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feat: Onboard Open Targets Platform dataset (#313)
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/** | ||
* Copyright 2021 Google LLC | ||
* | ||
* Licensed 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. | ||
*/ | ||
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resource "google_bigquery_dataset" "open_targets_platform" { | ||
dataset_id = "open_targets_platform" | ||
project = var.project_id | ||
description = "Open-Targets dataset" | ||
} | ||
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output "bigquery_dataset-open_targets_platform-dataset_id" { | ||
value = google_bigquery_dataset.open_targets_platform.dataset_id | ||
} |
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/** | ||
* Copyright 2021 Google LLC | ||
* | ||
* Licensed 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. | ||
*/ | ||
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provider "google" { | ||
project = var.project_id | ||
impersonate_service_account = var.impersonating_acct | ||
region = var.region | ||
} | ||
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data "google_client_openid_userinfo" "me" {} | ||
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output "impersonating-account" { | ||
value = data.google_client_openid_userinfo.me.email | ||
} |
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/** | ||
* Copyright 2021 Google LLC | ||
* | ||
* Licensed 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. | ||
*/ | ||
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variable "project_id" {} | ||
variable "bucket_name_prefix" {} | ||
variable "impersonating_acct" {} | ||
variable "region" {} | ||
variable "env" {} | ||
variable "iam_policies" { | ||
default = {} | ||
} | ||
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21
datasets/open_targets/pipelines/_images/copy_bq_datasets/Dockerfile
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# Copyright 2021 Google LLC | ||
# | ||
# Licensed 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. | ||
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FROM python:3.8 | ||
ENV PYTHONUNBUFFERED True | ||
COPY requirements.txt ./ | ||
RUN python3 -m pip install --no-cache-dir -r requirements.txt | ||
WORKDIR /custom | ||
COPY ./script.py . | ||
CMD ["python3", "script.py"] |
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datasets/open_targets/pipelines/_images/copy_bq_datasets/requirements.txt
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google-api-core | ||
google-cloud-bigquery-datatransfer | ||
protobuf |
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datasets/open_targets/pipelines/_images/copy_bq_datasets/script.py
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# Copyright 2022 Google LLC | ||
# | ||
# Licensed 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. | ||
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import logging | ||
import operator | ||
import os | ||
import time | ||
import typing | ||
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from google.api_core.exceptions import ResourceExhausted | ||
from google.cloud import bigquery_datatransfer_v1 | ||
from google.protobuf.timestamp_pb2 import Timestamp | ||
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RETRY_DELAY = 10 | ||
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class TimeoutError(Exception): | ||
"""Raised when the BQ transfer jobs haven't all finished within the allotted time""" | ||
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pass | ||
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def main( | ||
source_project_id: str, | ||
target_project_id: str, | ||
service_account: str, | ||
transfer_config_name: str, | ||
source_dataset_name: str, | ||
target_dataset_name: str, | ||
timeout: int, | ||
): | ||
client = bigquery_datatransfer_v1.DataTransferServiceClient() | ||
transfer_config_prefix = f"{transfer_config_name}-copy" | ||
transfer_configs = client.list_transfer_configs( | ||
request=bigquery_datatransfer_v1.types.ListTransferConfigsRequest( | ||
parent=f"projects/{target_project_id}" | ||
) | ||
) | ||
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existing_configs = [ | ||
config | ||
for config in transfer_configs | ||
if config.display_name.startswith(transfer_config_prefix) | ||
] | ||
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_running_configs = [] | ||
dataset_id = f"{source_dataset_name}" | ||
display_name = f"{transfer_config_prefix}-{source_dataset_name}" | ||
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_config = next( | ||
(config for config in existing_configs if config.display_name == display_name), | ||
None, | ||
) | ||
if not _config: | ||
_config = create_transfer_config( | ||
client, | ||
source_project_id, | ||
target_project_id, | ||
dataset_id, | ||
display_name, | ||
source_dataset_name, | ||
target_dataset_name, | ||
service_account, | ||
) | ||
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trigger_config(client, _config) | ||
_running_configs.append(_config) | ||
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wait_for_completion(client, _running_configs, timeout) | ||
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def wait_for_completion( | ||
client: bigquery_datatransfer_v1.DataTransferServiceClient, | ||
running_configs: typing.List[bigquery_datatransfer_v1.types.TransferConfig], | ||
timeout: int, | ||
) -> None: | ||
_start = int(time.time()) | ||
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while True: | ||
latest_runs = [] | ||
for config in running_configs: | ||
