Discover elifesciences/elife-tools Open Source project

A set of tools to allow PDF to XML conversion, utilising Apache Beam and other tools. The aim of this project is to bring multiple tools together to generate a full XML document.

363

sciencebeam-parser

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.

294

elife-xpub

Retrieve and extract citations from Crossref data

datacapsule-crossref

sciencebeam-gym

ScienceBeam Gym

Full XML of all eLife articles including each revision.

elife-article-xml

elife-bot

tools for creating an automatic publishing workflow.

eLife is an open-access journal that publishes promising research in the life and biomedical sciences

journal

elife-continuum-documentation

HTML

lens-browser

Lens Article Browser

A client-side NLM to Lens converter. Based on Substance.Converter.

lens-converter

Convert NLM XML files into the Lens JSON

elife-articles

xml of elife articles

refract

builder

Common steps used in eLife's Jenkins Pipelines

elife-jenkins-workflow-libs

Groovy

citation-context

Lens Indexer based on ElasticSearch.

lens-indexer

Stand-alone example of a reproducible document stack article

rds-example

RAML for the eLife Sciences API

api-raml

RAML

pattern-library

Pattern library driving https://elifesciences.org, the eLife journal.

Wrapper around https://github.com/kermitt2/delft

reference-schematron

sciencebeam-trainer-delft

proofreader-php is a tool for enforcing opinionated coding standards and conventions through static analysis of the code.

proofreader-php

Airflow pipeline for ScienceBeam related training and evaluation

sciencebeam-airflow

standalone article xml scraper for the pppp project

jats-scraper

Crossref deposit of journal articles

elife-crossref-xml-generation

lax

The Lens Reader as a module, for custom app integration

lens-reader

XML Validation service built on BaseX for validating XML against elife's schematron files

basex-validator-docker

XSLT

lens-elife

eLife integrations of Lens with custom extensions as well as official bundle

Extension for Behat that tests Drupal sites in isolation.

publisher-xml-fragment-examples

isolated-drupal-behat-extension

Visually outlines Substance documents.

lens-outline

journal-cms

jats-generator

jats-xml-to-pdf

peerscout

PeerScout® is a web application and machine learning trained API for suggesting peer reviewers from an existing pool, based on attributes of the papers they have reviewed and written

bot-lax-adaptor

Mapping the XML to new Continuum requirements and build of a new Kitchen sink

XML-mapping

eLife-JATS-schematron

Schematron for all JATS eLife content

XSLT

elife-pdfs

pdf versions of elife articles

threadbare

A partial replacement for eLife's usage of Fabric 1.x and Paramiko.

cermine-docker

Data Science project looking into the Peer Review Taxonomy

data-science-peertax

Definition of eLife's k8s cluster and deployments to it. Automatically applied via Flux.

elife-flux-cluster

eLife Medium articles API

medium

Dummy implementation of the eLife Sciences API

api-dummy

Lens Development Environment

lens-sandbox

manage scheduling future publications for eLife Continuum

elife-article-scheduler

PHP SDK for the eLife Sciences bus [in development]

bus-sdk-php

elife-metrics

This contains the markdown from gitbook for schematron.

schematron-wiki

XQuery

lens-starter

Minimal Lens integration, use as a starting point for development

elife-api

Data pipeline for loading eJP Xml files from S3 bucket into Bigquery

data-hub-ejp-xml-pipeline

data-science-dags

sciencebeam-utils

peerscout-dags

citation-sentiment-analysis

Utility functions related to elife-data-hub

elife-data-hub-utils

create custom airflow image used for running data-hub pipeline

data-hub-airflow-image

Makefile

enhanced-preprints-client

Enhanced Preprints client application

TypeScript

data-hub-core-airflow-dags

Contains non-sensitive Salt formulas configuration

builder-configuration

PHP implementation of the eLife patterns

patterns-php

A central place for resources relating to the eLife Data Pipeline tools

data-pipeline-sql-prototype

bigquery-views-manager

BigQuery Views Manager

elife version of drupal cookbook

packer-test

files for testing packer

Ruby

elife-drupal-cookbook

scripts for getting elife xml, parsing them, and populating our REST api

populate-elife-api

Are you a developer or hacker interested in using eLife's open-source resources? This page is for you! If you do build something using our code, we'd love to hear at [email protected] (we may be able to help you grow your project).

developer-resources

elife-alfred-formula

eLife upgrade to JATS xml

JATs-xml

api-gateway-formula

publishing dashboard for eLife Continuum

elife-dashboard

Enhanced Preprints import system

enhanced-preprints-import

TypeScript

elife-kickstart

Build script to make it easier to start building a distribution for a new Drupal project.

sciencebeam-editor

eif-article-json

PHP client for the eLife Sciences API

elife-data-hub-charts

Smarty

api-client-php

journal-cms-formula

Calculates PageRank over citation data

citerank

builder-base-formula

Library of eLife Articles, used as a landing page at lens.elifesciences.org

lens-library

elife-metrics-formula

Declares the deploys to kubernetes-aws--flux-test cluster using fluxcd

elife-flux-test

Testing repository. Contents may be DELETED at any time.

lens-s3

HTML

elife-article-xml-continuumtest

data-hub-api

Data Hup APIs

a collection of utility scripts used at eLife

elife-utility-scripts

PHP SDK for the eLife Sciences API

api-sdk-php

code to support uploading info to crossref on PAW articles

elife-crossref-feed

pubpub-css

To enable version control of the CSS in PubPub's static page system

CSS

elife-website

ScienceBeam Trainer for GROBID

sciencebeam-trainer-grobid

Minimal dummy to stand in for Hypothes.is inside eLife's testing infrastructure

hypothesis-dummy

bioprotocol-service

100

master-server-formula