Flyte Pipeline with Feast

This workflow makes use of the feature engineering tasks defined in the other file. We’ll build an end-to-end Flyte pipeline utilizing “Feast”. Here is the step-by-step process:

  • Fetch the SQLite3 data as a Pandas DataFrame

  • Perform mean-median-imputation

  • Build a feature store

  • Store the updated features in an offline store

  • Retrieve the features from an offline store

  • Perform univariate-feature-selection

  • Train a Naive Bayes model

  • Load features into an online store

  • Fetch one feature vector for inference

  • Generate prediction

import logging
import typing

Let’s import the libraries.

from datetime import datetime, timedelta
import random

import boto3
import joblib
import pandas as pd
from feast import Entity, Feature, FeatureStore, FeatureView, FileSource, ValueType
from flytekit import task, workflow, TaskMetadata
from flytekit.configuration import aws
from flytekit.extras.sqlite3.task import SQLite3Config, SQLite3Task
from flytekit.types.file import JoblibSerializedFile
from flytekit.types.schema import FlyteSchema
from sklearn.model_selection import train_test_split
from sklearn.naive_bayes import GaussianNB

from feast_dataobjects import FeatureStore, FeatureStoreConfig
from feature_eng_tasks import mean_median_imputer, univariate_selection

logger = logging.getLogger(__file__)

We define the necessary data holders.

# TODO: find a better way to define these features.
FEAST_FEATURES = [
    "horse_colic_stats:rectal temperature",
    "horse_colic_stats:total protein",
    "horse_colic_stats:peripheral pulse",
    "horse_colic_stats:surgical lesion",
    "horse_colic_stats:abdominal distension",
    "horse_colic_stats:nasogastric tube",
    "horse_colic_stats:outcome",
    "horse_colic_stats:packed cell volume",
    "horse_colic_stats:nasogastric reflux PH",
]
DATABASE_URI = "https://cdn.discordapp.com/attachments/545481172399030272/861575373783040030/horse_colic.db.zip"
DATA_CLASS = "surgical lesion"

This task exists just for the sandbox case, as feast needs an explicit S3 bucket and path. We will create it using an S3 client. Sadly this makes the workflow not as portable.

@task(cache=True, cache_version="1.0")
def create_bucket(bucket_name: str) -> str:
    client = boto3.client(
        's3',
        aws_access_key_id=aws.S3_ACCESS_KEY_ID.get(),
        aws_secret_access_key=aws.S3_SECRET_ACCESS_KEY.get(),
        use_ssl=False,
        endpoint_url=aws.S3_ENDPOINT.get(),
    )

    try:
        client.create_bucket(Bucket=bucket_name)
    except client.exceptions.BucketAlreadyOwnedByYou:
        logger.info(f"Bucket {bucket_name} has already been created by you.")
        pass
    return bucket_name

This is the first task and represents the data source. This can be any task, that fetches data, generates, modifies data ready for Feature ingestion. These can be arbitrary feature engineering tasks like data imputation, univariate selection etc as well.

load_horse_colic_sql = SQLite3Task(
    name="sqlite3.load_horse_colic",
    query_template="select * from data",
    output_schema_type=FlyteSchema,
    task_config=SQLite3Config(
        uri=DATABASE_URI,
        compressed=True,
    ),
    metadata=TaskMetadata(
        cache=True,
        cache_version="1.0",
    ),
)

We define two tasks, namely store_offline and load_historical_features to store and retrieve the historial features.

