workbench 0.8.162__py3-none-any.whl → 0.8.202__py3-none-any.whl
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- workbench/algorithms/dataframe/__init__.py +1 -2
- workbench/algorithms/dataframe/fingerprint_proximity.py +2 -2
- workbench/algorithms/dataframe/proximity.py +261 -235
- workbench/algorithms/graph/light/proximity_graph.py +10 -8
- workbench/api/__init__.py +2 -1
- workbench/api/compound.py +1 -1
- workbench/api/endpoint.py +11 -0
- workbench/api/feature_set.py +11 -8
- workbench/api/meta.py +5 -2
- workbench/api/model.py +16 -15
- workbench/api/monitor.py +1 -16
- workbench/core/artifacts/__init__.py +11 -2
- workbench/core/artifacts/artifact.py +11 -3
- workbench/core/artifacts/data_capture_core.py +355 -0
- workbench/core/artifacts/endpoint_core.py +256 -118
- workbench/core/artifacts/feature_set_core.py +265 -16
- workbench/core/artifacts/model_core.py +107 -60
- workbench/core/artifacts/monitor_core.py +33 -248
- workbench/core/cloud_platform/aws/aws_account_clamp.py +50 -1
- workbench/core/cloud_platform/aws/aws_meta.py +12 -5
- workbench/core/cloud_platform/aws/aws_parameter_store.py +18 -2
- workbench/core/cloud_platform/aws/aws_session.py +4 -4
- workbench/core/transforms/data_to_features/light/molecular_descriptors.py +4 -4
- workbench/core/transforms/features_to_model/features_to_model.py +42 -32
- workbench/core/transforms/model_to_endpoint/model_to_endpoint.py +36 -6
- workbench/core/transforms/pandas_transforms/pandas_to_features.py +27 -0
- workbench/core/views/training_view.py +113 -42
- workbench/core/views/view.py +53 -3
- workbench/core/views/view_utils.py +4 -4
- workbench/model_scripts/chemprop/chemprop.template +852 -0
- workbench/model_scripts/chemprop/generated_model_script.py +852 -0
- workbench/model_scripts/chemprop/requirements.txt +11 -0
- workbench/model_scripts/custom_models/chem_info/fingerprints.py +134 -0
- workbench/model_scripts/custom_models/chem_info/mol_descriptors.py +483 -0
- workbench/model_scripts/custom_models/chem_info/mol_standardize.py +450 -0
- workbench/model_scripts/custom_models/chem_info/molecular_descriptors.py +7 -9
- workbench/model_scripts/custom_models/chem_info/morgan_fingerprints.py +1 -1
- workbench/model_scripts/custom_models/proximity/feature_space_proximity.template +3 -5
- workbench/model_scripts/custom_models/proximity/proximity.py +261 -235
- workbench/model_scripts/custom_models/uq_models/bayesian_ridge.template +7 -8
- workbench/model_scripts/custom_models/uq_models/ensemble_xgb.template +20 -21
- workbench/model_scripts/custom_models/uq_models/gaussian_process.template +5 -11
- workbench/model_scripts/custom_models/uq_models/meta_uq.template +166 -62
- workbench/model_scripts/custom_models/uq_models/ngboost.template +30 -18
- workbench/model_scripts/custom_models/uq_models/proximity.py +261 -235
- workbench/model_scripts/custom_models/uq_models/requirements.txt +1 -3
- workbench/model_scripts/ensemble_xgb/ensemble_xgb.template +15 -17
- workbench/model_scripts/pytorch_model/generated_model_script.py +373 -190
- workbench/model_scripts/pytorch_model/pytorch.template +370 -187
- workbench/model_scripts/scikit_learn/generated_model_script.py +7 -12
- workbench/model_scripts/scikit_learn/scikit_learn.template +4 -9
- workbench/model_scripts/script_generation.py +17 -9
- workbench/model_scripts/uq_models/generated_model_script.py +605 -0
- workbench/model_scripts/uq_models/mapie.template +605 -0
- workbench/model_scripts/uq_models/requirements.txt +1 -0
- workbench/model_scripts/xgb_model/generated_model_script.py +37 -46
- workbench/model_scripts/xgb_model/xgb_model.template +44 -46
- workbench/repl/workbench_shell.py +28 -14
- workbench/scripts/endpoint_test.py +162 -0
- workbench/scripts/lambda_test.py +73 -0
- workbench/scripts/ml_pipeline_batch.py +137 -0
- workbench/scripts/ml_pipeline_sqs.py +186 -0
- workbench/scripts/monitor_cloud_watch.py +20 -100
- workbench/utils/aws_utils.py +4 -3
- workbench/utils/chem_utils/__init__.py +0 -0
- workbench/utils/chem_utils/fingerprints.py +134 -0
- workbench/utils/chem_utils/misc.py +194 -0
- workbench/utils/chem_utils/mol_descriptors.py +483 -0
- workbench/utils/chem_utils/mol_standardize.py +450 -0
- workbench/utils/chem_utils/mol_tagging.py +348 -0
- workbench/utils/chem_utils/projections.py +209 -0
- workbench/utils/chem_utils/salts.py +256 -0
- workbench/utils/chem_utils/sdf.py +292 -0
- workbench/utils/chem_utils/toxicity.py +250 -0
- workbench/utils/chem_utils/vis.py +253 -0
- workbench/utils/chemprop_utils.py +760 -0
- workbench/utils/cloudwatch_handler.py +1 -1
- workbench/utils/cloudwatch_utils.py +137 -0
- workbench/utils/config_manager.py +3 -7
- workbench/utils/endpoint_utils.py +5 -7
- workbench/utils/license_manager.py +2 -6
- workbench/utils/model_utils.py +95 -34
- workbench/utils/monitor_utils.py +44 -62
- workbench/utils/pandas_utils.py +3 -3
- workbench/utils/pytorch_utils.py +526 -0
- workbench/utils/shap_utils.py +10 -2
- workbench/utils/workbench_logging.py +0 -3
- workbench/utils/workbench_sqs.py +1 -1
- workbench/utils/xgboost_model_utils.py +371 -156
- workbench/web_interface/components/model_plot.py +7 -1
- workbench/web_interface/components/plugin_unit_test.py +5 -2
- workbench/web_interface/components/plugins/dashboard_status.py +3 -1
- workbench/web_interface/components/plugins/generated_compounds.py +1 -1
