Merge pull request #6 from beyondessential/update-20240530

Latest update for May 30 2024

.github/pull_request_template.md

@@ -2,22 +2,16 @@
 
 _Add a brief description of the changes in this PR to help give the reviewer context._
 
-### Checklist
+### Deploys
 
-- [ ] Code is finished
-- [ ] Tests are written
-- [ ] UI Screenshots added to the Linear issue
-- [ ] Testing notes added to the Linear issue
+- [ ] **Deploy to Tamanu Internal** <!-- #deploy -->
 
-_Upon merging:_
+### Remember to...
 
-- [ ] Update the changelog (find it [here](/~https://github.com/beyondessential/tamanu/releases) in the appropriate _draft_ release)
-  - [ ] with a ticket reference (e.g. `TAN-123: a one line description`, keep the lists sorted)
-  - [ ] any config/settings changes and manual deployment steps
-  - [ ] any db schema or other changes that could impact downstream data analysis
-- [ ] Update the [config reference](https://beyond-essential.slab.com/posts/reference-config-file-0c70ukly) or [settings reference](https://beyond-essential.slab.com/posts/reference-settings-0blw1x2q) as needed
-- [ ] Update the [relevant runbook(s)](https://beyond-essential.slab.com/topics/runbooks-bs04ml6c) as needed
+- ...write or update tests
+- ...add UI screenshots and **testing notes** to the Linear issue
+- ...add any **manual upgrade steps** to the Linear issue
+- ...update the [config reference](https://beyond-essential.slab.com/posts/reference-config-file-0c70ukly), [settings reference](https://beyond-essential.slab.com/posts/reference-settings-0blw1x2q), or any [relevant runbook(s)](https://beyond-essential.slab.com/topics/runbooks-bs04ml6c)
+- ...call out additions or changes to **config files** for the deployment team to take note of
 
-### Deploys
-
-- [ ] **Deploy to Tamanu Internal** <!-- #deploy -->
+<!-- Thank you! -->

.github/workflows/check-pr-title.yml

@@ -25,7 +25,7 @@ jobs:
       if: always()
       shell: bash
       run: |
-        if ! grep -qP '^(ci|config|db|deps|doc|feat|fix|fmt|merge|refactor|release|repo|revert|style|test|tweak)(\(\w+\))?:\s' <<< "$PR_TITLE"; then
+        if ! grep -qP '^(ci|config|db|deps|doc|feat|fix|fmt|merge|refactor|release|repo|revert|style|test|tweak|perf)(\(\w+\))?:\s' <<< "$PR_TITLE"; then
           echo "::warning::PR title Conventional Type is not on the list; refer to CONTRIBUTING.md"
           exit 1
         fi

.github/workflows/cleanup-auto-deploy.yml

@@ -17,7 +17,7 @@ concurrency:
   cancel-in-progress: false
 
 permissions:
-  contents: read # to checkout the repo
+  contents: write # to checkout the repo
   pull-requests: write # to parse PRs for config and update them
   issues: write # to parse special deploy issues and update them
 
@@ -79,6 +79,7 @@ jobs:
       deploy-name: ${{ matrix.name }}
       options: ${{ matrix.options }}
       check-branch: false
+      ref: not needed as check branch is false
     secrets:
       PULUMI_ACCESS_TOKEN: ${{ secrets.PULUMI_ACCESS_TOKEN }}
       TAILSCALE_OAUTH: ${{ secrets.TAILSCALE_DBPROXY_ACCESS_OAUTH }}

.github/workflows/cut-release-branch.yml

@@ -4,8 +4,12 @@ on:
   workflow_dispatch:
     inputs:
       version:
-        description: Next version number
+        description: Bump version on main to the next
         required: true
+        type: choice
+        options:
+          - minor
+          - major
         default: minor
 
 jobs:
@@ -61,15 +65,6 @@ jobs:
         git push origin "$NEW_BRANCH_NAME"
         git switch main
 
