From e67afb22506111ff80c3b12c822d03b9f7143144 Mon Sep 17 00:00:00 2001
From: Audrey Hamelers <hamelers@ebi.ac.uk>
Date: Tue, 22 Jan 2019 17:13:55 +0000
Subject: [PATCH] WIP: working with journals. #190, #159, #194
---
app/components/PubMedSearch.jsx | 6 ++---
app/components/dashboard/DashboardList.jsx | 2 +-
app/components/dashboard/operations.js | 5 ++++
app/components/submission-wizard/Citation.jsx | 4 ++--
.../submission-wizard/CreatePage.jsx | 11 ++++++---
.../submission-wizard/operations.js | 8 +++++++
.../entities/journal/data-access.js | 16 +++++++++++++
.../entities/manuscript/data-access.js | 6 ++---
.../entities/manuscript/helpers/transform.js | 23 +++++++++++++++++++
.../xpub-model/entities/manuscript/index.js | 18 ++++++++-------
.../entities/manuscript/resolvers.js | 1 -
.../entities/manuscript/typeDefs.graphqls | 1 +
12 files changed, 80 insertions(+), 21 deletions(-)
diff --git a/app/components/PubMedSearch.jsx b/app/components/PubMedSearch.jsx
index c92222707..b4d36c1b5 100755
--- a/app/components/PubMedSearch.jsx
+++ b/app/components/PubMedSearch.jsx
@@ -143,7 +143,7 @@ class PubMedSearch extends React.Component {
const indexedby = xml.match(/<IndexingSourceName(.*)<\/IndexingSourceName>/g)
console.log(indexedby) */
const date = new Date(result.sortpubdate)
- const metadata = {
+ const citationData = {
title: result.title,
articleIds: [
{
@@ -157,9 +157,9 @@ class PubMedSearch extends React.Component {
date,
},
],
- unmatchedJournal: result.source,
+ nlmId: result.nlmuniqueid,
}
- this.props.citationData(metadata)
+ this.props.citationData(citationData)
}
}
render() {
diff --git a/app/components/dashboard/DashboardList.jsx b/app/components/dashboard/DashboardList.jsx
index 3fbb90e97..eae4e0837 100644
--- a/app/components/dashboard/DashboardList.jsx
+++ b/app/components/dashboard/DashboardList.jsx
@@ -281,7 +281,7 @@ const DashboardList = ({
<span>{manuscript.id}</span>
{pmid && <span>PMID: {pmid.id}</span>}
<span>
- JOURNAL: {journal ? journal.journalTitle : unmatchedJournal}
+ JOURNAL: {journal ? journal.meta.nlmta : unmatchedJournal}
</span>
{releaseDelay && (
<span>
diff --git a/app/components/dashboard/operations.js b/app/components/dashboard/operations.js
index e1773ac5f..300b972fb 100644
--- a/app/components/dashboard/operations.js
+++ b/app/components/dashboard/operations.js
@@ -50,6 +50,11 @@ const DashboardFragment = gql`
status
updated
formState
+ journal {
+ meta {
+ nlmta
+ }
+ }
meta {
title
articleIds {
diff --git a/app/components/submission-wizard/Citation.jsx b/app/components/submission-wizard/Citation.jsx
index 987a3f74b..8cd791ec9 100755
--- a/app/components/submission-wizard/Citation.jsx
+++ b/app/components/submission-wizard/Citation.jsx
@@ -9,14 +9,14 @@ const Small = styled.span`
`
const Citation = props => {
- const { articleIds, title, journalMeta, unmatchedJournal } = props.metadata
+ const { title, articleIds, unmatchedJournal } = props.metadata
return (
<p>
<HTMLString string={title} />
<Small>
<span>
<HTMLString
- string={journalMeta ? journalMeta.title : unmatchedJournal}
+ string={props.journal ? props.journal.meta.nlmta : unmatchedJournal}
/>
</span>
{articleIds && articleIds.length > 0 && (
diff --git a/app/components/submission-wizard/CreatePage.jsx b/app/components/submission-wizard/CreatePage.jsx
index 3efab7ccb..41c2e2269 100755
--- a/app/components/submission-wizard/CreatePage.jsx
+++ b/app/components/submission-wizard/CreatePage.jsx
@@ -148,7 +148,7 @@ class Created extends React.Component {
render() {
const currentUser = this.context
const { currentStep, status, error, checked } = this.state
- const { id: mId, meta, files: allfiles } = this.props.manuscript
+ const { id: mId, meta, journal, files: allfiles } = this.props.manuscript
