bloom-lims 0.32.0

Templated Abstract Polymorphic LIMS - A Laboratory Information Management System

Bloom

Bloom is the LSMC beta authority for physical and material LIMS state.

Bloom owns:

• containers
• specimens
• derived samples
• plates and wells
• extraction outputs
• library prep outputs
• pools
• sequencing runs
• sequenced library assignments
• queue membership and queue-transition state for wet-lab execution

Bloom does not own:

• accessioning
• customer, TRF, Test, patient, provider, shipment, or kit truth
• workflow or workflow-step orchestration for the beta path

Beta Architecture

The active beta path is queue-driven and graph-native.

Canonical queues:

• extraction_prod
• extraction_rnd
• post_extract_qc
• ilmn_lib_prep
• ont_lib_prep
• ilmn_seq_pool
• ont_seq_pool
• ilmn_start_seq_run
• ont_start_seq_run

Atlas records intake outcomes first. Bloom accepts only Atlas-approved material, links that material to Atlas TRF/Test/process-item context through explicit graph-linked reference objects, and preserves lineage from specimen/container through plate and well placement, library prep, pooling, sequencing run creation, and sequenced library assignment. Accepted-material ingress queue membership is applied to the physical container (container_euid), with specimen queue reads falling back to containing-container queue state when needed.

Ursa resolves the canonical sequencing unit through Bloom with:

• run_euid
• flowcell_id
• lane
• library_barcode

Bloom returns:

• sequenced_library_assignment_euid
• atlas_tenant_id
• atlas_trf_euid
• atlas_test_euid
• atlas_test_process_item_euid

Public beta APIs return EUIDs only. Internal UUIDs are not part of the supported contract.

Active Beta APIs

Atlas and Ursa integration paths live under:

• /api/v1/external/atlas
• /api/v1/external/atlas/beta

Atlas Configuration Values Required For Bloom API Access

When configuring Atlas to call Bloom, set all three fields below in Atlas Bloom integration settings:

• bloom_base_url
  • Bloom API base URL Atlas calls (example: https://bloom.example.org).
• bloom_api_key_secret_ref
  • Secret reference Atlas resolves to the Bloom bearer token (for example env:MY_BLOOM_API_KEY).
• bloom_webhook_secret_ref
  • Secret reference Atlas uses to verify Bloom webhook signatures for inbound events.

The queue-driven beta endpoints are:

• POST /api/v1/external/atlas/beta/materials
• POST /api/v1/external/atlas/beta/queues/{queue_name}/items/{material_euid}
• POST /api/v1/external/atlas/beta/extractions
• POST /api/v1/external/atlas/beta/post-extract-qc
• POST /api/v1/external/atlas/beta/library-prep
• POST /api/v1/external/atlas/beta/pools
• POST /api/v1/external/atlas/beta/runs
• GET /api/v1/external/atlas/beta/runs/{run_euid}/resolve?flowcell_id=...&lane=...&library_barcode=...
• POST /api/v1/external/atlas/tests/{test_euid}/status-events

Embedded TapDB Admin Mount

Bloom mounts the TapDB admin FastAPI surface inside the same Bloom server process at:

• /admin/tapdb

Mounted-mode behavior:

• Bloom session auth is the only gate.
• Access is admin-only (role=admin).
• Unauthenticated browser requests are redirected to /login.
• Authenticated non-admin browser requests are redirected to /user_home?admin_required=1.
• JSON/XHR-style denied requests receive 401 (unauthenticated) or 403 (non-admin).
• TapDB local login/auth flow is disabled for mounted mode.

Runtime flags:

• BLOOM_TAPDB_MOUNT_ENABLED (default 1)
• BLOOM_TAPDB_MOUNT_PATH (default /admin/tapdb)

Legacy Isolation

Workflow/workset runtime surfaces are retired from active API/GUI mounts for the beta path. Any codepath that depends on workflow-step runtime, accession ownership, or UUID-based external contracts is not part of the supported beta system.

Development

Bloom runs on the TapDB-backed adapter layer used across the LSMC refactor. The beta queue flow uses explicit object creation, lineage writes, targeted lookup queries, process-item references, and idempotency keys on direct integration calls.

Focused validation commands for the beta path:

source bloom_activate.sh
pytest --no-cov tests/test_api_atlas_bridge.py tests/test_atlas_lookup_resilience.py tests/test_queue_flow.py tests/test_run_resolver.py tests/test_beta_cross_repo_smoke.py
ruff check bloom_lims tests

Cross-Repo References

• active Bloom beta API contract: docs/bloom_beta_api_contracts.md
• queue/runtime execution summary: docs/bloom_queue_refactor_execplan.md
• parent beta contract: /Users/jmajor/projects/lims3/_refactor/cross_repo_contracts.md