API Introduction

Any operation from the Emedgene graphical user interface (GUI) can also be performed by using the Emedgene API.

Following are some basic examples of how to use Emedgene API with Python.

For instructions on using the API with other programming languages, please refer to their respective documentation.

Prerequisites

• An installed copy of Python ()

• The Python package installer, pip ()

• The requests library installed (run pip install requests)

Authentication

In order to perform a secure session with Emedgene API servers you should first accomplish the authentication phase and retrieve the bearer token. The bearer token is further required to perform API requests on associated resources without extra identification. The token is valid for a predefined time. Once the bearer token is not valid, you will need to revalidate the token and accomplish the authentication phase again.

There are two ways to get your authentication token for your user before executing API calls:

Emedgene Domain users - https://<hostname>.emedgene.com

To generate the authorization token, use your username and password as follows:

This is your Bearer token that will be used for the following API requests.

Illumina Domain users - https://<hostname>.emg.illumina.com

For Illumina domain users there are two options to authenticate your user and retrieve the Bearer token.

1. Illumina credentials - use your username and password

1. Using your API Key to generate the authentication token. To generate an API Key take a look . Copy your API Key to the code below instead of 'my-api-key'.

Either of these options will produce your Bearer token that will be used for the following API requests.

API Reference

The different API commands can be found at https://<hostname>.emedgene.com/api/apidoc/swagger or https://<hostname>.emg.illumina.com/api/apidoc/swagger

It is useful to explore possible APIs and get an overview of the available parameters.

Creating Python requests from curl

The examples in the API Reference page use curl (Client URL), while Python uses requests.

In order to get the curl command:

1. Find the endpoint you want to use on the API Reference page.

2. Select Try it out.

3. Enter the necessary parameters.

Let's break down the parts of a curl command:

-X specifies the request method to use when communicating with the HTTP server. By default, curl performs a GET request, but you can use the -X option to set a different method, such as POST, PUT, DELETE, etc.

-H allows you to pass custom headers to the server.

-d is used to send data in a POST request to the server. This option implies using the POST method.

To translate a POST command to a Python request:

Translating a GET command would be similar:

Examples

In the examples below, <hostname>.emedgene.com and <hostname>.emg.illumina.com are used indifferently.

The following examples will build the requests step-by-step, allowing you to execute them individually to understand their functionality, using the output of one request as the input for the next.

You can also use the GUI to obtain all the parameters or record them after executing the individual API calls in this section. Then, use these values to construct your final API call.

Get list of cases

This example can be used as a simple way to verify your connection.

Checking the response

To validate the API request was completed successfully, check the HTTP response code.

HTTP 200 means the API call was successful. Learn more about HTTP response code .

In order to pretty-print the JSON response and view it in a formatted way:

Tip: when returning lists (like lists of cases) Emedgene API uses pagination. It is possible to get the next items from the list using from and size, shown below.

Get list of storage providers

Now that we are able to retrieve information with the API, let's continue by using it for a more practical request like retrieving the list of storage providers your user can access files from.

Your storage provider holds the sample files accessible for creating samples in a case.

Create new case

To create a new case, multiple parameters need to be defined such as samples, the relationship between samples, phenotypes, genes and more. All the required details can be found in the API Reference page under /api/cases/v2/cases .

Once the complete JSON defining the case details is complete, the case can be created as follows:

Once the case was created successfully, the response code expected is HTTP 201.

Use the case name to retrieve information about the case.

Check the status of a case

In order to know if the case has completed successfully, check the status as follows:

Get more information about a case

To get more information about a case, use the same API call as above without any test_fields

The response can be used to find which test fields are of interest and use them in the next API calls:

Get candidates of completed case

To retrieve the candidate variants of the completed case:

To retrieve candidate variants of the completed case with details such as transcript data, pathogenicity, ACMG tags and more:

Please contact support.

You can generate an API Key from your account console and use it with the API and command-line interface. Each user can create up to 10 API Keys. These keys are managed through the product dashboard, which you can access by logging into the Platform Dashboard (https://<domain>.login.illumina.com), navigating to the profile dropdown, and selecting "Manage API Keys."

To generate a new API Key, click Generate. You will need to name the API Key and decide whether to include all workgroups or select specific workgroups. The chosen workgroups will be accessible using this API Key.

After generating the API Key, it will be displayed (initially hidden). You can reveal the key to copy or download it to a file for secure storage. Remember, once you close the window, the key will no longer be accessible through the domain login page, so ensure it is stored securely for future use.

Store your API Key securely and refer to it when using the command-line interface or APIs.

For more information on how to use your API Key with Emedgene API, check out the .

Getting Started

Before exploring the examples, make sure to log in to the platform. More information on this can be found in the API Beginner Guide.

After authentication, you will receive a token, which remains valid for a certain period of time.

Use cases

• Automating Case Management: Creation and Status Check

• Assigning Participants

• Retrieving Case Info, Tags, Variants, and Changing Status

Automating Case Management: Creation and Status Check

This example demonstrates how to automate case management, including case creation, checking if the case status is "finalized," and generating a report.

Step 1: Create the Payload

First, construct a JSON payload with all the necessary case data.

Step 2: Send a POST Request

To create a case, send a POST request using the payload. Remember to replace any values enclosed in < > with your specific data.

Step 3: Retrieve Case Status and Name

After creating the case, you can retrieve the status and name from the API response.

Assigning Participants

Step 1: Retrieve Participant IDs by Email

Before assigning participants to cases, you can retrieve their IDs by searching for their email addresses.