const { notes } = meta
const files = allfiles
? allfiles.filter(
@@ -161,6 +161,11 @@ class Created extends React.Component {
return (
<Mutation mutation={UPDATE_MANUSCRIPT}>
{(updateManuscript, { data }) => {
+ const changeCitation = async meta => {
+ await updateManuscript({
+ variables: { data: { id: mId, meta } },
+ })
+ }
const updateEmbargo = async releaseDelay => {
await updateManuscript({
variables: { data: { id: mId, meta: { releaseDelay } } },
@@ -208,7 +213,7 @@ class Created extends React.Component {
<React.Fragment>
<H2>Citation</H2>
<PubMedSearch
- citationData={this.createNewManuscriptVersion}
+ citationData={changeCitation}
metadata={meta}
/>
</React.Fragment>
@@ -218,7 +223,7 @@ class Created extends React.Component {
Citation selected
</H2>
<Confirm>
- <Citation metadata={meta} />
+ <Citation journal={journal} metadata={meta} />
<Icon color="currentColor" size={5}>
check
</Icon>
diff --git a/app/components/submission-wizard/operations.js b/app/components/submission-wizard/operations.js
index f88e59e75..c52a14982 100644
--- a/app/components/submission-wizard/operations.js
+++ b/app/components/submission-wizard/operations.js
@@ -14,6 +14,14 @@ export const GET_MANUSCRIPT = gql`
id
status
formState
+ journal {
+ journalTitle
+ meta {
+ nlmta
+ pmcStatus
+ pubmedStatus
+ }
+ }
meta {
title
articleIds {
diff --git a/server/xpub-model/entities/journal/data-access.js b/server/xpub-model/entities/journal/data-access.js
index bf3773cf9..6ef633f05 100644
--- a/server/xpub-model/entities/journal/data-access.js
+++ b/server/xpub-model/entities/journal/data-access.js
@@ -27,6 +27,8 @@ class Journal extends EpmcBaseModel {
'meta,nlmuniqueid': { type: ['string', 'null'] },
'meta,pmcStatus': { type: 'boolean' },
'meta,pubmedStatus': { type: 'boolean' },
+ 'meta,firstYear': { type: 'string' },
+ 'meta,endYear': { type: 'string' },
},
}
}
@@ -58,6 +60,20 @@ class Journal extends EpmcBaseModel {
return rowToEntity(rows[0])
}
+ static async getIdByNlmId(nlmId) {
+ const row = await runQuery(
+ buildQuery
+ .select('journal.id')
+ .from('journal')
+ .where('meta,nlmuniqueid', nlmId)
+ .first(),
+ )
+ if (!row) {
+ throw new Error('journal not found')
+ }
+ return row.id
+ }
+
static async selectAll() {
const rows = await runQuery(buildQuery.select().from('journal'))
return rows.map(rowToEntity)
diff --git a/server/xpub-model/entities/manuscript/data-access.js b/server/xpub-model/entities/manuscript/data-access.js
index 55af7439f..07a188bfb 100644
--- a/server/xpub-model/entities/manuscript/data-access.js
+++ b/server/xpub-model/entities/manuscript/data-access.js
@@ -213,7 +213,7 @@ class Manuscript extends EpmcBaseModel {
manuscripts = await Manuscript.query()
.select('manuscript.*')
.where('manuscript.id', id)
- .eager('[teams.users, notes, files]')
+ .eager('[journal, teams.users, notes, files]')
} else {
manuscripts = await Manuscript.query().where('id', id)
}
@@ -237,7 +237,7 @@ class Manuscript extends EpmcBaseModel {
const manuscripts = await Manuscript.query()
.distinct('manuscript.id')
.select('manuscript.*')
- .eager('[teams.users, claiming]')
+ .eager('[teams.users, claiming, journal]')
.whereIn('status', status)
logger.debug('manuscripts: ', manuscripts)
return manuscripts
@@ -270,7 +270,7 @@ class Manuscript extends EpmcBaseModel {
.leftJoin('team', 'team.manuscript_id', 'manuscript.id')
.groupBy('manuscript.id', 'team.user_id', 'team.role_name')
.where('team.user_id', user)
- .eager('[teams.users]')
+ .eager('[teams.users, journal]')
return manuscripts
}
diff --git a/server/xpub-model/entities/manuscript/helpers/transform.js b/server/xpub-model/entities/manuscript/helpers/transform.js
index 32d655dc2..8ee0cf7f0 100644
