From 1627fb146ac0c5858df4332ef473e6aa23803b34 Mon Sep 17 00:00:00 2001
From: ahamelers <audrey@ahamelers.com>
Date: Wed, 23 Jan 2019 17:33:59 +0000
Subject: [PATCH] citations, normal journal added correctly now, WIP: still
working on unmatched citation
---
.../citation-search/PubMedSearch.jsx | 198 ++++---
.../citation-search/UnmatchedCitation.jsx | 2 +-
app/components/citation-search/operations.js | 45 ++
.../submission-wizard/CreatePage.jsx | 5 +-
.../submission-wizard/CreateSetupPage.jsx | 2 +-
.../submission-wizard/SubmitPage.jsx | 11 +-
.../submission-wizard/operations.js | 8 -
.../entities/journal/data-access.js | 13 +-
server/xpub-model/entities/journal/index.js | 1 +
.../xpub-model/entities/manuscript/index.js | 8 +-
server/xpub-model/index.js | 2 +
.../xpub-server/entities/journal/resolvers.js | 17 +
.../entities/journal/typeDefs.graphqls | 3 +
.../entities/manuscript/typeDefs.graphqls | 2 +-
.../entities/note/resolvers.test.js | 520 ------------------
server/xpub-server/index.js | 1 +
16 files changed, 199 insertions(+), 639 deletions(-)
create mode 100644 app/components/citation-search/operations.js
create mode 100644 server/xpub-server/entities/journal/resolvers.js
create mode 100644 server/xpub-server/entities/journal/typeDefs.graphqls
delete mode 100644 server/xpub-server/entities/note/resolvers.test.js
diff --git a/app/components/citation-search/PubMedSearch.jsx b/app/components/citation-search/PubMedSearch.jsx
index 7c40bf292..13ebd3c1e 100755
--- a/app/components/citation-search/PubMedSearch.jsx
+++ b/app/components/citation-search/PubMedSearch.jsx
@@ -1,6 +1,6 @@
import React from 'react'
import ReactDOM from 'react-dom'
-import { withRouter } from 'react-router-dom'
+import { ApolloConsumer } from 'react-apollo'
import styled from 'styled-components'
import { th } from '@pubsweet/ui-toolkit'
import { Action, Button, Icon, H2, Link } from '@pubsweet/ui'
@@ -18,6 +18,7 @@ import {
SearchForm,
ZebraList,
} from '../ui'
+import { JOURNAL_INFO } from './operations'
import PubMedSearchResult from './PubMedSearchResult'
import UnmatchedCitation from './UnmatchedCitation'
@@ -54,9 +55,9 @@ class PubMedSearch extends React.Component {
inEPMC: false,
unmatched:
this.props.metadata &&
- (!this.props.metadata.articleId ||
- this.props.metadata.articleId.length === 0),
- // pubProvided: null,
+ (!this.props.metadata.articleIds ||
+ this.props.metadata.articleIds.length === 0),
+ pubProvided: false,
}
this.onSearch = this.onSearch.bind(this)
this.onLoad = this.onLoad.bind(this)
@@ -117,7 +118,7 @@ class PubMedSearch extends React.Component {
}
this.setState({ loading: false })
}
- async onSelected(result) {
+ async onSelected(result, journal) {
const inPMC = result.articleids.find(id => id.idtype === 'pmc')
if (inPMC) {
const obj = {
@@ -134,43 +135,49 @@ class PubMedSearch extends React.Component {
obj.inEPMC = true
}
this.setState(obj)
+ } else if (journal.meta.pmcStatus) {
+ this.setState({ pubProvided: journal.journalTitle })
} else {
- // TODO: Add test for journals that participate in (are indexed by) PMC. Processing does not need to continue for these.
