LIMS Integration

Integration with a Laboratory Information Management System (LIMS) is achieved through a simple REST api; there are only two endpoints to get and set annotations for a particular specimen.

Support is enabled by command line options --lims-specimen-id and --lims-base-url, and optionally --lims-specimen-kind.

  • At application startup time to (1) retrieve the corresponding annotation from LIMS and load it by using the <base-url>/specimen_metadata/view endpoint and (2) to enable the “Upload Annotation” button

  • After user initiate annotation upload to LIMS while using the <base-url>/specimen_metadata/store endpoint.

The specimen_id parameter for both requests is set to the value of --lims-specimen-id, and the kind parameter is set to the value of --lims-specimen-kind.

For testing the functionality a simple reference LIMS server is implemented using flask; this server is only suitable for testing the API. See Endpoint Documentation for more information and sample requests.