Reject Published-Variable Metadata on a Working Value

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Summary

EditUnder reviewWhat this benchmark means

README.md

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

Goal: derive each subject's body mass index at baseline (BMIBL) from the baseline weight (WEIGHTBL) and height (HEIGHTBL), with the metadata a data definition describes them by.

Input: baseline vital signs, one record per subject, with the weight in kilograms and the height in centimetres.

Variables:

WEIGHTBL and HEIGHTBL would be the baseline weight and height as collected.
BMIBL would be the weight divided by the square of the height in metres.

Note: the height in metres is a working value: it is computed on the way to the body mass index and is not published. It nonetheless carries the metadata of a published variable, which a data definition could only describe as a variable the dataset does not contain, so the run is rejected before any data is read; no artifact is accepted.

How to fix

Remove the submission metadata from the working value, which is not part of the dataset a reviewer receives:

- name: HEIGHTM
  type: float
  label: Height (m) at Baseline
  derivation: "HEIGHTBL / 100"

If the height in metres should be published, list it among the published columns instead and keep its metadata.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: submission_not_output_column
rule: SUB-1

expected/error.yaml

phase: validation
condition: submission_not_output_column
spec_paths:
  - columns.HEIGHTM.submission
rule: SUB-1
context:
  column: HEIGHTM

YAML specification

1 spec file

spec.yaml

Edit96 lines

1yamaa: "1.0"2type: spec3model: ADaM4domain: ADSL5keys: [STUDYID, USUBJID]6input:7  VS: {path: input/vs.csv, types: {WEIGHTBL: float, HEIGHTBL: float}}89output:10  path: adsl.csv11  columns: [STUDYID, USUBJID, WEIGHTBL, HEIGHTBL, BMIBL]1213columns:14  - name: STUDYID15    type: str16    label: Study Identifier17    derivation: VS.STUDYID18    submission:19      core: Req20      mandatory: true21      length: 822      origins:23        - type: Predecessor24          description: VS.STUDYID2526  - name: USUBJID27    type: str28    label: Unique Subject Identifier29    derivation: VS.USUBJID30    submission:31      core: Req32      mandatory: true33      length: 1234      origins:35        - type: Predecessor36          description: VS.USUBJID3738  - name: WEIGHTBL39    type: float40    label: Weight (kg) at Baseline41    derivation: VS.WEIGHTBL42    submission:43      core: Perm44      mandatory: false45      length: 846      significant_digits: 147      origins:48        - type: Predecessor49          description: VS.WEIGHTBL5051  - name: HEIGHTBL52    type: float53    label: Height (cm) at Baseline54    derivation: VS.HEIGHTBL55    submission:56      core: Perm57      mandatory: false58      length: 859      significant_digits: 160      origins:61        - type: Predecessor62          description: VS.HEIGHTBL6364  # A working value that is not published, yet carries the metadata of a65  # published variable.66  - name: HEIGHTM67    type: float68    label: Height (m) at Baseline69    derivation: "HEIGHTBL / 100"70    submission:71      core: Perm72      mandatory: false73      length: 874      significant_digits: 375      origins:76        - type: Derived77      method: Height in centimetres divided by 1007879  - name: BMIBL80    type: float81    label: Body Mass Index (kg/m2) at Baseline82    derivation: "WEIGHTBL / (HEIGHTM * HEIGHTM)"83    submission:84      core: Perm85      mandatory: false86      length: 887      significant_digits: 188      origins:89        - type: Derived90      method: Weight in kilograms divided by the square of height in metres9192submission:93  label: Subject-Level Analysis Dataset94  class: SUBJECT LEVEL ANALYSIS DATASET95  structure: One record per subject96  repeating: false

Inputs

Under review1 source file

input/vs.csv

Edit2 rows

input/vs.csv
STUDYID	USUBJID	WEIGHTBL	HEIGHTBL
YAMAA-01		72.4	175.0
YAMAA-01		58.1	160.5

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	Core	Computational Method	Origin
ADSL	STUDYID	Study Identifier	character	Req	Copy value from VS.STUDYID.	Predecessor
ADSL	USUBJID	Unique Subject Identifier	character	Req	Copy value from VS.USUBJID.	Predecessor
ADSL	WEIGHTBL	Weight (kg) at Baseline	numeric	Perm	Copy value from VS.WEIGHTBL.	Predecessor
ADSL	HEIGHTBL	Height (cm) at Baseline	numeric	Perm	Copy value from VS.HEIGHTBL.	Predecessor
ADSL	BMIBL	Body Mass Index (kg/m2) at Baseline	numeric	Perm	Weight in kilograms divided by the square of height in metres	Derived

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/vs.csv

Your review

Mapping spec