-
- /* const journalUrl = `https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nlmcatalog&id=${result.nlmuniqueid}&retmode=xml`
- const response = await fetch(journalUrl)
- const xml = await response.text()
- const indexedby = xml.match(/<IndexingSourceName(.*)<\/IndexingSourceName>/g)
- console.log(indexedby) */
const date = new Date(result.sortpubdate)
const citationData = {
- title: result.title,
- articleIds: [
- {
- pubIdType: 'pmid',
- id: result.uid,
- },
- ],
- publicationDates: [
- {
- type: 'ppub',
- date,
- },
- ],
- nlmId: result.nlmuniqueid,
+ journalId: journal.id,
+ meta: {
+ title: result.title,
+ articleIds: [
+ {
+ pubIdType: 'pmid',
+ id: result.uid,
+ },
+ ],
+ publicationDates: [
+ {
+ type: 'ppub',
+ date,
+ },
+ ],
+ },
}
this.props.citationData(citationData)
}
}
render() {
- const { results, hitcount, loading, query, inPMC, pmcid } = this.state
- const { metadata } = this.props
- const { title, journalMeta, customMeta, notes } = metadata || {}
+ const {
+ results,
+ hitcount,
+ loading,
+ query,
+ inPMC,
+ inEPMC,
+ pubProvided,
+ pmcid,
+ } = this.state
+ const { manuscript } = this.props
+ const { meta, notes, journal } = manuscript || {}
const note = notes ? notes.find(n => n.notesType === 'user citation') : ''
- let journal = journalMeta
- if (!journal && customMeta && customMeta.unmatchedJournal) {
- journal = {
- title: customMeta.unmatchedJournal,
+ let journalInfo = journal
+ if (!journalInfo && meta && meta.unmatchedJournal) {
+ journalInfo = {
+ journalTitle: meta.unmatchedJournal,
}
}
if (this.state.unmatched) {
@@ -181,9 +188,9 @@ class PubMedSearch extends React.Component {
<CloseIcon onClick={() => this.setState({ unmatched: false })} />
</Close>
<UnmatchedCitation
- journal={journal}
+ journal={journalInfo}
note={note ? note.content : ''}
- title={title}
+ title={meta.title}
unmatchedInfo={this.handleUnmatchedInfo}
/>
</Page>
@@ -193,31 +200,43 @@ class PubMedSearch extends React.Component {
}
return (
<SearchArea>
- {inPMC ? (
- <div>
+ {inPMC || pubProvided ? (
+ <React.Fragment>
<H2>No further action is required for this manuscript</H2>
- <p>
- The full text of the article '
- <HTMLString string={inPMC} />
- '
- {` has already been sent to Europe PMC. Please use `}
- <B>{pmcid}</B>
- {` for grant reporting purposes.`}
- </p>
- {this.state.inEPMC && (
- <Links>
- <A href={`https://europepmc.org/articles/${pmcid}`}>
- <Icon color="currentColor">arrow-right-circle</Icon>
- View this article on Europe PMC
- </A>
- <br />
- <A
- href={`https://europepmc.org/orcid/import?3-1.ILinkListener-startwizard?query=${pmcid}`}
- >
- <Icon color="currentColor">arrow-right-circle</Icon>
- Claim this article to your ORCID
- </A>
- </Links>
+ {inPMC ? (
+ <React.Fragment>
+ <p>
+ The full text of the article '
+ <HTMLString string={inPMC} />
+ '
+ {` has already been sent to Europe PMC. Please use `}
+ <B>{pmcid}</B>
+ {` for grant reporting purposes.`}
+ </p>
+ {inEPMC && (
+ <Links>
+ <A href={`https://europepmc.org/articles/${pmcid}`}>
+ <Icon color="currentColor">arrow-right-circle</Icon>
+ View this article on Europe PMC
+ </A>
+ {/* TODO: ORCID claiming
+ <br />
+ <A
+ href={`https://europepmc.org/orcid/import?3-1.ILinkListener-startwizard?query=${pmcid}`}
+ >
+ <Icon color="currentColor">arrow-right-circle</Icon>
+ Claim this article to your ORCID
+ </A> */}
+ </Links>
+ )}
+ </React.Fragment>
+ ) : (
+ <p>
+ Your journal, {pubProvided.journalTitle}, participates in PMC.
+ Your article will be provided to Europe PMC, through PMC, by the
+ publisher. Please contact the publisher regarding any delays in
+ this process.
