workbench 0.8.166__tar.gz → 0.8.198__tar.gz
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- {workbench-0.8.166 → workbench-0.8.198}/.github/workflows/python-lint.yml +2 -3
- workbench-0.8.198/Dockerfile +7 -0
- {workbench-0.8.166 → workbench-0.8.198}/LICENSE +1 -1
- {workbench-0.8.166 → workbench-0.8.198}/PKG-INFO +24 -2
- {workbench-0.8.166 → workbench-0.8.198}/applications/aws_dashboard/Dockerfile +1 -1
- workbench-0.8.166/aws_setup/aws_account_check.py → workbench-0.8.198/aws_setup/aws_account_setup.py +25 -1
- workbench-0.8.198/aws_setup/workbench_compute/README.md +58 -0
- workbench-0.8.198/aws_setup/workbench_compute/app.py +64 -0
- workbench-0.8.198/aws_setup/workbench_compute/cdk.json +97 -0
- {workbench-0.8.166/aws_setup/workbench_core → workbench-0.8.198/aws_setup/workbench_compute}/requirements.txt +1 -2
- workbench-0.8.198/aws_setup/workbench_compute/tests/unit/test_workbench_compute_stack.py +17 -0
- workbench-0.8.198/aws_setup/workbench_compute/workbench_compute/workbench_compute_stack.py +279 -0
- workbench-0.8.198/aws_setup/workbench_core/app.py +75 -0
- workbench-0.8.198/aws_setup/workbench_core/requirements.txt +3 -0
- {workbench-0.8.166 → workbench-0.8.198}/aws_setup/workbench_core/workbench_core/workbench_core_stack.py +552 -103
- {workbench-0.8.166 → workbench-0.8.198}/aws_setup/workbench_dashboard_full/app.py +1 -1
- {workbench-0.8.166 → workbench-0.8.198}/aws_setup/workbench_dashboard_lite/app.py +1 -1
- {workbench-0.8.166 → workbench-0.8.198}/docs/api_classes/endpoint.md +3 -7
- {workbench-0.8.166 → workbench-0.8.198}/docs/api_classes/monitor.md +2 -2
- {workbench-0.8.166 → workbench-0.8.198}/docs/api_classes/overview.md +2 -7
- {workbench-0.8.166 → workbench-0.8.198}/docs/api_classes/views.md +2 -2
- {workbench-0.8.166 → workbench-0.8.198}/docs/aws_setup/core_stack.md +34 -6
- {workbench-0.8.166 → workbench-0.8.198}/docs/aws_setup/sso_assume_role.md +22 -4
- {workbench-0.8.166 → workbench-0.8.198}/docs/core_classes/views/overview.md +2 -2
- {workbench-0.8.166 → workbench-0.8.198}/examples/chem_utils/tautomerize_smiles.py +10 -4
- {workbench-0.8.166 → workbench-0.8.198}/examples/endpoint/endpoint_inference.py +3 -7
- {workbench-0.8.166 → workbench-0.8.198}/examples/full_ml_pipeline.py +1 -3
- workbench-0.8.198/examples/ml_pipelines/list_models.py +11 -0
- workbench-0.8.198/examples/ml_pipelines/wine_classifier.py +41 -0
- workbench-0.8.198/examples/models/smiles_to_md_v1.py +27 -0
- workbench-0.8.166/examples/models/uq/mapie_xgb.py → workbench-0.8.198/examples/models/uq/mapie.py +4 -4
- {workbench-0.8.166 → workbench-0.8.198}/examples/monitor/monitor_usage.py +1 -6
- {workbench-0.8.166 → workbench-0.8.198}/experiments/chem_info/bulk_sims.py +1 -1
- {workbench-0.8.166 → workbench-0.8.198}/experiments/chem_info/knn_sims.py +1 -1
- workbench-0.8.198/experiments/chemprop_model.py +492 -0
- workbench-0.8.198/experiments/mapie_model.py +477 -0
- {workbench-0.8.166 → workbench-0.8.198}/experiments/pytorch_model.py +2 -2
- workbench-0.8.198/ml_pipelines/hyper_uq.py +50 -0
- {workbench-0.8.166/model_docker_images/pytorch_inference → workbench-0.8.198/model_docker_images/inference}/Dockerfile +5 -2
- workbench-0.8.198/model_docker_images/inference/requirements.txt +9 -0
- workbench-0.8.198/model_docker_images/ml_pipelines/Dockerfile +38 -0
- workbench-0.8.198/model_docker_images/ml_pipelines/ml_pipeline_runner.py +73 -0
- workbench-0.8.198/model_docker_images/ml_pipelines/requirements.txt +16 -0
- {workbench-0.8.166 → workbench-0.8.198}/model_docker_images/scripts/build_deploy.sh +12 -8
- {workbench-0.8.166 → workbench-0.8.198}/model_docker_images/tests/example_model_script.py +2 -2
- {workbench-0.8.166 → workbench-0.8.198}/model_docker_images/training/Dockerfile +9 -2
- workbench-0.8.198/model_docker_images/training/requirements.txt +7 -0
- {workbench-0.8.166 → workbench-0.8.198}/notebooks/Inference_On_Legacy_Models.ipynb +2 -2
- {workbench-0.8.166 → workbench-0.8.198}/notebooks/ML_Pipeline_with_Workbench_2.ipynb +1 -1
- {workbench-0.8.166 → workbench-0.8.198}/pyproject.toml +5 -1
- workbench-0.8.198/scripts/delete_data_capture.py +72 -0
- workbench-0.8.166/scripts/endpoint_inference_launch.py → workbench-0.8.198/scripts/endpoint_timing.py +3 -26
- workbench-0.8.198/scripts/sagemaker_feature_group_issue.py +61 -0
- workbench-0.8.198/scripts/test_feature_set_creation.py +20 -0
- {workbench-0.8.166 → workbench-0.8.198}/scripts/tox21/test_tox_heuristic.py +1 -1
- workbench-0.8.198/scripts/tox21/tox21_to_df_store.py +186 -0
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/algorithms/dataframe/__init__.py +1 -2
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/algorithms/dataframe/fingerprint_proximity.py +2 -2
- workbench-0.8.198/src/workbench/algorithms/dataframe/proximity.py +403 -0
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/algorithms/graph/light/proximity_graph.py +10 -8
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/api/compound.py +1 -1
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/api/endpoint.py +2 -2
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/api/feature_set.py +4 -4
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/api/model.py +15 -14
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/api/monitor.py +1 -16
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/core/artifacts/artifact.py +11 -3
- workbench-0.8.198/src/workbench/core/artifacts/data_capture_core.py +355 -0
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/core/artifacts/endpoint_core.py +129 -34
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/core/artifacts/feature_set_core.py +197 -16
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/core/artifacts/model_core.py +70 -53
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/core/artifacts/monitor_core.py +33 -249
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/core/cloud_platform/aws/aws_account_clamp.py +50 -1
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/core/cloud_platform/aws/aws_meta.py +11 -4
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/core/cloud_platform/aws/aws_session.py +4 -4
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/core/transforms/data_to_features/light/molecular_descriptors.py +4 -4
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/core/transforms/features_to_model/features_to_model.py +12 -7
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/core/transforms/model_to_endpoint/model_to_endpoint.py +36 -6
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/core/transforms/pandas_transforms/pandas_to_features.py +27 -0
- workbench-0.8.198/src/workbench/core/views/training_view.py +231 -0
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/core/views/view.py +51 -1
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/core/views/view_utils.py +4 -4
- workbench-0.8.198/src/workbench/model_scripts/__pycache__/script_generation.cpython-312.pyc +0 -0
- workbench-0.8.198/src/workbench/model_scripts/__pycache__/script_generation.cpython-313.pyc +0 -0
- workbench-0.8.198/src/workbench/model_scripts/custom_models/chem_info/mol_descriptors.py +483 -0
- workbench-0.8.198/src/workbench/model_scripts/custom_models/chem_info/mol_standardize.py +450 -0
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/model_scripts/custom_models/chem_info/molecular_descriptors.py +7 -9
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/model_scripts/custom_models/proximity/feature_space_proximity.template +3 -5
