Merge branch 'shared-data-model' of...

Merge branch 'shared-data-model' of https://gitlab.coko.foundation/xpub/xpub-epmc.git into shared-data-model

app/component-pdf-viewer/client/index.js

+export { default } from './components'

app/component-pdf-viewer/index.js

+export { default } from './client'

app/component-pdf-viewer/package.json

+{
+  "name": "component-pdf-viewer",
+  "version": "0.0.1",
+  "description": "A component for viewing and highlighting PDFs",
+  "license": "MIT",
+  "author": "EBI",
+  "repository": {
+    "type": "git",
+    "url": "https://gitlab.coko.foundation/xpub/xpub-epmc",
+    "path": "/app/component-pdf-viewer"
+  },
+  "dependencies": {
+    "@pubsweet/ui": "9.0.0",
+    "@pubsweet/ui-toolkit": "2.0.0",
+    "styled-components": "^4.1.3",
+    "pdfjs-dist": "^2.0.489",
+    "react": "^16.2.0"
+  }
+}

app/components/ManuscriptPreview.jsx

 import React from 'react'
 import SimpleEditor from 'wax-editor-react'
-import PDFViewer from './pdf-viewer'
+import PDFViewer from '../component-pdf-viewer'
 import { A } from './ui'
 
 class ManuscriptPreview extends React.Component {

app/components/activity/EventDescription.jsx

@@ -86,7 +86,7 @@ const toggleHidden = button => {
   button.parentNode.nextElementSibling.classList.toggle('hidden')
 }
 
-const cleanUp = column => column.replace('meta,', '').replace('_', ' ')
+const cleanUp = column => column.replace('meta,', '').replace(/_/g, ' ')
 const isJson = str => {
   try {
     JSON.parse(str)

app/components/dashboard/DashboardPage.jsx

@@ -2,7 +2,7 @@ import React from 'react'
 import { Query, compose, graphql } from 'react-apollo'
 import styled from 'styled-components'
 import { H4, Link } from '@pubsweet/ui'
-import { pageSize } from 'config'
+import { pageSize, states } from 'config'
 import { Loading, LoadingIcon, Notification, Toggle, Pagination } from '../ui'
 import {
   ALL_MANUSCRIPTS,
@@ -117,15 +117,13 @@ const MyManuscripts = ({ currentUser, errors, history }) => {
             </Loading>
           )
         }
-
         // get the total number of manuscripts to decide whether the toggles are required
         const { countByStatus } = data
-        let totalTount = 0
-        countByStatus.forEach(status => {
-          totalTount += status.count
-        })
-        const togglesRequired = totalTount > pageSize
-
+        const totalCount = countByStatus.reduce(
+          (sum, status) => sum + parseInt(status.count, 10),
+          0,
+        )
+        const togglesRequired = totalCount > pageSize
         // determine the query and variables used to get manuscripts
         const query = togglesRequired ? MANUSCRIPTS_BY_STATUS : ALL_MANUSCRIPTS
         const params = new URLSearchParams(history.location.search)
@@ -133,17 +131,17 @@ const MyManuscripts = ({ currentUser, errors, history }) => {
         const completed = params.get('completed')
 
         const variables = {}
+        const done = states.indexOf('xml-complete')
         if (togglesRequired) {
           if (completed) {
-            variables.query = `xml-complete,ncbi-ready,published`
+            variables.query = states.slice(done).join(',')
             variables.page = params.get('page') ? params.get('page') - 1 : 0
             variables.pageSize = pageSize
           } else {
-            variables.query = `INITIAL,READY,submission-error,in-review,submitted,tagging,xml-qa,xml-triage,xml-review,being-withdrawn`
+            variables.query = states.slice(0, done).join(',')
             variables.page = -1
           }
         }
-
         return (
           <Query
             fetchPolicy="cache-and-network"
@@ -158,7 +156,6 @@ const MyManuscripts = ({ currentUser, errors, history }) => {
                   </Loading>
                 )
               }
-
               const { total, manuscripts } = togglesRequired
                 ? data.findByStatus
                 : data
@@ -211,30 +208,41 @@ const MyManuscripts = ({ currentUser, errors, history }) => {
               }
 
