Merge pull request #714 from joshunrau/v1.0

.env.template

@@ -3,14 +3,19 @@
 ## ---------------------------------
 
 # The domain name to use for your site in the production compose stack
-# If you set this to your own domain name, HTTPS will be enabled by default
-# Otherwise, if you do not want to use HTTPS, for example if your domain is
-# being handled by an additional, system-level reverse proxy, you can do so
-# by specifying the HTTP port as the address (e.g., localhost:80).
 SITE_ADDRESS=localhost:80
+# The domain name to use for the gateway service in the production compose stack
+GATEWAY_SITE_ADDRESS=localhost:3500
 
-# The port to listen on
+# The ports to listen on
 APP_PORT=5500
+PLAYGROUND_PORT=3750
+GATEWAY_PORT=3500
+
+# The Docker release to use (latest = stable)
+RELEASE_CHANNEL=main
+# The MongoDB version to use
+MONGODB_VERSION=7.0
 
 ## ---------------------------------
 ## PRODUCTION + DEVELOPMENT
@@ -41,8 +46,6 @@ GITHUB_REPO_URL=https://github.com/DouglasNeuroInformatics/OpenDataCapture
 GATEWAY_ENABLED=true
 # A link to the license governing distribution of the platform and all derivative work
 LICENSE_URL=https://www.gnu.org/licenses/agpl-3.0.en.html
-# The base URL for the gateway. In development, this should correspond to GATEWAY_DEV_SERVER_PORT
-GATEWAY_BASE_URL=http://localhost:3500
 # The interval (in miliseconds) at which the API will attempt to resync with the gateway
 GATEWAY_REFRESH_INTERVAL=10000
 # The path to the SQLite file for the gateway (e.g., file:/path/to/database.db)

.github/workflows/pull-request.yaml

@@ -3,12 +3,21 @@ on:
   pull_request:
     types: [opened, synchronize]
 jobs:
+  configure:
+    runs-on: ubuntu-latest
+    outputs:
+      mongodb_version: ${{ steps.define.outputs.MONGODB_VERSION }}
+    steps:
+      - id: define
+        run: |
+          cat .env.template | grep MONGODB_VERSION >> "$GITHUB_OUTPUT"
   build:
     name: Build, Lint, and Test
     runs-on: ubuntu-latest
+    needs: configure
     services:
       mongo:
-        image: mongo:7.0
+        image: mongo:${{needs.configure.outputs.mongodb_version}}
         ports:
           - 27017:27017
     steps:

README.md

@@ -28,39 +28,26 @@
 
 ![license](https://img.shields.io/github/license/DouglasNeuroInformatics/OpenDataCapture)
 ![version](https://img.shields.io/github/package-json/v/DouglasNeuroInformatics/OpenDataCapture)
+![build](https://github.com/DouglasNeuroInformatics/OpenDataCapture/actions/workflows/build.yaml/badge.svg)
 
-<!-- ![build](https://github.com/DouglasNeuroInformatics/OpenDataCapture/actions/workflows/build.yaml/badge.svg) -->
 <!-- [![codecov](https://codecov.io/gh/DouglasNeuroInformatics/OpenDataCapture/branch/main/graph/badge.svg?token=XHC7BY6PJ1)](https://codecov.io/gh/DouglasNeuroInformatics/OpenDataCapture) -->
 
 </div>
 <hr />
 
 ## About
 
-Open Data Capture is an integrated suite of applications tailored for the continuous and longitudinal collection of both clinical and research data. This platform is anchored on a few foundational principles:
+Open Data Capture is a web-based platform designed for continuous clinical data collection. Designed with clinician-researchers in mind, the platform enables both remote and in-person evaluations, encompassing a range of applications — from patient questionnaires completed at home to interactive memory tasks conducted in clinical settings. The platform is designed with a robust security framework, ensuring that all collected data is securely stored in a structured, standardized manner. It offers an intuitive, user-friendly interface to filter the stored data according to various criteria. Once filtered, the data can be used to generate dynamic graphs and tables, or exported for research purposes.
 
