feat: Onboard America Health Rankings dataset (#244)

datasets/america_health_rankings/_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
+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/america_health_rankings/_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 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"]),
+    )

datasets/america_health_rankings/_images/run_csv_transform_kub/requirements.txt

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+requests
+google-cloud-storage
+pandas
+openpyxl

datasets/america_health_rankings/_terraform/ahr_pipeline.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_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
+}

datasets/america_health_rankings/_terraform/america_health_rankings_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_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
+}

datasets/america_health_rankings/_terraform/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/america_health_rankings/_terraform/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" {}
+

datasets/america_health_rankings/ahr/ahr_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.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