- workbench-0.8.198/src/workbench/model_scripts/custom_models/proximity/proximity.py +403 -0
- workbench-0.8.198/src/workbench/model_scripts/custom_models/proximity/requirements.txt +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/model_scripts/custom_models/uq_models/bayesian_ridge.template +7 -8
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/model_scripts/custom_models/uq_models/ensemble_xgb.template +10 -17
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/model_scripts/custom_models/uq_models/gaussian_process.template +5 -11
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/model_scripts/custom_models/uq_models/meta_uq.template +156 -58
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/model_scripts/custom_models/uq_models/ngboost.template +20 -14
- workbench-0.8.198/src/workbench/model_scripts/custom_models/uq_models/proximity.py +403 -0
- workbench-0.8.198/src/workbench/model_scripts/custom_models/uq_models/requirements.txt +1 -0
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/model_scripts/ensemble_xgb/ensemble_xgb.template +5 -13
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/model_scripts/pytorch_model/generated_model_script.py +14 -23
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/model_scripts/pytorch_model/pytorch.template +9 -18
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/model_scripts/scikit_learn/scikit_learn.template +4 -9
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/model_scripts/script_generation.py +7 -2
- workbench-0.8.198/src/workbench/model_scripts/uq_models/generated_model_script.py +589 -0
- workbench-0.8.198/src/workbench/model_scripts/uq_models/mapie.template +589 -0
- workbench-0.8.198/src/workbench/model_scripts/uq_models/requirements.txt +1 -0
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/model_scripts/xgb_model/generated_model_script.py +34 -43
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/model_scripts/xgb_model/xgb_model.template +31 -40
- workbench-0.8.198/src/workbench/repl/__init__.py +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/repl/workbench_shell.py +7 -7
- workbench-0.8.198/src/workbench/scripts/lambda_launcher.py +63 -0
- workbench-0.8.198/src/workbench/scripts/ml_pipeline_batch.py +137 -0
- workbench-0.8.198/src/workbench/scripts/ml_pipeline_sqs.py +186 -0
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/scripts/monitor_cloud_watch.py +20 -100
- workbench-0.8.198/src/workbench/utils/__init__.py +0 -0
- workbench-0.8.198/src/workbench/utils/chem_utils/__init__.py +0 -0
- workbench-0.8.198/src/workbench/utils/chem_utils/fingerprints.py +134 -0
- workbench-0.8.198/src/workbench/utils/chem_utils/misc.py +194 -0
- workbench-0.8.198/src/workbench/utils/chem_utils/mol_descriptors.py +483 -0
- workbench-0.8.198/src/workbench/utils/chem_utils/mol_standardize.py +450 -0
- workbench-0.8.198/src/workbench/utils/chem_utils/mol_tagging.py +348 -0
- workbench-0.8.198/src/workbench/utils/chem_utils/projections.py +209 -0
- workbench-0.8.198/src/workbench/utils/chem_utils/salts.py +256 -0
- workbench-0.8.198/src/workbench/utils/chem_utils/sdf.py +292 -0
- workbench-0.8.198/src/workbench/utils/chem_utils/toxicity.py +250 -0
- workbench-0.8.198/src/workbench/utils/chem_utils/vis.py +253 -0
- workbench-0.8.198/src/workbench/utils/cloudwatch_utils.py +137 -0
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/utils/config_manager.py +2 -6
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/utils/endpoint_utils.py +5 -7
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/utils/license_manager.py +2 -6
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/utils/model_utils.py +95 -34
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/utils/monitor_utils.py +44 -62
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/utils/pandas_utils.py +3 -3
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/utils/shap_utils.py +10 -2
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/utils/workbench_sqs.py +1 -1
- workbench-0.8.198/src/workbench/utils/xgboost_model_utils.py +626 -0
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/web_interface/components/model_plot.py +7 -1
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/web_interface/components/plugin_unit_test.py +5 -2
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/web_interface/components/plugins/dashboard_status.py +3 -1
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/web_interface/components/plugins/generated_compounds.py +1 -1
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/web_interface/components/plugins/model_details.py +9 -7
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench/web_interface/components/plugins/scatter_plot.py +3 -3
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench.egg-info/PKG-INFO +24 -2
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench.egg-info/SOURCES.txt +70 -61
- {workbench-0.8.166 → workbench-0.8.198}/src/workbench.egg-info/entry_points.txt +3 -0
- {workbench-0.8.166/tests/create_test_artifacts → workbench-0.8.198/test_artifacts}/create_aqsol_uq_artifacts.py +9 -21
- workbench-0.8.198/test_artifacts/hyper_testing.py +70 -0
- workbench-0.8.198/test_artifacts/hyper_uq_testing.py +54 -0
- {workbench-0.8.166 → workbench-0.8.198}/tests/artifacts/endpoint_tests.py +7 -7
- {workbench-0.8.166 → workbench-0.8.198}/tests/chem_info/test_tautomerization.py +24 -6
- {workbench-0.8.166 → workbench-0.8.198}/tests/pytorch/pytorch_hello.py +2 -2
- {workbench-0.8.166 → workbench-0.8.198}/tox.ini +12 -7
- workbench-0.8.166/Dockerfile +0 -31
- workbench-0.8.166/aws_setup/event_bridge/dynamic_docker/Readme.md +0 -6
- workbench-0.8.166/aws_setup/event_bridge/dynamic_docker/app.py +0 -25
- workbench-0.8.166/aws_setup/event_bridge/dynamic_docker/lambda/lambda_replace_task.py +0 -56
- workbench-0.8.166/aws_setup/event_bridge/dynamic_docker/workbench_image_update_stack.py +0 -59
- workbench-0.8.166/aws_setup/workbench_core/app.py +0 -47
- workbench-0.8.166/aws_setup/workbench_dashboard_lite/cdk.json +0 -58
- workbench-0.8.166/examples/chem_utils/canonicalize_smiles.py +0 -22
- workbench-0.8.166/examples/pipelines/abalone_pipeline_v1.json +0 -43
- workbench-0.8.166/examples/pipelines/abalone_pipeline_v2.json +0 -45
- workbench-0.8.166/examples/pipelines/aqsol_pipeline_v1.json +0 -66
- workbench-0.8.166/examples/pipelines/pipeline_details.py +0 -5
- workbench-0.8.166/examples/pipelines/pipeline_execute.py +0 -11
- workbench-0.8.166/examples/pipelines/pipeline_manager.py +0 -18
- workbench-0.8.166/examples/storage/sagemaker_pipelines/all_steps.py +0 -27
- workbench-0.8.166/examples/storage/sagemaker_pipelines/hello.py +0 -1
- workbench-0.8.166/examples/storage/sagemaker_pipelines/ml_pipeline.py +0 -60
- workbench-0.8.166/examples/storage/sagemaker_pipelines/storage/full_pipeline_experiment/data_source.py +0 -27
- workbench-0.8.166/examples/storage/sagemaker_pipelines/storage/full_pipeline_experiment/endpoint.py +0 -5
- workbench-0.8.166/examples/storage/sagemaker_pipelines/storage/full_pipeline_experiment/feature_set.py +0 -5
- workbench-0.8.166/examples/storage/sagemaker_pipelines/storage/full_pipeline_experiment/ml_pipeline.py +0 -65
- workbench-0.8.166/examples/storage/sagemaker_pipelines/storage/full_pipeline_experiment/model.py +0 -13
- workbench-0.8.166/model_docker_images/inference/requirements.txt +0 -7
- workbench-0.8.166/model_docker_images/training/requirements.txt +0 -5
- workbench-0.8.166/scripts/endpoint_timing/endpoint_timing.py +0 -86
