Reject Missing Table

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: build one analysis row for each collected laboratory result, carrying SEX and AVAL through and adding ANRHI from a reference table of limits by test and sex.

Input: collected laboratory results carrying the collected result (LBSTRESN), test code (LBTESTCD), and sex (SEX), plus the reference table of upper limits by test code and sex.

Variables:

SEX would contain the subject's sex, carried from SEX in the laboratory results.
AVAL would contain the collected numeric result, carried from LBSTRESN.
ANRHI would be the upper limit of normal taken from the reference row whose test code matches the collected test code and whose sex matches the subject's sex; missing when no row matches or the sex is missing.

Note: the reference table is absent from the study, so the run is rejected before any data is read and no artifact is accepted.

How to fix

Decide first whether the study should carry reference limits: add the approved table when the limits exist, and state an explicit policy only when the study genuinely has none.

Add the approved limit table to the study under the name it is read by, input/lbref.csv, with one row per test and sex:

LBTESTCD,SEX,ANRHI
ALT,F,33
ALT,M,41

If a study genuinely has no reference limits for a test, say so explicitly by supplying a result for the unmatched case rather than by leaving the table out. A file that is simply absent cannot be told apart from one that was forgotten.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: resource_path_missing
requirement: REQ-0785

expected/error.yaml

phase: validation
condition: resource_path_missing
spec_paths:
  - input.LBREF.path
requirement: REQ-0785
context:
  dataset: LBREF
  path: input/lbref.csv

YAML specification

1 spec file

spec.yaml

Edit50 lines

1schema_version: "1.0"2domain: ADLB3keys: [STUDYID, USUBJID, PARAMCD]4input:5  LB: input/lb.csv6  # No such file in the study: rejected before any data is read.7  LBREF: input/lbref.csv8base: LB910output:11  path: adlb.csv12  columns: [STUDYID, USUBJID, PARAMCD, SEX, AVAL, ANRHI]1314intermediates:15  - id: LBREF_LOOKUP16    dataset: LBREF17    key: {LBTESTCD: PARAMCD, SEX: SEX}1819columns:20  - name: STUDYID21    type: str22    label: Study Identifier23    derivation: LB.STUDYID2425  - name: USUBJID26    type: str27    label: Unique Subject Identifier28    derivation: LB.USUBJID2930  - name: PARAMCD31    type: str32    label: Parameter Code33    derivation: LB.LBTESTCD3435  - name: SEX36    type: str37    label: Sex38    derivation: LB.SEX3940  - name: AVAL41    type: float42    label: Analysis Value43    derivation: LB.LBSTRESN4445  - name: ANRHI46    type: float47    label: Analysis Normal Range Upper Limit48    # The reference limit for the record's test code and sex; missing when49    # the table has no row for that pair or the sex is missing.50    derivation: LBREF_LOOKUP.ANRHI

Inputs

Under review1 source file

input/lb.csv

Edit2 rows

input/lb.csv
STUDYID	USUBJID	LBTESTCD	SEX	LBSTRESN
PILOT7		ALT	F	42
PILOT7		ALT	M	58

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

Comments

Mapping spec