Reject a Numeric Age Group Bound to a Text Codelist

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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 age (AGE) and numeric pooled age group (AGEGR1N) onto the subject-level analysis dataset, with the group restricted to the study's codelist for it.

Input: collected demographics, one record per subject, and the study's codelists in the project file: a text list of the age groups and a numeric list of their codes.

Variables:

AGE would be the age in years as collected.
AGEGR1N would be 1 for a subject younger than 65 and 2 otherwise; missing when no age was collected.

Note: the numeric age group is bound to the text list of the age groups, whose values are <65 and >=65. A number can never be one of those values, so the binding is a mistake rather than a check, and the run is rejected before any data is read; no artifact is accepted.

How to fix

Bind the numeric group to the numeric list of its codes:

submission:
  core: Perm
  mandatory: false
  length: 1
  codelist: AGEGR1N
  origins:
    - type: Derived
  method: 1 for an age below 65 years, 2 for 65 years or above

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: codelist_type_mismatch
rule: CT-8

expected/error.yaml

phase: validation
condition: codelist_type_mismatch
spec_paths:
  - columns.AGEGR1N.submission.codelist
rule: CT-8

YAML specification

1 spec file

spec.yaml

Edit74 lines

1yamaa: "1.0"2type: spec3model: ADaM4domain: ADSL5keys: [STUDYID, USUBJID]6input:7  DM: {path: input/dm.csv, types: {AGE: int}}89output:10  path: adsl.csv11  columns: [STUDYID, USUBJID, AGE, AGEGR1N]1213columns:14  - name: STUDYID15    type: str16    label: Study Identifier17    derivation: DM.STUDYID18    submission:19      core: Req20      mandatory: true21      length: 822      origins:23        - type: Predecessor24          description: DM.STUDYID2526  - name: USUBJID27    type: str28    label: Unique Subject Identifier29    derivation: DM.USUBJID30    submission:31      core: Req32      mandatory: true33      length: 1234      origins:35        - type: Predecessor36          description: DM.USUBJID3738  - name: AGE39    type: int40    label: Age41    derivation: DM.AGE42    submission:43      core: Req44      mandatory: false45      length: 346      origins:47        - type: Predecessor48          description: DM.AGE4950  # The numeric age group is bound to the text list of the age group, not51  # to its own numeric list.52  - name: AGEGR1N53    type: int54    label: Pooled Age Group 1 (N)55    derivation:56      case:57        - when: "AGE < 65"58          then: 159        - when: "AGE >= 65"60          then: 261    submission:62      core: Perm63      mandatory: false64      length: 165      codelist: AGEGR166      origins:67        - type: Derived68      method: 1 for an age below 65 years, 2 for 65 years or above6970submission:71  label: Subject-Level Analysis Dataset72  class: SUBJECT LEVEL ANALYSIS DATASET73  structure: One record per subject74  repeating: false

Inputs

Under review1 source file

input/dm.csv

Edit2 rows

input/dm.csv
STUDYID	USUBJID	AGE
YAMAA-01		52
YAMAA-01		77

Unexpected Output

Under reviewNo artifact is produced

No fixture files in this directory.

Shaded columns are derived— = missing value

Human review and assessment

Dataset Name	Variable Name	Variable Label	Type	Codelist/Controlled Terms	Core	Computational Method	Origin
ADSL	STUDYID	Study Identifier	character		Req	Copy value from DM.STUDYID.	Predecessor
ADSL	USUBJID	Unique Subject Identifier	character		Req	Copy value from DM.USUBJID.	Predecessor
ADSL	AGE	Age	numeric		Req	Copy value from DM.AGE.	Predecessor
ADSL	AGEGR1N	Pooled Age Group 1 (N)	numeric	Pooled Age Group 1	Perm	1 for an age below 65 years, 2 for 65 years or above	Derived

Codelist ID	Name	Value	Extensible
AGEGR1	Pooled Age Group 1	<65	No
AGEGR1	Pooled Age Group 1	>=65	No
AGEGR1N	Pooled Age Group 1 (N)	1	No
AGEGR1N	Pooled Age Group 1 (N)	2	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.csv

Your review

Mapping spec