.gitignore
.pre-commit-config.yaml
ACCESSIONING_WORKBENCH_PLAN.md
ACCESSIONING_WORKBENCH_README.md
AGENTS.md
README.md
alembic.ini
atlas_activate
atlas_env.yaml
augment_conda_pg.tgz
pyproject.toml
.augment/code_review_guidelines.yaml
.augment/default.md
.augment/rules/00-project-context.md
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.augment/rules/02-data-model-append-only.md
.augment/rules/03-security-phi.md
.augment/rules/04-python-quality.md
.augment/rules/05-domain-naming-and-status.md
.augment/rules/10-ui-style-lsmc.md
.augment/rules/11-api-conventions.md
.augment/rules/12-cross-system-api-boundary.md
.github/codeql/atlas-security.qls
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.github/workflows/ci.yml
.github/workflows/security-scans.yml
.github/workflows/weekly-package.yml
.ignore/ORIGINAL_REQUIREMENTS.md
.ignore/REFINED_ORIGINAL_REQUIREMENTS.md
app/__init__.py
app/domain_access.py
app/main.py
app/settings.py
app/worker.py
app/api/__init__.py
app/api/routes/__init__.py
app/api/routes/api_clients.py
app/api/routes/audit.py
app/api/routes/auth.py
app/api/routes/barcode.py
app/api/routes/bloom_auth.py
app/api/routes/bloom_integration.py
app/api/routes/bloom_lookups.py
app/api/routes/clinicians.py
app/api/routes/dewey_integration.py
app/api/routes/documents.py
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app/api/routes/fulfillment_runs.py
app/api/routes/graph.py
app/api/routes/groups.py
app/api/routes/intake.py
app/api/routes/internal.py
app/api/routes/manifests.py
app/api/routes/orgs.py
app/api/routes/people.py
app/api/routes/releases.py
app/api/routes/search_v2.py
app/api/routes/shipments.py
app/api/routes/support.py
app/api/routes/themes.py
app/api/routes/tracking.py
app/api/routes/trfs.py
app/api/routes/ursa_integration.py
app/api/routes/user_api_tokens.py
app/api/routes/webhooks.py
app/auth/__init__.py
app/auth/captcha.py
app/auth/cognito.py
app/auth/cognito_admin.py
app/auth/cognito_uri_validation.py
app/auth/dependencies.py
app/auth/middleware.py
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app/auth/rbac.py
app/auth/session.py
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app/cli/certs.py
app/cli/cognito.py
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app/cli/db.py
app/cli/integrations.py
app/cli/quality.py
app/cli/server.py
app/cli/tapdb.py
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app/cli/users.py
app/db/__init__.py
app/db/engine.py
app/domain/__init__.py
app/domain/enums.py
app/domain/policies/__init__.py
app/domain/policies/fulfillment_state_machine.py
app/domain/policies/permissions.py
app/domain/policies/rollups.py
app/domain/services/__init__.py
app/domain/services/accessioning_workbench.py
app/domain/services/api_clients.py
app/domain/services/audit.py
app/domain/services/audit_export.py
app/domain/services/audit_utils.py
app/domain/services/background_jobs.py
app/domain/services/barcode_printing.py
app/domain/services/bloom_bridge.py
app/domain/services/bloom_polling.py
app/domain/services/bloom_query_context.py
app/domain/services/bloom_status_events.py
app/domain/services/collection_events.py
app/domain/services/dashboard.py
app/domain/services/day_in_life_demo.py
app/domain/services/documents.py
app/domain/services/entity_links.py
app/domain/services/exceptions.py
app/domain/services/external_objects.py
app/domain/services/families.py
app/domain/services/fedex_tracking.py
app/domain/services/fulfillment_runs.py
app/domain/services/graph_viewer.py
app/domain/services/groups.py
app/domain/services/intake.py
app/domain/services/manifests.py
app/domain/services/order_relationships.py
app/domain/services/orgs.py
app/domain/services/patient_relationships.py
app/domain/services/people.py
