Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

feat: Onboard Broad Genome References dataset #316

Merged
merged 1 commit into from
Mar 21, 2022
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
28 changes: 28 additions & 0 deletions datasets/broad_references/infra/provider.tf
Original file line number Diff line number Diff line change
@@ -0,0 +1,28 @@
/**
* 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.
*/


provider "google" {
project = var.project_id
impersonate_service_account = var.impersonating_acct
region = var.region
}

data "google_client_openid_userinfo" "me" {}

output "impersonating-account" {
value = data.google_client_openid_userinfo.me.email
}
23 changes: 23 additions & 0 deletions datasets/broad_references/infra/variables.tf
Original file line number Diff line number Diff line change
@@ -0,0 +1,23 @@
/**
* 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.
*/


variable "project_id" {}
variable "bucket_name_prefix" {}
variable "impersonating_acct" {}
variable "region" {}
variable "env" {}

Original file line number Diff line number Diff line change
@@ -0,0 +1,48 @@
# 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.


from airflow import DAG
from airflow.providers.google.cloud.operators import cloud_storage_transfer_service

default_args = {
"owner": "Google",
"depends_on_past": False,
"start_date": "2022-03-01",
}


with DAG(
dag_id="broad_references.copy_gcs_bucket",
default_args=default_args,
max_active_runs=1,
schedule_interval="@daily",
catchup=False,
default_view="graph",
) as dag:

# Task to run a GCS to GCS operation using Google resources
gcs_bucket_transfer = cloud_storage_transfer_service.CloudDataTransferServiceGCSToGCSOperator(
task_id="gcs_bucket_transfer",
timeout=43200,
retries=0,
wait=True,
project_id="bigquery-public-data",
source_bucket="{{ var.json.broad_references.source_bucket }}",
destination_bucket="gcp-public-data--broad-references",
google_impersonation_chain="{{ var.json.broad_references.service_account }}",
transfer_options={"deleteObjectsUniqueInSink": False},
)

gcs_bucket_transfer
48 changes: 48 additions & 0 deletions datasets/broad_references/pipelines/copy_gcs_bucket/pipeline.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,48 @@
# 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.


---
resources: ~

dag:
airflow_version: 2
initialize:
dag_id: copy_gcs_bucket
default_args:
owner: "Google"
depends_on_past: False
start_date: '2022-03-01'
max_active_runs: 1
schedule_interval: "@daily"
catchup: False
default_view: graph

tasks:
- operator: "CloudDataTransferServiceGCSToGCSOperator"
description: "Task to run a GCS to GCS operation using Google resources"
args:
task_id: "gcs_bucket_transfer"
timeout: 43200 # 12 hours
retries: 0
wait: True
project_id: bigquery-public-data
source_bucket: "{{ var.json.broad_references.source_bucket }}"
destination_bucket: "gcp-public-data--broad-references"
google_impersonation_chain: "{{ var.json.broad_references.service_account }}"
transfer_options:
deleteObjectsUniqueInSink: False

graph_paths:
- "gcs_bucket_transfer"
22 changes: 22 additions & 0 deletions datasets/broad_references/pipelines/dataset.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,22 @@
# 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.

dataset:
name: broad_references
friendly_name: ~
description: ~
dataset_sources: ~
terms_of_use: ~

resources: ~