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

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

Variables:

ANRHI would be the upper limit of normal taken from the limit table where the test matches the collected test and the sex matches the carried sex.

Note: when the carried sex is blank, the pair that chooses a limit is incomplete and no entry can be looked for, so the run is rejected with no artifact accepted. Falling back to either sex, or to a combined limit, would answer with a range the study never stated.

How to fix

Recover and correct the missing sex when possible. If the intended result is a missing reference limit whenever any lookup input is missing, drop require_match: true so the lookup answers with missing:

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

That one answer also covers a complete test and sex that the reference table does not list: both find no entry (LOOKUP-24), and the run counts each under absent.

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.LBREF_LOOKUP
rule: LOOKUP-24
context:
  intermediate: LBREF_LOOKUP
  dataset: LBREF
  key:
    - LBTESTCD
    - SEX
  intermediate_key:
    LBTESTCD: ALT
    SEX:
  keys:
    - STUDYID: PILOT7
      USUBJID: P7-852
      PARAMCD: ALT

YAML specification

1 spec file

spec.yaml

Edit53 lines

1yamaa: "1.0"2type: spec3model: ADaM4domain: ADLB5keys: [STUDYID, USUBJID, PARAMCD]6input:7  LB: input/lb.csv8  LBREF: input/lbref.csv9base: LB1011output:12  path: adlb.csv13  columns: [STUDYID, USUBJID, PARAMCD, SEX, AVAL, ANRHI]1415intermediates:16  - id: LBREF_LOOKUP17    dataset: LBREF18    key: {LBTESTCD: PARAMCD, SEX: SEX}19    require_match: true2021columns:22  - name: STUDYID23    type: str24    label: Study Identifier25    derivation: LB.STUDYID2627  - name: USUBJID28    type: str29    label: Unique Subject Identifier30    derivation: LB.USUBJID3132  - name: PARAMCD33    type: str34    label: Parameter Code35    derivation: LB.LBTESTCD3637  - name: SEX38    type: str39    label: Sex40    derivation: LB.SEX4142  - name: AVAL43    type: float44    label: Analysis Value45    derivation: LB.LBSTRESN4647  # The upper limit for the parameter and sex. The lookup requires a match,48  # so a result that finds no limit, including one with a blank sex, stops49  # the run.50  - name: ANRHI51    type: float52    label: Analysis Normal Range Upper Limit53    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		ALT	—	38

input/lbref.csv

Edit2 rows

input/lbref.csv
LBTESTCD	SEX	ANRHI
ALT	F	33
ALT	M	41

Unexpected Output

Under reviewNo artifact is produced

No fixture files in this directory.

Shaded columns are derived— = missing value

Human review and assessment

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
1.7	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.csv

input/lbref.csv

Your review

Mapping spec