CrazyLIMS

Canonical entry point and documentation index for the CrazyLIMS database-first stack.

Start here

• Project overview, environment setup, and Make targets: docs/overview.md (formerly the full README).
• Quick start: make up (bring up services) → make ci (migrations, db tests, contract export, RBAC + UI smoke tests).
• Need local services without Docker? See scripts/local_dev.sh notes in docs/overview.md.

Documentation map

• Core references: docs/security-model.md, docs/database-schema.md, docs/domain-samples.md, docs/ui-handover-integration.md.
• ELN: jupyterlite-eln-plan.md, ui/public/eln/embed.html, eln-jupyterlite-embedding-attempts.md (experiment log). The bundled JupyterLite now ships a Pyodide-ready PostgREST client (crazylims_postgrest_client.pyodide.build_authenticated_client) plus offline wheels under /eln/lite/pypi.
• Transaction contexts & examples: docs/transaction-context-examples.md, docs/postman/transaction-context.postman_collection.json.
• Security redux & lineage-aware access: security-access-control-plan-phase1-and-2-security-redux.md.

Plans & roadmap

• Security backbone: phase1-redux-detailed-plan.md.
• Unified artefact/provenance platform: phase2-redux-detailed-plan.md.
• Historical plans kept for context: overarching-implementaion-plan.md, phase0-phase1-detailed-plan.md, phase2-detailed-plan.md, post-phase2-readiness-plan.md, tech-option-d-postgresql-schema-driven.md, minimal-eln-project-access.md.

API contracts

• PostgREST OpenAPI: contracts/postgrest/openapi.json.
• PostGraphile schema snapshots: contracts/postgraphile/.
• Use these for client generation (REST/GraphQL); keep them in sync with migrations via make contracts/export.

Services & UI

• PostgREST: http://localhost:7100 (override with POSTGREST_HOST_PORT).
• PostGraphile: http://localhost:7101 (override with POSTGRAPHILE_HOST_PORT).
• Dev console (persona switcher, security views, ELN workbench): make ui/dev → http://localhost:5173.

Assets & tokens

• Dev JWT fixtures: ops/examples/jwts (make jwt/dev regenerates and copies to ui/public/tokens).
• Vendored JupyterLite bundle (browser-only Pyodide runtime): make jupyterlite/vendor (outputs to ui/public/eln/lite/).

Repo helpers

• Migration workflow and test targets are documented in docs/overview.md.
• Makefile lists helper targets (logs, psql shell, db reset, UI tests).