+ </p>
)}
<Buttons>
<Link to="/">
@@ -229,15 +248,16 @@ class PubMedSearch extends React.Component {
inPMC: null,
pmcid: null,
inEPMC: false,
+ pubProvided: null,
})
}
>
Back to Search
</Button>
</Buttons>
- </div>
+ </React.Fragment>
) : (
- <div>
+ <React.Fragment>
<SearchForm
buttonLabel="Search"
disabled={!this.state.enabled}
@@ -266,39 +286,49 @@ class PubMedSearch extends React.Component {
</Notice>
)}
{results.length > 0 && (
- <ZebraList style={{ textAlign: 'center' }}>
- {results.map(
- result =>
- result.fulljournalname && (
- <PubMedSearchResult
- key={result.uid}
- onClick={() => this.onSelected(result)}
- result={result}
- />
- ),
- )}
- {loading && (
- <Loading>
- <LoadingIcon />
- </Loading>
- )}
- {results.length < hitcount && !loading && (
- <LoadMore onClick={this.onLoad} secondary>
- Load More Results
- </LoadMore>
+ <ApolloConsumer>
+ {client => (
+ <ZebraList style={{ textAlign: 'center' }}>
+ {results.map(
+ result =>
+ result.fulljournalname && (
+ <PubMedSearchResult
+ key={result.uid}
+ onClick={async () => {
+ const { data } = await client.query({
+ query: JOURNAL_INFO,
+ variables: { nlmId: result.nlmuniqueid },
+ })
+ this.onSelected(result, data.selectWithNLM)
+ }}
+ result={result}
+ />
+ ),
+ )}
+ {loading && (
+ <Loading>
+ <LoadingIcon />
+ </Loading>
+ )}
+ {results.length < hitcount && !loading && (
+ <LoadMore onClick={this.onLoad} secondary>
+ Load More Results
+ </LoadMore>
+ )}
+ </ZebraList>
)}
- </ZebraList>
+ </ApolloConsumer>
)}
{results.length === 0 && loading && (
<Loading>
<LoadingIcon />
</Loading>
)}
- </div>
+ </React.Fragment>
)}
</SearchArea>
)
}
}
-export default withRouter(PubMedSearch)
+export default PubMedSearch
diff --git a/app/components/citation-search/UnmatchedCitation.jsx b/app/components/citation-search/UnmatchedCitation.jsx
index 72de2aacb..cfa26696b 100755
--- a/app/components/citation-search/UnmatchedCitation.jsx
+++ b/app/components/citation-search/UnmatchedCitation.jsx
@@ -17,7 +17,7 @@ export default class UnmatchedCitation extends React.Component {
this.state = {
loading: false,
title: this.props.title,
- query: this.props.journal ? this.props.journal.title : '',
+ query: this.props.journal ? this.props.journal.journalTitle : '',
journal: this.props.journal,
note: this.props.note,
enabled: this.props.title && this.props.journal,
diff --git a/app/components/citation-search/operations.js b/app/components/citation-search/operations.js
new file mode 100644
index 000000000..c11190531
--- /dev/null
+++ b/app/components/citation-search/operations.js
@@ -0,0 +1,45 @@
+import gql from 'graphql-tag'
+
+export const JOURNAL_INFO = gql`
+ query($nlmId: String!) {
+ selectWithNLM(nlmId: $nlmId) {
+ id
+ journalTitle
+ meta {
+ nlmta
+ pmcStatus
+ pubmedStatus
+ }
+ }
+ }
+`
+
+export const CREATE_NOTE = gql`
+ mutation CreateNote($data: NewNoteInput!) {
+ createNote(data: $data) {
+ id
+ meta {
+ notes {
+ id
+ notesType
+ content
+ }
+ }
+ }
+ }
+`
+
+export const UPDATE_NOTE = gql`
+ mutation UpdateNote($data: NoteInput!) {
+ updateNote(data: $data) {
+ id
+ meta {
+ notes {
+ id
+ notesType
+ content
+ }
+ }
+ }
+ }
+`
diff --git a/app/components/submission-wizard/CreatePage.jsx b/app/components/submission-wizard/CreatePage.jsx
index 23e0b231e..c0d426166 100755
--- a/app/components/submission-wizard/CreatePage.jsx
+++ b/app/components/submission-wizard/CreatePage.jsx
@@ -147,7 +147,8 @@ class Created extends React.Component {
render() {
const currentUser = this.context
const { currentStep, status, error, checked } = this.state
- const { id: mId, meta, journal, files: allfiles } = this.props.manuscript
+ const { manuscript } = this.props
+ const { id: mId, meta, journal, files: allfiles } = manuscript
const { notes } = meta
const files = allfiles
? allfiles.filter(
@@ -213,7 +214,7 @@ class Created extends React.Component {
<H2>Citation</H2>
<PubMedSearch
citationData={changeCitation}
- metadata={meta}
+ manuscript={manuscript}
/>
</React.Fragment>
) : (
diff --git a/app/components/submission-wizard/CreateSetupPage.jsx b/app/components/submission-wizard/CreateSetupPage.jsx
index 073a4f16e..4c41f3871 100755
--- a/app/components/submission-wizard/CreateSetupPage.jsx
+++ b/app/components/submission-wizard/CreateSetupPage.jsx
@@ -17,7 +17,7 @@ const manuscriptSetup = async (
const created = await createManuscript()
const { id } = created.data.createManuscript
await updateManuscript({
- variables: { data: { id, meta: citationData } },
+ variables: { data: { id, ...citationData } },
})
const route = `/submission/${id}/create`
history.push(route)
diff --git a/app/components/submission-wizard/SubmitPage.jsx b/app/components/submission-wizard/SubmitPage.jsx
