Reject Missing Sex

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Summary

EditUnder reviewWhat this benchmark means

README.md

Public entries: Python and R. Passing coverage requires an installed inventory.

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, drop require_match: true; a result with a blank sex then gets a missing LBSTNRHI, counted under absent:

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

An incomplete key and a complete key the table does not contain share one absence policy (LOOKUP-24): both yield nothing, and require_match or absent 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
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: ALT
    SEX:
  keys:
    - STUDYID: YAMAA-01
      USUBJID: YAMAA-01-102
      LBSEQ: 1

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. A match is required, so a17  # result that finds no limit, including one with a blank sex, stops the18  # run.19  - id: REFRANGE20    dataset: LBRANGE21    key: [LBTESTCD, SEX]22    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

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

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