#1233 email grant PIs

app/components/activity/GrantsEdit.jsx

@@ -3,10 +3,8 @@ import { Mutation } from 'react-apollo'
 import styled from 'styled-components'
 import { th, darken } from '@pubsweet/ui-toolkit'
 import { Button, H3, Icon, RadioGroup, Action } from '@pubsweet/ui'
-import { states } from 'config'
 import { Buttons } from '../ui'
 import GrantSearch from '../grant-search'
-import { ALERT_PIS } from '../operations'
 import { EXCEPTION_ALERT, QUERY_ACTIVITY_INFO } from './operations'
 import { NoteMutations, WithFunders } from '../SubmissionMutations'
 
@@ -64,8 +62,6 @@ class GrantsEdit extends React.Component {
     const { close, fundingGroup, manuscript } = this.props
     const { notes } = manuscript.meta
     const planS = notes && notes.find(n => n.notesType === 'planS')
-    const noPIEmails =
-      states.indexOf(manuscript.status) < states.indexOf('tagging')
     return (
       <React.Fragment>
         <GrantSearch
@@ -135,85 +131,56 @@ class GrantsEdit extends React.Component {
             },
           ]}
         >
-          {(epmc_emailException, { data: data1 }) => (
-            <Mutation mutation={ALERT_PIS}>
-              {(epmc_emailGrantPis, { data: data2 }) => {
-                const checkException = async () => {
-                  const checkArray = ['newNote', 'deleteNote', 'updateGrants']
-                  await checkArray.reduce(async (promise, func) => {
-                    await promise
-                    const funcVal = this.state[func]
-                    if (funcVal) {
-                      return this.props[func](funcVal)
-                    }
-                    return Promise.resolve()
-                  }, Promise.resolve())
-
-                  const { isPlanS, selectedLicense } = this.state
-                  const { notes } = this.props.manuscript.meta
-                  const planS =
-                    notes && notes.find(n => n.notesType === 'planS')
-                  if (isPlanS && planS) {
-                    const changeLicense =
-                      (selectedLicense && !planS.content) ||
-                      (planS.content && planS.content !== selectedLicense)
-                    if (changeLicense) {
-                      await this.props.changeNote({
-                        id: planS.id,
-                        notesType: 'planS',
-                        content: selectedLicense,
-                      })
-                      if (selectedLicense) {
-                        await epmc_emailException({
-                          variables: {
-                            manuscriptId: manuscript.id,
-                            license: selectedLicense,
-                          },
-                        })
-                      }
-                    }
-                  }
+          {(epmc_emailException, { data }) => {
+            const checkException = async () => {
+              const checkArray = ['newNote', 'deleteNote', 'updateGrants']
+              await checkArray.reduce(async (promise, func) => {
+                await promise
+                const funcVal = this.state[func]
+                if (funcVal) {
+                  return this.props[func](funcVal)
                 }
-                const sendAlert = async () => {
-                  const { originalData, updateGrants } = this.state
-                  const newGrants = updateGrants.filter(
-                    p =>
-                      !originalData.some(
-                        o =>
-                          o.awardId === p.awardId &&
-                          o.fundingSource === p.fundingSource &&
-                          o.pi.surname === p.pi.surname,
-                      ),
-                  )
-                  await checkException()
-                  await epmc_emailGrantPis({
-                    variables: { manuscriptId: manuscript.id, newGrants },
+                return Promise.resolve()
+              }, Promise.resolve())
+
+              const { isPlanS, selectedLicense } = this.state
+              const { notes } = this.props.manuscript.meta
+              const planS = notes && notes.find(n => n.notesType === 'planS')
+              if (isPlanS && planS) {
+                const changeLicense =
+                  (selectedLicense && !planS.content) ||
+                  (planS.content && planS.content !== selectedLicense)
+                if (changeLicense) {
+                  await this.props.changeNote({
+                    id: planS.id,
+                    notesType: 'planS',
+                    content: selectedLicense,
                   })
-                  close()
+                  if (selectedLicense) {
+                    await epmc_emailException({
+                      variables: {
+                        manuscriptId: manuscript.id,
+                        license: selectedLicense,
+                      },
+                    })
+                  }
                 }
-                return (
-                  <Buttons right>
-                    <Button
-                      onClick={async () => {
-                        await checkException()
-                        close()
-                      }}
-                      primary
-                    >
-                      Save &amp; close
-                    </Button>
-                    <Button
-                      disabled={noPIEmails}
-                      onClick={() => sendAlert()}
-                      primary
-                    >
-                      Save &amp; send PI emails
-                    </Button>
-                  </Buttons>
-                )
-              }}
-            </Mutation>
-          )}
+              }
+            }
+            return (
+              <Buttons right>
+                <Button
+                  onClick={async () => {
+                    await checkException()
+                    close()
+                  }}
+                  primary
+                >
+                  Save &amp; close
+                </Button>
+              </Buttons>
+            )
+          }}
         </Mutation>
       </React.Fragment>
     )

