Define a Pipeline

To download the dataset

1. Download the dataset into your account's default Amazon S3 bucket.

   !mkdir -p data
   local_path = "data/abalone-dataset.csv"
   
   s3 = boto3.resource("s3")
   s3.Bucket(f"sagemaker-servicecatalog-seedcode-{region}").download_file(
       "dataset/abalone-dataset.csv",
       local_path
   )
   
   base_uri = f"s3://{default_bucket}/abalone"
   input_data_uri = sagemaker.s3.S3Uploader.upload(
       local_path=local_path, 
       desired_s3_uri=base_uri,
   )
   print(input_data_uri)

2. Download a second dataset for batch transformation after your model is created.

   local_path = "data/abalone-dataset-batch.csv"
   
   s3 = boto3.resource("s3")
   s3.Bucket(f"sagemaker-servicecatalog-seedcode-{region}").download_file(
       "dataset/abalone-dataset-batch",
       local_path
   )
   
   base_uri = f"s3://{default_bucket}/abalone"
   batch_data_uri = sagemaker.s3.S3Uploader.upload(
       local_path=local_path, 
       desired_s3_uri=base_uri,
   )
   print(batch_data_uri)

To create a processing step

1. Create a directory for the processing script.

   !mkdir -p abalone

2. Create a file in the /abalone directory named preprocessing.py with the following content. This preprocessing script is passed in to the processing step for execution on the input data. The training step then uses the preprocessed training features and labels to train a model, and the evaluation step uses the trained model and preprocessed test features and labels to evaluate the model. The script uses scikit-learn to do the following:

   • Fill in missing sex categorical data and encode it so it's suitable for training.

   • Scale and normalize all numerical fields except for rings and sex.

   • Split the data into training, test, and validation datasets.

   %%writefile abalone/preprocessing.py
   import argparse
   import os
   import requests
   import tempfile
   import numpy as np
   import pandas as pd
   
   
   from sklearn.compose import ColumnTransformer
   from sklearn.impute import SimpleImputer
   from sklearn.pipeline import Pipeline
   from sklearn.preprocessing import StandardScaler, OneHotEncoder
   
   
   # Because this is a headerless CSV file, specify the column names here.
   feature_columns_names = [
       "sex",
       "length",
       "diameter",
       "height",
       "whole_weight",
       "shucked_weight",
       "viscera_weight",
       "shell_weight",
   ]
   label_column = "rings"
   
   feature_columns_dtype = {
       "sex": str,
       "length": np.float64,
       "diameter": np.float64,
       "height": np.float64,
       "whole_weight": np.float64,
       "shucked_weight": np.float64,
       "viscera_weight": np.float64,
       "shell_weight": np.float64
   }
   label_column_dtype = {"rings": np.float64}
   
   
   def merge_two_dicts(x, y):
       z = x.copy()
       z.update(y)
       return z
   
   
   if __name__ == "__main__":
       base_dir = "/opt/ml/processing"
   
       df = pd.read_csv(
           f"{base_dir}/input/abalone-dataset.csv",
           header=None, 
           names=feature_columns_names + [label_column],
           dtype=merge_two_dicts(feature_columns_dtype, label_column_dtype)
       )
       numeric_features = list(feature_columns_names)
       numeric_features.remove("sex")
       numeric_transformer = Pipeline(
           steps=[
               ("imputer", SimpleImputer(strategy="median")),
               ("scaler", StandardScaler())
           ]
       )
   
       categorical_features = ["sex"]
       categorical_transformer = Pipeline(
           steps=[
               ("imputer", SimpleImputer(strategy="constant", fill_value="missing")),
               ("onehot", OneHotEncoder(handle_unknown="ignore"))
           ]
       )
   
       preprocess = ColumnTransformer(
           transformers=[
               ("num", numeric_transformer, numeric_features),
               ("cat", categorical_transformer, categorical_features)
           ]
       )
       
       y = df.pop("rings")
       X_pre = preprocess.fit_transform(df)
       y_pre = y.to_numpy().reshape(len(y), 1)
       
