atomic-ehr-codegen-python-us-core-profiles: doc fix + regenerate fhir_types (codegen canary)

.github/workflows/atomic-ehr-codegen-python-us-core-profiles.yaml

@@ -0,0 +1,122 @@
+name: atomic-ehr-codegen-python-us-core-profiles
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - 'developer-experience/atomic-ehr-codegen-python-us-core-profiles/**'
+      - '.github/workflows/atomic-ehr-codegen-python-us-core-profiles.yaml'
+  pull_request:
+    paths:
+      - 'developer-experience/atomic-ehr-codegen-python-us-core-profiles/**'
+      - '.github/workflows/atomic-ehr-codegen-python-us-core-profiles.yaml'
+  workflow_dispatch:
+
+defaults:
+  run:
+    working-directory: developer-experience/atomic-ehr-codegen-python-us-core-profiles
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    services:
+      aidbox_db:
+        image: healthsamurai/aidboxdb:17
+        env:
+          POSTGRES_USER: aidbox
+          POSTGRES_PASSWORD: aidboxpwd
+          POSTGRES_DB: aidbox
+        options: >-
+          --health-cmd "pg_isready -U aidbox"
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 10
+
+      aidbox:
+        image: healthsamurai/aidboxone:edge
+        ports:
+          - 8080:8080
+        env:
+          AIDBOX_LICENSE: ${{ secrets.AIDBOX_LICENSE }}
+          AIDBOX_CLIENT_ID: root
+          AIDBOX_CLIENT_SECRET: secret
+          AIDBOX_ADMIN_PASSWORD: secret
+          AIDBOX_PORT: 8080
+          AIDBOX_FHIR_PACKAGES: hl7.fhir.r4.core#4.0.1
+          AIDBOX_FHIR_SCHEMA_VALIDATION: true
+          BOX_SETTINGS_MODE: read-write
+          PGHOST: aidbox_db
+          PGPORT: 5432
+          PGUSER: aidbox
+          PGPASSWORD: aidboxpwd
+          PGDATABASE: aidbox
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: '22.12.0'
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Install Node dependencies
+        run: npm install
+
+      - name: Install @atomic-ehr/codegen 0.0.17
+        run: npm install --save-dev @atomic-ehr/codegen@0.0.17
+
+      - name: Regenerate fhir_types
+        run: npx tsx generate.ts
+
+      - name: Check generated fhir_types are up to date
+        run: |
+          if [ -n "$(git status --porcelain -- fhir_types)" ]; then
+            echo "::error::fhir_types/ changed after regeneration. Run 'npx tsx generate.ts' and commit the result."
+            git status --porcelain -- fhir_types
+            git diff -- fhir_types
+            exit 1
+          fi
+
+      - name: Install Python dependencies
+        run: pip install -r fhir_types/requirements.txt
+
+      - name: Typecheck
+        run: mypy .
+
+      - name: Build bundle
+        run: |
+          out=$(python load.py)
+          echo "$out"
+          echo "$out" | grep -qF 'Wrote bundle with 10 entries'
+
+      - name: Compute average BP and check output
+        run: |
+          out=$(python avg.py)
+          echo "$out"
+          echo "$out" | grep -qF 'Avg BP: 125.2/82.0 mmHg (n=5)'
+
+      - name: Wait for Aidbox
+        run: |
+          for i in $(seq 1 60); do
+            if curl -fsS http://localhost:8080/health >/dev/null 2>&1; then
+              echo "Aidbox is up"; exit 0
+            fi
+            echo "waiting for Aidbox ($i)"; sleep 3
+          done
+          echo "Aidbox did not become healthy in time"; exit 1
+
+      - name: POST bundle to Aidbox with fhirpy and read it back
+        env:
+          AIDBOX_URL: http://localhost:8080/fhir
+          AIDBOX_SECRET: secret
+        run: |
+          out=$(python post.py)
+          echo "$out"
+          echo "$out" | grep -qF 'Stored BP observations: 5'