- workbench-0.8.166/scripts/endpoint_timing/endpoint_timing_old.py +0 -139
- workbench-0.8.166/scripts/endpoint_timing/timing_plot.py +0 -54
- workbench-0.8.166/scripts/model_to_endpoint_debugging.py +0 -124
- workbench-0.8.166/scripts/tox21/tox21_to_df_store.py +0 -114
- workbench-0.8.166/src/workbench/algorithms/dataframe/proximity.py +0 -384
- workbench-0.8.166/src/workbench/core/views/training_view.py +0 -160
- workbench-0.8.166/src/workbench/model_scripts/custom_models/chem_info/local_utils.py +0 -769
- workbench-0.8.166/src/workbench/model_scripts/custom_models/chem_info/tautomerize.py +0 -83
- workbench-0.8.166/src/workbench/model_scripts/custom_models/proximity/generated_model_script.py +0 -138
- workbench-0.8.166/src/workbench/model_scripts/custom_models/proximity/proximity.py +0 -384
- workbench-0.8.166/src/workbench/model_scripts/custom_models/uq_models/generated_model_script.py +0 -393
- workbench-0.8.166/src/workbench/model_scripts/custom_models/uq_models/mapie_xgb.template +0 -203
- workbench-0.8.166/src/workbench/model_scripts/custom_models/uq_models/proximity.py +0 -384
- workbench-0.8.166/src/workbench/model_scripts/custom_models/uq_models/requirements.txt +0 -3
- workbench-0.8.166/src/workbench/model_scripts/ensemble_xgb/generated_model_script.py +0 -279
- workbench-0.8.166/src/workbench/model_scripts/quant_regression/quant_regression.template +0 -279
- workbench-0.8.166/src/workbench/model_scripts/scikit_learn/generated_model_script.py +0 -307
- workbench-0.8.166/src/workbench/model_scripts/xgb_model/requirements.txt +0 -1
- workbench-0.8.166/src/workbench/utils/chem_utils.py +0 -1556
- workbench-0.8.166/src/workbench/utils/fast_inference.py +0 -167
- workbench-0.8.166/src/workbench/utils/resource_utils.py +0 -39
- workbench-0.8.166/src/workbench/utils/xgboost_model_utils.py +0 -416
- workbench-0.8.166/tests/chem_info/test_canonicalize.py +0 -37
- {workbench-0.8.166 → workbench-0.8.198}/.flake8 +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/.github/PULL_REQUEST_TEMPLATE.md +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/.github/dependabot.yml +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/.github/workflows/deploy-docs.yml +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/.gitignore +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/CONTRIBUTING.md +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/Makefile +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/README.md +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/SECURITY.md +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/applications/aws_dashboard/README.md +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/applications/aws_dashboard/app.py +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/applications/aws_dashboard/assets/favicon.ico +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/applications/aws_dashboard/dashboard +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/applications/aws_dashboard/deploy.sh +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/applications/aws_dashboard/nginx.conf +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/applications/aws_dashboard/open_source_config.json +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/applications/aws_dashboard/pages/data_sources/callbacks.py +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/applications/aws_dashboard/pages/data_sources/layout.py +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/applications/aws_dashboard/pages/data_sources/page.py +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/applications/aws_dashboard/pages/endpoints/callbacks.py +0 -0
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- {workbench-0.8.166 → workbench-0.8.198}/tests/specific/column_changes.py +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/tests/specific/config_manager.py +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/tests/specific/deletion_tests.py +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/tests/specific/shap_tests.py +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/tests/transforms/data_to_data_tests.py +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/tests/transforms/data_to_features_tests.py +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/tests/transforms/features_to_model_tests.py +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/tests/transforms/model_to_endpoint_tests.py +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/tests/transforms/pandas_to_data_tests.py +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/tests/transforms/pandas_to_features_test.py +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/tests/views/view_tests.py +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/tests/views/view_tests_complex.py +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/tests/web_components/confusion_matrix_test.py +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/tests/web_components/correlation_matrix_test.py +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/tests/web_components/graph_plot_test.py +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/tests/web_components/plugin_interface_test.py +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/tests/web_components/scatter_plot_test.py +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/ui_testing/assets/custom.css +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/ui_testing/table_comparison.py +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/ui_testing/theme_switching.py +0 -0
- {workbench-0.8.166 → workbench-0.8.198}/ui_testing/theme_switching_2.py +0 -0
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@@ -12,9 +12,9 @@ jobs:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@
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uses: actions/setup-python@v5
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with:
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python-version: '3.
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python-version: '3.13'
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- name: Install dependencies
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run: |
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- name: Run Flake8 (Linting)
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run: |
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flake8 --exclude '*generated*' src/workbench applications tests
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-
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FROM python:3.12-slim
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ARG WORKBENCH_VERSION=
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RUN apt-get update && apt-get upgrade -y && \
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apt-get install -y --no-install-recommends libexpat1 libnghttp2-dev && \
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apt-get clean && rm -rf /var/lib/apt/lists/* && \
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pip install --no-cache-dir workbench${WORKBENCH_VERSION:+==$WORKBENCH_VERSION}
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@@ -1,15 +1,37 @@
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1
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Metadata-Version: 2.4
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Name: workbench
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Version: 0.8.