app/domain/services/releases.py
app/domain/services/shipments.py
app/domain/services/site_scope.py
app/domain/services/storage_policies.py
app/domain/services/story_graph_projection.py
app/domain/services/support.py
app/domain/services/test_definitions.py
app/domain/services/test_fulfillment_items.py
app/domain/services/testkit_trf_links.py
app/domain/services/timeline.py
app/domain/services/trfs.py
app/domain/services/ursa_integration.py
app/domain/services/user_api_tokens.py
app/domain/services/users.py
app/domain/services/webhook_emitter.py
app/domain/services/webhooks.py
app/etc/lsmc-atlas-config-template.yaml
app/integrations/__init__.py
app/integrations/bloom_client.py
app/integrations/dewey_client.py
app/integrations/tapdb_runtime.py
app/persistence/__init__.py
app/persistence/tapdb/__init__.py
app/persistence/tapdb/accessioning.py
app/persistence/tapdb/api_clients.py
app/persistence/tapdb/audit.py
app/persistence/tapdb/backend.py
app/persistence/tapdb/client.py
app/persistence/tapdb/collection_events.py
app/persistence/tapdb/documents.py
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app/persistence/tapdb/external_objects.py
app/persistence/tapdb/families.py
app/persistence/tapdb/fulfillment_run_repo.py
app/persistence/tapdb/groups.py
app/persistence/tapdb/logistics.py
app/persistence/tapdb/manifests.py
app/persistence/tapdb/orgs.py
app/persistence/tapdb/people.py
app/persistence/tapdb/projection.py
app/persistence/tapdb/releases_repo.py
app/persistence/tapdb/storage_policies.py
app/persistence/tapdb/support.py
app/persistence/tapdb/test_definitions.py
app/persistence/tapdb/test_fulfillment_items.py
app/persistence/tapdb/themes.py
app/persistence/tapdb/trfs.py
app/persistence/tapdb/user_api_tokens.py
app/persistence/tapdb/users.py
app/persistence/tapdb/webhooks.py
app/persistence/tapdb/orm_models/__init__.py
app/persistence/tapdb/orm_models/api_clients.py
app/persistence/tapdb/orm_models/assay_workflow.py
app/persistence/tapdb/orm_models/base.py
app/persistence/tapdb/orm_models/core.py
app/persistence/tapdb/orm_models/delivery.py
app/persistence/tapdb/orm_models/error_log.py
app/persistence/tapdb/orm_models/events.py
app/persistence/tapdb/orm_models/exceptions.py
app/persistence/tapdb/orm_models/groups.py
app/persistence/tapdb/orm_models/logistics.py
app/persistence/tapdb/orm_models/ordering.py
app/persistence/tapdb/orm_models/people.py
app/persistence/tapdb/orm_models/support.py
app/persistence/tapdb/orm_models/themes.py
app/persistence/tapdb/orm_models/user_api_tokens.py
app/persistence/tapdb/orm_models/webhooks.py
app/search/__init__.py
app/search/contracts.py
app/search/repository.py
app/search/service.py
app/util/__init__.py
app/util/security.py
app/web/__init__.py
app/web/exception_handler.py
app/web/flash.py
app/web/templates.py
app/web/routes/__init__.py
app/web/routes/accessioning.py
app/web/routes/admin_groups.py
app/web/routes/api_clients.py
app/web/routes/families.py
app/web/routes/graph.py
app/web/routes/pages.py
app/web/routes/search.py
app/web/routes/webhooks.py
app/web/static/favicon.svg
app/web/static/css/theme.css
app/web/static/css/themes/bold.css
app/web/static/css/themes/minimal.css
app/web/static/css/themes/professional.css
app/web/static/js/.gitkeep
app/web/static/js/graph_viewer.js
app/web/static/js/htmx.min.js
app/web/templates/base.html
app/web/templates/dashboard.html
app/web/templates/accessioning/_match_results.html
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app/web/templates/admin/organization_form.html
app/web/templates/admin/organization_site_form.html
app/web/templates/admin/organization_user_form.html
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app/web/templates/api_clients/form.html
