removed data-access methods to use index.js

server/ftp-integration/taggedXML.js

@@ -7,7 +7,7 @@ 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 manuscriptModel = require('../xpub-model/entities/manuscript')
 
 const ftpTagger = config.get('ftp_tagger')
 const {
@@ -74,7 +74,8 @@ 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.userId
     const tmpPath = await tar.createTempDir()
     const extractedFilePath = await tar.untar(path, tmpPath)
     const manifestFilename = await files.getManifestFilename(extractedFilePath)
@@ -82,10 +83,10 @@ async function processFile(path) {
       extractedFilePath,
       manifestFilename,
     )
-    const filesArr = await files.checkFiles(filesData, tmpPath, user)
+    const filesArr = await files.checkFiles(filesData, tmpPath, userId)
 
     // delete current existing 'tagging' files
-    await db.deleteTaggingFiles(manuscriptId, user)
+    await db.deleteTaggingFiles(manuscriptId, userId)
 
     // upload to minio
     for (let i = 0; i < filesArr.length; i += 1) {
@@ -108,17 +109,22 @@ async function processFile(path) {
 
     // create rows in 'file' table
     await db.createTaggersFiles(dbFilesArr)
+
+    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.findById(manuscriptId, userId)
 
     // send email to taggers
     processedTaggerEmail(
       ftpTagger.email,
       manuscriptId,
-      manuscriptObj[0]['meta,title'],
+      manuscriptObj['meta,title'],
       `${path}`,
     )
     // clean up tmp folder

server/utils/db.js

@@ -60,7 +60,7 @@ module.exports.upsertHtmlPrevFile = async function upsertHtmlPrevFile(
 
 module.exports.deleteTaggingFiles = async function deleteTaggingFiles(
   manuscriptId,
-  user,
+  userId,
 ) {
   const manFiles = await FileModel.selectByManuscriptId(manuscriptId)
   const submissionFilesTypes = ['manuscript', 'figure', 'table', 'supplement']
@@ -69,7 +69,7 @@ module.exports.deleteTaggingFiles = async function deleteTaggingFiles(
   )
   // delete tagging files
   for (let i = 0; i < taggingFiles.length; i += 1) {
-    await FileModel.deleteById(taggingFiles[i].id, user.userId)
+    await FileModel.deleteById(taggingFiles[i].id, userId)
   }
   logger.info(`${taggingFiles.length} files deleted.`)
 }