index c0fa9686f..df41cf01a 100755
--- a/app/components/submission-wizard/SubmitPage.jsx
+++ b/app/components/submission-wizard/SubmitPage.jsx
@@ -116,13 +116,8 @@ class Submit extends React.Component {
`${name.title ? `${name.title} ` : ''}${name.givenNames} ${name.surname}`
render() {
const currentUser = this.context
- const {
- id: mId,
- meta,
- files: allfiles,
- status,
- teams,
- } = this.props.manuscript
+ const { manuscript } = this.props
+ const { id: mId, meta, files: allfiles, status, teams } = manuscript
if (teams && allfiles) {
const { editing, references, regexes } = this.state
const fundingGroup = meta.fundingGroup ? meta.fundingGroup : []
@@ -170,7 +165,7 @@ class Submit extends React.Component {
<H3>Citation</H3>
<PubMedSearch
citationData={this.createNewManuscriptVersion}
- metadata={meta}
+ manuscript={manuscript}
/>
</div>
),
diff --git a/app/components/submission-wizard/operations.js b/app/components/submission-wizard/operations.js
index c52a14982..ec6b7347c 100644
--- a/app/components/submission-wizard/operations.js
+++ b/app/components/submission-wizard/operations.js
@@ -150,14 +150,6 @@ export const UPDATE_NOTE = gql`
}
`
-export const DELETE_NOTE = gql`
- mutation DeleteNote($id: ID!) {
- deleteNote(id: $id) {
- id
- }
- }
-`
-
export const SUBMIT_MANUSCRIPT = gql`
mutation SubmitManuscript($data: ManuscriptInput!) {
submitManuscript(data: $data) {
diff --git a/server/xpub-model/entities/journal/data-access.js b/server/xpub-model/entities/journal/data-access.js
index 6ef633f05..dc623e0b6 100644
--- a/server/xpub-model/entities/journal/data-access.js
+++ b/server/xpub-model/entities/journal/data-access.js
@@ -60,18 +60,17 @@ class Journal extends EpmcBaseModel {
return rowToEntity(rows[0])
}
- static async getIdByNlmId(nlmId) {
- const row = await runQuery(
+ static async selectByNlmId(nlmId) {
+ const rows = await runQuery(
buildQuery
- .select('journal.id')
+ .select('journal.*')
.from('journal')
- .where('meta,nlmuniqueid', nlmId)
- .first(),
+ .where('meta,nlmuniqueid', nlmId),
)
- if (!row) {
+ if (!rows) {
throw new Error('journal not found')
}
- return row.id
+ return rowToEntity(rows[0])
}
static async selectAll() {
diff --git a/server/xpub-model/entities/journal/index.js b/server/xpub-model/entities/journal/index.js
index 2c47dfdac..832a196d6 100755
--- a/server/xpub-model/entities/journal/index.js
+++ b/server/xpub-model/entities/journal/index.js
@@ -23,6 +23,7 @@ const JournalManager = {
return { ...journal, id }
},
+ selectWithNLM: async nlmId => Journal.selectByNlmId(nlmId),
}
module.exports = JournalManager
diff --git a/server/xpub-model/entities/manuscript/index.js b/server/xpub-model/entities/manuscript/index.js
index dfa41dbef..ca6dc2b31 100755
--- a/server/xpub-model/entities/manuscript/index.js
+++ b/server/xpub-model/entities/manuscript/index.js
@@ -9,7 +9,6 @@ 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 Journal = require('../journal/data-access')
const { dManuscriptUpdate, gManuscript } = require('./helpers/transform')
const mergeObjects = (...inputs) =>
@@ -139,12 +138,7 @@ const Manuscript = {
if (!originalMan) {
throw new Error('Manuscript not found')
}
- const newInput = input
- if (input.meta.nlmId) {
- input.journalId = await Journal.getIdByNlmId(input.meta.nlmId)
- delete newInput.meta.nlmId
- }
- const manuscriptUpdate = dManuscriptUpdate(newInput, userId)
+ const manuscriptUpdate = dManuscriptUpdate(input, userId)
lodash.assign(originalMan, manuscriptUpdate)
await originalMan.save()
const updatedMan = await ManuscriptAccess.selectById(input.id, true)
diff --git a/server/xpub-model/index.js b/server/xpub-model/index.js
index 5b8e19742..f31cd1750 100644
--- a/server/xpub-model/index.js
+++ b/server/xpub-model/index.js
@@ -5,6 +5,7 @@ const NoteManager = require('./entities/note')
const RoleManager = require('./entities/role')
const TeamManager = require('./entities/team')
const UserManager = require('./entities/user')
+const JournalManager = require('./entities/journal')
const OrganizationManager = require('./entities/organization')
module.exports = {
@@ -15,5 +16,6 @@ module.exports = {
RoleManager,
TeamManager,
UserManager,
+ JournalManager,
OrganizationManager,
}
diff --git a/server/xpub-server/entities/journal/resolvers.js b/server/xpub-server/entities/journal/resolvers.js
new file mode 100644
index 000000000..415fcf7c4
--- /dev/null
+++ b/server/xpub-server/entities/journal/resolvers.js
@@ -0,0 +1,17 @@
+const rfr = require('rfr')
+
+const { JournalManager } = rfr('server/xpub-model')
+
+const resolvers = {
+ Query: {
+ async selectWithNLM(_, { nlmId }, { user }) {
+ if (!user) {
+ throw new Error('You are not authenticated!')
