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SamStudio8 / ocarina2

on-computer agent (for) remembering input actions
MIT License
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Change biosample --is-surveillance to take `Y` or `N` rather than acting as a store_true flag #10

Closed SamStudio8 closed 3 years ago

SamStudio8 commented 3 years ago

Currently a surveillance sample requires --is-surveillance to be added as a command option, and a non-surveillance sample leaves this option off the CLI. The reason for this was to prevent the mandatory surveillance field from breaking existing command line scripts that use Ocarina to submit samples (thus just assuming all samples were non-surveillance unless told otherwise).

This is however not very easy to toggle and I'll be changing --is-surveillance to require a Y or N from the CLI in the next minor release. Users will need to update any script that uploads new biosamples and use --is-surveillance Y and --is-surveillance N as appropriate.

SamStudio8 commented 3 years ago

Implemented in v0.35.0 by https://github.com/SamStudio8/ocarina/commit/d900cb29ec3181ea3fd0214ffad1504603066bcc

SamStudio8 commented 3 years ago

In cases where users do not provide this field because it is unknown, we'll keep the default behaviour and assume N. This will prevent the PHA ingest pipelines from breaking. Implemented in v0.35.1 by https://github.com/SamStudio8/ocarina/commit/159bc8021e7ea6076ce15fb8e8392d3965cf8cb5