workbench 0.8.172__py3-none-any.whl → 0.8.174__py3-none-any.whl

workbench/algorithms/graph/light/proximity_graph.py

@@ -135,7 +135,8 @@ if __name__ == "__main__":
     from workbench.algorithms.dataframe.fingerprint_proximity import FingerprintProximity
     from workbench.web_interface.components.plugins.graph_plot import GraphPlot
     from workbench.api import DFStore
-    from workbench.utils.chem_utils import compute_morgan_fingerprints, project_fingerprints
+    from workbench.utils.chem_utils.fingerprints import compute_morgan_fingerprints
+    from workbench.utils.chem_utils.projections import project_fingerprints
     from workbench.utils.graph_utils import connected_sample, graph_layout
 
     def show_graph(graph, id_column):

workbench/api/compound.py

@@ -3,7 +3,7 @@ import logging
 from typing import List
 
 # Workbench Imports
-from workbench.utils.chem_utils import svg_from_smiles
+from workbench.utils.chem_utils.vis import svg_from_smiles
 
 
 @dataclass

workbench/api/monitor.py

@@ -15,7 +15,7 @@ class Monitor(MonitorCore):
 
     Common Usage:
        ```
-       mon = Endpoint(name).get_monitor()  # Pull from endpoint OR
+       mon = Endpoint(name).monitor()  # Pull from endpoint OR
        mon = Monitor(name)                 # Create using Endpoint Name
        mon.summary()
        mon.details()
@@ -29,7 +29,6 @@ class Monitor(MonitorCore):
        baseline_df = mon.get_baseline()
        constraints_df = mon.get_constraints()
        stats_df = mon.get_statistics()
-       input_df, output_df = mon.get_captured_data()
        ```
     """
 
@@ -81,15 +80,6 @@ class Monitor(MonitorCore):
         """
         super().create_monitoring_schedule(schedule)
 
-    def get_captured_data(self) -> (pd.DataFrame, pd.DataFrame):
-        """
-        Get the latest data capture input and output from S3.
-
-        Returns:
-            DataFrame (input), DataFrame(output): Flattened and processed DataFrames for input and output data.
-        """
-        return super().get_captured_data()
-
     def get_baseline(self) -> Union[pd.DataFrame, None]:
         """Code to get the baseline CSV from the S3 baseline directory
 
@@ -155,8 +145,3 @@ if __name__ == "__main__":
 
     print("\nStatistics...")
     print(mm.get_statistics())
-
-    # Get the latest data capture
-    input_df, output_df = mm.get_captured_data()
-    print(input_df.head())
-    print(output_df.head())

