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BernhardBuckel
52ea3b9c2f
Slice 1 of phase 3 of #1095. A Biomarker row keeps only its name, so nothing said which analyte it was. This adds the explicit alias list in the catalog the issue settled on, including the registry-only keys (urea, blood urea nitrogen, uric acid, total calcium, total bilirubin), and sets biomarkers.analyte_key (from migration 0385) from it. matchAnalyteKey equals a marker's folded name against the localised names of the catalog seeds the registry knows and against the alias list. It matches the whole name only, so "Calcium (ionisiert)" is not "Calcium"; a name two analytes claim matches neither; and the marker's own unit must be one the analyte reaches, so a marker called "Glucose" in a unit the registry cannot convert stays unlinked. The key is set when a marker is created (the biomarker route, the mint used by lab writes, the legacy backfill) and, for an existing marker, by ensureAnalyteKey the first time a reading needs it. It never overwrites a key that is set. There is no boot job for the existing markers: the conversion that uses the key fills it on first use, and a sweep can be added later if wanted. The key is returned on the biomarker API and in the OpenAPI schema. Refs #1095
docs/ — internal reference + operator playbooks
The user-facing documentation lives at https://docs.healthlog.dev — that's the canonical surface for self-hosting guides, integration walkthroughs, AI-provider setup, and the doctor-report workflow.
The files in this directory are the internal operator playbooks, audit notes, and machine-readable specs that ship alongside the source:
api/— the OpenAPI 3.1 spec for the native-client subset (iOS DTO codegen target). Seeapi/README.mdfor the preview commands. Also home to the MCP-server contract:api/mcp-capabilities.md(tools, resources, prompts, write model) andapi/mcp-skills.md(building a connector / skill).ops/— operator runbooks: deploy, backup / restore, encryption-key rotation, password reset and account recovery, env checks, TLS pinning, data repair. These are what an operator reaches for during an incident.self-hosting/— horizontal-scaling notes (HEALTHLOG_PROCESS_TYPE=web|worker|all) and the deploy-pipeline recipe. Routine install steps stay ondocs.healthlog.dev. Includesself-hosting/mcp.md— enabling the off-by-default MCP connector and pointing Claude.ai / ChatGPT / Claude Desktop at it, andself-hosting/sso.md— OIDC SSO login: IdP setup, the identity-pinning security model,OIDC_ONLYconsequences, and the break-glass runbook. Alsoself-hosting/geolite2.md— bringing your own offline GeoLite2 databases viaGEOLITE2_DIRinstead of sending login IPs to a third-party lookup. Andself-hosting/account-sharing.md— letting one account on the instance open another's health record: the three access levels, the eight sections a grant can be narrowed to, managed profiles for somebody with no login and the guardians who look after them, what revocation does and does not undo, and which trust properties of the instance are unchanged by any of it.using/— notes on using the app that sit close to the code.using/search.mdcovers the command palette's record search: opening it, what it finds, how matching works, and its limits on very large and shared records.migration/— migration notes. Currently only v1.3 to v1.4; later releases are covered byCHANGELOG.mdand https://docs.healthlog.dev.integrations/— per-integration reference (Withings, Fitbit, Google Health, WHOOP, Apple Health, AI providers, data import).adr/— architecture decision records.security/— threat-model notes.diagrams/— architecture diagrams rendered through docs.healthlog.dev.releases/— release imagery.apple-store-connect-checklist.md— the iOS submission gate.codex-protocol-spec.md— Codex / ChatGPT OAuth protocol reverse-engineering notes.ui-guidelines.md— UI / a11y house style.
If you're a self-hoster looking to spin up an instance, start at https://docs.healthlog.dev or jump to the Quick Start in the project README.