.github/workflows/atomic-ehr-codegen-typescript-us-core-profiles.yaml

@@ -0,0 +1,118 @@
+name: atomic-ehr-codegen-typescript-us-core-profiles
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - 'developer-experience/atomic-ehr-codegen-typescript-us-core-profiles/**'
+      - '.github/workflows/atomic-ehr-codegen-typescript-us-core-profiles.yaml'
+  pull_request:
+    paths:
+      - 'developer-experience/atomic-ehr-codegen-typescript-us-core-profiles/**'
+      - '.github/workflows/atomic-ehr-codegen-typescript-us-core-profiles.yaml'
+  workflow_dispatch:
+
+defaults:
+  run:
+    working-directory: developer-experience/atomic-ehr-codegen-typescript-us-core-profiles
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    services:
+      aidbox_db:
+        image: healthsamurai/aidboxdb:17
+        env:
+          POSTGRES_USER: aidbox
+          POSTGRES_PASSWORD: aidboxpwd
+          POSTGRES_DB: aidbox
+        options: >-
+          --health-cmd "pg_isready -U aidbox"
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 10
+
+      aidbox:
+        image: healthsamurai/aidboxone:edge
+        ports:
+          - 8080:8080
+        env:
+          AIDBOX_LICENSE: ${{ secrets.AIDBOX_LICENSE }}
+          AIDBOX_CLIENT_ID: root
+          AIDBOX_CLIENT_SECRET: secret
+          AIDBOX_ADMIN_PASSWORD: secret
+          AIDBOX_PORT: 8080
+          AIDBOX_FHIR_PACKAGES: hl7.fhir.r4.core#4.0.1
+          AIDBOX_FHIR_SCHEMA_VALIDATION: true
+          BOX_SETTINGS_MODE: read-write
+          PGHOST: aidbox_db
+          PGPORT: 5432
+          PGUSER: aidbox
+          PGPASSWORD: aidboxpwd
+          PGDATABASE: aidbox
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: '22.12.0'
+
+      - name: Install dependencies
+        run: npm install
+
+      - name: Install @atomic-ehr/codegen 0.0.17
+        run: npm install --save-dev @atomic-ehr/codegen@0.0.17
+
+      - name: Regenerate fhir-types
+        run: npx tsx generate.ts
+
+      - name: Check generated fhir-types are up to date
+        run: |
+          if [ -n "$(git status --porcelain -- fhir-types)" ]; then
+            echo "::error::fhir-types/ changed after regeneration. Run 'npx tsx generate.ts' and commit the result."
+            git status --porcelain -- fhir-types
+            git diff -- fhir-types
+            exit 1
+          fi
+
+      - name: Typecheck (including generated types)
+        run: npx tsc --noEmit
+
+      - name: Build bundle
+        run: |
+          out=$(npx tsx load.ts)
+          echo "$out"
+          echo "$out" | grep -qF 'Wrote bundle with 10 entries'
+
+      - name: Compute average BP and check output
+        run: |
+          out=$(npx tsx avg.ts)
+          echo "$out"
+          echo "$out" | grep -qF 'Avg BP: 125.2/82.0 mmHg (n=5)'
+
+      - name: Wait for Aidbox
+        run: |
+          for i in $(seq 1 60); do
+            if curl -fsS http://localhost:8080/health >/dev/null 2>&1; then
+              echo "Aidbox is up"; exit 0
+            fi
+            echo "waiting for Aidbox ($i)"; sleep 3
+          done
+          echo "Aidbox did not become healthy in time"; exit 1
+
+      - name: POST bundle to Aidbox and read it back
+        run: |
+          curl -fsS -u "root:secret" -X POST \
+            -H "Content-Type: application/fhir+json" \
+            --data @bundle.json http://localhost:8080/fhir > tx-response.json
+          echo "Transaction type: $(node -e "console.log(require('./tx-response.json').type)")"
+
+          curl -fsS -u "root:secret" \
+            "http://localhost:8080/fhir/Observation?code=http://loinc.org|85354-9" > obs.json
+          total=$(node -e "console.log(require('./obs.json').total)")
+          echo "Stored BP observations: $total"
+          test "$total" = "5"

developer-experience/atomic-ehr-codegen-python-us-core-profiles/README.md

@@ -1,6 +1,6 @@
 # US Core Profiles in Python with @atomic-ehr/codegen
 
-A small CSV-to-FHIR converter demonstrating [`@atomic-ehr/codegen`](https://github.com/atomic-ehr/codegen) profile class generation for US Core. The Python counterpart of [atomic-ehr-codegen-typescript-us-core-profiles](../atomic-ehr-codegen-typescript-us-core-profiles), generated for **Pydantic** with the **[fhirpy](https://github.com/beda-software/fhirpy)** async client enabled (`fhirpyClient: true`).
+A small CSV-to-FHIR converter demonstrating [`@atomic-ehr/codegen`](https://github.com/atomic-ehr/codegen) profile class generation for US Core. The Python counterpart of [atomic-ehr-codegen-typescript-us-core-profiles](../atomic-ehr-codegen-typescript-us-core-profiles), generated for **Pydantic** with the **[fhirpy](https://github.com/beda-software/fhirpy)** async client enabled (`client: "fhirpy"`).
 
 The example:
 
@@ -73,7 +73,7 @@ python post.py
 ## Notes on the Code
 
 - **The generator is a Node tool; the output is Python.** `generate.ts` runs once to emit `fhir_types/`. After that you only need Python + Pydantic (and fhirpy for `post.py`).
-- **`fhirpyClient: true`** makes the generated resources extend `FhirpyBaseModel`: they expose `resourceType` at class level and serialize via `model_dump`, which is everything fhirpy's typed client needs to `create` / `search` / `fetch` them.
+- **`client: "fhirpy"`** makes the generated resources extend `FhirpyBaseModel`: they expose `resourceType` at class level and serialize via `model_dump`, which is everything fhirpy's typed client needs to `create` / `search` / `fetch` them.
 - **camelCase attributes (`fieldFormat: "camelCase"`).** Resource fields use the FHIR wire names (`resourceType`, `birthDate`, `effectiveDateTime`), so attribute names match the JSON. This is what lets `client.resources(Observation).search(...).fetch()` be statically typed: fhirpy's `ResourceProtocol` looks for a `resourceType` attribute, which only exists as a real attribute under camelCase. (The generator also supports `snake_case`, but then `resourceType` is injected only at runtime and fhirpy's typed client can't see it statically.) Profile **method** names stay snake_case (`set_systolic`, `set_race`, `from_resource`).
 - **Must-support base fields** (`gender`, `birthDate`) aren't profiled further by US Core, so the profile class emits no `.set_gender()`-style setters. `load.py` sets them on the base `Patient`, then calls `UscorePatientProfile.apply()`. `validate()` warns if a must-support field is missing.
 - **No `is()` type guard.** Unlike the TypeScript API, the Python classes don't ship a `.filter()`-style guard. `avg.py` selects BP observations by `resourceType` + `meta.profile`, then calls `from_resource()`.