-    - name: Create next release draft
-      uses: actions/github-script@v7
-      with:
-        github-token: ${{ secrets.TAMANU_RELEASE_PAT }}
-        script: |
-          const cwd = '${{ github.workspace }}';
-          const { createNextDraft } = await import(`${cwd}/scripts/gha-release-ops.mjs`);
-          await createNextDraft(await import('fs'), github, context, cwd, '${{ github.event.inputs.version }}');
-
     - name: Bump version on main
       run: node scripts/version.mjs '${{ inputs.version }}'
 

.github/workflows/publish-release-version.yml

@@ -36,7 +36,8 @@ jobs:
         git config user.email github-actions@github.com
         version=$(jq -r .version package.json)
         git commit --allow-empty -am "release: v$version"
-        echo "current_version=$version" >> $GITHUB_OUTPUT
+        echo "current_version=$version" | tee -a $GITHUB_OUTPUT
+        echo "current_version_ref=$(git show-ref -s HEAD)" | tee -a $GITHUB_OUTPUT
         git tag -a "v$version" -m "release: v$version"
         git push --follow-tags
 
@@ -49,25 +50,43 @@ jobs:
         set -euxo pipefail
         version=$(jq -r .version package.json)
         git commit -am "release: Bump version to $version"
-        echo "next_version=$version" >> $GITHUB_OUTPUT
+        echo "next_version=$version" | tee -a $GITHUB_OUTPUT
         git push
 
     # do release management after the critical bits above as we care less if those fail
 
-    - name: Create draft for next release
-      uses: actions/github-script@v7
-      with:
-        github-token: ${{ secrets.GITHUB_TOKEN }}
-        script: |
-          const cwd = '${{ github.workspace }}';
-          const { createDraftRelease } = await import(`${cwd}/scripts/gha-release-ops.mjs`);
-          await createDraftRelease(await import('fs'), github, context, cwd, '${{ steps.nextv.outputs.next_version }}');
+    - name: Install git-cliff
+      run: npm install -g git-cliff@latest
+
+    - name: Generate release notes
+      run: |
+        version=${{ steps.tagged.outputs.current_version }}
+        pattern="^v$(cut -d. -f-2 <<< "$version" | sed 's/[.]/[.]/g')[.]"
+        # 2.6.1 -> ^v2[.]6[.]
+
+        git cliff --topo-order --strip all --latest \
+          --tag-pattern "$pattern" --tag "v$version" \
+          --output RELEASE_NOTES.md
+        cat RELEASE_NOTES.md
+
+    - name: Determine the true latest version
+      id: latest
+      run: |
+        set -euxo pipefail
+        git fetch --tags
+        git tag --list \
+          | grep -E '^v[0-9]+[.][0-9]+[.][0-9]+$' \
+          | cut -c2- \
+          | sort --version-sort \
+          | tail -n1 \
+          | sed 's/^/latest_version=/' \
+          | tee -a $GITHUB_OUTPUT
 
-    - name: Publish the draft release if one exists
-      uses: actions/github-script@v7
+    - name: Publish the release
+      uses: softprops/action-gh-release@v2
       with:
-        github-token: ${{ secrets.GITHUB_TOKEN }}
-        script: |
-          const cwd = '${{ github.workspace }}';
-          const { publishRelease } = await import(`${cwd}/scripts/gha-release-ops.mjs`);
-          await publishRelease(github, context, '${{ steps.tagged.outputs.current_version }}');
+        name: v${{ steps.tagged.outputs.current_version }}
+        tag_name: v${{ steps.tagged.outputs.current_version }}
+        target_commitish: ${{ steps.tagged.outputs.current_version_ref }}
+        body_path: RELEASE_NOTES.md
+        make_latest: ${{ steps.latest.outputs.latest_version == steps.tagged.outputs.current_version }}

.gitignore

@@ -69,3 +69,4 @@ lints.md
 .elasticbeanstalk/*
 !.elasticbeanstalk/*.cfg.yml
 !.elasticbeanstalk/*.global.yml
+

