diff --git a/app/components/dashboard/AdminDashboard.jsx b/app/components/dashboard/AdminDashboard.jsx
index 7865400c856200b3c10787466dc684b08ed5992a..52c007ba82b8438b049f6788b1669a815e5a0576 100755
--- a/app/components/dashboard/AdminDashboard.jsx
+++ b/app/components/dashboard/AdminDashboard.jsx
@@ -34,8 +34,8 @@ const TaggerQueue = { tagging: ['tagging'] }
const Completed = {
'approved for PMC': ['xml-complete'],
published: ['published'],
- removed: ['removed'],
- withdrawn: ['withdrawn'],
+ 'being withdrawn': ['being-withdrawn'],
+ deleted: ['deleted'],
}
const QueueTable = ({ title, queue, data }) => {
diff --git a/app/components/dashboard/DashboardList.jsx b/app/components/dashboard/DashboardList.jsx
index d6841119f15f2a3793abaaffc8fa849df1f7bf05..8bf123087003c4f23e5858a2898e829163546573 100644
--- a/app/components/dashboard/DashboardList.jsx
+++ b/app/components/dashboard/DashboardList.jsx
@@ -313,8 +313,8 @@ export const States = {
admin: adminState,
}
-const timeSince = date => {
- const seconds = Math.floor((new Date() - date) / 1000)
+export const timeSince = date => {
+ const seconds = Math.floor((new Date() - new Date(date)) / 1000)
let interval = Math.floor(seconds / 31536000)
if (interval >= 1) {
return `${interval} year${interval !== 1 ? 's' : ''}`
@@ -401,7 +401,7 @@ const DashboardList = ({
</div>
<Column>
<ItemStatus className={state.color}>{state.status}</ItemStatus>
- <B>{timeSince(new Date(updated))}</B>
+ <B>{timeSince(updated)}</B>
{userRole === 'admin' && claimStates.includes(status) && (
<React.Fragment>
{claimedBy ? (
diff --git a/app/components/dashboard/index.js b/app/components/dashboard/index.js
index c0a503e41a92494d77246d0e7c6686256b29c6d6..c79cb9aa9d4c0c590af53f71cd3dc75991f1e54a 100644
--- a/app/components/dashboard/index.js
+++ b/app/components/dashboard/index.js
@@ -1,4 +1,4 @@
export { default as SearchResultsPage } from './SearchResultsPage'
export { default as DashboardPage } from './DashboardPage'
-export { States } from './DashboardList'
+export { States, timeSince } from './DashboardList'
export { default as AdminDashboard } from './AdminDashboard'
diff --git a/app/components/submission-wizard/HandleDuplicates.jsx b/app/components/submission-wizard/HandleDuplicates.jsx
deleted file mode 100644
index 1ce0313c735676e7ebecdacbec25a5989884d2b8..0000000000000000000000000000000000000000
--- a/app/components/submission-wizard/HandleDuplicates.jsx
+++ /dev/null
@@ -1,123 +0,0 @@
-import React from 'react'
-import { withRouter } from 'react-router'
-import { Mutation } from 'react-apollo'
-import styled from 'styled-components'
-import { H3, Button, Action, Icon, Link } from '@pubsweet/ui'
-import { B, Buttons, Close, CloseButton, Portal } from '../ui'
-import { States } from '../dashboard'
-import Citation from './Citation'
-import { REPLACE_MANUSCRIPT, CHECK_DUPES } from './operations'
-
-const Columns = styled.div`
- display: flex;
- align-items: flex-start;
- justify-content: space-evenly;
- h3 {
- margin-top: 0;
- }
- button {
- display: flex;
- align-items: center;
- }
-`
-const HandleDuplicates = ({ close, current, duplicates }) => (
- <Mutation
- mutation={REPLACE_MANUSCRIPT}
- refetchQueries={result => {
- if (result.data.replaceManuscript) {
- return [
- {
- query: CHECK_DUPES,
- variables: {
- id: current.id,
- pmid:
- current.meta.articleIds &&
- current.meta.articleIds.find(id => id.pubIdType === 'pmid')
- ? current.meta.articleIds.find(id => id.pubIdType === 'pmid')
- .id
- : null,
- title: current.meta.title,
- },
- },
- ]
- }
- return []
- }}
- >
- {(replaceManuscript, { data }) => {
- const replace = async (keepId, throwId) => {
- const { data } = await replaceManuscript({
- variables: { keepId, throwId },
- })
- if (data.replaceManuscript && throwId === current.id) {
- this.props.history.push('/')
- }
- }
- return (
- <Portal transparent>
- <Close>
- <CloseButton onClick={close} />
- </Close>
- <Columns>
- <div>
- <H3>This manuscript</H3>
- <Citation journal={current.journal} metadata={current.meta} />
