icgc-argo / argo-clinical

Clinical data submission for ARGO programs.
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🐛 Clinical exception values reported as errors in `Submitted Data` view #1042

Open hknahal opened 1 year ago

hknahal commented 1 year ago

Describe the bug

Fields which have clinical exception values (ie. treatment_setting = Not applicable) are reported as errors in the downloaded error report TSV file

Steps To Reproduce

Link to view Treatment data in "Submitted Data" view in TEST-CA program on Staging: https://platform.staging.icgc-argo.org/submission/program/TEST-CA/clinical-data?donorId=&tab=treatment

Steps to reproduce the behaviour:

  1. Change pagination to 100 rows
  2. Click on 'Error Report' to download TSV file of errors: ERROR_report.csv
  3. TSV error report reports 4 rows that have errors because treatment_setting has a value that is not permissible. error_report_trt_setting

It appears the clinical exception value of Not applicable for the treatment_setting field is being reported as an error incorrectly, even though the treatment_setting field has a clinical exception (NOTE: The pink error box at the top does not report this error). treatment_setting Clinical API confirms treatment_setting has a clinical exception value of Not applicable: treatment_setting_exception

Expected behaviour

Fields which have clinical exception values should not be reported as an error in the downloaded TSV error report file.

hknahal commented 1 year ago

This issue is seen in Prod as well in the APGI-AU program. The Submitted Data view for Treatment data is reporting 2 errors for the treatment_setting field but the submitted values are valid. It's unclear which rows exactly are being reported as errors because the cells with the error are not highlighted in the table. The submitted value Not applicable is valid because a program-level exception has been applied to the treatment_setting field. The submitted value Advanced/Metastatic is also valid because it is an enum value from the dictionary for the treatment_setting field:

apgi-au_sd_error

Unclear why these are being reported as errors.