merge

.env.template

@@ -76,7 +76,8 @@ PLAYGROUND_DEV_SERVER_PORT=3750
 GATEWAY_DEV_SERVER_PORT=3500
 # The port to use for the Vite (full web app) development server
 WEB_DEV_SERVER_PORT=3000
-
+# Set an arbitrary delay (in milliseconds) for all responses (useful for testing suspense)
+API_RESPONSE_DELAY=
 # If set to 'true' and NODE_ENV === 'development', then login is automated
 VITE_DEV_BYPASS_AUTH=false
 # The username to use if VITE_DEV_BYPASS_AUTH is set to true
@@ -87,6 +88,8 @@ VITE_DEV_PASSWORD=Password12345678
 API_BASE_URL=http://localhost:5500
 # The number of miliseconds to delay the result of HTTP requests in development
 VITE_DEV_NETWORK_LATENCY=0
+# Whether to force clear queries when the pathname changes
+VITE_DEV_FORCE_CLEAR_QUERY_CACHE=false
 # Plausable analytics config (optional, set both to an empty string to disable)
 PLAUSIBLE_BASE_URL=
 PLAUSIBLE_WEB_DATA_DOMAIN=

apps/api/Dockerfile

@@ -1,4 +1,4 @@
-FROM node:iron-alpine AS base
+FROM node:iron AS base
 WORKDIR /app
 ARG RELEASE_VERSION
 ENV GATEWAY_DATABASE_URL="file:/dev/null"

apps/api/package.json

@@ -26,17 +26,17 @@
     "@douglasneuroinformatics/libnest": "catalog:",
     "@douglasneuroinformatics/libpasswd": "catalog:",
     "@douglasneuroinformatics/libstats": "catalog:",
-    "@faker-js/faker": "^9.0.0",
+    "@faker-js/faker": "^9.4.0",
     "@nestjs/axios": "^3.0.3",
     "@nestjs/common": "^10.4.1",
     "@nestjs/config": "^3.2.3",
     "@nestjs/core": "^10.4.1",
     "@nestjs/jwt": "^10.2.0",
-    "@nestjs/mapped-types": "2.0.5",
+    "@nestjs/mapped-types": "2.1.0",
     "@nestjs/passport": "^10.0.3",
     "@nestjs/platform-express": "^10.4.1",
     "@nestjs/swagger": "^7.4.0",
-    "@nestjs/throttler": "^6.2.1",
+    "@nestjs/throttler": "^6.3.0",
     "@opendatacapture/demo": "workspace:*",
     "@opendatacapture/instrument-library": "workspace:*",
     "@opendatacapture/instrument-utils": "workspace:*",
@@ -47,9 +47,9 @@
     "@opendatacapture/subject-utils": "workspace:*",
     "@prisma/client": "catalog:",
     "axios": "catalog:",
-    "express": "^4.19.2",
+    "express": "^4.21.2",
     "lodash-es": "workspace:lodash-es__4.x@*",
-    "mongodb": "^6.8.1",
+    "mongodb": "^6.12.0",
     "passport": "^0.7.0",
     "passport-jwt": "4.0.1",
     "reflect-metadata": "^0.1.14",
@@ -62,15 +62,15 @@
     "@nestjs/testing": "^10.4.1",
     "@opendatacapture/instrument-stubs": "workspace:*",
     "@types/express": "^4.17.21",
-    "@types/passport": "^1.0.16",
+    "@types/passport": "^1.0.17",
     "@types/passport-jwt": "^4.0.1",
     "@types/supertest": "^6.0.2",
-    "concurrently": "^9.0.0",
+    "concurrently": "^9.1.2",
     "esbuild": "catalog:",
     "esbuild-plugin-tsc": "^0.4.0",
     "nodemon": "catalog:",
     "prisma": "catalog:",
-    "prisma-json-types-generator": "^3.0.4",
+    "prisma-json-types-generator": "^3.2.2",
     "supertest": "^7.0.0",
     "type-fest": "workspace:type-fest__4.x@*"
   },

apps/api/src/app.module.ts

@@ -1,6 +1,7 @@
 import { CryptoModule } from '@douglasneuroinformatics/libnest/crypto';
 import { LoggingModule } from '@douglasneuroinformatics/libnest/logging';
 import { Module } from '@nestjs/common';
+import type { MiddlewareConsumer, NestModule } from '@nestjs/common';
 import { APP_GUARD } from '@nestjs/core';
 import { ThrottlerGuard, ThrottlerModule } from '@nestjs/throttler';
 
@@ -10,6 +11,7 @@ import { AuthenticationGuard } from './auth/guards/authentication.guard';
 import { AuthorizationGuard } from './auth/guards/authorization.guard';
 import { ConfigurationModule } from './configuration/configuration.module';
 import { ConfigurationService } from './configuration/configuration.service';
+import { DelayMiddleware } from './core/middleware/delay.middleware';
 import { GatewayModule } from './gateway/gateway.module';
 import { GroupsModule } from './groups/groups.module';
 import { InstrumentsModule } from './instruments/instruments.module';
@@ -93,4 +95,13 @@ import { UsersModule } from './users/users.module';
     }
   ]
 })
-export class AppModule {}
+export class AppModule implements NestModule {
+  constructor(private readonly configurationService: ConfigurationService) {}
+
+  configure(consumer: MiddlewareConsumer) {
+    const isDev = this.configurationService.get('NODE_ENV') === 'development';
+    if (isDev) {
+      consumer.apply(DelayMiddleware).forRoutes('*');
+    }
+  }
+}