- <p>
- <B>Status:</B> {current.status}
- </p>
- <p>
- <B>Grants: </B>
- {current.meta.fundingGroup.map((f, t) => (
- <span key={f.awardId}>
- {`${f.fundingSource} ${f.awardId}`}
- {t !== current.meta.fundingGroup.length - 1 && ', '}
- </span>
- ))}
- </p>
- <Action onClick={() => replace(current.id, duplicates[0].id)}>
- Remove this & transfer grants
- <Icon color="currentColor">arrow-right</Icon>
- </Action>
- </div>
- <div>
- <H3>Duplicate(s)</H3>
- {duplicates.map(dupe => (
- <React.Fragment>
- <Link
- target="_blank"
- to={`/submission/${dupe.id}/${
- States.admin[dupe.status].url
- }`}
- >
- <Citation journal={dupe.journal} metadata={dupe.meta} />
- </Link>
- <p>
- <B>Status:</B> {dupe.status}
- </p>
- <p>
- <B>Grants: </B>
- {dupe.meta.fundingGroup.map((f, t) => (
- <span key={f.awardId}>
- {`${f.fundingSource} ${f.awardId}`}
- {t !== dupe.meta.fundingGroup.length - 1 && ', '}
- </span>
- ))}
- </p>
- <Action onClick={() => replace(current.id, dupe.id)}>
- <Icon color="currentColor">arrow-left</Icon>
- Transfer grants & remove this
- </Action>
- </React.Fragment>
- ))}
- </div>
- </Columns>
- <Buttons>
- <Button onClick={close}>Exit</Button>
- </Buttons>
- </Portal>
- )
- }}
- </Mutation>
-)
-
-export default withRouter(HandleDuplicates)
diff --git a/app/components/submission-wizard/ResolveDuplicates.jsx b/app/components/submission-wizard/ResolveDuplicates.jsx
new file mode 100644
index 0000000000000000000000000000000000000000..f4b2ee281a3d3496469e3c5254ed46f839a59130
--- /dev/null
+++ b/app/components/submission-wizard/ResolveDuplicates.jsx
@@ -0,0 +1,179 @@
+import React from 'react'
+import { withRouter } from 'react-router'
+import { Mutation } from 'react-apollo'
+import styled from 'styled-components'
+import { th } from '@pubsweet/ui-toolkit'
+import { H3, H4, Button, Action, Icon, Link } from '@pubsweet/ui'
+import { B, Buttons, Close, CloseButton, Portal, Notification } from '../ui'
+import { States, timeSince } from '../dashboard'
+import Citation from './Citation'
+import { REPLACE_MANUSCRIPT, CHECK_DUPES } from './operations'
+
+const Columns = styled.div`
+ display: flex;
+ flex-wrap: wrap;
+ align-items: stretch;
+ justify-content: flex-end;
+ h3 {
+ margin-top: 0;
+ }
+ h4 {
+ margin: 0;
+ }
+ button {
+ display: flex;
+ align-items: center;
+ }
+ & > * {
+ width: 48%;
+ box-sizing: border-box;
+ margin-right: 1%;
+ margin-left: 1%;
+ }
+ & > div {
+ margin-top: ${th('gridUnit')};
+ display: flex;
+ align-items: stretch;
+ justify-content: space-between;
+ flex-direction: column;
+ border: ${th('borderWidth')} ${th('borderStyle')} ${th('colorBorder')};
+ padding: calc(${th('gridUnit')} * 2);
+ }
+`
+const Current = styled.div`
+ background-color: ${th('colorBackground')};
+`
+const Dupes = styled.div`
+ background-color: ${th('colorBackgroundHue')};
+`
+const FlexP = styled.div`
+ display: flex;
+ flex-wrap: wrap;
+ align-items: center;
+ justify-content: space-between;
+`
+const ResolveDuplicates = ({ close, current, duplicates }) => (
+ <Mutation
+ mutation={REPLACE_MANUSCRIPT}
+ refetchQueries={result => {
+ if (result.data.replaceManuscript) {
+ return [
+ {
+ query: CHECK_DUPES,
+ variables: {
+ id: current.id,
+ pmid:
+ current.meta.articleIds &&
+ current.meta.articleIds.find(id => id.pubIdType === 'pmid')
+ ? current.meta.articleIds.find(id => id.pubIdType === 'pmid')
+ .id
+ : null,
+ title: current.meta.title,
+ },
+ },
+ ]
+ }
+ return []
+ }}
+ >
+ {(replaceManuscript, { data }) => {
+ const replace = async (keepId, throwId) => {
+ const { data } = await replaceManuscript({
+ variables: { keepId, throwId },
+ })
+ if (data.replaceManuscript && throwId === current.id) {
+ this.props.history.push('/')
+ }
+ }
+ console.log(duplicates)
+ return (
+ <Portal transparent>
+ <Close>
+ <CloseButton onClick={close} />
+ </Close>
+ <Columns>
+ <H3>This manuscript</H3>
+ <H3>Duplicate(s)</H3>
+ <p style={{ flex: '0 0 100%' }}>
+ <Notification type="error">
+ Two articles cannot have the same PMID.