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Version: 0.8.198
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Summary: Workbench: A Dashboard and Python API for creating and deploying AWS SageMaker Model Pipelines
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Author-email: SuperCowPowers LLC <support@supercowpowers.com>
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License
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License: MIT License
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Copyright (c) 2021-2026 SuperCowPowers LLC
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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+
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Project-URL: Homepage, https://github.com/SuperCowPowers/workbench
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Keywords: SageMaker,Machine Learning,AWS,Python,Utilities
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Classifier: Development Status :: 4 - Beta
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Classifier: Programming Language :: Python :: 3.10
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Classifier: Programming Language :: Python :: 3.11
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Classifier: Programming Language :: Python :: 3.12
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Classifier: Programming Language :: Python :: 3.13
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Classifier: Topic :: Scientific/Engineering
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Requires-Python: >=3.10
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Description-Content-Type: text/markdown
|
workbench-0.8.166/aws_setup/aws_account_check.py → workbench-0.8.198/aws_setup/aws_account_setup.py
RENAMED
|
@@ -39,12 +39,31 @@ class AWSAccountCheck:
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self.log.error(f"AccessDeniedException {e}")
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self.log.error(f"Access denied while trying to create/access the catalog database '{catalog_db}'.")
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self.log.error("Create the database manually in the AWS Glue Console, or run this command:")
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-
self.log.error('aws glue create-database --database-input \'{"Name": "
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self.log.error(f'aws glue create-database --database-input \'{{"Name": "{catalog_db}"}}\'')
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sys.exit(1)
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else:
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self.log.error(f"Unexpected error: {e}")
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sys.exit(1)
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+
def ensure_athena_results_bucket(self):
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"""Ensure that the Athena results S3 bucket exists"""
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+
bucket_name = f"aws-athena-query-results-{self.aws_clamp.account_id}-{self.aws_clamp.region}"
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self.log.important(f"Checking if Athena results bucket {bucket_name} exists...")
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try:
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s3_client = self.aws_clamp.boto3_session.client("s3")
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s3_client.head_bucket(Bucket=bucket_name)
|
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+
self.log.info(f"Athena results bucket {bucket_name} already exists")
|
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+
except ClientError as e:
|
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58
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+
if e.response["Error"]["Code"] == "404":
|
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+
self.log.error(f"Athena results bucket {bucket_name} does not exist.")
|
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60
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+
self.log.error("Create the bucket manually using this AWS CLI command:")
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self.log.error(f"aws s3 mb s3://{bucket_name}")
|
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sys.exit(1)
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else:
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self.log.error(f"Error checking bucket {bucket_name}: {e}")
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sys.exit(1)
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+
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def check(self):
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"""Check if the AWS Account is set up Correctly"""
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50
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self.log.info("*** Caller/Base AWS Identity Check ***")
|
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@@ -71,6 +90,11 @@ class AWSAccountCheck:
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71
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self.ensure_aws_catalog_db(catalog_db)
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print("\n")
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92
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+
# Check that the Athena Results Bucket exists
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self.log.info("*** AWS Athena Results Bucket Check ***")
|
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+
self.ensure_athena_results_bucket()
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print("\n")
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self.log.info("AWS Account Clamp: AOK!")
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@@ -0,0 +1,58 @@
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1
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+
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# Welcome to your CDK Python project!
|
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+
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|
4
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This is a blank project for CDK development with Python.
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The `cdk.json` file tells the CDK Toolkit how to execute your app.
|
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7
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This project is set up like a standard Python project. The initialization
|
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process also creates a virtualenv within this project, stored under the `.venv`
|
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+
directory. To create the virtualenv it assumes that there is a `python3`
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(or `python` for Windows) executable in your path with access to the `venv`
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package. If for any reason the automatic creation of the virtualenv fails,
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you can create the virtualenv manually.
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+
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+
To manually create a virtualenv on MacOS and Linux:
|
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+
|
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```
|
|
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$ python3 -m venv .venv
|
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19
|
+
```
|
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20
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+
|
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+
After the init process completes and the virtualenv is created, you can use the following
|
|
22
|
+
step to activate your virtualenv.
|
|
23
|
+
|
|
24
|
+
```
|
|
25
|
+
$ source .venv/bin/activate
|
|
26
|
+
```
|
|
27
|
+
|
|
28
|
+
If you are a Windows platform, you would activate the virtualenv like this:
|
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+
|
|
30
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+
```
|
|
31
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+
% .venv\Scripts\activate.bat
|
|
32
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+
```
|
|
33
|
+
|
|
34
|
+
Once the virtualenv is activated, you can install the required dependencies.
|
|
35
|
+
|
|
36
|
+
```
|
|
37
|
+
$ pip install -r requirements.txt
|
|
38
|
+
```
|
|
39
|
+
|
|
40
|
+
At this point you can now synthesize the CloudFormation template for this code.
|
|
41
|
+
|
|
42
|
+
```
|
|
43
|
+
$ cdk synth
|
|
44
|
+
```
|
|
45
|
+
|
|
46
|
+
To add additional dependencies, for example other CDK libraries, just add
|
|
47
|
+
them to your `setup.py` file and rerun the `pip install -r requirements.txt`
|
|
48
|
+
command.
|
|
49
|
+
|
|
50
|
+
## Useful commands
|
|
51
|
+
|
|
52
|
+
* `cdk ls` list all stacks in the app
|
|
53
|
+
* `cdk synth` emits the synthesized CloudFormation template
|
|
54
|
+
* `cdk deploy` deploy this stack to your default AWS account/region
|
|
55
|
+
* `cdk diff` compare deployed stack with current state
|
|
56
|
+
* `cdk docs` open CDK documentation
|
|
57
|
+
|
|
58
|
+
Enjoy!
|
|
@@ -0,0 +1,64 @@
|
|
|
1
|
+
import boto3
|
|
2
|
+
import aws_cdk as cdk
|
|
3
|
+
from aws_cdk import Fn
|
|
4
|
+
from workbench_compute.workbench_compute_stack import WorkbenchComputeStack, WorkbenchComputeStackProps
|
|
5
|
+
|
|
6
|
+
# Initialize Workbench ConfigManager
|
|
7
|
+
try:
|
|
8
|
+
from workbench.utils.config_manager import ConfigManager
|
|
9
|
+
|
|
10
|
+
cm = ConfigManager()
|
|
11
|
+
except ImportError:
|
|
12
|
+
print("Workbench Configuration Manager Not Found...")
|
|
13
|
+
print("Set the WORKBENCH_CONFIG Env var and run again...")
|
|
14
|
+
raise SystemExit(1)
|
|
15
|
+
|
|
16
|
+
# Grab the account and region using boto3
|
|
17
|
+
session = boto3.session.Session()
|
|
18
|
+
aws_account = session.client("sts").get_caller_identity().get("Account")
|
|
19
|
+
aws_region = session.region_name
|
|
20
|
+
print(f"Account: {aws_account}")
|
|
21
|
+
print(f"Region: {aws_region}")
|
|
22
|
+
|
|
23
|
+
# Get configurations needed for compute stack
|
|
24
|
+
workbench_bucket = cm.get_config("WORKBENCH_BUCKET")
|
|
25
|
+
if not workbench_bucket:
|
|
26
|
+
print("Error: WORKBENCH_BUCKET is required but not found in config.")
