NAME}", "/tmp"], }, {"imageUri": "bash", "commands": ["-c", "echo Hello, world"]}, { "imageUri": "google/cloud-sdk", "commands": [ "gsutil", "cp", f"gs://{BUCKET_NAME}/{FILE_NAME}", f"gs://{BUCKET_NAME}/output.in", ], }, ], "resources": { "regions": [f"{LOCATION}"], "virtualMachine": { "machineType": "n1-standard-1", }, }, } }
# [END howto_configure_multiple_action_pipeline] with DAG( DAG_ID, schedule="@once", start_date=datetime(2021, 1, 1), catchup=False, tags=["example"], ) as dag:
[docs] create_bucket = GCSCreateBucketOperator(task_id="create_bucket", bucket_name=BUCKET_NAME)
upload_file = LocalFilesystemToGCSOperator( task_id="upload_file", src=FILE_LOCAL_PATH, dst=FILE_NAME, bucket=BUCKET_NAME, ) # [START howto_run_pipeline] simple_life_science_action_pipeline = LifeSciencesRunPipelineOperator( task_id="simple-action-pipeline", body=SIMPLE_ACTION_PIPELINE, project_id=PROJECT_ID, location=LOCATION, ) # [END howto_run_pipeline] multiple_life_science_action_pipeline = LifeSciencesRunPipelineOperator( task_id="multi-action-pipeline", body=MULTI_ACTION_PIPELINE, project_id=PROJECT_ID, location=LOCATION ) delete_bucket = GCSDeleteBucketOperator( task_id="delete_bucket", bucket_name=BUCKET_NAME, trigger_rule=TriggerRule.ALL_DONE ) chain( # TEST SETUP create_bucket, upload_file, # TEST BODY simple_life_science_action_pipeline, multiple_life_science_action_pipeline, # TEST TEARDOWN delete_bucket, ) from tests.system.utils.watcher import watcher # This test needs watcher in order to properly mark success/failure # when "tearDown" task with trigger rule is part of the DAG list(dag.tasks) >> watcher() from tests.system.utils import get_test_run # noqa: E402 # Needed to run the example DAG with pytest (see: tests/system/README.md#run_via_pytest)
[docs]test_run = get_test_run(dag)

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