-
Notifications
You must be signed in to change notification settings - Fork 62
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 Human Variant Annotation dataset #438
Changes from 5 commits
7a7128e
8909da6
a75a989
899fdcb
8db3422
fb76413
File filter
Filter by extension
Conversations
Jump to
Diff view
Diff view
There are no files selected for viewing
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,32 @@ | ||
/** | ||
* 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. | ||
*/ | ||
|
||
|
||
resource "google_storage_bucket" "human-variant-annotation" { | ||
name = "${var.bucket_name_prefix}-human-variant-annotation" | ||
force_destroy = true | ||
location = "US" | ||
uniform_bucket_level_access = true | ||
lifecycle { | ||
ignore_changes = [ | ||
logging, | ||
] | ||
} | ||
} | ||
|
||
output "storage_bucket-human-variant-annotation-name" { | ||
value = google_storage_bucket.human-variant-annotation.name | ||
} |
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 | ||
} |
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,26 @@ | ||
/** | ||
* 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" {} | ||
variable "iam_policies" { | ||
default = {} | ||
} | ||
|
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,37 @@ | ||
# 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. | ||
|
||
# The base image for this build | ||
FROM python:3.8 | ||
|
||
# Allow statements and log messages to appear in Cloud logs | ||
ENV PYTHONUNBUFFERED True | ||
|
||
# Copy the requirements file into the image | ||
COPY requirements.txt ./ | ||
|
||
# Install the packages specified in the requirements file | ||
RUN python3 -m pip install --no-cache-dir -r requirements.txt | ||
|
||
# The WORKDIR instruction sets the working directory for any RUN, CMD, | ||
# ENTRYPOINT, COPY and ADD instructions that follow it in the Dockerfile. | ||
# If the WORKDIR doesn’t exist, it will be created even if it’s not used in | ||
# any subsequent Dockerfile instruction | ||
WORKDIR /custom | ||
|
||
# Copy the specific data processing script/s in the image under /custom/* | ||
COPY ./csv_transform.py . | ||
|
||
# Command to run the data processing script when the container is run | ||
CMD ["python3", "csv_transform.py"] |
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,112 @@ | ||
# 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. | ||
|
||
import datetime | ||
import logging | ||
import os | ||
import pathlib | ||
import typing | ||
|
||
import requests | ||
from google.cloud import storage | ||
|
||
|
||
def main( | ||
base_url: str, | ||
folder: pathlib.Path, | ||
version: str, | ||
gcs_bucket: str, | ||
target_gcs_folder: str, | ||
pipeline: str, | ||
): | ||
logging.info( | ||
f"Human Variant Annotation Dataset {pipeline} pipeline process started at " | ||
+ str(datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S")) | ||
) | ||
logging.info(f"Creating './files/{folder}'") | ||
pathlib.Path(f"./files/{folder}").mkdir(parents=True, exist_ok=True) | ||
dates = get_dates() | ||
for date in dates: | ||
date_time = datetime.datetime.strptime(date, "%Y%m%d") | ||
get_files(date_time, base_url, version, folder, gcs_bucket, target_gcs_folder) | ||
|
||
logging.info( | ||
f"Human Variant Annotation Dataset {pipeline} pipeline process completed at " | ||
+ str(datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S")) | ||
) | ||
|
||
|
||
def get_dates() -> typing.List[str]: | ||
today = datetime.datetime.now() | ||
start_date = datetime.datetime(today.year, today.month - 1, 1) | ||
end_date = today | ||
delta = datetime.timedelta(days=1) | ||
dates = [] | ||
while start_date <= end_date: | ||
dates.append(start_date.strftime("%Y%m%d")) | ||
start_date += delta | ||
return dates | ||
|
||
|
||
def get_files( | ||
date_time: datetime.datetime, | ||
base_url: str, | ||
version: str, | ||
folder: pathlib.Path, | ||
gcs_bucket: str, | ||
target_gcs_folder: str, | ||
): | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. return type None There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. ok done |
||
file_name = f"clinvar_{date_time.strftime('%Y%m%d')}.vcf.gz" | ||
source_url = base_url + f"archive_{version}/{date_time.strftime('%Y')}/{file_name}" | ||
source_file = f"./files/{folder}/{file_name}" | ||
status_code = download_gzfile(source_url, source_file) | ||
if status_code == 200: | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. else: There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. ok done |
||
target_gcs_path = f"{target_gcs_folder}{file_name}" | ||
upload_file_to_gcs(source_file, gcs_bucket, target_gcs_path) | ||
|
||
|
||
def download_gzfile(source_url: str, source_file: str) -> int: | ||
logging.info(f"Downloading data from {source_url} to {source_file} .") | ||
res = requests.get(source_url, stream=True) | ||
if res.status_code == 200: | ||
