workbench 0.8.162__py3-none-any.whl → 0.8.202__py3-none-any.whl

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  1. workbench/algorithms/dataframe/__init__.py +1 -2
  2. workbench/algorithms/dataframe/fingerprint_proximity.py +2 -2
  3. workbench/algorithms/dataframe/proximity.py +261 -235
  4. workbench/algorithms/graph/light/proximity_graph.py +10 -8
  5. workbench/api/__init__.py +2 -1
  6. workbench/api/compound.py +1 -1
  7. workbench/api/endpoint.py +11 -0
  8. workbench/api/feature_set.py +11 -8
  9. workbench/api/meta.py +5 -2
  10. workbench/api/model.py +16 -15
  11. workbench/api/monitor.py +1 -16
  12. workbench/core/artifacts/__init__.py +11 -2
  13. workbench/core/artifacts/artifact.py +11 -3
  14. workbench/core/artifacts/data_capture_core.py +355 -0
  15. workbench/core/artifacts/endpoint_core.py +256 -118
  16. workbench/core/artifacts/feature_set_core.py +265 -16
  17. workbench/core/artifacts/model_core.py +107 -60
  18. workbench/core/artifacts/monitor_core.py +33 -248
  19. workbench/core/cloud_platform/aws/aws_account_clamp.py +50 -1
  20. workbench/core/cloud_platform/aws/aws_meta.py +12 -5
  21. workbench/core/cloud_platform/aws/aws_parameter_store.py +18 -2
  22. workbench/core/cloud_platform/aws/aws_session.py +4 -4
  23. workbench/core/transforms/data_to_features/light/molecular_descriptors.py +4 -4
  24. workbench/core/transforms/features_to_model/features_to_model.py +42 -32
  25. workbench/core/transforms/model_to_endpoint/model_to_endpoint.py +36 -6
  26. workbench/core/transforms/pandas_transforms/pandas_to_features.py +27 -0
  27. workbench/core/views/training_view.py +113 -42
  28. workbench/core/views/view.py +53 -3
  29. workbench/core/views/view_utils.py +4 -4
  30. workbench/model_scripts/chemprop/chemprop.template +852 -0
  31. workbench/model_scripts/chemprop/generated_model_script.py +852 -0
  32. workbench/model_scripts/chemprop/requirements.txt +11 -0
  33. workbench/model_scripts/custom_models/chem_info/fingerprints.py +134 -0
  34. workbench/model_scripts/custom_models/chem_info/mol_descriptors.py +483 -0
  35. workbench/model_scripts/custom_models/chem_info/mol_standardize.py +450 -0
  36. workbench/model_scripts/custom_models/chem_info/molecular_descriptors.py +7 -9
  37. workbench/model_scripts/custom_models/chem_info/morgan_fingerprints.py +1 -1
  38. workbench/model_scripts/custom_models/proximity/feature_space_proximity.template +3 -5
  39. workbench/model_scripts/custom_models/proximity/proximity.py +261 -235
  40. workbench/model_scripts/custom_models/uq_models/bayesian_ridge.template +7 -8
  41. workbench/model_scripts/custom_models/uq_models/ensemble_xgb.template +20 -21
  42. workbench/model_scripts/custom_models/uq_models/gaussian_process.template +5 -11
  43. workbench/model_scripts/custom_models/uq_models/meta_uq.template +166 -62
  44. workbench/model_scripts/custom_models/uq_models/ngboost.template +30 -18
  45. workbench/model_scripts/custom_models/uq_models/proximity.py +261 -235
  46. workbench/model_scripts/custom_models/uq_models/requirements.txt +1 -3
  47. workbench/model_scripts/ensemble_xgb/ensemble_xgb.template +15 -17
  48. workbench/model_scripts/pytorch_model/generated_model_script.py +373 -190
  49. workbench/model_scripts/pytorch_model/pytorch.template +370 -187
  50. workbench/model_scripts/scikit_learn/generated_model_script.py +7 -12
  51. workbench/model_scripts/scikit_learn/scikit_learn.template +4 -9
  52. workbench/model_scripts/script_generation.py +17 -9
  53. workbench/model_scripts/uq_models/generated_model_script.py +605 -0
  54. workbench/model_scripts/uq_models/mapie.template +605 -0
