Fhir: tooling to auto-generate an adaptor

[josephjclark]

Summary

This PR adds tooling to auto-generate a FHIR adaptor from a FHIR spec.

Closes #798

Usage guide

First time (to generate packages/fhir-jembi):

pnpm generate-fhir jembi --spec https://build.fhir.org/ig/jembi/ethiopia-hiv/branches/master/definitions.json.zip

To rebuild from the same spec:

pnpm generate-fhir jembi

To update/redownload the spec:
To rebuild from the same spec:

pnpm generate-fhir jembi --respec

Steps

• Moved the gen code into a single central command pnpm generate-fhir
• Re-generated fhir-ndr-et with no diffs in builders.js
• Generated PASSING (but basic) unit tests for each builder function
• Generate skipped tests for each example in the spec
• Generate a FHIR v4 adaptor
• Work out what to do about datatype helpers (I saw them being hand-written for each base fhir version, but the generator needs to know their APIs)
• Re-base fhir-ndr-et on the fhir 4 adaptor

AI Usage

Please disclose how you've used AI in this work (it's cool, we just want to know!):

• Code generation (copilot but not intellisense)
• Learning or fact checking
• Strategy / design
• Optimisation / refactoring
• Translation / spellchecking / doc gen
• Other
• I have not used AI

You can read more details in our Responsible AI Policy

[josephjclark]

Refer to #812 for guidance on how to handle types.

I don't think it's a copy and paste solution but it at least shows where we were going wrong.

[josephjclark]

Here's the a no-diff diff from builders.js in a02d9c0

> pnpm generate-fhir jembi --spec https://build.fhir.org/ig/jembi/ethiopia-hiv/branches/master/definitions.json.zip

> diff --color packages/fhir-jembi/src/builders.js packages/fhir-ndr-et/src/builders.js 
31239c31239
< }
---
> }
\ No newline at end of file

This depends on mappings file (because of course it does!), which I've temporarily checked in. It uses ordered generation too.

Pretty pleased with this: I've externalised the tooling into a pretty elegant command.

The commits from this point will start to diverge the code

[josephjclark]

Auto-generated unit tests 😎

They don't do a lot, but they do verify that the generated code works and resources can be created

  art-follow-up-careplan
    ✔ should create a simple art-follow-up-careplan

  cervical-cancer-care-plan
    ✔ should create a simple cervical-cancer-care-plan

  cotrimoxazole-preventive-therapy-careplan
    ✔ should create a simple cotrimoxazole-preventive-therapy-careplan

  tb-treatment-careplan
    ✔ should create a simple tb-treatment-careplan

  tpt-careplan
    ✔ should create a simple tpt-careplan

  entry-from-outside-target-facility-encounter
    ✔ should create a simple entry-from-outside-target-facility-encounter

  target-facility-encounter
    ✔ should create a simple target-facility-encounter

  arv-regimen-medication
    ✔ should create a simple arv-regimen-medication

  oi-medication
    ✔ should create a simple oi-medication

  tpt-medication
    ✔ should create a simple tpt-medication

  arv-medication-administration
    ✔ should create a simple arv-medication-administration

  cotrimoxazole-preventive-therapy-medication-administration
    ✔ should create a simple cotrimoxazole-preventive-therapy-medication-administration

  fluconazole-preventive-therapy-medication-administration
    ✔ should create a simple fluconazole-preventive-therapy-medication-administration

  arv-medication-dispense
    ✔ should create a simple arv-medication-dispense

  cotrimoxazole-preventive-therapy-medication-dispense
    ✔ should create a simple cotrimoxazole-preventive-therapy-medication-dispense

  generic-medication-dispense
    ✔ should create a simple generic-medication-dispense

  arv-medication-request
    ✔ should create a simple arv-medication-request

  cotrimoxazole-preventive-therapy-medication-request
    ✔ should create a simple cotrimoxazole-preventive-therapy-medication-request

  generic-medication-request
    ✔ should create a simple generic-medication-request

  tpt-medication-request
    ✔ should create a simple tpt-medication-request

  active-tb-observation
    ✔ should create a simple active-tb-observation

  alt-ast-observation
    ✔ should create a simple alt-ast-observation

  alternate-tb-prophylaxis-type-observation
    ✔ should create a simple alternate-tb-prophylaxis-type-observation