with open(source_file, "wb") as fb: | ||
for chunk in res: | ||
fb.write(chunk) | ||
logging.info(f"\tDownloaded data from {source_url} into {source_file}") | ||
else: | ||
logging.info(f"Couldn't download {source_url}: Error {res.status_code}") | ||
return res.status_code | ||
|
||
|
||
def upload_file_to_gcs( | ||
source_file: pathlib.Path, target_gcs_bucket: str, target_gcs_path: str | ||
) -> None: | ||
logging.info(f"Uploading output file to gs://{target_gcs_bucket}/{target_gcs_path}") | ||
storage_client = storage.Client() | ||
bucket = storage_client.bucket(target_gcs_bucket) | ||
blob = bucket.blob(target_gcs_path) | ||
blob.upload_from_filename(source_file) | ||
logging.info("Successfully uploaded file to gcs bucket.") | ||
|
||
|
||
if __name__ == "__main__": | ||
logging.getLogger().setLevel(logging.INFO) | ||
main( | ||
base_url=os.environ.get("BASE_URL", ""), | ||
folder=pathlib.Path(os.environ.get("FOLDER", "")).expanduser(), | ||
version=os.environ.get("VERSION", "2.0"), | ||
gcs_bucket=os.environ.get("GCS_BUCKET", ""), | ||
target_gcs_folder=os.environ.get("TARGET_GCS_FOLDER", ""), | ||
pipeline=os.environ.get("PIPELINE", ""), | ||
) |
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,2 @@ | ||
google-cloud-storage | ||
requests |
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,99 @@ | ||
# 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.cncf.kubernetes.operators import kubernetes_pod | ||
from airflow.providers.google.cloud.transfers import gcs_to_gcs | ||
|
||
default_args = { | ||
"owner": "Google", | ||
"depends_on_past": False, | ||
"start_date": "2021-03-01", | ||
} | ||
|
||
|
||
with DAG( | ||
dag_id="human_variant_annotation.clinvar", | ||
default_args=default_args, | ||
max_active_runs=1, | ||
schedule_interval="@daily", | ||
catchup=False, | ||
default_view="graph", | ||
) as dag: | ||
|
||
# Run CSV transform within kubernetes pod | ||
clinvar_vcf_grch37 = kubernetes_pod.KubernetesPodOperator( | ||
task_id="clinvar_vcf_grch37", | ||
startup_timeout_seconds=600, | ||
name="name_basics", | ||
namespace="composer", | ||
service_account_name="datasets", | ||
image_pull_policy="Always", | ||
image="{{ var.json.human_variant_annotation.container_registry.run_csv_transform_kub }}", | ||
env_vars={ | ||
"BASE_URL": "https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/", | ||
"FOLDER": "vcf_GRCh37", | ||
"VERSION": "2.0", | ||
"GCS_BUCKET": "{{ var.value.composer_bucket }}", | ||
"TARGET_GCS_FOLDER": "data/human_variant_annotation/clinVar-vcf_GRCh37/", | ||
"PIPELINE": "clinvar", | ||
}, | ||
resources={"limit_memory": "1G", "limit_cpu": "1"}, | ||
) | ||
|
||
# Task to run a GoogleCloudStorageToGoogleCloudStorageOperator | ||
copy_clinvar_v1_to_gcs_destination_bucket = gcs_to_gcs.GCSToGCSOperator( | ||
task_id="copy_clinvar_v1_to_gcs_destination_bucket", | ||
source_bucket="{{ var.value.composer_bucket }}", | ||
source_object="data/human_variant_annotation/clinVar-vcf_GRCh37/*", | ||
destination_bucket="{{ var.json.human_variant_annotation.destination_bucket }}", | ||
destination_object="human-variant-annotation/clinVar-vcf_GRCh37/", | ||
move_object=False, | ||
replace=False, | ||
) | ||
|
||
# Run CSV transform within kubernetes pod | ||
clinvar_vcf_grch38 = kubernetes_pod.KubernetesPodOperator( | ||
task_id="clinvar_vcf_grch38", | ||
startup_timeout_seconds=600, | ||
name="name_basics", | ||
namespace="composer", | ||
service_account_name="datasets", | ||
image_pull_policy="Always", | ||
image="{{ var.json.human_variant_annotation.container_registry.run_csv_transform_kub }}", | ||
env_vars={ | ||
"BASE_URL": "https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/", | ||
"FOLDER": "vcf_GRCh38", | ||
"VERSION": "2.0", | ||
"GCS_BUCKET": "{{ var.value.composer_bucket }}", | ||
"TARGET_GCS_FOLDER": "data/human_variant_annotation/clinVar-vcf_GRCh38/", | ||
"PIPELINE": "db_snp", | ||
}, | ||
resources={"limit_memory": "1G", "limit_cpu": "1"}, | ||
) | ||
|
||
# Task to run a GoogleCloudStorageToGoogleCloudStorageOperator | ||
copy_clinvar_v2_to_gcs_destination_bucket = gcs_to_gcs.GCSToGCSOperator( | ||
task_id="copy_clinvar_v2_to_gcs_destination_bucket", | ||
source_bucket="{{ var.value.composer_bucket }}", | ||
source_object="data/human_variant_annotation/clinVar-vcf_GRCh38/*", | ||
destination_bucket="{{ var.json.human_variant_annotation.destination_bucket }}", | ||
destination_object="human-variant-annotation/clinVar-vcf_GRCh38/", | ||
move_object=False, | ||
replace=False, | ||
) | ||
|
||
clinvar_vcf_grch37 >> copy_clinvar_v1_to_gcs_destination_bucket | ||
clinvar_vcf_grch38 >> copy_clinvar_v2_to_gcs_destination_bucket |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Always incorporate a return type. For no return type use:
def fn(...) -> None:
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Ok done