CanCOGeN export to LIMS: Patient Symptomatic needs to be changed in LIMS export

cidgoh / DataHarmonizer

A standardized browser-based spreadsheet editor and validator that can be run offline and locally, and which includes templates for SARS-CoV-2 and Monkeypox sampling data. This project, created by the Centre for Infectious Disease Genomics and One Health (CIDGOH), at Simon Fraser University, is now an open-source collaboration with contributions from the National Microbiome Data Collaborative (NMDC), the LinkML development team, and others.

MIT License

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CanCOGeN export to LIMS: Patient Symptomatic needs to be changed in LIMS export #149

Closed griffie closed 3 years ago

griffie commented 3 years ago

Currently, there is a field called Patient Symptomatic with values "yes" or "no" based on whether there are symptoms listed, that is exported in the CNPHI export file based on hard coded logic (this field is not in our template). This field should be renamed VE_SYMP_AVAIL in the NML LIMS export. Values should be renamed as Y and N.

ddooley commented 3 years ago

This is included in Cancogen nml lims v0.1 #155 pull request.