-- Versatility in Instruments: Whether it's surveys, clinical questionnaires, interactive tasks, or neuroimaging data, our platform can handle it all under the umbrella of a generic instrument.
-- User-Friendly Design: Designed with the user in mind, its intuitive interface ensures that even those without specialized knowledge can navigate and utilize the platform with ease.
-- Streamlined Deployment: With our one-liner deployment solution, leverage Docker Compose for a hassle-free, automated setup.
+## Quick Start
 
-## Deployment
+Assuming that Docker and Docker Compose are already installed on your system, you can deploy an instance of Open Data Capture using the following command:
 
-### Download Repository
-
-```shell
-git clone https://github.com/DouglasNeuroInformatics/OpenDataCapture
-cd OpenDataCapture
-```
-
-### Launch Application
-
-```shell
-./scripts/generate-env.sh
-docker compose up -d
-docker compose exec mongo mongosh --eval "rs.initiate({_id: 'rs0', members: [{_id: 0, host: 'localhost:27017'}]});"
+```sh
+./scripts/generate-env.sh && docker compose up -d
 ```
 
-By default, the application will run on port 5500. So, navigate to `http://localhost:5500` in your browser and you should be greeted with the setup screen.
+By default, the application will run on port 5500. So, navigate to `http://localhost:5500` in your browser and you should be greeted with the setup screen. After getting started, we highly recommend reading our [deployment guide](http://localhost:4000/en/tutorials/deployment/) for additional information on how to configure Open Data Capture to best meet the needs of your organization.
 
 ## Contribution
 

apps/api/Dockerfile

@@ -1,4 +1,4 @@
-FROM node:lts-iron as base
+FROM node:lts-alpine as base
 WORKDIR /app
 ENV PNPM_HOME="/pnpm"
 ENV PATH="$PNPM_HOME:$PATH"
@@ -8,10 +8,14 @@ RUN corepack enable
 # PRUNE WORKSPACE
 FROM base AS builder
 COPY . .
+RUN apk add --no-cache libc6-compat
+RUN apk update
 RUN pnpm dlx turbo prune @open-data-capture/api --docker
 
 # INSTALL DEPENDENCIES
 FROM base AS installer
+RUN apk add --no-cache libc6-compat
+RUN apk update
 COPY .gitignore jsconfig.json ./
 COPY --from=builder /app/out/json/ .
 RUN pnpm install --frozen-lockfile 
@@ -25,9 +29,6 @@ RUN pnpm dlx turbo build --filter=@open-data-capture/api
 FROM base AS runner
 COPY --from=installer /app/apps/api/dist/ /app/dist/
 COPY --from=installer /app/apps/api/public/ /app/public/
-RUN addgroup --system --gid 1001 app
-RUN adduser --system --uid 1001 app
-RUN chown -R app:app /app
-USER app
 RUN echo '{ "type": "module" }' > package.json
+USER node
 CMD [ "node", "./dist/app.mjs" ]

apps/api/package.json

@@ -10,7 +10,7 @@
     "dev": "NODE_ENV=development env-cmd -f ../../.env concurrently \"pnpm build:watch\" \"sleep 1 && nodemon dist/app.mjs\"",
     "format": "prettier --write src",
     "lint": "tsc && eslint --fix src",
-    "start": "env-cmd -f ../../.env --use-shell 'NODE_OPTIONS=\"--enable-source-maps\" API_PROD_SERVER_PORT=$API_DEV_SERVER_PORT NODE_ENV=production ESBUILD_BINARY_PATH=dist/bin/esbuild node dist/app.mjs'",
+    "start": "env-cmd -f ../../.env --use-shell 'NODE_OPTIONS=\"--enable-source-maps\" API_PROD_SERVER_PORT=$API_DEV_SERVER_PORT NODE_ENV=production ESBUILD_BINARY_PATH=dist/bin/esbuild GATEWAY_SITE_ADDRESS=http://localhost:$GATEWAY_DEV_SERVER_PORT  node dist/app.mjs'",
     "test": "env-cmd -f ../../.env vitest run"
   },
   "dependencies": {
@@ -53,6 +53,7 @@
   "devDependencies": {
     "@nestjs/testing": "^10.3.0",
     "@open-data-capture/esbuild-plugin-native-modules": "workspace:*",
+    "@open-data-capture/esbuild-plugin-prisma": "workspace:*",
     "@open-data-capture/esbuild-plugin-runtime": "workspace:*",
     "@types/express": "^4.17.21",
     "@types/lodash": "^4.14.202",