app/components/operations.js

@@ -201,12 +201,6 @@ export const UPDATE_NOTE = gql`
   }
 `
 
-export const ALERT_PIS = gql`
-  mutation EmailGrantPis($manuscriptId: ID!, $newGrants: [FundingGroupInput]) {
-    epmc_emailGrantPis(manuscriptId: $manuscriptId, newGrants: $newGrants)
-  }
-`
-
 export const GET_PREPRINT_SELECTIONS = gql`
   query($id: ID!) {
     getPreprintSelections(manuscriptId: $id) {

app/components/submission-wizard/SubmitApprove.jsx

@@ -4,7 +4,6 @@ import { withRouter } from 'react-router'
 import { europepmcUrl } from 'config'
 import { Button, CheckboxGroup, Icon } from '@pubsweet/ui'
 import { A, Portal, Buttons, Fieldset } from '../ui'
-import { ALERT_PIS } from '../operations'
 import { SUBMIT_MANUSCRIPT } from './operations'
 
 const SubmitApprove = ({
@@ -69,25 +68,13 @@ const SubmitApprove = ({
           (preprint && adminButton === 'review')
         ) {
           return (
-            <Mutation mutation={ALERT_PIS}>
-              {(epmc_emailGrantPis, { data }) => {
-                const sendAlert = async () => {
-                  await epmc_emailGrantPis({ variables: { manuscriptId } })
-                }
-                return (
-                  <Button
-                    disabled={disabled}
-                    onClick={() => {
-                      sendAlert()
-                      submit('tagging')
-                    }}
-                    primary
-                  >
-                    Approve for tagging
-                  </Button>
-                )
-              }}
-            </Mutation>
+            <Button
+              disabled={disabled}
+              onClick={() => submit('tagging')}
+              primary
+            >
+              Approve for tagging
+            </Button>
           )
         }
         if (adminButton === 'review') {

server/ebi-integration/grantLinkCheck.js

 const logger = require('@pubsweet/logger')
 const { checkJobStatus, uncaughtError } = require('../job-runner')
 const Manuscript = require('../xpub-model/entities/manuscript/data-access')
-const {
-  gManuscript,
-} = require('../xpub-model/entities/manuscript/helpers/transform')
 const { transaction } = require('objection')
 const { errorDevEmail } = require('../email')
 const { createGrantLinks } = require('./linkGrants')
@@ -51,10 +48,12 @@ async function grantLinkCheck() {
     const linkingManuscripts = await Manuscript.query()
       .where('fundingState', 'Linking grants')
       .whereNull('manuscript.deleted')
+      .eager('teams.users.identities')
+      .modifyEager('teams', builder => {
+        builder.whereNull('deleted')
+      })
     if (linkingManuscripts.length > 0) {
-      const grantLinkDone = await createGrantLinks(
-        linkingManuscripts.map(manuscript => gManuscript(manuscript)),
-      )
+      const grantLinkDone = await createGrantLinks(linkingManuscripts)
       if (!grantLinkDone.success) {
         throw new Error(grantLinkDone.message)
       }

