#652

handle xml parsing on write stream finish

server/ncbi-integration/fromNcbi.js

@@ -12,6 +12,7 @@ const {
 } = require('../xpub-model/entities/manuscript/helpers/transform')
 
 const NCBI_RESPONSE_EXT = new RegExp(/\S+.ld.response.xml$/i)
+let c = new Client()
 
 ;(async () => {
   const beforeUpdate = Date.now()
@@ -23,11 +24,11 @@ function close(c) {
   c.end()
   ManuscriptAccess.knex().destroy()
   c = null
+  logger.info('connection terminated')
   process.exit()
 }
 
 async function fromNcbi() {
-  let c = new Client()
   c.on('ready', () => {
     c.list(
       `/${config.get('ncbi-ftp')['receive-folder']}`,
@@ -50,16 +51,22 @@ async function fromNcbi() {
           c.get(remoteFilePath, (err, stream) => {
             if (err) return
             const path = `${os.tmpdir()}/${file.name}`
-            stream.pipe(fs.createWriteStream(path))
-            processFile(path).then(response => {
-              updateManuscriptNcbiStatus(file.name, response).then(() => {
-                c.rename(remoteFilePath, `${remoteFilePath}.processed`, err => {
-                  if (err) {
-                    logger.info(err)
-                  }
-                  if (index === array.length - 1) {
-                    close(c)
-                  }
+            const writeStream = stream.pipe(fs.createWriteStream(path))
+            writeStream.on('finish', () => {
+              processFile(path).then(response => {
+                updateManuscriptNcbiStatus(file.name, response).then(() => {
+                  c.rename(
+                    remoteFilePath,
+                    `${remoteFilePath}.processed`,
+                    err => {
+                      if (err) {
+                        logger.info(err)
+                      }
+                      if (index === array.length - 1) {
+                        close(c)
+                      }
+                    },
+                  )
                 })
               })
             })
@@ -72,6 +79,17 @@ async function fromNcbi() {
   c.connect({ host, user, password })
 }
 
+process
+  .on('uncaughtException', err => {
+    logger.error('Uncaught Exception thrown: ', err)
+    close(c)
+  })
+  .on('unhandledRejection', (reason, promise) => {
+    logger.error('Unhandled Rejection at Promise: ', promise)
+    logger.error('Reason: ', reason)
+    close(c)
+  })
+
 function processFile(path) {
   return new Promise((resolve, reject) => {
     fs.readFile(path, 'utf8', (err, data) => {
@@ -96,6 +114,9 @@ async function updateManuscriptNcbiStatus(fileName, response) {
   // filename example: ems76395.2019_01_01-08_30_06.ld.response.xml
   const manuscriptId = fileName.split('.')[0].toUpperCase()
   const manuscript = await ManuscriptAccess.selectById(manuscriptId)
+  if (!manuscript) {
+    throw new Error('manuscript not found in db')
+  }
   const newIds = manuscript['meta,articleIds'].filter(
     id => id.pubIdType !== 'pmcid',
   )