apps/api/scripts/build.js

@@ -4,6 +4,7 @@ import path from 'path';
 import url from 'url';
 
 import { nativeModulesPlugin } from '@open-data-capture/esbuild-plugin-native-modules';
+import { prismaPlugin } from '@open-data-capture/esbuild-plugin-prisma';
 import { runtimePlugin } from '@open-data-capture/esbuild-plugin-runtime';
 import esbuild from 'esbuild';
 import esbuildPluginTsc from 'esbuild-plugin-tsc';
@@ -36,21 +37,7 @@ const { __dirname, __filename, require } = await (async () => {
 })();
 `;
 
-// Copy Prisma
-async function copyPrisma() {
-  const coreDatabasePath = path.dirname(require.resolve('@open-data-capture/database/core'));
-  const files = await fs.readdir(coreDatabasePath);
-  const engineFilename = files.find((filename) => {
-    return filename.startsWith('libquery_engine') && filename.endsWith('.node');
-  });
-  if (!engineFilename) {
-    throw new Error(`Failed to resolve prisma engine from path: ${coreDatabasePath}`);
-  }
-  await fs.mkdir(path.join(outdir, 'core'));
-  await fs.copyFile(path.join(coreDatabasePath, engineFilename), path.join(outdir, 'core', engineFilename));
-}
-
-// Copy Prisma
+// Copy ESBuild
 async function copyEsbuild() {
   const filepath = require.resolve('esbuild/bin/esbuild');
   await fs.copyFile(filepath, path.join(binDir, 'esbuild'));
@@ -73,6 +60,7 @@ const options = {
       tsconfigPath: tsconfig
     }),
     runtimePlugin({ outdir }),
+    prismaPlugin({ outdir: path.join(outdir, 'core') }),
     nativeModulesPlugin()
   ],
   target: ['node18', 'es2022'],
@@ -82,13 +70,12 @@ const options = {
 if (process.argv.includes('--watch')) {
   const ctx = await esbuild.context({
     ...options,
-    external: [...options.external, 'esbuild'],
+    external: [...(options.external ?? []), 'esbuild'],
     sourcemap: true
   });
   await ctx.watch();
   console.log('Watching...');
 } else {
-  await copyPrisma();
   await copyEsbuild();
   await esbuild.build(options);
   console.log('Done!');

apps/api/src/assignments/assignments.service.ts

@@ -15,14 +15,20 @@ import { CreateAssignmentDto } from './dto/create-assignment.dto';
 
 @Injectable()
 export class AssignmentsService {
-  private readonly gatewayBaseUrl: string;
+  private readonly assignmentBaseUrl: string;
 
   constructor(
     @InjectModel('Assignment') private readonly assignmentModel: Model<'Assignment'>,
     configurationService: ConfigurationService,
     private readonly gatewayService: GatewayService
   ) {
-    this.gatewayBaseUrl = configurationService.get('GATEWAY_BASE_URL');
+    if (configurationService.get('NODE_ENV') === 'production') {
+      const siteAddress = configurationService.get('GATEWAY_SITE_ADDRESS')!;
+      this.assignmentBaseUrl = siteAddress.origin;
+    } else {
+      const gatewayPort = configurationService.get('GATEWAY_DEV_SERVER_PORT')!;
+      this.assignmentBaseUrl = `http://localhost:${gatewayPort}`;
+    }
   }
 
   async create({ expiresAt, instrumentId, subjectId }: CreateAssignmentDto): Promise<Assignment> {
@@ -44,7 +50,7 @@ export class AssignmentsService {
             id: subjectId
           }
         },
-        url: `${this.gatewayBaseUrl}/assignments/${id}`
+        url: `${this.assignmentBaseUrl}/assignments/${id}`
       }
     });
     try {

apps/api/src/configuration/configuration.schema.ts

@@ -1,22 +1,60 @@
 import { $BooleanString } from '@open-data-capture/common/core';
 import { z } from 'zod';
 
-export const $Configuration = z.object({
-  API_DEV_SERVER_PORT: z.coerce.number().positive().int().optional(),
-  API_PROD_SERVER_PORT: z.coerce.number().positive().int().default(80),
-  DEBUG: $BooleanString,
-  GATEWAY_API_KEY: z.string().min(32),
-  GATEWAY_BASE_URL: z.string().url(),
-  GATEWAY_ENABLED: $BooleanString,
