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feat: Onboard COVID19-Italy dataset (#148)
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datasets/covid19_italy/_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 | ||
# limitations under the License. | ||
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# The base image for this build | ||
# FROM gcr.io/google.com/cloudsdktool/cloud-sdk:slim | ||
FROM python:3.8 | ||
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# Allow statements and log messages to appear in Cloud logs | ||
ENV PYTHONUNBUFFERED True | ||
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# Copy the requirements file into the image | ||
COPY requirements.txt ./ | ||
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# Install the packages specified in the requirements file | ||
RUN python3 -m pip install --no-cache-dir -r requirements.txt | ||
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# 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 | ||
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# Copy the specific data processing script/s in the image under /custom/* | ||
COPY ./csv_transform.py . | ||
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# Command to run the data processing script when the container is run | ||
CMD ["python3", "csv_transform.py"] |
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datasets/covid19_italy/_images/run_csv_transform_kub/Pipfile
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[[source]] | ||
url = "https://pypi.org/simple" | ||
verify_ssl = true | ||
name = "pypi" | ||
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[packages] | ||
requests = "*" | ||
vaex = "*" | ||
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[dev-packages] | ||
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[requires] | ||
python_version = "3.9" |
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datasets/covid19_italy/_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. | ||
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import datetime | ||
import json | ||
import logging | ||
import os | ||
import pathlib | ||
import typing | ||
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import pandas as pd | ||
import requests | ||
from google.cloud import storage | ||
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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: | ||
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logging.info( | ||
"Covid-19 Italy process started at " | ||
+ str(datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S")) | ||
) | ||
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logging.info("creating 'files' folder") | ||
pathlib.Path("./files").mkdir(parents=True, exist_ok=True) | ||
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logging.info(f"Downloading file {source_url}") | ||
download_file(source_url, source_file) | ||
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logging.info(f"Opening file {source_file}") | ||
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df = pd.read_csv(str(source_file)) | ||
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logging.info(f"Transformation Process Starting.. {source_file}") | ||
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logging.info(f"Transform: Renaming Headers.. {source_file}") | ||
rename_headers(df, rename_mappings) | ||
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logging.info(f"Transform: Creating Geometry Column.. {pipeline_name}") | ||
if pipeline_name == "data_by_province" or pipeline_name == "data_by_region": | ||
df["location_geom"] = ( | ||
"POINT(" | ||
+ df["longitude"].astype(str).replace("nan", "") | ||
+ " " | ||
+ df["latitude"].astype(str).replace("nan", "") | ||
+ ")" | ||
) | ||
df.location_geom = df.location_geom.replace("POINT( )", "") | ||
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logging.info("Transform: Reordering headers..") | ||
df = df[headers] | ||
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logging.info(f"Transformation Process complete .. {source_file}") | ||
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logging.info(f"Saving to output file.. {target_file}") | ||
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try: | ||
save_to_new_file(df, file_path=str(target_file)) | ||
except Exception as e: | ||
logging.error(f"Error saving output file: {e}.") | ||
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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) | ||
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logging.info( | ||
"Covid-19 Italy process completed at " | ||
+ str(datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S")) | ||
) | ||
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def convert_dt_format(date_str: str, time_str: str) -> None: | ||
return str(datetime.datetime.strptime(date_str, "%m/%d/%Y").date()) + " " + time_str | ||
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def rename_headers(df: pd.DataFrame, rename_mappings: dict) -> None: | ||
df.rename(columns=rename_mappings, inplace=True) | ||
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def save_to_new_file(df: pd.DataFrame, file_path: str) -> None: | ||
df.to_csv(file_path, float_format="%.0f", index=False) | ||
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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}") | ||
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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) | ||
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if __name__ == "__main__": | ||
logging.getLogger().setLevel(logging.INFO) | ||
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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"], | ||
) |
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datasets/covid19_italy/_images/run_csv_transform_kub/requirements.txt
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requests | ||
google-cloud-storage | ||
pandas |
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datasets/covid19_italy/_terraform/covid19_italy_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. | ||
*/ | ||
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resource "google_bigquery_dataset" "covid19_italy" { | ||
dataset_id = "covid19_italy" | ||
project = var.project_id | ||
description = "COVID-19 Italy" | ||
} | ||
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output "bigquery_dataset-covid19_italy-dataset_id" { | ||
value = google_bigquery_dataset.covid19_italy.dataset_id | ||
} |
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datasets/covid19_italy/_terraform/data_by_province_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. | ||
*/ | ||
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resource "google_bigquery_table" "data_by_province" { | ||
project = var.project_id | ||
dataset_id = "covid19_italy" | ||
table_id = "data_by_province" | ||
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description = "COVID-19 Italy Data By Province" | ||
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depends_on = [ | ||
google_bigquery_dataset.covid19_italy | ||
] | ||
} | ||
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output "bigquery_table-data_by_province-table_id" { | ||
value = google_bigquery_table.data_by_province.table_id | ||
} | ||
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output "bigquery_table-data_by_province-id" { | ||
value = google_bigquery_table.data_by_province.id | ||
} |
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datasets/covid19_italy/_terraform/data_by_region_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. | ||
*/ | ||
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resource "google_bigquery_table" "data_by_region" { | ||
project = var.project_id | ||
dataset_id = "covid19_italy" | ||
table_id = "data_by_region" | ||
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description = "COVID-19 Italy Data By Region" | ||
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depends_on = [ | ||
google_bigquery_dataset.covid19_italy | ||
] | ||
} | ||
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output "bigquery_table-data_by_region-table_id" { | ||
value = google_bigquery_table.data_by_region.table_id | ||
} | ||
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output "bigquery_table-data_by_region-id" { | ||
value = google_bigquery_table.data_by_region.id | ||
} |
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datasets/covid19_italy/_terraform/national_trends_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. | ||
*/ | ||
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resource "google_bigquery_table" "national_trends" { | ||
project = var.project_id | ||
dataset_id = "covid19_italy" | ||
table_id = "national_trends" | ||
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description = "COVID-19 Italy National Trends" | ||
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depends_on = [ | ||
google_bigquery_dataset.covid19_italy | ||
] | ||
} | ||
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output "bigquery_table-national_trends-table_id" { | ||
value = google_bigquery_table.national_trends.table_id | ||
} | ||
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output "bigquery_table-national_trends-id" { | ||
value = google_bigquery_table.national_trends.id | ||
} |
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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. | ||
*/ | ||
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provider "google" { | ||
project = var.project_id | ||
impersonate_service_account = var.impersonating_acct | ||
region = var.region | ||
} | ||
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data "google_client_openid_userinfo" "me" {} | ||
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output "impersonating-account" { | ||
value = data.google_client_openid_userinfo.me.email | ||
} |
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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. | ||
*/ | ||
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variable "project_id" {} | ||
variable "bucket_name_prefix" {} | ||
variable "impersonating_acct" {} | ||
variable "region" {} | ||
variable "env" {} | ||
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