Encoda

Announcement

For some time our main focus has been a rewrite of our Stencila platform (v2). We are porting over codecs and other functionality from this repo to the v2 of our Stencila platform.

This means that we are unable to be so active with contributions to this project. eLife have volunteered to continue development on this repository until such a time as the v2 of Stencila can meet their needs. They only have need of the codecs to convert from JATS to JSON.

From v2.0.0 of this project we will only continue to support the conversion from JATS to JSON. If you want to use any other formats then please see if they are available in Stencila or use the v1.0.3 release.

We have chosen at this time to leave the rest of the README.md as it was before the removal of much of the code. This does mean that the README.md is out of date. We may prioritise updating it in future.

Codecs for structured, semantic, composable, and executable documents

Introduction

"A codec is a device or computer program for encoding or decoding a digital data stream or signal. Codec is a portmanteau of coder-decoder. - Wikipedia

Encoda provides a collection of codecs for converting between, and composing together, documents in various formats. The aim is not to achieve perfect lossless conversion between alternative document formats; there are already several tools for that. Instead the focus of Encoda is to use existing tools to encode and compose semantic documents in alternative formats.

Formats

As far as possible, Encoda piggybacks on top of existing tools for parsing and serializing documents in various formats. It uses extensions to schema.org as the central data model for all documents and for many formats, it simply transforms the data model of the external tool (e.g. Pandoc types, SheetJS spreadsheet model) to that schema ("decoding") and back again ("encoding"). In this sense, you can think of Encoda as a Rosetta Stone with schema.org at it's centre.

⚡ Tip: If a codec for your favorite format is missing below, see if there is already an issue for it and 👍 or comment. If there is no issue regarding the converter you need, feel free to create one.

Format	Codec	Powered by	Status
Text
Plain text	txt	toString	✔
Markdown	md	Remark	✔
LaTex	latex	Pandoc	α
Microsoft Word	docx	Pandoc	β
Google Docs	gdoc	JSON	β
Open Document Text	odt	Pandoc	α
HTML	html	jsdom, hyperscript	✔
JATS XML	jats	xml-js	✔
	jats-pandoc	Pandoc	β
Portable Document Format	pdf	pdf-lib, Puppeteer	β
Math
TeX	tex	mathconverter	✔
MathML	mathml	MathJax	✔
Visualization
Plotly	plotly	Plotly.js	✔
Vega / Vega-Lite	vega	Vega	✔
Bibliographic
Citation Style Language JSON	csl	Citation.js	✔
BibTeX	bib	Citation.js	✔
Notebooks
Jupyter	ipynb	JSON	✔
RMarkdown	xmd	Remark	✔
Spreadsheets
Microsoft Excel	xlsx	SheetJS	β
Open Document Spreadsheet	ods	SheetJS	β
Tabular data
CSV	csv	SheetJS	β
Tabular Data Package	tdp	datapackage-js	α
Collections
Filesystem Directory	dir	fs	β
Data interchange, other
JSON	json	JSON	✔
JSON-LD	jsonld	jsonld.js	✔
JSON5	json5	json5	✔
YAML	yaml	js-yaml	✔
Pandoc	pandoc	Pandoc	✔
Reproducible PNG	rpng	Puppeteer	✔
XML	xml	xml-js	✔

Key

• ✗: Not yet implemented
• α: Alpha, initial implementation
• β: Beta, ready for user testing
• ✔: Ready for production use

Publishers

Several of the codecs in Encoda, deal with fetching content from a particular publisher. For example, to get an eLife article and read it in Markdown:

stencila convert https://elifesciences.org/articles/45187v2 ye-et-al-2019.md

Some of these publisher codecs deal with meta data. e.g.

stencila convert "Watson and Crick 1953" - --from crossref --to yaml

type: Article
title: Genetical Implications of the Structure of Deoxyribonucleic Acid
authors:
  - familyNames:
      - WATSON
    givenNames:
      - J. D.
    type: Person
  - familyNames:
      - CRICK
    givenNames:
      - F. H. C.
    type: Person
datePublished: '1953,5'
isPartOf:
  issueNumber: '4361'
  isPartOf:
    volumeNumber: '171'
    isPartOf:
      title: Nature
      type: Periodical
    type: PublicationVolume
  type: PublicationIssue

Source	Codec	Base codec/s	Status	Coverage
General
HTTP	http	Based on Content-Type or extension	β	![][http-cov]
Person
ORCID	orcid	jsonld	β	![][orcid-cov]
Article metadata
DOI	doi	csl	β	![][doi-cov]
Crossref	crossref	jsonld	β	![][crossref-cov]
Article content
eLife	elife	jats	β	![][elife-cov]
PLoS	plos	jats	β	![][plos-cov]

Install

The easiest way to use Encoda is to install the stencila command line tool. Encoda powers stencila convert, and other commands, in that CLI. However, the version of Encoda in stencila, can lag behind the version in this repo. So if you want the latest functionality, install Encoda as a Node.js package:

npm install @stencila/encoda --global

Use

Encoda is intended to be used primarily as a library for other applications. However, it comes with a simple command line script which allows you to use the convert function directly.

