6. Developing with Escher¶

If you are interested in developing software using Escher as a dependency, this is the place to start. If want contribute to development of Escher, then check out the GitHub repository (instruction for building and testing the project are in the README):

https://github.com/zakandrewking/escher

You might also want to check out the the Gitter chat room and the Development Roadmap.

6.1. Using the static JavaScript and CSS files¶

You can include the compiled Escher JavaScript and CSS files in any HTML document.

The compiled files are available from unpkg:

https://unpkg.com/escher/dist/escher.js
https://unpkg.com/escher/dist/escher.min.js

Source maps are also hosted there:

https://unpkg.com/escher/dist/escher.js.map
https://unpkg.com/escher/dist/escher.min.js.map

If you want a particular version of escher, add a version tag like this:

https://unpkg.com/escher@1.7.0-beta.19/dist/escher.js

Or, if you use NPM, you can simply install escher:

npm install --save escher

Or with yarn:

yarn add escher

For an example of the boilerplate code that is required to begin developing with Escher, have a look at the escher-demo repository. For projects built with npm, use the escher-test repository as a guide.

You can also follow the Developer Tutorial for an example of extending Escher to create custom tooltips.

6.2. Import Escher¶

The Escher JavaScript file uses UMD, so you can include it in almost any project.

If you are using JavaScript ES6 import syntax, the default export is Builder:

import Builder from 'escher'
import * as escher from 'escher'

6.3. Generating and reading Escher and COBRA files¶

6.3.1. The Escher file format¶

Escher layouts are defined by JSON files that follow a specific schema, using json schema. The latest schema for Escher JSON files is here. The Escher schemas are versioned, with inspiration from SchemaVer. The escher.validate module can be used to validate models against the schema.

The Escher layout schema is designed to be as simple as possible. For example, the core metabolism map of Escherichia coli is layed out like this:

[
    {
        "map_name": "E coli core.Core metabolism",
        "map_id": "2938hoq32a1",
        "map_description": "E. coli core metabolic network\nLast Modified Fri Dec 05 2014 16:39:44 GMT-0800 (PST)",
        "homepage": "https://escher.github.io",
        "schema": "https://escher.github.io/escher/jsonschema/1-0-0#"
    },
    {
        "reactions": { ... },
        "nodes": { ... },
        "text_label": { ... },
        "canvas": {
            "x": 7.857062530517567,
            "y": 314.36893920898433,
            "width": 5894.515691375733,
            "height": 4860.457037353515
        }
    },
]

The map_name includes the model that was used to build this layout, followed by a period and then a readable name for the map. The map_id is a unique identifier for this map. The map_description describes the map and the last time it was modified. Both the homepage and the schema entries must have exactly these values for the Escher map to be valid.

In the next section, the reactions, nodes, labels, and canvas are all defined. For reactions, nodes, and text labels, each element has a key that is an arbitrary integer. As long as there are no repeated IDs (e.g. no 2 segments with the ID 517), then everything should work fine.

Read through the schema (here) for more detail on the format.

6.3.2. The COBRA file format¶

COBRA models are also saved as JSON files. This format has not been documented with a schema, but you can browse through the core metabolism model as a guide to generating valid COBRA models.

6.3.3. Contributing to the Escher Source Code¶

We welcome open source contributions to the Escher source code. You can find installation instructions for developing Escher in the README:

https://github.com/zakandrewking/escher/blob/master/README.md

And instructions (work in progress :):

https://github.com/zakandrewking/escher/blob/master/CONTRIBUTING.md

And our code of conduct:

https://github.com/zakandrewking/escher/blob/master/CODE_OF_CONDUCT.md

6.3.4. I still need help!¶

If you are interested in developing with or contributing to Escher and you need more information than what is provided in the documentation, please contact Zachary King <zaking@ucsd.edu>.