- workbench/web_interface/components/plugins/model_details.py +9 -7
- workbench/web_interface/components/plugins/scatter_plot.py +3 -3
- {workbench-0.8.162.dist-info → workbench-0.8.202.dist-info}/METADATA +27 -6
- {workbench-0.8.162.dist-info → workbench-0.8.202.dist-info}/RECORD +101 -85
- {workbench-0.8.162.dist-info → workbench-0.8.202.dist-info}/entry_points.txt +4 -0
- {workbench-0.8.162.dist-info → workbench-0.8.202.dist-info}/licenses/LICENSE +1 -1
- workbench/model_scripts/custom_models/chem_info/local_utils.py +0 -769
- workbench/model_scripts/custom_models/chem_info/tautomerize.py +0 -83
- workbench/model_scripts/custom_models/proximity/generated_model_script.py +0 -138
- workbench/model_scripts/custom_models/uq_models/generated_model_script.py +0 -393
- workbench/model_scripts/custom_models/uq_models/mapie_xgb.template +0 -203
- workbench/model_scripts/ensemble_xgb/generated_model_script.py +0 -279
- workbench/model_scripts/quant_regression/quant_regression.template +0 -279
- workbench/model_scripts/quant_regression/requirements.txt +0 -1
- workbench/utils/chem_utils.py +0 -1556
- workbench/utils/execution_environment.py +0 -211
- workbench/utils/fast_inference.py +0 -167
- workbench/utils/resource_utils.py +0 -39
- {workbench-0.8.162.dist-info → workbench-0.8.202.dist-info}/WHEEL +0 -0
- {workbench-0.8.162.dist-info → workbench-0.8.202.dist-info}/top_level.txt +0 -0
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"""DataCaptureCore class for managing SageMaker endpoint data capture"""
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import logging
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import re
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import time
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from datetime import datetime
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from typing import Tuple
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import pandas as pd
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from sagemaker import Predictor
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from sagemaker.model_monitor import DataCaptureConfig
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import awswrangler as wr
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# Workbench Imports
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from workbench.core.artifacts.endpoint_core import EndpointCore
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from workbench.core.cloud_platform.aws.aws_account_clamp import AWSAccountClamp
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from workbench.utils.monitor_utils import process_data_capture
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# Setup logging
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log = logging.getLogger("workbench")
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class DataCaptureCore:
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"""Manages data capture configuration and retrieval for SageMaker endpoints"""
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def __init__(self, endpoint_name: str):
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"""DataCaptureCore Class
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Args:
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endpoint_name (str): Name of the endpoint to manage data capture for
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"""
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self.log = logging.getLogger("workbench")
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self.endpoint_name = endpoint_name
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self.endpoint = EndpointCore(self.endpoint_name)
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# Initialize Class Attributes
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self.sagemaker_session = self.endpoint.sm_session
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self.sagemaker_client = self.endpoint.sm_client
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self.data_capture_path = self.endpoint.endpoint_data_capture_path
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self.workbench_role_arn = AWSAccountClamp().aws_session.get_workbench_execution_role_arn()
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def summary(self) -> dict:
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"""Return the summary of data capture configuration
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Returns:
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dict: Summary of data capture status
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"""
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if self.endpoint.is_serverless():
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return {"endpoint_type": "serverless", "data_capture": "not supported"}
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else:
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return {
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"endpoint_type": "realtime",
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"data_capture_enabled": self.is_enabled(),
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"capture_percentage": self.capture_percentage(),
