Reject Boolean str_contains Result in a Text Column

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 dermatitis or erythema, writing the structured str_contains result straight into SKIN_FLAG.

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

Variables:

SKIN_FLAG would hold whether the event term contains DERMATITIS or ERYTHEMA, and UNKNOWN when the term is missing.

The structured form returns true or false, and no column type accepts a boolean: the first record's match yields true, which has no text form, so the run fails and no artifact is accepted. The missing value is accepted and stands in for a missing term, but a record that carries a term yields true or false whether or not it matches, so a run succeeds only when every term is missing.

How to fix

Map the boolean to flag values with the predicate-text form inside a case, which is the spelling that stores text:

- name: SKIN_FLAG
  type: str
  derivation:
    case:
      - when: "AE.AEDECOD IS NULL"
        then: {literal: UNKNOWN}
      - when: "str_contains(AE.AEDECOD, 'DERMATITIS|ERYTHEMA')"
        then: {literal: Y}
      - otherwise: {literal: N}

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: convert
condition: conversion_failed
requirement: REQ-0013

expected/error.yaml

phase: convert
condition: conversion_failed
spec_paths:
  - columns.SKIN_FLAG
requirement: REQ-0013
context:
  from: bool
  to: str
  value: true
  keys:
    - STUDYID: YAMAA-01
      USUBJID: YAMAA-01-001
      AESEQ: 1

YAML specification

1 spec file

spec.yaml

Edit39 lines

1schema_version: "1.0"2domain: ADAE3keys: [STUDYID, USUBJID, AESEQ]4input:5  AE: input/ae.csv67output:8  path: adae.csv9  columns: [STUDYID, USUBJID, AESEQ, SKIN_FLAG]1011columns:12  - name: STUDYID13    type: str14    label: Study Identifier15    derivation: AE.STUDYID1617  - name: USUBJID18    type: str19    label: Unique Subject Identifier20    derivation: AE.USUBJID2122  - name: AESEQ23    type: int24    label: Sequence Number25    derivation: AE.AESEQ2627  # The defect: the structured str_contains form returns a boolean, and28  # no column type accepts one, so storing the result in SKIN_FLAG fails29  # the run. The missing value is accepted by validation and stands in30  # for a missing term, but any term, matching or not, yields a boolean,31  # so this run stops at the first record.32  - name: SKIN_FLAG33    type: str34    label: Skin Event Flag35    derivation:36      str_contains:37        source: AE.AEDECOD38        pattern: "DERMATITIS|ERYTHEMA"39        missing: "UNKNOWN"

Inputs

Under review1 source file

input/ae.csv

Edit3 rows

input/ae.csv
STUDYID	AESEQ	AEDECOD
YAMAA-01	1	APPLICATION SITE DERMATITIS
YAMAA-01	2	HEADACHE
YAMAA-01	3	—

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	AESEQ	Sequence Number	numeric	Copy value from AE.AESEQ.	Predecessor
ADAE	SKIN_FLAG	Skin Event Flag	character	True when AE.AEDECOD matches DERMATITIS\|ERYTHEMA anywhere, false when it does not; a missing source → "UNKNOWN".	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