       X = np.concatenate((y_pre, X_pre), axis=1)
       
       np.random.shuffle(X)
       train, validation, test = np.split(X, [int(.7*len(X)), int(.85*len(X))])
   
       
       pd.DataFrame(train).to_csv(f"{base_dir}/train/train.csv", header=False, index=False)
       pd.DataFrame(validation).to_csv(f"{base_dir}/validation/validation.csv", header=False, index=False)
       pd.DataFrame(test).to_csv(f"{base_dir}/test/test.csv", header=False, index=False)

3. Create an instance of an SKLearnProcessor to pass in to the processing step.

   from sagemaker.sklearn.processing import SKLearnProcessor
   
   
   framework_version = "0.23-1"
   
   sklearn_processor = SKLearnProcessor(
       framework_version=framework_version,
       instance_type="ml.m5.xlarge",
       instance_count=processing_instance_count,
       base_job_name="sklearn-abalone-process",
       sagemaker_session=pipeline_session,
       role=role,
   )

4. Create a processing step. This step takes in the SKLearnProcessor, the input and output channels, and the preprocessing.py script that you created. This is very similar to a processor instance's run method in the SageMaker Python SDK. The input_data parameter passed into ProcessingStep is the input data of the step itself. This input data is used by the processor instance when it runs.

   Note the  "train, "validation, and "test" named channels specified in the output configuration for the processing job. Step Properties such as these can be used in subsequent steps and resolve to their runtime values at execution.

   from sagemaker.processing import ProcessingInput, ProcessingOutput
   from sagemaker.workflow.steps import ProcessingStep
      
   
   processor_args = sklearn_processor.run(
       inputs=[
         ProcessingInput(source=input_data, destination="/opt/ml/processing/input"),  
       ],
       outputs=[
           ProcessingOutput(output_name="train", source="/opt/ml/processing/train"),
           ProcessingOutput(output_name="validation", source="/opt/ml/processing/validation"),
           ProcessingOutput(output_name="test", source="/opt/ml/processing/test")
       ],
       code="abalone/preprocessing.py",
   ) 
   
   step_process = ProcessingStep(
       name="AbaloneProcess",
       step_args=processor_args
   )

To define a training step

1. Specify the model path where you want to save the models from training.

   model_path = f"s3://{default_bucket}/AbaloneTrain"

2. Configure an estimator for the XGBoost algorithm and the input dataset. The training instance type is passed into the estimator. A typical training script loads data from the input channels, configures training with hyperparameters, trains a model, and saves a model to model_dir so that it can be hosted later. SageMaker uploads the model to Amazon S3 in the form of a model.tar.gz at the end of the training job.

   from sagemaker.estimator import Estimator
   
   
   image_uri = sagemaker.image_uris.retrieve(
       framework="xgboost",
       region=region,
       version="1.0-1",
       py_version="py3",
       instance_type="ml.m5.xlarge"
   )
   xgb_train = Estimator(
       image_uri=image_uri,
       instance_type="ml.m5.xlarge",
       instance_count=1,
       output_path=model_path,
       sagemaker_session=pipeline_session,
       role=role,
   )
   xgb_train.set_hyperparameters(
       objective="reg:linear",
       num_round=50,
       max_depth=5,
       eta=0.2,
       gamma=4,
       min_child_weight=6,
       subsample=0.7,
       silent=0
   )

3. Create a TrainingStep using the estimator instance and properties of the ProcessingStep. In particular, pass in the S3Uri of the "train" and "validation" output channel to the TrainingStep. 

   from sagemaker.inputs import TrainingInput
   from sagemaker.workflow.steps import TrainingStep
   
   
   train_args = xgb_train.fit(
       inputs={
           "train": TrainingInput(
               s3_data=step_process.properties.ProcessingOutputConfig.Outputs[
                   "train"
               ].S3Output.S3Uri,
               content_type="text/csv"
           ),
           "validation": TrainingInput(
               s3_data=step_process.properties.ProcessingOutputConfig.Outputs[
                   "validation"
               ].S3Output.S3Uri,
               content_type="text/csv"
           )
       },
   )
   
   step_train = TrainingStep(
       name="AbaloneTrain",
       step_args = train_args
   )

To define a processing step for model evaluation

1. Create a file in the /abalone directory named evaluation.py. This script is used in a processing step to perform model evaluation. It takes a trained model and the test dataset as input, then produces a JSON file containing classification evaluation metrics.

