refactor(*): remove most pubsweet dependencies

.gitignore

@@ -64,8 +64,6 @@ temp/
 # Container data
 data/
 minio/
-
-# Pubsweet
 uploads/
 
 # IDE

.npmignore

@@ -64,8 +64,6 @@ temp/
 # Container data
 data/
 minio/
-
-# Pubsweet
 uploads/
 
 # IDE

Dockerfile

 FROM node:20
 
-RUN apt-get update \ 
-    && apt-get upgrade -y \
-    && apt-get install -y ranger vim
+RUN apt-get update && \ 
+    apt-get install -y ranger vim
 
 WORKDIR /home/node/app
 

dev/config/components.js

 module.exports = [
+  './src/models/__tests__/helpers/fake',
+  './src/models/activityLog',
+  './src/models/chatMessage',
+  './src/models/chatThread',
+  './src/models/file',
+  './src/models/identity',
+  './src/models/serviceCredential',
   './src/models/team',
   './src/models/teamMember',
   './src/models/user',
-  './src/models/identity',
-  './src/models/activityLog',
 ]

dev/scripts/setupDevServer.sh

@@ -3,7 +3,8 @@ set -x
 export NODE_CONFIG_DIR='./dev/config'
 
 # This is run through docker. Its CWD will be the root folder.
-node_modules/.bin/pubsweet migrate
+chmod +x src/cli/coko-server.js
+src/cli/coko-server.js migrate
 node ./dev/scripts/seedGlobalTeams.js
 node ./dev/scripts/ensureTempFolderExists.js
 node ./dev/scripts/seedAdmin.js

jest.config.js

 module.exports = {
   collectCoverage: false,
-  // collectCoverageFrom: [
-  //   '<rootDir>/src/models/**/*.model.js',
-  //   '<rootDir>/src/models/**/*.controller.js',
-  //   '<rootDir>/src/models/useTransaction.js',
-  //   '!<rootDir>/src/models/__tests__/helpers/**',
-  // ],
-  // coverageDirectory: '<rootDir>/coverage',
-  projects: [
-    {
-      displayName: 'models',
-      testEnvironment: 'node',
-      testRegex: 'src/models/__tests__/.+model.test.js$',
-      globalSetup: '<rootDir>/src/models/__tests__/_setup.js',
-      // globalTeardown: '<rootDir>/src/models/__tests__/_teardown.js',
-    },
-    {
-      displayName: 'controllers',
-      testEnvironment: 'node',
-      testRegex: 'src/models/__tests__/.+controller.test.js$',
-      globalSetup: '<rootDir>/src/models/__tests__/_setup.js',
-      // globalTeardown: '<rootDir>/src/models/__tests__/_teardown.js',
-    },
-    {
-      displayName: 'api',
-      testEnvironment: 'node',
-      testRegex: 'src/models/__tests__/.+api.test.js$',
-      globalSetup: '<rootDir>/src/models/__tests__/_setup.js',
-      // globalTeardown: '<rootDir>/src/models/__tests__/_teardown.js',
-    },
-    {
-      displayName: 'services',
-      testEnvironment: 'node',
-      testRegex: 'src/services/__tests__/.+service.test.js$',
-      // globalSetup: '<rootDir>/src/models/__tests__/_setup.js',
-      // globalTeardown: '<rootDir>/src/models/__tests__/_teardown.js',
-    },
-    {
-      displayName: 'utils',
-      testEnvironment: 'node',
-      testRegex: 'src/utils/__tests__/.+test.js$',
-      // globalSetup: '<rootDir>/src/models/__tests__/_setup.js',
-      // globalTeardown: '<rootDir>/src/models/__tests__/_teardown.js',
-    },
-    {
-      displayName: 'app',
-      testEnvironment: 'node',
-      testRegex: 'src/__tests__/.*\\.test\\.js$',
-      globalSetup: '<rootDir>/src/models/__tests__/_setup.js',
-      // globalTeardown: '<rootDir>/src/models/__tests__/_teardown.js',
-    },
-  ],
   maxWorkers: 1,
+  globalSetup: '<rootDir>/src/models/__tests__/_setup.js',
+  testEnvironment: 'node',
+  testRegex: '(/src/.*\\.test\\.js$|/__tests__/.*\\.test\\.js$)',
 }