server/ebi-integration/linkGrants.js

@@ -3,10 +3,12 @@ const logger = require('@pubsweet/logger')
 const moment = require('moment')
 const Client = require('ftp')
 const { Readable } = require('stream')
+const { grantEmail } = require('../email')
 
 module.exports.createGrantLinks = async function createGrantLinks(
   manuscripts,
   removeFundingGroup,
+  addFundingGroup,
 ) {
   try {
     const filename = `grants${
@@ -14,14 +16,14 @@ module.exports.createGrantLinks = async function createGrantLinks(
     }.${moment().format('YYYY_MM_DD-HH_mm_SS')}.xml`
     const sendManuscripts = manuscripts.reduce((list, manuscript) => {
       const articleIds =
-        manuscript.meta.articleIds &&
-        manuscript.meta.articleIds
+        manuscript['meta,article_ids'] &&
+        manuscript['meta,article_ids']
           .filter(a => ['pmcid', 'pmid'].includes(a.pubIdType))
           .sort((a, b) => (a.pubIdType > b.pubIdType ? 1 : -1))
       const fundingGroup =
-        (manuscript.meta.fundingGroup &&
-          manuscript.meta.fundingGroup.length > 0 &&
-          manuscript.meta.fundingGroup) ||
+        (manuscript['meta,funding_group'] &&
+          manuscript['meta,funding_group'].length > 0 &&
+          manuscript['meta,funding_group']) ||
         undefined
       if (
         articleIds &&
@@ -29,10 +31,9 @@ module.exports.createGrantLinks = async function createGrantLinks(
         (fundingGroup || removeFundingGroup)
       ) {
         list.push({
-          id: manuscript.id,
+          manuscript,
           articleIds,
           fundingGroup,
-          removeFundingGroup,
         })
       } else {
         logger.info(`${manuscript.id} No grants to link or no ID to link to`)
@@ -47,9 +48,10 @@ module.exports.createGrantLinks = async function createGrantLinks(
           const grantList = await createGrantXML(
             each.articleIds,
             each.fundingGroup,
-            each.removeFundingGroup,
+            removeFundingGroup,
           )
-          logger.info(`${each.id} Grant list created`)
+          logger.info(`${each.manuscript.id} Grant list created`)
+          emailGrantPis(each.manuscript, addFundingGroup || each.fundingGroup)
           return grantList
         }),
       )
@@ -114,3 +116,43 @@ function sendXML(contents, filename) {
     ftp.connect({ host, user, password })
   })
 }
+
+async function emailGrantPis(manuscript, grantList) {
+  const { teams, id } = manuscript
+  const releaseDelay = manuscript['meta,release_delay']
+  const title = manuscript['meta,title']
+  const fundingGroup = manuscript['meta,funding_group']
+  const emails = teams.map(t => t.users[0].identities[0].email)
+  const { teamMembers: rTeam } = teams.find(t => t.role === 'reviewer') || {}
+  const [reviewer] = rTeam || []
+  if (!fundingGroup || fundingGroup.length === 0) return true
+  if (fundingGroup.some(g => emails.includes(g.pi.email))) return true
+
+  const piList = grantList.reduce((pis, curr) => {
+    const exists = pis.findIndex(p => p.pi.email === curr.pi.email)
+    const award = {
+      awardId: curr.awardId,
+      fundingSource: curr.fundingSource,
+      title: curr.title,
+    }
+    if (exists > -1) {
+      pis[exists].awards.push(award)
+    } else {
+      pis.push({
+        pi: curr.pi,
+        awards: [award],
+      })
+    }
+    return pis
+  }, [])
+  const manInfo = {
+    id,
+    title,
+    releaseDelay,
+  }
+  const reviewerName = reviewer && reviewer.alias.name
+  await Promise.all(
+    piList.map(async li => grantEmail(li.pi, li.awards, manInfo, reviewerName)),
+  )
+  return true
+}