               const attention = []
-              const review = []
+              const warning = []
+              const processing = []
               const complete = []
-              const other = []
+              const highlight = [
+                'INITIAL',
+                'READY',
+                'submission-error',
+                'in-review',
+                'xml-review',
+              ]
               manuscripts.forEach(m => {
                 const reviewer = m.teams.find(t => t.role === 'reviewer')
                 const submitter = m.teams.find(t => t.role === 'submitter')
-                if (
-                  reviewer &&
-                  reviewer.teamMembers[0].user.id === currentUser.id &&
-                  ['in-review', 'xml-review'].includes(m.status)
-                ) {
-                  review.push(m)
-                } else if (
-                  submitter.teamMembers[0].user.id === currentUser.id &&
-                  ['INITIAL', 'READY', 'submission-error'].includes(m.status)
-                ) {
-                  attention.push(m)
+                if (highlight.includes(m.status)) {
+                  if (
+                    reviewer &&
+                    reviewer.teamMembers[0].user.id === currentUser.id &&
+                    highlight.slice(-2).includes(m.status)
+                  ) {
+                    attention.push(m)
+                  } else if (
+                    submitter.teamMembers[0].user.id === currentUser.id &&
+                    highlight.slice(0, 3).includes(m.status)
+                  ) {
+                    attention.push(m)
+                  } else {
+                    warning.push(m)
+                  }
                 } else if (
                   !togglesRequired &&
-                  ['xml-complete', 'ncbi-ready', 'published'].includes(m.status)
+                  states.slice(done).includes(m.status)
                 ) {
                   complete.push(m)
                 } else {
-                  other.push(m)
+                  processing.push(m)
                 }
               })
               return (
@@ -256,25 +264,30 @@ const MyManuscripts = ({ currentUser, errors, history }) => {
                   ))}
                   {attention.length > 0 && (
                     <React.Fragment>
-                      <H4>Needs attention ({attention.length})</H4>
+                      <H4>Needs your attention ({attention.length})</H4>
                       <DashboardList
+                        currentUser={currentUser}
                         listData={attention}
-                        sectionRole="submitter"
                       />
                     </React.Fragment>
                   )}
-                  {review.length > 0 && (
+                  {warning.length > 0 && (
                     <React.Fragment>
-                      <H4>Waiting for author review ({review.length})</H4>
-                      <DashboardList listData={review} sectionRole="reviewer" />
+                      <H4>
+                        Waiting for action by another user ({warning.length})
+                      </H4>
+                      <DashboardList
+                        currentUser={currentUser}
+                        listData={warning}
+                      />
                     </React.Fragment>
                   )}
-                  {other.length > 0 && (
+                  {processing.length > 0 && (
                     <React.Fragment>
-                      <H4>In process at Europe PMC ({other.length})</H4>
+                      <H4>In process at Europe PMC ({processing.length})</H4>
                       <DashboardList
                         currentUser={currentUser}
-                        listData={other}
+                        listData={processing}
                       />
                     </React.Fragment>
                   )}

app/components/dashboard/index.js

@@ -5,7 +5,7 @@ const submitterState = {
     url: 'create',
   },
   READY: {
-    status: 'Not yet submitted',
+    status: 'Incomplete',
     color: 'error',
     url: 'submit',
   },
@@ -15,12 +15,12 @@ const submitterState = {
     url: 'submit',
   },
   'in-review': {
-    status: 'Submitted',
-    color: 'normal',
+    status: 'Initial review',
+    color: 'warning',
     url: 'submit',
   },
   submitted: {
-    status: 'Submitted',
+    status: 'Europe PMC QA',
     color: 'normal',
     url: 'submit',
   },
@@ -35,8 +35,8 @@ const submitterState = {
     url: 'submit',
   },
   'xml-review': {
-    status: 'Processing',
-    color: 'normal',
+    status: 'Final proof',
+    color: 'warning',
     url: 'submit',
   },
   'xml-triage': {
@@ -45,17 +45,17 @@ const submitterState = {
     url: 'submit',
   },
   'xml-complete': {
-    status: 'Approved for archive',
+    status: 'Approved for Europe PMC',
     color: 'success',
     url: 'submit',
   },
   'ncbi-ready': {
-    status: 'Approved for archive',
+    status: 'Approved for Europe PMC',
     color: 'success',
     url: 'submit',
   },
   published: {
-    status: 'Available in archive',
+    status: 'Available in Europe PMC',
     color: 'success',
     url: 'submit',
   },
@@ -68,13 +68,13 @@ const submitterState = {
 