package.json

@@ -12,6 +12,10 @@
   "license": "MIT",
   "author": "Yannis Barlas",
   "main": "src/index.js",
+  "bin": {
+    "coko-server": "./cli/coko-server.js",
+    "cs": "./cli/coko-server.js"
+  },
   "scripts": {
     "cz": "git-cz",
     "prepare": "husky install",
@@ -32,11 +36,7 @@
     "pg": "^8.7.3"
   },
   "dependencies": {
-    "@pubsweet/base-model": "^4.0.10",
-    "@pubsweet/component-send-email": "^0.4.13",
-    "@pubsweet/db-manager": "^3.1.21",
-    "@pubsweet/errors": "^2.0.46",
-    "@pubsweet/logger": "^0.2.56",
+    "@hapi/joi": "^14.3.0",
     "@pubsweet/models": "^0.3.21",
     "apollo-server-express": "^2.11.0",
     "aws-sdk": "^2.1046.0",
@@ -45,6 +45,7 @@
     "bcrypt": "5.1.1",
     "body-parser": "^1.19.0",
     "command-exists": "^1.2.9",
+    "commander": "^2.20.0",
     "config": "^3.3.2",
     "cookie-parser": "^1.4.5",
     "cors": "^2.8.5",
@@ -62,12 +63,14 @@
     "http-status-codes": "^1.4.0",
     "image-size": "^1.0.2",
     "jsonwebtoken": "^8.4.0",
+    "knex": "^0.21.1",
     "lodash": "^4.17.20",
     "mime-types": "^2.1.34",
     "moment": "^2.29.1",
     "morgan": "^1.10.0",
     "multer": "^1.1.0",
     "node-cron": "^2.0.3",
+    "nodemailer": "^6.4.18",
     "objection": "^2.2.15",
     "passport": "^0.4.1",
     "passport-anonymous": "^1.0.1",
@@ -75,9 +78,10 @@
     "passport-local": "^1.0.0",
     "pg": "^8.7.3",
     "pg-boss": "^5.2.0",
-    "pubsweet": "^5.1.25",
     "sharp": "^0.29.3",
     "subscriptions-transport-ws": "^0.9.19",
+    "tmp-promise": "^2.0.0",
+    "umzug": "^2.1.0",
     "uuid": "^8.3.2",
     "waait": "^1.0.5"
   },
@@ -85,10 +89,12 @@
     "@coko/lint": "^2.0.0",
     "faker": "^5.5.3",
     "jest": "^26.6.3",
+    "jest-environment-node": "^26.6.2",
     "node-wait-for-it": "^0.2.0",
     "nodemon": "^3.0.1",
     "standard-version": "^7.1.0",
-    "supertest": "^3.1.0"
+    "supertest": "^3.1.0",
+    "winston": "^2.3.1"
   },
   "publishConfig": {
     "access": "public"

src/__tests__/apiFileUpload.test.js

 const fs = require('fs')
 const path = require('path')
-const { migrate } = require('@pubsweet/db-manager')
+const migrate = require('../dbManager/migrate')
 const { User } = require('../models')
 
 const api = require('./helpers/api')

src/__tests__/apiLocals.test.js

 const api = require('../app')(require('express')())
 
+const db = require('../dbManager/db')
 const clearDb = require('../models/__tests__/_clearDb')
 const { User } = require('../models')
 
@@ -16,6 +17,10 @@ describe('api/app locals', () => {
     return User.insert(userData)
   })
 
