daylily-ursa 0.1.20

Daylily Ursa beta analysis API

daylily-ursa

Daylily Ursa beta analysis API.

Ursa is the analysis-only service in the beta stack. It no longer owns customer, biospecimen, manifest, portal, or workset truth.

Scope

Ursa now handles:

• run-linked analysis ingest
• Bloom resolver lookups for run_euid + flowcell_id + lane + library_barcode
• TapDB-backed analysis execution and review state
• analysis artifact registration
• Atlas result and artifact return

Ursa no longer serves:

• workset lifecycle APIs
• customer portal routes
• biospecimen or manifest ownership APIs
• file-registry-as-primary ownership
• monitor or workflow-runtime beta entrypoints

Runtime Contract

1. Atlas and Bloom create the order, material, queue, and run context.
2. Ursa ingests run_euid, flowcell_id, lane, and library_barcode.
3. Ursa resolves Atlas TRF/Test/process-item identity through Bloom.
4. Ursa records analysis state, review state, and artifacts under the resolved identity.
5. Ursa requires explicit APPROVED review state before returning result and artifact references to Atlas.

Quick Start

source ./ursa_activate

export TAPDB_STRICT_NAMESPACE=1
export TAPDB_CLIENT_ID=local
export TAPDB_DATABASE_NAME=ursa
export TAPDB_ENV=dev

export URSA_INTERNAL_API_KEY=ursa-dev-internal-key
export BLOOM_BASE_URL=https://localhost:8912
export BLOOM_VERIFY_SSL=false
export ATLAS_BASE_URL=https://localhost:8915
export ATLAS_VERIFY_SSL=false
export ATLAS_INTERNAL_API_KEY=replace-me

ursa server start

Important Environment Variables

AWS_PROFILE=your-profile
URSA_ALLOWED_REGIONS=us-west-2

TAPDB_STRICT_NAMESPACE=1
TAPDB_CLIENT_ID=local
TAPDB_DATABASE_NAME=ursa
TAPDB_ENV=dev

URSA_INTERNAL_API_KEY=ursa-dev-internal-key
BLOOM_BASE_URL=https://localhost:8912
BLOOM_API_TOKEN=
BLOOM_VERIFY_SSL=false
ATLAS_BASE_URL=https://localhost:8915
ATLAS_INTERNAL_API_KEY=
ATLAS_VERIFY_SSL=false
URSA_HOST=0.0.0.0
URSA_PORT=8914

API Surface

• POST /api/analyses/ingest
• GET /api/analyses/{analysis_euid}
• POST /api/analyses/{analysis_euid}/status
• POST /api/analyses/{analysis_euid}/artifacts
• POST /api/analyses/{analysis_euid}/review
• POST /api/analyses/{analysis_euid}/return

All write routes require:

• X-API-Key
• Idempotency-Key on ingest and result return

The ingest payload includes:

• run_euid
• flowcell_id
• lane
• library_barcode

The stored and returned Atlas context includes:

• sequenced_library_assignment_euid
• atlas_tenant_id
• atlas_trf_euid
• atlas_test_euid
• atlas_test_process_item_euid

Repo Notes

• execution plan: docs/ursa_refactor_execplan.md
• Atlas return contract: docs/ursa_atlas_return_contract.md

Validation

pytest tests/test_tapdb_backend.py tests/test_file_metadata.py tests/test_analysis_ingest.py tests/test_result_return.py tests/test_bloom_resolver_client.py tests/test_console_scripts.py
ruff check daylib_ursa tests/test_tapdb_backend.py tests/test_file_metadata.py tests/test_analysis_ingest.py tests/test_result_return.py tests/test_bloom_resolver_client.py tests/test_console_scripts.py