Reject Parent Escape

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

This fixture retains the reference engine's historical containment rejection and locked expected report. Under the approved declaring-file policy (#1905), absolute and parent-relative local spellings are permitted; an absent file fails at the declared location. Current public Python/R path behavior is qualified by independently authored installed tests. This fixture records reference-only policy history until the coordinated reference transition and is not evidence that the replacement public routes reject these path forms.

Goal: one record for each subject and collected laboratory parameter carrying SEX, AVAL, and ANRHI.

Input: collected laboratory results carrying the collected result (LBSTRESN), test code (LBTESTCD), and sex (SEX), together with a reference table of upper limits read from ../reference/lbref.csv, a location above the study.

Variables:

SEX would be the sex the limits are chosen by, taken from SEX.
AVAL would be the collected result, taken from LBSTRESN.
ANRHI would be the upper limit of normal for that test and sex, taken from the reference entry whose test code and sex equal LBTESTCD and SEX; missing when no entry matches or the sex is missing.

Note: the limits live outside the study, so the historical reference engine rejects this fixture before any data is read and accepts no artifact.

How to fix

For the retained reference engine, bring the governed limits into the study and read them from there:

input:
  LBREF:
    path: input/lbref.csv

If the limits are maintained centrally, copy the approved version into the study when it is approved. That preserves the historical reference policy. The replacement public routes permit the parent-relative declaration under OS/caller permissions and retain the actual input bytes for the run.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: resource_path_outside_project
requirement: REQ-0784

expected/error.yaml

phase: validation
condition: resource_path_outside_project
spec_paths:
  - input.LBREF.path
requirement: REQ-0784
context:
  dataset: LBREF
  path: ../reference/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  # Climbs above the study folder: rejected before any data is read.7  LBREF: ../reference/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