|
|
27
|
+
exit(1)
|
|
28
|
+
|
|
29
|
+
|
|
30
|
+
# Get the Batch and Lambda Roles from WorkbenchCore stack outputs
|
|
31
|
+
batch_role_arn = Fn.import_value("WorkbenchCore-BatchRoleArn")
|
|
32
|
+
lambda_role_arn = Fn.import_value("WorkbenchCore-LambdaRoleArn")
|
|
33
|
+
|
|
34
|
+
# VPC and subnet configuration (optional)
|
|
35
|
+
existing_vpc_id = cm.get_config("WORKBENCH_VPC_ID")
|
|
36
|
+
subnet_ids = cm.get_config("WORKBENCH_SUBNET_IDS") or []
|
|
37
|
+
|
|
38
|
+
# Log the configuration for transparency
|
|
39
|
+
print("Configuration:")
|
|
40
|
+
print(f" WORKBENCH_BUCKET: {workbench_bucket}")
|
|
41
|
+
print(f" WORKBENCH_BATCH_ROLE_ARN: {batch_role_arn}")
|
|
42
|
+
print(f" WORKBENCH_LAMBDA_ROLE_ARN: {lambda_role_arn}")
|
|
43
|
+
print(f" WORKBENCH_VPC_ID: {existing_vpc_id}")
|
|
44
|
+
print(f" WORKBENCH_SUBNET_IDS: {subnet_ids}")
|
|
45
|
+
|
|
46
|
+
# Our CDK App and Environment
|
|
47
|
+
app = cdk.App()
|
|
48
|
+
env = cdk.Environment(account=aws_account, region=aws_region)
|
|
49
|
+
|
|
50
|
+
# Create the Workbench Compute Stack
|
|
51
|
+
compute_stack = WorkbenchComputeStack(
|
|
52
|
+
app,
|
|
53
|
+
"WorkbenchCompute",
|
|
54
|
+
env=env,
|
|
55
|
+
props=WorkbenchComputeStackProps(
|
|
56
|
+
workbench_bucket=workbench_bucket,
|
|
57
|
+
batch_role_arn=batch_role_arn,
|
|
58
|
+
lambda_role_arn=lambda_role_arn,
|
|
59
|
+
existing_vpc_id=existing_vpc_id,
|
|
60
|
+
subnet_ids=subnet_ids,
|
|
61
|
+
),
|
|
62
|
+
)
|
|
63
|
+
|
|
64
|
+
app.synth()
|
|
@@ -0,0 +1,97 @@
|
|
|
1
|
+
{
|
|
2
|
+
"app": "python3 app.py",
|
|
3
|
+
"watch": {
|
|
4
|
+
"include": [
|
|
5
|
+
"**"
|
|
6
|
+
],
|
|
7
|
+
"exclude": [
|
|
8
|
+
"README.md",
|
|
9
|
+
"cdk*.json",
|
|
10
|
+
"requirements*.txt",
|
|
11
|
+
"source.bat",
|
|
12
|
+
"**/__init__.py",
|
|
13
|
+
"**/__pycache__",
|
|
14
|
+
"tests"
|
|
15
|
+
]
|
|
16
|
+
},
|
|
17
|
+
"context": {
|
|
18
|
+
"@aws-cdk/aws-lambda:recognizeLayerVersion": true,
|
|
19
|
+
"@aws-cdk/core:checkSecretUsage": true,
|
|
20
|
+
"@aws-cdk/core:target-partitions": [
|
|
21
|
+
"aws",
|
|
22
|
+
"aws-cn"
|
|
23
|
+
],
|
|
24
|
+
"@aws-cdk-containers/ecs-service-extensions:enableDefaultLogDriver": true,
|
|
25
|
+
"@aws-cdk/aws-ec2:uniqueImdsv2TemplateName": true,
|
|
26
|
+
"@aws-cdk/aws-ecs:arnFormatIncludesClusterName": true,
|
|
27
|
+
"@aws-cdk/aws-iam:minimizePolicies": true,
|
|
28
|
+
"@aws-cdk/core:validateSnapshotRemovalPolicy": true,
|
|
29
|
+
"@aws-cdk/aws-codepipeline:crossAccountKeyAliasStackSafeResourceName": true,
|
|
30
|
+
"@aws-cdk/aws-s3:createDefaultLoggingPolicy": true,
|
|
31
|
+
"@aws-cdk/aws-sns-subscriptions:restrictSqsDescryption": true,
|
|
32
|
+
"@aws-cdk/aws-apigateway:disableCloudWatchRole": true,
|
|
33
|
+
"@aws-cdk/core:enablePartitionLiterals": true,
|
|
34
|
+
"@aws-cdk/aws-events:eventsTargetQueueSameAccount": true,
|
|
35
|
+
"@aws-cdk/aws-ecs:disableExplicitDeploymentControllerForCircuitBreaker": true,
|
|
36
|
+
"@aws-cdk/aws-iam:importedRoleStackSafeDefaultPolicyName": true,
|
|
37
|
+
"@aws-cdk/aws-s3:serverAccessLogsUseBucketPolicy": true,
|
|
38
|
+
"@aws-cdk/aws-route53-patters:useCertificate": true,
|
|
39
|
+
"@aws-cdk/customresources:installLatestAwsSdkDefault": false,
|
|
40
|
+
"@aws-cdk/aws-rds:databaseProxyUniqueResourceName": true,
|
|
41
|
+
"@aws-cdk/aws-codedeploy:removeAlarmsFromDeploymentGroup": true,
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"@aws-cdk/aws-apigateway:authorizerChangeDeploymentLogicalId": true,
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"@aws-cdk/aws-ec2:launchTemplateDefaultUserData": true,
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"@aws-cdk/aws-secretsmanager:useAttachedSecretResourcePolicyForSecretTargetAttachments": true,
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"@aws-cdk/aws-redshift:columnId": true,
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"@aws-cdk/aws-stepfunctions-tasks:enableEmrServicePolicyV2": true,
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"@aws-cdk/aws-ec2:restrictDefaultSecurityGroup": true,
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"@aws-cdk/aws-apigateway:requestValidatorUniqueId": true,
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"@aws-cdk/aws-kms:aliasNameRef": true,
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"@aws-cdk/aws-kms:applyImportedAliasPermissionsToPrincipal": true,
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"@aws-cdk/aws-autoscaling:generateLaunchTemplateInsteadOfLaunchConfig": true,
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"@aws-cdk/core:includePrefixInUniqueNameGeneration": true,
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"@aws-cdk/aws-efs:denyAnonymousAccess": true,
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"@aws-cdk/aws-opensearchservice:enableOpensearchMultiAzWithStandby": true,
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"@aws-cdk/aws-lambda-nodejs:useLatestRuntimeVersion": true,
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"@aws-cdk/aws-efs:mountTargetOrderInsensitiveLogicalId": true,
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"@aws-cdk/aws-rds:auroraClusterChangeScopeOfInstanceParameterGroupWithEachParameters": true,
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"@aws-cdk/aws-appsync:useArnForSourceApiAssociationIdentifier": true,
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"@aws-cdk/aws-rds:preventRenderingDeprecatedCredentials": true,
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"@aws-cdk/aws-codepipeline-actions:useNewDefaultBranchForCodeCommitSource": true,