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"capture_modes": self.capture_modes() if self.is_enabled() else [],
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"data_capture_path": self.data_capture_path if self.is_enabled() else None,
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}
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def enable(self, capture_percentage=100, capture_options=None, force_redeploy=False):
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"""
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Enable data capture for the SageMaker endpoint.
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Args:
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capture_percentage (int): Percentage of data to capture. Defaults to 100.
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capture_options (list): List of what to capture - ["REQUEST"], ["RESPONSE"], or ["REQUEST", "RESPONSE"].
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Defaults to ["REQUEST", "RESPONSE"] to capture both.
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force_redeploy (bool): If True, force redeployment even if data capture is already enabled.
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"""
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# Early returns for cases where we can't/don't need to add data capture
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if self.endpoint.is_serverless():
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self.log.warning("Data capture is not supported for serverless endpoints.")
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return
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# Default to capturing both if not specified
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if capture_options is None:
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capture_options = ["REQUEST", "RESPONSE"]
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# Validate capture_options
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valid_options = {"REQUEST", "RESPONSE"}
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if not all(opt in valid_options for opt in capture_options):
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self.log.error("Invalid capture_options. Must be a list containing 'REQUEST' and/or 'RESPONSE'")
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return
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if self.is_enabled() and not force_redeploy:
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self.log.important(f"Data capture already configured for {self.endpoint_name}.")
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return
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# Get the current endpoint configuration name for later deletion
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current_endpoint_config_name = self.endpoint.endpoint_config_name()
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# Log the data capture operation
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self.log.important(f"Enabling Data Capture for {self.endpoint_name} --> {self.data_capture_path}")
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self.log.important(f"Capturing: {', '.join(capture_options)} at {capture_percentage}% sampling")
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self.log.important("This will redeploy the endpoint...")
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# Create and apply the data capture configuration
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data_capture_config = DataCaptureConfig(
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enable_capture=True,
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sampling_percentage=capture_percentage,
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destination_s3_uri=self.data_capture_path,
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capture_options=capture_options,
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)
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# Update endpoint with the new capture configuration
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Predictor(self.endpoint_name, sagemaker_session=self.sagemaker_session).update_data_capture_config(
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data_capture_config=data_capture_config
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)
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# Clean up old endpoint configuration
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try:
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self.sagemaker_client.delete_endpoint_config(EndpointConfigName=current_endpoint_config_name)
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self.log.info(f"Deleted old endpoint configuration: {current_endpoint_config_name}")
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except Exception as e:
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self.log.warning(f"Could not delete old endpoint configuration {current_endpoint_config_name}: {e}")
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def disable(self):
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"""
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Disable data capture for the SageMaker endpoint.
