diff --git a/datasets/covid19_cds_eu/_images/run_csv_transform_kub/Dockerfile b/datasets/covid19_cds_eu/_images/run_csv_transform_kub/Dockerfile new file mode 100644 index 000000000..7265a1b71 --- /dev/null +++ b/datasets/covid19_cds_eu/_images/run_csv_transform_kub/Dockerfile @@ -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. + +# 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"] diff --git a/datasets/covid19_cds_eu/_images/run_csv_transform_kub/csv_transform.py b/datasets/covid19_cds_eu/_images/run_csv_transform_kub/csv_transform.py new file mode 100644 index 000000000..b623f7fc1 --- /dev/null +++ b/datasets/covid19_cds_eu/_images/run_csv_transform_kub/csv_transform.py @@ -0,0 +1,154 @@ +# 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 math +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( + f"COVID-19 CDS EU {pipeline_name} 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 from {source_url}...") + download_file(source_url, source_file) + + logging.info(f"Opening file {source_file}...") + df = pd.read_csv(source_file) + + logging.info("Transforming... ") + + logging.info("Transform: Rename columns... ") + rename_headers(df, rename_mappings) + + logging.info("Transform: Create new column location_geom... ") + df["location_geom"] = ( + "POINT(" + + df["longitude"].astype(str).replace("nan", "") + + " " + + df["latitude"].astype(str).replace("nan", "") + + ")" + ).replace("POINT( )", "") + + logging.info("Transform: Convert datatype to integer... ") + convert_datatype_to_integer_string(df) + + logging.info("Transform: Reordering headers..") + df = df[headers] + + 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"COVID-19 CDS EU {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, index=False) + + +def convert_to_integer_string(input: typing.Union[str, float]) -> str: + str_val = "" + if not input or (math.isnan(input)): + str_val = "" + else: + str_val = str(int(round(input, 0))) + return str_val + + +def convert_datatype_to_integer_string(df: pd.DataFrame) -> None: + dt_cols = [ + "population", + "cases", + "deaths", + "recovered", + "active", + "tested", + "hospitalized", + "discharged", + ] + + for dt_col in dt_cols: + df[dt_col] = df[dt_col].apply(convert_to_integer_string) + + +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/covid19_cds_eu/_images/run_csv_transform_kub/requirements.txt b/datasets/covid19_cds_eu/_images/run_csv_transform_kub/requirements.txt new file mode 100644 index 000000000..3e4d10c7e --- /dev/null +++ b/datasets/covid19_cds_eu/_images/run_csv_transform_kub/requirements.txt @@ -0,0 +1,3 @@ +google-cloud-storage +pandas +requests diff --git a/datasets/covid19_cds_eu/_terraform/covid19_cds_eu_dataset.tf b/datasets/covid19_cds_eu/_terraform/covid19_cds_eu_dataset.tf new file mode 100644 index 000000000..c96af4545 --- /dev/null +++ b/datasets/covid19_cds_eu/_terraform/covid19_cds_eu_dataset.tf @@ -0,0 +1,42 @@ +/** + * 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" "covid19_cds_eu" { + dataset_id = "covid19_cds_eu" + project = var.project_id + description = "COVID-19 CDS EU dataset" +} + +output "bigquery_dataset-covid19_cds_eu-dataset_id" { + value = google_bigquery_dataset.covid19_cds_eu.dataset_id +} + +resource "google_storage_bucket" "covid19-cds-eu" { + name = "${var.bucket_name_prefix}-covid19-cds-eu" + force_destroy = true + location = "US" + uniform_bucket_level_access = true + lifecycle { + ignore_changes = [ + logging, + ] + } +} + +output "storage_bucket-covid19-cds-eu-name" { + value = google_storage_bucket.covid19-cds-eu.name +} diff --git a/datasets/covid19_cds_eu/_terraform/global_cases_by_province_pipeline.tf b/datasets/covid19_cds_eu/_terraform/global_cases_by_province_pipeline.tf new file mode 100644 index 000000000..c8f25207e --- /dev/null +++ b/datasets/covid19_cds_eu/_terraform/global_cases_by_province_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" "covid19_cds_eu_global_cases_by_province" { + project = var.project_id + dataset_id = "covid19_cds_eu" + table_id = "global_cases_by_province" + + description = "Global cases by province table" + + + + + depends_on = [ + google_bigquery_dataset.covid19_cds_eu + ] +} + +output "bigquery_table-covid19_cds_eu_global_cases_by_province-table_id" { + value = google_bigquery_table.covid19_cds_eu_global_cases_by_province.table_id +} + +output "bigquery_table-covid19_cds_eu_global_cases_by_province-id" { + value = google_bigquery_table.covid19_cds_eu_global_cases_by_province.id +} diff --git a/datasets/covid19_cds_eu/_terraform/provider.tf b/datasets/covid19_cds_eu/_terraform/provider.tf new file mode 100644 index 000000000..23ab87dcd --- /dev/null +++ b/datasets/covid19_cds_eu/_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/covid19_cds_eu/_terraform/variables.tf b/datasets/covid19_cds_eu/_terraform/variables.tf new file mode 100644 index 000000000..c3ec7c506 --- /dev/null +++ b/datasets/covid19_cds_eu/_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/covid19_cds_eu/dataset.yaml b/datasets/covid19_cds_eu/dataset.yaml new file mode 100644 index 000000000..248136b5e --- /dev/null +++ b/datasets/covid19_cds_eu/dataset.yaml @@ -0,0 +1,30 @@ +# 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: covid19_cds_eu + friendly_name: ~ + description: ~ + dataset_sources: ~ + terms_of_use: ~ + + +resources: + - type: bigquery_dataset + dataset_id: covid19_cds_eu + description: COVID-19 CDS EU dataset + - type: storage_bucket + name: covid19-cds-eu + uniform_bucket_level_access: True + location: US diff --git a/datasets/covid19_cds_eu/global_cases_by_province/global_cases_by_province_dag.py b/datasets/covid19_cds_eu/global_cases_by_province/global_cases_by_province_dag.py new file mode 100644 index 000000000..ae570bf03 --- /dev/null +++ b/datasets/covid19_cds_eu/global_cases_by_province/global_cases_by_province_dag.py @@ -0,0 +1,213 @@ +# 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="covid19_cds_eu.global_cases_by_province", + default_args=default_args, + max_active_runs=1, + schedule_interval="@daily", + catchup=False, + default_view="graph", +) as dag: + + # Run CSV transform within kubernetes pod + global_cases_by_province_transform_csv = kubernetes_pod_operator.KubernetesPodOperator( + task_id="global_cases_by_province_transform_csv", + startup_timeout_seconds=600, + name="global_cases_by_province", + 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.covid19_cds_eu.container_registry.run_csv_transform_kub }}", + env_vars={ + "SOURCE_URL": "https://coronadatascraper.com/timeseries.csv", + "SOURCE_FILE": "files/data.csv", + "TARGET_FILE": "files/data_output.csv", + "TARGET_GCS_BUCKET": "{{ var.value.composer_bucket }}", + "TARGET_GCS_PATH": "data/covid19_cds_eu/global_cases_by_province/data_output.csv", + "PIPELINE_NAME": "global_cases_by_province", + "CSV_HEADERS": '["name","level","date","city","county","state","country","population","latitude","longitude","aggregate","tz","cases","deaths","recovered","active","tested","hospitalized","discharged","growth_factor","url","location_geom"]', + "RENAME_MAPPINGS": '{"lat":"latitude","long":"longitude","growthFactor":"growth_factor"}', + }, + resources={"request_memory": "2G", "request_cpu": "1"}, + ) + + # Task to load CSV data to a BigQuery table + load_global_cases_by_province_to_bq = ( + gcs_to_bq.GoogleCloudStorageToBigQueryOperator( + task_id="load_global_cases_by_province_to_bq", + bucket="{{ var.value.composer_bucket }}", + source_objects=[ + "data/covid19_cds_eu/global_cases_by_province/data_output.csv" + ], + source_format="CSV", + destination_project_dataset_table="covid19_cds_eu.global_cases_by_province", + skip_leading_rows=1, + allow_quoted_newlines=True, + write_disposition="WRITE_TRUNCATE", + schema_fields=[ + { + "name": "name", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "level", + "type": "string", + "description": "", + "mode": "nullable", + }, + {"name": "date", "type": "date", "description": "", "mode": "nullable"}, + { + "name": "city", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "county", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "state", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "country", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "population", + "type": "integer", + "description": "", + "mode": "nullable", + }, + { + "name": "latitude", + "type": "float", + "description": "", + "mode": "nullable", + }, + { + "name": "longitude", + "type": "float", + "description": "", + "mode": "nullable", + }, + { + "name": "aggregate", + "type": "string", + "description": "", + "mode": "nullable", + }, + {"name": "tz", "type": "string", "description": "", "mode": "nullable"}, + { + "name": "cases", + "type": "integer", + "description": "", + "mode": "nullable", + }, + { + "name": "deaths", + "type": "integer", + "description": "", + "mode": "nullable", + }, + { + "name": "recovered", + "type": "integer", + "description": "", + "mode": "nullable", + }, + { + "name": "active", + "type": "integer", + "description": "", + "mode": "nullable", + }, + { + "name": "tested", + "type": "integer", + "description": "", + "mode": "nullable", + }, + { + "name": "hospitalized", + "type": "integer", + "description": "", + "mode": "nullable", + }, + { + "name": "discharged", + "type": "integer", + "description": "", + "mode": "nullable", + }, + { + "name": "growth_factor", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "url", + "type": "string", + "description": "", + "mode": "nullable", + }, + { + "name": "location_geom", + "type": "geography", + "description": "", + "mode": "nullable", + }, + ], + ) + ) + + global_cases_by_province_transform_csv >> load_global_cases_by_province_to_bq diff --git a/datasets/covid19_cds_eu/global_cases_by_province/pipeline.yaml b/datasets/covid19_cds_eu/global_cases_by_province/pipeline.yaml new file mode 100644 index 000000000..cc242986d --- /dev/null +++ b/datasets/covid19_cds_eu/global_cases_by_province/pipeline.yaml @@ -0,0 +1,171 @@ +# 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: global_cases_by_province + description: "Global cases by province table" + +dag: + airflow_version: 1 + initialize: + dag_id: global_cases_by_province + 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: "global_cases_by_province_transform_csv" + startup_timeout_seconds: 600 + name: "global_cases_by_province" + 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.covid19_cds_eu.container_registry.run_csv_transform_kub }}" + env_vars: + SOURCE_URL: "https://coronadatascraper.com/timeseries.csv" + SOURCE_FILE: "files/data.csv" + TARGET_FILE: "files/data_output.csv" + TARGET_GCS_BUCKET: "{{ var.value.composer_bucket }}" + TARGET_GCS_PATH: "data/covid19_cds_eu/global_cases_by_province/data_output.csv" + PIPELINE_NAME: "global_cases_by_province" + CSV_HEADERS: >- + ["name","level","date","city","county","state","country","population","latitude","longitude","aggregate","tz","cases","deaths","recovered","active","tested","hospitalized","discharged","growth_factor","url","location_geom"] + RENAME_MAPPINGS: >- + {"lat":"latitude","long":"longitude","growthFactor":"growth_factor"} + resources: + request_memory: "2G" + request_cpu: "1" + + - operator: "GoogleCloudStorageToBigQueryOperator" + description: "Task to load CSV data to a BigQuery table" + args: + task_id: "load_global_cases_by_province_to_bq" + bucket: "{{ var.value.composer_bucket }}" + source_objects: ["data/covid19_cds_eu/global_cases_by_province/data_output.csv"] + source_format: "CSV" + destination_project_dataset_table: "covid19_cds_eu.global_cases_by_province" + skip_leading_rows: 1 + allow_quoted_newlines: True + write_disposition: "WRITE_TRUNCATE" + + schema_fields: + - name: "name" + type: "string" + description: "" + mode: "nullable" + - name: "level" + type: "string" + description: "" + mode: "nullable" + - name: "date" + type: "date" + description: "" + mode: "nullable" + - name: "city" + type: "string" + description: "" + mode: "nullable" + - name: "county" + type: "string" + description: "" + mode: "nullable" + - name: "state" + type: "string" + description: "" + mode: "nullable" + - name: "country" + type: "string" + description: "" + mode: "nullable" + - name: "population" + type: "integer" + description: "" + mode: "nullable" + - name: "latitude" + type: "float" + description: "" + mode: "nullable" + - name: "longitude" + type: "float" + description: "" + mode: "nullable" + - name: "aggregate" + type: "string" + description: "" + mode: "nullable" + - name: "tz" + type: "string" + description: "" + mode: "nullable" + - name: "cases" + type: "integer" + description: "" + mode: "nullable" + - name: "deaths" + type: "integer" + description: "" + mode: "nullable" + - name: "recovered" + type: "integer" + description: "" + mode: "nullable" + - name: "active" + type: "integer" + description: "" + mode: "nullable" + - name: "tested" + type: "integer" + description: "" + mode: "nullable" + - name: "hospitalized" + type: "integer" + description: "" + mode: "nullable" + - name: "discharged" + type: "integer" + description: "" + mode: "nullable" + - name: "growth_factor" + type: "string" + description: "" + mode: "nullable" + - name: "url" + type: "string" + description: "" + mode: "nullable" + - name: "location_geom" + type: "geography" + description: "" + mode: "nullable" + + graph_paths: + - "global_cases_by_province_transform_csv >> load_global_cases_by_province_to_bq"