Wired in prototype
Phase 0 · Today
Shipped
omh-shim and jupyterhealth-client integrated in pause_ingest. Vendor JSON → Open mHealth (IEEE 1752.1) → FHIR R5 Observation path is end-to-end runnable in the Python worker, including DBDP HRV feature computation → derived Observation upload with derivedFrom provenance. Wire-level contract test (tests/jhe_mock_server.py + test_exchange_integration.py) exercises the full pipeline against an in-process JHE mock — the production exchange.upload_observation, hrv_features_to_fhir_observation, and read_recent_observations code paths run unmodified. The same contract assertions also run against a real JHE instance via an opt-in PAUSE_USE_REAL_JHE=1 pytest marker (tests/conftest.py + tests/test_exchange_real_jhe.py); 7 / 7 real-JHE tests green against the jhe-local Docker stack. Surfaced a real bug in the jupyterhealth-client integration that lenient unit-test doubles missed, plus two more mock-vs-real divergences on the first real-mode run (POST response shape; unknown-patient list filter) now pinned in both directions. Reference FHIR R5 Bundle shape also served live at /api/mulesoft/patient/anika-patel/timeline.
Wired in prototype
Phase 1 · Local dev loop against real JHE
Shipped 2026-06-16 (extended 2026-06-23)
Real JupyterHealth Exchange Django container brought up against a Docker postgres on the maintainer's box, OIDC RS256 key generated, seeded with the canonical RBAC fixtures, an OAuth client_credentials app named pause-ingest bound to a real Patient + Oura DataSource through a Study with explicit per-scope consent rows + a FhirSource row, and pause_ingest's full pipeline ran end-to-end through BOTH JHE write paths: the raw OMH heart-rate observation routes to JHE's mapped Observation handler (server-issued integer pk) and the derived HRV-time-domain feature observation (with derivedFrom pointer to the raw row's server id) routes to the auxiliary FhirAuxResource handler (server-issued UUID pk) via the X-JHE-FHIR-Source-ID header threaded through IngestConfig.fhir_source_id. Three real-JHE-only gotchas the wire-level mock had not pinned were surfaced and fixed in the same session: pause_ingest was requesting OAuth scope strings (observation.read / observation.write) JHE's vocabulary rejects with invalid_scope; pause_ingest used Content-Type: application/fhir+json which JHE's parser rejects (must be application/json); and pause_ingest's OMH coding system / code shape did not match JHE's mapped-Observation routing criteria (system https://w3id.org/openmhealth, code omh:<schema>:<version>), so writes silently fell through to the auxiliary handler which then 400'd on the missing X-JHE-FHIR-Source-ID header. The wire-level mock now mirrors the routing contract (codings outside https://w3id.org/openmhealth require the header) so future drift on either write path fails the contract test instead of silently routing wrong against real JHE. Extended 2026-06-23 by shipping the JHE_SETUP_RUNBOOK's Path B sketch as a real opt-in pytest marker — PAUSE_USE_REAL_JHE=1 swaps the in-process JheMockServer fixture for IngestConfig.from_env() and runs the same 7 contract assertions against the live jhe-local stack; 7/7 green on the first real-mode invocation. Two more wire-level surprises the mock had papered over were surfaced in that run and pinned in both directions: real JHE's POST /Observation response omits valueAttachment (only the envelope; mock echoed the full posted resource); real JHE's GET /Observation?patient=<unknown> returns the OAuth client's full authorized set, not an empty Bundle. Full transcript at docs/JHE_REAL_RUN_2026-06-16.md; runbook Path B at docs/JHE_SETUP_RUNBOOK.md.
Designed
Phase 2 · Real wearable ingest
2–3 weeks
Vendor OAuth for Oura, then HealthKit bridge for Apple Health. Background worker polls samples and runs the convert → upload pipeline at scale.
Designed
Phase 3 · Provider read path
2–3 weeks
FastAPI assembles a patient timeline via jupyterhealth-client. Wire the menopause classifier and RAG over the guideline corpus. Clinician view in the Pause web app.
Designed
Phase 4 · Provider write path
3–4 weeks
Write Observation, CarePlan, and DocumentReference back to JHE. Capture clinician accept / edit / reject as outcomes-registry events.
Future
Phase 5 · Customer-VPC deployment
4+ weeks per design partner
Deploy JHE into the customer VPC via Helm. Wire SAML SSO. Deploy Pause inference alongside in federated mode — model weights leave the VPC; PHI does not.