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"""
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# Early return if data capture isn't configured
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if not self.is_enabled():
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self.log.important(f"Data capture is not currently enabled for {self.endpoint_name}.")
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return
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# Get the current endpoint configuration name for later deletion
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current_endpoint_config_name = self.endpoint.endpoint_config_name()
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# Log the operation
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self.log.important(f"Disabling Data Capture for {self.endpoint_name}")
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self.log.important("This normally redeploys the endpoint...")
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# Create a configuration with capture disabled
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data_capture_config = DataCaptureConfig(enable_capture=False, destination_s3_uri=self.data_capture_path)
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# Update endpoint with the new configuration
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Predictor(self.endpoint_name, sagemaker_session=self.sagemaker_session).update_data_capture_config(
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data_capture_config=data_capture_config
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)
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# Clean up old endpoint configuration
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self.sagemaker_client.delete_endpoint_config(EndpointConfigName=current_endpoint_config_name)
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def is_enabled(self) -> bool:
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"""
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Check if data capture is enabled on the endpoint.
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Returns:
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bool: True if data capture is enabled, False otherwise.
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"""
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try:
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endpoint_config_name = self.endpoint.endpoint_config_name()
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endpoint_config = self.sagemaker_client.describe_endpoint_config(EndpointConfigName=endpoint_config_name)
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data_capture_config = endpoint_config.get("DataCaptureConfig", {})
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# Check if data capture is enabled
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is_enabled = data_capture_config.get("EnableCapture", False)
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return is_enabled
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except Exception as e:
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self.log.error(f"Error checking data capture configuration: {e}")
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return False
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def capture_percentage(self) -> int:
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"""
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Get the data capture percentage from the endpoint configuration.
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Returns:
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int: Data capture percentage if enabled, None otherwise.
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"""
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try:
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endpoint_config_name = self.endpoint.endpoint_config_name()
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endpoint_config = self.sagemaker_client.describe_endpoint_config(EndpointConfigName=endpoint_config_name)
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data_capture_config = endpoint_config.get("DataCaptureConfig", {})
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# Check if data capture is enabled and return the percentage
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if data_capture_config.get("EnableCapture", False):
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return data_capture_config.get("InitialSamplingPercentage", 0)
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else:
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return None
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except Exception as e:
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self.log.error(f"Error checking data capture percentage: {e}")
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return None
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def get_config(self) -> dict:
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"""
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Returns the complete data capture configuration from the endpoint config.
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Returns:
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dict: Complete DataCaptureConfig from AWS, or None if not configured
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"""
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config_name = self.endpoint.endpoint_config_name()
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response = self.sagemaker_client.describe_endpoint_config(EndpointConfigName=config_name)
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data_capture_config = response.get("DataCaptureConfig")
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if not data_capture_config:
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self.log.error(f"No data capture configuration found for endpoint config {config_name}")
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return None
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return data_capture_config
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def capture_modes(self) -> list:
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"""Get the current capture modes (REQUEST/RESPONSE)"""
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if not self.is_enabled():
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return []
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config = self.get_config()
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if not config:
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return []
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capture_options = config.get("CaptureOptions", [])
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modes = [opt.get("CaptureMode") for opt in capture_options]
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return ["REQUEST" if m == "Input" else "RESPONSE" for m in modes if m]
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def get_captured_data(self, from_date: str = None, add_timestamp: bool = True) -> Tuple[pd.DataFrame, pd.DataFrame]:
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"""
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Read and process captured data from S3.
