Laboratory Workflow Simulator – Impersonating instruments for automated E2E testing

garethreid123gmailcom

Automated testing is a required part of any development but can be hard to achieve when using physical instruments and dynamically changing real-life samples. Here I will describe my solution to this, which impersonates laboratory instruments and randomly generates different sample characteristics.

If you are reading this externally I refer to Holly which is our Laboratory Information Management Systems (LIMS). This is the software used to manage the samples and instruments within the sample workflow.

Purpose

  • Generate a set of samples and add them to Holly via Babble (HL7 interface)
  • Generate each instruments out file set for interaction in Holly
  • Add dummy workflow & test information to allow final dashboard testing
  • Cross check data matches across each step automatically, data checked:
    • Patient demographics
    • Barcodes
    • Plate position
    • Id’s
    • Re-extraction & failed actions
    • Volumes, concentration & dilution info

Description – Workflow Simulator

DNA/RNA preparation workflow simulator

Generates:

With in/out sample ids and appropriate metrics and attributes

  • HL7 data file – Auslab (external LIS) impersonator
  • QiaSymphony (DNA extraction instrument) input driver file
  • QiaSymphony rackfiles – QiaSymphony instrument impersonator
  • Synergy Hx PlateReader driver file
  • Hamilton MicroLab driver file (load Qubit plate on liquid handler)
  • Qubit results file – PlateReader instrument impersonator
  • Hamilton driver file (dilutions)
  • Dilutions results file – Hamilton MicroLab instrument impersonator
  • XL9 Label input file
  • XL9 Label output file – XL9 instrument impersonator

Runs:

  • Babble import of HL7 file
  • Creates random workflow & sample metrics for dashboard (Lab work Impersonator)

By running this every time a change is made to software we can auto detect any issues from a software change. Inversely we can use these files to test instrument protocols when a change is made to the instruments onboard logic.

Code is kept in private source control but please email me if you are interested and I will put a modified version in git.

Published by garethreid123gmailcom

I am software developer with 15 years experience. I started out at a web company, at the start of the .Net boom, 15 years ago and have learned with the industry keeping up with changing front and back end concepts as well as the ever changing architecture and design pattern landscape. I consider myself a senior developer with excellent design knowledge and people management. In the last 7 years I have moved my programming expertise into the are of medicine and bioinformatics. I apply my skillset, including web dashboards, backend transactional systems, process automation and robotics instrument programming, to create entire process ecosystems.

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