+ }
+
+ return JournalManager.selectWithNLM(nlmId)
+ },
+ },
+}
+
+module.exports = resolvers
diff --git a/server/xpub-server/entities/journal/typeDefs.graphqls b/server/xpub-server/entities/journal/typeDefs.graphqls
new file mode 100644
index 000000000..4b5b4c416
--- /dev/null
+++ b/server/xpub-server/entities/journal/typeDefs.graphqls
@@ -0,0 +1,3 @@
+extend type Query {
+ selectWithNLM(nlmId: String!): Journal!
+}
\ No newline at end of file
diff --git a/server/xpub-server/entities/manuscript/typeDefs.graphqls b/server/xpub-server/entities/manuscript/typeDefs.graphqls
index 54d9d236d..ef2a633ad 100644
--- a/server/xpub-server/entities/manuscript/typeDefs.graphqls
+++ b/server/xpub-server/entities/manuscript/typeDefs.graphqls
@@ -29,6 +29,7 @@ extend type Mutation {
input ManuscriptInput {
id: ID!
status: String
+ journalId: ID
meta: ManuscriptMetaInput
}
@@ -39,7 +40,6 @@ input ManuscriptMetaInput {
fundingGroup: [FundingGroupInput]
releaseDelay: String
unmatchedJournal: String
- nlmId: String
}
input ArticleIdInput {
diff --git a/server/xpub-server/entities/note/resolvers.test.js b/server/xpub-server/entities/note/resolvers.test.js
deleted file mode 100644
index 3e3d26d07..000000000
--- a/server/xpub-server/entities/note/resolvers.test.js
+++ /dev/null
@@ -1,520 +0,0 @@
-/* jest.mock('@pubsweet/logger')
-jest.mock('@elifesciences/xpub-meca-export', () => ({
- mecaExport: jest.fn(() => Promise.resolve()),
-}))
-
-const lodash = require('lodash')
-const config = require('config')
-const fs = require('fs-extra')
-const stream = require('stream')
-const logger = require('@pubsweet/logger')
-const { createTables } = require('@pubsweet/db-manager')
-const mailer = require('@pubsweet/component-send-email')
-// const { mecaExport } = require('@elifesciences/xpub-meca-export')
-const startS3rver = require('../../test/mock-s3-server')
-const {
- UserManager: User,
- FileManager,
- ManuscriptManager: Manuscript,
-} = require('@elifesciences/xpub-model')
-const { Mutation, Query } = require('./resolvers')
-const {
- userData,
- badUserData,
- expectedManuscript,
- manuscriptInput,
-} = require('./resolvers.test.data')
-
-// const replaySetup = require('../../../../test/helpers/replay-setup')
-
-describe('Manuscripts', () => {
- const profileId = userData.identities[0].identifier
- const badProfileId = badUserData.identities[0].identifier
- let userId
-
- beforeEach(async () => {
- // replaySetup('success')
- await Promise.all([
- fs.remove(config.get('pubsweet-server.uploads')),
- createTables(true),
- ])
- const [user] = await Promise.all([
- User.save(userData),
- User.save(badUserData),
- ])
- userId = user.id
- mailer.clearMails()
- })
-
- describe('manuscript', () => {
- it('Gets form data', async () => {
- const manuscriptData = {
- createdBy: userId,
- meta: { title: 'title' },
- status: 'INITIAL',
- }
- const { id } = await Manuscript.save(manuscriptData)
-
- const manuscript = await Query.manuscript({}, { id }, { user: profileId })
- expect(manuscript).toMatchObject(manuscriptData)
- })
- })
-
- describe('createManuscript', () => {
- it('fails if no authenticated user', async () => {
- await expect(Mutation.createManuscript({}, {}, {})).rejects.toThrow(
- 'Not logged in',
- )
- })
-
- it('adds new manuscript to the db for current user with status INITIAL', async () => {
- const manuscript = await Mutation.createManuscript(
- {},
- {},
- { user: profileId },
- )
-
- const manuscripts = await Manuscript.findByStatus('INITIAL', userId)
- expect(manuscripts.length).toBeGreaterThan(0)
- expect(manuscripts[0].id).toBe(manuscript.id)
- })
- })
-
- describe('updateManuscript', () => {
- it("fails if manuscript doesn't belong to user", async () => {
- const blankManuscript = Manuscript.new({ createdBy: userId })
- const manuscript = await Manuscript.save(blankManuscript)
- await expect(
- Mutation.updateManuscript(
- {},
- { data: { id: manuscript.id } },