@task(cache=True, cache_version="1.0")
def store_offline(feature_store: FeatureStore, dataframe: FlyteSchema) -> FeatureStore:
    horse_colic_entity = Entity(name="Hospital Number", value_type=ValueType.STRING)

    horse_colic_feature_view = FeatureView(
        name="horse_colic_stats",
        entities=["Hospital Number"],
        features=[
            Feature(name="rectal temperature", dtype=ValueType.FLOAT),
            Feature(name="total protein", dtype=ValueType.FLOAT),
            Feature(name="peripheral pulse", dtype=ValueType.FLOAT),
            Feature(name="surgical lesion", dtype=ValueType.STRING),
            Feature(name="abdominal distension", dtype=ValueType.FLOAT),
            Feature(name="nasogastric tube", dtype=ValueType.STRING),
            Feature(name="outcome", dtype=ValueType.STRING),
            Feature(name="packed cell volume", dtype=ValueType.FLOAT),
            Feature(name="nasogastric reflux PH", dtype=ValueType.FLOAT),
        ],
        batch_source=FileSource(
            path=str(dataframe.remote_path),
            event_timestamp_column="timestamp",
        ),
        ttl=timedelta(days=1),
    )

    # Ingest the data into feast
    feature_store.apply([horse_colic_entity, horse_colic_feature_view])

    return feature_store


@task(cache=True, cache_version="1.0")
def load_historical_features(feature_store: FeatureStore) -> FlyteSchema:
    entity_df = pd.DataFrame.from_dict(
        {
            "Hospital Number": [
                "530101",
                "5290409",
                "5291329",
                "530051",
                "529518",
                "530101",
                "529340",
                "5290409",
                "530034",
            ],
            "event_timestamp": [
                datetime(2021, 6, 25, 16, 36, 27),
                datetime(2021, 6, 25, 16, 36, 27),
                datetime(2021, 6, 25, 16, 36, 27),
                datetime(2021, 6, 25, 16, 36, 27),
                datetime(2021, 6, 25, 16, 36, 27),
                datetime(2021, 7, 5, 11, 36, 1),
                datetime(2021, 6, 25, 16, 36, 27),
                datetime(2021, 7, 5, 11, 50, 40),
                datetime(2021, 6, 25, 16, 36, 27),
            ],
        }
    )

    return feature_store.get_historical_features(entity_df=entity_df, features=FEAST_FEATURES)  # noqa

Next, we train a naive bayes model using the data from the feature store.

@task(cache=True, cache_version="1.0")
def train_model(dataset: pd.DataFrame, data_class: str) -> JoblibSerializedFile:
    x_train, _, y_train, _ = train_test_split(
        dataset[dataset.columns[~dataset.columns.isin([data_class])]],
        dataset[data_class],
        test_size=0.33,
        random_state=42,
    )
    model = GaussianNB()
    model.fit(x_train, y_train)
    model.feature_names = list(x_train.columns.values)
    fname = "/tmp/model.joblib.dat"
    joblib.dump(model, fname)
    return fname

To perform inferencing, we define two tasks: store_online and retrieve_online.

Decoding the Feast Nomenclature

materialize()

Materialize data from the offline store into the online store.

get_online_features()

Retrieves the latest online feature data.

Note

One key difference between an online and offline store is that only the latest feature values are stored per entity key in an online store, unlike an offline store where all feature values are stored. Our dataset has two such entries with the same Hospital Number but different time stamps. Only data point with the latest timestamp will be stored in the online store.

@task(cache=True, cache_version="1.0")
def store_online(feature_store: FeatureStore) -> FeatureStore:
    feature_store.materialize(
        start_date=datetime.utcnow() - timedelta(days=250),
        end_date=datetime.utcnow() - timedelta(minutes=10),
    )
    return feature_store

We define a task to test our model using the inference point fetched earlier.

@task(cache=True, cache_version="1.0")
def predict(model_ser: JoblibSerializedFile, features: dict) -> typing.List[str]:
    # Load model
    model = joblib.load(model_ser)
    f_names = model.feature_names

    test_list = []
    for each_name in f_names:
        test_list.append(features[each_name][0])
    prediction = model.predict([test_list])
    return prediction

Next, we need to convert timestamp column in the underlying dataframe, otherwise its type is written as string.

