Reject a Second List of Sex Codes

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Summary

EditUnder reviewWhat this benchmark means

README.md

Public entries: Python and R. Passing coverage requires an installed inventory.

Goal: carry the collected sex (SEX) for each subject, coded with the study's controlled terminology for sex.

Input: collected demographics with the study and subject identifiers and the recorded sex code.

Variables:

SEX would be the subject's recorded sex, one of the codes the terminology lists: F, M or U.

Note: the accepted codes are stated once. The terminology the column is bound to already lists every accepted code, so a second list of the same codes is rejected before any record is read, even when the two lists agree.

How to fix

Remove the allowed_values check. The bound SEX codelist lists its items, and every non-missing value must equal one of them:

- name: SEX
  type: str
  label: Sex
  derivation: DM_RAW.SEX
  submission:
    codelist: SEX
    origins:
      - type: Collected
        source: Investigator

To accept fewer codes than the published list, bind a sponsor codelist that lists only those codes instead of narrowing the binding with a second list.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: redundant_declaration
rule: CT-9

expected/error.yaml

phase: validation
condition: redundant_declaration
spec_paths:
  - columns.SEX.verifications[0].allowed_values
rule: CT-9
context:
  column: SEX
  codelist: SEX
  stated_by: columns.SEX.submission.codelist

YAML specification

1 spec file

spec.yaml

Edit37 lines

1yamaa: "1.0"2type: spec3model: SDTM4domain: DM5keys: [STUDYID, USUBJID]6input:7  DM_RAW: input/dm_raw.csv89output:10  path: dm.csv11  columns: [STUDYID, USUBJID, SEX]1213columns:14  - name: STUDYID15    type: str16    label: Study Identifier17    derivation: DM_RAW.STUDYID1819  - name: USUBJID20    type: str21    label: Unique Subject Identifier22    derivation: DM_RAW.USUBJID2324  # The bound list already names every accepted code; the list of values25  # beside it states the same codes a second time.26  - name: SEX27    type: str28    label: Sex29    derivation: DM_RAW.SEX30    verifications:31      - allowed_values:32          values: [F, M, U]33    submission:34      codelist: SEX35      origins:36        - type: Collected37          source: Investigator

Inputs

Under review1 source file

input/dm_raw.csv

Edit2 rows

input/dm_raw.csv
STUDYID	USUBJID	SEX
YAMAA-01		F
YAMAA-01		M

Unexpected Output

Under reviewNo artifact is produced

No fixture files in this directory.

Shaded columns are derived— = missing value

Human review and assessment

Variable Name	Variable Label	Type	Controlled Terms or Format	Origin	Conversion Definition	Variable Type	Variable Order
STUDYID	Study Identifier	Char		Collected	Copy value from DM_RAW.STUDYID.	SDTM	1
USUBJID	Unique Subject Identifier	Char		Collected	Copy value from DM_RAW.USUBJID.	SDTM	2
SEX	Sex	Char	Sex	Collected	Copy value from DM_RAW.SEX.	SDTM	3

Codelist ID	Name	Value	Decode	Codelist NCI alias	Value NCI alias	Extensible
SEX	Sex	F	Female	C66731	C16576	No
SEX	Sex	M	Male	C66731	C20197	No
SEX	Sex	U	Unknown	C66731	C17998	No

Version	Date	Author	Description
1.7	2026-10-20	yamaa docs build	Read a specification in the 1.0 surface as its 0.5 counterpart; state that missing values stay missing where a mapping declares no missing handler, and leave out a declared missing answer that restates a handler's default
1.6	2026-10-17	yamaa docs build	Describe collected date parts written as ISO 8601 date text and times of day counted in seconds since midnight
1.5	2026-10-17	yamaa docs build	Name collected precision in words instead of letter codes; state imputation fallbacks, minimum source precision, bounds ignored outside the collected period, and invalid text with no handler as an error; describe date and datetime shifts, imputation flag codes, and partial text giving no date part
1.4	2026-10-15	yamaa docs build	State datetime precision codes through the hour and minute, and complete only the time parts a collected datetime lacks
1.3	2026-09-29	yamaa docs build	Show study codelist names, external dictionaries, and ISO 8601 formats in variable rows; list the document's codelist values and metadata
1.2	2026-09-29	yamaa docs build	Classify ADaM copies from a declared input as Predecessor and recodes as Derived, and SDTM recodes of locally derived columns as Derived
1.1	2026-09-29	yamaa docs build	Resolve lookups into the donor record they select, and give every derivation shape a plain-language rule instead of its raw YAML
1.0		yamaa docs build	Initial generation from spec.yaml

How to fix

input/dm_raw.csv

Your review

Mapping spec