- { user: badProfileId },
- ),
- ).rejects.toThrow('Manuscript not found')
- })
-
- it('fails if manuscript has already been submitted', async () => {
- const blankManuscript = Manuscript.new({
- createdBy: userId,
- status: Manuscript.statuses.MECA_EXPORT_PENDING,
- })
- const manuscript = await Manuscript.save(blankManuscript)
- await expect(
- Mutation.updateManuscript(
- {},
- { data: { id: manuscript.id } },
- { user: profileId },
- ),
- ).rejects.toThrow(
- 'Cannot update manuscript with status of MECA_EXPORT_PENDING',
- )
- })
-
- it('updates the current submission for user with data and emails', async () => {
- const NUM_EMAILS = 1
- const blankManuscript = Manuscript.new({ createdBy: userId })
- const manuscript = await Manuscript.save(blankManuscript)
-
- await Mutation.updateManuscript(
- {},
- { data: { id: manuscript.id, ...manuscriptInput } },
- { user: profileId },
- )
- await waitforEmails(NUM_EMAILS)
-
- const allEmails = mailer.getMails()
- expect(allEmails).toHaveLength(NUM_EMAILS)
-
- // Check the dashboard email
- expect(allEmails[0]).toMatchObject({
- to: 'mymail@mail.com',
- subject: 'Libero Submission System: New Submission',
- })
-
- const actualManuscript = await Manuscript.find(manuscript.id, userId)
- expect(actualManuscript).toMatchObject(expectedManuscript)
- })
- })
-
- describe('submitManuscript', () => {
- let id, initialManuscript
-
- beforeAll(() =>
- jest
- .spyOn(FileManager, 'getContent')
- .mockImplementation(() => 'A real PDF'))
-
- afterAll(() => FileManager.getContent.mockRestore())
-
- beforeEach(async () => {
- jest.clearAllMocks()
-
- initialManuscript = Manuscript.new({ createdBy: userId })
- initialManuscript.files = [
- {
- url: 'fake-path.pdf',
- filename: 'FakeManuscript.pdf',
- type: 'MANUSCRIPT_SOURCE',
- },
- ]
-
- const manuscript = await Manuscript.save(initialManuscript)
- id = manuscript.id
- })
-
- it('stores data with new status', async () => {
- const returnedManuscript = await Mutation.submitManuscript(
- {},
- { data: { ...manuscriptInput, id } },
- { user: profileId },
- )
-
- expect(returnedManuscript.status).toBe(
- Manuscript.statuses.MECA_EXPORT_PENDING,
- )
-
- const storedManuscript = await Manuscript.find(id, userId)
-
- expect(storedManuscript).toMatchObject({
- ...expectedManuscript,
- status: expect.stringMatching(/^MECA_EXPORT_(SUCCEEDED|PENDING)/),
- })
- })
-
- it('calls meca export with correct arguments', async () => {
- const ip = '1.2.3.4'
- await Mutation.submitManuscript(
- {},
- { data: { ...manuscriptInput, id } },
- { user: profileId, ip },
- )
-
- expect(mecaExport).toHaveBeenCalled()
- const [
- actualManuscript,
- actualContent,
- actualIp,
- ] = mecaExport.mock.calls[0]
- expect(actualManuscript.id).toBe(id)
- expect(actualContent).toBe('A real PDF')
- expect(actualIp).toBe(ip)
- })
-
- it('removes blank optional reviewer rows', async () => {
- const manuscript = lodash.cloneDeep(manuscriptInput)
- manuscript.id = id
- manuscript.suggestedReviewers = [
- { name: 'Reviewer 1', email: 'reviewer1@mail.com' },
- { name: 'Reviewer 2', email: 'reviewer2@mail.com' },
- { name: 'Reviewer 3', email: 'reviewer3@mail.com' },
- { name: '', email: '' },
- { name: 'Reviewer 4', email: 'reviewer4@mail.com' },
- { name: '', email: '' },
- ]
- await Mutation.submitManuscript(
- {},
- { data: manuscript },
- { user: profileId },
- )
-
- const storedManuscript = await Manuscript.find(id, userId)
- const team = storedManuscript.teams.find(
- t => t.role === 'suggestedReviewer',
- )
- expect(team.teamMembers.map(member => member.meta)).toEqual([
- { name: 'Reviewer 1', email: 'reviewer1@mail.com' },
- { name: 'Reviewer 2', email: 'reviewer2@mail.com' },
- { name: 'Reviewer 3', email: 'reviewer3@mail.com' },
- { name: 'Reviewer 4', email: 'reviewer4@mail.com' },
- ])
- })
-
- it("fails if manuscript doesn't belong to user", async () => {