@task(cache=True, cache_version="1.0")
def convert_timestamp_column(
        dataframe: FlyteSchema, timestamp_column: str
) -> FlyteSchema:
    df = dataframe.open().all()
    df[timestamp_column] = pd.to_datetime(df[timestamp_column])
    return df

The build_feature_store task is a medium to access Feast methods by building a feature store.

@task(cache=True, cache_version="1.0")
def build_feature_store(s3_bucket: str, registry_path: str, online_store_path: str) -> FeatureStore:
    feature_store_config = FeatureStoreConfig(project="horsecolic", s3_bucket=s3_bucket, registry_path=registry_path,
                                              online_store_path=online_store_path)
    return FeatureStore(config=feature_store_config)

A sample method that randomly selects one datapoint from the input dataset to run predictions on

Note

Note this is not ideal and can be just embedded in the predict method. But, for introspection and demo, we are splitting it up

@task
def retrieve_online(feature_store: FeatureStore, dataset: pd.DataFrame) -> dict:
    inference_data = random.choice(dataset["Hospital Number"])
    logger.info(f"Hospital Number chosen for inference is: {inference_data}")
    entity_rows = [{"Hospital Number": inference_data}]

    return feature_store.get_online_features(FEAST_FEATURES, entity_rows)

the following workflow is a separate workflow that can be run indepedently to create features and store them offline This can be run periodically or triggered independently

@workflow
def featurize(feature_store: FeatureStore, imputation_method: str = "mean") -> (FlyteSchema, FeatureStore):
    # Load parquet file from sqlite task
    df = load_horse_colic_sql()

    # Perform mean median imputation
    df = mean_median_imputer(dataframe=df, imputation_method=imputation_method)

    # Convert timestamp column from string to datetime.
    converted_df = convert_timestamp_column(
        dataframe=df, timestamp_column="timestamp"
    )

    return df, store_offline(feature_store=feature_store, dataframe=converted_df)

The following workflow can be run independently to train a model, given the Dataframe, either from Feature store or locally

@workflow
def trainer(df: FlyteSchema, num_features_univariate: int = 7) -> JoblibSerializedFile:
    # Perform univariate feature selection
    selected_features = univariate_selection(
        dataframe=df,  # noqa
        num_features=num_features_univariate,
        data_class=DATA_CLASS,
    )

    # Train the Naive Bayes model
    trained_model = train_model(
        dataset=selected_features,
        data_class=DATA_CLASS,
    )

    return trained_model

Finally, we define a workflow that streamlines the whole pipeline building and feature serving process. To show how to compose and end to end workflow that includes featurization, training and example predictions, we construct the following workflow, composing other workflows

@workflow
def feast_workflow(
        imputation_method: str = "mean",
        num_features_univariate: int = 7,
        s3_bucket: str = "feast-integration",
        registry_path: str = "registry.db",
        online_store_path: str = "online.db",
) -> (FeatureStore, JoblibSerializedFile, typing.List[str]):
    # Create bucket if it does not already exist
    # & Build feature store
    feature_store = build_feature_store(s3_bucket=create_bucket(bucket_name=s3_bucket), registry_path=registry_path,
                                        online_store_path=online_store_path)
    # Feature engineering
    df, loaded_feature_store = featurize(feature_store=feature_store, imputation_method=imputation_method)

    # Demonstrate how to load features from offline store
    historical_features = load_historical_features(feature_store=loaded_feature_store)

    model = trainer(df=historical_features, num_features_univariate=num_features_univariate)

    online_feature_store = store_online(feature_store=loaded_feature_store)

    # Use a feature retrieved from the online store for inference
    predictions = predict(model_ser=model, features=retrieve_online(feature_store=online_feature_store, dataset=df))  # noqa

    return online_feature_store, model, predictions


if __name__ == "__main__":
    print(f"{feast_workflow()}")

You should see prediction against the test input as the workflow output.

Total running time of the script: ( 0 minutes 0.000 seconds)

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