latest_runs.append(latest_transfer_run(client, config)) | ||
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logging.info(f"States: {[str(run.state) for run in latest_runs]}") | ||
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# Mark as complete when all runs have succeeded | ||
if all([str(run.state) == "TransferState.SUCCEEDED" for run in latest_runs]): | ||
return | ||
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# Stop the process when it's longer than the allotted time | ||
if int(time.time()) - _start > timeout: | ||
raise TimeoutError | ||
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time.sleep(RETRY_DELAY) | ||
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def latest_transfer_run( | ||
client: bigquery_datatransfer_v1.DataTransferServiceClient, | ||
config: bigquery_datatransfer_v1.types.TransferConfig, | ||
) -> bigquery_datatransfer_v1.types.TransferRun: | ||
transfer_runs = client.list_transfer_runs(parent=config.name) | ||
return max(transfer_runs, key=operator.attrgetter("run_time")) | ||
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def create_transfer_config( | ||
client: bigquery_datatransfer_v1.DataTransferServiceClient, | ||
source_project_id: str, | ||
target_project_id: str, | ||
dataset_id: str, | ||
display_name: str, | ||
source_dataset_name: str, | ||
target_dataset_name: str, | ||
service_account: str, | ||
) -> bigquery_datatransfer_v1.types.TransferConfig: | ||
transfer_config = bigquery_datatransfer_v1.TransferConfig( | ||
destination_dataset_id=f"{target_dataset_name}", | ||
display_name=display_name, | ||
data_source_id="cross_region_copy", | ||
dataset_region="US", | ||
params={ | ||
"source_project_id": source_project_id, | ||
"source_dataset_id": dataset_id, | ||
}, | ||
schedule_options=bigquery_datatransfer_v1.ScheduleOptions( | ||
disable_auto_scheduling=True | ||
), | ||
) | ||
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request = bigquery_datatransfer_v1.types.CreateTransferConfigRequest( | ||
parent=client.common_project_path(target_project_id), | ||
transfer_config=transfer_config, | ||
service_account_name=service_account, | ||
) | ||
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return client.create_transfer_config(request=request) | ||
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def trigger_config( | ||
client: bigquery_datatransfer_v1.DataTransferServiceClient, | ||
config: bigquery_datatransfer_v1.types.TransferConfig, | ||
) -> None: | ||
now = time.time() | ||
seconds = int(now) | ||
nanos = int((now - seconds) * pow(10, 9)) | ||
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try: | ||
client.start_manual_transfer_runs( | ||
request=bigquery_datatransfer_v1.types.StartManualTransferRunsRequest( | ||
parent=config.name, | ||
requested_run_time=Timestamp(seconds=seconds, nanos=nanos), | ||
) | ||
) | ||
except ResourceExhausted: | ||
logging.info( | ||
f"Transfer job is currently running for config ({config.display_name}) {config.name}." | ||
) | ||
return | ||
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if __name__ == "__main__": | ||
logging.getLogger().setLevel(logging.INFO) | ||
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main( | ||
source_project_id=os.environ["SOURCE_PROJECT_ID"], | ||
target_project_id=os.environ["TARGET_PROJECT_ID"], | ||
service_account=os.environ["SERVICE_ACCOUNT"], | ||
transfer_config_name=os.environ["TRANSFER_CONFIG_NAME"], | ||
source_dataset_name=os.environ["SOURCE_DATASET_NAME"], | ||
target_dataset_name=os.environ["TARGET_DATASET_NAME"], | ||
timeout=int(os.getenv("TIMEOUT", 1200)), | ||
) |
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58
datasets/open_targets/pipelines/copy_platform_data/copy_platform_data_dag.py
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# Copyright 2021 Google LLC | ||
# | ||
# Licensed 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. | ||
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from airflow import DAG | ||
from airflow.providers.cncf.kubernetes.operators import kubernetes_pod | ||
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default_args = { | ||
"owner": "Google", | ||
"depends_on_past": False, | ||
"start_date": "2021-03-23", | ||
} | ||
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with DAG( | ||
dag_id="open_targets.copy_platform_data", | ||
default_args=default_args, | ||
max_active_runs=1, | ||
schedule_interval="@monthly", | ||
catchup=False, | ||
default_view="graph", | ||
) as dag: | ||
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# Transfer Open Targets Databases | ||
copy_bq_datasets = kubernetes_pod.KubernetesPodOperator( | ||
task_id="copy_bq_datasets", | ||
name="copy_bq_datasets", | ||
namespace="composer", | ||
service_account_name="datasets", | ||
image_pull_policy="Always", | ||
image="{{ var.json.open_targets.container_registry.copy_bq_datasets }}", | ||
env_vars={ | ||
"SOURCE_PROJECT_ID": "{{ var.json.open_targets.source_project_id }}", | ||
"TARGET_PROJECT_ID": "{{ var.json.open_targets.target_project_id }}", | ||
"SERVICE_ACCOUNT": "{{ var.json.open_targets.service_account }}", | ||
"TRANSFER_CONFIG_NAME": "open-targets", | ||
"SOURCE_DATASET_NAME": "{{ var.json.open_targets.platform.source_dataset_name }}", | ||
"TARGET_DATASET_NAME": "{{ var.json.open_targets.platform.target_dataset_name }}", | ||
}, | ||
resources={ | ||
"request_memory": "128M", | ||
"request_cpu": "200m", | ||
"request_ephemeral_storage": "5G", | ||
}, | ||
) | ||
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copy_bq_datasets |
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