Reject Mismatched Lists

Review ask

As a clinical trial statistician or programmer, challenge anything in this benchmark: describe a problem in Comments, or propose a fix with the Edit button on any source file.

Task: Is this a specification error a study team could realistically make, and should the build stop on it rather than continue?
Inputs: Do they trigger the failure for the reason the summary gives?
Expected failure: Is this the right error, raised at the right point, and would it tell the programmer what to fix?

The other tabs beside Comments are background for assessment, not under review.

Summary

EditUnder reviewWhat this benchmark means

README.md

Goal: attach the reference-range upper limit (LBSTNRHI) to each collected result, carrying its test code and sex.

Input: collected results carrying test code (LBTESTCD), sex (SEX), and numeric result (LBSTRESN), plus a reference-limit table carrying the upper limit (NRHI) by test code and sex.

Variables:

LBSTNRHI would contain the upper limit value from the reference-limit table for the test code and sex of the result.

Note: the lookup names three limit-table columns, and each listed column matches the same-named current-row value. The collected results carry no unit, so the UNIT column would match against nothing. The unknown current-row value is rejected before any data is read; no artifact is accepted.

How to fix

If the limit table holds one unit per test code, match on test code and sex alone, since the collected results carry no unit:

intermediates:
  - id: REFRANGE
    dataset: LBRANGE
    key: [LBTESTCD, SEX]

When a current-row name differs from the table's, map the table column to it, as in key: {LBTESTCD: PARAMCD, SEX: SEX}.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: unknown_field
requirement: REQ-0117

expected/error.yaml

phase: validation
condition: unknown_field
spec_paths:
  - intermediates[0].key
requirement: REQ-0117
context:
  identifier: UNIT
  intermediate: REFRANGE

YAML specification

1 spec file

spec.yaml

Edit50 lines

1schema_version: "1.0"2domain: LB3keys: [STUDYID, USUBJID, LBSEQ]4input:5  LB_RAW: input/lb_raw.csv6  LBRANGE: input/lbrange.csv7base: LB_RAW89output:10  path: lb.csv11  columns: [STUDYID, USUBJID, LBSEQ, LBTESTCD, SEX, LBSTNRHI]1213intermediates:14  # The reference range for the result's test code and sex. Each listed15  # table column matches the same-named current-row value, and the16  # collected results carry no UNIT.17  - id: REFRANGE18    dataset: LBRANGE19    key: [LBTESTCD, SEX, UNIT]2021columns:22  - name: STUDYID23    type: str24    label: Study Identifier25    derivation: LB_RAW.STUDYID2627  - name: USUBJID28    type: str29    label: Unique Subject Identifier30    derivation: LB_RAW.USUBJID3132  - name: LBSEQ33    type: int34    label: Sequence Number35    derivation: LB_RAW.LBSEQ3637  - name: LBTESTCD38    type: str39    label: Lab Test or Examination Short Name40    derivation: LB_RAW.LBTESTCD4142  - name: SEX43    type: str44    label: Sex45    derivation: LB_RAW.SEX4647  - name: LBSTNRHI48    type: float49    label: Reference Range Upper Limit-Std Units50    derivation: REFRANGE.NRHI

Inputs

Under review2 source files

input/lb_raw.csv

Edit2 rows

input/lb_raw.csv
STUDYID	USUBJID	LBSEQ	LBTESTCD	SEX	LBSTRESN
YAMAA-01		1	ALT	F	42
YAMAA-01		1	ALT	M	35

input/lbrange.csv

Edit2 rows

input/lbrange.csv
LBTESTCD	SEX	UNIT	NRLO	NRHI
ALT	F	U/L	0	40
ALT	M	U/L	0	40

Unexpected Output

Under reviewNo artifact is produced

No fixture files in this directory.

Shaded columns are derived— = missing value

Comments and assessment materials

Variable Name	Variable Label	Type	Origin	Conversion Definition	Variable Type	Variable Order
STUDYID	Study Identifier	Char	Collected	Copy value from LB_RAW.STUDYID.	SDTM	1
USUBJID	Unique Subject Identifier	Char	Collected	Copy value from LB_RAW.USUBJID.	SDTM	2
LBSEQ	Sequence Number	Num	Collected	Copy value from LB_RAW.LBSEQ.	SDTM	3
LBTESTCD	Lab Test or Examination Short Name	Char	Collected	Copy value from LB_RAW.LBTESTCD.	SDTM	4
SEX	Sex	Char	Collected	Copy value from LB_RAW.SEX.	SDTM	5
LBSTNRHI	Reference Range Upper Limit-Std Units	Num	Derived	Take NRHI from the LBRANGE record matching on LBTESTCD, SEX and UNIT, and a row with no match is an error.	SDTM	6

Version	Date	Author	Description
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/lb_raw.csv

input/lbrange.csv

Comments

Mapping spec