Get config.json from collaboration server (#371)

* Add a JBrowse module

* Tracks added - ready for test

* tmp commit

* tmp commit

* Get Apollo tracks from Mongo and include those in config.json

* tmp commit

* user can add track to Mongo from track info menu

* user can add/delete track to Mongo from track info menu

* Ready for draft PR

* Jbrowse -> JBrowse

* Use a 'none' role instead of public endpoints

* Add "Log out" Apollo menu item

* Fetch authenticated config.json from collab server

* Misc. fixes

* Store whole JBrowse config instead of just tracks

* Save session tracks to Apollo JBrowse config

* Fix feature selection refresh crash

* Remove static serving from collaboration server

* Fix/skip a few more tests

* Remove unused variable

* Fix CLI test env

* Move env variables to the correct place

---------

Co-authored-by: Garrett Stevens <[email protected]>

.github/workflows/pull_request.yml

@@ -41,7 +41,7 @@ jobs:
       - name: Start apollo
         run: |
           yarn --cwd packages/apollo-shared start &
-          yarn --cwd packages/apollo-collaboration-server start &
+          ALLOW_ROOT_USER=true ROOT_USER_NAME=admin ROOT_USER_PASSWORD=pass yarn --cwd packages/apollo-collaboration-server start &
       - name: Run CLI tests
         run: python3 ./test/test.py TestCLI
         working-directory: packages/apollo-cli

docs/apollo.env

@@ -75,12 +75,6 @@ ALLOW_GUEST_USER=true
 # Possible values are admin, readOnly and user; defaults to readonly
 GUEST_USER_ROLE=readOnly
 
-# Apollo by default uses The Sequence Ontology. You can override this by
-# providing a path to an ontology file in the OBO Graphs JSON format. You can
-# use `robot` to convert an OBO or OWL to OBO Graphs JSON.
-# http://robot.obolibrary.org/convert
-# ONTOLOGY_FILE = '/data/ontology.json'
-
 # Comma-separated list of Apollo plugins to use
 # PLUGIN_URLS=https://example.com/apollo-plugin-example.umd.production.min.js
 # Alternatively, can be a path to a file with a list of plugin URLs, one URL per

packages/apollo-collaboration-server/.development.env

@@ -5,6 +5,9 @@
 # URL
 URL=http://localhost:3999
 
+# Name of your server (shown during the login process)
+NAME=Demo Server
+
 # MongoDB connection
 MONGODB_URI=mongodb://127.0.0.1:27017/apolloDb
 # Alternatively, can be a path to a file with the URI
@@ -48,6 +51,13 @@ MICROSOFT_CLIENT_SECRET=~Gr8Q~h6RTU7SMC-fjNxXy_~nabTD-ME_rFyLa.M
 ## OPTIONAL ##
 ##############
 
+# Description of what is hosted on your server
+DESCRIPTION=A server for Apollo development purposes
+
+# URL (relative or absolute) of the Apollo JBrowse plugin.
+# Defaults to relative URL 'apollo.js'
+PLUGIN_LOCATION=http://localhost:9000/dist/jbrowse-plugin-apollo.umd.development.js
+
 # Application port, defaults to 3999
 # PORT=3999
 
@@ -69,28 +79,25 @@ CHUNK_SIZE=500
 # Whether to broadcast users locations, defaults to true
 # BROADCAST_USER_LOCATION=true
 
+# Whether to allow a root user that can log in with a name and password. All
+# other users (besides guest) must sign in with an authentication provider.
+# Defaults to false
+# ALLOW_ROOT_USER=false
+# The root user name, required if ALLOW_ROOT_USER is true
+# ROOT_USER_NAME=root
+# The root user password, required if ALLOW_ROOT_USER is true
+# ROOT_USER_PASSWORD=password
+# Alternatively, can be a path to a file with the root user password
+# ROOT_USER_PASSWORD_FILE=/run/secrets/root-user-password
+
 # Whether to allow guest users who do not have to log in, defaults to false
 ALLOW_GUEST_USER=true
 # If guest users are allowed, what role will they have
 # Possible values are admin, readOnly and user; defaults to readonly
 # GUEST_USER_ROLE=readOnly
 