  55. workbench/model_scripts/uq_models/requirements.txt +1 -0
  56. workbench/model_scripts/xgb_model/generated_model_script.py +37 -46
  57. workbench/model_scripts/xgb_model/xgb_model.template +44 -46
  58. workbench/repl/workbench_shell.py +28 -14
  59. workbench/scripts/endpoint_test.py +162 -0
  60. workbench/scripts/lambda_test.py +73 -0
  61. workbench/scripts/ml_pipeline_batch.py +137 -0
  62. workbench/scripts/ml_pipeline_sqs.py +186 -0
  63. workbench/scripts/monitor_cloud_watch.py +20 -100
  64. workbench/utils/aws_utils.py +4 -3
  65. workbench/utils/chem_utils/__init__.py +0 -0
  66. workbench/utils/chem_utils/fingerprints.py +134 -0
  67. workbench/utils/chem_utils/misc.py +194 -0
  68. workbench/utils/chem_utils/mol_descriptors.py +483 -0
  69. workbench/utils/chem_utils/mol_standardize.py +450 -0
  70. workbench/utils/chem_utils/mol_tagging.py +348 -0
  71. workbench/utils/chem_utils/projections.py +209 -0
  72. workbench/utils/chem_utils/salts.py +256 -0
  73. workbench/utils/chem_utils/sdf.py +292 -0
  74. workbench/utils/chem_utils/toxicity.py +250 -0
  75. workbench/utils/chem_utils/vis.py +253 -0
  76. workbench/utils/chemprop_utils.py +760 -0
  77. workbench/utils/cloudwatch_handler.py +1 -1
  78. workbench/utils/cloudwatch_utils.py +137 -0
  79. workbench/utils/config_manager.py +3 -7
  80. workbench/utils/endpoint_utils.py +5 -7
  81. workbench/utils/license_manager.py +2 -6
  82. workbench/utils/model_utils.py +95 -34
  83. workbench/utils/monitor_utils.py +44 -62
  84. workbench/utils/pandas_utils.py +3 -3
  85. workbench/utils/pytorch_utils.py +526 -0
  86. workbench/utils/shap_utils.py +10 -2
  87. workbench/utils/workbench_logging.py +0 -3
  88. workbench/utils/workbench_sqs.py +1 -1
  89. workbench/utils/xgboost_model_utils.py +371 -156
  90. workbench/web_interface/components/model_plot.py +7 -1
  91. workbench/web_interface/components/plugin_unit_test.py +5 -2
  92. workbench/web_interface/components/plugins/dashboard_status.py +3 -1
  93. workbench/web_interface/components/plugins/generated_compounds.py +1 -1
  94. workbench/web_interface/components/plugins/model_details.py +9 -7
  95. workbench/web_interface/components/plugins/scatter_plot.py +3 -3
  96. {workbench-0.8.162.dist-info → workbench-0.8.202.dist-info}/METADATA +27 -6
  97. {workbench-0.8.162.dist-info → workbench-0.8.202.dist-info}/RECORD +101 -85
  98. {workbench-0.8.162.dist-info → workbench-0.8.202.dist-info}/entry_points.txt +4 -0
  99. {workbench-0.8.162.dist-info → workbench-0.8.202.dist-info}/licenses/LICENSE +1 -1
  100. workbench/model_scripts/custom_models/chem_info/local_utils.py +0 -769
  101. workbench/model_scripts/custom_models/chem_info/tautomerize.py +0 -83
  102. workbench/model_scripts/custom_models/proximity/generated_model_script.py +0 -138
  103. workbench/model_scripts/custom_models/uq_models/generated_model_script.py +0 -393
  104. workbench/model_scripts/custom_models/uq_models/mapie_xgb.template +0 -203
  105. workbench/model_scripts/ensemble_xgb/generated_model_script.py +0 -279
  106. workbench/model_scripts/quant_regression/quant_regression.template +0 -279
  107. workbench/model_scripts/quant_regression/requirements.txt +0 -1
  108. workbench/utils/chem_utils.py +0 -1556
  109. workbench/utils/execution_environment.py +0 -211
  110. workbench/utils/fast_inference.py +0 -167
  111. workbench/utils/resource_utils.py +0 -39
  112. {workbench-0.8.162.dist-info → workbench-0.8.202.dist-info}/WHEEL +0 -0
  113. {workbench-0.8.162.dist-info → workbench-0.8.202.dist-info}/top_level.txt +0 -0
@@ -2,12 +2,10 @@
2
2
 