workbench/core/artifacts/data_capture_core.py

@@ -0,0 +1,348 @@
+"""DataCaptureCore class for managing SageMaker endpoint data capture"""
+
+import logging
+import re
+import time
+from datetime import datetime
+from typing import Tuple
+import pandas as pd
+from sagemaker import Predictor
+from sagemaker.model_monitor import DataCaptureConfig
+import awswrangler as wr
+
+# Workbench Imports
+from workbench.core.artifacts.endpoint_core import EndpointCore
+from workbench.core.cloud_platform.aws.aws_account_clamp import AWSAccountClamp
+from workbench.utils.monitor_utils import process_data_capture
+
+# Setup logging
+log = logging.getLogger("workbench")
+
+
+class DataCaptureCore:
+    """Manages data capture configuration and retrieval for SageMaker endpoints"""
+
+    def __init__(self, endpoint_name: str):
+        """DataCaptureCore Class
+
+        Args:
+            endpoint_name (str): Name of the endpoint to manage data capture for
+        """
+        self.log = logging.getLogger("workbench")
+        self.endpoint_name = endpoint_name
+        self.endpoint = EndpointCore(self.endpoint_name)
+
+        # Initialize Class Attributes
+        self.sagemaker_session = self.endpoint.sm_session
+        self.sagemaker_client = self.endpoint.sm_client
+        self.data_capture_path = self.endpoint.endpoint_data_capture_path
+        self.workbench_role_arn = AWSAccountClamp().aws_session.get_workbench_execution_role_arn()
+
+    def summary(self) -> dict:
+        """Return the summary of data capture configuration
+
+        Returns:
+            dict: Summary of data capture status
+        """
+        if self.endpoint.is_serverless():
+            return {"endpoint_type": "serverless", "data_capture": "not supported"}
+        else:
+            return {
+                "endpoint_type": "realtime",
+                "data_capture_enabled": self.is_enabled(),
+                "capture_percentage": self.capture_percentage(),
+                "capture_modes": self.capture_modes() if self.is_enabled() else [],
+                "data_capture_path": self.data_capture_path if self.is_enabled() else None,
+            }
+
+    def enable(self, capture_percentage=100, capture_options=None, force_redeploy=False):
+        """
+        Enable data capture for the SageMaker endpoint.
+
+        Args:
+            capture_percentage (int): Percentage of data to capture. Defaults to 100.
+            capture_options (list): List of what to capture - ["REQUEST"], ["RESPONSE"], or ["REQUEST", "RESPONSE"].
+                                    Defaults to ["REQUEST", "RESPONSE"] to capture both.
+            force_redeploy (bool): If True, force redeployment even if data capture is already enabled.
+        """
+        # Early returns for cases where we can't/don't need to add data capture
+        if self.endpoint.is_serverless():
+            self.log.warning("Data capture is not supported for serverless endpoints.")
+            return
+
+        # Default to capturing both if not specified
+        if capture_options is None:
+            capture_options = ["REQUEST", "RESPONSE"]
+
+        # Validate capture_options
+        valid_options = {"REQUEST", "RESPONSE"}
+        if not all(opt in valid_options for opt in capture_options):
+            self.log.error("Invalid capture_options. Must be a list containing 'REQUEST' and/or 'RESPONSE'")
+            return
+
+        if self.is_enabled() and not force_redeploy:
+            self.log.important(f"Data capture already configured for {self.endpoint_name}.")
+            return
+
+        # Get the current endpoint configuration name for later deletion
+        current_endpoint_config_name = self.endpoint.endpoint_config_name()
+
+        # Log the data capture operation
+        self.log.important(f"Enabling Data Capture for {self.endpoint_name} --> {self.data_capture_path}")
+        self.log.important(f"Capturing: {', '.join(capture_options)} at {capture_percentage}% sampling")
+        self.log.important("This will redeploy the endpoint...")
+
+        # Create and apply the data capture configuration
+        data_capture_config = DataCaptureConfig(
+            enable_capture=True,
+            sampling_percentage=capture_percentage,
+            destination_s3_uri=self.data_capture_path,
+            capture_options=capture_options,
+        )
+
+        # Update endpoint with the new capture configuration
+        Predictor(self.endpoint_name, sagemaker_session=self.sagemaker_session).update_data_capture_config(
+            data_capture_config=data_capture_config
+        )
+
+        # Clean up old endpoint configuration
+        try:
+            self.sagemaker_client.delete_endpoint_config(EndpointConfigName=current_endpoint_config_name)
+            self.log.info(f"Deleted old endpoint configuration: {current_endpoint_config_name}")
+        except Exception as e:
+            self.log.warning(f"Could not delete old endpoint configuration {current_endpoint_config_name}: {e}")
+
+    def disable(self):
+        """
+        Disable data capture for the SageMaker endpoint.
+        """
+        # Early return if data capture isn't configured
+        if not self.is_enabled():