-  GATEWAY_REFRESH_INTERVAL: z.coerce.number().positive().int(),
-  MONGO_DIRECT_CONNECTION: z.string().optional(),
-  MONGO_REPLICA_SET: z.string().optional(),
-  MONGO_RETRY_WRITES: z.string().optional(),
-  MONGO_URI: z.string().url(),
-  MONGO_WRITE_CONCERN: z.string().optional(),
-  NODE_ENV: z.enum(['development', 'production', 'test']),
-  SECRET_KEY: z.string().min(32),
-  VERBOSE: $BooleanString
-});
+const $OptionalURL = z.preprocess(
+  (arg) => arg || undefined,
+  z
+    .string()
+    .url()
+    .optional()
+    .transform((arg) => (arg ? new URL(arg) : undefined))
+);
+
+export const $Configuration = z
+  .object({
+    API_DEV_SERVER_PORT: z.coerce.number().positive().int().optional(),
+    API_PROD_SERVER_PORT: z.coerce.number().positive().int().default(80),
+    DEBUG: $BooleanString,
+    GATEWAY_API_KEY: z.string().min(32),
+    GATEWAY_DEV_SERVER_PORT: z.coerce.number().positive().int().optional(),
+    GATEWAY_ENABLED: $BooleanString,
+    GATEWAY_INTERNAL_NETWORK_URL: $OptionalURL,
+    GATEWAY_REFRESH_INTERVAL: z.coerce.number().positive().int(),
+    GATEWAY_SITE_ADDRESS: $OptionalURL,
+    MONGO_DIRECT_CONNECTION: z.string().optional(),
+    MONGO_REPLICA_SET: z.string().optional(),
+    MONGO_RETRY_WRITES: z.string().optional(),
+    MONGO_URI: z
+      .string()
+      .url()
+      .transform((arg) => new URL(arg)),
+    MONGO_WRITE_CONCERN: z.string().optional(),
+    NODE_ENV: z.enum(['development', 'production', 'test']),
+    SECRET_KEY: z.string().min(32),
+    VERBOSE: $BooleanString
+  })
+  .superRefine((env, ctx) => {
+    if (env.NODE_ENV === 'production') {
+      if (!env.GATEWAY_SITE_ADDRESS) {
+        ctx.addIssue({
+          code: z.ZodIssueCode.custom,
+          message: 'GATEWAY_SITE_ADDRESS must be defined in production'
+        });
+      }
+    } else if (env.NODE_ENV === 'development') {
+      if (!env.API_DEV_SERVER_PORT) {
+        ctx.addIssue({
+          code: z.ZodIssueCode.custom,
+          message: 'API_DEV_SERVER_PORT must be defined in production'
+        });
+      }
+      if (!env.GATEWAY_DEV_SERVER_PORT) {
+        ctx.addIssue({
+          code: z.ZodIssueCode.custom,
+          message: 'GATEWAY_DEV_SERVER_PORT must be defined in production'
+        });
+      }
+    }
+  });
 
 export type Configuration = z.infer<typeof $Configuration>;

apps/api/src/configuration/configuration.service.ts

@@ -8,6 +8,6 @@ export class ConfigurationService {
   constructor(private readonly configService: ConfigService) {}
 
   get<TKey extends Extract<keyof Configuration, string>>(key: TKey) {
-    return this.configService.get<Configuration[TKey]>(key)!;
+    return this.configService.get<Configuration[TKey]>(key) as Configuration[TKey];
   }
 }

apps/api/src/gateway/gateway.module.ts

@@ -17,7 +17,21 @@ import { GatewaySynchronizer } from './gateway.synchronizer';
     HttpModule.registerAsync({
       inject: [ConfigurationService],
       useFactory: (configurationService: ConfigurationService) => {
+        let baseURL: string;
+        if (configurationService.get('NODE_ENV') === 'production') {
+          const internalNetworkUrl = configurationService.get('GATEWAY_INTERNAL_NETWORK_URL');
+          const siteAddress = configurationService.get('GATEWAY_SITE_ADDRESS')!;
+          if (siteAddress.hostname === 'localhost' && internalNetworkUrl) {
+            baseURL = internalNetworkUrl.origin;
+          } else {
+            baseURL = siteAddress.origin;
+          }
+        } else {
+          const gatewayPort = configurationService.get('GATEWAY_DEV_SERVER_PORT')!;
+          baseURL = `http://localhost:${gatewayPort}`;
+        }
         return {
+          baseURL,
           headers: {
             Authorization: `Bearer ${configurationService.get('GATEWAY_API_KEY')}`
           }