-# Apollo by default uses The Sequence Ontology. You can override this by
-# providing a path to an ontology file in the OBO Graphs JSON format. You can
-# use `robot` to convert an OBO or OWL to OBO Graphs JSON.
-# http://robot.obolibrary.org/convert
-# ONTOLOGY_FILE = '/data/ontology.json'
-
 # Comma-separated list of Apollo plugins to use
 # PLUGIN_URLS=https://example.com/apollo-plugin-example.umd.production.min.js
 # Alternatively, can be a path to a file with a list of plugin URLs, one URL per
 # line
 # PLUGIN_URLS_FILE=/data/plugin-urls
-
-##############################################################################
-## To login via username and password
-##############################################################################
-ALLOW_ROOT_USER=false
-ROOT_USER_NAME=admin
-ROOT_USER_PASSWORD=pass
-ROOT_USER_PASSWORD_FILE

packages/apollo-collaboration-server/package.json

@@ -46,6 +46,7 @@
     "@nestjs/terminus": "^10.0.1",
     "@nestjs/websockets": "^10.1.0",
     "connect-mongodb-session": "^3.1.1",
+    "deepmerge": "^4.3.1",
     "express": "^4.18.0",
     "express-session": "^1.17.3",
     "generic-filehandle": "^3.0.0",

packages/apollo-collaboration-server/src/app.module.ts

@@ -1,11 +1,9 @@
 import fs from 'node:fs/promises'
-import path from 'node:path'
 
 import { Module } from '@nestjs/common'
 import { ConfigModule, ConfigService } from '@nestjs/config'
 import { APP_GUARD } from '@nestjs/core'
 import { MongooseModule, MongooseModuleFactoryOptions } from '@nestjs/mongoose'
-import { ServeStaticModule } from '@nestjs/serve-static'
 import Joi from 'joi'
 import { Connection } from 'mongoose'
 
@@ -18,6 +16,7 @@ import { ExportModule } from './export/export.module'
 import { FeaturesModule } from './features/features.module'
 import { FilesModule } from './files/files.module'
 import { HealthModule } from './health/health.module'
+import { JBrowseModule } from './jbrowse/jbrowse.module'
 import { MessagesModule } from './messages/messages.module'
 import { OperationsModule } from './operations/operations.module'
 import { PluginsModule } from './plugins/plugins.module'
@@ -38,6 +37,7 @@ const nodeEnv = process.env.NODE_ENV ?? 'production'
 const validationSchema = Joi.object({
   // Required
   URL: Joi.string().uri().required(),
+  NAME: Joi.string().required(),
   MONGODB_URI: Joi.string(),
   MONGODB_URI_FILE: Joi.string(),
   FILE_UPLOAD_FOLDER: Joi.string().required(),
@@ -53,8 +53,9 @@ const validationSchema = Joi.object({
   JWT_SECRET_FILE: Joi.string(),
   SESSION_SECRET: Joi.string(),
   SESSION_SECRET_FILE: Joi.string(),
-  ONTOLOGY_FILE: Joi.string(),
   // Optional
+  DESCRIPTION: Joi.string(),
+  PLUGIN_LOCATION: Joi.string(),
   ALLOW_ROOT_USER: Joi.boolean().default(false),
   ROOT_USER_NAME: Joi.string(),
   ROOT_USER_PASSWORD: Joi.string(),
@@ -164,10 +165,8 @@ async function mongoDBURIFactory(
     RefSeqChunksModule,
     RefSeqsModule,
     SequenceModule,
-    ServeStaticModule.forRoot({
-      rootPath: path.join(__dirname, '..', 'public'),
-    }),
     UsersModule,
+    JBrowseModule,
   ],
   providers: [
     { provide: APP_GUARD, useClass: JwtAuthGuard },

packages/apollo-collaboration-server/src/authentication/authentication.controller.ts

@@ -13,14 +13,15 @@ import {
 } from '@nestjs/common'
 
 import { GoogleAuthGuard } from '../utils/google.guard'
-import { Public } from '../utils/jwt-auth.guard'
 import { MicrosoftAuthGuard } from '../utils/microsoft.guard'
 import {
   AuthenticationService,
   RequestWithUserToken,
 } from './authentication.service'
+import { Validations } from '../utils/validation/validatation.decorator'
+import { Role } from '../utils/role/role.enum'
 
-@Public()
+@Validations(Role.None)
 @Controller('auth')
 export class AuthenticationController {
   private readonly logger = new Logger(AuthenticationController.name)

packages/apollo-collaboration-server/src/authentication/authentication.service.ts

