Setup environment variable collection

.github/workflows/container-ecr-viewer.yaml

@@ -111,7 +111,7 @@ jobs:
           node-version: ${{env.NODE_VERSION}}
 
       - name: Start app
-        run: docker compose --env-file .env.test --profile postgres --profile ecr-viewer up -d
+        run: COLLECTION=AWS_SQLSERVER_NON_INTEGRATED docker compose --profile AWS_SQLSERVER_NON_INTEGRATED --profile ecr-viewer up -d
         working-directory: ./containers/${{env.CONTAINER}}
 
       - name: Wait for Application to be ready
@@ -147,6 +147,7 @@ jobs:
 
   convert-data:
     runs-on: ubuntu-latest
+    timeout-minutes: 20
     steps:
       - name: Checkout
         uses: actions/checkout@v4

containers/ecr-viewer/.env.sample

@@ -1,6 +1,5 @@
-APP_ENV=test
-NEXT_PUBLIC_NON_INTEGRATED_VIEWER=true
-SOURCE=postgres
+COLLECTION=AWS_SQLSERVER_NON_INTEGRATED
+# NBS_AUTH=false
 
 # Azure Connection
 AZURE_STORAGE_CONNECTION_STRING="DefaultEndpointsProtocol=http;AccountName=devstoreaccount1;AccountKey=Eby8vdM02xNOcqFlqUwJPLlmEtlCDXJ1OUzFT50uSRZ6IFsuFq2UVErCz4I6tq/K1SZFPTOtr/KBHBeksoGMGw==;BlobEndpoint=http://localhost:10000/devstoreaccount1;"
@@ -13,10 +12,8 @@ ECR_BUCKET_NAME=ecr-viewer-files
 AWS_ACCESS_KEY_ID=123
 AWS_SECRET_ACCESS_KEY=xyz
 
-# Metadata
+# Postgres
 DATABASE_URL=postgres://postgres:pw@localhost:5432/ecr_viewer_db
-METADATA_DATABASE_TYPE=postgres
-METADATA_DATABASE_SCHEMA=core
 
 # SQL Server
 SQL_SERVER_USER=sa

containers/ecr-viewer/.env.test

@@ -1,3 +1,3 @@
 DATABASE_URL=postgres://postgres:pw@postgres:5432/ecr_viewer_db
-APP_ENV=test
+NBS_AUTH=false
 AZURE_CONTAINER_NAME=ecr-viewer-files

containers/ecr-viewer/Dockerfile

@@ -27,6 +27,10 @@ RUN npm run build
 FROM base AS runner
 WORKDIR /app
 
+# Install dotenvx
+RUN apk add --no-cache curl
+RUN curl -sfS https://dotenvx.sh | sh
+
 # Uncomment the following line in case you want to disable telemetry during runtime.
 ENV NEXT_TELEMETRY_DISABLED 1
 
@@ -43,6 +47,7 @@ RUN chown nextjs:nodejs .next
 # https://nextjs.org/docs/advanced-features/output-file-tracing
 COPY --from=builder --chown=nextjs:nodejs /app/.next/standalone ./
 COPY --from=builder --chown=nextjs:nodejs /app/.next/static ./.next/static
+COPY --from=builder --chown=nextjs:nodejs /app/env ./env
 
 USER nextjs
 
@@ -64,4 +69,4 @@ ENV OTEL_EXPORTER_OTLP_TRACES_ENDPOINT=http://otel-collector:4318/v1/traces
 
 # server.js is created by next build from the standalone output
 # https://nextjs.org/docs/pages/api-reference/next-config-js/output
-CMD node server.js
+CMD ["sh", "-c", "dotenvx run --env-file=./env/.env.$COLLECTION -- node server.js"]

containers/ecr-viewer/api-documentation.md

@@ -4,10 +4,11 @@ Display an eCR
 
 **URL** : `/view-data?id=:id&snomed-code=:snomed&auth=:auth`
 
-**URL Parameters** : 
+**URL Parameters** :
+
 - `id=[string]` where `id` is the ID of the eCR.
 - `snomed-code=[string]` where `snomed-code` is the condition the user is viewing the eCR for. OPTIONAL.
-- `auth=[string]` where `auth` is the authentication token for the user. Only required if app_env is production.
+- `auth=[string]` where `auth` is the authentication token for the user. Only required if NBS_AUTH is true.
 