+  afterAll(() => {
+    db.destroy()
+  })
+
   it('exposes models', async () => {
     const userInstance = new api.locals.models.User()
     expect(userInstance.type).toEqual('user')

src/__tests__/graphql/authentication.test.js

@@ -7,6 +7,7 @@ const clearDb = require('../../models/__tests__/_clearDb')
 const api = require('../helpers/api')
 const authentication = require('../../authentication')
 const { User } = require('../../models')
+const db = require('../../dbManager/db')
 
 describe('GraphQL authentication', () => {
   let token
@@ -23,6 +24,10 @@ describe('GraphQL authentication', () => {
     token = authentication.token.create(user)
   })
 
+  afterAll(() => {
+    db.destroy()
+  })
+
   describe('loginUser mutation', () => {
     it('can log in', async () => {
       const { body } = await api.graphql.query(

src/__tests__/graphql/errors.test.js

 const { User } = require('@pubsweet/models')
-const errors = require('@pubsweet/errors')
+const errors = require('../../errors')
 const api = require('../helpers/api')
 const authentication = require('../../authentication')
 const clearDb = require('../../models/__tests__/_clearDb')
+const db = require('../../dbManager/db')
 
 /* eslint-disable-next-line jest/no-disabled-tests */
 describe.skip('GraphQL errors', () => {
@@ -20,6 +21,10 @@ describe.skip('GraphQL errors', () => {
     token = authentication.token.create(user)
   })
 
+  afterAll(() => {
+    db.destroy()
+  })
+
   it('should pass GraphQLError to clients', async () => {
     const { body } = await api.graphql.query(
       `mutation($input: UserInput) {

src/__tests__/graphql/mutations.test.js

@@ -4,6 +4,7 @@ const api = require('../helpers/api')
 const authentication = require('../../authentication')
 const { User } = require('../../models')
 const clearDb = require('../../models/__tests__/_clearDb')
+const db = require('../../dbManager/db')
 
 describe('GraphQL core mutations', () => {
   let token
@@ -20,6 +21,10 @@ describe('GraphQL core mutations', () => {
     token = authentication.token.create(user)
   })
 
+  afterAll(() => {
+    db.destroy()
+  })
+
   describe('mutations', () => {
     // it.skip('can create a user', async () => {
     //   const { body } = await api.graphql.query(

src/__tests__/graphql/queries.test.js

@@ -2,6 +2,7 @@ const { Team, TeamMember, User } = require('../../models')
 const clearDb = require('../../models/__tests__/_clearDb')
 const api = require('../helpers/api')
 const authentication = require('../../authentication')
+const db = require('../../dbManager/db')
 
 describe('GraphQL core queries', () => {
   let token
@@ -18,6 +19,10 @@ describe('GraphQL core queries', () => {
     token = authentication.token.create(user)
   })
 
+  afterAll(() => {
+    db.destroy()
+  })
+
   it('can resolve all users', async () => {
     const { body } = await api.graphql.query(
       `{ users { result { username } } }`,