 const reviewerState = {
   INITIAL: {
-    status: 'With submitter',
-    color: 'normal',
+    status: 'Incomplete',
+    color: 'warning',
     url: 'submit',
   },
   READY: {
-    status: 'With submitter',
-    color: 'normal',
+    status: 'Incomplete',
+    color: 'warning',
     url: 'submit',
   },
   'submission-error': {
@@ -83,12 +83,12 @@ const reviewerState = {
     url: 'submit',
   },
   'in-review': {
-    status: 'Needs review',
+    status: 'Initial review',
     color: 'error',
     url: 'submit',
   },
   submitted: {
-    status: 'Submitted',
+    status: 'Europe PMC QA',
     color: 'normal',
     url: 'submit',
   },
@@ -103,27 +103,27 @@ const reviewerState = {
     url: 'submit',
   },
   'xml-review': {
-    status: 'Needs final review',
+    status: 'Final proof',
     color: 'error',
     url: 'review',
   },
   'xml-triage': {
     status: 'Processing',
-    color: 'warning',
+    color: 'normal',
     url: 'submit',
   },
   'xml-complete': {
-    status: 'Approved for archive',
+    status: 'Approved for Europe PMC',
     color: 'success',
     url: 'submit',
   },
   'ncbi-ready': {
-    status: 'Approved for archive',
+    status: 'Approved for Europe PMC',
     color: 'success',
     url: 'submit',
   },
   published: {
-    status: 'Available in archive',
+    status: 'Available in Europe PMC',
     color: 'success',
     url: 'submit',
   },
@@ -136,12 +136,12 @@ const reviewerState = {
 
 const adminState = {
   INITIAL: {
-    status: 'Not yet submitted',
+    status: 'Incomplete',
     color: 'normal',
     url: 'create',
   },
   READY: {
-    status: 'Not yet submitted',
+    status: 'Incomplete',
     color: 'normal',
     url: 'submit',
   },
@@ -151,7 +151,7 @@ const adminState = {
     url: 'submit',
   },
   'in-review': {
-    status: 'Needs review',
+    status: 'Initial review',
     color: 'normal',
     url: 'submit',
   },
@@ -171,7 +171,7 @@ const adminState = {
     url: 'review',
   },
   'xml-review': {
-    status: 'Final review',
+    status: 'Final proof',
     color: 'normal',
     url: 'review',
   },
@@ -186,12 +186,12 @@ const adminState = {
     url: 'activity',
   },
   'ncbi-ready': {
-    status: 'Approved for archive',
+    status: 'Approved for Europe PMC',
     color: 'success',
     url: 'activity',
   },
   published: {
-    status: 'Available in archive',
+    status: 'Available in Europe PMC',
     color: 'success',
     url: 'activity',
   },

app/components/preview-files/FileLightbox.jsx

@@ -3,7 +3,7 @@ import ReactDOM from 'react-dom'
 import styled from 'styled-components'
 import { Action } from '@pubsweet/ui'
 import { th } from '@pubsweet/ui-toolkit'
-import PDFViewer from '../pdf-viewer'
+import PDFViewer from '../../component-pdf-viewer'
 import { A, Page, Center, Cover, Close, CloseButton } from '../ui'
 import { ImageTypes } from './'
 

app/components/review-wizard/Review.jsx

@@ -19,7 +19,7 @@ import UploadFiles, {
   AllTypes,
 } from '../upload-files'
 import ManuscriptPreview from '../ManuscriptPreview'
-import PDFViewer from '../pdf-viewer'
+import PDFViewer from '../../component-pdf-viewer'
 import { GET_MANUSCRIPT } from '../operations'
 import HTMLPreview from './HTMLPreview'
 import ReviewForm from './ReviewForm'

app/components/upload-files/uploadtypes.js

@@ -24,6 +24,8 @@ export const FileTypes = [
   'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet',
   'application/xml',
   'application/gzip',
+  'application/x-gzip',
+  'application/x-gzip-compressed',
   'text/xml',
 
   'audio/midi',

config/components.json

@@ -11,7 +11,6 @@
   "./node_modules/@pubsweet/job-xsweet",
   "./server/minio-server",
   "./server/grist",
-  "./server/ftp-integration",
   "./server/eutils",
   "./server/email",
   "./server/xml-validation",

runShellScript.sh

@@ -4,11 +4,13 @@ cmd=$1
 
 echo "runShellScript.sh $cmd"
 