+ </Notification>
+ </p>
+ <Current>
+ <H4>{current.id}</H4>
+ <Citation journal={current.journal} metadata={current.meta} />
+ <FlexP>
+ <span>
+ <B>Status:</B> {current.status}
+ </span>
+ <span>
+ <B>Last updated:</B> {timeSince(current.updated)}
+ </span>
+ </FlexP>
+ <p>
+ <B>Grants: </B>
+ {current.meta.fundingGroup && current.meta.fundingGroup.map((f, t) => (
+ <span key={f.awardId}>
+ {`${f.fundingSource} ${f.awardId}`}
+ {t !== current.meta.fundingGroup.length - 1 && ', '}
+ </span>
+ ))}
+ </p>
+ <Button onClick={() => replace(current.id, duplicates[0].id)} primary>
+ Remove this & transfer grants
+ <Icon color="currentColor">arrow-right</Icon>
+ </Button>
+ </Current>
+ {duplicates.map((dupe, i) => (
+ <React.Fragment>
+ <Dupes key={dupe.id}>
+ <H4>{dupe.id}</H4>
+ <Link
+ target="_blank"
+ to={`/submission/${dupe.id}/${
+ States.admin[dupe.status].url
+ }`}
+ >
+ <Citation journal={dupe.journal} metadata={dupe.meta} />
+ </Link>
+ <FlexP>
+ <span>
+ <B>Status:</B> {dupe.status}
+ </span>
+ <span>
+ <B>Last updated:</B> {timeSince(dupe.updated)}
+ </span>
+ </FlexP>
+ <p>
+ <B>Grants: </B>
+ {dupe.meta.fundingGroup && dupe.meta.fundingGroup.map((f, t) => (
+ <span key={f.awardId}>
+ {`${f.fundingSource} ${f.awardId}`}
+ {t !== dupe.meta.fundingGroup.length - 1 && ', '}
+ </span>
+ ))}
+ </p>
+ <Button onClick={() => replace(current.id, dupe.id)} primary>
+ <Icon color="currentColor">arrow-left</Icon>
+ Transfer grants & remove this
+ </Button>
+ </Dupes>
+ {i === 0 && (
+ <p style={{ flex: '0 0 100%', textAlign: 'center' }}>
+ <Button style={{ margin: '0 auto' }}>These two are not duplicates!</Button>
+ </p>
+ )}
+ {i !== duplicates.length - 1 && <br />}
+ </React.Fragment>
+ ))}
+ </Columns>
+ <Buttons>
+ <Button onClick={close}>Exit</Button>
+ </Buttons>
+ </Portal>
+ )
+ }}
+ </Mutation>
+)
+
+export default withRouter(ResolveDuplicates)
diff --git a/app/components/submission-wizard/Submit.jsx b/app/components/submission-wizard/Submit.jsx
index a297be0c36d9273495e80739d0bc5377b11c6f73..a1a6d3463f5af5f35b944044f269de5507fa6ffa 100644
--- a/app/components/submission-wizard/Submit.jsx
+++ b/app/components/submission-wizard/Submit.jsx
@@ -19,7 +19,7 @@ import {
} from '../ui'
import Citation from './Citation'
import GrantSearch from './GrantSearch'
-import HandleDuplicates from './HandleDuplicates'
+import ResolveDuplicates from './ResolveDuplicates'
import SelectReviewer from './SelectReviewer'
import SubmitForm from './SubmitForm'
import SubmitHighlights from './SubmitHighlights'
@@ -169,7 +169,7 @@ class Submit extends React.Component {
onClick={() => this.setState({ prune: true })}
primary
>
- Handle duplicates
+ Resolve duplicates
</Button>
<ErrorMessage>
<Icon color="currentColor" size={2}>
@@ -367,7 +367,7 @@ class Submit extends React.Component {
<div>
<PanelHeader>
<H2>
- {status === 'submission-error' ? 'Edit' : 'Confirm'}
+ {status === 'submission-error' && 'Edit' || status === 'submitted' && 'Review' || 'Confirm'}
{` input & approve`}
</H2>
</PanelHeader>
@@ -410,7 +410,7 @@ class Submit extends React.Component {
</div>
</EditPanel>
{duplicates && prune && (
- <HandleDuplicates
+ <ResolveDuplicates
close={() => this.setState({ prune: false })}
current={manuscript}
duplicates={duplicates}