3
3
  import logging
4
4
  import json
5
- from typing import Union, Tuple
5
+ from typing import Union
6
6
  import pandas as pd
7
- from sagemaker import Predictor
8
7
  from sagemaker.model_monitor import (
9
8
  CronExpressionGenerator,
10
- DataCaptureConfig,
11
9
  DefaultModelMonitor,
12
10
  DatasetFormat,
13
11
  )
@@ -15,29 +13,32 @@ import awswrangler as wr
15
13
 
16
14
  # Workbench Imports
17
15
  from workbench.core.artifacts.endpoint_core import EndpointCore
16
+ from workbench.core.artifacts.data_capture_core import DataCaptureCore
18
17
  from workbench.api import Model, FeatureSet
19
18
  from workbench.core.cloud_platform.aws.aws_account_clamp import AWSAccountClamp
20
19
  from workbench.utils.s3_utils import read_content_from_s3, upload_content_to_s3
21
20
  from workbench.utils.datetime_utils import datetime_string
22
21
  from workbench.utils.monitor_utils import (
23
- process_data_capture,
24
22
  get_monitor_json_data,
25
23
  parse_monitoring_results,
26
24
  preprocessing_script,
27
25
  )
28
26
 
29
- # Note: This resource might come in handy when doing code refactoring
27
+ # Note: These resources might come in handy when doing code refactoring
30
28
  # https://github.com/aws-samples/amazon-sagemaker-from-idea-to-production/blob/master/06-monitoring.ipynb
31
29
  # https://docs.aws.amazon.com/sagemaker/latest/dg/model-monitor-pre-and-post-processing.html
32
30
  # https://github.com/aws/amazon-sagemaker-examples/blob/main/sagemaker_model_monitor/introduction/SageMaker-ModelMonitoring.ipynb
33
31
 
34
32
 
35
33
  class MonitorCore:
34
+ """Manages monitoring, baselines, and monitoring schedules for SageMaker endpoints"""
35
+
36
36
  def __init__(self, endpoint_name, instance_type="ml.m5.large"):
37
37
  """MonitorCore Class
38
+
38
39
  Args:
39
40
  endpoint_name (str): Name of the endpoint to set up monitoring for
40
- instance_type (str): Instance type to use for monitoring. Defaults to "ml.t3.medium".
41
+ instance_type (str): Instance type to use for monitoring. Defaults to "ml.m5.large".
41
42
  """
42
43
  self.log = logging.getLogger("workbench")
43
44
  self.endpoint_name = endpoint_name
@@ -46,7 +47,6 @@ class MonitorCore:
46
47
  # Initialize Class Attributes
47
48
  self.sagemaker_session = self.endpoint.sm_session
48
49
  self.sagemaker_client = self.endpoint.sm_client
49
- self.data_capture_path = self.endpoint.endpoint_data_capture_path
50
50
  self.monitoring_path = self.endpoint.endpoint_monitoring_path
51
51
  self.monitoring_schedule_name = f"{self.endpoint_name}-monitoring-schedule"
52
52
  self.baseline_dir = f"{self.monitoring_path}/baseline"
@@ -57,6 +57,10 @@ class MonitorCore:
57
57
  self.workbench_role_arn = AWSAccountClamp().aws_session.get_workbench_execution_role_arn()
58
58
  self.instance_type = instance_type
59
59
 
60
+ # Create DataCaptureCore instance for composition
61
+ self.data_capture = DataCaptureCore(endpoint_name)
62
+ self.data_capture_path = self.data_capture.data_capture_path
63
+
60
64
  # Check if a monitoring schedule already exists for this endpoint
61
65
  existing_schedule = self.monitoring_schedule_exists()
62
66
 
@@ -74,23 +78,20 @@ class MonitorCore:
74
78
  self.log.info(f"Initialized new model monitor for {self.endpoint_name}")
75
79
 
76
80
  def summary(self) -> dict:
77
- """Return the summary of information about the endpoint monitor
81
+ """Return the summary of monitoring configuration
78
82
 
79
83
  Returns:
80
- dict: Summary of information about the endpoint monitor
84
+ dict: Summary of monitoring status
81
85
  """
82
86
  if self.endpoint.is_serverless():
83
87
  return {
84
88
  "endpoint_type": "serverless",
85
- "data_capture": "not supported",
86
89
  "baseline": "not supported",
87
90
  "monitoring_schedule": "not supported",
88
91
  }
89
92
  else:
90
93
  summary = {
91
94
  "endpoint_type": "realtime",
92
- "data_capture": self.data_capture_enabled(),
93
- "capture_percent": self.data_capture_percent(),
94
95
  "baseline": self.baseline_exists(),
95
96
  "monitoring_schedule": self.monitoring_schedule_exists(),
96
97
  "preprocessing": self.preprocessing_exists(),
@@ -103,22 +104,15 @@ class MonitorCore:
103
104
  Returns:
104
105
  dict: The monitoring details for the endpoint
105
106
  """
106
- # Get the actual data capture path
107
- actual_capture_path = self.data_capture_config()["DestinationS3Uri"]
108
- if actual_capture_path != self.data_capture_path:
109
- self.log.warning(
110
- f"Data capture path mismatch: Expected {self.data_capture_path}, "
111
- f"but found {actual_capture_path}. Using the actual path."
112
- )
113
- self.data_capture_path = actual_capture_path
114
107
  result = self.summary()
115
108
  info = {
116
- "data_capture_path": self.data_capture_path if self.data_capture_enabled() else None,
117
- "preprocessing_script_file": self.preprocessing_script_file if self.preprocessing_exists() else None,
118
109
  "monitoring_schedule_status": "Not Scheduled",
119
110
  }
120
111
  result.update(info)
121
112
 
113
+ if self.preprocessing_exists():
114
+ result["preprocessing_script_file"] = self.preprocessing_script_file
115
+
122
116
  if self.baseline_exists():
123
117
  result.update(
124
118
  {
@@ -144,7 +138,6 @@ class MonitorCore:
144
138
 
145
139
  last_run = schedule_details.get("LastMonitoringExecutionSummary", {})
146
140
  if last_run:
147
-
148
141
  # If no inference was run since the last monitoring schedule, the
149
142
  # status will be "Failed" with reason "Job inputs had no data",
150
143
  # so we check for that and set the status to "No New Data"
@@ -162,187 +155,22 @@ class MonitorCore:
162
155
 