- const blankManuscript = Manuscript.new({ createdBy: userId })
- const manuscript = await Manuscript.save(blankManuscript)
- await expect(
- Mutation.submitManuscript(
- {},
- { data: { id: manuscript.id } },
- { user: badProfileId },
- ),
- ).rejects.toThrow('Manuscript not found')
- })
-
- it('fails if manuscript has already been submitted', async () => {
- const blankManuscript = Manuscript.new({
- createdBy: userId,
- status: Manuscript.statuses.MECA_EXPORT_PENDING,
- })
- const manuscript = await Manuscript.save(blankManuscript)
- await expect(
- Mutation.submitManuscript(
- {},
- { data: { id: manuscript.id } },
- { user: profileId },
- ),
- ).rejects.toThrow(
- 'Cannot submit manuscript with status of MECA_EXPORT_PENDING',
- )
- })
-
- // TODO more tests needed here
- it('fails when manuscript has incomplete data', async () => {
- const badManuscript = {
- id,
- title: 'Some Title',
- }
- await expect(
- Mutation.submitManuscript(
- {},
- { data: badManuscript },
- { user: profileId },
- ),
- ).rejects.toThrow()
- })
-
- it('fails when manuscript has bad data types', async () => {
- const badManuscript = lodash.cloneDeep(manuscriptInput)
- lodash.merge(badManuscript, {
- id,
- title: 100,
- manuscriptType: {},
- })
- await expect(
- Mutation.submitManuscript(
- {},
- { data: badManuscript },
- { user: profileId },
- ),
- ).rejects.toThrow(
- '"title" is not allowed. "manuscriptType" is not allowed',
- )
- })
-
- it('sends email and updates status when export fails', async () => {
- const NUM_EMAILS = 1
- jest.spyOn(logger, 'error').mockImplementationOnce(() => {})
- mecaExport.mockImplementationOnce(() =>
- Promise.reject(new Error('Broked')),
- )
-
- const manuscript = lodash.cloneDeep(manuscriptInput)
- manuscript.id = id
- await Mutation.submitManuscript(
- {},
- { data: manuscript },
- { user: profileId },
- )
-
- await waitforEmails(NUM_EMAILS)
-
- const allEmails = mailer.getMails()
- expect(allEmails).toHaveLength(NUM_EMAILS)
-
- // Check the MECA fail email
- expect(allEmails[0]).toMatchObject({
- to: 'test@example.com',
- subject: 'MECA export failed',
- })
-
- expect(logger.error).toHaveBeenCalled()
- const updatedManuscript = await Manuscript.find(manuscript.id, userId)
- expect(updatedManuscript.status).toBe(
- Manuscript.statuses.MECA_EXPORT_FAILED,
- )
- })
- })
-
- describe('uploadManuscript', () => {
- let s3Server
-
- beforeEach(async () => {
- const server = await startS3rver({
- ...config.get('aws.credentials'),
- ...config.get('aws.s3'),
- })
- s3Server = server.instance
- })
-
- afterEach(done => {
- s3Server.close(done)
- })
-
- it("fails if manuscript doesn't belong to user", async () => {
- const blankManuscript = Manuscript.new()
- blankManuscript.createdBy = userId
- const manuscript = await Manuscript.save(blankManuscript)
-
- await expect(
- Mutation.uploadManuscript(
- {},
- { id: manuscript.id },
- { user: badProfileId },
- ),
- ).rejects.toThrow('Manuscript not found')
- })
-
- it('saves manuscript to S3', async () => {
- const blankManuscript = Manuscript.new()
- blankManuscript.createdBy = userId
- const { id } = await Manuscript.save(blankManuscript)
- const file = {
- filename: 'manuscript.pdf',
- stream: fs.createReadStream(
- `${__dirname}/../../../../test/fixtures/dummy-manuscript-2.pdf`,
- ),
- mimetype: 'application/pdf',
- }
- const manuscript = await Mutation.uploadManuscript(
- {},
- { id, file, fileSize: 73947 },
- { user: profileId },
- )
-
- const pdfBinary = await FileManager.getContent(
- Manuscript.getSource(manuscript),
- )
- expect(pdfBinary.toString().substr(0, 6)).toEqual('%PDF-1')
- })
-
- it('fails if S3 upload fails', async () => {
- jest
- .spyOn(FileManager, 'putContent')
- .mockImplementationOnce(() =>
- Promise.reject(new Error('Failed to persist file')),
- )
- const blankManuscript = Manuscript.new({ createdBy: userId })
- const { id } = await Manuscript.save(blankManuscript)
- const file = {
