Exceptions validation script changes

[hknahal]

Related to https://github.com/icgc-argo/argo-dictionary/issues/407

Updated validation scripts for fields that are conditional on fields that could have exception values ("not applicable" or "unknown").

Summary

Updated validation script for lymph_nodes_examined_method:

• If lymph_nodes_examined_status has an exception value of either Not applicable or Unknown, then lymph_nodes_examined_method is not allowed to be one of the enum values in the dictionary. It must also be either Not applicable or Unknown.

Updated validation script for tumour_grade:

• Whentumour_grading_system has an exception value of either Not applicable or Unknown, the error message was not clear. Updated validation script to indicate accepted values if tumour_grading_system has an exception value (ie. if tumour_grading_system = Not applicable, then tumour_grade can only be Not applicable).

[hknahal]

Tested in QA using TEST-CA

• Applied program exceptions on TEST-CA for several fields: TEST-CA_program_exceptions.csv

1. Submitted tumour_grading_system = Not applicable and tumour_grade = G3. This fails validation as expected and returns a more clear message indicating that tumour_grade can only be Not applicable.

2. Submitted enum value from dictionary for lymph_nodes_examined_method when there is an exception value (Unknown) for lymph_nodes_examined_status. This correctly displays an error message indicating that lymph_nodes_examined_method should not be submitted if lymph_nodes_examined_status = Unknown:

[joneubank]

@hknahal Your changes look good, but I just want to confirm with you that for this to work both fields would need to have an exception provided... ie. lymph_nodes_examined_status and lymph_nodes_examined_method have been given the same exception value.

If we are agreed about that then this can proceed.

[hknahal]

Thanks @joneubank. Yes agreed, both fields (ie. lymph_nodes_examined_status and lymph_nodes_examined_method) would need the same exception value.