daylily-ursa 0.4.0

Daylily Ursa beta analysis API

daylily-ursa

Daylily Ursa is the analysis execution, review, artifact-linking, and result-return service. It sits downstream of wet-lab execution and upstream of customer-visible delivery, coordinating analysis ingest, review state, Dewey artifact linkage, and Atlas return.

Ursa owns:

• analysis ingest records linked to sequencing context
• analysis and review state
• Dewey artifact-link and registration flows for analysis inputs and outputs
• Atlas result return after approval

Ursa does not own:

• customer portal routes
• storage policy authority
• file or file-set identity
• generic shared DB or auth lifecycle

Component View

flowchart LR
    Ingest["analysis ingest"] --> Ursa["Ursa API and review service"]
    Bloom["Bloom run context"] --> Ursa
    Ursa --> Dewey["artifact resolution and registration"]
    Ursa --> Atlas["approved result return"]
    Ursa --> TapDB["TapDB persistence"]

Prerequisites

• Python 3.10+
• local PostgreSQL/TapDB-compatible runtime
• API keys and base URLs if you want live Bloom, Dewey, or Atlas integration
• optional Playwright/test dependencies for E2E flows

Getting Started

Quickstart

source ./activate <deploy-name>
ursa config init
ursa server start --port 8913

ursa server start uses the shared TLS resolver by default. Pass --no-ssl for HTTP-only local testing, or --cert and --key to override the deployment-scoped cert pair.

Validation:

pytest -q

Architecture

Technology

• FastAPI + Jinja2-facing service/UI pieces
• Typer-based ursa CLI
• TapDB for persistence
• HTTP integration clients for Bloom, Dewey, and Atlas

Core Object Model

Ursa centers on:

• analyses and ingest payloads
• review state and approval
• input references to storage URIs or Dewey artifacts
• output artifacts registered or resolved through Dewey
• result-return requests back into Atlas

Runtime Shape

• app factory: daylib_ursa.workset_api:create_app
• CLI: ursa
• alternate entrypoint: daylily-workset-api

Request Lifecycle

1. ingest analysis input and sequencing context
2. resolve upstream run context as needed
3. attach outputs and artifact links
4. review and approve
5. return approved results to Atlas

Cost Estimates

Approximate only.

• Local development: workstation plus local database.
• Shared sandbox: usually a service-level slice of the wider Dayhoff environment.
• Production-like use grows with retained analysis metadata, integration traffic, and uptime requirements rather than unusual Ursa-specific infrastructure.

Development Notes

• Canonical local entry path: source ./activate
• Use ursa ... for Ursa-owned runtime operations
• Use tapdb ... only where Ursa explicitly delegates shared DB/runtime lifecycle
• Use daycog ... only where Ursa explicitly delegates shared auth lifecycle

Useful checks:

source ./activate
ursa --help
pytest -q

Sandboxing

• Safe: docs work, tests, ursa --help, and local-only runtime work
• Local-stateful: config init and local DB bootstrap paths
• Requires extra care: live Atlas/Bloom/Dewey integrations and any deployed environment changes

Current Docs

• Docs index
• Ursa-Atlas return contract

References

• FastAPI
• TapDB
• Dewey