Reject Invalid Regex in str_contains

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?

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Summary

EditUnder reviewWhat this benchmark means

README.md

Goal: flag adverse events whose term mentions severe intensity.

Input: collected adverse events with one record for each event, carrying the event term.

Variables:

AESEV would hold SEVERE when the event term contains SEVERE anywhere, and MILD otherwise, including when the term is missing.

The pattern SEVERE[ is not a valid portable regex: the [ opens a character class that never closes. The request is rejected before any data is read, and no artifact is accepted.

How to fix

Decide what the term must contain. To flag a term that mentions severe intensity, as the goal states, remove the bracket:

derivation:
  case:
    - when: "str_contains(AE.AETERM, 'SEVERE')"
      then: {literal: SEVERE}
    - otherwise: {literal: MILD}

Only if the literal text SEVERE[ is meant, escape the bracket:

derivation:
  case:
    - when: "str_contains(AE.AETERM, 'SEVERE\\[')"
      then: {literal: SEVERE}
    - otherwise: {literal: MILD}

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: invalid_predicate
requirement: REQ-1244

expected/error.yaml

phase: validation
condition: invalid_predicate
spec_paths:
  - columns.AESEV.derivation.case[0].when
requirement: REQ-1244
context:
  position: 24
  predicate: "str_contains(AE.AETERM, 'SEVERE[')"

YAML specification

1 spec file

spec.yaml

Edit32 lines

1schema_version: "1.0"2domain: ADAE3keys: [STUDYID, USUBJID]4input:5  AE: input/ae.csv67output:8  path: adae.csv9  columns: [STUDYID, USUBJID, AESEV]1011columns:12  - name: STUDYID13    type: str14    label: Study Identifier15    derivation: AE.STUDYID1617  - name: USUBJID18    type: str19    label: Unique Subject Identifier20    derivation: AE.USUBJID2122  # The defect: '[' opens a character class that never closes, so the23  # pattern is not a valid regex and the spec is rejected before any data24  # is read.25  - name: AESEV26    type: str27    label: Severity/Intensity28    derivation:29      case:30        - when: "str_contains(AE.AETERM, 'SEVERE[')"31          then: {literal: SEVERE}32        - otherwise: {literal: MILD}

Inputs

Under review1 source file

input/ae.csv

Edit2 rows

input/ae.csv
STUDYID	USUBJID	AETERM
CATH		HEADACHE SEVERE
CATH		NAUSEA MILD

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
ADAE	STUDYID	Study Identifier	character	Copy value from AE.STUDYID.	Predecessor
ADAE	USUBJID	Unique Subject Identifier	character	Copy value from AE.USUBJID.	Predecessor
ADAE	AESEV	Severity/Intensity	character	If str_contains(AE.AETERM, 'SEVERE[') then "SEVERE"; otherwise "MILD".	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/ae.csv

Comments

Mapping spec