Merge branch 'main' of https://github.com/beyondessential/tamanu into…

… epic-medication-enhancements-and-mar-2

.github/workflows/ci-non-deterministic.yml

@@ -1,4 +1,4 @@
-name: Test Migrations for Determinism
+name: Migration determinism
 
 on:
   workflow_dispatch:
@@ -17,9 +17,6 @@ env:
 
 jobs:
   test-for-non-determinism:
-    permissions:
-      id-token: write # allow accessing OIDC token for AWS
-      contents: read
     strategy:
       fail-fast: false
       matrix:
@@ -28,18 +25,28 @@ jobs:
           - "14"
           - "15"
           - "16"
-    name: Test Migrations for Determinism on pg${{ matrix.postgres }}
+          - "17"
+    name: on pg=${{ matrix.postgres }}
     runs-on: ubuntu-latest
+    permissions:
+      contents: read
     steps:
-      - name: Configure AWS Credentials
-        uses: aws-actions/configure-aws-credentials@v3
-        with:
-          aws-region: ap-southeast-2
-          role-to-assume: arn:aws:iam::143295493206:role/gha-tamanu-test-data-snapshots-s3
-          role-session-name: GHA@fake=generate
       - uses: actions/checkout@v4
         with:
-          fetch-depth: 4000
+          fetch-depth: 0
+          ref: ${{ github.base_ref }}
+      - run: git switch ${{ github.event.pull_request.head.ref || github.ref_name }}
+
+      # Deal with the case where base_ref diverges from this branch
+      # (e.g. main has gone beyond the point where this branch forked)
+      #
+      # Test from the base of the PR or one commit back if on main/release.
+      - name: Find base
+        id: base
+        run: |
+          realbase=$(git merge-base ${{ github.base_ref || 'HEAD~1' }} HEAD)
+          echo "realbase=$realbase" | tee -a "$GITHUB_OUTPUT"
+
       - uses: actions/setup-node@v4
         with:
           node-version-file: '.nvmrc'
@@ -49,25 +56,36 @@ jobs:
           key: ${{ runner.os }}-npm-${{ hashFiles('package-lock.json') }}
           path: ${{ env.NODE_MODULES_PATHS }}
 
-      - run: npm install
+      - run: npm ci
       - run: npm run build-shared
 
+      - name: Precheck
+        id: precheck
+        run: |
+          set +e
+          npm run --silent --workspace scripts test-determinism -- --since-ref ${{ steps.base.outputs.realbase }} --check-precondition --skip-db-check --skip-env-check
+          code=$?
+          echo "code=$code" | tee -a "$GITHUB_OUTPUT"
+          [[ "$code" = "1" ]] && exit 1
+          true
+
       - name: Install and start postgres ${{ matrix.postgres }}
+        if: steps.precheck.outputs.code != '2'
         run: |
           source .github/scripts/install-postgres-ubuntu.sh ${{ matrix.postgres }}
           .github/scripts/setup-postgres-for-one-package.sh fake
 
-      - run: python3 -m pip install boto3
-
-      - id: commit-finder
-        run: |
-          commit=$(.github/scripts/find-dumped.py)
-          (( $? == 0 )) || exit 1
-          echo "commit=$commit" >> $GITHUB_OUTPUT
-
-      - run: aws s3 cp s3://bes-tamanu-test-data-snapshots/${{ steps.commit-finder.outputs.commit }}/fake-pg${{ matrix.postgres }}.dump ./ --no-progress
+      - name: Test central migrations
+        if: steps.precheck.outputs.code != '2'
+        env:
+          NODE_CONFIG_DIR: ${{ github.workspace }}/packages/central-server/config
+        run: npm run --silent --workspace scripts test-determinism -- --since-ref ${{ steps.base.outputs.realbase }}
 
-      - run: npm run --workspace scripts test-determinism -- --dump-path $(realpath fake-pg${{ matrix.postgres }}.dump)
+      - name: Test facility migrations
+        if: steps.precheck.outputs.code != '2'
+        env:
+          NODE_CONFIG_DIR: ${{ github.workspace }}/packages/facility-server/config
+        run: npm run --silent --workspace scripts test-determinism -- --since-ref ${{ steps.base.outputs.realbase }}
 