diff --git a/app/components/submission-wizard/SubmitPage.jsx b/app/components/submission-wizard/SubmitPage.jsx
index 3eceddbdfea9bbbe1d09571f59da8c0c6df65318..f26226bd43d1c6b750e689342b70492a7d261245 100755
--- a/app/components/submission-wizard/SubmitPage.jsx
+++ b/app/components/submission-wizard/SubmitPage.jsx
@@ -27,7 +27,7 @@ const DupeCheckSubmitPage = ({ manuscript, ...props }) => {
)
}
const duplicates =
- data.checkDuplicates.length > 0 && data.checkDuplicates
+ data.checkDuplicates.length > 0 && data.checkDuplicates || null
return (
<SubmitWithHeader
duplicates={duplicates}
diff --git a/app/components/submission-wizard/operations.js b/app/components/submission-wizard/operations.js
index 580654bafe9b7bf91867674c74c48efdcc3b2aca..13ebd2bd2e5c53a1a2f0c0bec4a5e966fdfc64fa 100644
--- a/app/components/submission-wizard/operations.js
+++ b/app/components/submission-wizard/operations.js
@@ -20,6 +20,7 @@ const ManuscriptFragment = gql`
fragment ManuscriptFragment on Manuscript {
id
status
+ updated
formState
journal {
journalTitle
diff --git a/config/authsome.js b/config/authsome.js
index d332f54c5580bbad5533cba163bc997d23f7085b..a24d72ce6335de13ab6eeea5f22075f3fa86824b 100755
--- a/config/authsome.js
+++ b/config/authsome.js
@@ -28,8 +28,8 @@ const authorisationMap = {
Manuscript: {
roles: {
admin: states,
- submitter: states.slice(0, states.length - 2),
- reviewer: states.slice(0, states.length - 2),
+ submitter: states.slice(0, states.length - 1),
+ reviewer: states.slice(0, states.length - 1),
tagger: ['tagging'],
'external-admin': ['xml-qa'],
},
diff --git a/config/states.json b/config/states.json
index b75a41175c4fcb933740a1d4eeda6bc20f040f84..7be3a7ccc976cbd1185fa77d7a61931509ed1a10 100644
--- a/config/states.json
+++ b/config/states.json
@@ -11,6 +11,5 @@
"xml-complete",
"ncbi-ready",
"published",
- "removed",
- "withdrawn"
+ "being-withdrawn"
]
\ No newline at end of file
diff --git a/server/email/templates/rejectSubmission.js b/server/email/templates/rejectSubmission.js
index 49f289c01e7d250e48c3d3dc37fded4ecc15afbe..63ef20b6c59ef78063ca70e59d4b4e3ed2149873 100644
--- a/server/email/templates/rejectSubmission.js
+++ b/server/email/templates/rejectSubmission.js
@@ -10,7 +10,7 @@ const rejectSubmissionTemplate = (
<p>Your manuscript submission, <b>${title}</b> was rejected by the reviewer.<p>
<p>The reviewer, ${reviewer}, sent the following message:</p>
<blockquote style="white-space: pre-wrap">${message}</blockquote>
- <p>Please go to your manuscript at <a style="color:#20699C" href="${link}"></a> to correct any errors in the submission.</p>
+ <p>Please go to your manuscript at <a style="color:#20699C" href="${link}">${link}</a> to correct any errors in the submission.</p>
<p>Kind regards,</p>
<p>The Europe PMC plus system</p>
`
diff --git a/server/xpub-model/entities/manuscript/data-access.js b/server/xpub-model/entities/manuscript/data-access.js
index eb7a6d1e0d6322bab62f67d19280718db3312ee2..1bc7a8049d2a2329b6bc02a958d48b99a0c73b83 100644
--- a/server/xpub-model/entities/manuscript/data-access.js
+++ b/server/xpub-model/entities/manuscript/data-access.js
@@ -219,10 +219,10 @@ class Manuscript extends EpmcBaseModel {
static async selectById(id, eager = false) {
let manuscripts
if (eager) {
+ // don't whereNull deleted here
manuscripts = await Manuscript.query()