src/__tests__/graphql/subscriptions.bak.js

+/* eslint-disable jest/no-commented-out-tests */
+
+// const { User } = require('@pubsweet/models')
+// const { fixtures } = require('@pubsweet/model-user/test')
+
+// const WebSocket = require('ws')
+
+// const {
+//   ApolloClient,
+//   createHttpLink,
+//   gql,
+//   InMemoryCache,
+//   split,
+// } = require('@apollo/client')
+
+// const { WebSocketLink } = require('@apollo/client/link/ws')
+// const { getMainDefinition } = require('@apollo/client/utilities')
+
+// const FormData = require('form-data')
+// const fetch = require('node-fetch')
+// const wait = require('waait')
+// const { startServer } = require('../../src')
+// const authentication = require('../../src/authentication')
+// const cleanDB = require('../helpers/db_cleaner')
+
+// function generateFetchOptions(token, fileSize) {
+//   // This dance needs to happen because apollo-upload-client is 'untestable':
+//   // https://github.com/jaydenseric/apollo-upload-client/issues/32#issuecomment-327694315
+
+//   let variables
+//   let size
+//   let query
+
+//   if (fileSize) {
+//     variables = {
+//       file: null,
+//       fileSize,
+//     }
+//     query =
+//       'mutation uploadFile($file: Upload!, $fileSize: Int) { upload(file: $file, fileSize: $fileSize) { url, __typename }}'
+//     size = fileSize
+//   } else {
+//     variables = {
+//       file: null,
+//     }
+//     query =
+//       'mutation uploadFile($file: Upload!) { upload(file: $file) { url, __typename }}'
+//     size = 1000000
+//   }
+
+//   const body = new FormData()
+//   body.append(
+//     'operations',
+//     JSON.stringify({
+//       operationName: 'uploadFile',
+//       variables,
+//       query,
+//     }),
+//   )
+
+//   body.append('map', JSON.stringify({ 1: ['variables.file'] }))
+//   body.append('1', 'a'.repeat(size), { filename: 'a.txt' })
+
+//   const options = {
+//     method: 'POST',
+//     body,
+//     headers: {
+//       Authorization: `Bearer ${token}`,
+//     },
+//   }
+
+//   return options
+// }
+
+// describe('GraphQL subscriptions', () => {
+//   let token
+//   let user
+//   let server
+//   let apolloClient
+//   let wsLink
+
+//   beforeAll(async () => {
+//     server = await startServer()
+//   })
+//   beforeEach(async () => {
+//     await cleanDB()
+//     user = await new User(fixtures.user).save()
+//     token = authentication.token.create(user)
+//     wsLink = new WebSocketLink({
+//       uri: `ws://localhost:4000/subscriptions`,
+//       options: {
+//         connectionParams: {
+//           authToken: token,
+//         },
+//       },
+//       reconnect: false,
+//       webSocketImpl: WebSocket,
+//     })
+//     const httpLink = createHttpLink({ fetch })
+
+//     const link = split(
+//       ({ query }) => {
+//         const { kind, operation } = getMainDefinition(query)
+//         return kind === 'OperationDefinition' && operation === 'subscription'
+//       },
+//       wsLink,
+//       httpLink,
+//     )
+
+//     const config = {
+//       link,
+//       cache: new InMemoryCache(),
+//     }
+
+//     apolloClient = new ApolloClient(config)
+//   })
+
+//   afterEach(async () => {
+//     await wsLink.subscriptionClient.client.close()
+//   })
+
+//   afterAll(done => server.close(done))
+
+//   it('reports progress when fileSize is given', async () => {
+//     let done
+//     let progress = 0
+
+//     const subscriptionPromise = new Promise((resolve, reject) => {
+//       apolloClient
+//         .subscribe({
+//           query: gql`
+//             subscription onUploadProgress {
+//               uploadProgress
+//             }
+//           `,
+//         })
+//         .subscribe({
+//           next: async res => {
+//             expect(res.data.uploadProgress).toBeGreaterThanOrEqual(progress)
+//             progress = res.data.uploadProgress
+//             expect(progress).toBeGreaterThan(-1)
+//             expect(progress).toBeLessThanOrEqual(100)
+//             // sometimes the last notification is sent slightly before
+//             // fetch completes, resulting in an unresolved promise, so
+//             // we just wait a tiny bit.
+//             await wait(100)
+//             if (done) resolve('done')
+//           },
+//           error: reject,
+//         })
+//     })
+
+//     await fetch(
+//       `http://localhost:4000/graphql`,
+//       generateFetchOptions(token, 1000000),
+//     )
+//     done = true
+//     expect(await subscriptionPromise).toBe('done')
+//   })
+
+//   it('reports progress when fileSize is not given', async () => {
+//     let done
+//     let progress = 0
+
+//     const subscriptionPromise = new Promise((resolve, reject) => {
+//       apolloClient
+//         .subscribe({
+//           query: gql`
+//             subscription onUploadProgress {
+//               uploadProgress
+//             }
+//           `,
+//         })
+//         .subscribe({
+//           next: async res => {
+//             expect(res.data.uploadProgress).toBeGreaterThanOrEqual(progress)
+//             progress = res.data.uploadProgress
+//             expect(progress).toBeGreaterThan(-1)
+//             expect(progress).toBeLessThanOrEqual(1000000)
+//             // sometimes the last notification is sent slightly before
+//             // fetch completes, resulting in an unresolved promise, so
+//             // we just wait a tiny bit.
+//             await wait(100)
+//             if (done) resolve('done')
+//           },
+//           error: reject,
+//         })
+//     })
+
+//     await fetch(`http://localhost:4000/graphql`, generateFetchOptions(token))
+//     done = true
+//     expect(await subscriptionPromise).toBe('done')
+//   })
+// })

