Feat: Onboard Human Variant Annotation dataset

datasets/human_variant_annotation/infra/human_variant_annotation_dataset.tf

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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.
+ */
+
+
+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
+}

datasets/human_variant_annotation/infra/provider.tf

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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.
+ */
+
+
+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
+}

datasets/human_variant_annotation/infra/variables.tf

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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.
+ */
+
+
+variable "project_id" {}
+variable "bucket_name_prefix" {}
+variable "impersonating_acct" {}
+variable "region" {}
+variable "env" {}
+variable "iam_policies" {
+  default = {}
+}
+

datasets/human_variant_annotation/pipelines/_images/run_csv_transform_kub/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.
+
+# 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"]

datasets/human_variant_annotation/pipelines/_images/run_csv_transform_kub/csv_transform.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.
+
+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,
+) -> None:
+    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,
+) -> None:
+    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:
+        target_gcs_path = f"{target_gcs_folder}{file_name}"
+        upload_file_to_gcs(source_file, gcs_bucket, target_gcs_path)
+    else:
+        pass
+
+
+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", ""),
+    )

datasets/human_variant_annotation/pipelines/_images/run_csv_transform_kub/requirements.txt

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+google-cloud-storage
+requests

datasets/human_variant_annotation/pipelines/clinvar/clinvar_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.
+
+
+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