Reject Duplicate Subject

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Summary

EditUnder reviewWhat this benchmark means

README.md

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

Goal: build one record for every subject carrying the collected age (AGE) and sex (SEX). Each subject may appear only once in the result.

Input: collected demographics records carrying age (AGE) and sex (SEX).

Variables:

AGE would be the collected age, carried into the result unchanged.
SEX would be the sex collected in the demographics records, carried into the result unchanged.

Note: the result is built one row per collected record, so a subject entered twice reaches the result twice. That rejects the run even when the two records agree; here they also disagree on the age, and keeping either record, or merging the two, would report an age the collected data does not support. The expected file shows the completed rows as they reach the one-row-per-subject check, but the repeated subject still rejects the run and no artifact is accepted.

How to fix

Reconcile the two source records and correct the governed demographics input so it contains one supported age for the subject. If multiple source records are legitimate, build the rows from a list holding each subject once and declare an ordered record-selection rule for the demographics record; do not rely on source order to discard one. The completed output must contain exactly one row for each key.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: output
condition: duplicate_key
rule: OUTPUT-3

expected/error.yaml

phase: output
condition: duplicate_key
spec_paths:
  - keys
rule: OUTPUT-3
context:
  duplicate_count: 1
  keys:
    - STUDYID: PILOT7
      USUBJID: P7-722

YAML specification

1 spec file

spec.yaml

Edit38 lines

1yamaa: "1.0"2type: spec3model: ADaM4domain: ADSL5keys: [STUDYID, USUBJID]6input:7  DM: input/dm.csv89output:10  path: adsl.csv11  columns: [STUDYID, USUBJID, AGE, SEX]1213columns:14  - name: STUDYID15    type: str16    label: Study Identifier17    derivation: DM.STUDYID1819  - name: USUBJID20    type: str21    label: Unique Subject Identifier22    derivation: DM.USUBJID2324  - name: AGE25    type: int26    label: Age27    derivation: DM.AGE2829  - name: SEX30    type: str31    label: Sex32    derivation: DM.SEX3334# One output row per DM record, so a subject entered twice reaches the35# output twice and fails the key check. Without rows the output would hold36# one row per subject, and the two ages would clash earlier instead.37rows:38  - id: record

Inputs

Under review1 source file

input/dm.csv

Edit3 rows

input/dm.csv
STUDYID	AGE	SEX
PILOT7	64	F
PILOT7	58	M
PILOT7	59	M

Unexpected Output

Under review3 rows presented to the failing check - not an accepted artifact

expected/adsl.csv

Edit3 rows

expected/adsl.csv
STUDYID	AGE	SEX
PILOT7	64	F
PILOT7	58	M
PILOT7	59	M

Shaded columns are derived— = missing value

Human review and assessment

Dataset Name	Variable Name	Variable Label	Type	Computational Method	Origin
ADSL	STUDYID	Study Identifier	character	Copy value from DM.STUDYID.	Predecessor
ADSL	USUBJID	Unique Subject Identifier	character	Copy value from DM.USUBJID.	Predecessor
ADSL	AGE	Age	numeric	Copy value from DM.AGE.	Predecessor
ADSL	SEX	Sex	character	Copy value from DM.SEX.	Predecessor

Template	Include when
record

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

expected/adsl.csv

Your review

Mapping spec