feat: Onboard CMS Medicare (#185)

datasets/cms_medicare/_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/cms_medicare/_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 fnmatch
+import json
+import logging
+import os
+import pathlib
+import typing
+from zipfile import ZipFile
+
+import pandas as pd
+import requests
+from google.cloud import storage
+
+PIPELINES_NAME_INPATIENT = [
+    "inpatient_charges_2011",
+    "inpatient_charges_2012",
+    "inpatient_charges_2013",
+    "inpatient_charges_2014",
+    "inpatient_charges_2015",
+]
+PIPELINES_NAME_OUTPATIENT = [
+    "outpatient_charges_2011",
+    "outpatient_charges_2012",
+    "outpatient_charges_2013",
+    "outpatient_charges_2014",
+]
+
+
+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,
+    pipeline_name: str,
+) -> None:
+
+    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}")
+
+    if pipeline_name in (PIPELINES_NAME_INPATIENT + PIPELINES_NAME_OUTPATIENT):
+        with ZipFile(source_file) as zipped_files:
+            file_list = zipped_files.namelist()
+            csv_file = fnmatch.filter(file_list, "*.csv")
+            data = zipped_files.open(*csv_file)
+            df = pd.read_csv(data)
+    else:
+        df = pd.read_csv(str(source_file))
+
+    logging.info(f"Transformation Process Starting.. {source_file}")
+
+    rename_headers(df, rename_mappings)
+
+    filter_null_rows(
+        df, PIPELINES_NAME_INPATIENT, PIPELINES_NAME_OUTPATIENT, pipeline_name
+    )
+
+    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(
+        "CMS Medicare process completed at "
+        + str(datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S"))
+    )
+
+
+def rename_headers(df: pd.DataFrame, rename_mappings: dict) -> None:
+    df.rename(columns=rename_mappings, inplace=True)
+
+
+def filter_null_rows(
+    df: pd.DataFrame,
+    PIPELINES_NAME_INPATIENT: typing.List[str],
+    PIPELINES_NAME_OUTPATIENT: typing.List[str],
+    pipeline_name: str,
+) -> pd.DataFrame:
+    if pipeline_name in PIPELINES_NAME_INPATIENT:
+        return df.dropna(subset=["drg_definition", "provider_id"], inplace=True)
+    elif pipeline_name in PIPELINES_NAME_OUTPATIENT:
+        return df.dropna(subset=["apc", "provider_id"], inplace=True)
+    else:
+        return df
+
+
+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"]),
+        pipeline_name=os.environ["PIPELINE_NAME"],
+    )

datasets/cms_medicare/_images/run_csv_transform_kub/requirements.txt

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+requests
+google-cloud-storage
+pandas

datasets/cms_medicare/_terraform/cms_medicare_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" "cms_medicare" {
+  dataset_id  = "cms_medicare"
+  project     = var.project_id
+  description = "CMS Medicare"
+}
+
+output "bigquery_dataset-cms_medicare-dataset_id" {
+  value = google_bigquery_dataset.cms_medicare.dataset_id
+}

datasets/cms_medicare/_terraform/hospital_general_info_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" "hospital_general_info" {
+  project    = var.project_id
+  dataset_id = "cms_medicare"
+  table_id   = "hospital_general_info"
+
+  description = "CMS Medicare Hospital General Info"
+
+
+
+
+  depends_on = [
+    google_bigquery_dataset.cms_medicare
+  ]
+}
+
+output "bigquery_table-hospital_general_info-table_id" {
+  value = google_bigquery_table.hospital_general_info.table_id
+}
+
+output "bigquery_table-hospital_general_info-id" {
+  value = google_bigquery_table.hospital_general_info.id
+}

datasets/cms_medicare/_terraform/inpatient_charges_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" "inpatient_charges_2011" {
+  project    = var.project_id
+  dataset_id = "cms_medicare"
+  table_id   = "inpatient_charges_2011"
+
+  description = "CMS Medicare Inpatient Charges 2011"
+
+
+
+
+  depends_on = [
+    google_bigquery_dataset.cms_medicare
+  ]
+}
+
+output "bigquery_table-inpatient_charges_2011-table_id" {
+  value = google_bigquery_table.inpatient_charges_2011.table_id
+}
+
+output "bigquery_table-inpatient_charges_2011-id" {
+  value = google_bigquery_table.inpatient_charges_2011.id
+}
+
+resource "google_bigquery_table" "inpatient_charges_2012" {
+  project    = var.project_id
+  dataset_id = "cms_medicare"
+  table_id   = "inpatient_charges_2012"
+
+  description = "CMS Medicare Inpatient Charges 2012"
+
+
+
+
+  depends_on = [
+    google_bigquery_dataset.cms_medicare
+  ]
+}
+
+output "bigquery_table-inpatient_charges_2012-table_id" {
+  value = google_bigquery_table.inpatient_charges_2012.table_id
+}
+
+output "bigquery_table-inpatient_charges_2012-id" {
+  value = google_bigquery_table.inpatient_charges_2012.id
+}
+
+resource "google_bigquery_table" "inpatient_charges_2013" {
+  project    = var.project_id
+  dataset_id = "cms_medicare"
+  table_id   = "inpatient_charges_2013"
+
+  description = "CMS Medicare Inpatient Charges 2013"
+
+
+
+
+  depends_on = [
+    google_bigquery_dataset.cms_medicare
+  ]
+}
+
+output "bigquery_table-inpatient_charges_2013-table_id" {
+  value = google_bigquery_table.inpatient_charges_2013.table_id
+}
+
+output "bigquery_table-inpatient_charges_2013-id" {
+  value = google_bigquery_table.inpatient_charges_2013.id
+}
+
+resource "google_bigquery_table" "inpatient_charges_2014" {
+  project    = var.project_id
+  dataset_id = "cms_medicare"
+  table_id   = "inpatient_charges_2014"
+
+  description = "CMS Medicare Inpatient Charges 2014"
+
+
+
+
+  depends_on = [
+    google_bigquery_dataset.cms_medicare
+  ]
+}
+
+output "bigquery_table-inpatient_charges_2014-table_id" {
+  value = google_bigquery_table.inpatient_charges_2014.table_id
+}
+
+output "bigquery_table-inpatient_charges_2014-id" {
+  value = google_bigquery_table.inpatient_charges_2014.id
+}
+
+resource "google_bigquery_table" "inpatient_charges_2015" {
+  project    = var.project_id
+  dataset_id = "cms_medicare"
+  table_id   = "inpatient_charges_2015"
+
+  description = "CMS Medicare Inpatient Charges 2015"
+
+
+
+
+  depends_on = [
+    google_bigquery_dataset.cms_medicare
+  ]
+}
+
+output "bigquery_table-inpatient_charges_2015-table_id" {
+  value = google_bigquery_table.inpatient_charges_2015.table_id
+}
+
+output "bigquery_table-inpatient_charges_2015-id" {
+  value = google_bigquery_table.inpatient_charges_2015.id
+}