diff --git a/app/components/dashboard/AdminDashboard.jsx b/app/components/dashboard/AdminDashboard.jsx
index 3920ccfbda070d34ebb37c5034aa1e8202a20025..a6941461c398396684e2f423e5d08a02ad0b0b34 100755
--- a/app/components/dashboard/AdminDashboard.jsx
+++ b/app/components/dashboard/AdminDashboard.jsx
@@ -17,8 +17,8 @@ const ListTable = styled(Table)`
`
const HelpdeskQueue = {
'needs submission QA': ['submitted'],
- 'needs xml QA': ['xml-qa'],
- 'xml error reported': ['xml-triage'],
+ 'needs XML QA': ['xml-qa'],
+ 'XML errors': ['xml-triage'],
'needs citation': ['xml-complete'],
}
diff --git a/docker-compose.prod.yml b/docker-compose.prod.yml
index fe4536943ae81f2610a57d35ba4e4eb6b65766f0..d8076206c4a24048a8131a2cbf7c0d987d8efdbf 100755
--- a/docker-compose.prod.yml
+++ b/docker-compose.prod.yml
@@ -4,13 +4,13 @@ services:
app:
volumes: # remember to replace /folder_on_disk/ with the path to where you want to store the files on the host machine
- "ftpdata:/home/xpub/ftpdata/"
- ports:
- - "80:80"
environment:
NODE_ENV: production
PORT: "80"
env_file:
- .env.prod
+ expose:
+ - "80"
postgres:
ports:
diff --git a/server/ncbi-integration/fromNcbi.js b/server/ncbi-integration/fromNcbi.js
index 3093dfc95a9741ec1ddf4351a2103e7c2b8e7063..e05676b6da4511b4de9a420c3d124c55aa9c70ac 100644
--- a/server/ncbi-integration/fromNcbi.js
+++ b/server/ncbi-integration/fromNcbi.js
@@ -4,55 +4,69 @@ const fs = require('fs')
const os = require('os')
const Dom = require('xmldom').DOMParser
const logger = require('@pubsweet/logger')
-const ManuscriptManager = require('../xpub-model/entities/manuscript')
+const lodash = require('lodash')
const ManuscriptAccess = require('../xpub-model/entities/manuscript/data-access')
+const {
+ dManuscriptUpdate,
+ gManuscript,
+} = require('../xpub-model/entities/manuscript/helpers/transform')
const NCBI_RESPONSE_EXT = new RegExp(/\S+.ld.response.xml$/i)
;(async () => {
const beforeUpdate = Date.now()
await fromNcbi()
- logger.info(`Published check was finished in ${Date.now() - beforeUpdate} ms`)
+ logger.info(`from ncbi check was finished in ${Date.now() - beforeUpdate} ms`)
})()
+function close(c) {
+ c.end()
+ ManuscriptAccess.knex().destroy()
+ c = null
+ process.exit()
+}
+
async function fromNcbi() {
let c = new Client()
c.on('ready', () => {
- c.list(`/${config.get('ncbi-ftp')['send-folder']}`, false, (err, list) => {
- if (err) {
- c = null
- return
- }
- const responseFiles = list.filter(file =>
- NCBI_RESPONSE_EXT.test(file.name),
- )
- if (!responseFiles.length) {
- c.end()
- }
- responseFiles.forEach((file, index, array) => {
- const remoteFilePath = `/${config.get('ncbi-ftp')['send-folder']}/${
- file.name
- }`
- c.get(remoteFilePath, (err, stream) => {
- if (err) return
- const path = `${os.tmpdir()}/${file.name}`
- stream.pipe(fs.createWriteStream(path))
- processFile(path).then(response => {
- updateManuscriptNcbiStatus(file.name, response).then(() => {
- c.rename(remoteFilePath, `${remoteFilePath}.processed`, err => {
- if (err) {
- logger.info(err)
- }
- if (index === array.length - 1) {
- c.end()
- c = null
- }
+ c.list(
+ `/${config.get('ncbi-ftp')['receive-folder']}`,
+ false,
+ (err, list) => {
+ if (err) {
+ c = null
+ return
+ }
+ const responseFiles = list.filter(file =>
+ NCBI_RESPONSE_EXT.test(file.name),
+ )
+ if (!responseFiles.length) {
+ close(c)
+ }
+ responseFiles.forEach((file, index, array) => {
+ const remoteFilePath = `/${
+ config.get('ncbi-ftp')['receive-folder']
+ }/${file.name}`
+ c.get(remoteFilePath, (err, stream) => {
+ if (err) return
+ const path = `${os.tmpdir()}/${file.name}`
+ stream.pipe(fs.createWriteStream(path))
+ processFile(path).then(response => {