Converting files

encoda convert notebook.ipynb notebook.docx

Encoda will determine the input and output formats based on the file extensions. You can override these using the --from and --to options. e.g.

encoda convert notebook.ipynb notebook.xml --to jats

You can also convert to more than one file / format (in this case the --to argument only applies to the first output file) e.g.

encoda convert report.docx report.Rmd report.html report.jats

Converting folders

You can decode an entire directory into a Collection. Encoda will traverse the directory, including subdirectories, decoding each file matching your glob pattern. You can then encode the Collection using the dir codec into a tree of HTML files e.g.

encoda convert myproject myproject-published --to dir --pattern '**/*.{rmd, csv}'

Converting command line input

You can also read content from the first argument. In that case, you'll need to specifying the --from format e.g.

encoda convert "{type: 'Paragraph', content: ['Hello world!']}" --from json5 paragraph.md

You can send output to the console by using - as the second argument and specifying the --to format e.g.

encoda convert paragraph.md - --to yaml

Option	Description
--from	The format of the input content e.g. --from md
--to	The format for the output content e.g. --to html
--theme	The theme for the output (only applies to HTML, PDF and RPNG output) e.g. --theme eLife. Either a Thema theme name or a path/URL to a directory containing a styles.css and a index.js file.
--standalone	Generate a standalone document, not a fragment (default true)
--bundle	Bundle all assets (e.g images, CSS and JS) into the document (default false)
--debug	Print debugging information

Using with Executa

Encoda exposes the decode and encode methods of the Executa API. Register Encoda so that it can be discovered by other executors on your machine,

npm run register

You can then use Encoda as a plugin for Executa that provides additional format conversion capabilities. For example, you can use the query REPL on a Markdown document:

npx executa query CHANGELOG.md --repl

You can then use the REPL to explore the structure of the document and do things like create summary documents from it. For example, lets say from some reason we wanted to create a short JATS XML file with the five most recent releases of this package:

jmp > %format jats
jmp > %dest latest-releases.jats.xml
jmp > {type: 'Article', content: content[? type==`Heading` && depth==`1`] | [1:5]}

Which creates the latest-major-releases.jats.xml file:

<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD v1.1 20151215//EN" "JATS-archivearticle1.dtd">
<article xmlns:xlink="http://www.w3.org/1999/xlink" article-type="research-article">
    <front>
        <title-group>
            <article-title/>
        </title-group>
        <contrib-group/>
    </front>
    <body>
        <sec>
            <title>
                <ext-link ext-link-type="uri" xlink:href="https://github.com/stencila/encoda/compare/v0.79.0...v0.80.0">0.80.0</ext-link> (2019-09-30)
            </title>
        </sec>
...

You can query a document in any format supported by Encoda. As another example, lets' fetch a CSV file from Github and get the names of it's columns:

npx executa query https://gist.githubusercontent.com/jncraton/68beb88e6027d9321373/raw/381dcf8c0d4534d420d2488b9c60b1204c9f4363/starwars.csv --repl
🛈 INFO  encoda:http Fetching "https://gist.githubusercontent.com/jncraton/68beb88e6027d9321373/raw/381dcf8c0d4534d420d2488b9c60b1204c9f4363/starwars.csv"
jmp > columns[].name
[
  'SetID',
  'Number',
  'Variant',
  'Theme',
  'Subtheme',
  'Year',
  'Name',
  'Minifigs',
  'Pieces',
  'UKPrice',
  'USPrice',
  'CAPrice',
  'EUPrice',
  'ImageURL',
  'Owned',
  'Wanted',
  'QtyOwned',
]
jmp >

See the %help REPL command for more examples.

Note: If you have executa installed globally, then the npx prefix above is not necessary.

Documentation

Self-hoisted (documentation converted from various formats to html) and API documentation (generated from source code) is available at: https://stencila.github.io/encoda.

Develop

Check how to contribute back to the project. All PRs are most welcome! Thank you!

