From 26e1e9fd98c6a7d24b2dae895e73185511d19d84 Mon Sep 17 00:00:00 2001 From: Varshika Gupta Date: Mon, 6 Dec 2021 11:08:51 +0000 Subject: [PATCH 1/2] fix: Onboard CDC Places Dataset --- .../_images/run_csv_transform_kub/Dockerfile | 34 ++++ .../run_csv_transform_kub/csv_transform.py | 112 +++++++++++ .../run_csv_transform_kub/requirements.txt | 3 + .../_terraform/cdc_places_dataset.tf | 26 +++ ..._for_better_health_county_data_pipeline.tf | 39 ++++ datasets/cdc_places/_terraform/provider.tf | 28 +++ datasets/cdc_places/_terraform/variables.tf | 23 +++ datasets/cdc_places/dataset.yaml | 58 ++++++ ..._data_for_better_health_county_data_dag.py | 113 +++++++++++ .../pipeline.yaml | 185 ++++++++++++++++++ 10 files changed, 621 insertions(+) create mode 100644 datasets/cdc_places/_images/run_csv_transform_kub/Dockerfile create mode 100644 datasets/cdc_places/_images/run_csv_transform_kub/csv_transform.py create mode 100644 datasets/cdc_places/_images/run_csv_transform_kub/requirements.txt create mode 100644 datasets/cdc_places/_terraform/cdc_places_dataset.tf create mode 100644 datasets/cdc_places/_terraform/local_data_for_better_health_county_data_pipeline.tf create mode 100644 datasets/cdc_places/_terraform/provider.tf create mode 100644 datasets/cdc_places/_terraform/variables.tf create mode 100644 datasets/cdc_places/dataset.yaml create mode 100644 datasets/cdc_places/local_data_for_better_health_county_data/local_data_for_better_health_county_data_dag.py create mode 100644 datasets/cdc_places/local_data_for_better_health_county_data/pipeline.yaml diff --git a/datasets/cdc_places/_images/run_csv_transform_kub/Dockerfile b/datasets/cdc_places/_images/run_csv_transform_kub/Dockerfile new file mode 100644 index 000000000..62b210f95 --- /dev/null +++ b/datasets/cdc_places/_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/cdc_places/_images/run_csv_transform_kub/csv_transform.py b/datasets/cdc_places/_images/run_csv_transform_kub/csv_transform.py new file mode 100644 index 000000000..7af6ce290 --- /dev/null +++ b/datasets/cdc_places/_images/run_csv_transform_kub/csv_transform.py @@ -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 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, + 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}") + + df = pd.read_csv(str(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( + f"Local Data for Better Health, County Data {pipeline_name} 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 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"], + ) diff --git a/datasets/cdc_places/_images/run_csv_transform_kub/requirements.txt b/datasets/cdc_places/_images/run_csv_transform_kub/requirements.txt new file mode 100644 index 000000000..1c45cdfc3 --- /dev/null +++ b/datasets/cdc_places/_images/run_csv_transform_kub/requirements.txt @@ -0,0 +1,3 @@ +requests +google-cloud-storage +pandas diff --git a/datasets/cdc_places/_terraform/cdc_places_dataset.tf b/datasets/cdc_places/_terraform/cdc_places_dataset.tf new file mode 100644 index 000000000..66e1fc4bb --- /dev/null +++ b/datasets/cdc_places/_terraform/cdc_places_dataset.tf @@ -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. + */ + + +resource "google_bigquery_dataset" "cdc_places" { + dataset_id = "cdc_places" + project = var.project_id + description = "Local Data for Better Health, County Data" +} + +output "bigquery_dataset-cdc_places-dataset_id" { + value = google_bigquery_dataset.cdc_places.dataset_id +} diff --git a/datasets/cdc_places/_terraform/local_data_for_better_health_county_data_pipeline.tf b/datasets/cdc_places/_terraform/local_data_for_better_health_county_data_pipeline.tf new file mode 100644 index 000000000..4342dd46d --- /dev/null +++ b/datasets/cdc_places/_terraform/local_data_for_better_health_county_data_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" "cdc_places_local_data_for_better_health_county_data" { + project = var.project_id + dataset_id = "cdc_places" + table_id = "local_data_for_better_health_county_data" + + description = "Local Data for Better Health, County Data" + + + + + depends_on = [ + google_bigquery_dataset.cdc_places + ] +} + +output "bigquery_table-cdc_places_local_data_for_better_health_county_data-table_id" { + value = google_bigquery_table.cdc_places_local_data_for_better_health_county_data.table_id +} + +output "bigquery_table-cdc_places_local_data_for_better_health_county_data-id" { + value = google_bigquery_table.cdc_places_local_data_for_better_health_county_data.id +} diff --git a/datasets/cdc_places/_terraform/provider.tf b/datasets/cdc_places/_terraform/provider.tf new file mode 100644 index 000000000..23ab87dcd --- /dev/null +++ b/datasets/cdc_places/_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/cdc_places/_terraform/variables.tf b/datasets/cdc_places/_terraform/variables.tf new file mode 100644 index 000000000..c3ec7c506 --- /dev/null +++ b/datasets/cdc_places/_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/cdc_places/dataset.yaml b/datasets/cdc_places/dataset.yaml new file mode 100644 index 000000000..5240106c9 --- /dev/null +++ b/datasets/cdc_places/dataset.yaml @@ -0,0 +1,58 @@ +# 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: + # The `dataset` block includes properties for your dataset that will be shown + # to users of your data on the Google Cloud website. + + # Must be exactly the same name as the folder name your dataset.yaml is in. + name: cdc_places + + # A friendly, human-readable name of the dataset + friendly_name: cdc_places + + # A short, descriptive summary of the dataset. + description: Local Data for Better Health, County Data + + # A list of sources the dataset is derived from, using the YAML list syntax. + dataset_sources: ~ + + # A list of terms and conditions that users of the dataset should agree on, + # using the YAML list syntax. + terms_of_use: ~ + + +resources: + # A list of Google Cloud resources needed by your dataset. In principle, all + # pipelines under a dataset should be able to share these resources. + # + # The currently supported resources are shown below. Use only the resources + # you need, and delete the rest as needed by your pipeline. + # + # We will keep adding to the list below to support more Google Cloud resources + # over time. If a resource you need isn't supported, please file an issue on + # the repository. + + - type: bigquery_dataset + # Google BigQuery dataset to namespace all tables managed by this folder + # + # Required Properties: + # dataset_id + # + # Optional Properties: + # friendly_name (A user-friendly name of the dataset) + # description (A user-friendly description of the dataset) + # location (The geographic location where the dataset should reside) + dataset_id: cdc_places + description: "Local Data for Better Health, County Data" diff --git a/datasets/cdc_places/local_data_for_better_health_county_data/local_data_for_better_health_county_data_dag.py b/datasets/cdc_places/local_data_for_better_health_county_data/local_data_for_better_health_county_data_dag.py new file mode 100644 index 000000000..6a7cece93 --- /dev/null +++ b/datasets/cdc_places/local_data_for_better_health_county_data/local_data_for_better_health_county_data_dag.py @@ -0,0 +1,113 @@ +# 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="cdc_places.local_data_for_better_health_county_data", + default_args=default_args, + max_active_runs=1, + schedule_interval="@daily", + catchup=False, + default_view="graph", +) as dag: + + # Run CSV transform within kubernetes pod + local_data_transform_csv = kubernetes_pod_operator.KubernetesPodOperator( + task_id="local_data_transform_csv", + startup_timeout_seconds=600, + name="cdc_places_local_data_for_better_health_county_data", + 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.cdc_places.container_registry.run_csv_transform_kub }}", + env_vars={ + "SOURCE_URL": "https://chronicdata.cdc.gov/resource/swc5-untb.csv", + "SOURCE_FILE": "files/data.csv", + "TARGET_FILE": "files/data_output.csv", + "TARGET_GCS_BUCKET": "{{ var.value.composer_bucket }}", + "TARGET_GCS_PATH": "data/cdc_places/local_data_for_better_health_county_data/data_output.csv", + "CSV_HEADERS": '["year","stateabbr","statedesc","locationname","datasource","category","measure","data_value_unit","data_value_type","data_value","data_value_footnote_symbol","data_value_footnote","low_confidence_limit","high_confidence_limit","totalpopulation","locationid","categoryid","measureid","datavaluetypeid","short_question_text","geolocation"]', + "RENAME_MAPPINGS": '{"year": "year","stateabbr": "stateabbr","statedesc": "statedesc","locationname": "locationname","datasource": "datasource","category": "category","measure": "measure","data_value_unit": "data_value_unit","data_value_type": "data_value_type","data_value": "data_value","data_value_footnote_symbol": "data_value_footnote_symbol","data_value_footnote": "data_value_footnote","low_confidence_limit": "low_confidence_limit","high_confidence_limit": "high_confidence_limit","totalpopulation": "totalpopulation","locationid": "locationid","categoryid": "categoryid","measureid": "measureid","datavaluetypeid": "datavaluetypeid","short_question_text": "short_question_text","geolocation": "geolocation"}', + "PIPELINE_NAME": "local_data_for_better_health_county_data", + }, + resources={"limit_memory": "4G", "limit_cpu": "2"}, + ) + + # Task to load CSV data to a BigQuery table + load_local_data_to_bq = gcs_to_bq.GoogleCloudStorageToBigQueryOperator( + task_id="load_local_data_to_bq", + bucket="{{ var.value.composer_bucket }}", + source_objects=[ + "data/cdc_places/local_data_for_better_health_county_data/data_output.csv" + ], + source_format="CSV", + destination_project_dataset_table="cdc_places.local_data_for_better_health_county_data", + skip_leading_rows=1, + write_disposition="WRITE_TRUNCATE", + schema_fields=[ + {"name": "year", "type": "INTEGER", "mode": "NULLABLE"}, + {"name": "stateabbr", "type": "STRING", "mode": "NULLABLE"}, + {"name": "statedesc", "type": "STRING", "mode": "NULLABLE"}, + {"name": "locationname", "type": "STRING", "mode": "NULLABLE"}, + {"name": "datasource", "type": "STRING", "mode": "NULLABLE"}, + {"name": "category", "type": "STRING", "mode": "NULLABLE"}, + {"name": "measure", "type": "STRING", "mode": "NULLABLE"}, + {"name": "data_value_unit", "type": "STRING", "mode": "NULLABLE"}, + {"name": "data_value_type", "type": "STRING", "mode": "NULLABLE"}, + {"name": "data_value", "type": "FLOAT", "mode": "NULLABLE"}, + { + "name": "data_value_footnote_symbol", + "type": "STRING", + "mode": "NULLABLE", + }, + {"name": "data_value_footnote", "type": "STRING", "mode": "NULLABLE"}, + {"name": "low_confidence_limit", "type": "FLOAT", "mode": "NULLABLE"}, + {"name": "high_confidence_limit", "type": "FLOAT", "mode": "NULLABLE"}, + {"name": "totalpopulation", "type": "INTEGER", "mode": "NULLABLE"}, + {"name": "locationid", "type": "INTEGER", "mode": "NULLABLE"}, + {"name": "categoryid", "type": "STRING", "mode": "NULLABLE"}, + {"name": "measureid", "type": "STRING", "mode": "NULLABLE"}, + {"name": "datavaluetypeid", "type": "STRING", "mode": "NULLABLE"}, + {"name": "short_question_text", "type": "STRING", "mode": "NULLABLE"}, + {"name": "geolocation", "type": "GEOGRAPHY", "mode": "NULLABLE"}, + ], + ) + + local_data_transform_csv >> load_local_data_to_bq diff --git a/datasets/cdc_places/local_data_for_better_health_county_data/pipeline.yaml b/datasets/cdc_places/local_data_for_better_health_county_data/pipeline.yaml new file mode 100644 index 000000000..f2a394f42 --- /dev/null +++ b/datasets/cdc_places/local_data_for_better_health_county_data/pipeline.yaml @@ -0,0 +1,185 @@ +# 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 + # Required