src/__tests__/graphql/upload.test.js

@@ -2,6 +2,7 @@ const api = require('../helpers/api')
 const authentication = require('../../authentication')
 const clearDb = require('../../models/__tests__/_clearDb')
 const { User } = require('../../models')
+const db = require('../../dbManager/db')
 
 describe('GraphQL uploads', () => {
   let token
@@ -18,6 +19,10 @@ describe('GraphQL uploads', () => {
     token = authentication.token.create(user)
   })
 
+  afterAll(() => {
+    db.destroy()
+  })
+
   it('can upload a file', async () => {
     const { body } = await api.request
       .post('/graphql')

src/__tests__/helpers/customApp.js

 /* eslint-disable no-param-reassign */
 
 const configureApp = app => {
-  // console.log('og', app)
-
   app.get('/verify', (req, res) => res.send('hi'))
 
   // Actions to perform when the HTTP server starts listening

src/__tests__/job.test.js

@@ -2,6 +2,7 @@
 
 const { boss, subscribeJobsToQueue } = require('../jobs')
 const { jobs } = require('../services')
+const db = require('../dbManager/db')
 // const { renewAuthTokens } = require('../utils/tokens')
 
 const freezeTime = 1701856542000
@@ -86,6 +87,10 @@ describe.skip('jobs service', () => {
     await subscribeJobsToQueue()
   })
 
+  afterAll(() => {
+    db.destroy()
+  })
+
   it('registers jobs', async () => {
     expect(Object.keys(boss.subscriptions)).toEqual([
       jobs.REFRESH_TOKEN_EXPIRED,

src/__tests__/pubsweetJobs/jobs.test.js

 /* eslint-disable jest/no-disabled-tests, jest/no-done-callback */
 
 const { startJobQueue } = require('../../jobs')
+const db = require('../../dbManager/db')
 
 const someHandler = async job => {
   expect(job.data.param).toEqual('aThing')
@@ -14,6 +15,10 @@ describe.skip('jobs', () => {
     jobQueue = await startJobQueue()
   })
 
+  afterAll(() => {
+    db.destroy()
+  })
+
   it('submits a job, runs it, and notifies on completion', async done => {
     const queueName = 'aJobQueue'
 

src/__tests__/pubsweetJobs/jobsDifferentProcess.test.js

@@ -3,6 +3,7 @@
 const path = require('path')
 const { spawn } = require('child_process')
 const { startJobQueue } = require('../../jobs')
+const db = require('../../dbManager/db')
 
 describe('job runner in a different process', () => {
   let jobQueue
@@ -11,6 +12,10 @@ describe('job runner in a different process', () => {
     jobQueue = await startJobQueue()
   })
 
+  afterAll(() => {
+    db.destroy()
+  })
+
   it('submits a job and gets notified on completion', async done => {
     const queueName = 'aJobQueue2'
 

src/__tests__/pubsweetJobs/jobsIntegration.test.js

 /* eslint-disable jest/no-disabled-tests, jest/no-done-callback */
 
 const startServer = require('../../startServer')
-
+const db = require('../../dbManager/db')
 const { connectToJobQueue } = require('../../jobs')
 
 const someHandler = async job => {
@@ -16,6 +16,10 @@ describe.skip('integrated job queue', () => {
     server = await startServer()
   })
 
+  afterAll(() => {
+    db.destroy()
+  })
+
   // This is to verify that pg-boss has been setup with pg-boss.start()
   // in the process of starting pubsweet-server
   it('ready to connect and process jobs when server starts', async done => {