.select('manuscript.*')
.where('manuscript.id', id)
- .whereNull('manuscript.deleted')
.eager('[journal, teams.users, notes, files, claiming]')
.modifyEager('teams', builder => {
builder.whereNull('deleted')
@@ -271,6 +271,33 @@ class Manuscript extends EpmcBaseModel {
return parseInt(count[0].count, 10)
}
+ static async countDeleted() {
+ const count = await knex('manuscript')
+ .count('*')
+ .whereNotNull('deleted')
+ return parseInt(count[0].count, 10)
+ }
+
+ static async getDeleted(page = 0, pageSize = PAGE_SIZE, user) {
+ const manuscripts =
+ page === -1
+ ? await Manuscript.query()
+ .distinct('manuscript.id')
+ .select('manuscript.*')
+ .eager('[teams.users, claiming, journal]')
+ .whereNotNull('manuscript.deleted')
+ .orderBy('manuscript.updated', 'desc')
+ : await Manuscript.query()
+ .distinct('manuscript.id')
+ .select('manuscript.*')
+ .eager('[teams.users, claiming, journal]')
+ .whereNotNull('manuscript.deleted')
+ .orderBy('manuscript.updated', 'desc')
+ .page(page, pageSize)
+ logger.debug('manuscripts: ', manuscripts)
+ return manuscripts
+ }
+
static async selectActivityById(id) {
const manuscripts = await Manuscript.query()
.where('manuscript.id', id)
diff --git a/server/xpub-model/entities/manuscript/index.js b/server/xpub-model/entities/manuscript/index.js
index f2d2bbaf4b2c1ecfbee27eec7006376adb44dd68..028945587f40066fb170362a560e142d9d28fe8d 100755
--- a/server/xpub-model/entities/manuscript/index.js
+++ b/server/xpub-model/entities/manuscript/index.js
@@ -33,12 +33,10 @@ const Manuscript = {
},
findByStatus: async (query, page, pageSize, user) => {
- const manuscripts = await ManuscriptAccess.selectByStatus(
- query,
- page,
- pageSize,
- user,
- )
+ const manuscripts =
+ query === 'deleted'
+ ? await ManuscriptAccess.getDeleted(page, pageSize, user)
+ : await ManuscriptAccess.selectByStatus(query, page, pageSize, user)
const rtn =
page === -1
? manuscripts.map(manuscript => gManuscript(manuscript))
@@ -113,6 +111,8 @@ const Manuscript = {
const count = await ManuscriptAccess.countByStatus(type)
return { type, count }
})
+ const deleted = await ManuscriptAccess.countDeleted()
+ counts.push({ type: 'deleted', count: deleted })
return counts
},
@@ -151,26 +151,16 @@ const Manuscript = {
findByDepositStatesNull: ManuscriptAccess.selectByPdfDepositStatesNull,
delete: async (id, userId) => {
- let trx
try {
- trx = await transaction.start(ManuscriptAccess.knex())
const manuscript = await ManuscriptAccess.selectById(id)
if (manuscript) {
- await ManuscriptAccess.delete(id, userId, trx)
- await FileAccess.deleteByManuscriptId(id, userId, trx)
- await ReviewAccess.deleteByManuscriptId(id, userId, trx)
- await NoteAccess.deleteByManuscriptId(id, userId, trx)
- await trx.commit()
+ await ManuscriptAccess.delete(id, userId)
return true
}
return false
} catch (error) {
- if (trx) {
- await trx.rollback()
- }
- logger.error('Nothing was deleted')
- logger.error(error)
- throw error
+ logger.error(`Nothing was deleted: ${error}`)
+ return false
}
},
@@ -278,7 +268,7 @@ const Manuscript = {
lodash.assign(keepMan, input)
try {
await keepMan.save()
- await Manuscript.delete(throwId, userId)
+ await ManuscriptAccess.delete(throwId, userId)
await removeDuplicateEmail(user, throwMan, keepMan)
} catch (error) {
logger.error(error)