Properties: + table_id: local_data_for_better_health_county_data + + # Description of the table + description: "Local Data for Better Health, County Data" + +dag: + + airflow_version: 1 + + initialize: + dag_id: local_data_for_better_health_county_data + default_args: + owner: "Google" + + # When set to True, keeps a task from getting triggered if the previous schedule for the task hasn’t succeeded + depends_on_past: False + start_date: '2021-03-01' + max_active_runs: 1 + schedule_interval: "@daily" + catchup: False + default_view: graph + + tasks: + + - operator: "KubernetesPodOperator" + + # Task description + description: "Run CSV transform within kubernetes pod" + + args: + + task_id: "local_data_transform_csv" + startup_timeout_seconds: 600 + + # The name of the pod in which the task will run. This will be used (plus a random suffix) to generate a pod id + name: "cdc_places_local_data_for_better_health_county_data" + + # The namespace to run within Kubernetes. Always set its value to "default" because we follow the guideline that KubernetesPodOperator will only be used for very light workloads, i.e. use the Cloud Composer environment's resources without starving other pipelines. + namespace: "default" + + affinity: + nodeAffinity: + requiredDuringSchedulingIgnoredDuringExecution: + nodeSelectorTerms: + - matchExpressions: + - key: cloud.google.com/gke-nodepool + operator: In + values: + - "pool-e2-standard-4" + + image_pull_policy: "Always" + + # Docker images will be built and pushed to GCR by default whenever the `scripts/generate_dag.py` is run. To skip building and pushing images, use the optional `--skip-builds` flag. + image: "{{ var.json.cdc_places.container_registry.run_csv_transform_kub }}" + + # Set the environment variables you need initialized in the container. Use these as input variables for the script your container is expected to perform. + env_vars: + SOURCE_URL: "https://chronicdata.cdc.gov/resource/swc5-untb.csv" + SOURCE_FILE: "files/data.csv" + TARGET_FILE: "files/data_output.csv" + TARGET_GCS_BUCKET: "{{ var.value.composer_bucket }}" + TARGET_GCS_PATH: "data/cdc_places/local_data_for_better_health_county_data/data_output.csv" + CSV_HEADERS: >- + ["year","stateabbr","statedesc","locationname","datasource","category","measure","data_value_unit","data_value_type","data_value","data_value_footnote_symbol","data_value_footnote","low_confidence_limit","high_confidence_limit","totalpopulation","locationid","categoryid","measureid","datavaluetypeid","short_question_text","geolocation"] + RENAME_MAPPINGS: >- + {"year": "year","stateabbr": "stateabbr","statedesc": "statedesc","locationname": "locationname","datasource": "datasource","category": "category","measure": "measure","data_value_unit": "data_value_unit","data_value_type": "data_value_type","data_value": "data_value","data_value_footnote_symbol": "data_value_footnote_symbol","data_value_footnote": "data_value_footnote","low_confidence_limit": "low_confidence_limit","high_confidence_limit": "high_confidence_limit","totalpopulation": "totalpopulation","locationid": "locationid","categoryid": "categoryid","measureid": "measureid","datavaluetypeid": "datavaluetypeid","short_question_text": "short_question_text","geolocation": "geolocation"} + PIPELINE_NAME: "local_data_for_better_health_county_data" + + # Set resource limits for the pod here. For resource units in Kubernetes, see https://kubernetes.io/docs/concepts/configuration/manage-resources-containers/#resource-units-in-kubernetes + resources: + limit_memory: "4G" + limit_cpu: "2" + + - operator: "GoogleCloudStorageToBigQueryOperator" + description: "Task to load CSV data to a BigQuery table" + + args: + task_id: "load_local_data_to_bq" + + # The GCS bucket where the CSV file is located in. + bucket: "{{ var.value.composer_bucket }}" + + # The GCS object path for the CSV file + source_objects: ["data/cdc_places/local_data_for_better_health_county_data/data_output.csv"] + source_format: "CSV" + destination_project_dataset_table: "cdc_places.local_data_for_better_health_county_data" + + # Use this if your CSV file contains a header row + skip_leading_rows: 1 + + # How to write data to the table: overwrite, append, or write if empty + # See https://cloud.google.com/bigquery/docs/reference/auditlogs/rest/Shared.Types/WriteDisposition + write_disposition: "WRITE_TRUNCATE" + + # The BigQuery table schema based on the CSV file. For more info, see + # https://cloud.google.com/bigquery/docs/schemas. + # Always use snake_case and lowercase for column names, and be explicit, + # i.e. specify modes for all columns. + # types: "INTEGER", "TIMESTAMP", "STRING" + schema_fields: + - name: "year" + type: "INTEGER" + mode: "NULLABLE" + - name: "stateabbr" + type: "STRING" + mode: "NULLABLE" + - name: "statedesc" + type: "STRING" + mode: "NULLABLE" + - name: "locationname" + type: "STRING" + mode: "NULLABLE" + - name: "datasource" + type: "STRING" + mode: "NULLABLE" + - name: "category" + type: "STRING" + mode: "NULLABLE" + - name: "measure" + type: "STRING" + mode: "NULLABLE" + - name: "data_value_unit" + type: "STRING" + mode: "NULLABLE" + - name: "data_value_type" + type: "STRING" + mode: "NULLABLE" + - name: "data_value" + type: "FLOAT" + mode: "NULLABLE" + - name: "data_value_footnote_symbol" + type: "STRING" + mode: "NULLABLE" + - name: "data_value_footnote" + type: "STRING" + mode: "NULLABLE" + - name: "low_confidence_limit" + type: "FLOAT" + mode: "NULLABLE" + - name: "high_confidence_limit" + type: "FLOAT" + mode: "NULLABLE" + - name: "totalpopulation" + type: "INTEGER" + mode: "NULLABLE" + - name: "locationid" + type: "INTEGER" + mode: "NULLABLE" + - name: "categoryid" + type: "STRING" + mode: "NULLABLE" + - name: "measureid" + type: "STRING" + mode: "NULLABLE" + - name: "datavaluetypeid" + type: "STRING" + mode: "NULLABLE" + - name: "short_question_text" + type: "STRING" + mode: "NULLABLE" + - name: "geolocation" + type: "GEOGRAPHY" + mode: "NULLABLE" + + graph_paths: + - "local_data_transform_csv >> load_local_data_to_bq" From a2a57db838da252e38eb99ab499f03c293ff13b8 Mon Sep 17 00:00:00 2001 From: Varshika Gupta Date: Wed, 8 Dec 2021 15:39:39 +0000 Subject: [PATCH 2/2] fix: Onboard CDC Places Dataset --- .../run_csv_transform_kub/csv_transform.py | 4 ---- datasets/cdc_places/dataset.yaml | 9 --------- .../pipeline.yaml | 20 ------------------- 3 files changed, 33 deletions(-) diff --git a/datasets/cdc_places/_images/run_csv_transform_kub/csv_transform.py b/datasets/cdc_places/_images/run_csv_transform_kub/csv_transform.py index 7af6ce290..a18f19605 100644 --- a/datasets/cdc_places/_images/run_csv_transform_kub/csv_transform.py +++ b/datasets/cdc_places/_images/run_csv_transform_kub/csv_transform.py @@ -42,17 +42,13 @@ def main( download_file(source_url, source_file) logging.info(f"Opening file {source_file}") - df = pd.read_csv(str(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: diff --git a/datasets/cdc_places/dataset.yaml b/datasets/cdc_places/dataset.yaml index 5240106c9..8691d97d4 100644 --- a/datasets/cdc_places/dataset.yaml +++ b/datasets/cdc_places/dataset.yaml @@ -45,14 +45,5 @@ resources: # the repository. - type: bigquery_dataset - # Google BigQuery dataset to namespace all tables managed by this folder - # - # Required Properties: - # dataset_id - # - # Optional Properties: - # friendly_name (A user-friendly name of the dataset) - # description (A user-friendly description of the dataset) - # location (The geographic location where the dataset should reside) dataset_id: cdc_places description: "Local Data for Better Health, County Data" diff --git a/datasets/cdc_places/local_data_for_better_health_county_data/pipeline.yaml b/datasets/cdc_places/local_data_for_better_health_county_data/pipeline.yaml index f2a394f42..49edfac9f 100644 --- a/datasets/cdc_places/local_data_for_better_health_county_data/pipeline.yaml +++ b/datasets/cdc_places/local_data_for_better_health_county_data/pipeline.yaml @@ -16,10 +16,8 @@ resources: - type: bigquery_table - # Required Properties: table_id: local_data_for_better_health_county_data - # Description of the table description: "Local Data for Better Health, County Data" dag: @@ -31,7 +29,6 @@ dag: default_args: owner: "Google" - # When set to True, keeps a task from getting triggered if the previous schedule for the task hasn’t succeeded depends_on_past: False start_date: '2021-03-01' max_active_runs: 1 @@ -43,7 +40,6 @@ dag: - operator: "KubernetesPodOperator" - # Task description description: "Run CSV transform within kubernetes pod" args: @@ -51,10 +47,8 @@ dag: task_id: "local_data_transform_csv" startup_timeout_seconds: 600 - # The name of the pod in which the task will run. This will be used (plus a random suffix) to generate a pod id name: "cdc_places_local_data_for_better_health_county_data" - # The namespace to run within Kubernetes. Always set its value to "default" because we follow the guideline that KubernetesPodOperator will only be used for very light workloads, i.e. use the Cloud Composer environment's resources without starving other pipelines. namespace: "default" affinity: @@ -69,10 +63,8 @@ dag: image_pull_policy: "Always" - # Docker images will be built and pushed to GCR by default whenever the `scripts/generate_dag.py` is run. To skip building and pushing images, use the optional `--skip-builds` flag. image: "{{ var.json.cdc_places.container_registry.run_csv_transform_kub }}" - # Set the environment variables you need initialized in the container. Use these as input variables for the script your container is expected to perform. env_vars: SOURCE_URL: "https://chronicdata.cdc.gov/resource/swc5-untb.csv" SOURCE_FILE: "files/data.csv" @@ -85,7 +77,6 @@ dag: {"year": "year","stateabbr": "stateabbr","statedesc": "statedesc","locationname": "locationname","datasource": "datasource","category": "category","measure": "measure","data_value_unit": "data_value_unit","data_value_type": "data_value_type","data_value": "data_value","data_value_footnote_symbol": "data_value_footnote_symbol","data_value_footnote": "data_value_footnote","low_confidence_limit": "low_confidence_limit","high_confidence_limit": "high_confidence_limit","totalpopulation": "totalpopulation","locationid": "locationid","categoryid": "categoryid","measureid": "measureid","datavaluetypeid": "datavaluetypeid","short_question_text": "short_question_text","geolocation": "geolocation"} PIPELINE_NAME: "local_data_for_better_health_county_data" - # Set resource limits for the pod here. For resource units in Kubernetes, see https://kubernetes.io/docs/concepts/configuration/manage-resources-containers/#resource-units-in-kubernetes resources: limit_memory: "4G" limit_cpu: "2" @@ -96,26 +87,15 @@ dag: args: task_id: "load_local_data_to_bq" - # The GCS bucket where the CSV file is located in. bucket: "{{ var.value.composer_bucket }}" - # The GCS object path for the CSV file source_objects: ["data/cdc_places/local_data_for_better_health_county_data/data_output.csv"] source_format: "CSV" destination_project_dataset_table: "cdc_places.local_data_for_better_health_county_data" - # Use this if your CSV file contains a header row skip_leading_rows: 1 - - # How to write data to the table: overwrite, append, or write if empty - # See https://cloud.google.com/bigquery/docs/reference/auditlogs/rest/Shared.Types/WriteDisposition write_disposition: "WRITE_TRUNCATE" - # The BigQuery table schema based on the CSV file. For more info, see - # https://cloud.google.com/bigquery/docs/schemas. - # Always use snake_case and lowercase for column names, and be explicit, - # i.e. specify modes for all columns. - # types: "INTEGER", "TIMESTAMP", "STRING" schema_fields: - name: "year" type: "INTEGER"