Email Notifications

Stakeholders are interested in the progress of samples as they move through a workflow. Email alerts of events can provide them with real-time notifications.

Some possible uses of notifications include the following:

• Completion of a workflow for the billing department
• Manager review requests
• Notice of new files added via the LabLink interface
• Updates on samples that are not following a standard path through a workflow

BaseSpace Clarity LIMS provides a simple way of accomplishing this using a combination of the Clarity LIMS API, EPP / automation triggers, and Simple Mail Transfer Protocol (SMTP).

The send_email() method uses the Python smptlib module to create a Simple Mail Transfer Protocol (SMPT) object to build and send the email. The attached script does the following:

1. Gathers relevant data from the Clarity LIMS API endpoints.
2. Generates an email body according to a template.
3. Calls the send_email() function.

Connect to Clarity LIMS SMTP with:

host='localhost', port=25

Because of server restrictions, the script can send emails from only:

noreply.clarity@illumina.com

The automation / EPP command is configured to pass the following parameters:

-u

The username of the current user (Required)

-p

The password of the current user (Required)

-s

The URI of the step that launches the script (Required)

Example command line:

python /opt/gls/clarity/customextensions/emails_from_Clarity.py -u {username} -p {password} -s {stepURI}

• The script can be executed using a Clarity LIMS automation / EPP command, and triggered by one of the following methods:
– Manually, via a button on theRecord Details screen.
– Automatically, at a step milestone (on entry to or exit from a screen).
• The script can also be triggered outside of a Clarity LIMS workflow, using a time-based job scheduler such as cron.
• You are running a version of Python supported by Clarity LIMS, as documented in the Technical Requirements.
• The example code is provided for illustrative purposes only. It does not contain sufficient exception handling for use 'as is' in a production environment.

emails_from_clarity.py.txt