code from Koosum

server/ftp-integration/taggedXML.js

@@ -7,7 +7,9 @@ const db = require('../utils/db.js')
 const { execSync } = require('child_process')
 const uuidv4 = require('uuid/v4')
 const config = require('config')
-const manuscriptModel = require('../xpub-model/entities/manuscript/data-access')
+const Manuscript = require('../xpub-model/entities/manuscript/data-access')
+// const manuscriptModel = require('../xpub-model/entities/manuscript')
+const Team = require('../xpub-model/entities/team/data-access')
 
 const ftpTagger = config.get('ftp_tagger')
 const {
@@ -16,10 +18,10 @@ const {
   errorDevEmail,
 } = require('../email')
 
+// const parentRootPath = '/home/yogmatee/projects/PLAY/chokidar/ftp_mock'
 const parentRootPath = `${process.env.HOME}/${config.get('ftp_directory')}/${
   ftpTagger.username
 }`
-
 const rootPath = `${parentRootPath}/Done`
 
 const ignoreNewFolder = `${parentRootPath}/New`
@@ -74,7 +76,9 @@ async function processFile(path) {
   try {
     logger.info(`Processing tagged XML packages: ${path}`)
 
-    const user = await getUser.getFTPUser(rootPath, path)
+    const user = await getUser.getFTPUser()
+    const userId = user.id
+
     const tmpPath = await tar.createTempDir()
     const extractedFilePath = await tar.untar(path, tmpPath)
     const manifestFilename = await files.getManifestFilename(extractedFilePath)
@@ -82,7 +86,17 @@ async function processFile(path) {
       extractedFilePath,
       manifestFilename,
     )
-    const filesArr = await files.checkFiles(filesData, tmpPath, user)
+    const filesArr = await files.checkFiles(filesData, tmpPath, userId)
+
+    // create team
+    /* await Team.insert(
+      {
+        manuscriptId,
+        userId,
+        roleName: 'reviewer',
+      },
+      userId,
+    )*/
 
     // delete current existing 'tagging' files
     await db.deleteTaggingFiles(manuscriptId, user)
@@ -90,36 +104,63 @@ async function processFile(path) {
     // upload to minio
     for (let i = 0; i < filesArr.length; i += 1) {
       const uuid = uuidv4()
-      const minioFileName = `${uuid}${filesArr[i].extension}`
+      filesArr[i].minioFileName = `${uuid}${filesArr[i].extension}`
       files.uploadFileToMinio(
-        minioFileName,
+        filesArr[i].minioFileName,
         filesArr[i].filename,
         filesArr[i].url,
         filesArr[i].mimeType,
       )
-      filesArr[i].filename = minioFileName
     }
 
+    const rows = await Manuscript.findByFieldEager(
+      'id',
+      manuscriptId,
+      '[files]',
+    )
+    const manuscript = rows[0]
+
     const dbFilesArr = filesArr.map(obj => {
-      obj.url = `/download/${obj.filename}`
+      obj.url = `/download/${obj.minioFileName}`
       delete obj.extension
+      delete obj.minioFileName
       return obj
     })
 
+    manuscript.files = manuscript.files.concat(dbFilesArr)
+
     // create rows in 'file' table
-    await db.createTaggersFiles(dbFilesArr)
-    await manuscriptModel.updatePdfDepositState(manuscriptId)
+    // await db.createTaggersFiles(dbFilesArr)
+
+    manuscript.pdfDepositState = 'WAITING_FOR_PDF_CONVERSION'
+    //await manuscriptModel.updatePdfDepositState(manuscriptId)
+
+    const manuscriptDb = await new Manuscript(manuscript).saveWithUserAndRole(
+      {
+        relate: true,
+        unrelate: true,
+      },
+      userId,
+      'tagger',
+    )
+
+    /*
+    manuscriptModel.update(
+      { id: manuscriptId, pdfDepositState: 'WAITING_FOR_PDF_CONVERSION' },
+      user.id,
+    )
+*/
     await files.renameFile(path)
 
     logger.info('Uploading to Minio and the database has been completed.')
 
-    const manuscriptObj = await manuscriptModel.getManuscriptById(manuscriptId)
+    //const manuscriptObj = await manuscriptModel.getManuscriptById(manuscriptId)
 
     // send email to taggers
     processedTaggerEmail(
       ftpTagger.email,
       manuscriptId,
-      manuscriptObj[0]['meta,title'],
+      manuscriptDb['meta,title'],
       `${path}`,
     )
     // clean up tmp folder

server/utils/files.js

@@ -64,7 +64,7 @@ module.exports.getManifestFileData = function getManifestFileData(
   })
 }
 
-module.exports.checkFiles = function checkFiles(files, tmpPath, user) {
+module.exports.checkFiles = function checkFiles(files, tmpPath, userId) {
   return new Promise((resolve, reject) => {
     const filesArr = []
     for (let i = 0; i < files.length; i += 1) {
@@ -95,7 +95,7 @@ module.exports.checkFiles = function checkFiles(files, tmpPath, user) {
         size: fileSizeInBytes,
         url: file,
         label: fileLabel,
-        updatedBy: user.userId,
+        updatedBy: userId,
       })
     }
     resolve(filesArr)

server/utils/user.js

@@ -5,27 +5,11 @@ const Identity = rfr('server/xpub-model/entities/identity/data-access')
 const User = rfr('server/xpub-model/entities/user/data-access')
 const ftpUsers = config.get('users')
 
-module.exports.getFTPUser = function getFTPUser(rootPath, filename) {
+module.exports.getFTPUser = function getFTPUser() {
   return new Promise((resolve, reject) => {
-    const userName = 'taggers'
-
-    Identity.findByFieldEager(
-      'meta',
-      `{"ftpUserName": "${userName}"}`,
-      '[user]',
-    )
-      .then(identityDb => {
-        const user = ftpUsers.find(user =>
-          user.identities
-            .filter(identity => identity.meta)
-            .find(identity => identity.meta.ftpUserName === userName),
-        )
-        const identity = user.identities
-          .filter(identity => identity.meta)
-          .find(identity => identity.meta.ftpUserName === userName)
-        /* eslint-disable dot-notation */
-        identity['userId'] = identityDb[0].userId
-        resolve(identity)
+    User.findByEmail('taggers@internal.ebi.ac.uk')
+      .then(user => {
+        resolve(user)
       })
       .catch(error => reject(error))
   })

server/xpub-model/entities/team/data-access.js

@@ -16,8 +16,8 @@ class Team extends EpmcBaseModel {
   // static idColumn = ['article_id', 'member_id'];
 
   static get idColumn() {
-    // return ['manuscript_id', 'user_id', 'role_name']
-    return 'id'
+    return ['manuscript_id', 'user_id', 'role_name']
+    // return 'id'
   }
 
   /*