diff --git a/datasets/ml_datasets/infra/iris_pipeline.tf b/datasets/ml_datasets/infra/iris_pipeline.tf new file mode 100644 index 000000000..a94ebc483 --- /dev/null +++ b/datasets/ml_datasets/infra/iris_pipeline.tf @@ -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 + * limitations under the License. + */ + + +resource "google_bigquery_table" "ml_datasets_iris" { + project = var.project_id + dataset_id = "ml_datasets" + table_id = "iris" + description = "iris table" + depends_on = [ + google_bigquery_dataset.ml_datasets + ] +} + +output "bigquery_table-ml_datasets_iris-table_id" { + value = google_bigquery_table.ml_datasets_iris.table_id +} + +output "bigquery_table-ml_datasets_iris-id" { + value = google_bigquery_table.ml_datasets_iris.id +} diff --git a/datasets/ml_datasets/infra/ml_datasets_dataset.tf b/datasets/ml_datasets/infra/ml_datasets_dataset.tf index a25fd55f9..511083702 100644 --- a/datasets/ml_datasets/infra/ml_datasets_dataset.tf +++ b/datasets/ml_datasets/infra/ml_datasets_dataset.tf @@ -33,3 +33,19 @@ resource "google_bigquery_dataset" "ml_datasets_uscentral1" { output "bigquery_dataset-ml_datasets_uscentral1-dataset_id" { value = google_bigquery_dataset.ml_datasets_uscentral1.dataset_id } + +resource "google_storage_bucket" "ml-datasets" { + name = "${var.bucket_name_prefix}-ml-datasets" + force_destroy = true + location = "US" + uniform_bucket_level_access = true + lifecycle { + ignore_changes = [ + logging, + ] + } +} + +output "storage_bucket-ml-datasets-name" { + value = google_storage_bucket.ml-datasets.name +} diff --git a/datasets/ml_datasets/infra/penguins_pipeline.tf b/datasets/ml_datasets/infra/penguins_pipeline.tf index 15cdfe137..914e318c2 100644 --- a/datasets/ml_datasets/infra/penguins_pipeline.tf +++ b/datasets/ml_datasets/infra/penguins_pipeline.tf @@ -19,12 +19,6 @@ resource "google_bigquery_table" "ml_datasets_penguins" { project = var.project_id dataset_id = "ml_datasets" table_id = "penguins" - - - - - - depends_on = [ google_bigquery_dataset.ml_datasets ] @@ -42,12 +36,6 @@ resource "google_bigquery_table" "ml_datasets_uscentral1_penguins" { project = var.project_id dataset_id = "ml_datasets_uscentral1" table_id = "penguins" - - - - - - depends_on = [ google_bigquery_dataset.ml_datasets_uscentral1 ] diff --git a/datasets/ml_datasets/pipelines/_images/run_csv_transform_kub/Dockerfile b/datasets/ml_datasets/pipelines/_images/run_csv_transform_kub/Dockerfile new file mode 100644 index 000000000..7265a1b71 --- /dev/null +++ b/datasets/ml_datasets/pipelines/_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/ml_datasets/pipelines/_images/run_csv_transform_kub/csv_transform.py b/datasets/ml_datasets/pipelines/_images/run_csv_transform_kub/csv_transform.py new file mode 100644 index 000000000..fbae88eb6 --- /dev/null +++ b/datasets/ml_datasets/pipelines/_images/run_csv_transform_kub/csv_transform.py @@ -0,0 +1,119 @@ +# 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( + f"ML datasets {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(str(source_file)) + + logging.info(f"Transforming {source_file}... ") + + logging.info("Transform: Rename columns... ") + rename_headers(df, rename_mappings) + + logging.info("Transform: Replacing values... ") + df = df.replace(to_replace={"species": {"Iris-": ""}}) + + 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"ML datasets {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 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/ml_datasets/pipelines/_images/run_csv_transform_kub/requirements.txt b/datasets/ml_datasets/pipelines/_images/run_csv_transform_kub/requirements.txt new file mode 100644 index 000000000..3e4d10c7e --- /dev/null +++ b/datasets/ml_datasets/pipelines/_images/run_csv_transform_kub/requirements.txt @@ -0,0 +1,3 @@ +google-cloud-storage +pandas +requests diff --git a/datasets/ml_datasets/pipelines/dataset.yaml b/datasets/ml_datasets/pipelines/dataset.yaml index f520316e4..1209f32cd 100644 --- a/datasets/ml_datasets/pipelines/dataset.yaml +++ b/datasets/ml_datasets/pipelines/dataset.yaml @@ -68,3 +68,7 @@ resources: dataset_id: ml_datasets_uscentral1 location: us-central1 description: ~ + - type: storage_bucket + name: ml-datasets + uniform_bucket_level_access: True + location: US diff --git a/datasets/ml_datasets/pipelines/iris/iris_dag.py b/datasets/ml_datasets/pipelines/iris/iris_dag.py new file mode 100644 index 000000000..2fe7efd16 --- /dev/null +++ b/datasets/ml_datasets/pipelines/iris/iris_dag.py @@ -0,0 +1,105 @@ +# 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="ml_datasets.iris", + default_args=default_args, + max_active_runs=1, + schedule_interval="@daily", + catchup=False, + default_view="graph", +) as dag: + + # Run CSV transform within kubernetes pod + iris_transform_csv = kubernetes_pod_operator.KubernetesPodOperator( + task_id="iris_transform_csv", + startup_timeout_seconds=600, + name="iris", + namespace="composer", + service_account_name="datasets", + image_pull_policy="Always", + image="{{ var.json.ml_datasets.container_registry.run_csv_transform_kub }}", + env_vars={ + "SOURCE_URL": "https://www.openml.org/data/get_csv/61/dataset_61_iris.csv", + "SOURCE_FILE": "files/data.csv", + "TARGET_FILE": "files/data_output.csv", + "TARGET_GCS_BUCKET": "{{ var.value.composer_bucket }}", + "TARGET_GCS_PATH": "data/ml_datasets/iris/data_output.csv", + "PIPELINE_NAME": "iris", + "CSV_HEADERS": '["sepal_length","sepal_width","petal_length","petal_width","species"]', + "RENAME_MAPPINGS": '{"sepallength": "sepal_length","sepalwidth": "sepal_width","petallength": "petal_length","petalwidth": "petal_width","class": "species"}', + }, + resources={ + "request_memory": "2G", + "request_cpu": "1", + "request_ephemeral_storage": "5G", + }, + ) + + # Task to load CSV data to a BigQuery table + load_iris_to_bq = gcs_to_bq.GoogleCloudStorageToBigQueryOperator( + task_id="load_iris_to_bq", + bucket="{{ var.value.composer_bucket }}", + source_objects=["data/ml_datasets/iris/data_output.csv"], + source_format="CSV", + destination_project_dataset_table="ml_datasets.iris", + skip_leading_rows=1, + allow_quoted_newlines=True, + write_disposition="WRITE_TRUNCATE", + schema_fields=[ + { + "name": "sepal_length", + "type": "float", + "description": "", + "mode": "nullable", + }, + { + "name": "sepal_width", + "type": "float", + "description": "", + "mode": "nullable", + }, + { + "name": "petal_length", + "type": "float", + "description": "", + "mode": "nullable", + }, + { + "name": "petal_width", + "type": "float", + "description": "", + "mode": "nullable", + }, + { + "name": "species", + "type": "string", + "description": "", + "mode": "nullable", + }, + ], + ) + + iris_transform_csv >> load_iris_to_bq diff --git a/datasets/ml_datasets/pipelines/iris/pipeline.yaml b/datasets/ml_datasets/pipelines/iris/pipeline.yaml new file mode 100644 index 000000000..923f2d6f7 --- /dev/null +++ b/datasets/ml_datasets/pipelines/iris/pipeline.yaml @@ -0,0 +1,96 @@ +# 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: iris + description: "iris table" + +dag: + airflow_version: 1 + initialize: + dag_id: iris + 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: "iris_transform_csv" + startup_timeout_seconds: 600 + name: "iris" + namespace: "composer" + service_account_name: "datasets" + image_pull_policy: "Always" + image: "{{ var.json.ml_datasets.container_registry.run_csv_transform_kub }}" + env_vars: + SOURCE_URL: "https://www.openml.org/data/get_csv/61/dataset_61_iris.csv" + SOURCE_FILE: "files/data.csv" + TARGET_FILE: "files/data_output.csv" + TARGET_GCS_BUCKET: "{{ var.value.composer_bucket }}" + TARGET_GCS_PATH: "data/ml_datasets/iris/data_output.csv" + PIPELINE_NAME: "iris" + CSV_HEADERS: >- + ["sepal_length","sepal_width","petal_length","petal_width","species"] + RENAME_MAPPINGS: >- + {"sepallength": "sepal_length","sepalwidth": "sepal_width","petallength": "petal_length","petalwidth": "petal_width","class": "species"} + resources: + request_memory: "2G" + request_cpu: "1" + request_ephemeral_storage: "5G" + + - operator: "GoogleCloudStorageToBigQueryOperator" + description: "Task to load CSV data to a BigQuery table" + args: + task_id: "load_iris_to_bq" + bucket: "{{ var.value.composer_bucket }}" + source_objects: ["data/ml_datasets/iris/data_output.csv"] + source_format: "CSV" + destination_project_dataset_table: "ml_datasets.iris" + skip_leading_rows: 1 + allow_quoted_newlines: True + write_disposition: "WRITE_TRUNCATE" + + schema_fields: + - name: "sepal_length" + type: "float" + description: "" + mode: "nullable" + - name: "sepal_width" + type: "float" + description: "" + mode: "nullable" + - name: "petal_length" + type: "float" + description: "" + mode: "nullable" + - name: "petal_width" + type: "float" + description: "" + mode: "nullable" + - name: "species" + type: "string" + description: "" + mode: "nullable" + + graph_paths: + - "iris_transform_csv >> load_iris_to_bq"