   %%writefile abalone/evaluation.py
   import json
   import pathlib
   import pickle
   import tarfile
   import joblib
   import numpy as np
   import pandas as pd
   import xgboost
   
   
   from sklearn.metrics import mean_squared_error
   
   
   if __name__ == "__main__":
       model_path = f"/opt/ml/processing/model/model.tar.gz"
       with tarfile.open(model_path) as tar:
           tar.extractall(path=".")
       
       model = pickle.load(open("xgboost-model", "rb"))
   
       test_path = "/opt/ml/processing/test/test.csv"
       df = pd.read_csv(test_path, header=None)
       
       y_test = df.iloc[:, 0].to_numpy()
       df.drop(df.columns[0], axis=1, inplace=True)
       
       X_test = xgboost.DMatrix(df.values)
       
       predictions = model.predict(X_test)
   
       mse = mean_squared_error(y_test, predictions)
       std = np.std(y_test - predictions)
       report_dict = {
           "regression_metrics": {
               "mse": {
                   "value": mse,
                   "standard_deviation": std
               },
           },
       }
   
       output_dir = "/opt/ml/processing/evaluation"
       pathlib.Path(output_dir).mkdir(parents=True, exist_ok=True)
       
       evaluation_path = f"{output_dir}/evaluation.json"
       with open(evaluation_path, "w") as f:
           f.write(json.dumps(report_dict))

2. Create an instance of a ScriptProcessor that is used to create a ProcessingStep.

   from sagemaker.processing import ScriptProcessor
   
   
   script_eval = ScriptProcessor(
       image_uri=image_uri,
       command=["python3"],
       instance_type="ml.m5.xlarge",
       instance_count=1,
       base_job_name="script-abalone-eval",
       sagemaker_session=pipeline_session,
       role=role,
   )

3. Create a ProcessingStep using the processor instance, the input and output channels, and the  evaluation.py script. In particular, pass in the S3ModelArtifacts property from the step_train training step, as well as the S3Uri of the "test" output channel of the step_process processing step. This is very similar to a processor instance's run method in the SageMaker Python SDK. 

   from sagemaker.workflow.properties import PropertyFile
   
   
   evaluation_report = PropertyFile(
       name="EvaluationReport",
       output_name="evaluation",
       path="evaluation.json"
   )
   
   eval_args = script_eval.run(
           inputs=[
           ProcessingInput(
               source=step_train.properties.ModelArtifacts.S3ModelArtifacts,
               destination="/opt/ml/processing/model"
           ),
           ProcessingInput(
               source=step_process.properties.ProcessingOutputConfig.Outputs[
                   "test"
               ].S3Output.S3Uri,
               destination="/opt/ml/processing/test"
           )
       ],
       outputs=[
           ProcessingOutput(output_name="evaluation", source="/opt/ml/processing/evaluation"),
       ],
       code="abalone/evaluation.py",
   )
   
   step_eval = ProcessingStep(
       name="AbaloneEval",
       step_args=eval_args,
       property_files=[evaluation_report],
   )

To define a CreateModelStep for batch transformation

1. Create a SageMaker model. Pass in the S3ModelArtifacts property from the step_train training step.

   from sagemaker.model import Model
   
   
   model = Model(
       image_uri=image_uri,
       model_data=step_train.properties.ModelArtifacts.S3ModelArtifacts,
       sagemaker_session=pipeline_session,
       role=role,
   )

2. Define the model input for your SageMaker model.

   from sagemaker.inputs import CreateModelInput
   
   
   inputs = CreateModelInput(
       instance_type="ml.m5.large",
       accelerator_type="ml.eia1.medium",
   )