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+
|
|
214
|
+
Args:
|
|
215
|
+
from_date (str, optional): Only process files from this date onwards (YYYY-MM-DD format).
|
|
216
|
+
Defaults to None to process all files.
|
|
217
|
+
add_timestamp (bool, optional): Whether to add a timestamp column to the DataFrame.
|
|
218
|
+
|
|
219
|
+
Returns:
|
|
220
|
+
Tuple[pd.DataFrame, pd.DataFrame]: Processed input and output DataFrames.
|
|
221
|
+
"""
|
|
222
|
+
files = wr.s3.list_objects(self.data_capture_path)
|
|
223
|
+
if not files:
|
|
224
|
+
self.log.warning(f"No data capture files found in {self.data_capture_path}.")
|
|
225
|
+
return pd.DataFrame(), pd.DataFrame()
|
|
226
|
+
|
|
227
|
+
# Filter by date if specified
|
|
228
|
+
if from_date:
|
|
229
|
+
from_date_obj = datetime.strptime(from_date, "%Y-%m-%d").date()
|
|
230
|
+
files = [f for f in files if self._file_date_filter(f, from_date_obj)]
|
|
231
|
+
self.log.info(f"Processing {len(files)} files from {from_date} onwards.")
|
|
232
|
+
else:
|
|
233
|
+
self.log.info(f"Processing all {len(files)} files...")
|
|
234
|
+
|
|
235
|
+
# Check if any files remain after filtering
|
|
236
|
+
if not files:
|
|
237
|
+
self.log.info("No files to process after date filtering.")
|
|
238
|
+
return pd.DataFrame(), pd.DataFrame()
|
|
239
|
+
|
|
240
|
+
# Sort files by name (assumed to include timestamp)
|
|
241
|
+
files.sort()
|
|
242
|
+
|
|
243
|
+
# Get all timestamps in one batch if needed
|
|
244
|
+
timestamps = {}
|
|
245
|
+
if add_timestamp:
|
|
246
|
+
# Batch describe operation - much more efficient than per-file calls
|
|
247
|
+
timestamps = wr.s3.describe_objects(path=files)
|
|
248
|
+
|
|
249
|
+
# Process files using concurrent.futures
|
|
250
|
+
start_time = time.time()
|
|
251
|
+
|
|
252
|
+
def process_single_file(file_path):
|
|
253
|
+
"""Process a single file and return input/output DataFrames."""
|
|
254
|
+
try:
|
|
255
|
+
log.debug(f"Processing file: {file_path}...")
|
|
256
|
+
df = wr.s3.read_json(path=file_path, lines=True)
|
|
257
|
+
if not df.empty:
|
|
258
|
+
input_df, output_df = process_data_capture(df)
|
|
259
|
+
if add_timestamp and file_path in timestamps:
|
|
260
|
+
output_df["timestamp"] = timestamps[file_path]["LastModified"]
|
|
261
|
+
return input_df, output_df
|
|
262
|
+
return pd.DataFrame(), pd.DataFrame()
|
|
263
|
+
except Exception as e:
|
|
264
|
+
self.log.warning(f"Error processing {file_path}: {e}")
|
|
265
|
+
return pd.DataFrame(), pd.DataFrame()
|
|
266
|
+
|
|
267
|
+
# Use ThreadPoolExecutor for I/O-bound operations
|
|
268
|
+
from concurrent.futures import ThreadPoolExecutor
|
|
269
|
+
|
|
270
|
+
max_workers = min(32, len(files)) # Cap at 32 threads or number of files
|
|
271
|
+
|
|
272
|
+
all_input_dfs, all_output_dfs = [], []
|
|
273
|
+
with ThreadPoolExecutor(max_workers=max_workers) as executor:
|
|
274
|
+
futures = [executor.submit(process_single_file, file_path) for file_path in files]
|
|
275
|
+
for future in futures:
|
|
276
|
+
input_df, output_df = future.result()
|
|
277
|
+
if not input_df.empty:
|
|
278
|
+
all_input_dfs.append(input_df)
|
|
279
|
+
if not output_df.empty:
|
|
280
|
+
all_output_dfs.append(output_df)
|
|
281
|
+
|
|
282
|
+
if not all_input_dfs:
|
|
283
|
+
self.log.warning("No valid data was processed.")
