Reject Duplicate 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 numeric result into the output and choose the upper limit of normal (ANRHI) from a reference table by test and sex.

Input: collected laboratory records 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, taken from the reference table row matching the collected test code and sex.

Note: a result whose test and sex match more than one line of the reference table has no single line to take its limit from. Taking either line, or the first the file happens to list, would make the result depend on file order rather than on the study's reference ranges, so the run is rejected with no artifact accepted, even when the lines agree.

How to fix

Make the lookup table unique on [LBTESTCD, SEX] by resolving the conflicting ALT/F reference limits under the study's governed reference-range rules. A lookup cannot choose one duplicate by file order.

If both rows are valid for different conditions, such as different assay methods, carry that condition on both the collected records and the table, and add it to the key, pairing the table column with the collected value. A collected field that is not an output column is named with its dataset prefix:

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

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: join
condition: multiple_matches
requirement: REQ-0127

expected/error.yaml

phase: join
condition: multiple_matches
spec_paths:
  - intermediates[0]
requirement: REQ-0127
context:
  intermediate: LBREF_LOOKUP
  dataset: LBREF
  key:
    - LBTESTCD
    - SEX
  intermediate_key:
    LBTESTCD: ALT
    SEX: F
  match_count: 2
  keys:
    - STUDYID: PILOT7
      USUBJID: P7-831
      PARAMCD: ALT

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. Nothing orders the table45  # rows, so a test and sex listed on two rows 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

Edit1 row

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

input/lbref.csv

Edit3 rows

input/lbref.csv
LBTESTCD	SEX	ANRHI
ALT	F	33
ALT	F	35
ALT	M	41

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