   # Dummy job to have a stable name for PR requirements
   tests-pass:

common.tsconfig.json

@@ -7,15 +7,15 @@
     "ignoreDeprecations": "5.0",
     "verbatimModuleSyntax": false,
     "isolatedModules": true,
-    "module": "ES2020",
-    "lib": ["es2020"],
+    "module": "ES2022",
+    "lib": ["es2022"],
     "noEmit": true,
     "noUnusedLocals": true,
     "noUnusedParameters": true,
     "pretty": true,
     "skipLibCheck": true,
     "strict": true,
-    "target": "es2020"
+    "target": "es2022"
   },
   "exclude": [
     "build",

database/model/central-server/fhir/encounters.yml

@@ -58,3 +58,8 @@ sources:
             description: "{{ doc('fhir__generic__is_live') }} in encounters."
             data_tests:
               - not_null
+          - name: resolved
+            data_type: boolean
+            description: "{{ doc('fhir__generic__resolved') }} in encounters."
+            data_tests:
+              - not_null

database/model/central-server/fhir/generic.md

@@ -30,3 +30,7 @@ Timestamp of when this FHIR resource was last materialised.
 {% docs fhir__generic__is_live %}
 Whether or not a FHIR resource is live. If a resource is not live, it won't be rematerialised if upstream changes are made.
 {% enddocs %}
+
+{% docs fhir__generic__resolved %}
+If this FHIR resource has resolved all of its references to other resources.
+{% enddocs %}

database/model/central-server/fhir/immunizations.yml

@@ -78,3 +78,8 @@ sources:
             description: "{{ doc('fhir__generic__is_live') }} in immunizations."
             data_tests:
               - not_null
+          - name: resolved
+            data_type: boolean
+            description: "{{ doc('fhir__generic__resolved') }} in immunizations."
+            data_tests:
+              - not_null

database/model/central-server/fhir/non_fhir_medici_report.yml

@@ -139,3 +139,8 @@ sources:
             description: "{{ doc('fhir__generic__is_live') }} in non_fhir_medici_report."
             data_tests:
               - not_null
+          - name: resolved
+            data_type: boolean
+            description: "{{ doc('fhir__generic__resolved') }} in non_fhir_medici_report."
+            data_tests:
+              - not_null

database/model/central-server/fhir/organizations.yml

@@ -45,3 +45,8 @@ sources:
             description: "{{ doc('fhir__generic__is_live') }} in organizations."
             data_tests:
               - not_null
+          - name: resolved
+            data_type: boolean
+            description: "{{ doc('fhir__generic__resolved') }} in organizations."
+            data_tests:
+              - not_null

database/model/central-server/fhir/patients.yml

@@ -78,3 +78,8 @@ sources:
             description: "{{ doc('fhir__generic__is_live') }} in patients."
             data_tests:
               - not_null
+          - name: resolved
+            data_type: boolean
+            description: "{{ doc('fhir__generic__resolved') }} in patients."
+            data_tests:
+              - not_null

database/model/central-server/fhir/practitioners.yml

@@ -43,3 +43,8 @@ sources:
             description: "{{ doc('fhir__generic__is_live') }} in practitioners."
             data_tests:
               - not_null
+          - name: resolved
+            data_type: boolean
+            description: "{{ doc('fhir__generic__resolved') }} in practitioners."
+            data_tests:
+              - not_null

database/model/central-server/fhir/service_requests.yml

@@ -105,3 +105,8 @@ sources:
             description: "{{ doc('fhir__generic__is_live') }} in service_requests."
             data_tests:
               - not_null
+          - name: resolved
+            data_type: boolean
+            description: "{{ doc('fhir__generic__resolved') }} in service_requests."
+            data_tests:
+              - not_null

database/model/central-server/fhir/specimens.yml

@@ -43,3 +43,8 @@ sources:
             description: "{{ doc('fhir__generic__is_live') }} in specimens."
             data_tests:
               - not_null
+          - name: resolved
+            data_type: boolean
+            description: "{{ doc('fhir__generic__resolved') }} in specimens."
+            data_tests:
+              - not_null