CONTRIBUTING.md

@@ -128,6 +128,7 @@ The following types are conventional:
 - `fix` for bug fixes
 - `fmt` for automatic formatting changes (ignored in changelogs)
 - `merge` for merging between branches (generally between `main` and `release/*`)
+- `perf` for code changes that improve performance
 - `refactor` for code refactoring
 - `release` for changes that are part of the release process (generally automated commits, not manual use)
 - `repo` for changes to the repository structure, or for config/dotfiles (e.g. `.gitignore`, `.editorconfig`, etc)

README.md

@@ -4,16 +4,14 @@
 
 | Package | Runbook | Description |
 | ------- | ------- | ----------- |
-| [@tamanu/central-server](packages/central-server) | [central-server runbook](https://beyond-essential.slab.com/posts/tamanu-central-server-runbook-et0trny5) | The central server, which facility server and mobile client instances communicate with to synchronise data *|
+| [@tamanu/central-server](packages/central-server) | [central-server runbook](https://beyond-essential.slab.com/posts/tamanu-central-server-runbook-et0trny5) | The central server, which facility server and mobile client instances communicate with to synchronise data |
 | [@tamanu/facility-server](packages/facility-server) | [facility-server runbook](https://beyond-essential.slab.com/posts/todo-tamanu-lan-runbook-ezljl0qk) | The facility server, which the app communicates with |
 | [@tamanu/meta-server](packages/meta-server) | [meta-server runbook](https://beyond-essential.slab.com/posts/todo-tamanu-meta-server-runbook-0zbgw7m7) | The metadata server, which serves information about app versions and known central-server installations |
 | [@tamanu/web-frontend](packages/web) | [web runbook](https://beyond-essential.slab.com/posts/todo-tamanu-desktop-runbook-i2bmy57c) | The web app |
 | [mobile](packages/mobile) | [mobile runbook](https://beyond-essential.slab.com/posts/todo-tamanu-mobile-runbook-8vj8qceu) | The mobile app  |
 | [@tamanu/shared](packages/shared) | N/A | Shared code monolith among Tamanu components |
 | [@tamanu/build-tooling](packages/build-tooling) | N/A | Shared build tooling code |
-| [csca](packages/csca) | [csca runbook](https://beyond-essential.slab.com/posts/csca-runbook-be1td5ml), [signer runbook](https://beyond-essential.slab.com/posts/signer-runbook-hcws6er3) | A tool to create and manage a CSCA / ICAO eMRTD PKI* |
-
-<sub>*omitted from public repo for security reasons</sub>
+| [csca](packages/csca) | [csca runbook](https://beyond-essential.slab.com/posts/csca-runbook-be1td5ml), [signer runbook](https://beyond-essential.slab.com/posts/signer-runbook-hcws6er3) | A tool to create and manage a CSCA / ICAO eMRTD PKI |
 
 The latest version for each Tamanu service (Servers, Web Client & Mobile Client) can be retrieved with a HTTP GET request via their respective public API routes:
 