+ updateManuscriptNcbiStatus(file.name, response).then(() => {
+ c.rename(remoteFilePath, `${remoteFilePath}.processed`, err => {
+ if (err) {
+ logger.info(err)
+ }
+ if (index === array.length - 1) {
+ close(c)
+ }
+ })
})
})
})
})
- })
- })
+ },
+ )
})
const { host, user, password } = config.get('ncbi-ftp')
c.connect({ host, user, password })
@@ -88,7 +102,7 @@ async function updateManuscriptNcbiStatus(fileName, response) {
if (!response.status && response.pmcid) {
newIds.push({ pubIdType: 'pmcid', id: response.pmcid })
}
- return ManuscriptManager.update({
+ return updateManuscript({
id: manuscriptId,
status: response.status
? config.get('ncbiFailedState')
@@ -97,3 +111,15 @@ async function updateManuscriptNcbiStatus(fileName, response) {
'meta,articleIds': response.pmcid ? newIds : manuscript['meta,articleIds'],
})
}
+
+async function updateManuscript(input) {
+ const originalMan = await ManuscriptAccess.selectById(input.id)
+ if (!originalMan) {
+ throw new Error('Manuscript not found')
+ }
+ const manuscriptUpdate = dManuscriptUpdate(input)
+ lodash.assign(originalMan, manuscriptUpdate)
+ await originalMan.save()
+ const updatedMan = await ManuscriptAccess.selectById(input.id, true)
+ return gManuscript(updatedMan)
+}
diff --git a/server/ncbi-integration/toNcbi.js b/server/ncbi-integration/toNcbi.js
index 52c1aad159fb5a9730f3e043eee56dcb634e0b9e..7a1a9a48de8d8ac0dadcc4d281a538cb499d4154 100644
--- a/server/ncbi-integration/toNcbi.js
+++ b/server/ncbi-integration/toNcbi.js
@@ -7,41 +7,56 @@ const os = require('os')
const config = require('config')
const md5File = require('md5-file')
const Client = require('ftp')
+const lodash = require('lodash')
const pubsweetServer = config.get('pubsweet-server.baseUrl')
// const ftpLocation = '/home/mselim/test'
const ncbiFileTypes = config.get('ncbiFileTypes')
-const ManuscriptManager = require('../xpub-model/entities/manuscript')
+// const ManuscriptManager = require('../xpub-model/entities/manuscript')
+const ManuscriptAccess = require('../xpub-model/entities/manuscript/data-access')
+const {
+ dManuscriptUpdate,
+ gManuscript,
+} = require('../xpub-model/entities/manuscript/helpers/transform')
const NCBI_PACKAGE_EXT = '.ld'
;(async () => {
const beforeUpdate = Date.now()
await toNcbi()
- logger.info(`Published check was finished in ${Date.now() - beforeUpdate} ms`)
+ logger.info(`ncbi check in ${Date.now() - beforeUpdate} ms`)
})()
async function toNcbi() {
- ManuscriptManager.findNcbiReady().then(manuscripts => {
- manuscripts.forEach(manuscript => {
- logger.info(`Sending package ${manuscript.id} to ncbi FTP location.`)
- createTempDir(manuscript).then(tmpPath =>
- getFiles(tmpPath, manuscript).then(() =>
- getFunderInfo(manuscript).then(funders =>
- createManifest(tmpPath, manuscript, funders).then(() =>
- compress(tmpPath, manuscript).then(destination => {
- send(destination, manuscript).then(() => {
- tidyUp(tmpPath)
- updateManuscriptNcbiStatus(manuscript)
- })
- }),
+ ManuscriptAccess.findNcbiReady()
+ .then(manuscripts => {
+ manuscripts.forEach(manuscript => {
+ logger.info(`Sending package ${manuscript.id} to ncbi FTP location.`)
+ createTempDir(manuscript).then(tmpPath =>
+ getFiles(tmpPath, manuscript).then(() =>
+ getFunderInfo(manuscript).then(funders =>
+ createManifest(tmpPath, manuscript, funders).then(() =>
+ compress(tmpPath, manuscript).then(destination => {
+ send(destination, manuscript).then(() => {
+ tidyUp(tmpPath)
+ updateManuscriptNcbiStatus(manuscript).then(() => {
+ ManuscriptAccess.knex().destroy()
+ process.exit()
+ })
+ })
+ }),
+ ),
),
),
- ),
- )
+ )
+ })
+ if (!manuscripts.length) {
+ ManuscriptAccess.knex().destroy()
+ process.exit()
+ }
})
- })
