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Summary
EditUnder reviewWhat this benchmark meansREADME.mdPublic entries: Python and R. Passing coverage requires an installed inventory.
Goal: flag adverse events whose term mentions severe intensity.
Input: collected adverse events with one record for each event, carrying the event term.
Variables:
AESEVwould holdSEVEREwhen the event term containsSEVEREanywhere, andMILDotherwise, 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: "'SEVERE'"
- otherwise: "'MILD'"
Only if the literal text SEVERE[ is meant, escape the bracket:
derivation:
case:
- when: "str_contains(AE.AETERM, 'SEVERE\\[')"
then: "'SEVERE'"
- otherwise: "'MILD'"
Expected failure
Editthe run is rejected; no artifact is acceptedexpected/error.yaml- phase
- validation
- condition
- invalid_expression
- rule
- FORMULA-8
expected/error.yaml
phase: validation
condition: invalid_expression
spec_paths:
- columns.AESEV.derivation.case[0].when
rule: FORMULA-8
context:
position: 24
predicate: "str_contains(AE.AETERM, 'SEVERE[')"
Inputs
Under review1 source fileinput/ae.csv
Edit2 rows| STUDYID | USUBJID | AETERM |
|---|---|---|
| CATH | HEADACHE SEVERE | |
| CATH | NAUSEA MILD |
Unexpected Output
Under reviewNo artifact is producedNo fixture files in this directory.
Human review and assessment
| Dataset Name | Variable Name | Variable Label | Type | Codelist/Controlled Terms | Core | 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 | Reviewer | Sign-off |
|---|---|---|---|---|---|
| 1.7 | 2026-10-20 | yamaa docs build | Read a specification in the 1.0 surface as its 0.5 counterpart; state that missing values stay missing where a mapping declares no missing handler, and leave out a declared missing answer that restates a handler's default | ||
| 1.6 | 2026-10-17 | yamaa docs build | Describe collected date parts written as ISO 8601 date text and times of day counted in seconds since midnight | ||
| 1.5 | 2026-10-17 | yamaa docs build | Name collected precision in words instead of letter codes; state imputation fallbacks, minimum source precision, bounds ignored outside the collected period, and invalid text with no handler as an error; describe date and datetime shifts, imputation flag codes, and partial text giving no date part | ||
| 1.4 | 2026-10-15 | yamaa docs build | State datetime precision codes through the hour and minute, and complete only the time parts a collected datetime lacks | ||
| 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 |