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

@@ -1,3 +1,4 @@
+import { isNumberLike, parseNumber } from '@douglasneuroinformatics/libjs';
 import { $BooleanString } from '@opendatacapture/schemas/core';
 import { z } from 'zod';
 
@@ -10,17 +11,27 @@ const $OptionalURL = z.preprocess(
     .transform((arg) => (arg ? new URL(arg) : undefined))
 );
 
+const $ParsedNumber = <TSchema extends z.ZodTypeAny>(schema: TSchema) => {
+  return z.preprocess((arg) => {
+    if (!isNumberLike(arg)) {
+      return undefined;
+    }
+    return parseNumber(arg);
+  }, schema);
+};
+
 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),
+    API_DEV_SERVER_PORT: $ParsedNumber(z.number().positive().int().optional()),
+    API_PROD_SERVER_PORT: $ParsedNumber(z.number().positive().int().default(80)),
+    API_RESPONSE_DELAY: $ParsedNumber(z.number().positive().int().optional()),
     DANGEROUSLY_DISABLE_PBKDF2_ITERATION: $BooleanString.default(false),
     DEBUG: $BooleanString,
     GATEWAY_API_KEY: z.string().min(32),
-    GATEWAY_DEV_SERVER_PORT: z.coerce.number().positive().int().optional(),
+    GATEWAY_DEV_SERVER_PORT: $ParsedNumber(z.number().positive().int().optional()),
     GATEWAY_ENABLED: $BooleanString,
     GATEWAY_INTERNAL_NETWORK_URL: $OptionalURL,
-    GATEWAY_REFRESH_INTERVAL: z.coerce.number().positive().int(),
+    GATEWAY_REFRESH_INTERVAL: $ParsedNumber(z.number().positive().int()),
     GATEWAY_SITE_ADDRESS: $OptionalURL,
     MONGO_DIRECT_CONNECTION: z.string().optional(),
     MONGO_REPLICA_SET: z.string().optional(),

apps/api/src/core/middleware/delay.middleware.ts

@@ -0,0 +1,18 @@
+import { Injectable, type NestMiddleware } from '@nestjs/common';
+
+import { ConfigurationService } from '@/configuration/configuration.service';
+
+@Injectable()
+export class DelayMiddleware implements NestMiddleware {
+  constructor(private readonly configurationService: ConfigurationService) {}
+
+  use(_req: any, _res: any, next: (error?: any) => void) {
+    const responseDelay = this.configurationService.get('API_RESPONSE_DELAY');
+    if (!responseDelay) {
+      return next();
+    }
+    setTimeout(() => {
+      next();
+    }, responseDelay);
+  }
+}

apps/api/src/instrument-records/instrument-records.service.ts

@@ -11,7 +11,7 @@ import type {
   LinearRegressionResults,
   UploadInstrumentRecordsData
 } from '@opendatacapture/schemas/instrument-records';
-import type { InstrumentRecordModel, Prisma, SessionModel } from '@prisma/generated-client';
+import { type InstrumentRecordModel, Prisma, type SessionModel } from '@prisma/generated-client';
 import { isNumber, pickBy } from 'lodash-es';
 
 import { accessibleQuery } from '@/ability/ability.utils';
@@ -274,91 +274,84 @@ export class InstrumentRecordsService {
       );
     }
 
-    const createdRecordsArray: InstrumentRecordModel[] = [];
     const createdSessionsArray: SessionModel[] = [];
 
     try {
-      for (let i = 0; i < records.length; i++) {
-        const { data: rawData, date, subjectId } = records[i]!;
-        await this.createSubjectIfNotFound(subjectId);
-
-        const session = await this.sessionsService.create({
-          date: date,
-          groupId: groupId ? groupId : null,
-          subjectData: {
-            id: subjectId
-          },
-          type: 'RETROSPECTIVE'
-        });
+      const preProcessedRecords = await Promise.all(
+        records.map(async (record) => {
+          const { data: rawData, date, subjectId } = record;
+
+          // Validate data
+          const parseResult = instrument.validationSchema.safeParse(this.parseJson(rawData));
+          if (!parseResult.success) {
+            console.error(parseResult.error.issues);
+            throw new UnprocessableEntityException(
+              `Data received for record does not pass validation schema of instrument '${instrument.id}'`
+            );
+          }
 
-        createdSessionsArray.push(session);
+          // Ensure subject exists
+          await this.createSubjectIfNotFound(subjectId);
 
-        const sessionId = session.id;
+          const session = await this.sessionsService.create({
+            date: date,
+            groupId: groupId ?? null,
+            subjectData: { id: subjectId },
+            type: 'RETROSPECTIVE'
+          });
 