 **Method** : `GET`
 
@@ -16,6 +17,7 @@ Display an eCR
 **Permissions required** : None
 
 ## Example Architecture
+
 ![NBS -> ECR Viewer sequence diagram](assets/nbs-ecr-viewer-arch.png)
 
 ## Success Response

containers/ecr-viewer/cypress/docker-compose.yml

@@ -29,4 +29,4 @@ services:
       - "3000:3000"
     environment:
       - DATABASE_URL=${DATABASE_URL:-postgres://postgres:pw@db:5432/ecr_viewer_db}
-      - APP_ENV=${APP_ENV:-prod}
+      - NBS_AUTH=${NBS_AUTH:-true}

containers/ecr-viewer/design-review/design-review.sh

@@ -89,19 +89,25 @@ npm i
 
 # Write env vars to .env.local
 npm run setup-local-env
-echo "NEXT_PUBLIC_NON_INTEGRATED_VIEWER=$IS_NON_INTEGRATED" >> .env.local
+echo "NBS_AUTH=false" >> .env.local
+
+if [ "$IS_NON_INTEGRATED" = true ]; then
+    echo "COLLECTION=AWS_SQLSERVER_NON_INTEGRATED" >> .env.local
+else 
+    echo "COLLECTION=AWS_INTEGRATED" >> .env.local
+fi
 
 # Run FHIR conversion on seed data
 if [ "$CONVERT_SEED_DATA" = true ]; then
   echo "Running seed data FHIR conversion..."
-  docker compose -f ./docker-compose-seed.yml --profile "*" down -v
+  npm run clear-local
   npm run convert-seed-data:build
 else
   echo "Skipping seed data FHIR conversion..."
 fi
 
 # Run ecr viewer
-npx @dotenvx/dotenvx run -f .env.local -- sh -c 'docker compose -f ./docker-compose.yml --profile ${SOURCE} --profile ${METADATA_DATABASE_TYPE} --profile ecr-viewer up -d'
+npm run local-docker
 
 # Wait for eCR Viewer to be available
 URL="http://localhost:3000/ecr-viewer"

containers/ecr-viewer/docker-compose.yml

@@ -8,21 +8,21 @@ services:
     ports:
       - "3000:3000"
     environment:
-      - APP_ENV=${APP_ENV:-test}
-      - METADATA_DATABASE_TYPE=${METADATA_DATABASE_TYPE:-postgres}
-      - SOURCE=${SOURCE:-postgres}
+      - COLLECTION=${COLLECTION:-AWS_SQLSERVER_NON_INTEGRATED}
+      # POSTGRES
       - DATABASE_URL=postgres://postgres:pw@postgres:5432/ecr_viewer_db
+      # AWS
       - AWS_CUSTOM_ENDPOINT=http://aws-storage:4566
       - AWS_REGION=${AWS_REGION:-us-east-1}
       - ECR_BUCKET_NAME=${ECR_BUCKET_NAME:-ecr-viewer-files}
       - AWS_ACCESS_KEY_ID=${AWS_ACCESS_KEY_ID:-123}
       - AWS_SECRET_ACCESS_KEY=${AWS_SECRET_ACCESS_KEY:-xyz}
+      # Azure
       - AZURE_STORAGE_CONNECTION_STRING=DefaultEndpointsProtocol=http;AccountName=devstoreaccount1;AccountKey=Eby8vdM02xNOcqFlqUwJPLlmEtlCDXJ1OUzFT50uSRZ6IFsuFq2UVErCz4I6tq/K1SZFPTOtr/KBHBeksoGMGw==;BlobEndpoint=http://azure-storage:10000/devstoreaccount1;
       - AZURE_CONTAINER_NAME=${AZURE_CONTAINER_NAME:-ecr-viewer-files}
-      - NEXT_PUBLIC_NON_INTEGRATED_VIEWER=${NEXT_PUBLIC_NON_INTEGRATED_VIEWER:-true}
-      - METADATA_DATABASE_SCHEMA=${METADATA_DATABASE_SCHEMA:-core}
-      - SQL_SERVER_USER=${SQL_SERVER_USER}
-      - SQL_SERVER_PASSWORD=${SQL_SERVER_PASSWORD}
+      # SQL Server
+      - SQL_SERVER_USER=${SQL_SERVER_USER:-sa}
+      - SQL_SERVER_PASSWORD=${SQL_SERVER_PASSWORD:-Password1!}
       - SQL_SERVER_HOST=${SQL_SERVER_HOST:-sqlserver}
     profiles:
       - ecr-viewer
@@ -47,13 +47,14 @@ services:
       timeout: 5s
       retries: 20
     profiles:
-      - postgres
+      - AWS_PG_NON_INTEGRATED
+      - AZURE_PG_NON_INTEGRATED
 