163
156
  return result
164
157
 
165
- def enable_data_capture(self, capture_percentage=100, force=False):
166
- """
167
- Enable data capture for the SageMaker endpoint.
158
+ def enable_data_capture(self, capture_percentage=100):
159
+ """Enable data capture for the endpoint
168
160
 
169
161
  Args:
170
- capture_percentage (int): Percentage of data to capture. Defaults to 100.
171
- force (bool): If True, force reconfiguration even if data capture is already enabled.
162
+ capture_percentage (int): Percentage of requests to capture (0-100, default 100)
172
163
  """
173
- # Early returns for cases where we can't/don't need to add data capture
174
164
  if self.endpoint.is_serverless():
175
165
  self.log.warning("Data capture is not supported for serverless endpoints.")
176
166
  return
177
167
 
178
- if self.data_capture_enabled() and not force:
179
- self.log.important(f"Data capture already configured for {self.endpoint_name}.")
180
- return
181
-
182
- # Get the current endpoint configuration name for later deletion
183
- current_endpoint_config_name = self.endpoint.endpoint_config_name()
184
-
185
- # Log the data capture operation
186
- self.log.important(f"Enabling Data Capture for {self.endpoint_name} --> {self.data_capture_path}")
187
- self.log.important("This normally redeploys the endpoint...")
188
-
189
- # Create and apply the data capture configuration
190
- data_capture_config = DataCaptureConfig(
191
- enable_capture=True, # Required parameter
192
- sampling_percentage=capture_percentage,
193
- destination_s3_uri=self.data_capture_path,
194
- )
195
-
196
- # Update endpoint with the new capture configuration
197
- Predictor(self.endpoint_name, sagemaker_session=self.sagemaker_session).update_data_capture_config(
198
- data_capture_config=data_capture_config
199
- )
200
-
201
- # Clean up old endpoint configuration
202
- self.sagemaker_client.delete_endpoint_config(EndpointConfigName=current_endpoint_config_name)
203
-
204
- def data_capture_config(self):
205
- """
206
- Returns the complete data capture configuration from the endpoint config.
207
- Returns:
208
- dict: Complete DataCaptureConfig from AWS, or None if not configured
209
- """
210
- config_name = self.endpoint.endpoint_config_name()
211
- response = self.sagemaker_client.describe_endpoint_config(EndpointConfigName=config_name)
212
- data_capture_config = response.get("DataCaptureConfig")
213
- if not data_capture_config:
214
- self.log.error(f"No data capture configuration found for endpoint config {config_name}")
215
- return None
216
- return data_capture_config
217
-
218
- def disable_data_capture(self):
219
- """
220
- Disable data capture for the SageMaker endpoint.
221
- """
222
- # Early return if data capture isn't configured
223
- if not self.data_capture_enabled():
224
- self.log.important(f"Data capture is not currently enabled for {self.endpoint_name}.")
168
+ if self.data_capture.is_enabled():
169
+ self.log.info(f"Data capture is already enabled for {self.endpoint_name}.")
225
170
  return
226
171
 