3. Create your CreateModelStep using the CreateModelInput and SageMaker model instance you defined.

   from sagemaker.workflow.steps import CreateModelStep
   
   
   step_create_model = CreateModelStep(
       name="AbaloneCreateModel",
       model=model,
       inputs=inputs,
   )

To define a TransformStep to perform batch transformation

1. Create a transformer instance with the appropriate compute instance type, instance count, and desired output Amazon S3 bucket URI. Pass in the ModelName property from the step_create_model CreateModel step.

   from sagemaker.transformer import Transformer
   
   
   transformer = Transformer(
       model_name=step_create_model.properties.ModelName,
       instance_type="ml.m5.xlarge",
       instance_count=1,
       output_path=f"s3://{default_bucket}/AbaloneTransform"
   )

2. Create a TransformStep using the transformer instance you defined and the batch_data pipeline parameter.

   from sagemaker.inputs import TransformInput
   from sagemaker.workflow.steps import TransformStep
   
   
   step_transform = TransformStep(
       name="AbaloneTransform",
       transformer=transformer,
       inputs=TransformInput(data=batch_data)
   )

To define a RegisterModel step to create a model package

• Construct a RegisterModel step using the estimator instance you used for the training step . Pass in the S3ModelArtifacts property from the step_train training step and specify a ModelPackageGroup. SageMaker Pipelines creates this ModelPackageGroup for you.

  from sagemaker.model_metrics import MetricsSource, ModelMetrics 
  from sagemaker.workflow.step_collections import RegisterModel
  
  
  model_metrics = ModelMetrics(
      model_statistics=MetricsSource(
          s3_uri="{}/evaluation.json".format(
              step_eval.arguments["ProcessingOutputConfig"]["Outputs"][0]["S3Output"]["S3Uri"]
          ),
          content_type="application/json"
      )
  )
  step_register = RegisterModel(
      name="AbaloneRegisterModel",
      estimator=xgb_train,
      model_data=step_train.properties.ModelArtifacts.S3ModelArtifacts,
      content_types=["text/csv"],
      response_types=["text/csv"],
      inference_instances=["ml.t2.medium", "ml.m5.xlarge"],
      transform_instances=["ml.m5.xlarge"],
      model_package_group_name=model_package_group_name,
      approval_status=model_approval_status,
      model_metrics=model_metrics
  )

To define a condition step to verify model accuracy

1. Define a ConditionLessThanOrEqualTo condition using the accuracy value found in the output of the model evaluation processing step, step_eval. Get this output using the property file you indexed in the processing step and the respective JSONPath of the mean squared error value, "mse".

   from sagemaker.workflow.conditions import ConditionLessThanOrEqualTo
   from sagemaker.workflow.condition_step import ConditionStep
   from sagemaker.workflow.functions import JsonGet
   
   
   cond_lte = ConditionLessThanOrEqualTo(
       left=JsonGet(
           step_name=step_eval.name,
           property_file=evaluation_report,
           json_path="regression_metrics.mse.value"
       ),
       right=6.0
   )

2. Construct a ConditionStep. Pass the ConditionEquals condition in, then set the model package registration and batch transformation steps as the next steps if the condition passes.

   step_cond = ConditionStep(
       name="AbaloneMSECond",
       conditions=[cond_lte],
       if_steps=[step_register, step_create_model, step_transform],
       else_steps=[], 
   )

To create a pipeline

1. Define the following for your pipeline: name, parameters, and steps. Names must be unique within an (account, region) pair.

   Note

   A step can only appear once in either the pipeline's step list or the if/else step lists of the condition step. It cannot appear in both.

   from sagemaker.workflow.pipeline import Pipeline
   
   
   pipeline_name = f"AbalonePipeline"
   pipeline = Pipeline(
       name=pipeline_name,
       parameters=[
           processing_instance_count,
           model_approval_status,
           input_data,
           batch_data,
       ],
       steps=[step_process, step_train, step_eval, step_cond],
   )

2. (Optional) Examine the JSON pipeline definition to ensure that it's well-formed.

   import json
   
   json.loads(pipeline.definition())