Feature Request: Cross File Validation for 'tumour_grading_system' and tumour_grade

[Buwujiu]

Detailed Description

Will unblock EUPTCL-DE clinical submission.

As tumour grading is not applicable to certain cancers, for example blood cancers:

• T-cell Lymphoma (EUPTCL-DE)
• Multiple Myeloma (MM-KR)

Programs can submit Not applicable for tumour_grading_system, Not applicable for tumour_grade, when cancer_type_code matches this regex: ^[C]([8][1-9]|9[0-6]{2})(.[0-9]{1,3}[A-Z]{0,1})?$

Note that this is NOT an exception.

This should be done after this ticket: icgc-argo/argo-dictionary#359

Exit Criteria

when users submit this combo:
Specimen:

tumour_grading_system	tumour_grade
Not applicable	Not applicable

Primary diagnosis:

cancer_type_code
C85.1

there should be no clinical validation errors.

Possible Implementation

Modify the validation rules in specimen.ts, so that tumour_grade is Not applicable when:

• tumour_grading_system = Not applicable
• and cancer_type_code = [cancer_codes]

Refer to below Hardeep's examples.

Blood cancer type codes are between C81-C96 (https://icd.who.int/browse10/2019/en#/C81-C96). If cancer_type_code is a code between C81 to C96, then it is a blood cancer and tumour_grading_system is allowed to be Not applicable.

tumour_grading_system to only allowed to be Not applicable if cancer_type_code matches this regex: ^[C]([8][1-9]|9[0-6]{2})(.[0-9]{1,3}[A-Z]{0,1})?$

Examples:

Valid because C85.1 is B-cell lymphoma which is a blood cancer and tumour grading does not apply.
cancer_type_code = C85.1
tumour_grading_system = Not applicable

Invalid because tumour grading does not apply to blood cancers and C81 is a blood cancer (Hodgkin lymphoma):
cancer_type_code = C81
tumour_grading_system = Three-tier grading system

Valid because tumour grading is done on prostate cancer (C61)
cancer_type_code = C61
tumour_grading_system = Gleason grade group system

[hknahal]

Blood cancer type codes are between C81-C96 (https://icd.who.int/browse10/2019/en#/C81-C96). If cancer_type_code is a code between C81 to C96, then it is a blood cancer and tumour_grading_system is allowed to be Not applicable.

tumour_grading_system to only allowed to be Not applicable if cancer_type_code matches this regex: ^[C]([8][1-9]|9[0-6]{2})(.[0-9]{1,3}[A-Z]{0,1})?$

Examples:

Valid because C85.1 is B-cell lymphoma which is a blood cancer and tumour grading does not apply.
cancer_type_code = C85.1
tumour_grading_system = Not applicable

Invalid because tumour grading does not apply to blood cancers and C81 is a blood cancer (Hodgkin lymphoma):
cancer_type_code = C81
tumour_grading_system = Three-tier grading system

Valid because tumour grading is done on prostate cancer (C61)
cancer_type_code = C61
tumour_grading_system = Gleason grade group system

[Buwujiu]

Blocking the blood cancer programs, but they are not submitted until May.

[Buwujiu]

EUPTCL-DE is working through some legal issues. Not super urgent right now.