227
- # Get the current endpoint configuration name for later deletion
228
- current_endpoint_config_name = self.endpoint.endpoint_config_name()
229
-
230
- # Log the operation
231
- self.log.important(f"Disabling Data Capture for {self.endpoint_name}")
232
- self.log.important("This normally redeploys the endpoint...")
233
-
234
- # Create a configuration with capture disabled
235
- data_capture_config = DataCaptureConfig(enable_capture=False, destination_s3_uri=self.data_capture_path)
236
-
237
- # Update endpoint with the new configuration
238
- Predictor(self.endpoint_name, sagemaker_session=self.sagemaker_session).update_data_capture_config(
239
- data_capture_config=data_capture_config
240
- )
241
-
242
- # Clean up old endpoint configuration
243
- self.sagemaker_client.delete_endpoint_config(EndpointConfigName=current_endpoint_config_name)
244
-
245
- def data_capture_enabled(self):
246
- """
247
- Check if data capture is already configured on the endpoint.
248
- Args:
249
- capture_percentage (int): Expected data capture percentage.
250
- Returns:
251
- bool: True if data capture is already configured, False otherwise.
252
- """
253
- try:
254
- endpoint_config_name = self.endpoint.endpoint_config_name()
255
- endpoint_config = self.sagemaker_client.describe_endpoint_config(EndpointConfigName=endpoint_config_name)
256
- data_capture_config = endpoint_config.get("DataCaptureConfig", {})
257
-
258
- # Check if data capture is enabled and the percentage matches
259
- is_enabled = data_capture_config.get("EnableCapture", False)
260
- return is_enabled
261
- except Exception as e:
262
- self.log.error(f"Error checking data capture configuration: {e}")
263
- return False
264
-
265
- def data_capture_percent(self):
266
- """
267
- Get the data capture percentage from the endpoint configuration.
268
-
269
- Returns:
270
- int: Data capture percentage if enabled, None otherwise.
271
- """
272
- try:
273
- endpoint_config_name = self.endpoint.endpoint_config_name()
274
- endpoint_config = self.sagemaker_client.describe_endpoint_config(EndpointConfigName=endpoint_config_name)
275
- data_capture_config = endpoint_config.get("DataCaptureConfig", {})
276
-
277
- # Check if data capture is enabled and return the percentage
278
- if data_capture_config.get("EnableCapture", False):
279
- return data_capture_config.get("InitialSamplingPercentage", 0)
280
- else:
281
- return None
282
- except Exception as e:
283
- self.log.error(f"Error checking data capture percentage: {e}")
284
- return None
285
-
286
- def get_captured_data(self, max_files=None, add_timestamp=True) -> Tuple[pd.DataFrame, pd.DataFrame]:
287
- """
288
- Read and process captured data from S3.
289
-
290
- Args:
291
- max_files (int, optional): Maximum number of files to process.
292
- Defaults to None to process all files.
293
- add_timestamp (bool, optional): Whether to add a timestamp column to the DataFrame.
294
-
295
- Returns:
296
- Tuple[pd.DataFrame, pd.DataFrame]: Processed input and output DataFrames.
297
- """
298
- # List files in the specified S3 path
299
- files = wr.s3.list_objects(self.data_capture_path)
300
- if not files:
301
- self.log.warning(f"No data capture files found in {self.data_capture_path}.")
302
- return pd.DataFrame(), pd.DataFrame()
303
-
304
- self.log.info(f"Found {len(files)} files in {self.data_capture_path}.")
305
-
306
- # Sort files by timestamp (assuming the naming convention includes timestamp)
307
- files.sort()
308
-
309
- # Select files to process
310
- if max_files is None:
311
- files_to_process = files
312
- self.log.info(f"Processing all {len(files)} files.")
313
- else:
314
- files_to_process = files[-max_files:] if files else []
315
- self.log.info(f"Processing the {len(files_to_process)} most recent file(s).")
316
-
317
- # Process each file
318
- all_input_dfs = []
319
- all_output_dfs = []
320
- for file_path in files_to_process:
321
- self.log.info(f"Processing {file_path}...")
322
- try:
323
- # Read the JSON lines file
324
- df = wr.s3.read_json(path=file_path, lines=True)
325
- if not df.empty:
326
- input_df, output_df = process_data_capture(df)
327
- # Generate a timestamp column if requested
328
- if add_timestamp:
329
- # Get file metadata to extract last modified time
330
- file_metadata = wr.s3.describe_objects(path=file_path)
331
- timestamp = file_metadata[file_path]["LastModified"]
332
- output_df["timestamp"] = timestamp
333
-
334
- # Append the processed DataFrames to the lists
335
- all_input_dfs.append(input_df)
336
- all_output_dfs.append(output_df)
337
- except Exception as e:
338
- self.log.warning(f"Error processing file {file_path}: {e}")
339
-
340
- # Combine all DataFrames
341
- if not all_input_dfs or not all_output_dfs:
342
- self.log.warning("No valid data was processed from the captured files.")
343
- return pd.DataFrame(), pd.DataFrame()
344
-
345
- return pd.concat(all_input_dfs, ignore_index=True), pd.concat(all_output_dfs, ignore_index=True)
172
+ self.data_capture.enable(capture_percentage=capture_percentage)
173
+ self.log.important(f"Enabled data capture for {self.endpoint_name} at {self.data_capture_path}")
346
174
 
347
175
  def baseline_exists(self) -> bool:
348
176
  """
@@ -533,6 +361,11 @@ class MonitorCore:
533
361
  self.log.warning("If you want to create another one, delete existing schedule first.")
534
362
  return
535
363
 
364
+ # Check if data capture is enabled, if not enable it
365
+ if not self.data_capture.is_enabled():
366
+ self.log.warning("Data capture is not enabled for this endpoint. Enabling it now...")
367
+ self.enable_data_capture(capture_percentage=100)
368
+
536
369
  # Set up a NEW monitoring schedule
537
370
  schedule_args = {
538
371
  "monitor_schedule_name": self.monitoring_schedule_name,
@@ -577,33 +410,6 @@ class MonitorCore:
577
410
  self.model_monitor.delete_monitoring_schedule()
578
411
  self.log.important(f"Deleted monitoring schedule for {self.endpoint_name}.")
579
412
 
