Introduction

Resources for JSON

• What are JSON files and how do you use them?

• What is a JSON file?

JSON File Basics

• JavaScript Object Notation

• Common format for communicating with Application Program Interface (API)

• Used to access DNAnexus API servers

Why Should You Learn JSON?

• Reading and modifying JSON is at the heart of building and running apps

• Understanding JSON responses from the API will help you debug jobs

• Automation and Batch submissions: running the same app on multiple files

  • Find which jobs have failed and why

  • Run the failed jobs again

Elements and Reading JSON

A valid JSON document is enclosed in one of two data structures, either a list of values contained in square brackets:

[
    {
        "project": "project-Gg2QQx002Q7yY4kFQF7GKYPV",
        "id": "applet-G1951vj0YyjJjbvGJ9FZB967",
        "describe": {
            "id": "applet-G1951vj0YyjJjbvGJ9FZB967",
            "project": "project-Gg2QQx002Q7yY4kFQF7GKYPV"
        }
    },
    {
        "project": "project-Gg2QQx002Q7yY4kFQF7GKYPV",
        "id": "file-GGy7Pbj0Xf47XZk125k22g9v",
        "describe": {
            "id": "file-GGy7Pbj0Xf47XZk125k22g9v",
            "project": "project-Gg2QQx002Q7yY4kFQF7GKYPV"
        }
    }
]

Or an object composed of key/value pairs contained in curly brackets:

Example:

{
   "report_html": {
       "dnanexus_link": "file-G4x7GX80VBzQy64k4jzgjqgY"
   },
   "stats_txt": {
       "dnanexus_link": "file-G4x7GXQ0VBzZxFxz4fqV120B"
   }
}

A JSON value may be any of the following:

• single- or double-quoted string, e.g., "samtools" or 'file-G4x7GX80VBzQy64k4jzgjqgY'

• integer, e.g. 19 or -4

• float, e.g., 3.14 or 6.67384e-11

• boolean, e.g., true or false

• null

• object

Lists

• Lists are braced in square brackets [ ]

• Similar to Python syntax

• Used for multiple values separated by commas

Example:

{
    "dnanexus-link": [
        "file-G4x7GXQ0VBzZxFxz4fqV120B", "file-G4x7GX80VBzQy64k4jzgjqgY"
    ]
}

Objects

• An object starts and ends with curly braces

• An object contains key/value pairs

• Keys must be quoted strings

• Values may be any JSON value, including another object

Example:

{ 
    "report_html": {
        "dnanexus_link": "file-G4x7GX80VBzQy64k4jzgjqgY"
    }
}

Resources

Full Documentation

To create a support ticket if there are technical issues:

1. Go to the Help header (same section where Projects and Tools are) inside the platform

2. Select "Contact Support"

3. Fill in the Subject and Message to submit a support ticket.