Clone the repository and install a development environment:

git clone https://github.com/stencila/encoda.git
cd encoda
npm install

You can manually test conversion using current TypeScript src using:

npm start -- convert simple.md simple.html

That can be slow because the TypeScript has to be compiled on the fly (using ts-node). Alternatively, compile the TypeScript to JavaScript first, and then run node on the dist folder:

npm run build:dist
node dist convert simple.md simple.html

If you are using VSCode, you can use the Auto Attach feature to attach to the CLI when running the debug NPM script:

npm run debug -- convert simple.gdoc simple.ipynb

A simple script to convert JATS to JSON:

cat simple-jats.xml | npm run convert-jats --silent > simple.json

Testing

Running tests locally

Run the test suite using:

npm test

Or, run a single test file e.g.

npx jest tests/xlsx.test.ts --watch

To display debug logs during testing set the environment variable DEBUG=1, e.g.

DEBUG=1 npm test

To get coverage statistics:

npm run cover

There's also a Makefile if you prefer to run tasks that way e.g.

make lint cover

Running test in Docker

You can also test this package using with a Docker container:

npm run test:docker

Writing tests

Recording and using network fixtures

As far as possible, tests should be able to run with no network access. We use Nock Back to record and play back network requests and responses. Use the nockRecord helper function for this with the convention of starting the fixture file with nock-record- e.g.

const stopRecording = await nockRecord('nock-record-<name-of-test>.json')
// Do some things that connect to the interwebs
stopRecording()

Note that the HTTP fetcher implements caching so that you may need to remove the cache for the recording of fixtures to work e.g. rm -rf /tmp/stencila/encoda/cache/.

If there are changes in the URLs that your test fetches, or you want to check that your test is still works against an external API that may have changed, remove the Nock recording and rerun the test e.g.,

rm src/codecs/elife/__fixtures__/nock-record-*.json
npx jest src/codecs/elife/ --testTimeout 30000

Contribute

We 💕 contributions! All contributions: ideas 🤔, examples 💡, bug reports 🐛, documentation 📖, code 💻, questions 💬. See CONTRIBUTING.md for more on where to start. You can also provide your feedback on the Community Forum and Gitter channel.

Contributors

Aleksandra Pawlik 💻 📖 🐛	Nokome Bentley 💻 📖 🐛	Jacqueline 📖 🎨	Hamish Mackenzie 💻 📖	Alex Ketch 💻 📖 🎨	Ben Shaw 💻 🐛	Phil Neff 🐛
Raniere Silva 📖	Lorenzo Cangiano 🐛	FAtherden-eLife 🐛 🎨	Giorgio Sironi 👀

Add a contributor...

To add youself, or someone else, to the above list, either,

1. Ask the @all-contributors bot to do it for you by commenting on an issue or PR like this:

   @all-contributors please add @octocat for bugs, tests and code

2. Use the all-contributors CLI to do it yourself:

   npx all-contributors add octocat bugs, tests, code

See the list of contribution types.

Acknowledgments

Encoda relies on many awesome opens source tools (see package.json for the complete list). We are grateful ❤ to their developers and contributors for all their time and energy. In particular, these tools do a lot of the heavy lifting 💪 under the hood.

Tool	Use
	Ajv is "the fastest JSON Schema validator for Node.js and browser". Ajv is not only fast, it also has an impressive breadth of functionality. We use Ajv for the validate() and coerce() functions to ensure that ingested data is valid against the Stencila schema.
	Citation.js converts bibliographic formats like BibTeX, BibJSON, DOI, and Wikidata to CSL-JSON. We use it to power the codecs for those formats and APIs.
	datapackage-js from the team at Frictionless Data is a Javascript library for working with Data Packages. It does a lot of the work in converting between Tabular Data Packages and Stencila Datatables.
	Glitch Digital's structured-data-testing-tool is a library and command line tool to help inspect and test for Structured Data. We use it to check that the HTML generated by Encoda can be read by bots 🤖
	Pa11y provides a range of free and open source tools to help designers and developers make their web pages more accessible. We use pa11y to test that HTML generated produced by Encoda meets the Web Content Accessibility Guidelines (WCAG) and Axe rule set.
Pandoc	Pandoc is a "universal document converter". It's able to convert between an impressive number of formats for textual documents. Our Typescript definitions for Pandoc's AST allow us to leverage this functionality from within Node.js while maintaining type safety. Pandoc powers our converters for Word, JATS and Latex. We have contributed to Pandoc, including developing its JATS reader.
	Puppeteer is a Node library which provides a high-level API to control Chrome. We use it to take screenshots of HTML snippets as part of generating rPNGs and we plan to use it for generating PDFs.
	Remark is an ecosystem of plugins for processing Markdown. It's part of the unified framework for processing text with syntax trees - a similar approach to Pandoc but in Javascript. We use Remark as our Markdown parser because of it's extensibility.
	SheetJs is a Javascript library for parsing and writing various spreadsheet formats. We use their community edition to power converters for CSV, Excel, and Open Document Spreadsheet formats. They also have a pro version if you need extra support and functionality.

Many thanks ❤ to the Alfred P. Sloan Foundation and eLife for funding development of this tool.