Allow `specimen_acquisition_interval` to accept negative numbers

lindaxiang commented 2 months ago

In the current data model, specimen_acquisition_interval indicates the interval between primary diagnosis and specimen acquisition in days. It is an integer larger than 0.

However, for program MONSTAR,

They use date of enrolment as date of diagnosis
Their tissue NGS is performed with archival tissue for the majority of cases, so sample collection is often performed prior to enrolment

Considering the specimen table can be expanded to collect any specimens associated with a donor not only related to one given diagnosis. We can allow the specimen_acquisition_interval to accept negative numbers.

Implementation

remove the restrictions: https://github.com/icgc-argo/argo-dictionary/blob/develop/schemas/specimen.json#L152-L157

edsu7 commented 1 month ago

tested in QA, waiting for Bhavik to test

lindaxiang commented 1 month ago

Addressed by PR: https://github.com/icgc-argo/argo-dictionary/pull/433

edsu7 commented 3 weeks ago

Tested in QA. PR merged

things left to do

update dictionary and deploy in prod

icgc-argo / argo-dictionary

Allow `specimen_acquisition_interval` to accept negative numbers #432