cliff.toml

@@ -0,0 +1,63 @@
+[changelog]
+trim = true
+header = """
+# Changelog\n
+All notable changes to this project will be documented in this file.\n
+See [conventional commits](https://www.conventionalcommits.org/) for commit guidelines.\n
+"""
+footer = """
+<!-- generated by git-cliff -->
+"""
+body = """
+## Release notes 📋
+
+{%- for commit in commits | sort(attribute="group") %}
+	{%- if commit.group -%}
+	{% else -%}
+        - **{{ commit.scope | striptags | trim }}:** \
+			{{ commit.message | upper_first }}\
+      {%- if commit.message is not matching(".*\\s+\\(#\\d+\\)\\s*$") %} ([`{{ commit.id | truncate(length=10, end="") }}`]($REPO/commit/{{ commit.id }})){%- endif -%}
+	{% endif -%}
+{% endfor -%}
+
+{% for group, commits in commits | filter(attribute="scope") | group_by(attribute="group") %}
+    ### {{ group | striptags | trim | upper_first }}
+    {% for commit in commits | sort(attribute="scope") %}
+        - **{{ commit.scope | striptags | trim }}:** \
+            {{ commit.message | upper_first }}\
+            {%- if commit.message is not matching(".*\\s+\\(#\\d+\\)\\s*$") %} ([`{{ commit.id | truncate(length=10, end="") }}`]($REPO/commit/{{ commit.id }})){%- endif -%}
+    {%- endfor -%}
+    {% raw %}\n{% endraw %}\
+{% endfor %}\n
+"""
+postprocessors = [
+  { pattern = '\b((?i)(?:EPI|KAM|MAUI|MDEV|NASS|NOTAM|SAV|TAM3|TAMOC|TAN|TAV|VIT|WAITM)-[1-9][0-9]*)\b', replace = "[$1](https://linear.app/bes/issue/$1)" }, # linear
+  { pattern = '\(#(\d+)\)', replace = "([#$1]($$REPO/pull/$1))"}, # github
+  { pattern = '\$REPO', replace = "/~https://github.com/beyondessential/tamanu" }, # replace repository URL
+]
+
+[git]
+conventional_commits = true
+filter_unconventional = true
+split_commits = true
+protect_breaking_commits = true
+filter_commits = true
+tag_pattern = "v[0-9].*"
+sort_commits = "oldest"
+
+commit_parsers = [
+  { message = "^feat", group = "Features ⭐" },
+  { message = "^fix", group = "Bugfixes 🐛" },
+  { message = "^tweak", group = "Tweaks ⚖️" },
+  { message = "^config", group = "Configuration ⚙️" },
+  { message = "^db", group = "Database 📊" },
+  { message = "^doc", group = "Documentation 📚" },
+  { message = "^perf", group = "Performance 🌊" },
+  { message = "^refactor", group = "Refactors 🛠️" },
+  { message = "^test", group = "Testing 🧪" },
+  { message = "^deps", group = "Dependencies 📦" },
+  { message = "^repo", group = "Repo 📖" },
+  { message = "^(chore|ci|draft|fmt|merge|release|style|wip)", skip = true },
+  { body = ".*security", group = "Security ⚠️" },
+  { message = "^revert", group = "Revert ⏪" },
+]

package.json

@@ -1,6 +1,6 @@
 {
   "name": "tamanu",
-  "version": "2.6.0",
+  "version": "2.9.0",
   "description": "This repo contains all the packages for Tamanu",
   "homepage": "/~https://github.com/beyondessential/tamanu.git#readme",
   "repository": "git@github.com:beyondessential/tamanu.git",
@@ -59,6 +59,7 @@
       "packages/meta-server",
       "packages/shared",
       "packages/constants",
+      "packages/settings",
       "packages/api-client"
     ],
     "nohoist": [

packages/api-client/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@tamanu/api-client",
-  "version": "2.6.0",
+  "version": "2.9.0",
   "private": true,
   "description": "API client for Tamanu Facility Server",
   "main": "dist/cjs/index.js",

packages/api-client/src/TamanuApi.js

@@ -67,13 +67,14 @@ export class TamanuApi {
       permissions,
       centralHost,
       role,
+      settings,
     } = await response.json();
     server.type = serverType;
     server.centralHost = centralHost;
     this.setToken(token);
 
     const { user, ability } = await this.fetchUserData(permissions);
-    return { user, token, localisation, server, ability, role };
+    return { user, token, localisation, server, ability, role, settings };
   }
 
   async fetchUserData(permissions) {

packages/build-tooling/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@tamanu/build-tooling",
-  "version": "2.6.0",
+  "version": "2.9.0",
   "description": "Build tooling for Tamanu packages",
   "main": "index.mjs",
   "type": "module",

packages/constants/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@tamanu/constants",
-  "version": "2.6.0",
+  "version": "2.9.0",
   "private": true,
   "description": "Shared constants",
   "main": "dist/cjs/index.js",