   sqlserver:
     image: mcr.microsoft.com/mssql/server:2022-latest
     environment:
       - ACCEPT_EULA=Y
-      - MSSQL_SA_PASSWORD=${SQL_SERVER_PASSWORD}
+      - MSSQL_SA_PASSWORD=${SQL_SERVER_PASSWORD:-Password1!}
     ports:
       - "1433:1433"
     volumes:
@@ -70,7 +71,8 @@ services:
       timeout: 10s
       retries: 5
     profiles:
-      - sqlserver
+      - AWS_SQLSERVER_NON_INTEGRATED
+      - AZURE_SQLSERVER_NON_INTEGRATED
 
   aws-storage:
     image: gresau/localstack-persist:3
@@ -80,39 +82,38 @@ services:
       - aws-data:/persisted-data
       - ./seed-scripts/aws:/etc/localstack/init/ready.d
     profiles:
-      - s3
+      - AWS_INTEGRATED
+      - AWS_PG_NON_INTEGRATED
+      - AWS_SQLSERVER_NON_INTEGRATED
 
   azure-storage:
-    image: mcr.microsoft.com/azure-storage/azurite
+    build:
+      context: ./seed-scripts
+      dockerfile: azurite.Dockerfile
     hostname: azurite
     restart: always
-    command: "azurite --blobHost 0.0.0.0 --blobPort 10000 -l data --debug /data/debug.log"
+    command:
+      - /bin/sh
+      - -c
+      - |
+        azurite --blobHost 0.0.0.0 --blobPort 10000 -l data --debug /data/debug.log &
+        sleep 5
+        az storage container create --name ecr-viewer-files
+        tail -f /dev/null
     volumes:
       - azure-data:/opt/azurite/data
+    environment:
+      AZURE_STORAGE_CONNECTION_STRING: DefaultEndpointsProtocol=http;AccountName=devstoreaccount1;AccountKey=Eby8vdM02xNOcqFlqUwJPLlmEtlCDXJ1OUzFT50uSRZ6IFsuFq2UVErCz4I6tq/K1SZFPTOtr/KBHBeksoGMGw==;BlobEndpoint=http://localhost:10000/devstoreaccount1;
     healthcheck:
       test: nc 127.0.0.1 10000 -z
       interval: 1s
       retries: 30
     ports:
       - "10000:10000"
     profiles:
-      - azure
-
-  azure-storage-init:
-    image: mcr.microsoft.com/azure-cli:latest
-    command:
-      - /bin/sh
-      - -c
-      - |
-        az storage container create --name ecr-viewer-files
-    depends_on:
-      azure-storage:
-        condition: service_healthy
-    environment:
-      # https://github.com/Azure/Azurite/blob/main/README.md#usage-with-azure-storage-sdks-or-tools
-      AZURE_STORAGE_CONNECTION_STRING: DefaultEndpointsProtocol=http;AccountName=devstoreaccount1;AccountKey=Eby8vdM02xNOcqFlqUwJPLlmEtlCDXJ1OUzFT50uSRZ6IFsuFq2UVErCz4I6tq/K1SZFPTOtr/KBHBeksoGMGw==;BlobEndpoint=http://azure-storage:10000/devstoreaccount1;
-    profiles:
-      - azure
+      - AZURE_INTEGRATED
+      - AZURE_PG_NON_INTEGRATED
+      - AZURE_SQLSERVER_NON_INTEGRATED
 
 volumes:
   db:

containers/ecr-viewer/env/.env.AWS_INTEGRATED

@@ -0,0 +1,3 @@
+NBS_AUTH=true
+NEXT_PUBLIC_NON_INTEGRATED_VIEWER=false
+SOURCE=s3

containers/ecr-viewer/env/.env.AWS_PG_NON_INTEGRATED

@@ -0,0 +1,5 @@
+NBS_AUTH=false
+NEXT_PUBLIC_NON_INTEGRATED_VIEWER=true
+SOURCE=s3
+METADATA_DATABASE_TYPE=postgres
+METADATA_DATABASE_SCHEMA=core

containers/ecr-viewer/env/.env.AWS_SQLSERVER_NON_INTEGRATED

@@ -0,0 +1,5 @@
+NBS_AUTH=false
+NEXT_PUBLIC_NON_INTEGRATED_VIEWER=true
+SOURCE=s3
+METADATA_DATABASE_TYPE=sqlserver
+METADATA_DATABASE_SCHEMA=extended

containers/ecr-viewer/env/.env.AZURE_INTEGRATED

@@ -0,0 +1,3 @@
+NBS_AUTH=true
+NEXT_PUBLIC_NON_INTEGRATED_VIEWER=false
+SOURCE=azure

containers/ecr-viewer/env/.env.AZURE_PG_NON_INTEGRATED

@@ -0,0 +1,5 @@
+NBS_AUTH=false
+NEXT_PUBLIC_NON_INTEGRATED_VIEWER=true
+SOURCE=azure
+METADATA_DATABASE_TYPE=postgres
+METADATA_DATABASE_SCHEMA=core

containers/ecr-viewer/env/.env.AZURE_SQLSERVER_NON_INTEGRATED

@@ -0,0 +1,5 @@
+NBS_AUTH=false
+NEXT_PUBLIC_NON_INTEGRATED_VIEWER=true
+SOURCE=azure
+METADATA_DATABASE_TYPE=sqlserver
+METADATA_DATABASE_SCHEMA=extended

containers/ecr-viewer/environment.d.ts

@@ -1,7 +1,6 @@
 /* eslint-disable unused-imports/no-unused-vars */
 namespace NodeJS {
   interface ProcessEnv {
-    APP_ENV: "test" | "dev" | "middleware" | "prod";
     AWS_ACCESS_KEY_ID: string;
     AWS_CUSTOM_ENDPOINT: string;
     AWS_REGION: string;
@@ -15,6 +14,7 @@ namespace NodeJS {
     GITHUB_SECRET: string;
     METADATA_DATABASE_SCHEMA?: "core" | "extended";
     METADATA_DATABASE_TYPE?: "postgres" | "sqlserver";
+    NBS_AUTH: "true" | "false";
     NBS_PUB_KEY: string;
     NEXT_PUBLIC_NON_INTEGRATED_VIEWER: "true" | "false";
     NEXT_RUNTIME: string;

containers/ecr-viewer/jest.config.js

@@ -9,6 +9,7 @@ const createJestConfig = nextJest({
 const customJestConfig = {
   setupFilesAfterEnv: ["<rootDir>/jest.setup.ts"],
   testEnvironment: "jest-environment-jsdom",
+  modulePathIgnorePatterns: ["<rootDir>/.next"],
   moduleNameMapper: {
     "^mssql$": "<rootDir>/src/app/tests/__mocks__/mssql.js",
     "^tedious$": "<rootDir>/src/app/tests/__mocks__/mssql.js",