- filename: 'manuscript.pdf',
- stream: fs.createReadStream(
- `${__dirname}/../../../../test/fixtures/dummy-manuscript-2.pdf`,
- ),
- mimetype: 'application/pdf',
- }
- await expect(
- Mutation.uploadManuscript(
- {},
- { id, file, fileSize: 73947 },
- { user: profileId },
- ),
- ).rejects.toThrow('Failed to persist file')
-
- const manuscript = await Manuscript.find(id, userId)
- expect(manuscript.files).toHaveLength(0)
- })
-
- it('sets empty title if ScienceBeam fails', async () => {
- jest.spyOn(logger, 'warn').mockImplementationOnce(() => {})
- // replaySetup('error')
- const blankManuscript = Manuscript.new()
- blankManuscript.createdBy = userId
- const { id } = await Manuscript.save(blankManuscript)
- const file = {
- filename: 'manuscript.pdf',
- stream: fs.createReadStream(
- `${__dirname}/../../../../test/fixtures/dummy-manuscript-2.pdf`,
- ),
- mimetype: 'application/pdf',
- }
- const manuscript = await Mutation.uploadManuscript(
- {},
- { id, file, fileSize: 73947 },
- { user: profileId },
- )
- expect(manuscript).toMatchObject({
- id,
- meta: { title: '' },
- files: [{ filename: 'manuscript.pdf' }],
- })
- expect(logger.warn).toHaveBeenCalled()
- })
-
- it('extracts title from PDF', async () => {
- const blankManuscript = Manuscript.new()
- blankManuscript.createdBy = userId
- const { id } = await Manuscript.save(blankManuscript)
- const file = {
- filename: 'manuscript.pdf',
- stream: fs.createReadStream(
- `${__dirname}/../../../../test/fixtures/dummy-manuscript-2.pdf`,
- ),
- mimetype: 'application/pdf',
- }
- const manuscript = await Mutation.uploadManuscript(
- {},
- { id, file, fileSize: 73947 },
- { user: profileId },
- )
- expect(manuscript).toMatchObject({
- id,
- meta: {
- title:
- 'The Relationship Between Lamport Clocks and Interrupts Using Obi',
- },
- files: [{ filename: 'manuscript.pdf' }],
- })
- })
-
- it(`fails if manuscript size is bigger than ${config.get(
- 'fileUpload.maxSizeMB',
- )}MB`, async () => {
- const blankManuscript = Manuscript.new()
- blankManuscript.createdBy = userId
- const { id } = await Manuscript.save(blankManuscript)
-
- const maxFileSize = config.get('fileUpload.maxSizeMB')
- const fileSize = maxFileSize * 1e6 + 1
- const bufferStream = new stream.PassThrough()
- bufferStream.end(Buffer.alloc(fileSize))
- const file = {
- filename: 'manuscript.pdf',
- stream: bufferStream,
- mimetype: 'application/pdf',
- }
- await expect(
- Mutation.uploadManuscript(
- {},
- { id, file, fileSize },
- { user: profileId },
- ),
- ).rejects.toThrow(`File size shouldn't exceed ${maxFileSize}MB`)
- })
- })
-
- describe('deleteManuscript', () => {
- it("fails if manuscript doesn't belong to user", async () => {
- const blankManuscript = Manuscript.new()
- blankManuscript.createdBy = userId
- const manuscript = await Manuscript.save(blankManuscript)
-
- await expect(
- Mutation.deleteManuscript(
- {},
- { id: manuscript.id },
- { user: badProfileId },
- ),
- ).rejects.toThrow('Manuscript not found')
- })
-
- it('removes manuscript from database', async () => {
- const blankManuscript = Manuscript.new()
- blankManuscript.createdBy = userId
- const manuscript = await Manuscript.save(blankManuscript)
- await Mutation.deleteManuscript(
- {},
- { id: manuscript.id },
- { user: profileId },
- )
-
- const manuscripts = await Manuscript.all(userId)
- expect(manuscripts).toEqual([])
- })
- })
-})
-async function waitforEmails(NUM_EMAILS) {
- for (let i = 0; i < 100 && mailer.getMails().length < NUM_EMAILS; i += 1) {
- // eslint-disable-next-line no-await-in-loop
- await new Promise(resolve => setTimeout(resolve, 10))
- }
-} */
diff --git a/server/xpub-server/index.js b/server/xpub-server/index.js
index 39898cdaa..cc800fec3 100644
--- a/server/xpub-server/index.js
+++ b/server/xpub-server/index.js
@@ -8,6 +8,7 @@ const entities = [
'file',
'identity',
'manuscript',
+ 'journal',
'note',
'team',
'role',
--
GitLab