Step 2: Assign Participants to the Case

Finally, assign participants to the case using their IDs.

Retrieving Case Info, Tags, Variants, and Changing Status

This example demonstrates how to retrieve tagged variants and the associated variant information from a case, and change the case status.

Step 1: Obtain the Case Name

If you don't have the case name yet, follow the steps outlined in Steps 1 and 2 of to create a case and retrieve the case name.

Step 2: Retrieve case info

Use this API route to get some basic information on a case: creation time, creator, last updated time, case name, case status.

Step 3: Send a GET Request to Retrieve Case Tags

To pull the case data, including tagged variants, send a GET request.

Step 4: Update Case Status to a Custom Status

After retrieving the case, update the status to "custom_status_1".

Managing Finalized Cases and Generating Reports

Step 1: Retrieve Cases Finalized in the Last 24 Hours

Retrieve cases that were finalized within the last 24 hours.

Another option for retrieving a finalized case is to use . This option allows to receive notifications on case status change instead of checking via API.

Step 2: Generate a Report

Reports can only be generated for finalized cases. To generate a report, send the following GET request:

Creating a Custom Preset Group with Additional Gene Panels

This example demonstrates how to create a custom preset group by combining an existing preset group (created with a case) and adding additional gene lists, HPO terms, inheritance modes, or other data on top of it.

Step 1: Create a Case with an Existing Preset Group

Before creating a custom preset group, ensure that a case has already been created using an existing preset group. For details on how to create a case, refer to .

Step 2: Create a Custom Preset Group

Once the case is created, use the API to add custom gene lists on top of the existing preset group associated with the case. Here's the Python code to achieve this:

Emedgene Integration Using Webhooks

Emedgene allows seamless integration with other platforms via webhooks. By configuring webhooks, you can receive real-time updates on genomic data analyses. When an event occurs, Emedgene pushes relevant data to your specified URL, enabling automated workflows and immediate data synchronization with your systems. This integration simplifies data sharing and enhances the efficiency of your operations by keeping your platforms in sync with insights from Emedgene.

Prerequisites

1. Have a BaseSpace account

2. Have an Emedgene account

3. Add this BaseSpace as a Storage Provider in Emedgene -

4. Add your BaseSpace user to the Emedgene Connect App whitelist

   1. Go to

      https://<domain>.api.basespace.illumina.com/v1pre3/users/current

   2. Send the Href value to Tech Support with the subject "BaseSpace Emedgene Connect app" "Href": "v1pre3/users/00000000"

Workflow setup

1. On BaseSpace, go to Apps and search for Emedgene Connect Beta under All Categories

1. Click on the app and press Launch Application

1. Fill out the application setup

   1. Choose an Analysis Name - this will be used for the setup analysis run

   2. Choose a Biosample and Project for the setup - other projects and biosamples can be used later on

1. When the app launches, an additional URL will be printed to the logs. Copy this URL to another tab and give the requested access to the app. The access granted will created the workflows used later in the BioSample Workflow Sheet.

2. Once the app setup analysis is completed successfully, press View Files next to the Logs window.

1. Go to Files and find the BioSample Workflow CSV template in the outputs directory.

BioSample Workflow Sheet setup

• Columns A-J hold the data to queue the Emedgene Connect Beta app launch.

  • BioSample Name

  • Default Project - the BaseSpace project to save the outputs to. Can be different than the project used for setting up the app.

Sample Sheet setup

• Sample_ID needs to match the BioSampleName in the BioSample Workflow Sheet

• ProjectName needs to match the Default Project in the BioSample Workflow Sheet

Run upload

Upload the run with the Sample Sheet to BaseSpace via CLI (Command Line interface).

To set up the BaseSpace CLI see .

<bs-path> upload run -n '<RunName>' -t <Instrument> . --concurrency=high

1. <RunName> should be set to the RunName from the Sample Sheet Headers

2. <Instrument> should be set to the InstrumentPlatform from the Sample Sheet Headers

3. <bs-path> should be set to the output of the command which bs

Next Steps

Once BCL Convert is completed for a BioSample from the BioSample Workflow sheet, the selected Analysis Workflow from the BioSample Workflow sheet will launch the Emedgene Connect Beta.

Overview

This feature enables automatic case creation in Emedgene following the successful completion of specific array analysis events on ICA. The automation supports efficient and standardized case generation, ensuring timely downstream review and interpretation.

When It Applies

This feature is triggered when a DRAGEN Array - Cytogenetics analysis with Emedgene tertiary interpretation analysis is completed successfully on ICA.

Prerequisites

Before automatic case creation can occur, ensure the following conditions are met:

1. The user needs to have access to BSSH and Emedgene in the same workgroup.

2. The managed ICA project must be to the Emedgene workgroup:

   • The managed ICA project needs to be the one was created automatically by BSSH after running the first analysis (BSSH {workgroup name}, for example "BSSH MyWG").

Automatic Case Creation Workflow

Upon successful analysis completion, the system will:

1. Create a New Case in EMG

   • Case Type: Set to Array.

     • Note: No ROI file will be associated with the case.

Limitations

Please note the following limitations of the automatic case creation feature:

1. Supports only singleton cases

   • Cases involving multiple individuals (e.g., trios or families) are not supported.

2. No phenotype support

Benefits

• Streamlined and seamless workflow between ICA and Emedgene.

• Reduces manual intervention and potential for data entry errors.