+            self.log.important(f"Data capture is not currently enabled for {self.endpoint_name}.")
+            return
+
+        # Get the current endpoint configuration name for later deletion
+        current_endpoint_config_name = self.endpoint.endpoint_config_name()
+
+        # Log the operation
+        self.log.important(f"Disabling Data Capture for {self.endpoint_name}")
+        self.log.important("This normally redeploys the endpoint...")
+
+        # Create a configuration with capture disabled
+        data_capture_config = DataCaptureConfig(enable_capture=False, destination_s3_uri=self.data_capture_path)
+
+        # Update endpoint with the new configuration
+        Predictor(self.endpoint_name, sagemaker_session=self.sagemaker_session).update_data_capture_config(
+            data_capture_config=data_capture_config
+        )
+
+        # Clean up old endpoint configuration
+        self.sagemaker_client.delete_endpoint_config(EndpointConfigName=current_endpoint_config_name)
+
+    def is_enabled(self) -> bool:
+        """
+        Check if data capture is enabled on the endpoint.
+
+        Returns:
+            bool: True if data capture is enabled, False otherwise.
+        """
+        try:
+            endpoint_config_name = self.endpoint.endpoint_config_name()
+            endpoint_config = self.sagemaker_client.describe_endpoint_config(EndpointConfigName=endpoint_config_name)
+            data_capture_config = endpoint_config.get("DataCaptureConfig", {})
+
+            # Check if data capture is enabled
+            is_enabled = data_capture_config.get("EnableCapture", False)
+            return is_enabled
+        except Exception as e:
+            self.log.error(f"Error checking data capture configuration: {e}")
+            return False
+
+    def capture_percentage(self) -> int:
+        """
+        Get the data capture percentage from the endpoint configuration.
+
+        Returns:
+            int: Data capture percentage if enabled, None otherwise.
+        """
+        try:
+            endpoint_config_name = self.endpoint.endpoint_config_name()
+            endpoint_config = self.sagemaker_client.describe_endpoint_config(EndpointConfigName=endpoint_config_name)
+            data_capture_config = endpoint_config.get("DataCaptureConfig", {})
+
+            # Check if data capture is enabled and return the percentage
+            if data_capture_config.get("EnableCapture", False):
+                return data_capture_config.get("InitialSamplingPercentage", 0)
+            else:
+                return None
+        except Exception as e:
+            self.log.error(f"Error checking data capture percentage: {e}")
+            return None
+
+    def get_config(self) -> dict:
+        """
+        Returns the complete data capture configuration from the endpoint config.
+
+        Returns:
+            dict: Complete DataCaptureConfig from AWS, or None if not configured
+        """
+        config_name = self.endpoint.endpoint_config_name()
+        response = self.sagemaker_client.describe_endpoint_config(EndpointConfigName=config_name)
+        data_capture_config = response.get("DataCaptureConfig")
+        if not data_capture_config:
+            self.log.error(f"No data capture configuration found for endpoint config {config_name}")
+            return None
+        return data_capture_config
+
+    def capture_modes(self) -> list:
+        """Get the current capture modes (REQUEST/RESPONSE)"""
+        if not self.is_enabled():
+            return []
+
+        config = self.get_config()
+        if not config:
+            return []
+
+        capture_options = config.get("CaptureOptions", [])
+        modes = [opt.get("CaptureMode") for opt in capture_options]
+        return ["REQUEST" if m == "Input" else "RESPONSE" for m in modes if m]
+
+    def get_captured_data(self, from_date: str = None, add_timestamp: bool = True) -> Tuple[pd.DataFrame, pd.DataFrame]:
+        """
+        Read and process captured data from S3.
+
+        Args:
+            from_date (str, optional): Only process files from this date onwards (YYYY-MM-DD format).
+                                       Defaults to None to process all files.
+            add_timestamp (bool, optional): Whether to add a timestamp column to the DataFrame.
+
+        Returns:
+            Tuple[pd.DataFrame, pd.DataFrame]: Processed input and output DataFrames.
+        """
+        files = wr.s3.list_objects(self.data_capture_path)
+        if not files:
+            self.log.warning(f"No data capture files found in {self.data_capture_path}.")
+            return pd.DataFrame(), pd.DataFrame()
+
+        # Filter by date if specified
+        if from_date:
+            from_date_obj = datetime.strptime(from_date, "%Y-%m-%d").date()
+            files = [f for f in files if self._file_date_filter(f, from_date_obj)]
+            self.log.info(f"Processing {len(files)} files from {from_date} onwards.")
+        else:
+            self.log.info(f"Processing all {len(files)} files...")
+        files.sort()
+
+        # Get all timestamps in one batch if needed
+        timestamps = {}
+        if add_timestamp:
+            # Batch describe operation - much more efficient than per-file calls
