Reject Missing Sex

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: look up the sex-specific reference upper limit (LBSTNRHI) for each collected laboratory result by its test code and sex.

Input: collected results carrying the test code (LBTESTCD), sex (SEX), and numeric result (LBSTRESN), plus a limits table carrying the upper limit (NRHI) by test code and sex.

Variables:

LBSTNRHI would be the upper limit from the limits table for the matching test code and sex.

Note: a result with a blank sex has an incomplete lookup key and cannot find its sex-specific limit. Every result is required to find one, so such a result rejects the run with no artifact accepted.

How to fix

Recover the missing sex when possible. If an incomplete lookup key is intended to leave the upper limit missing, declare no_match: null; a result with a blank sex then gets a missing LBSTNRHI:

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

An incomplete key and a complete key the table does not contain share one absence policy (REQ-0129, REQ-0131): both yield nothing, and no_match decides whether that fails or answers with a value.

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: ALT
    SEX:
  keys:
    - STUDYID: YAMAA-01
      USUBJID: YAMAA-01-102
      LBSEQ: 1

YAML specification

1 spec file

spec.yaml

Edit50 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 that finds no limit, including one with a blank sex, stops the16  # run.17  - id: REFRANGE18    dataset: LBRANGE19    key: [LBTESTCD, SEX]2021columns:22  - name: STUDYID23    type: str24    label: Study Identifier25    derivation: LB_RAW.STUDYID2627  - name: USUBJID28    type: str29    label: Unique Subject Identifier30    derivation: LB_RAW.USUBJID3132  - name: LBSEQ33    type: int34    label: Sequence Number35    derivation: LB_RAW.LBSEQ3637  - name: LBTESTCD38    type: str39    label: Lab Test or Examination Short Name40    derivation: LB_RAW.LBTESTCD4142  - name: SEX43    type: str44    label: Sex45    derivation: LB_RAW.SEX4647  - name: LBSTNRHI48    type: float49    label: Reference Range Upper Limit-Std Units50    derivation: REFRANGE.NRHI

Inputs

Under review2 source files

input/lb_raw.csv

Edit4 rows

input/lb_raw.csv
STUDYID	LBSEQ	LBTESTCD	SEX	LBSTRESN
YAMAA-01	1	ALT	F	42
YAMAA-01	1	ALT	—	38
YAMAA-01	1	ALT	M	35
YAMAA-01	1	AST	F	28

input/lbrange.csv

Edit3 rows

input/lbrange.csv
LBTESTCD	SEX	UNIT	NRHI
ALT	F	U/L	40
ALT	M	U/L	40
AST	F	U/L	35

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