+ .catch(e => logger.error(e))
}
function createTempDir(manuscript) {
@@ -198,7 +213,7 @@ function send(dest, manuscript) {
c.on('ready', () => {
c.put(
dest,
- `/${config.get('ncbi-ftp')['receive-folder']}/${path.basename(dest)}`,
+ `/${config.get('ncbi-ftp')['send-folder']}/${path.basename(dest)}`,
err => {
if (err) {
reject(err)
@@ -247,7 +262,7 @@ function getFileMd5(filePath) {
}
function updateManuscriptNcbiStatus(manuscript) {
- ManuscriptManager.update(
+ updateManuscript(
{
id: manuscript.id,
status: config.get('ncbiSentState'),
@@ -258,3 +273,15 @@ function updateManuscriptNcbiStatus(manuscript) {
logger.info(`Created package ${manuscript.id} to ncbi FTP location.`),
)
}
+
+async function updateManuscript(input) {
+ const originalMan = await ManuscriptAccess.selectById(input.id)
+ if (!originalMan) {
+ throw new Error('Manuscript not found')
+ }
+ const manuscriptUpdate = dManuscriptUpdate(input)
+ lodash.assign(originalMan, manuscriptUpdate)
+ await originalMan.save()
+ const updatedMan = await ManuscriptAccess.selectById(input.id, true)
+ return gManuscript(updatedMan)
+}
diff --git a/server/privacyNotice/privacyNoticeCheck.js b/server/privacyNotice/privacyNoticeCheck.js
index 092923259ef56c1a47b5d814122461408dbd734a..6c745868c85416f36c5a4fedefae8cd84d57ea88 100644
--- a/server/privacyNotice/privacyNoticeCheck.js
+++ b/server/privacyNotice/privacyNoticeCheck.js
@@ -2,7 +2,7 @@ const https = require('https')
const PrivacyNotice = require('../xpub-model/entities/privacyNotice/data-access')
-const privacyNoticeCheck = () => {
+const privacyNoticeCheck = async () => {
PrivacyNotice.selectLastVersion().then(privacyNotice => {
getLatestVersion().then(data => {
const privacyNotesData = data.nodes[0].node
@@ -13,11 +13,13 @@ const privacyNoticeCheck = () => {
privacyNotesData.changed.split('-')[0].trim(),
),
}
- PrivacyNotice.insert(latestPrivacyNotice).then(() =>
- PrivacyNotice.knex().destroy(),
- )
+ PrivacyNotice.insert(latestPrivacyNotice).then(() => {
+ PrivacyNotice.knex().destroy()
+ process.exit()
+ })
} else {
PrivacyNotice.knex().destroy()
+ process.exit()
}
})
})
diff --git a/server/xpub-model/entities/manuscript/index.js b/server/xpub-model/entities/manuscript/index.js
index 25eeb10cf007a8f5a52b9b9545aff7c232545691..1a6553de207f6c642993f3a1767b0f6906b9c2a0 100755
--- a/server/xpub-model/entities/manuscript/index.js
+++ b/server/xpub-model/entities/manuscript/index.js
@@ -547,7 +547,6 @@ const Manuscript = {
}
return true
},
-
modelName: 'Manuscript',
model: ManuscriptAccess,
diff --git a/server/xpub-model/entities/team/data-access.js b/server/xpub-model/entities/team/data-access.js
index b4be60f968ba75a60499806e0a1bce52774be542..939006c22ce3af09827a815e11e423ad9dc26d57 100755
--- a/server/xpub-model/entities/team/data-access.js
+++ b/server/xpub-model/entities/team/data-access.js
@@ -16,8 +16,8 @@ class Team extends EpmcBaseModel {
// static idColumn = ['article_id', 'member_id'];
static get idColumn() {
- return ['manuscript_id', 'user_id', 'role_name']
- // return 'id'
+ // return ['manuscript_id', 'user_id', 'role_name']
+ return 'id'
}
/*
diff --git a/wrapperScript.sh b/wrapperScript.sh
index 486dda96720c4b0803f8cedf65f135abb46f980e..c170cbd3866f65c727e72a3c16abb9c6433160c4 100755
--- a/wrapperScript.sh
+++ b/wrapperScript.sh
@@ -9,7 +9,7 @@ echo "Wait up to 3 minutes for server to respond, check every 20 seconds"
COUNTER=0
while [ $COUNTER -lt 15 ]; do
- RUNNING=$(curl --silent --connect-timeout 20 "$PUBSWEET_URL" | grep "/assets/")
+ RUNNING=$(curl --silent --connect-timeout 20 "http://localhost:$PORT" | grep "/assets/")
if [ -n "$RUNNING" ] ; then
echo "xPub is running"
#echo "Creating the Users"