Reject Absolute Path

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: attempt one record per subject and laboratory test carrying the collected result in AVAL and the upper limit of normal for that test and the subject's sex in ANRHI.

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

Variables:

SEX would be the collected sex, taken from SEX in the collected records, and also chooses the limit.
AVAL would be the collected numeric result, taken from LBSTRESN.
ANRHI would be the upper limit of normal from the reference table for the record's test code and sex; missing when the table has no limit for that pair or the sex is missing.

Note: the reference table is named by an absolute location, /shared/reference/lbref.csv, which names a place on the machine that runs the study rather than a file the study carries. The historical reference-engine run opens only files inside the study or in a location the runner approved, so it rejects this fixture before any data is read and no artifact is accepted.

How to fix

For the retained reference engine, copy the governed reference limits into the study and name them where the study keeps its data:

input:
  LBREF:
    path: input/lbref.csv

Under the historical reference policy, keep a shared limit table outside the study only when the runner approves its directory as a data root, then name it by its rooted path. The replacement public routes use the declared local location under OS/caller permissions; no data-root approval is interpreted. Give each study the version it was run against either way: a shared location that is edited between runs changes results that were already reported.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: resource_path_not_relative
requirement: REQ-0781

expected/error.yaml

phase: validation
condition: resource_path_not_relative
spec_paths:
  - input.LBREF.path
requirement: REQ-0781
context:
  dataset: LBREF
  path: /shared/reference/lbref.csv

YAML specification

1 spec file

spec.yaml

Edit51 lines

1schema_version: "1.0"2domain: ADLB3keys: [STUDYID, USUBJID, PARAMCD]4input:5  LB: input/lb.csv6  # An absolute location on the machine that runs the study, not a file7  # the study carries: rejected before any data is read.8  LBREF: /shared/reference/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}1920columns:21  - name: STUDYID22    type: str23    label: Study Identifier24    derivation: LB.STUDYID2526  - name: USUBJID27    type: str28    label: Unique Subject Identifier29    derivation: LB.USUBJID3031  - name: PARAMCD32    type: str33    label: Parameter Code34    derivation: LB.LBTESTCD3536  - name: SEX37    type: str38    label: Sex39    derivation: LB.SEX4041  - name: AVAL42    type: float43    label: Analysis Value44    derivation: LB.LBSTRESN4546  - name: ANRHI47    type: float48    label: Analysis Normal Range Upper Limit49    # The reference limit for the record's test code and sex; missing when50    # the table has no row for that pair or the sex is missing.51    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