From 8ecbfda2ce4dfd279e85606aa8a7d0a3405dbdb3 Mon Sep 17 00:00:00 2001 From: varshika06 <81638548+varshika06@users.noreply.github.com> Date: Wed, 22 Dec 2021 01:29:27 +0530 Subject: [PATCH] feat: Onboard America Health Rankings dataset (#244) --- .../_images/run_csv_transform_kub/Dockerfile | 34 +++++ .../run_csv_transform_kub/csv_transform.py | 115 +++++++++++++++++ .../run_csv_transform_kub/requirements.txt | 4 + .../_terraform/ahr_pipeline.tf | 39 ++++++ .../america_health_rankings_dataset.tf | 37 ++++++ .../_terraform/provider.tf | 28 +++++ .../_terraform/variables.tf | 23 ++++ .../america_health_rankings/ahr/ahr_dag.py | 95 ++++++++++++++ .../america_health_rankings/ahr/pipeline.yaml | 118 ++++++++++++++++++ datasets/america_health_rankings/dataset.yaml | 31 +++++ 10 files changed, 524 insertions(+) create mode 100644 datasets/america_health_rankings/_images/run_csv_transform_kub/Dockerfile create mode 100644 datasets/america_health_rankings/_images/run_csv_transform_kub/csv_transform.py create mode 100644 datasets/america_health_rankings/_images/run_csv_transform_kub/requirements.txt create mode 100644 datasets/america_health_rankings/_terraform/ahr_pipeline.tf create mode 100644 datasets/america_health_rankings/_terraform/america_health_rankings_dataset.tf create mode 100644 datasets/america_health_rankings/_terraform/provider.tf create mode 100644 datasets/america_health_rankings/_terraform/variables.tf create mode 100644 datasets/america_health_rankings/ahr/ahr_dag.py create mode 100644 datasets/america_health_rankings/ahr/pipeline.yaml create mode 100644 datasets/america_health_rankings/dataset.yaml diff --git a/datasets/america_health_rankings/_images/run_csv_transform_kub/Dockerfile b/datasets/america_health_rankings/_images/run_csv_transform_kub/Dockerfile new file mode 100644 index 000000000..62b210f95 --- /dev/null +++ b/datasets/america_health_rankings/_images/run_csv_transform_kub/Dockerfile @@ -0,0 +1,34 @@ +# 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 +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"] diff --git a/datasets/america_health_rankings/_images/run_csv_transform_kub/csv_transform.py b/datasets/america_health_rankings/_images/run_csv_transform_kub/csv_transform.py new file mode 100644 index 000000000..3ce817e10 --- /dev/null +++ b/datasets/america_health_rankings/_images/run_csv_transform_kub/csv_transform.py @@ -0,0 +1,115 @@ +# 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 json +import logging +import os +import pathlib +import typing + +import pandas as pd +import requests +from google.cloud import storage + + +def main( + source_url: str, + source_file: pathlib.Path, + target_file: pathlib.Path, + target_gcs_bucket: str, + target_gcs_path: str, + headers: typing.List[str], + rename_mappings: dict, +) -> None: + + logging.info( + "America Health Rankings process started at " + + str(datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S")) + ) + + logging.info("Creating 'files' folder") + pathlib.Path("./files").mkdir(parents=True, exist_ok=True) + + logging.info(f"Downloading file {source_url}") + download_file(source_url, source_file) + + logging.info(f"Opening file {source_file}") + df = pd.read_excel(source_file) + + logging.info(f"Transformation Process Starting.. {source_file}") + rename_headers(df, rename_mappings) + df = df[headers] + + logging.info(f"Transformation Process complete .. {source_file}") + logging.info(f"Saving to output file.. {target_file}") + + try: + save_to_new_file(df, file_path=str(target_file)) + except Exception as e: + logging.error(f"Error saving output file: {e}.") + + logging.info( + f"Uploading output file to.. gs://{target_gcs_bucket}/{target_gcs_path}" + ) + upload_file_to_gcs(target_file, target_gcs_bucket, target_gcs_path) + + logging.info( + "America Health Rankings process