Metadata-Version: 2.4
Name: bloom_lims
Version: 0.32.1
Summary: Templated Abstract Polymorphic LIMS - A Laboratory Information Management System
License: MIT
Project-URL: Homepage, https://github.com/Daylily-Informatics/bloom
Project-URL: Repository, https://github.com/Daylily-Informatics/bloom.git
Project-URL: Issues, https://github.com/Daylily-Informatics/bloom/issues
Keywords: lims,laboratory,informatics,bioinformatics,sample-management
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Healthcare Industry
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Requires-Python: >=3.12
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: daylily-tapdb==0.1.35
Requires-Dist: daylily-cognito==0.1.24
Requires-Dist: pydantic>=2.6.0
Requires-Dist: pydantic-settings>=2.0.0
Requires-Dist: psutil>=5.9.0
Provides-Extra: dev
Requires-Dist: pytest>=8.0; extra == "dev"
Requires-Dist: pytest-cov>=4.1.0; extra == "dev"
Requires-Dist: pytest-asyncio>=0.23.0; extra == "dev"
Requires-Dist: ruff>=0.1.0; extra == "dev"
Requires-Dist: mypy>=1.0; extra == "dev"
Dynamic: license-file

# Bloom

Bloom is the wet-lab and material-state authority in this workspace.

It owns the physical side of the beta LIMS flow:

- containers and placements
- specimens and derived materials
- extraction, QC, library-prep, pool, and run objects
- sequenced library assignments
- wet-lab queue membership and queue-transition state
- Bloom-side lineage linking to Atlas fulfillment context

It does not own:

- customer-portal data and tenant administration
- patient, clinician, shipment, TRF, or test truth
- artifact registry authority
- analysis execution or result-return workflows

## Runtime Shape

Bloom is a FastAPI application with both API and server-rendered GUI surfaces.

Primary entrypoints:

- app entrypoint: `main.py`
- app factory: `bloom_lims.app:create_app`
- CLI entrypoint: `bloom`

Primary CLI groups:

- `bloom server`: start, stop, status, logs
- `bloom db`: TapDB lifecycle and Bloom template seeding
- `bloom integrations atlas`: show and validate Atlas integration config
- `bloom test`, `bloom quality`, `bloom users`, `bloom config`

## API Surface

Canonical API router prefix: `/api/v1`

Core route groups mounted today:

- `/api/v1/objects`
- `/api/v1/containers`
- `/api/v1/content`
- `/api/v1/equipment`
- `/api/v1/templates`
- `/api/v1/subjects`
- `/api/v1/lineages`
- `/api/v1/search`
- `/api/v1/search/v2`
- `/api/v1/object-creation`
- `/api/v1/tracking`
- `/api/v1/user-tokens`
- `/api/v1/admin/*`
- `/api/v1/external/specimens`
- `/api/v1/external/atlas`
- `/api/v1/external/atlas/beta`

Server-rendered GUI routes remain active under the root app, including login, operational views, and graph screens.

## Cross-Repo Boundaries

- Atlas sends accepted-material and status traffic into Bloom.
- Bloom links physical execution state back to Atlas TRF/test/fulfillment-item context.
- Bloom can register run artifacts in Dewey when Dewey integration is enabled.
- Ursa resolves sequencing context from Bloom using run and lane identifiers.

## TapDB Mount

Bloom can mount the TapDB admin surface inside the same server process.

Mounted path defaults to `/admin/tapdb`.

Mounted-mode rules:

- Bloom session auth is the gate.
- access is admin-only
- unauthenticated browser requests redirect to `/login`
- mounted TapDB local login is disabled

## Timezone Policy

- Bloom persists timestamps in UTC.
- display timezone is user-configurable via TapDB-backed `system_user` preferences
- canonical preference key: `display_timezone`

## Local Development

Typical local flow:

```bash
source bloom_activate.sh
pip install -e .
bloom db build
bloom server start --foreground
```

Focused validation commands:

```bash
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
```

## Current Docs

- [Docs index](docs/README.md)
- [Bloom beta API contracts](docs/bloom_beta_api_contracts.md)
- [Search V2](docs/SEARCH_V2.md)
- [Authentication](docs/AUTHENTICATION.md)

Historical execution plans remain in `docs/`, but they are reference material rather than the primary source of truth.

<!-- release-sweep: 2026-03-10 -->