580
- # Put this functionality into this class
581
- """
582
- executions = my_monitor.list_executions()
583
- latest_execution = executions[-1]
584
-
585
- latest_execution.describe()['ProcessingJobStatus']
586
- latest_execution.describe()['ExitMessage']
587
- Here are the possible terminal states and what each of them means:
588
-
589
- - Completed - This means the monitoring execution completed and no issues were found in the violations report.
590
- - CompletedWithViolations - This means the execution completed, but constraint violations were detected.
591
- - Failed - The monitoring execution failed, maybe due to client error
592
- (perhaps incorrect role premissions) or infrastructure issues. Further
593
- examination of the FailureReason and ExitMessage is necessary to identify what exactly happened.
594
- - Stopped - job exceeded the max runtime or was manually stopped.
595
- You can also get the S3 URI for the output with latest_execution.output.destination and analyze the results.
596
-
597
- Visualize results
598
- You can use the monitor object to gather reports for visualization:
599
-
600
- suggested_constraints = my_monitor.suggested_constraints()
601
- baseline_statistics = my_monitor.baseline_statistics()
602
-
603
- latest_monitoring_violations = my_monitor.latest_monitoring_constraint_violations()
604
- latest_monitoring_statistics = my_monitor.latest_monitoring_statistics()
605
- """
606
-
607
413
  def get_monitoring_results(self, max_results=10) -> pd.DataFrame:
608
414
  """Get the results of monitoring executions
609
415
 
@@ -758,7 +564,7 @@ class MonitorCore:
758
564
  Returns:
759
565
  str: String representation of this MonitorCore object
760
566
  """
761
- summary_dict = {} # Disabling for now self.summary()
567
+ summary_dict = self.summary()
762
568
  summary_items = [f" {repr(key)}: {repr(value)}" for key, value in summary_dict.items()]
763
569
  summary_str = f"{self.__class__.__name__}: {self.endpoint_name}\n" + ",\n".join(summary_items)
764
570
  return summary_str
@@ -775,7 +581,6 @@ if __name__ == "__main__":
775
581
 
776
582
  # Create the Class and test it out
777
583
  endpoint_name = "abalone-regression-rt"
778
- endpoint_name = "logd-dev-reg-rt"
779
584
  my_endpoint = EndpointCore(endpoint_name)
780
585
  if not my_endpoint.exists():
781
586
  print(f"Endpoint {endpoint_name} does not exist.")
@@ -788,11 +593,10 @@ if __name__ == "__main__":
788
593
  # Check the details of the monitoring class
789
594
  pprint(mm.details())
790
595
 
791
- # Enable data capture on the endpoint
792
- mm.enable_data_capture()
596
+ # Enable data capture (if not already enabled)
597
+ mm.enable_data_capture(capture_percentage=100)
793
598
 
794
599
  # Create a baseline for monitoring
795
- # mm.create_baseline(recreate=True)
796
600
  mm.create_baseline()
797
601
 
798
602
  # Check the monitoring outputs
@@ -804,30 +608,11 @@ if __name__ == "__main__":
804
608
  pprint(mm.get_constraints())
805
609
 
806
610
  print("\nStatistics...")
807
- print(mm.get_statistics())
611
+ print(str(mm.get_statistics())[:1000]) # Print only first 1000 characters
808
612
 
809
613
  # Set up the monitoring schedule (if it doesn't already exist)
810
614
  mm.create_monitoring_schedule()
811
615
 
812
- #
813
- # Test the data capture by running some predictions
814
- #
815
-
816
- # Make predictions on the Endpoint using the FeatureSet evaluation data
817
- # pred_df = my_endpoint.auto_inference()
818
- # print(pred_df.head())
819
-
820
- # Check that data capture is working
821
- input_df, output_df = mm.get_captured_data()
822
- if input_df.empty or output_df.empty:
823
- print("No data capture files found, for a new endpoint it may take a few minutes to start capturing data")
824
- else:
825
- print("Found data capture files")
826
- print("Input")
827
- print(input_df.head())
828
- print("Output")
829
- print(output_df.head())
830
-
831
616
  # Test update_constraints (commented out for now)
832
617
  # print("\nTesting constraint updates...")
833
618
  # custom_constraints = {"sex": {"allowed_values": ["M", "F", "I"]}, "length": {"min": 0.0, "max": 1.0}}
@@ -846,7 +631,7 @@ if __name__ == "__main__":
846
631
  print("\nTesting execution details retrieval...")
847
632
  if not results_df.empty:
848
633
  latest_execution_arn = results_df.iloc[0]["processing_job_arn"]
849
- execution_details = mm.get_execution_details(latest_execution_arn)
634
+ execution_details = mm.get_execution_details(latest_execution_arn) if latest_execution_arn else None
850
635
  if execution_details:
851
636
  print(f"Execution details for {latest_execution_arn}:")
852
637
  pprint(execution_details)
@@ -54,7 +54,11 @@ class AWSAccountClamp:
54
54
 
55
55
  # Check our Assume Role
56
56
  self.log.info("Checking Workbench Assumed Role...")
57
- self.aws_session.assumed_role_info()
57
+ role_info = self.aws_session.assumed_role_info()
58
+ self.log.info(f"Assumed Role: {role_info}")
59
+
60
+ # Check if we have tag write permissions (if we don't, we are read-only)
61
+ self.read_only = not self.check_tag_permissions()
58
62
 
59
63
  # Check our Workbench API Key and Load the License
60
64
  self.log.info("Checking Workbench API License...")
@@ -138,6 +142,45 @@ class AWSAccountClamp:
138
142
  """
139
143
  return self.boto3_session.client("sagemaker")
140
144
 
