From ba27dacb54765832fd14f1bd5d12ab5cf6f3dfe3 Mon Sep 17 00:00:00 2001
From: Nikos Marinos <nmarinos@ebi.ac.uk>
Date: Thu, 14 Mar 2019 13:07:39 +0000
Subject: [PATCH] Fixes to xsweet converter with Koosum
---
package.json | 2 +-
server/ftp-integration/api.js | 23 ++++++++++++-------
.../xpub-model/entities/file/data-access.js | 2 +-
server/xsweet-conversion/index.js | 23 +++++++++++--------
4 files changed, 31 insertions(+), 19 deletions(-)
diff --git a/package.json b/package.json
index 1a688482d..a6fd3edc3 100755
--- a/package.json
+++ b/package.json
@@ -164,7 +164,7 @@
"reset": "pubsweet setupdb --clobber",
"start": "docker-compose -f ./docker-compose.yml -f ./docker-compose.dev.yml up --build",
"start:production": "docker-compose -f ./docker-compose.yml -f ./docker-compose.prod.yml up --build",
- "start:services": "docker-compose up postgres ftpd_server minio",
+ "start:services": "docker-compose up postgres ftpd_server minio xsweet",
"start:services:dev": "docker-compose -f ./docker-compose.yml -f ./docker-compose.dev.yml up postgres ftpd_server minio",
"ftp:listener": "./runFtpMonitor.sh &",
"server": "crontab crontab && pubsweet server",
diff --git a/server/ftp-integration/api.js b/server/ftp-integration/api.js
index 6beb16d7c..1c78f65ae 100644
--- a/server/ftp-integration/api.js
+++ b/server/ftp-integration/api.js
@@ -73,7 +73,11 @@ async function tidyUp(filePath, tmpPath, manuscript, isError) {
// node couldn't execute the command
reject(err)
}
- logger.info(`Finished Bulk import process for ${filePath}`)
+ logger.info(
+ `Finished Bulk import process for ${filePath} as manuscript ${
+ manuscript.id
+ }.`,
+ )
resolve(true)
})
})
@@ -516,6 +520,15 @@ function uploadFile(
})
}
+async function submitManuscript(manuscriptdb, submitter) {
+ const input = {
+ id: manuscriptdb.id,
+ status: 'submitted',
+ }
+ const { userId } = submitter
+ await ManuscriptManager.submit(input, userId)
+}
+
async function createManuscript(
pubsweetServer,
xmlObj,
@@ -690,13 +703,7 @@ async function createManuscript(
)[0].fileURI
await xsweetConverter.xsweetConvert(manuscriptFileURI, manuscriptdb.id)
-
- const input = {
- id: manuscriptdb.id,
- status: 'submitted',
- }
- const { userId } = submitter
- await ManuscriptManager.submit(input, userId)
+ await submitManuscript(manuscriptdb, submitter)
})
return manuscriptdb
}
diff --git a/server/xpub-model/entities/file/data-access.js b/server/xpub-model/entities/file/data-access.js
index 437ece15b..ef8b75055 100644
--- a/server/xpub-model/entities/file/data-access.js
+++ b/server/xpub-model/entities/file/data-access.js
@@ -28,7 +28,7 @@ class File extends EpmcBaseModel {
type: { type: 'string' },
size: { type: 'int' },
url: { type: 'string' },
- label: { type: 'string' },
+ label: { type: ['string', 'null'] },
deleted: { type: 'timestamp' },
updatedBy: { type: 'uuid' },
},
diff --git a/server/xsweet-conversion/index.js b/server/xsweet-conversion/index.js
index bf89c5dc3..38bfed8a7 100644
--- a/server/xsweet-conversion/index.js
+++ b/server/xsweet-conversion/index.js
@@ -1,3 +1,4 @@
+const config = require('config')
const fs = require('fs')
const rp = require('request-promise')
const tar = require('../utils/unTar.js')
@@ -9,6 +10,8 @@ const path = require('path')
const files = require('../utils/files.js')
const db = require('../utils/db.js')
+const pubsweetServer = config.get('pubsweet-server.baseUrl')
+const label = 'xsweet conversion'
/*
xsweetConvert(
'/home/yogmatee/projects/xmlValidation_files/xweet_files/tiana.docx',
@@ -16,14 +19,15 @@ xsweetConvert(
)
*/
-module.exports.xsweetConvert = function xsweetConvert(fileUrl, manuscriptId) {
+module.exports.xsweetConvert = async function xsweetConvert(
+ fileUrl,
+ manuscriptId,
+) {
const options = {
method: 'POST',
- uri: 'http://localhost:3000/convertDocxToHTML',
+ uri: `${pubsweetServer}/convertDocxToHTML`,
formData: {
- docx: fs.createReadStream(
- '/home/yogmatee/projects/xmlValidation_files/xweet_files/tiana.docx',
- ),
+ docx: fs.createReadStream(fileUrl),
},
headers: {
/* 'content-type': 'multipart/form-data' */
@@ -31,7 +35,7 @@ module.exports.xsweetConvert = function xsweetConvert(fileUrl, manuscriptId) {
},
}
- rp(options)
+ await rp(options)
.then(async body => {
try {
const tmpPath = await tar.createTempDir()
@@ -42,6 +46,7 @@ module.exports.xsweetConvert = function xsweetConvert(fileUrl, manuscriptId) {
`${tmpPath}/${manuscriptId}.html`,
manuscriptId,
user,
+ label,
)
const uuid = uuidv4()
@@ -58,7 +63,7 @@ module.exports.xsweetConvert = function xsweetConvert(fileUrl, manuscriptId) {
delete fileInfo.extension
await db.upsertHtmlPrevFile(fileInfo, manuscriptId)
- logger.info('file has been uploaded to Minio and to db')
+ logger.info('HTML converted file has been uploaded to Minio and to db')
} catch (err) {
throw err
}
@@ -68,7 +73,7 @@ module.exports.xsweetConvert = function xsweetConvert(fileUrl, manuscriptId) {
})
}
-function getFileInfo(filepath, manuscriptId, user) {
+function getFileInfo(filepath, manuscriptId, user, label) {
const filename = filepath.substring(filepath.lastIndexOf('/') + 1)
const fileExt = path.extname(filepath)
const fileSize = fs.statSync(filepath).size
@@ -77,7 +82,7 @@ function getFileInfo(filepath, manuscriptId, user) {
url: filepath,
filename,
type: 'source',
- label: '',
+ label,
size: fileSize,
extension: fileExt,
mimeType: `${mime.contentType(fileExt)}`,
--
GitLab