Reject Unmatched Key

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 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. A result whose test code and sex have no reference entry has no stated answer, so it 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, declare no_match: null:

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

The lookup then returns a missing value for every column read through it when a complete key has no match.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: join
condition: unmatched_key
requirement: REQ-0124

expected/error.yaml

phase: join
condition: unmatched_key
spec_paths:
  - intermediates[0]
requirement: REQ-0124
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

Edit49 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 limit for the result's test code and sex. With no no_match answer,15  # a result whose test code and sex match no table row stops the run.16  - id: REFRANGE17    dataset: LBRANGE18    key: [LBTESTCD, SEX]1920columns:21  - name: STUDYID22    type: str23    label: Study Identifier24    derivation: LB_RAW.STUDYID2526  - name: USUBJID27    type: str28    label: Unique Subject Identifier29    derivation: LB_RAW.USUBJID3031  - name: LBSEQ32    type: int33    label: Sequence Number34    derivation: LB_RAW.LBSEQ3536  - name: LBTESTCD37    type: str38    label: Lab Test or Examination Short Name39    derivation: LB_RAW.LBTESTCD4041  - name: SEX42    type: str43    label: Sex44    derivation: LB_RAW.SEX4546  - name: LBSTNRHI47    type: float48    label: Reference Range Upper Limit-Std Units49    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

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 and SEX, 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