containers/ecr-viewer/package.json

@@ -6,16 +6,18 @@
   "private": true,
   "scripts": {
     "dev": "next dev",
-    "local-dev": "npx @dotenvx/dotenvx run -f .env.local -- sh -c 'docker compose -f ./docker-compose.yml --profile ${SOURCE} --profile ${METADATA_DATABASE_TYPE} up -d && npm run dev'",
+    "local-dev": "npx @dotenvx/dotenvx run -f .env.local -- npm run local-dev:sub",
+    "local-dev:sub": "npx @dotenvx/dotenvx run -f ./env/.env.${COLLECTION} -- sh -c 'docker compose -f ./docker-compose.yml --profile ${COLLECTION} up -d && npm run dev'",
+    "local-docker": "npx @dotenvx/dotenvx run -f .env.local -- sh -c 'docker compose -f ./docker-compose.yml --profile ${COLLECTION} --profile ecr-viewer up -d'",
     "setup-local-env": "./setup-env.sh",
     "build": "next build",
     "start": "next start",
     "lint": "next lint",
     "test": "TZ=America/New_York jest",
     "test:watch": "TZ=America/New_York jest --watch",
-    "clear-local": "docker compose -f ./docker-compose.yml --profile \"*\" down -v",
-    "convert-seed-data": "npx @dotenvx/dotenvx run -f .env.local -- sh -c 'docker compose -f ./seed-scripts/docker-compose-seed.yml --profile ${SOURCE} --profile ${METADATA_DATABASE_TYPE} --profile ecr-viewer up --abort-on-container-exit'",
-    "convert-seed-data:build": "npx @dotenvx/dotenvx run -f .env.local -- sh -c 'docker compose -f ./seed-scripts/docker-compose-seed.yml --profile ${SOURCE} --profile ${METADATA_DATABASE_TYPE} --profile ecr-viewer up --abort-on-container-exit --build'",
+    "clear-local": "docker compose -f ./docker-compose.yml --profile \"*\" down -v && docker compose -f ./seed-scripts/docker-compose-seed.yml --profile \"*\" down -v",
+    "convert-seed-data": "npx @dotenvx/dotenvx run -f .env.local -- sh -c 'docker compose -f ./seed-scripts/docker-compose-seed.yml --profile ${COLLECTION} --profile ecr-viewer up --abort-on-container-exit'",
+    "convert-seed-data:build": "npx @dotenvx/dotenvx run -f .env.local -- sh -c 'docker compose -f ./seed-scripts/docker-compose-seed.yml --profile ${COLLECTION} --profile ecr-viewer up --abort-on-container-exit --build'",
     "update-cypress-data": "docker compose -f ./seed-scripts/docker-compose-create-sql.yml up --build --abort-on-container-exit",
     "cypress:open": "cypress open",
     "cypress:run": "cypress run",
@@ -65,7 +67,7 @@
     "sanitize-html": "^2.13.1"
   },
   "devDependencies": {
-    "@dotenvx/dotenvx": "^1.22.0",
+    "@dotenvx/dotenvx": "^1.25.1",
     "@next/eslint-plugin-next": "^14.2.5",
     "@smithy/util-stream": "^2.1.2",
     "@testing-library/jest-dom": "^6.1.5",

containers/ecr-viewer/seed-scripts/azurite.Dockerfile

@@ -0,0 +1,9 @@
+FROM mcr.microsoft.com/azure-storage/azurite:latest
+
+RUN apk add py3-pip
+RUN apk add gcc musl-dev python3-dev libffi-dev openssl-dev cargo make
+RUN pip install --upgrade pip
+RUN pip install azure-cli
+
+WORKDIR /data
+CMD ["/bin/sh"]

containers/ecr-viewer/seed-scripts/create-seed-data.py

@@ -36,9 +36,15 @@ def _process_files(args):
     requests = []
     folder_paths = []
     configName = "integrated.json"
-    if os.getenv("METADATA_DATABASE_SCHEMA") == "extended":
+    if (
+        os.getenv("COLLECTION") == "AWS_SQLSERVER_NON_INTEGRATED"
+        or os.getenv("COLLECTION") == "AZURE_SQLSERVER_NON_INTEGRATED"
+    ):
         configName = "non-integrated-extended.json"
-    elif os.getenv("METADATA_DATABASE_SCHEMA") == "core":
+    elif (
+        os.getenv("COLLECTION") == "AZURE_PG_NON_INTEGRATED"
+        or os.getenv("COLLECTION") == "AWS_PG_NON_INTEGRATED"
+    ):
         configName = "non-integrated-core.json"
 
     def _process_eicrs(subfolder, folder, folder_path, payload):

containers/ecr-viewer/seed-scripts/docker-compose-seed.yml

@@ -75,4 +75,4 @@ services:
     volumes:
       - ./baseECR:/code/baseECR
     environment:
-      - METADATA_DATABASE_SCHEMA=${METADATA_DATABASE_SCHEMA}
+      - COLLECTION=${COLLECTION}