app/web/templates/api_clients/list.html
app/web/templates/api_clients/show_key.html
app/web/templates/clinicians/create.html
app/web/templates/clinicians/detail.html
app/web/templates/clinicians/edit.html
app/web/templates/clinicians/list.html
app/web/templates/clinicians/user_create.html
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app/web/templates/collection_events/edit.html
app/web/templates/collection_events/list.html
app/web/templates/components/document_upload.html
app/web/templates/components/timeline.html
app/web/templates/documents/detail.html
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app/web/templates/intake/exception_queue.html
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app/web/templates/manifests/list.html
app/web/templates/manifests/upload.html
app/web/templates/my_organization/index.html
app/web/templates/my_organization/settings_edit.html
app/web/templates/my_organization/site_detail.html
app/web/templates/my_organization/site_form.html
app/web/templates/my_organization/sites.html
app/web/templates/my_organization/user_form.html
app/web/templates/my_organization/user_tokens.html
app/web/templates/my_organization/users.html
app/web/templates/partials/tube_panel.html
app/web/templates/patients/create.html
app/web/templates/patients/detail.html
app/web/templates/patients/edit.html
app/web/templates/patients/list.html
app/web/templates/results/create.html
app/web/templates/results/detail.html
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app/web/templates/results/set_detail.html
app/web/templates/results/sets.html
app/web/templates/search/index.html
app/web/templates/settings/show_api_token.html
app/web/templates/shipments/add_specimen.html
app/web/templates/shipments/create.html
app/web/templates/shipments/detail.html
app/web/templates/shipments/edit.html
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app/web/templates/support/create.html
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app/web/templates/support/index.html
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app/web/templates/testkits/detail.html
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app/web/templates/trfs/detail.html
app/web/templates/trfs/edit.html
app/web/templates/trfs/list.html
app/web/templates/trfs/test_detail.html
app/web/templates/tubes/detail.html
app/web/templates/webhooks/detail.html
app/web/templates/webhooks/form.html
app/web/templates/webhooks/list.html
config/lsmc-atlas-config-example.yaml
config/tapdb-config-lsmc-atlas.yaml
docs/2026-03-09-zero-compat-rename-refactor-plan.md
docs/ARCHITECTURE.md
docs/ATLAS_BLOOM_TUBE_KIT_LINKING_EXEC_PLAN.md
docs/ATLAS_TAPDB_DOMAIN_MAPPING.md
docs/ATLAS_TUBE_COLLECTION_EVENT_HARD_CUT_EXEC_PLAN.md
docs/AUTHENTICATION.md
docs/BLOOM_CONTAINER_SPECIMEN_RUNBOOK.md
docs/DATABASE_HOSTING_STRATEGY.md
docs/GRAPH_VIEWER.md
docs/GUI_OBJECT_MATRIX_EXEC_PLAN.md
docs/ORG_SOFT_DELETE_EXEC_PLAN.md
docs/RBAC_TESTING_GUIDE.md
docs/README.md
docs/SEARCH_V2.md
docs/SITE_SCOPED_LINKAGE_HARD_CUTOVER_EXEC_PLAN.md
docs/TOKEN_SCOPES.md
docs/atlas_bloom_contract.md
docs/atlas_refactor_execplan.md
docs/security-audit-SWE-2.md
lsmc_atlas.egg-info/PKG-INFO
lsmc_atlas.egg-info/SOURCES.txt
lsmc_atlas.egg-info/dependency_links.txt
lsmc_atlas.egg-info/entry_points.txt
lsmc_atlas.egg-info/requires.txt
lsmc_atlas.egg-info/top_level.txt
scripts/__init__.py
scripts/_get_session.py
scripts/_run_demo.sh
scripts/api_demo_create_order_flow.py
scripts/audit_routes.py
scripts/audit_test_coverage.py
scripts/audit_web_coverage.py
scripts/day_in_life_demo.py
scripts/kill_by_port.sh
scripts/kill_by_port.sh~
scripts/provision_local_user.py
scripts/report_legacy_orm_residue.sh
scripts/run_audit.sh
scripts/run_tests.py