--- a/server/xpub-model/entities/manuscript/helpers/transform.js
+++ b/server/xpub-model/entities/manuscript/helpers/transform.js
@@ -28,12 +28,32 @@ const dManuscriptUpdate = (data, userId) => {
if (data.claimedBy) {
properties.claimedBy = data.claimedBy
}
+ if (data.journalId) {
+ properties.journalId = data.journalId
+ }
if (userId) {
properties.updatedBy = userId
}
return new Manuscript(properties)
}
+const gJournal = model => {
+ const journal = {
+ journalTitle: model.journalTitle,
+ meta: {
+ publisherName: model['meta,publisherName'],
+ issn: model['meta,issn'],
+ nlmta: model['meta,nlmta'],
+ nlmuniqueid: model['meta,nlmuniqueid'],
+ pmcStatus: model['meta,pmcStatus'],
+ pubmedStatus: model['meta,pubmedStatus'],
+ firstYear: model['meta,firstYear'],
+ endYear: model['meta,endYear'],
+ },
+ }
+ return journal
+}
+
// Transform from Database model to GraphQL data
const gManuscript = model => {
const manuscript = {}
@@ -41,6 +61,9 @@ const gManuscript = model => {
manuscript.updated = model.updated
manuscript.status = model.status
manuscript.formState = model.formState
+ if (model.journal) {
+ manuscript.journal = gJournal(model.journal)
+ }
manuscript.meta = {}
if (model['meta,title']) {
manuscript.meta.title = model['meta,title']
diff --git a/server/xpub-model/entities/manuscript/index.js b/server/xpub-model/entities/manuscript/index.js
index f0bd12fcb..dfa41dbef 100755
--- a/server/xpub-model/entities/manuscript/index.js
+++ b/server/xpub-model/entities/manuscript/index.js
@@ -9,7 +9,7 @@ const FileAccess = require('../file/data-access')
const NoteAccess = require('../note/data-access')
const ReviewAccess = require('../review/data-access')
const Team = require('../team/data-access')
-const UserAccess = require('../user/data-access')
+const Journal = require('../journal/data-access')
const { dManuscriptUpdate, gManuscript } = require('./helpers/transform')
const mergeObjects = (...inputs) =>
@@ -134,18 +134,20 @@ const Manuscript = {
return savedMan
},
- update: async (input, userId, eager = false) => {
+ update: async (input, userId) => {
const originalMan = await ManuscriptAccess.selectById(input.id)
if (!originalMan) {
throw new Error('Manuscript not found')
}
-
- const manuscriptUpdate = dManuscriptUpdate(input, userId)
- lodash.assign(originalMan, manuscriptUpdate)
- const updatedMan = await originalMan.save()
- if (eager) {
- updatedMan.claiming = await UserAccess.findById(userId)
+ const newInput = input
+ if (input.meta.nlmId) {
+ input.journalId = await Journal.getIdByNlmId(input.meta.nlmId)
+ delete newInput.meta.nlmId
}
+ const manuscriptUpdate = dManuscriptUpdate(newInput, userId)
+ lodash.assign(originalMan, manuscriptUpdate)
+ await originalMan.save()
+ const updatedMan = await ManuscriptAccess.selectById(input.id, true)
return gManuscript(updatedMan)
},
diff --git a/server/xpub-server/entities/manuscript/resolvers.js b/server/xpub-server/entities/manuscript/resolvers.js
index 98e891f3b..2edd1c7f6 100644
--- a/server/xpub-server/entities/manuscript/resolvers.js
+++ b/server/xpub-server/entities/manuscript/resolvers.js
@@ -80,7 +80,6 @@ const resolvers = {
const updatedMan = await ManuscriptManager.update(
{ id, claimedBy: user },
user,
- true,
)
return updatedMan
},
diff --git a/server/xpub-server/entities/manuscript/typeDefs.graphqls b/server/xpub-server/entities/manuscript/typeDefs.graphqls
index eb5374a60..54d9d236d 100644
--- a/server/xpub-server/entities/manuscript/typeDefs.graphqls
+++ b/server/xpub-server/entities/manuscript/typeDefs.graphqls
@@ -39,6 +39,7 @@ input ManuscriptMetaInput {
fundingGroup: [FundingGroupInput]
releaseDelay: String
unmatchedJournal: String
+ nlmId: String
}
input ArticleIdInput {
--
GitLab