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"@aws-cdk/aws-cloudwatch-actions:changeLambdaPermissionLogicalIdForLambdaAction": true,
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"@aws-cdk/aws-codepipeline:crossAccountKeysDefaultValueToFalse": true,
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"@aws-cdk/aws-codepipeline:defaultPipelineTypeToV2": true,
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"@aws-cdk/aws-kms:reduceCrossAccountRegionPolicyScope": true,
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"@aws-cdk/aws-eks:nodegroupNameAttribute": true,
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"@aws-cdk/aws-ec2:ebsDefaultGp3Volume": true,
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"@aws-cdk/aws-ecs:removeDefaultDeploymentAlarm": true,
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"@aws-cdk/custom-resources:logApiResponseDataPropertyTrueDefault": false,
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"@aws-cdk/aws-s3:keepNotificationInImportedBucket": false,
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"@aws-cdk/core:explicitStackTags": true,
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"@aws-cdk/aws-ecs:enableImdsBlockingDeprecatedFeature": false,
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"@aws-cdk/aws-ecs:disableEcsImdsBlocking": true,
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"@aws-cdk/aws-ecs:reduceEc2FargateCloudWatchPermissions": true,
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"@aws-cdk/aws-dynamodb:resourcePolicyPerReplica": true,
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"@aws-cdk/aws-ec2:ec2SumTImeoutEnabled": true,
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"@aws-cdk/aws-appsync:appSyncGraphQLAPIScopeLambdaPermission": true,
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"@aws-cdk/aws-rds:setCorrectValueForDatabaseInstanceReadReplicaInstanceResourceId": true,
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+
"@aws-cdk/core:cfnIncludeRejectComplexResourceUpdateCreatePolicyIntrinsics": true,
|
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79
|
+
"@aws-cdk/aws-lambda-nodejs:sdkV3ExcludeSmithyPackages": true,
|
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80
|
+
"@aws-cdk/aws-stepfunctions-tasks:fixRunEcsTaskPolicy": true,
|
|
81
|
+
"@aws-cdk/aws-ec2:bastionHostUseAmazonLinux2023ByDefault": true,
|
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82
|
+
"@aws-cdk/aws-route53-targets:userPoolDomainNameMethodWithoutCustomResource": true,
|
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83
|
+
"@aws-cdk/aws-elasticloadbalancingV2:albDualstackWithoutPublicIpv4SecurityGroupRulesDefault": true,
|
|
84
|
+
"@aws-cdk/aws-iam:oidcRejectUnauthorizedConnections": true,
|
|
85
|
+
"@aws-cdk/core:enableAdditionalMetadataCollection": true,
|
|
86
|
+
"@aws-cdk/aws-lambda:createNewPoliciesWithAddToRolePolicy": false,
|
|
87
|
+
"@aws-cdk/aws-s3:setUniqueReplicationRoleName": true,
|
|
88
|
+
"@aws-cdk/aws-events:requireEventBusPolicySid": true,
|
|
89
|
+
"@aws-cdk/core:aspectPrioritiesMutating": true,
|
|
90
|
+
"@aws-cdk/aws-dynamodb:retainTableReplica": true,
|
|
91
|
+
"@aws-cdk/aws-stepfunctions:useDistributedMapResultWriterV2": true,
|
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92
|
+
"@aws-cdk/s3-notifications:addS3TrustKeyPolicyForSnsSubscriptions": true,
|
|
93
|
+
"@aws-cdk/aws-ec2:requirePrivateSubnetsForEgressOnlyInternetGateway": true,
|
|
94
|
+
"@aws-cdk/aws-s3:publicAccessBlockedByDefault": true,
|
|
95
|
+
"@aws-cdk/aws-lambda:useCdkManagedLogGroup": true
|
|
96
|
+
}
|
|
97
|
+
}
|
|
@@ -0,0 +1,17 @@
|
|
|
1
|
+
import aws_cdk as core
|
|
2
|
+
import aws_cdk.assertions as assertions
|
|
3
|
+
|
|
4
|
+
from workbench_compute.workbench_compute_stack import WorkbenchComputeStack
|
|
5
|
+
|
|
6
|
+
|
|
7
|
+
# example tests. To run these tests, uncomment this file along with the example
|
|
8
|
+
# resource in workbench_compute/workbench_compute_stack.py
|
|
9
|
+
def test_sqs_queue_created():
|
|
10
|
+
app = core.App()
|
|
11
|
+
stack = WorkbenchComputeStack(app, "workbench-compute")
|
|
12
|
+
template = assertions.Template.from_stack(stack)
|
|
13
|
+
|
|
14
|
+
|
|
15
|
+
# template.has_resource_properties("AWS::SQS::Queue", {
|
|
16
|
+
# "VisibilityTimeout": 300
|
|
17
|
+
# })
|
|
@@ -0,0 +1,279 @@
|
|
|
1
|
+
from aws_cdk import (
|
|
2
|
+
Environment,
|
|
3
|
+
Stack,
|
|
4
|
+
aws_iam as iam,
|
|
5
|
+
aws_ec2 as ec2,
|
|
6
|
+
aws_ecs as ecs,
|
|
7
|
+
aws_ecr as ecr,
|
|
8
|
+
aws_batch as batch,
|
|
9
|
+
aws_sqs as sqs,
|
|
10
|
+
aws_lambda as lambda_,
|
|
11
|
+
aws_lambda_event_sources as lambda_events,
|
|
12
|
+
aws_logs as logs,
|
|
13
|
+
Duration,
|
|
14
|
+
Size,
|
|
15
|
+
)
|
|
16
|
+
from constructs import Construct
|
|
17
|
+
from typing import Any, List, Dict
|
|
18
|
+
from dataclasses import dataclass, field
|
|
19
|
+
from textwrap import dedent
|
|
20
|
+
|
|
21
|
+
|
|
22
|
+
@dataclass
|
|
23
|
+
class WorkbenchComputeStackProps:
|
|
24
|
+
workbench_bucket: str
|
|
25
|
+
batch_role_arn: str
|
|
26
|
+
lambda_role_arn: str
|
|
27
|
+
existing_vpc_id: str = None
|
|
28
|
+
subnet_ids: List[str] = field(default_factory=list) # Optional subnets ids for the Batch compute environment
|
|
29
|
+
|
|
30
|
+
|
|
31
|
+
class WorkbenchComputeStack(Stack):
|
|
32
|
+
def __init__(
|
|
33
|
+
self,
|
|
34
|
+
scope: Construct,
|
|
35
|
+
construct_id: str,
|
|
36
|
+
env: Environment,
|
|
37
|
+
props: WorkbenchComputeStackProps,
|
|
38
|
+
**kwargs: Any,
|
|
39
|
+
) -> None:
|
|
40
|
+
desc = "Workbench Compute: Defines the compute infrastructure for Workbench including Batch resources."