-        const parseResult = instrument.validationSchema.safeParse(this.parseJson(rawData));
-        if (!parseResult.success) {
-          console.error(parseResult.error.issues);
-          throw new UnprocessableEntityException(
-            `Data received for record at index '${i}' does not pass validation schema of instrument '${instrument.id}'`
-          );
-        }
+          createdSessionsArray.push(session);
 
-        const createdRecord = await this.instrumentRecordModel.create({
-          data: {
-            computedMeasures: instrument.measures
-              ? this.instrumentMeasuresService.computeMeasures(instrument.measures, parseResult.data)
-              : null,
+          const computedMeasures = instrument.measures
+            ? this.instrumentMeasuresService.computeMeasures(instrument.measures, parseResult.data)
+            : null;
+
+          return {
+            computedMeasures,
             data: this.serializeData(parseResult.data),
             date,
-            group: groupId
-              ? {
-                  connect: { id: groupId }
-                }
-              : undefined,
-            instrument: {
-              connect: {
-                id: instrumentId
-              }
-            },
-            session: {
-              connect: {
-                id: sessionId
-              }
-            },
-            subject: {
-              connect: {
-                id: subjectId
-              }
-            }
-          }
-        });
+            groupId,
+            instrumentId,
+            sessionId: session.id,
+            subjectId
+          };
+        })
+      );
 
-        createdRecordsArray.push(createdRecord);
-      }
-    } catch (err) {
-      await this.instrumentRecordModel.deleteMany({
+      await this.instrumentRecordModel.createMany({
+        data: preProcessedRecords
+      });
+
+      return this.instrumentRecordModel.findMany({
         where: {
-          id: {
-            in: createdRecordsArray.map((record) => record.id)
-          }
+          groupId,
+          instrumentId
         }
       });
+    } catch (err) {
       await this.sessionsService.deleteByIds(createdSessionsArray.map((session) => session.id));
       throw err;
     }
-
-    return createdRecordsArray;
   }
 
   private async createSubjectIfNotFound(subjectId: string) {
     try {
-      await this.subjectsService.findById(subjectId);
+      return await this.subjectsService.findById(subjectId);
     } catch (exception) {
       if (exception instanceof NotFoundException) {
         const addedSubject: CreateSubjectDto = {
           id: subjectId
         };
-        await this.subjectsService.create(addedSubject);
+        try {
+          return await this.subjectsService.create(addedSubject);
+        } catch (prismaError) {
+          if (prismaError instanceof Prisma.PrismaClientKnownRequestError && prismaError.code === 'P2002') {
+            console.error(prismaError);
+            return await this.subjectsService.findById(subjectId);
+          } else {
+            throw prismaError;
+          }
+        }
       } else {
         throw exception;
       }

apps/api/src/users/users.service.ts

@@ -107,9 +107,14 @@ export class UsersService {
     return user;
   }
 
-  async updateById(id: string, data: UpdateUserDto, { ability }: EntityOperationOptions = {}) {
+  async updateById(id: string, { groupIds, ...data }: UpdateUserDto, { ability }: EntityOperationOptions = {}) {
     return this.userModel.update({
-      data,
+      data: {
+        ...data,
+        groups: {
+          connect: groupIds?.map((id) => ({ id }))
+        }
+      },
       where: { AND: [accessibleQuery(ability, 'update', 'User')], id }
     });
   }

apps/gateway/Dockerfile

@@ -1,4 +1,4 @@
-FROM node:iron-alpine AS base
+FROM node:iron AS base
 WORKDIR /app
 ARG RELEASE_VERSION
 ENV GATEWAY_DATABASE_URL=file:/app/sqlite/gateway.db

apps/gateway/package.json

@@ -25,10 +25,10 @@
     "@opendatacapture/schemas": "workspace:*",
     "@prisma/client": "catalog:",
     "axios": "catalog:",
-    "compression": "^1.7.4",
-    "express": "^4.19.2",
+    "compression": "^1.7.5",
+    "express": "^4.21.2",
     "lodash-es": "workspace:lodash-es__4.x@*",
-    "pino-http": "^10.3.0",
+    "pino-http": "^10.4.0",
     "pino-pretty": "^11.2.2",
     "react": "workspace:react__18.x@*",
     "react-dom": "workspace:react-dom__18.x@*",
@@ -42,15 +42,15 @@
     "@opendatacapture/vite-plugin-runtime": "workspace:*",
     "@types/compression": "^1.7.5",
     "@types/express": "^4.17.21",
-    "@vitejs/plugin-react-swc": "^3.7.0",
+    "@vitejs/plugin-react-swc": "^3.7.2",
     "autoprefixer": "^10.4.20",
     "esbuild": "catalog:",
     "nodemon": "catalog:",
-    "postcss": "^8.4.45",
+    "postcss": "^8.5.1",
     "prisma": "catalog:",
-    "tailwindcss": "^3.4.10",
+    "tailwindcss": "^3.4.17",
     "type-fest": "workspace:type-fest__4.x@*",
-    "vite": "^5.4.3"
+    "vite": "catalog:"
   },
   "trustedDependencies": [
     "prisma",