Complete AJCC Script Based Validation across all examples

[icgc-argo]

Complete AJCC Script Based Validation across all examples

[wajiha-oicr]

Hi, I've been able to identify the following fields with the word staging system in their names:

• follow_up.json

  • recurrence_tumour_staging_system
  • posttherapy_tumour_staging_system

• primary_diagnosis.json

  • clinical_tumour_staging_system

• specimen.json

  • pathological_tumour_staging_system

Just want to confirm, will this script apply to each of these 5 fields? Am I missing any?

[wajiha-oicr]

@wajiha-oicr They will NOT have a codelist, but the will probably have a regex. An empty string should not be allowed for now:

Here is a list of possibilities for the TNM scenarios that need to be codified into regex:

T[0-4]
T[0-4][a-e]
T[0-4][a-e][0-2]
T[0-4][a-e][mi]
TX
Ta
Tis
Tis \(DCIS\)
Tis \(LCIS\)
Tis \(Paget's\)

N[0-4]
N[0-4][a-c]
N1(bI|bII|bIII|bIV|mi)
N0 (i+)
N0 (i-)
N0 (mol-)
N0 (mol-)
NX

M[0-2]
M[0-2][a-c]
MX
cM0 \(i+\)

I see, thanks. I'm assuming we will work on creating the validations for those fields as part of a separate ticket.

[wajiha-oicr]

Also, are there recent tsv sample files available for these schemas? Particularly specimen.tsv and primary_diagnosis.tsv; I'm not seeing any columns for the m, n, t, or stage fields.

[rosibaj]

@wajiha-oicr Yes, those are all the correct spots!

[wajiha-oicr]

@rosibaj , will the fields (i.e t,n,m category, stage group, stage suffix) eventually get codelists for which values are permitted? Or can the user enter any string they like?

Wondering if I need to check for empty strings or not; when there's a codelist that's already taken care of.

[rosibaj]

@wajiha-oicr They will NOT have a codelist, but the will probably have a regex. An empty string should not be allowed for now:

Here is a list of possibilities for the TNM scenarios that need to be codified into regex:

T[0-4]
T[0-4][a-e]
T[0-4][a-e][0-2]
T[0-4][a-e][mi]
TX
Ta
Tis
Tis \(DCIS\)
Tis \(LCIS\)
Tis \(Paget's\)

N[0-4]
N[0-4][a-c]
N1(bI|bII|bIII|bIV|mi)
N0 (i+)
N0 (i-)
N0 (mol-)
N0 (mol-)
NX

M[0-2]
M[0-2][a-c]
MX
cM0 \(i+\)

[rosibaj]

@wajiha-oicr yes, thats a future update :) list is still being verified.