Merge branch 'epic-medication-enhancements-and-mar' into epic-medicat…

…ion-enhancements-and-mar-2

.github/workflows/cd.yml

@@ -160,9 +160,9 @@ jobs:
       matrix:
         platform:
           - arch: amd64
-            runs-on: ubuntu-latest
+            runs-on: ubuntu-24.04
           - arch: arm64
-            runs-on: Linux-ARM64-Ubuntu-24.04
+            runs-on: ubuntu-24.04-arm
         package:
           - name: central
             path: central-server

.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:

.vscode/extensions.json

@@ -0,0 +1,9 @@
+{
+  "recommendations": [
+    "dbaeumer.vscode-eslint",
+    "esbenp.prettier-vscode",
+    "humao.rest-client",
+    "streetsidesoftware.code-spell-checker",
+    "styled-components.vscode-styled-components"
+  ]
+}

alerts/certificate-notification-error.yml

@@ -2,22 +2,21 @@ sql: |
   SELECT *
   FROM certificate_notifications
   WHERE status = 'Error'
-  AND created_at > $1;
+  AND created_at > $1
+  ORDER BY created_at DESC
 
 send:
   - target: external
     id: default
     subject: '[Tamanu Alert] Certificate notification error ({{ hostname }})'
     template: |
-      <p>Server: {{ hostname }}</p>
-      <h1>Patient notifications errored</h1>
-      <p>There are {{ rows | length }} certificate notifications that have failed to process.</p>
-      <ul>
-        {% for row in rows | slice(end=5) %}
-        <li><b>{{ row.id }}</b>: {{ row.type }} - <i>{{ row.error }}</i></li>
-        {% endfor %}
-        {% if rows | length > 5 %}
-        <li>... and {{ rows | length - 5 }} more</li>
-        {% endif %}
-      </ul>
-      <p>For more information, please check the logs.</p>
+      - Server: {{ hostname }}
+      - Alert: {{ filename }}
+
+      There are {{ rows | length }} certificate notifications that have failed to process:
+      {% for row in rows | slice(end=5) %}
+      - **{{ row.type }} ({{ row.id }})**: {{ row.error }}
+      {% endfor %}
+      {% if rows | length > 5 %}
+      - ... and {{ rows | length - 5 }} more
+      {% endif %}

alerts/fhir-error.yml

@@ -2,22 +2,21 @@ sql: |
   SELECT *
   FROM fhir.jobs
   WHERE error IS NOT NULL
-  AND created_at > $1;
+  AND created_at > $1
+  ORDER BY created_at DESC
 
 send:
   - target: external
     id: default
     subject: '[Tamanu Alert] FHIR job error ({{ hostname }})'
     template: |
-      <p>Server: {{ hostname }}</p>
-      <h1>FHIR jobs errored</h1>
-      <p>There are {{ rows | length }} FHIR jobs that have failed to process.</p>
-      <ul>
-        {% for row in rows | slice(end=5) %}
-        <li><b>{{ row.created_at }}</b>: {{ row.topic }} - <i>{{ row.error }}</i></li>
-        {% endfor %}
-        {% if rows | length > 5 %}
-        <li>... and {{ rows | length - 5 }} more</li>
-        {% endif %}
-      </ul>
-      <p>For more information, please check the logs.</p>
+      - Server: {{ hostname }}
+      - Alert: {{ filename }}
+
+      There are {{ rows | length }} FHIR jobs that have failed to process:
+      {% for row in rows | slice(end=5) %}
+      - **{{ row.topic }} ({{ row.created_at }})**: {{ row.error }}
+      {% endfor %}
+      {% if rows | length > 5 %}
+      - ... and {{ rows | length - 5 }} more
+      {% endif %}

alerts/fhir-queue-incredibly-large.yml

@@ -3,14 +3,14 @@ sql: |
     COUNT(*) AS job_count
   FROM fhir.jobs
   WHERE status = 'Queued'
-  HAVING COUNT(*) > 1000;
+  HAVING COUNT(*) > 1000
 
 send:
   - target: external
     id: default
     subject: '[Tamanu Alert] FHIR job queue abnormally large ({{ hostname }})'
     template: |
-      <p>Server: {{ hostname }}</p>
-      <p>Alert: {{ filename }}</p>
-      <h1>FHIR queued jobs count is abnormally high</h1>
-      <p>Currently queued jobs: {{ rows[0].job_count }}</p>
+      - Server: {{ hostname }}
+      - Alert: {{ filename }}
+
+      Currently queued jobs: {{ rows[0].job_count }}

alerts/fhir-queued-job-long.yml

@@ -1,26 +1,26 @@
 sql: |
   SELECT
     id,
+    topic,
     payload->>'resource' AS resource,
-    ROUND(EXTRACT(EPOCH FROM (NOW() - created_at)) / 60)::text AS duration_minutes
+    ROUND(EXTRACT(EPOCH FROM (CURRENT_TIMESTAMP - created_at)) / 60)::text AS duration_minutes
   FROM fhir.jobs
   WHERE status = 'Queued'
-    AND NOW() - created_at > INTERVAL '15 minutes';
+    AND CURRENT_TIMESTAMP - created_at > INTERVAL '15 minutes'
+    AND topic != 'fhir.resolver'
+  ORDER BY created_at ASC
 
 send:
   - target: external
     id: default
     subject: '[Tamanu Alert] Long queued FHIR jobs ({{ hostname }})'
     template: |
-      <p>Server: {{ hostname }}</p>
-      <p>Alert: {{ filename }}</p>
-      <h1>Long queued FHIR jobs detected</h1>
-      <ul>
-        {% for row in rows | slice(end=5) %}
-        <li><b>{{row.resource}}</> ID: <b>{{ row.id }}</b> - Duration: <i>{{ row.duration_minutes }} minutes</i></li>
-        {% endfor %}
-        {% if rows | length > 5 %}
-        <li>... and {{ rows | length - 5 }} more</li>
-        {% endif %}
-      </ul>
-      <p>For more information, please check the logs.</p>
+      - Server: {{ hostname }}
+      - Alert: {{ filename }}
+
+      {% for row in rows | slice(end=5) %}
+      - **{{ row.topic }}** {{row.resource}} ({{ row.id }}) for {{ row.duration_minutes }} minutes
+      {% endfor %}
+      {% if rows | length > 5 %}
+      - ... and {{ rows | length - 5 }} more
+      {% endif %}