Reject Unmapped 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: carry sex and the collected result into the output and attach the upper limit of normal (ANRHI) chosen by test and sex.

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

Variables:

ANRHI would be the upper limit of normal for that test and sex, read from the reference table where the collected test code and sex match a table entry. A collected test and sex with no table entry has no stated answer. Leaving the limit missing would hide that the result was never checked against a range, so the run is rejected with no artifact accepted.

How to fix

Add the governed AST/M reference range to the reference table when one exists. If the analysis intentionally leaves the limit missing when a complete key is not in the table, declare that missing-value answer:

intermediates:
  - id: LBREF_LOOKUP
    dataset: LBREF
    key: {LBTESTCD: PARAMCD, SEX: SEX}
    no_match: null

The same answer also covers a result whose test code or sex is blank: both find no entry (REQ-0129, REQ-0131).

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: LBREF_LOOKUP
  dataset: LBREF
  key:
    - LBTESTCD
    - SEX
  intermediate_key:
    LBTESTCD: AST
    SEX: M
  keys:
    - STUDYID: PILOT7
      USUBJID: P7-842
      PARAMCD: AST

YAML specification

1 spec file

spec.yaml

Edit49 lines

1schema_version: "1.0"2domain: ADLB3keys: [STUDYID, USUBJID, PARAMCD]4input:5  LB: input/lb.csv6  LBREF: input/lbref.csv7base: LB89output:10  path: adlb.csv11  columns: [STUDYID, USUBJID, PARAMCD, SEX, AVAL, ANRHI]1213intermediates:14  - id: LBREF_LOOKUP15    dataset: LBREF16    key: {LBTESTCD: PARAMCD, SEX: SEX}1718columns:19  - name: STUDYID20    type: str21    label: Study Identifier22    derivation: LB.STUDYID2324  - name: USUBJID25    type: str26    label: Unique Subject Identifier27    derivation: LB.USUBJID2829  - name: PARAMCD30    type: str31    label: Parameter Code32    derivation: LB.LBTESTCD3334  - name: SEX35    type: str36    label: Sex37    derivation: LB.SEX3839  - name: AVAL40    type: float41    label: Analysis Value42    derivation: LB.LBSTRESN4344  # The upper limit for the parameter and sex. With no no_match answer, a45  # result whose test and sex match no table row stops the run.46  - name: ANRHI47    type: float48    label: Analysis Normal Range Upper Limit49    derivation: LBREF_LOOKUP.ANRHI

Inputs

Under review2 source files

input/lb.csv

Edit2 rows

input/lb.csv
STUDYID	USUBJID	LBTESTCD	SEX	LBSTRESN
PILOT7		ALT	F	42
PILOT7		AST	M	55

input/lbref.csv

Edit3 rows

input/lbref.csv
LBTESTCD	SEX	ANRHI
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

Dataset Name	Variable Name	Variable Label	Type	Computational Method	Origin
ADLB	STUDYID	Study Identifier	character	Copy value from LB.STUDYID.	Predecessor
ADLB	USUBJID	Unique Subject Identifier	character	Copy value from LB.USUBJID.	Predecessor
ADLB	PARAMCD	Parameter Code	character	Copy value from LB.LBTESTCD.	Predecessor
ADLB	SEX	Sex	character	Copy value from LB.SEX.	Predecessor
ADLB	AVAL	Analysis Value	numeric	Copy value from LB.LBSTRESN.	Predecessor
ADLB	ANRHI	Analysis Normal Range Upper Limit	numeric	Take ANRHI from the LBREF record whose LBTESTCD equals PARAMCD and SEX equals SEX, and a row with no match is an error.	Derived

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.csv

input/lbref.csv

Comments

Mapping spec