-# Start the first process
-ps aux | grep "$cmd" | grep -q -v grep
-PROCESS_1_STATUS=$?
-echo "PROCESS_1_STATUS: $PROCESS_1_STATUS"
-if [ $PROCESS_1_STATUS -ne 0 ]; then
+# Start the process
+PROCESS_RESULT=`ps aux | grep "$cmd" | grep -v "runShellScript.sh" | grep -v grep`
+
+echo "$PROCESS_RESULT"
+
+if [ -z "$PROCESS_RESULT" ]
+then
     echo "Executing: $cmd"
     $cmd
     status=$?
@@ -21,30 +23,3 @@ else
     echo "Process $cmd already running"
     exit 1
 fi
-
-# Start the second process
-#./my_second_process -D
-#status=$?
-#if [ $status -ne 0 ]; then
-#  echo "Failed to start my_second_process: $status"
-#  exit $status
-#fi
-
-# Naive check runs checks once a minute to see if either of the processes exited.
-# This illustrates part of the heavy lifting you need to do if you want to run
-# more than one service in a container. The container exits with an error
-# if it detects that either of the processes has exited.
-# Otherwise it loops forever, waking up every 60 seconds
-while sleep 60; do
-  ps aux |grep "$cmd" |grep -q -v grep
-  PROCESS_1_STATUS=$?
-#  ps aux |grep my_second_process |grep -q -v grep
-#  PROCESS_2_STATUS=$?
-  # If the greps above find anything, they exit with 0 status
-  # If they are not both 0, then something is wrong
-  if [ $PROCESS_1_STATUS -ne 0 ]; then
-#  if [ $PROCESS_1_STATUS -ne 0 -o $PROCESS_2_STATUS -ne 0 ]; then
-    echo "One of the processes has already exited."
-    exit 1
-  fi
-done
\ No newline at end of file

server/email/index.js

 const config = require('config')
 const Email = require('@pubsweet/component-send-email')
+const lodash = require('lodash')
 const logger = require('@pubsweet/logger')
 const {
   htmlEmailBase,
@@ -19,6 +20,8 @@ const {
 const tagger = config.ftp_tagger.email
 const { sender, url, testAddress, system, dev } = config['epmc-email']
 
+const parsed = string => lodash.unescape(string)
+
 const sendMail = (to, subject, message, from = null, cc = null, bcc = null) => {
   const mailData = {
     from: from || sender,
@@ -54,13 +57,13 @@ const taggerErrorEmail = (subject, message) => {
 }
 
 const taggerEmail = (email, manId, title, link) => {
-  const html = newPackageForTaggingTemplate(manId, title, link)
+  const html = newPackageForTaggingTemplate(manId, parsed(title), link)
   const subject = 'New Package Available for Tagging'
   sendMail(email, subject, html, null, null, system)
 }
 
 const processedTaggerEmail = (email, manId, title, packageName) => {
-  const html = processedTaggingFilesTemplate(manId, title, packageName)
+  const html = processedTaggingFilesTemplate(manId, parsed(title), packageName)
   const subject = 'Tagging files have been uploaded'
   sendMail(email, subject, html, null, null, system)
 }
@@ -88,15 +91,16 @@ const reviewerEmail = ({ reviewer, manInfo, submitter, token }) => {
   const submitterName = `${title ? `${title} ` : ''}${givenNames} ${surname}`
   const { title: t, givenNames: g, surname: s } = reviewer.name
   const salutation = `${t ? `${t} ` : ''}${g} ${s}`
-  let link = `${url}submission/${manInfo.id}/submit`
+  const link = `${url}submission/${manInfo.id}/submit`
+  const args = [salutation, parsed(manInfo.title), submitterName, link]
   let html = ''
   if (token === 'correction') {
-    html = checkReviewerTemplate(salutation, manInfo.title, submitterName, link)
+    html = checkReviewerTemplate(...args)
   } else if (reviewer.id) {
-    html = setReviewerTemplate(salutation, manInfo.title, submitterName, link)
+    html = setReviewerTemplate(...args)
   } else {
-    link = `${url}dashboard?accept=${token}`
-    html = newReviewerTemplate(salutation, manInfo.title, submitterName, link)
+    args[4] = `${url}dashboard?accept=${token}`
+    html = newReviewerTemplate(...args)
   }
   const subject = `Approve submission of ${manInfo.id}`
   sendMail(reviewer.email, subject, html, null, null, system)
@@ -111,7 +115,7 @@ const submitterRejectEmail = ({ reviewer, manInfo, submitter, message }) => {
   const link = `${url}submission/${manInfo.id}/submit`
   const html = rejectSubmissionTemplate(
     salutation,
-    manInfo.title,
+    parsed(manInfo.title),
     reviewerName,
     message,
     link,
@@ -132,7 +136,7 @@ const removeDuplicateEmail = (user, badInfo, goodInfo) => {
   const html = removeDupeTemplate(
     salutation,
     badInfo.id,
-    badInfo['meta,title'],
+    parsed(badInfo['meta,title']),
     goodInfo.id,
     pmcid,
   )
@@ -153,7 +157,7 @@ const finalReviewEmail = (reviewer, manInfo) => {
         }`
   const html = finalReviewTemplate(
     salutation,
-    manInfo.title,
+    parsed(manInfo.title),
     link,
     releaseDelay,
   )