#
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not use this file except in compliance
# with the License. You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,
# software distributed under the License is distributed on an
# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
# KIND, either express or implied. See the License for the
# specific language governing permissions and limitations
# under the License.
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]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)