fix(disatch): Fix open api schema

biosimulations · Apr 16, 2021 · ff15503 · ff15503
1 parent 1f6c4fc
commit ff15503
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Showing 7 changed files with 48 additions and 15 deletions.
diff --git a/biosimulations/apps/dispatch-api/src/images/images.controller.ts b/biosimulations/apps/dispatch-api/src/images/images.controller.ts
@@ -12,11 +12,11 @@ import {
   Post,
 } from '@nestjs/common';
 import { ClientProxy } from '@nestjs/microservices';
-import { ApiBody, ApiOperation, ApiResponse, ApiTags } from '@nestjs/swagger';
+import { ApiBody, ApiOperation,  ApiTags } from '@nestjs/swagger';
 import { refreshImageBody } from './image.dto';
 
 @Controller('images')
-@ApiResponse({})
+
 @ApiTags('Internal management')
 export class ImagesController {
   constructor(@Inject('NATS_CLIENT') private client: ClientProxy) {}

diff --git a/biosimulations/apps/dispatch-api/src/logs/logs.controller.ts b/biosimulations/apps/dispatch-api/src/logs/logs.controller.ts
@@ -46,6 +46,7 @@ export class LogsController {
     throw new NotImplementedException('Not Implemented');
   }
   @ApiResponse({
+    status: 200,
     type: CombineArchiveLog,
   })
   @Get(':id')
@@ -65,6 +66,10 @@ export class LogsController {
   }
 
   @Post()
+  @ApiResponse({
+    status: 201,
+    type: CombineArchiveLog,
+  })
   public async createLogs(
     @Body() body: CreateSimulationRunLogBody,
   ): Promise<CombineArchiveLog> {

diff --git a/biosimulations/apps/dispatch-api/src/main.ts b/biosimulations/apps/dispatch-api/src/main.ts
@@ -11,7 +11,10 @@ import { NestFactory } from '@nestjs/core';
 import { AppModule } from './app/app.module';
 import { DocumentBuilder, SwaggerModule } from '@nestjs/swagger';
 import { CustomOrigin } from '@nestjs/common/interfaces/external/cors-options.interface';
-import { SecuritySchemeObject } from '@nestjs/swagger/dist/interfaces/open-api-spec.interface';
+import {
+  ScopesObject,
+  SecuritySchemeObject,
+} from '@nestjs/swagger/dist/interfaces/open-api-spec.interface';
 import { ConfigService } from '@nestjs/config';
 import { json } from 'body-parser';
 import { Resolver } from '@stoplight/json-ref-resolver';
@@ -79,7 +82,7 @@ async function bootstrap() {
     {
       name: 'Authentication testing',
       description:
-        'Operations for checking whether a user is logged in and retrieving information about a user\'s privileges.',
+        "Operations for checking whether a user is logged in and retrieving information about a user's privileges.",
     },
     {
       name: 'Internal management',
@@ -112,11 +115,12 @@ async function bootstrap() {
     builder.addTag(tag.name, tag.description);
   }
 
-  const scopes = [
-    'read:SimulationRuns',
-    'write:SimulationRuns',
-    'delete:SimulationsRuns',
-  ];
+  const scopes: ScopesObject = {
+    'read:SimulationRuns': 'Get information about a submitted run',
+    'write:SimulationRuns': 'Modify a run, including status',
+    'delete:SimulationsRuns': 'Delete runs from the database',
+    // TODO add all scopes/find a way to automate this from auth0
+  };
   const authorizationUrl =
     'https://auth.biosimulations.org/authorize?audience=dispatch.biosimulations.org';
   const openIdConnectUrl =
@@ -163,7 +167,7 @@ async function bootstrap() {
     customCss: removeIcon,
     swaggerOptions: {
       oauth: {
-        clientId: 'pMatIe0TqLPbnXBn6gcDjdjnpIrlKG3a',
+        clientId: clientId,
       },
       //tagsSorter: 'alpha',
       operationsSorter: 'alpha',
@@ -177,7 +181,9 @@ async function bootstrap() {
   const resolver = new Resolver();
   const resolvedDocument = await resolver.resolve(document);
   const schema = resolvedDocument.result.components.schemas.CombineArchiveLog;
-  httpAdapter.get('/schema/CombineArchiveLog.json', (req, res) => res.json(toJsonSchema(schema)));
+  httpAdapter.get('/schema/CombineArchiveLog.json', (req, res) =>
+    res.json(toJsonSchema(schema)),
+  );
 