  alternate-tpt-at-follow-up-observation
    ✔ should create a simple alternate-tpt-at-follow-up-observation

  art-eligibility-status-observation
    ✔ should create a simple art-eligibility-status-observation

  art-followup-status-observation
    ✔ should create a simple art-followup-status-observation

  art-followup-stopped-reasons-observation
    ✔ should create a simple art-followup-stopped-reasons-observation

  art-not-started-plan-next-step-observation
    ✔ should create a simple art-not-started-plan-next-step-observation

  arv-adherence-observation
    ✔ should create a simple arv-adherence-observation

  arv-change-category-type-observation
    ✔ should create a simple arv-change-category-type-observation

  arv-poor-adherence-reasons-observation
    ✔ should create a simple arv-poor-adherence-reasons-observation

  arv-regimen-change-reason-observation
    ✔ should create a simple arv-regimen-change-reason-observation

  arv-regimen-changed-observation
    ✔ should create a simple arv-regimen-changed-observation

  arv-regimen-side-effects-observation
    ✔ should create a simple arv-regimen-side-effects-observation

  assessed-for-pain-observation
    ✔ should create a simple assessed-for-pain-observation

  blood-pressure
    ✔ should create a simple blood-pressure

  bmi-observation
    ✔ should create a simple bmi-observation

  breastfeeding-status-observation
    ✔ should create a simple breastfeeding-status-observation

  cd4-absolute-observation
    ✔ should create a simple cd4-absolute-observation

  cd4-percentage-observation
    ✔ should create a simple cd4-percentage-observation

  cervical-cancer-screening-accepted-observation
    ✔ should create a simple cervical-cancer-screening-accepted-observation

  cervical-cancer-screening-counselling-status-observation
    ✔ should create a simple cervical-cancer-screening-counselling-status-observation

  cervical-cancer-screening-method-observation
    ✔ should create a simple cervical-cancer-screening-method-observation

  cervical-cancer-screening-observation
    ✔ should create a simple cervical-cancer-screening-observation

  cervical-cancer-screening-result-observation
    ✔ should create a simple cervical-cancer-screening-result-observation

  cervical-cancer-screening-type-observation
    ✔ should create a simple cervical-cancer-screening-type-observation

  cervical-cancer-treatment-received-observation
    ✔ should create a simple cervical-cancer-treatment-received-observation

  children-developmental-milestone-observation
    ✔ should create a simple children-developmental-milestone-observation

  confirmed-hiv-positive-observation
    ✔ should create a simple confirmed-hiv-positive-observation

  cotrimoxazole-preventive-therapy-adherence-observation
    ✔ should create a simple cotrimoxazole-preventive-therapy-adherence-observation

  cotrimoxazole-preventive-therapy-observation
    ✔ should create a simple cotrimoxazole-preventive-therapy-observation

  counseled-for-hiv-observation
    ✔ should create a simple counseled-for-hiv-observation

  creatine-observation
    ✔ should create a simple creatine-observation

  current-art-duration-observation
    ✔ should create a simple current-art-duration-observation

  delivery-mode-observation
    ✔ should create a simple delivery-mode-observation

  delivery-place-observation
    ✔ should create a simple delivery-place-observation

  differentiated-service-delivery-observation
    ✔ should create a simple differentiated-service-delivery-observation

  disclosure-status-observation
    ✔ should create a simple disclosure-status-observation

  edema-observation
    ✔ should create a simple edema-observation

  elicited-index-case-contacts-observation
    ✔ should create a simple elicited-index-case-contacts-observation

  enhanced-adherence-counselling-observation
    ✔ should create a simple enhanced-adherence-counselling-observation

  estimated-delivery-date-observation
    ✔ should create a simple estimated-delivery-date-observation

  family-member-hiv-status-observation
    ✔ should create a simple family-member-hiv-status-observation

  family-planning-method-observation
    ✔ should create a simple family-planning-method-observation

  fluconazole-preventive-therapy-observation
    ✔ should create a simple fluconazole-preventive-therapy-observation

  future-pregnancy-plans-observation
    ✔ should create a simple future-pregnancy-plans-observation

  generic-observation
    ✔ should create a simple generic-observation

  head-circumference-observation
    ✔ should create a simple head-circumference-observation

