Reject Mismatched Lists

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Summary

EditUnder reviewWhat this benchmark means

README.md

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

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
rule: LOOKUP-5

expected/error.yaml

phase: validation
condition: unknown_field
spec_paths:
  - intermediates.REFRANGE.key
rule: LOOKUP-5
context:
  identifier: UNIT
  intermediate: REFRANGE

YAML specification

1 spec file

spec.yaml

Edit53 lines

1yamaa: "1.0"2type: spec3model: SDTM4domain: LB5keys: [STUDYID, USUBJID, LBSEQ]6input:7  LB_RAW: input/lb_raw.csv8  LBRANGE: input/lbrange.csv9base: LB_RAW1011output:12  path: lb.csv13  columns: [STUDYID, USUBJID, LBSEQ, LBTESTCD, SEX, LBSTNRHI]1415intermediates:16  # The reference range for the result's test code and sex. Each listed17  # table column matches the same-named current-row value, and the18  # collected results carry no UNIT.19  - id: REFRANGE20    dataset: LBRANGE21    key: [LBTESTCD, SEX, UNIT]22    require_match: true2324columns:25  - name: STUDYID26    type: str27    label: Study Identifier28    derivation: LB_RAW.STUDYID2930  - name: USUBJID31    type: str32    label: Unique Subject Identifier33    derivation: LB_RAW.USUBJID3435  - name: LBSEQ36    type: int37    label: Sequence Number38    derivation: LB_RAW.LBSEQ3940  - name: LBTESTCD41    type: str42    label: Lab Test or Examination Short Name43    derivation: LB_RAW.LBTESTCD4445  - name: SEX46    type: str47    label: Sex48    derivation: LB_RAW.SEX4950  - name: LBSTNRHI51    type: float52    label: Reference Range Upper Limit-Std Units53    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

Human review and assessment

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
1.7	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/lb_raw.csv

input/lbrange.csv

Your review

Mapping spec