145
+ def check_tag_permissions(self):
146
+ """Check if current role has permission to add tags to SageMaker endpoints.
147
+
148
+ Returns:
149
+ bool: True if AddTags is allowed, False otherwise
150
+ """
151
+ try:
152
+ sagemaker = self.boto3_session.client("sagemaker")
153
+
154
+ # Use a non-existent endpoint name
155
+ fake_endpoint = "workbench-permission-check-dummy-endpoint"
156
+
157
+ # Try to add tags to the non-existent endpoint
158
+ sagemaker.add_tags(
159
+ ResourceArn=f"arn:aws:sagemaker:{self.region}:{self.account_id}:endpoint/{fake_endpoint}",
160
+ Tags=[{"Key": "PermissionCheck", "Value": "Test"}],
161
+ )
162
+
163
+ # If we get here, we have permission (but endpoint doesn't exist)
164
+ return True
165
+
166
+ except ClientError as e:
167
+ error_code = e.response["Error"]["Code"]
168
+
169
+ # AccessDeniedException = no permission
170
+ if error_code == "AccessDeniedException":
171
+ self.log.debug("No AddTags permission (AccessDeniedException)")
172
+ return False
173
+
174
+ # ResourceNotFound = we have permission, but endpoint doesn't exist
175
+ elif error_code in ["ResourceNotFound", "ValidationException"]:
176
+ self.log.debug("AddTags permission verified (resource not found)")
177
+ return True
178
+
179
+ # Unexpected error, assume no permission for safety
180
+ else:
181
+ self.log.debug(f"Unexpected error checking permissions: {error_code}")
182
+ return False
183
+
141
184
 
142
185
  if __name__ == "__main__":
143
186
  """Exercise the AWS Account Clamp Class"""
@@ -162,3 +205,9 @@ if __name__ == "__main__":
162
205
  print("\n\n*** AWS Sagemaker Session/Client Check ***")
163
206
  sm_client = aws_account_clamp.sagemaker_client()
164
207
  print(sm_client.list_feature_groups()["FeatureGroupSummaries"])
208
+
209
+ print("\n\n*** AWS Tag Permission Check ***")
210
+ if aws_account_clamp.check_tag_permissions():
211
+ print("Tag Permission Check Success...")
212
+ else:
213
+ print("Tag Permission Check Failed...")
@@ -196,7 +196,9 @@ class AWSMeta:
196
196
 
197
197
  # Return the summary as a DataFrame
198
198
  df = pd.DataFrame(data_summary).convert_dtypes()
199
- return df.sort_values(by="Created", ascending=False)
199
+ if not df.empty:
200
+ df.sort_values(by="Created", ascending=False, inplace=True)
201
+ return df
200
202
 
201
203
  def models(self, details: bool = False) -> pd.DataFrame:
202
204
  """Get a summary of the Models in AWS.
@@ -256,7 +258,9 @@ class AWSMeta:
256
258
 
257
259
  # Return the summary as a DataFrame
258
260
  df = pd.DataFrame(model_summary).convert_dtypes()
259
- return df.sort_values(by="Created", ascending=False)
261
+ if not df.empty:
262
+ df.sort_values(by="Created", ascending=False, inplace=True)
263
+ return df
260
264
 
261
265
  def endpoints(self, details: bool = False) -> pd.DataFrame:
262
266
  """Get a summary of the Endpoints in AWS.
@@ -308,7 +312,7 @@ class AWSMeta:
308
312
  "Status": endpoint_details.get("EndpointStatus", "-"),
309
313
  "Config": endpoint_details.get("EndpointConfigName", "-"),
310
314
  "Variant": endpoint_details["config"]["variant"],
311
- "Capture": str(endpoint_details.get("DataCaptureConfig", {}).get("EnableCapture", "False")),
315
+ "Capture": str(endpoint_details.get("DataCaptureConfig", {}).get("EnableCapture", "-")),
312
316
  "Samp(%)": str(endpoint_details.get("DataCaptureConfig", {}).get("CurrentSamplingPercentage", "-")),
313
317
  "Tags": aws_tags.get("workbench_tags", "-"),
314
318
  "Monitored": endpoint_details["monitored"],
@@ -317,7 +321,9 @@ class AWSMeta:
317
321
 
318
322
  # Return the summary as a DataFrame
319
323
  df = pd.DataFrame(data_summary).convert_dtypes()
320
- return df.sort_values(by="Created", ascending=False)
324
+ if not df.empty:
325
+ df.sort_values(by="Created", ascending=False, inplace=True)
326
+ return df
321
327
 
322
328
  def _endpoint_config_info(self, endpoint_config_name: str) -> dict:
323
329
  """Internal: Get the Endpoint Configuration information for the given endpoint config name.
@@ -657,7 +663,8 @@ class AWSMeta:
657
663
  df = pd.DataFrame(data_summary).convert_dtypes()
658
664
 
659
665
  # Sort by the Modified column
660
- df = df.sort_values(by="Modified", ascending=False)
666
+ if not df.empty:
667
+ df = df.sort_values(by="Modified", ascending=False)
661
668
  return df
662
669
 