@@ -34,15 +34,15 @@ interface ConfigValues {
   GOOGLE_CLIENT_ID?: string
   GOOGLE_CLIENT_ID_FILE?: string
   ALLOW_GUEST_USER: boolean
-  DEFAULT_NEW_USER_ROLE: Role | 'none'
+  DEFAULT_NEW_USER_ROLE: Role
   ROOT_USER_NAME: string
   ROOT_USER_PASSWORD: string
 }
 
 @Injectable()
 export class AuthenticationService {
   private readonly logger = new Logger(AuthenticationService.name)
-  private defaultNewUserRole: Role | 'none'
+  private defaultNewUserRole: Role
 
   constructor(
     private readonly usersService: UsersService,
@@ -183,9 +183,10 @@ export class AuthenticationService {
         // If there is not a non-guest user yet, the 1st user role will be admin
         newUserRole = hasAdmin ? this.defaultNewUserRole : Role.Admin
       }
-      const newUser: CreateUserDto = { email, username: name }
-      if (newUserRole !== 'none') {
-        newUser.role = newUserRole
+      const newUser: CreateUserDto = {
+        email,
+        username: name,
+        role: newUserRole,
       }
       user = await this.usersService.addNew(newUser)
     }

packages/apollo-collaboration-server/src/changes/changes.module.ts

@@ -8,6 +8,7 @@ import { AssembliesModule } from '../assemblies/assemblies.module'
 import { CountersModule } from '../counters/counters.module'
 import { FeaturesModule } from '../features/features.module'
 import { FilesModule } from '../files/files.module'
+import { JBrowseModule } from '../jbrowse/jbrowse.module'
 import { MessagesModule } from '../messages/messages.module'
 import { RefSeqChunksModule } from '../refSeqChunks/refSeqChunks.module'
 import { RefSeqsModule } from '../refSeqs/refSeqs.module'
@@ -37,6 +38,7 @@ import { ChangesService } from './changes.service'
     UsersModule,
     CountersModule,
     MessagesModule,
+    JBrowseModule,
   ],
 })
 export class ChangesModule {}

packages/apollo-collaboration-server/src/changes/changes.service.ts

@@ -17,6 +17,8 @@ import {
   RefSeqChunk,
   RefSeqChunkDocument,
   RefSeqDocument,
+  JBrowseConfig,
+  JBrowseConfigDocument,
   User,
   UserDocument,
 } from '@apollo-annotation/schemas'
@@ -54,6 +56,8 @@ export class ChangesService {
     private readonly fileModel: Model<FileDocument>,
     @InjectModel(User.name)
     private readonly userModel: Model<UserDocument>,
+    @InjectModel(JBrowseConfig.name)
+    private readonly jbrowseConfigModel: Model<JBrowseConfigDocument>,
     @InjectModel(Change.name)
     private readonly changeModel: Model<ChangeDocument>,
     private readonly filesService: FilesService,
@@ -110,6 +114,7 @@ export class ChangesService {
           refSeqChunkModel: this.refSeqChunkModel,
           fileModel: this.fileModel,
           userModel: this.userModel,
+          jbrowseConfigModel: this.jbrowseConfigModel,
           session,
           filesService: this.filesService,
           counterService: this.countersService,

packages/apollo-collaboration-server/src/checks/checks.controller.ts

@@ -1,12 +1,11 @@
 import { Controller, Get, Logger, Param, Query } from '@nestjs/common'
 
 import { FeatureRangeSearchDto } from '../entity/gff3Object.dto'
-import { Public } from '../utils/jwt-auth.guard'
 import { Role } from '../utils/role/role.enum'
 import { Validations } from '../utils/validation/validatation.decorator'
 import { ChecksService } from './checks.service'
 
-@Public()
+@Validations(Role.ReadOnly)
 @Controller('checks')
 export class ChecksController {
   constructor(private readonly checksService: ChecksService) {}
@@ -28,7 +27,6 @@ export class ChecksController {
    * @param searchDto - range
    * @returns an array of checkResult -documents
    */
-  @Validations(Role.ReadOnly)
   @Get('range')
   getFeatures(@Query() request: FeatureRangeSearchDto) {
     this.logger.debug(

packages/apollo-collaboration-server/src/export/export.controller.ts

@@ -9,7 +9,6 @@ import {
 } from '@nestjs/common'
 import { Response as ExpressResponse } from 'express'
 
