Reject a Reference Limit That Is Both Required and Optional

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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 upper limit (LBSTNRHI) to each collected result by test and sex.

Input: collected results carrying test code (LBTESTCD) and sex (SEX), plus a reference table carrying an upper limit (NRHI) per test code and sex.

Variables:

LBSTNRHI would be the upper limit read from the reference table matched on test code and sex.

Note: every result is required to find its reference entry, and a result without one is also given an answer. The two contradict each other, so the run is rejected before any record is read, with no artifact accepted.

How to fix

Decide whether a result without a reference entry is an error or has an answer. If every result must be checked against a range, keep only require_match: true:

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

If a missing limit is acceptable, keep only the answer, or omit both: an intermediate without absent answers with a missing limit, and the run counts each such result. When only some results must find a limit, keep require_match: true and read the limit under a condition that selects those results; a result that never reads the limit never fails:

derivation:
  case:
    - when: "LBTESTCD = 'ALT'"
      then: REFRANGE.NRHI

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: conflicting_absence_policy
rule: LOOKUP-24

expected/error.yaml

phase: validation
condition: conflicting_absence_policy
spec_paths:
  - intermediates.REFRANGE.absent
  - intermediates.REFRANGE.require_match
rule: LOOKUP-24
context:
  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 limit for the result's test code and sex. It both requires every17  # result to find a limit and states what a result without one gives.18  - id: REFRANGE19    dataset: LBRANGE20    key: [LBTESTCD, SEX]21    absent: null22    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
PILOT7		1	ALT	F
PILOT7		1	AST	M

input/lbrange.csv

Edit3 rows

input/lbrange.csv
LBTESTCD	SEX	NRHI
ALT	F	33
ALT	M	41
AST	F	32

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 and SEX, 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