server/xpub-model/entities/manuscript/index.js

@@ -57,7 +57,7 @@ const grantCheck = (origMan, changeMan) => {
           ),
       )
       if (added.length > 0 || removed.length > 0) {
-        return { send: true, removeGroup: removed }
+        return { send: true, added, removed }
       }
     }
   }
@@ -376,13 +376,13 @@ const Manuscript = {
       const teams = await TeamAccess.selectByManuscriptId(id)
       const subTeam = teams.find(t => t.roleName === 'submitter')
       if (userId === subTeam.userId) {
-        const submitter = await UserAccess.findById(subTeam.userId)
+        const [submitter] = subTeam.users
         const emails = submitter ? [submitter.identities[0].email] : []
         const manInfo = { id, title: manuscript['meta,title'] }
         const revTeam = teams.find(t => t.roleName === 'reviewer')
         let reviewer = null
         if (revTeam && revTeam.userId !== subTeam.userId) {
-          reviewer = await UserAccess.findById(revTeam.userId)
+          ;[reviewer] = revTeam.user
           if (reviewer) {
             emails.push(reviewer.identities[0].email)
           }
@@ -526,7 +526,7 @@ const Manuscript = {
       const emailTeam =
         teams.find(t => t.roleName === 'reviewer') ||
         teams.find(t => t.roleName === 'submitter')
-      const emailPerson = await UserAccess.findById(emailTeam.userId)
+      const [emailPerson] = emailTeam.users
       await alreadyCompleteEmail(emailPerson, manuscript)
       return {
         success: true,
@@ -556,8 +556,8 @@ const Manuscript = {
     const teams = await TeamAccess.selectByManuscriptId(input.manuscriptId)
     const subTeam = teams.find(t => t.roleName === 'submitter')
     const revTeam = teams.find(t => t.roleName === 'reviewer')
-    const submitter = await UserAccess.findById(subTeam.userId)
-    const reviewer = await UserAccess.findById(revTeam.userId)
+    const [submitter] = subTeam.users
+    const [reviewer] = revTeam.users
     const email = JSON.parse(input.content)
     const errors = []
     try {
@@ -615,11 +615,11 @@ const Manuscript = {
   replace: async (keepId, throwId, userId) => {
     const keepMan = await ManuscriptAccess.selectById(keepId)
     const throwMan = await ManuscriptAccess.selectById(throwId, true)
-    const emailId =
-      (throwMan.teams.find(t => t.roleName === 'reviewer') &&
-        throwMan.teams.find(t => t.roleName === 'reviewer').users[0].id) ||
-      throwMan.teams.find(t => t.roleName === 'submitter').users[0].id
-    const user = await UserAccess.findById(emailId)
+    const teams = await TeamAccess.selectByManuscriptId(throwId)
+    const emailTeam =
+      teams.find(t => t.roleName === 'reviewer') ||
+      teams.find(t => t.roleName === 'submitter')
+    const [user] = emailTeam.users
     const keepFunds = keepMan['meta,fundingGroup'] || []
     const throwFunds = throwMan['meta,fundingGroup'] || []
     const newFunds = keepFunds.concat(
@@ -641,12 +641,13 @@ const Manuscript = {
       'meta,fundingGroup': newFunds,
       updatedBy: userId,
     }
-    const { send, removeGroup } = await grantCheck(keepMan, input)
+    const { send, added, removed } = await grantCheck(keepMan, input)
     lodash.assign(keepMan, input)
     try {
       await keepMan.save()
       if (send) {
-        await createGrantLinks([gManuscript(keepMan)], removeGroup)
+        keepMan.teams = await TeamAccess.selectByManuscriptId(keepId)
+        await createGrantLinks([keepMan], removed, added)
       }
       await ManuscriptAccess.delete(throwId, userId)
       await removeDuplicateEmail(user, throwMan, keepMan)
@@ -1021,7 +1022,7 @@ const Manuscript = {
         }
       }
       const manuscriptUpdate = dManuscriptUpdate(input, userId)
-      const { send, removeGroup } = await grantCheck(
+      const { send, added, removed } = await grantCheck(
         originalMan,
         manuscriptUpdate,
       )
@@ -1030,7 +1031,8 @@ const Manuscript = {
       const updatedMan = await ManuscriptAccess.selectById(input.id, true, trx)
       const manuscript = gManuscript(updatedMan)
       if (send) {
-        await createGrantLinks([manuscript], removeGroup)
+        updatedMan.teams = await TeamAccess.selectByManuscriptId(input.id)
+        await createGrantLinks([updatedMan], removed, added)
       }
       if (commit) {
         await trx.commit()