-import { Public } from '../utils/jwt-auth.guard'
 import { Role } from '../utils/role/role.enum'
 import { Validations } from '../utils/validation/validatation.decorator'
 import { ExportService } from './export.service'
@@ -39,7 +38,7 @@ export class ExportController {
    * @param res -
    * @returns A StreamableFile of the GFF3
    */
-  @Public()
+  @Validations(Role.None)
   @Get()
   async exportGFF3(
     @Query() request: { exportID: string; fastaWidth?: number },

packages/apollo-collaboration-server/src/features/features.controller.ts

@@ -1,12 +1,12 @@
 import { Controller, Get, Logger, Param, Query } from '@nestjs/common'
 
 import { FeatureRangeSearchDto } from '../entity/gff3Object.dto'
-import { Public } from '../utils/jwt-auth.guard'
 import { Role } from '../utils/role/role.enum'
 import { Validations } from '../utils/validation/validatation.decorator'
 import { FeatureCountRequest } from './dto/feature.dto'
 import { FeaturesService } from './features.service'
 
+@Validations(Role.ReadOnly)
 @Controller('features')
 export class FeaturesController {
   constructor(private readonly featuresService: FeaturesService) {}
@@ -17,7 +17,6 @@ export class FeaturesController {
    * For testing try to go to:
    * http://localhost:3999/features/searchFeatures?term=exonerate
    */
-  @Public()
   @Get('searchFeatures')
   async searchFeatures(@Query() request: { term: string; assemblies: string }) {
     return this.featuresService.searchFeatures(request)
@@ -29,7 +28,6 @@ export class FeaturesController {
    * @returns Return 'HttpStatus.OK' and array of features if search was successful
    * or if search data was not found or in case of error throw exception
    */
-  @Validations(Role.ReadOnly)
   @Get('getFeatures')
   getFeatures(@Query() request: FeatureRangeSearchDto) {
     this.logger.debug(
@@ -39,7 +37,6 @@ export class FeaturesController {
     return this.featuresService.findByRange(request)
   }
 
-  @Validations(Role.ReadOnly)
   @Get('count')
   async getFeatureCount(@Query() featureCountRequest: FeatureCountRequest) {
     this.logger.debug(
@@ -56,14 +53,12 @@ export class FeaturesController {
    * @returns Return 'HttpStatus.OK' and the feature(s) if search was successful
    * or if search data was not found or in case of error throw exception
    */
-  @Validations(Role.ReadOnly)
   @Get(':featureid')
   getFeature(@Param('featureid') featureid: string) {
     this.logger.debug(`Get feature by featureId: ${featureid}`)
     return this.featuresService.findById(featureid)
   }
 
-  @Public()
   @Get('check/:featureid')
   checkFeature(@Param('featureid') featureid: string) {
     return this.featuresService.checkFeature(featureid)
@@ -74,7 +69,6 @@ export class FeaturesController {
    * @returns Return 'HttpStatus.OK' and array of features if search was successful
    * or if search data was not found or in case of error throw exception
    */
-  @Validations(Role.ReadOnly)
   @Get()
   getAll() {
     this.logger.debug('Get all features')

packages/apollo-collaboration-server/src/health/health.controller.ts

@@ -1,13 +1,14 @@
 import { Controller, Get } from '@nestjs/common'
 import { HealthCheck, HealthCheckService } from '@nestjs/terminus'
 
-import { Public } from '../utils/jwt-auth.guard'
+import { Validations } from '../utils/validation/validatation.decorator'
+import { Role } from '../utils/role/role.enum'
 
 @Controller('health')
 export class HealthController {
   constructor(private health: HealthCheckService) {}
 
-  @Public()
+  @Validations(Role.None)
   @Get()
   @HealthCheck()
   check() {

packages/apollo-collaboration-server/src/jbrowse/dto/create-track.dto.ts

@@ -0,0 +1,5 @@
+export class CreateTrackDto {
+  readonly type: string
+  readonly trackId: string
+  readonly config: string[]
+}

packages/apollo-collaboration-server/src/jbrowse/jbrowse.controller.spec.ts

@@ -0,0 +1,19 @@
+import { Test, TestingModule } from '@nestjs/testing'
+
+import { JBrowseController } from './jbrowse.controller'
+
+describe('JBrowseController', () => {
+  let controller: JBrowseController
+
+  beforeEach(async () => {
+    const module: TestingModule = await Test.createTestingModule({
+      controllers: [JBrowseController],
+    }).compile()
+
+    controller = module.get<JBrowseController>(JBrowseController)
+  })
+
+  it('should be defined', () => {
+    expect(controller).toBeDefined()
+  })
+})