scripts/seed_day_in_life_baseline.py
scripts/seed_dev_data.py
scripts/seed_tapdb_overlay.py
tests/__init__.py
tests/conftest.py
tests/tapdb_test_helpers.py
tests/test_accessioning_workbench_matching.py
tests/test_accessioning_workbench_service.py
tests/test_accessioning_workbench_web.py
tests/test_admin_groups_web.py
tests/test_admin_test_definition_bloom_link.py
tests/test_api_clients_tapdb_cutover.py
tests/test_api_smoke.py
tests/test_append_only.py
tests/test_atlas_activate.py
tests/test_audit_tapdb_cutover.py
tests/test_auth_cognito.py
tests/test_background_jobs.py
tests/test_barcode_printing.py
tests/test_bloom_bridge_service.py
tests/test_bloom_client_paths.py
tests/test_bloom_https_validation.py
tests/test_bloom_identity_hard_cut.py
tests/test_bloom_integration_api.py
tests/test_bloom_lookups_api.py
tests/test_bloom_polling.py
tests/test_bloom_status_events.py
tests/test_bloom_status_events_service.py
tests/test_bloom_tube_kit_linking_web.py
tests/test_captcha.py
tests/test_cli_cognito_daycog.py
tests/test_cli_command_helpers.py
tests/test_cli_db_tapdb.py
tests/test_cli_integrations_bloom.py
tests/test_cli_users.py
tests/test_cognito_provisioning.py
tests/test_cognito_uri_validation.py
tests/test_day_in_life_demo.py
tests/test_deployment_chrome.py
tests/test_dewey_integration_api.py
tests/test_docs_access.py
tests/test_documents.py
tests/test_documents_tapdb_cutover.py
tests/test_domain_access.py
tests/test_euid_helpers.py
tests/test_exceptions_tapdb_cutover.py
tests/test_ext_admin.py
tests/test_families_web.py
tests/test_fedex_tracking.py
tests/test_fulfillment_runs.py
tests/test_fulfillment_runs_api.py
tests/test_fulfillment_state_machine.py
tests/test_graph_viewer_api.py
tests/test_graph_viewer_service.py
tests/test_graph_viewer_web.py
tests/test_groups.py
tests/test_groups_tapdb_cutover.py
tests/test_gui_object_creation_matrix.py
tests/test_health.py
tests/test_intake_outcomes.py
tests/test_legacy_orm_residue_helper.py
tests/test_manifests_tapdb_cutover.py
tests/test_no_direct_postgres_commands.py
tests/test_orgs_tapdb_cutover.py
tests/test_packaging_metadata.py
tests/test_people_tapdb_cutover.py
tests/test_postgres_setup.py
tests/test_rate_limiting.py
tests/test_release_repo_relationships.py
tests/test_rollups.py
tests/test_route_surface_coverage.py
tests/test_search_v2_api.py
tests/test_search_v2_web.py
tests/test_security_fixes.py
tests/test_security_fixes_2.py
tests/test_security_fixes_3.py
tests/test_server_cognito_startup_validation.py
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tests/test_storage_policy_api.py
tests/test_storage_policy_service.py
tests/test_support_tapdb_cutover.py
tests/test_tapdb_cutover_guards.py
tests/test_templates_timezone.py
tests/test_tenant_isolation.py
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tests/test_test_fulfillment_items.py
tests/test_themes.py
tests/test_themes_tapdb_routes.py
tests/test_trf_order_api.py
tests/test_trf_test_family_linking_web.py
tests/test_ursa_integration_api.py
tests/test_ursa_result_return_service.py
tests/test_user_api_tokens.py
tests/test_user_api_tokens_tapdb_cutover.py
tests/test_users_tapdb_cutover.py
tests/test_web_crud.py
tests/test_web_smoke.py
tests/test_webhooks.py
tests/test_webhooks_sql_pagination.py
tests/test_webhooks_tapdb_cutover.py
tests/e2e/README.md
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tests/e2e/conftest.py
tests/e2e/test_admin_tools_e2e.py
tests/e2e/test_auth_e2e.py
tests/e2e/test_data_flows_e2e.py
tests/e2e/test_documents_e2e.py
tests/e2e/test_example_e2e.py
tests/e2e/test_logistics_e2e.py
tests/e2e/test_organization_e2e.py
tests/e2e/test_patient_clinician_e2e.py
tests/e2e/test_search_graph_e2e.py
tests/e2e/test_trf_e2e.py