|
|
284
|
+
return pd.DataFrame(), pd.DataFrame()
|
|
285
|
+
|
|
286
|
+
input_df = pd.concat(all_input_dfs, ignore_index=True)
|
|
287
|
+
output_df = pd.concat(all_output_dfs, ignore_index=True)
|
|
288
|
+
|
|
289
|
+
elapsed_time = time.time() - start_time
|
|
290
|
+
self.log.info(f"Processed {len(files)} files in {elapsed_time:.2f} seconds.")
|
|
291
|
+
return input_df, output_df
|
|
292
|
+
|
|
293
|
+
def _file_date_filter(self, file_path, from_date_obj):
|
|
294
|
+
"""Extract date from S3 path and compare with from_date."""
|
|
295
|
+
try:
|
|
296
|
+
# Match YYYY/MM/DD pattern in the path
|
|
297
|
+
date_match = re.search(r"/(\d{4})/(\d{2})/(\d{2})/", file_path)
|
|
298
|
+
if date_match:
|
|
299
|
+
year, month, day = date_match.groups()
|
|
300
|
+
file_date = datetime(int(year), int(month), int(day)).date()
|
|
301
|
+
return file_date >= from_date_obj
|
|
302
|
+
return False # No date pattern found
|
|
303
|
+
except ValueError:
|
|
304
|
+
return False
|
|
305
|
+
|
|
306
|
+
def __repr__(self) -> str:
|
|
307
|
+
"""String representation of this DataCaptureCore object
|
|
308
|
+
|
|
309
|
+
Returns:
|
|
310
|
+
str: String representation of this DataCaptureCore object
|
|
311
|
+
"""
|
|
312
|
+
summary_dict = self.summary()
|
|
313
|
+
summary_items = [f" {repr(key)}: {repr(value)}" for key, value in summary_dict.items()]
|
|
314
|
+
summary_str = f"{self.__class__.__name__}: {self.endpoint_name}\n" + ",\n".join(summary_items)
|
|
315
|
+
return summary_str
|
|
316
|
+
|
|
317
|
+
|
|
318
|
+
# Test function for the class
|
|
319
|
+
if __name__ == "__main__":
|
|
320
|
+
"""Exercise the MonitorCore class"""
|
|
321
|
+
from pprint import pprint
|
|
322
|
+
|
|
323
|
+
# Set options for actually seeing the dataframe
|
|
324
|
+
pd.set_option("display.max_columns", None)
|
|
325
|
+
pd.set_option("display.width", None)
|
|
326
|
+
|
|
327
|
+
# Create the Class and test it out
|
|
328
|
+
endpoint_name = "abalone-regression-rt"
|
|
329
|
+
my_endpoint = EndpointCore(endpoint_name)
|
|
330
|
+
if not my_endpoint.exists():
|
|
331
|
+
print(f"Endpoint {endpoint_name} does not exist.")
|
|
332
|
+
exit(1)
|
|
333
|
+
dc = my_endpoint.data_capture()
|
|
334
|
+
|
|
335
|
+
# Check the summary of the data capture class
|
|
336
|
+
pprint(dc.summary())
|
|
337
|
+
|
|
338
|
+
# Enable data capture on the endpoint
|
|
339
|
+
# dc.enable(force_redeploy=True)
|
|
340
|
+
my_endpoint.enable_data_capture()
|
|
341
|
+
|
|
342
|
+
# Test the data capture by running some predictions
|
|
343
|
+
# pred_df = my_endpoint.auto_inference()
|
|
344
|
+
# print(pred_df.head())
|
|
345
|
+
|
|
346
|
+
# Check that data capture is working
|
|
347
|
+
input_df, output_df = dc.get_captured_data(from_date="2025-09-01")
|
|
348
|
+
if input_df.empty and output_df.empty:
|
|
349
|
+
print("No data capture files found, for a new endpoint it may take a few minutes to start capturing data")
|
|
350
|
+
else:
|
|
351
|
+
print("Found data capture files")
|
|
352
|
+
print("Input")
|
|
353
|
+
print(input_df.head())
|
|
354
|
+
print("Output")
|
|
355
|
+
print(output_df.head())
|