packages/constants/src/comms.ts

@@ -2,6 +2,7 @@ export const PATIENT_COMMUNICATION_CHANNELS = {
   EMAIL: 'Email',
   SMS: 'Sms',
   WHATSAPP: 'WhatsApp',
+  TELEGRAM: 'Telegram'
 };
 
 export const PATIENT_COMMUNICATION_CHANNELS_VALUES = Object.values(
@@ -11,6 +12,7 @@ export const PATIENT_COMMUNICATION_CHANNELS_VALUES = Object.values(
 export const PATIENT_COMMUNICATION_TYPES = {
   REFERRAL_CREATED: 'Referral created',
   CERTIFICATE: 'Certificate',
+  VACCINATION_REMINDER: 'Vaccination reminder',
 };
 
 export const PATIENT_COMMUNICATION_TYPES_VALUES = Object.values(

packages/constants/src/fhir.ts

@@ -233,6 +233,15 @@ export const FHIR_DIAGNOSTIC_REPORT_STATUS = {
   UNKNOWN: 'unknown',
 };
 
+export const FHIR_IMAGING_STUDY_STATUS = {
+  REGISTERED: 'registered',
+  AVAILABLE: 'available',
+  FINAL_INVALID_LEGACY: 'final', // this needs to be supported but is not valid FHIR
+  CANCELLED: 'cancelled',
+  ENTERED_IN_ERROR: 'entered-in-error',
+  UNKNOWN: 'unknown',
+};
+
 export const FHIR_ENCOUNTER_CLASS_DISPLAY = {
   IMP: 'inpatient encounter',
   AMB: 'ambulatory encounter',
@@ -297,3 +306,13 @@ export const IPS_REQUEST_STATUSES = {
   ERROR: 'Error',
   IGNORE: 'Ignore',
 };
+
+export const HTTP_BODY_DATA_PATHS = {
+  DIAGNOSTIC_REPORT_ATTACHMENT: '$.presentedForm[*].data',
+};
+
+export const SCRUBBED_DATA_MESSAGE = 'Raw data removed from logs';
+export const SUPPORTED_CONTENT_TYPES = {
+  PDF: 'application/pdf',
+};
+export const DEFAULT_REASON_CANCELLED_BY_API = 'cancelled externally via api';

packages/constants/src/importable.ts

@@ -7,12 +7,15 @@ export const GENERAL_IMPORTABLE_DATA_TYPES = [
   'angiogramImagingArea',
   'arrivalMode',
   'carePlan',
+  'catchment',
   'certifiableVaccine',
   'colonoscopyImagingArea',
+  'contactRelationship',
   'country',
   'ctScanImagingArea',
   'department',
   'diagnosis',
+  'diet',
   'dischargeDisposition',
   'division',
   'drug',
@@ -76,7 +79,9 @@ export const REFERENCE_TYPES = {
   ICD10: 'icd10',
   ALLERGY: 'allergy',
   CONDITION: 'condition',
+  CONTACT_RELATIONSHIP: 'contactRelationship',
   DRUG: 'drug',
+  DIET: 'diet',
   TRIAGE_REASON: 'triageReason',
   PROCEDURE_TYPE: 'procedureType',
   IMAGING_TYPE: 'imagingType',
@@ -115,6 +120,7 @@ export const REFERENCE_TYPES = {
   VACCINE_CIRCUMSTANCE: 'vaccineCircumstance',
   ADDITIONAL_INVOICE_LINE: 'additionalInvoiceLine',
   SPECIMEN_TYPE: 'specimenType',
+  CATCHMENT: 'catchment',
   REACTION: 'reaction',
   ...IMAGING_AREA_TYPES,
 };

packages/constants/src/index.ts

@@ -31,3 +31,4 @@ export * from './programRegistry.js';
 export * from './vaccines.js';
 export * from './settings.js';
 export * from './encounterHistory.js';
+export * from './webSocket.js';