663
670
  def _aws_pipelines(self) -> pd.DataFrame:
@@ -4,6 +4,7 @@ from typing import Union
4
4
  import logging
5
5
  import json
6
6
  import zlib
7
+ import time
7
8
  import base64
8
9
  from botocore.exceptions import ClientError
9
10
 
@@ -77,7 +78,7 @@ class AWSParameterStore:
77
78
  all_parameters = []
78
79
 
79
80
  # Make the initial call to describe parameters
80
- response = self.ssm_client.describe_parameters(**params)
81
+ response = self._call_with_retry(self.ssm_client.describe_parameters, **params)
81
82
 
82
83
  # Aggregate the names from the initial response
83
84
  all_parameters.extend(param["Name"] for param in response["Parameters"])
@@ -86,7 +87,7 @@ class AWSParameterStore:
86
87
  while "NextToken" in response:
87
88
  # Update the parameters with the NextToken for subsequent calls
88
89
  params["NextToken"] = response["NextToken"]
89
- response = self.ssm_client.describe_parameters(**params)
90
+ response = self._call_with_retry(self.ssm_client.describe_parameters, **params)
90
91
 
91
92
  # Aggregate the names from the subsequent responses
92
93
  all_parameters.extend(param["Name"] for param in response["Parameters"])
@@ -183,6 +184,21 @@ class AWSParameterStore:
183
184
  self.log.critical(f"Failed to add/update parameter '{name}': {e}")
184
185
  raise
185
186
 
187
+ def _call_with_retry(self, func, **kwargs):
188
+ """Call AWS API with exponential backoff on throttling."""
189
+ max_retries = 5
190
+ base_delay = 1
191
+ for attempt in range(max_retries):
192
+ try:
193
+ return func(**kwargs)
194
+ except ClientError as e:
195
+ if e.response["Error"]["Code"] == "ThrottlingException" and attempt < max_retries - 1:
196
+ delay = base_delay * (2**attempt)
197
+ self.log.warning(f"Throttled, retrying in {delay}s...")
198
+ time.sleep(delay)
199
+ else:
200
+ raise
201
+
186
202
  @staticmethod
187
203
  def _compress_value(value) -> str:
188
204
  """Compress a value with precision reduction."""
@@ -10,7 +10,7 @@ import logging
10
10
 
11
11
  # Workbench Imports
12
12
  from workbench.utils.config_manager import ConfigManager
13
- from workbench.utils.execution_environment import running_on_lambda, running_on_glue
13
+ from workbench_bridges.utils.execution_environment import running_as_service
14
14
 
15
15
  # Attempt to import IPython-related utilities
16
16
  try:
@@ -66,10 +66,10 @@ class AWSSession:
66
66
  return self._cached_boto3_session
67
67
 
68
68
  def _create_boto3_session(self):
69
- """Internal: Get the AWS Boto3 Session, defaulting to the Workbench Role if possible."""
69
+ """Internal: Get the AWS Boto3 Session, assuming the Workbench Role if necessary."""
70
70
 
71
- # Check the execution environment and determine if we need to assume the Workbench Role
72
- if running_on_lambda() or running_on_glue() or self.is_workbench_role():
71
+ # Check if we're running as a service or already using the Workbench Role
72
+ if running_as_service() or self.is_workbench_role():
73
73
  self.log.important("Using the default Boto3 session...")
74
74
  return boto3.Session(region_name=self.region)
75
75
 
@@ -1,7 +1,7 @@
1
1
  """MolecularDescriptors: Compute a Feature Set based on RDKit Descriptors
2
2
 
3
- Note: An alternative to using this class is to use the `compute_molecular_descriptors` function directly.
4
- df_features = compute_molecular_descriptors(df)
3
+ Note: An alternative to using this class is to use the `compute_descriptors` function directly.
4
+ df_features = compute_descriptors(df)
5
5
  to_features = PandasToFeatures("my_feature_set")
6
6
  to_features.set_input(df_features, id_column="id")
7
7
  to_features.set_output_tags(["blah", "whatever"])
@@ -10,7 +10,7 @@ Note: An alternative to using this class is to use the `compute_molecular_descri
10
10
 
11
11
  # Local Imports
12
12
  from workbench.core.transforms.data_to_features.light.data_to_features_light import DataToFeaturesLight
13
- from workbench.utils.chem_utils import compute_molecular_descriptors
13
+ from workbench.utils.chem_utils.mol_descriptors import compute_descriptors
14
14
 
15
15
 
16
16
  class MolecularDescriptors(DataToFeaturesLight):
@@ -39,7 +39,7 @@ class MolecularDescriptors(DataToFeaturesLight):
39
39
  """Compute a Feature Set based on RDKit Descriptors"""
40
40
 
41
41
  # Compute/add all the Molecular Descriptors
42
- self.output_df = compute_molecular_descriptors(self.input_df)
42
+ self.output_df = compute_descriptors(self.input_df)
43
43
 
44
44
 
45
45
  if __name__ == "__main__":