  health-status-observation
    ✔ should create a simple health-status-observation

  heart-rate-observation
    ✔ should create a simple heart-rate-observation

  height-observation
    ✔ should create a simple height-observation

  hgb-observation
    ✔ should create a simple hgb-observation

  highest-education-observation
    ✔ should create a simple highest-education-observation

  hiv-prevention-plan-observation
    ✔ should create a simple hiv-prevention-plan-observation

  hiv-program-final-outcome-known-observation
    ✔ should create a simple hiv-program-final-outcome-known-observation

  hiv-program-final-outcome-observation
    ✔ should create a simple hiv-program-final-outcome-observation

  hiv-program-reason-art-not-started-observation
    ✔ should create a simple hiv-program-reason-art-not-started-observation

  hiv-program-status-observation
    ✔ should create a simple hiv-program-status-observation

  hiv-status-disclosure-at-enrollment-observation
    ✔ should create a simple hiv-status-disclosure-at-enrollment-observation

  hiv-test-results-observation
    ✔ should create a simple hiv-test-results-observation

  hiv-treatment-prior-enrollment-observation
    ✔ should create a simple hiv-treatment-prior-enrollment-observation

  inh-at-follow-up-observation
    ✔ should create a simple inh-at-follow-up-observation

  last-menstrual-period-observation
    ✔ should create a simple last-menstrual-period-observation

  level-of-pain-observation
    ✔ should create a simple level-of-pain-observation

  maternal-hiv-status-observation
    ✔ should create a simple maternal-hiv-status-observation

  muac-observation
    ✔ should create a simple muac-observation

  nutritional-screening-result-observation
    ✔ should create a simple nutritional-screening-result-observation

  nutritional-status-observation
    ✔ should create a simple nutritional-status-observation

  nutritional-suppliments-provided-observation
    ✔ should create a simple nutritional-suppliments-provided-observation

  otz-observation
    ✔ should create a simple otz-observation

  patient-functional-status-observation
    ✔ should create a simple patient-functional-status-observation

  patient-occupation-observation
    ✔ should create a simple patient-occupation-observation

  patient-who-stage-observation
    ✔ should create a simple patient-who-stage-observation

  physical-examinations-observation
    ✔ should create a simple physical-examinations-observation

  pregnancy-status-observation
    ✔ should create a simple pregnancy-status-observation

  presenting-symptom-observation
    ✔ should create a simple presenting-symptom-observation

  reason-eligible-for-art-observation
    ✔ should create a simple reason-eligible-for-art-observation

  reason-not-eligbile-for-tpt-observation
    ✔ should create a simple reason-not-eligbile-for-tpt-observation

  resides-in-catchment-area-observation
    ✔ should create a simple resides-in-catchment-area-observation

  respiratory-rate-observation
    ✔ should create a simple respiratory-rate-observation

  screened-for-tb-observation
    ✔ should create a simple screened-for-tb-observation

  target-population-observation
    ✔ should create a simple target-population-observation

  tb-diagnostic-test-result-observation
    ✔ should create a simple tb-diagnostic-test-result-observation

  tb-prophylaxis-type-observation
    ✔ should create a simple tb-prophylaxis-type-observation

  tb-screening-result-observation
    ✔ should create a simple tb-screening-result-observation

  tb-treatment-started-observation
    ✔ should create a simple tb-treatment-started-observation

  tb-treatment-status-observation
    ✔ should create a simple tb-treatment-status-observation

  temperature-observation
    ✔ should create a simple temperature-observation

  tested-for-hiv-observation
    ✔ should create a simple tested-for-hiv-observation

  therapeutic-supplementary-food-observation
    ✔ should create a simple therapeutic-supplementary-food-observation

  tpt-eligbility-observation
    ✔ should create a simple tpt-eligbility-observation

  tpt-started-observation
    ✔ should create a simple tpt-started-observation

  treatment-completed-observation
    ✔ should create a simple treatment-completed-observation

  treatment-discontinued-observation
    ✔ should create a simple treatment-discontinued-observation

  viral-load-count-observation
    ✔ should create a simple viral-load-count-observation

  viral-load-indication-observation
    ✔ should create a simple viral-load-indication-observation

  viral-load-performed-observation
    ✔ should create a simple viral-load-performed-observation

  weight-observation
    ✔ should create a simple weight-observation

  patient
    ✔ should create a simple patient

  related-person
    ✔ should create a simple related-person