Reject Sex Codes Checked Without the Study's Terminology

Review ask

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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 each subject's sex (SEX), coded with the study's sex terminology.

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

Variables:

SEX would be the subject's sex as collected, one of the codes the study's sex terminology lists.

Note: the study declares its sex terminology once, beside its list of datasets, and every dataset that codes sex refers to it. Built on its own, the demographics dataset has no terminology to check its codes against, so the run is refused before any record is read instead of publishing codes that nobody checked.

How to fix

Build the dataset as part of its study: open it from the study's project file, which declares the sex terminology and lists the dataset, for example yamaa_project("project.yaml")$spec("DM")$run() in R, yamaa.project("project.yaml").spec("DM").run() in Python, or yamaa run project.yaml --spec DM on the command line:

yamaa: "1.0"
type: project
codelists:
  - codelists:
      - id: SEX
        name: Sex
        data_type: text
        items: [{value: F}, {value: M}, {value: U}]
sdtm:
  specs: [spec.yaml]

A study without a project file yet needs one before its datasets can refer to shared terminology.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: project_binding_missing
rule: CT-13

expected/error.yaml

phase: validation
condition: project_binding_missing
spec_paths:
  - columns.SEX.submission.codelist
rule: CT-13
context:
  binding: codelist
  column: SEX
  codelist: SEX

YAML specification

1 spec file

spec.yaml

Edit58 lines

1yamaa: "1.0"23type: spec45model: SDTM6domain: DM7keys: [STUDYID, USUBJID]8input:9  DM_RAW: input/dm_raw.csv1011output:12  path: dm.csv13  columns: [STUDYID, USUBJID, SEX]1415columns:16  - name: STUDYID17    type: str18    label: Study Identifier19    derivation: DM_RAW.STUDYID20    submission:21      core: Req22      role: Identifier23      length: 724      origins:25        - type: Protocol26          source: Sponsor2728  - name: USUBJID29    type: str30    label: Unique Subject Identifier31    derivation: DM_RAW.USUBJID32    submission:33      core: Req34      role: Identifier35      length: 1136      origins:37        - type: Collected38          source: Investigator3940  # The sex terminology is declared once, in the study's project file.41  - name: SEX42    type: str43    label: Sex44    derivation: DM_RAW.SEX45    submission:46      core: Req47      role: Record Qualifier48      length: 149      codelist: SEX50      origins:51        - type: Collected52          source: Investigator5354submission:55  label: Demographics56  class: SPECIAL PURPOSE57  structure: One record per subject58  repeating: false

Inputs

Under review1 source file

input/dm_raw.csv

Edit3 rows

input/dm_raw.csv
STUDYID	USUBJID	SEX
STUDY01		F
STUDY01		M
STUDY01		F

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	Length	Controlled Terms or Format	Origin	Core	Conversion Definition	Variable Type	Variable Order
STUDYID	Study Identifier	Char	7		Protocol	Req	Copy value from DM_RAW.STUDYID.	SDTM	1
USUBJID	Unique Subject Identifier	Char	11		Collected	Req	Copy value from DM_RAW.USUBJID.	SDTM	2
SEX	Sex	Char	1	SEX	Collected	Req	Copy value from DM_RAW.SEX.	SDTM	3

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