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

@@ -87,6 +87,7 @@ class Team extends EpmcBaseModel {
 
   static async selectByManuscriptId(manId, trx) {
     const manuscriptRoles = await Team.query(trx)
+      .eager('users.identities')
       .where({
         'team.manuscript_id': manId,
       })

server/xpub-server/entities/email/resolvers.js

@@ -2,9 +2,7 @@ const rfr = require('rfr')
 const logger = require('@pubsweet/logger')
 const authentication = require('../user/authentication')
 
-const { userMessage, resetPassword, grantEmail, licenseEmail } = rfr(
-  'server/email',
-)
+const { userMessage, resetPassword, licenseEmail } = rfr('server/email')
 const {
   ManuscriptManager,
   UserManager,
@@ -65,58 +63,6 @@ const resolvers = {
       await NoteManager.create(note, user)
       return true
     },
-    async epmc_emailGrantPis(_, { manuscriptId, newGrants = null }, { user }) {
-      const manuscript = await ManuscriptManager.findById(manuscriptId, user)
-      const { meta, teams } = manuscript
-      const { fundingGroup, releaseDelay, title } = meta
-      if (!fundingGroup) return true
-      const { teamMembers: sTeam } =
-        teams.find(team => team.role === 'submitter') || {}
-      const [submitter] = sTeam || []
-      const sEmail =
-        submitter && (await UserManager.findEmail(submitter.user.id))
-      const { teamMembers: rTeam } =
-        teams.find(team => team.role === 'reviewer') || {}
-      const [reviewer] = rTeam || []
-      const rEmail = reviewer && (await UserManager.findEmail(reviewer.user.id))
-      if (
-        sEmail &&
-        rEmail &&
-        fundingGroup.some(g => [rEmail, sEmail].includes(g.pi.email))
-      ) {
-        return true
-      }
-      const grantList = newGrants || fundingGroup
-      const piList = grantList.reduce((pis, curr) => {
-        const exists = pis.findIndex(p => p.pi.email === curr.pi.email)
-        const award = {
-          awardId: curr.awardId,
-          fundingSource: curr.fundingSource,
-          title: curr.title,
-        }
-        if (exists > -1) {
-          pis[exists].awards.push(award)
-        } else {
-          pis.push({
-            pi: curr.pi,
-            awards: [award],
-          })
-        }
-        return pis
-      }, [])
-      const manInfo = {
-        id: manuscriptId,
-        title,
-        releaseDelay,
-      }
-      const reviewerName = reviewer && reviewer.alias.name
-      await Promise.all(
-        piList.map(async li =>
-          grantEmail(li.pi, li.awards, manInfo, reviewerName),
-        ),
-      )
-      return true
-    },
     async epmc_emailException(_, { manuscriptId, license: l }, { user }) {
       const manuscript = await ManuscriptManager.findById(manuscriptId, user)
       const { meta, teams, status, version } = manuscript

server/xpub-server/entities/email/typeDefs.graphqls

@@ -5,9 +5,6 @@ extend type Mutation {
   # Send email to reset password
   epmc_emailPasswordResetLink(email: String!): Boolean!
 
-  # Check and send email to grant PIs
-  epmc_emailGrantPis(manuscriptId: ID!, newGrants: [FundingGroupInput]): Boolean!
-
   # Send email to confirm license exception
   epmc_emailException(manuscriptId: ID!, license: String): Boolean!
 }