elifesciences / elife-xpub

eLife is an open-access journal and technology provider that publishes promising research in the life and biomedical sciences. This is their implementation of a submission and peer review system based on Coko PubSweet and xPub.

eLife xPub

Description

An eLife specific implementation of the xPub submission and peer-review system for scholarly journals. xPub is a journal publishing workflow implementation of PubSweet, an open toolkit for building publishing workflows.

This is a collaboration between eLife and the Collaborative Knowledge Foundation (Coko), more information in our press release.

This repo contains scripts to synchronise the selected commit of xPub so that it can be deployed to eLife's instance on AWS using https://github.com/elifesciences/elife-xpub-formula. This repo will also contain any eLife specific components or configuration.

Documentation

All documents relevant to this project can be found in the docs folder within the repository.

elife-xpub's Issues

Complete tasks in pubsweet-client for 1.0 milestone

See https://gitlab.coko.foundation/pubsweet/pubsweet-client/milestones/3

Set up continuous deployment for elife-xpub

• Fix config bugs
• Upgrade kubernetes

Validate article IDs for related work (considered previously & co-submissions) based on query to eLife API

• (1) Retrieve subject areas and article types from elife API - moved to issue #42
• (2) Validate related work against existing article ids

Use case:
A paper has been previously rejected and the authors go away, revise and resubmit. The paper needs to be seen by the same editors and reviewers, who will need easy access to the previous submission so they can re-familiarise themselves with the original issues and evaluate if the authors have adequately addressed them.

Create a deployment pipeline for xpub

Subtasks are being tracked here: https://gitlab.coko.foundation/xpub/xpub/issues/16#note_10798

Migrate from css modules to styled-components

Send email to author on form submission

Create subject area control molecule (wireframe 006)

Latest wireframes:

requirements here

---

Old version:

Tasks

• Build UI molecule
• Request list of subject areas from eLife API on page load

Prepare this repo for being public:

• update readme
• ensure licence is set correctly
• update description
• check for secrets

Bring pubsweet-starter up to do date such that it uses the latest pubsweet-server

GraphQL frontend

Refactor pubsweet-cli to incorporate db-manager and speed up tests

Create latex conversion step for INK (in Node)

Integrating INK

Create reviewer suggestions page layout (wireframe 008)

WARNING: subject to change

Create mechanism for running migrations

Backend changes to postgres

Copy xpub app and remove unneeded elements

• copy files from xpub/xpub into xpub/xpub-elife (do not preserve git history)
• remove unnecessary files like app/config/*
• make initial commit

Create author details page layout (wireframe 002)

Connect file upload page to storage back-end (wireframe 004)

Extract db-manager from pubsweet-cli

Deploy elife-xpub with couchdb (instead of leveldb).

Create customised drop zone molecule (wireframe 003)

Create correspondent delegation/assignment control molecule (wireframe 002)

Add more e2e tests in pubsweet-starter

https://gitlab.coko.foundation/pubsweet/pubsweet-starter/issues/5

Add responsiveness preview to styleguide

https://gitlab.coko.foundation/xpub/xpub/issues/69

Create seed data for editors

Needed to have data to populate the people picker.

Add and connect steps molecule to form pages

GraphQL server backend

Complete remaining tasks in pubsweet-server for 1.0 milestone

See https://gitlab.coko.foundation/pubsweet/pubsweet-server/milestones/4

Create Graphcool test implementation

Add latest version of xpub-collabra to elife-xpub

Improve accessibility

Add theming support to xpub

Create manuscript metadata page layout (wireframe 006)

Wireframes

Overall page:

When a user checks the box, a border appears and a new field for entry:

Set up continuous deployment for elife-xpub

Create dummy manuscript view

Connect reviewer suggestions page (wireframe 008) to the backend

Form data should be saved (e.g. when moving between pages) on the backend.

Make this repo public

Create ORCID login molecule

Add and connect app-bar molecule

pubsweet molecule may require modification

Allow collection and fragment teams to be retrieved from the API

https://gitlab.coko.foundation/pubsweet/pubsweet-server/issues/59

Create author details validated form fields (wireframe 002)

Fixing bugs in xpub

See https://gitlab.coko.foundation/xpub/xpub/milestones/3

Investigation gitlab's auto-deploy for xpub

https://gitlab.coko.foundation/xpub/xpub/issues/16

Bring atoms and molecules up to standards agreed at the PubSweetMeet

Create manuscript and cover letter upload page layout (wireframe 004)

Ensure form progress is saved

Pre-populate form fields using Orcid data

Implement redesigned pubsweet startup process

https://gitlab.coko.foundation/pubsweet/pubsweet-cli/issues/90

Connect author details page (wireframe 002)

Mocked connection to ink