|
|
41
|
+
super().__init__(scope, construct_id, env=env, description=desc, **kwargs)
|
|
42
|
+
|
|
43
|
+
# Print the environment details
|
|
44
|
+
print("Environment")
|
|
45
|
+
print(env)
|
|
46
|
+
|
|
47
|
+
# Grab our properties
|
|
48
|
+
self.workbench_bucket = props.workbench_bucket
|
|
49
|
+
self.batch_role_arn = props.batch_role_arn
|
|
50
|
+
self.existing_vpc_id = props.existing_vpc_id
|
|
51
|
+
self.subnet_ids = props.subnet_ids
|
|
52
|
+
|
|
53
|
+
# Import the Batch role
|
|
54
|
+
self.workbench_batch_role = iam.Role.from_role_arn(self, "ImportedBatchRole", self.batch_role_arn)
|
|
55
|
+
|
|
56
|
+
# Import the Lambda role
|
|
57
|
+
self.workbench_lambda_role = iam.Role.from_role_arn(self, "ImportedLambdaRole", props.lambda_role_arn)
|
|
58
|
+
|
|
59
|
+
# Create Batch resources first (Lambda will reference them)
|
|
60
|
+
self.batch_compute_environment = self.create_batch_compute_environment()
|
|
61
|
+
self.batch_job_queue = self.create_batch_job_queue()
|
|
62
|
+
self.batch_job_definitions = self.create_batch_job_definitions()
|
|
63
|
+
|
|
64
|
+
# Create ML Pipeline SQS Queue and Lambda (after Batch resources)
|
|
65
|
+
self.ml_pipeline_queue = self.create_ml_pipeline_queue()
|
|
66
|
+
self.batch_trigger_lambda = self.create_batch_trigger_lambda()
|
|
67
|
+
|
|
68
|
+
#####################
|
|
69
|
+
# Batch Compute #
|
|
70
|
+
#####################
|
|
71
|
+
def create_batch_compute_environment(self) -> batch.FargateComputeEnvironment:
|
|
72
|
+
"""Create the Batch compute environment with Fargate."""
|
|
73
|
+
|
|
74
|
+
# Check if we have an existing VPC to use
|
|
75
|
+
if self.existing_vpc_id:
|
|
76
|
+
vpc = ec2.Vpc.from_lookup(self, "ImportedVPC", vpc_id=self.existing_vpc_id)
|
|
77
|
+
vpc_subnets = None
|
|
78
|
+
|
|
79
|
+
# Use specific subnets if provided
|
|
80
|
+
if self.subnet_ids:
|
|
81
|
+
vpc_subnets = ec2.SubnetSelection(
|
|
82
|
+
subnets=[
|
|
83
|
+
ec2.Subnet.from_subnet_id(self, f"BatchSubnet{i}", subnet_id)
|
|
84
|
+
for i, subnet_id in enumerate(self.subnet_ids)
|
|
85
|
+
]
|
|
86
|
+
)
|
|
87
|
+
else:
|
|
88
|
+
raise ValueError(
|
|
89
|
+
'Please provide the Workbench Config entry: "WORKBENCH_VPC_ID":"vpc-123456789abcdef0". '
|
|
90
|
+
"Default VPC networks cannot pull ECR images for Batch jobs."
|
|
91
|
+
)
|
|
92
|
+
|
|
93
|
+
return batch.FargateComputeEnvironment(
|
|
94
|
+
self,
|
|
95
|
+
"WorkbenchBatchComputeEnvironment",
|
|
96
|
+
compute_environment_name="workbench-compute-env",
|
|
97
|
+
vpc=vpc,
|
|
98
|
+
vpc_subnets=vpc_subnets,
|
|
99
|
+
maxv_cpus=16, # Limit to 16 vCPU to minimize AWS Throttling issues
|
|
100
|
+
)
|
|
101
|
+
|
|
102
|
+
def create_batch_job_queue(self) -> batch.JobQueue:
|
|
103
|
+
"""Create the Batch job queue."""
|
|
104
|
+
return batch.JobQueue(
|
|
105
|
+
self,
|
|
106
|
+
"WorkbenchBatchJobQueue",
|
|
107
|
+
job_queue_name="workbench-job-queue",
|
|
108
|
+
compute_environments=[
|
|
109
|
+
batch.OrderedComputeEnvironment(compute_environment=self.batch_compute_environment, order=1)
|
|
110
|
+
],
|
|
111
|
+
)
|
|
112
|
+
|
|
113
|
+
def create_batch_job_definitions(self) -> Dict[str, batch.EcsJobDefinition]:
|
|
114
|
+
"""Create ML pipeline job definitions in small/medium/large tiers."""
|
|
115
|
+
|
|
116
|
+
# Using ECR image for ML pipelines
|
|
117
|
+
ecr_image = ecs.ContainerImage.from_ecr_repository(
|
|
118
|
+
repository=ecr.Repository.from_repository_arn(
|
|
119
|
+
self,
|
|
120
|
+
"MLPipelineRepo",
|
|
121
|
+
repository_arn=f"arn:aws:ecr:{self.region}:507740646243:repository/aws-ml-images/py312-ml-pipelines",
|
|
122
|
+
),
|
|
123
|
+
tag="0.2",
|
|
124
|
+
)
|
|
125
|
+
|
|
126
|
+
# Job Definition Tiers
|
|
127
|
+
tiers = {
|
|
128
|
+
"small": (2, 4096), # 2 vCPU, 4GB RAM
|
|
129
|
+
"medium": (4, 8192), # 4 vCPU, 8GB RAM
|
|
130
|
+
"large": (8, 16384), # 8 vCPU, 16GB RAM
|
|
131
|
+
}
|
|
132
|
+
|
|
133
|
+
job_definitions = {}
|
|
134
|
+
for size, (cpu, memory_mib) in tiers.items():
|
|
135
|
+
job_definitions[size] = batch.EcsJobDefinition(
|
|
136
|
+
self,
|
|
137
|
+
f"JobDef{size.capitalize()}",
|
|
138
|
+
job_definition_name=f"workbench-batch-{size}",
|
|
139
|
+
container=batch.EcsFargateContainerDefinition(
|
|
140
|
+
self,
|
|
141
|
+
f"Container{size.capitalize()}",
|
|
142
|
+
cpu=cpu,
|
|
143
|
+
memory=Size.mebibytes(memory_mib),
|
|
144
|
+
image=ecr_image,
|
|
145
|
+
job_role=self.workbench_batch_role,
|
|
146
|
+
execution_role=self.workbench_batch_role,
|
|
147
|
+
environment={
|
|
148
|
+
"WORKBENCH_BUCKET": self.workbench_bucket,
|
|
149
|
+
"PYTHONUNBUFFERED": "1",
|
|
150
|
+
},
|
|
151
|
+
),
|
|
152
|
+
timeout=Duration.hours(3),
|
|
153
|
+
)
|
|
154
|
+
return job_definitions
|
|
155
|
+
|
|
156
|
+
###########################
|
|
157
|
+
# ML Pipeline SQS Queue #
|
|
158
|
+
###########################
|
|
159
|
+
def create_ml_pipeline_queue(self) -> sqs.Queue:
|
|
160
|
+
"""Create SQS FIFO queue for ML pipeline orchestration with deduplication."""
