Reject Unmatched Key

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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. Every result is required to find its reference entry, so a result whose test code and sex have none rejects the run with no artifact accepted.

How to fix

Add the governed AST/M range to the reference table when one exists. If an absent range is intentionally represented by a missing value, drop require_match: true:

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

The lookup then returns a missing value for every column read through it when a complete key has no match, and the run counts each such answer under absent. Declaring absent beside require_match: true is refused as a contradiction.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: join
condition: unmatched_key
rule: LOOKUP-24

expected/error.yaml

phase: join
condition: unmatched_key
spec_paths:
  - intermediates.REFRANGE
rule: LOOKUP-24
context:
  intermediate: REFRANGE
  dataset: LBRANGE
  key: [LBTESTCD, SEX]
  intermediate_key:
    LBTESTCD: AST
    SEX: M
  keys:
    - STUDYID: PILOT7
      USUBJID: P7-542
      LBSEQ: 1

YAML specification

1 spec file

spec.yaml

Edit52 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. A match is required, so a17  # result whose test code and sex match no table row stops the run.18  - id: REFRANGE19    dataset: LBRANGE20    key: [LBTESTCD, SEX]21    require_match: true2223columns:24  - name: STUDYID25    type: str26    label: Study Identifier27    derivation: LB_RAW.STUDYID2829  - name: USUBJID30    type: str31    label: Unique Subject Identifier32    derivation: LB_RAW.USUBJID3334  - name: LBSEQ35    type: int36    label: Sequence Number37    derivation: LB_RAW.LBSEQ3839  - name: LBTESTCD40    type: str41    label: Lab Test or Examination Short Name42    derivation: LB_RAW.LBTESTCD4344  - name: SEX45    type: str46    label: Sex47    derivation: LB_RAW.SEX4849  - name: LBSTNRHI50    type: float51    label: Reference Range Upper Limit-Std Units52    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