+            timestamps = wr.s3.describe_objects(path=files)
+
+        # Process files using concurrent.futures
+        start_time = time.time()
+
+        def process_single_file(file_path):
+            """Process a single file and return input/output DataFrames."""
+            try:
+                log.debug(f"Processing file: {file_path}...")
+                df = wr.s3.read_json(path=file_path, lines=True)
+                if not df.empty:
+                    input_df, output_df = process_data_capture(df)
+                    if add_timestamp and file_path in timestamps:
+                        output_df["timestamp"] = timestamps[file_path]["LastModified"]
+                    return input_df, output_df
+                return pd.DataFrame(), pd.DataFrame()
+            except Exception as e:
+                self.log.warning(f"Error processing {file_path}: {e}")
+                return pd.DataFrame(), pd.DataFrame()
+
+        # Use ThreadPoolExecutor for I/O-bound operations
+        from concurrent.futures import ThreadPoolExecutor
+
+        max_workers = min(32, len(files))  # Cap at 32 threads or number of files
+
+        all_input_dfs, all_output_dfs = [], []
+        with ThreadPoolExecutor(max_workers=max_workers) as executor:
+            futures = [executor.submit(process_single_file, file_path) for file_path in files]
+            for future in futures:
+                input_df, output_df = future.result()
+                if not input_df.empty:
+                    all_input_dfs.append(input_df)
+                if not output_df.empty:
+                    all_output_dfs.append(output_df)
+
+        if not all_input_dfs:
+            self.log.warning("No valid data was processed.")
+            return pd.DataFrame(), pd.DataFrame()
+
+        input_df = pd.concat(all_input_dfs, ignore_index=True)
+        output_df = pd.concat(all_output_dfs, ignore_index=True)
+
+        elapsed_time = time.time() - start_time
+        self.log.info(f"Processed {len(files)} files in {elapsed_time:.2f} seconds.")
+        return input_df, output_df
+
+    def _file_date_filter(self, file_path, from_date_obj):
+        """Extract date from S3 path and compare with from_date."""
+        try:
+            # Match YYYY/MM/DD pattern in the path
+            date_match = re.search(r"/(\d{4})/(\d{2})/(\d{2})/", file_path)
+            if date_match:
+                year, month, day = date_match.groups()
+                file_date = datetime(int(year), int(month), int(day)).date()
+                return file_date >= from_date_obj
+            return False  # No date pattern found
+        except ValueError:
+            return False
+
+    def __repr__(self) -> str:
+        """String representation of this DataCaptureCore object
+
+        Returns:
+            str: String representation of this DataCaptureCore object
+        """
+        summary_dict = self.summary()
+        summary_items = [f"  {repr(key)}: {repr(value)}" for key, value in summary_dict.items()]
+        summary_str = f"{self.__class__.__name__}: {self.endpoint_name}\n" + ",\n".join(summary_items)
+        return summary_str
+
+
+# Test function for the class
+if __name__ == "__main__":
+    """Exercise the MonitorCore class"""
+    from pprint import pprint
+
+    # Set options for actually seeing the dataframe
+    pd.set_option("display.max_columns", None)
+    pd.set_option("display.width", None)
+
+    # Create the Class and test it out
+    endpoint_name = "abalone-regression-rt"
+    my_endpoint = EndpointCore(endpoint_name)
+    if not my_endpoint.exists():
+        print(f"Endpoint {endpoint_name} does not exist.")
+        exit(1)
+    dc = my_endpoint.data_capture()
+
+    # Check the summary of the data capture class
+    pprint(dc.summary())
+
+    # Enable data capture on the endpoint
+    # dc.enable(force_redeploy=True)
+    my_endpoint.enable_data_capture()
+
+    # Test the data capture by running some predictions
+    # pred_df = my_endpoint.auto_inference()
+    # print(pred_df.head())
+
+    # Check that data capture is working
+    input_df, output_df = dc.get_captured_data()
+    if input_df.empty and output_df.empty:
+        print("No data capture files found, for a new endpoint it may take a few minutes to start capturing data")
+    else:
+        print("Found data capture files")
+        print("Input")
+        print(input_df.head())
+        print("Output")
+        print(output_df.head())

workbench/core/artifacts/endpoint_core.py

@@ -164,11 +164,17 @@ class EndpointCore(Artifact):
         """
         return "Serverless" in self.endpoint_meta["InstanceType"]
 
-    def add_data_capture(self):
+    def data_capture(self):
+        """Get the MonitorCore class for this endpoint"""
+        from workbench.core.artifacts.data_capture_core import DataCaptureCore
+
+        return DataCaptureCore(self.endpoint_name)
+
+    def enable_data_capture(self):
         """Add data capture to the endpoint"""
-        self.get_monitor().add_data_capture()
+        self.data_capture().enable()
 
-    def get_monitor(self):
+    def monitor(self):
         """Get the MonitorCore class for this endpoint"""
         from workbench.core.artifacts.monitor_core import MonitorCore