|
|
161
|
+
|
|
162
|
+
# Dead letter queue for failed messages (also FIFO)
|
|
163
|
+
dlq = sqs.Queue(
|
|
164
|
+
self,
|
|
165
|
+
"MLPipelineDLQ",
|
|
166
|
+
queue_name="workbench-ml-pipeline-dlq.fifo", # Must end with .fifo
|
|
167
|
+
fifo=True,
|
|
168
|
+
retention_period=Duration.days(14),
|
|
169
|
+
)
|
|
170
|
+
|
|
171
|
+
# Main FIFO queue with deduplication
|
|
172
|
+
return sqs.Queue(
|
|
173
|
+
self,
|
|
174
|
+
"MLPipelineQueue",
|
|
175
|
+
queue_name="workbench-ml-pipeline-queue.fifo", # Must end with .fifo
|
|
176
|
+
fifo=True,
|
|
177
|
+
content_based_deduplication=True, # Auto-dedupe based on message content
|
|
178
|
+
visibility_timeout=Duration.minutes(15),
|
|
179
|
+
retention_period=Duration.days(1),
|
|
180
|
+
dead_letter_queue=sqs.DeadLetterQueue(max_receive_count=1, queue=dlq),
|
|
181
|
+
)
|
|
182
|
+
|
|
183
|
+
def create_batch_trigger_lambda(self) -> lambda_.Function:
|
|
184
|
+
"""Create Lambda function to process SQS messages and trigger Batch jobs."""
|
|
185
|
+
|
|
186
|
+
# Create a mapping of job definition names to pass to Lambda
|
|
187
|
+
job_def_names = {size: f"workbench-batch-{size}" for size in ["small", "medium", "large"]}
|
|
188
|
+
|
|
189
|
+
batch_trigger_lambda = lambda_.Function(
|
|
190
|
+
self,
|
|
191
|
+
"BatchTriggerLambda",
|
|
192
|
+
function_name="workbench-batch-trigger",
|
|
193
|
+
runtime=lambda_.Runtime.PYTHON_3_12,
|
|
194
|
+
handler="index.lambda_handler",
|
|
195
|
+
code=lambda_.Code.from_inline(self._get_lambda_code()),
|
|
196
|
+
timeout=Duration.minutes(5),
|
|
197
|
+
log_retention=logs.RetentionDays.ONE_WEEK,
|
|
198
|
+
environment={
|
|
199
|
+
"WORKBENCH_BUCKET": self.workbench_bucket,
|
|
200
|
+
"JOB_QUEUE": self.batch_job_queue.job_queue_name,
|
|
201
|
+
"JOB_DEF_SMALL": job_def_names["small"],
|
|
202
|
+
"JOB_DEF_MEDIUM": job_def_names["medium"],
|
|
203
|
+
"JOB_DEF_LARGE": job_def_names["large"],
|
|
204
|
+
},
|
|
205
|
+
role=self.workbench_lambda_role,
|
|
206
|
+
)
|
|
207
|
+
|
|
208
|
+
# Connect SQS to Lambda
|
|
209
|
+
batch_trigger_lambda.add_event_source(
|
|
210
|
+
lambda_events.SqsEventSource(
|
|
211
|
+
self.ml_pipeline_queue, batch_size=1 # One message at a time for precise error handling
|
|
212
|
+
)
|
|
213
|
+
)
|
|
214
|
+
return batch_trigger_lambda
|
|
215
|
+
|
|
216
|
+
@staticmethod
|
|
217
|
+
def _get_lambda_code() -> str:
|
|
218
|
+
"""Return the Lambda function code as a string."""
|
|
219
|
+
return dedent(
|
|
220
|
+
'''
|
|
221
|
+
import json
|
|
222
|
+
import boto3
|
|
223
|
+
import os
|
|
224
|
+
from datetime import datetime
|
|
225
|
+
from pathlib import Path
|
|
226
|
+
|
|
227
|
+
batch = boto3.client('batch')
|
|
228
|
+
s3 = boto3.client('s3')
|
|
229
|
+
|
|
230
|
+
WORKBENCH_BUCKET = os.environ['WORKBENCH_BUCKET']
|
|
231
|
+
JOB_QUEUE = os.environ['JOB_QUEUE']
|
|
232
|
+
JOB_DEFINITIONS = {
|
|
233
|
+
'small': os.environ['JOB_DEF_SMALL'],
|
|
234
|
+
'medium': os.environ['JOB_DEF_MEDIUM'],
|
|
235
|
+
'large': os.environ['JOB_DEF_LARGE'],
|
|
236
|
+
}
|
|
237
|
+
|
|
238
|
+
def lambda_handler(event, context):
|
|
239
|
+
"""Process SQS messages and submit Batch jobs."""
|
|
240
|
+
|
|
241
|
+
for record in event['Records']:
|
|
242
|
+
try:
|
|
243
|
+
message = json.loads(record['body'])
|
|
244
|
+
script_path = message['script_path'] # s3://bucket/path/to/script.py
|
|
245
|
+
size = message.get('size', 'small')
|
|
246
|
+
extra_env = message.get('environment', {})
|
|
247
|
+
|
|
248
|
+
script_name = Path(script_path).stem
|
|
249
|
+
job_name = f"workbench_{script_name}_{datetime.now():%Y%m%d_%H%M%S}"
|
|
250
|
+
|
|
251
|
+
# Get job definition name from environment variables
|
|
252
|
+
job_def_name = JOB_DEFINITIONS.get(size, JOB_DEFINITIONS['small'])
|
|
253
|
+
|
|
254
|
+
# Build environment variables
|
|
255
|
+
env_vars = [
|
|
256
|
+
{'name': 'ML_PIPELINE_S3_PATH', 'value': script_path},
|
|
257
|
+
{'name': 'WORKBENCH_BUCKET', 'value': WORKBENCH_BUCKET},
|
|
258
|
+
*[{'name': k, 'value': v} for k, v in extra_env.items()]
|
|
259
|
+
]
|
|
260
|
+
|
|
261
|
+
# Submit Batch job to the queue
|
|
262
|
+
response = batch.submit_job(
|
|
263
|
+
jobName=job_name,
|
|
264
|
+
jobQueue=JOB_QUEUE,
|
|
265
|
+
jobDefinition=job_def_name,
|
|
266
|
+
containerOverrides={
|
|
267
|
+
'environment': env_vars
|
|
268
|
+
}
|
|
269
|
+
)
|
|
270
|
+
|
|
271
|
+
print(f"Submitted job: {job_name} ({response['jobId']})")
|
|
272
|
+
|
|
273
|
+
except Exception as e:
|
|
274
|
+
print(f"Error processing message: {e}")
|
|
275
|
+
raise # Let SQS retry via DLQ
|
|
276
|
+
|
|
277
|
+
return {'statusCode': 200}
|
|
278
|
+
'''
|
|
279
|
+
).strip()
|