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” buttonAfter 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.