   const configService = app.get(ConfigService);
   const limit = configService.get('server.limit');

diff --git a/biosimulations/apps/dispatch-service/src/app/app.module.ts b/biosimulations/apps/dispatch-service/src/app/app.module.ts
@@ -1,4 +1,5 @@
 import { Module, HttpModule } from '@nestjs/common';
+import { BullModule } from '@nestjs/bull';
 
 import { HpcService } from './services/hpc/hpc.service';
 import { SbatchService } from './services/sbatch/sbatch.service';
@@ -27,6 +28,15 @@ import { LogService } from './results/log.service';
     SharedNatsClientModule,
     DispatchNestClientModule,
     ScheduleModule.forRoot(),
+    BullModule.forRoot({
+      redis: {
+        host: 'localhost',
+        port: 6379,
+      },
+    }),
+    BullModule.registerQueue({
+      name: 'jobmonitor',
+    }),
   ],
   controllers: [SubmissionController, ResultsController],
   providers: [

diff --git a/biosimulations/apps/dispatch-service/src/app/submission/monitoring.service.ts b/biosimulations/apps/dispatch-service/src/app/submission/monitoring.service.ts
@@ -0,0 +1,8 @@
+import { Injectable } from '@nestjs/common';
+import { Queue } from 'bull';
+import { InjectQueue } from '@nestjs/bull';
+
+@Injectable()
+export class MonitoringService {
+  constructor(@InjectQueue('jobmonitoring') private monitorQueue: Queue) {}
+}
diff --git a/biosimulations/apps/dispatch/src/app/app.module.ts b/biosimulations/apps/dispatch/src/app/app.module.ts
@@ -29,9 +29,10 @@ const routes: Routes = [
   {
     path: 'create',
     loadChildren: () =>
-      import('apps/dispatch/src/app/components/create-simulation-project/create-simulation-project.module').then(
-        (m) => m.CreateSimulationProjectModule,
-      ),
+      // eslint-disable-next-line @nrwl/nx/enforce-module-boundaries
+      import(
+        'apps/dispatch/src/app/components/create-simulation-project/create-simulation-project.module'
+      ).then((m) => m.CreateSimulationProjectModule),
     data: {
       breadcrumb: 'Create simulation project',
     },
@@ -40,6 +41,7 @@ const routes: Routes = [
   {
     path: 'run',
     loadChildren: () =>
+      // eslint-disable-next-line @nrwl/nx/enforce-module-boundaries
       import('apps/dispatch/src/app/components/run/run.module').then(
         (m) => m.RunModule,
       ),
@@ -51,6 +53,7 @@ const routes: Routes = [
   {
     path: 'simulations',
     loadChildren: () =>
+      // eslint-disable-next-line @nrwl/nx/enforce-module-boundaries
       import(
         'apps/dispatch/src/app/components/simulations/simulations.module'
       ).then((m) => m.SimulationsModule),
@@ -61,6 +64,7 @@ const routes: Routes = [
   {
     path: 'help',
     loadChildren: () =>
+      // eslint-disable-next-line @nrwl/nx/enforce-module-boundaries
       import('apps/dispatch/src/app/components/help/help.module').then(
         (m) => m.HelpModule,
       ),

diff --git a/biosimulations/libs/dispatch/api-models/src/lib/simulationRun.ts b/biosimulations/libs/dispatch/api-models/src/lib/simulationRun.ts
@@ -24,7 +24,7 @@ export class SimulationRun {
   @ApiProperty({
     type: String,
     description: 'The name of a BioSimulators compliant simulator',
-    examples: ['vcell', 'gillespy2', 'cobrapy', 'copasi', 'bionetgen', 'tellurium'],
+    example: 'vcell',
     externalDocs: {
       url: 'https://biosimulators.org/simulators',
       description: 'Simulators List',