completed at " + + str(datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S")) + ) + + +def convert_dt_format(date_str: str, time_str: str) -> None: + return str(datetime.datetime.strptime(date_str, "%m/%d/%Y").date()) + " " + time_str + + +def rename_headers(df: pd.DataFrame, rename_mappings: dict) -> None: + df.rename(columns=rename_mappings, inplace=True) + + +def save_to_new_file(df: pd.DataFrame, file_path: str) -> None: + df.to_csv(file_path, float_format="%.0f", index=False) + + +def download_file(source_url: str, source_file: pathlib.Path) -> None: + logging.info(f"Downloading {source_url} into {source_file}") + r = requests.get(source_url, stream=True) + if r.status_code == 200: + with open(source_file, "wb") as f: + for chunk in r: + f.write(chunk) + else: + logging.error(f"Couldn't download {source_url}: {r.text}") + + +def upload_file_to_gcs(file_path: pathlib.Path, gcs_bucket: str, gcs_path: str) -> None: + storage_client = storage.Client() + bucket = storage_client.bucket(gcs_bucket) + blob = bucket.blob(gcs_path) + blob.upload_from_filename(file_path) + + +if __name__ == "__main__": + logging.getLogger().setLevel(logging.INFO) + + main( + source_url=os.environ["SOURCE_URL"], + source_file=pathlib.Path(os.environ["SOURCE_FILE"]).expanduser(), + target_file=pathlib.Path(os.environ["TARGET_FILE"]).expanduser(), + target_gcs_bucket=os.environ["TARGET_GCS_BUCKET"], + target_gcs_path=os.environ["TARGET_GCS_PATH"], + headers=json.loads(os.environ["CSV_HEADERS"]), + rename_mappings=json.loads(os.environ["RENAME_MAPPINGS"]), + ) diff --git a/datasets/america_health_rankings/_images/run_csv_transform_kub/requirements.txt b/datasets/america_health_rankings/_images/run_csv_transform_kub/requirements.txt new file mode 100644 index 000000000..a49d7af9c --- /dev/null +++ b/datasets/america_health_rankings/_images/run_csv_transform_kub/requirements.txt @@ -0,0 +1,4 @@ +requests +google-cloud-storage +pandas +openpyxl diff --git a/datasets/america_health_rankings/_terraform/ahr_pipeline.tf b/datasets/america_health_rankings/_terraform/ahr_pipeline.tf new file mode 100644 index 000000000..875c64d85 --- /dev/null +++ b/datasets/america_health_rankings/_terraform/ahr_pipeline.tf @@ -0,0 +1,39 @@ +/** + * 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_bigquery_table" "america_health_rankings_america_health_rankings" { + project = var.project_id + dataset_id = "america_health_rankings" + table_id = "america_health_rankings" + + description = "America Health Rankings" + + + + + depends_on = [ + google_bigquery_dataset.america_health_rankings + ] +} + +output "bigquery_table-america_health_rankings_america_health_rankings-table_id" { + value = google_bigquery_table.america_health_rankings_america_health_rankings.table_id +} + +output "bigquery_table-america_health_rankings_america_health_rankings-id" { + value = google_bigquery_table.america_health_rankings_america_health_rankings.id +} diff --git a/datasets/america_health_rankings/_terraform/america_health_rankings_dataset.tf b/datasets/america_health_rankings/_terraform/america_health_rankings_dataset.tf new file mode 100644 index 000000000..7deb9059d --- /dev/null +++ b/datasets/america_health_rankings/_terraform/america_health_rankings_dataset.tf @@ -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. + */ + + +resource "google_bigquery_dataset" "america_health_rankings" { + dataset_id = "america_health_rankings" + project = var.project_id + description = "America Health Rankings" +} + +output "bigquery_dataset-america_health_rankings-dataset_id" { + value = google_bigquery_dataset.america_health_rankings.dataset_id +} + +resource "google_storage_bucket" "america-health-rankings" { + name = "${var.bucket_name_prefix}-america-health-rankings" + force_destroy = true + location = "US" + uniform_bucket_level_access = true +} + +output "storage_bucket-america-health-rankings-name" { + value = google_storage_bucket.america-health-rankings.name +} diff --git a/datasets/america_health_rankings/_terraform/provider.tf b/datasets/america_health_rankings/_terraform/provider.tf new file mode 100644 index 000000000..23ab87dcd --- /dev/null +++ b/datasets/america_health_rankings/_terraform/provider.tf @@ -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 +} diff --git a/datasets/america_health_rankings/_terraform/variables.tf b/datasets/america_health_rankings/_terraform/variables.tf new file mode 100644 index 000000000..c3ec7c506 --- /dev/null +++ b/datasets/america_health_rankings/_terraform/variables.tf @@ -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" {} + diff --git a/datasets/america_health_rankings/ahr/ahr_dag.py b/datasets/america_health_rankings/ahr/ahr_dag.py new file mode 100644 index 000000000..79c58b2d8 --- /dev/null +++ b/datasets/america_health_rankings/ahr/ahr_dag.py @@ -0,0 +1,95 @@ +# 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.contrib.operators import gcs_to_bq, kubernetes_pod_operator + +default_args = { + "owner": "Google", + "depends_on_past": False, + "start_date": "2021-03-01", +} + + +with DAG( + dag_id="america_health_rankings.ahr", + default_args=default_args, + max_active_runs=1, + schedule_interval="@daily", + catchup=False, + default_view="graph", +) as dag: + + # Run CSV transform within kubernetes pod + ahr_transform_csv = kubernetes_pod_operator.KubernetesPodOperator( + task_id="ahr_transform_csv", + startup_timeout_seconds=600, + name="america_health_rankings_ahr", + namespace="default", + affinity={ + "nodeAffinity": { + "requiredDuringSchedulingIgnoredDuringExecution": { + "nodeSelectorTerms": [ + { + "matchExpressions": [ + { + "key": "cloud.google.com/gke-nodepool", + "operator": "In", + "values": ["pool-e2-standard-4"], + } + ] + } + ] + } + } + }, + image_pull_policy="Always", + image="{{ var.json.america_health_rankings.container_registry.run_csv_transform_kub }}", + env_vars={ + "SOURCE_URL": "https://assets.americashealthrankings.org/app/uploads/ahr_heath-disparities_data.xlsx", + "SOURCE_FILE": "files/data.xlsx", + "TARGET_FILE": "files/data_output.csv", + "TARGET_GCS_BUCKET": "{{ var.value.composer_bucket }}", + "TARGET_GCS_PATH": "data/america_health_rankings/ahr/data_output.csv", + "CSV_HEADERS": '["edition","report_type","measure_name","state_name","subpopulation","value","lower_ci","upper_ci","source","source_date"]', + "RENAME_MAPPINGS": '{"Edition": "edition","Report Type": "report_type","Measure Name": "measure_name","State Name": "state_name","Subpopulation": "subpopulation","Value": "value","Lower CI": "lower_ci","Upper CI": "upper_ci","Source": "source","Source Date": "source_date"}', + }, + resources={"limit_memory": "2G", "limit_cpu": "1"}, + ) + + # Task to load CSV data to a BigQuery table + load_ahr_to_bq = gcs_to_bq.GoogleCloudStorageToBigQueryOperator( + task_id="load_ahr_to_bq", + bucket="{{ var.value.composer_bucket }}", + source_objects=["data/america_health_rankings/ahr/data_output.csv"], + source_format="CSV", + destination_project_dataset_table="america_health_rankings.ahr", + skip_leading_rows=1, + write_disposition="WRITE_TRUNCATE", + schema_fields=[ + {"name": "edition", "type": "INTEGER", "mode": "NULLABLE"}, + {"name": "report_type", "type": "STRING", "mode": "NULLABLE"}, + {"name": "measure_name", "type": "STRING", "mode": "NULLABLE"}, + {"name": "state_name", "type": "STRING", "mode": "NULLABLE"}, + {"name": "subpopulation", "type": "STRING", "mode": "NULLABLE"}, + {"name": "value", "type": "FLOAT", "mode": "NULLABLE"}, + {"name": "lower_ci", "type": "FLOAT", "mode": "NULLABLE"}, + {"name": "upper_ci", "type": "FLOAT", "mode": "NULLABLE"}, + {"name": "source", "type": "STRING", "mode": "NULLABLE"}, + {"name": "source_date", "type": "STRING", "mode": "NULLABLE"}, + ], + ) + + ahr_transform_csv >> load_ahr_to_bq diff --git a/datasets/america_health_rankings/ahr/pipeline.yaml b/datasets/america_health_rankings/ahr/pipeline.yaml new file mode 100644 index 000000000..a3878593f --- /dev/null +++ b/datasets/america_health_rankings/ahr/pipeline.yaml @@ -0,0 +1,118 @@ +# 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: + + - type: bigquery_table + table_id: america_health_rankings + description: "America Health Rankings" + +dag: + + airflow_version: 1 + initialize: + dag_id: ahr + default_args: + owner: "Google" + depends_on_past: False + start_date: '2021-03-01' + max_active_runs: 1 + schedule_interval: "@daily" + catchup: False + default_view: graph + + tasks: + + - operator: "KubernetesPodOperator" + description: "Run CSV transform within kubernetes pod" + args: + task_id: "ahr_transform_csv" + startup_timeout_seconds: 600 + name: "america_health_rankings_ahr" + namespace: "default" + affinity: + nodeAffinity: + requiredDuringSchedulingIgnoredDuringExecution: + nodeSelectorTerms: + - matchExpressions: + - key: cloud.google.com/gke-nodepool + operator: In + values: + - "pool-e2-standard-4" + + image_pull_policy: "Always" + image: "{{ var.json.america_health_rankings.container_registry.run_csv_transform_kub }}" + + env_vars: + SOURCE_URL: "https://assets.americashealthrankings.org/app/uploads/ahr_heath-disparities_data.xlsx" + SOURCE_FILE: "files/data.xlsx" + TARGET_FILE: "files/data_output.csv" + TARGET_GCS_BUCKET: "{{ var.value.composer_bucket }}" + TARGET_GCS_PATH: "data/america_health_rankings/ahr/data_output.csv" + CSV_HEADERS: >- + ["edition","report_type","measure_name","state_name","subpopulation","value","lower_ci","upper_ci","source","source_date"] + RENAME_MAPPINGS: >- + {"Edition": "edition","Report Type": "report_type","Measure Name": "measure_name","State Name": "state_name","Subpopulation": "subpopulation","Value": "value","Lower CI": "lower_ci","Upper CI": "upper_ci","Source": "source","Source Date": "source_date"} + + resources: + limit_memory: "2G" + limit_cpu: "1" + + - operator: "GoogleCloudStorageToBigQueryOperator" + description: "Task to load CSV data to a BigQuery table" + + args: + task_id: "load_ahr_to_bq" + bucket: "{{ var.value.composer_bucket }}" + source_objects: ["data/america_health_rankings/ahr/data_output.csv"] + source_format: "CSV" + destination_project_dataset_table: "america_health_rankings.ahr" + skip_leading_rows: 1 + write_disposition: "WRITE_TRUNCATE" + + schema_fields: + - name: "edition" + type: "INTEGER" + mode: "NULLABLE" + - name: "report_type" + type: "STRING" + mode: "NULLABLE" + - name: "measure_name" + type: "STRING" + mode: "NULLABLE" + - name: "state_name" + type: "STRING" + mode: "NULLABLE" + - name: "subpopulation" + type: "STRING" + mode: "NULLABLE" + - name: "value" + type: "FLOAT" + mode: "NULLABLE" + - name: "lower_ci" + type: "FLOAT" + mode: "NULLABLE" + - name: "upper_ci" + type: "FLOAT" + mode: "NULLABLE" + - name: "source" + type: "STRING" + mode: "NULLABLE" + - name: "source_date" + type: "STRING" + mode: "NULLABLE" + + graph_paths: + - "ahr_transform_csv >> load_ahr_to_bq" diff --git a/datasets/america_health_rankings/dataset.yaml b/datasets/america_health_rankings/dataset.yaml new file mode 100644 index 000000000..98c8e1cd6 --- /dev/null +++ b/datasets/america_health_rankings/dataset.yaml @@ -0,0 +1,31 @@ +# 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: cms_medicare + friendly_name: cms_medicare + description: CMS Medicare + dataset_sources: ~ + terms_of_use: ~ + + +resources: + + - type: bigquery_dataset + dataset_id: america_health_rankings + description: "America Health Rankings" + - type: storage_bucket + name: america-health-rankings + uniform_bucket_level_access: True + location: US