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Summary
EditUnder reviewWhat this benchmark meansREADME.mdPublic entries: Python and R. Passing coverage requires an installed inventory.
Goal: carry each adverse event's reported term (AETERM) and coded term
(AEDECOD), requiring a coded term on every event with a reported term.
Input: collected adverse events, one record per subject and event, with the term as reported and its dictionary code.
Variables:
AETERMwould be the event's term as the investigator reported it, missing where none was reported.AEDECODwould be the dictionary-derived term for the reported term, required wherever a term was reported; a record without a reported term may lack it.
Note: one event reports a term without its coded term, so the check on the completed dataset fails and no artifact is accepted. The record that reports no term lacks a coded term too, which the rule allows.
How to fix
Code the reported term at the source, where the dictionary coding is governed, and rerun. A reported term that has not been coded yet is not a reason to relax the rule for every record; when coding is still under way and the dataset must build, report the uncoded events instead of failing, which needs a run report file:
output:
report: ae-checks.csv
columns:
- name: AEDECOD
verifications:
- not_missing: {when: "AETERM IS NOT NULL", severity: warning}
Do not copy the reported term into the coded term, which claims a coding nobody did.
Expected failure
Editthe run is rejected; no artifact is acceptedexpected/error.yaml- phase
- verification
- condition
- not_missing_failed
- rule
- CHECK-5
expected/error.yaml
phase: verification
condition: not_missing_failed
spec_paths:
- columns.AEDECOD.verifications[0].not_missing
rule: CHECK-5
context:
column: AEDECOD
failure_count: 1
keys:
- STUDYID: YAMAA-01
USUBJID: P01
AESEQ: 2
Inputs
Under review1 source fileinput/ae_raw.csv
Edit4 rows| STUDYID | USUBJID | AESEQ | AETERM | AEDECOD |
|---|---|---|---|---|
| YAMAA-01 | 1 | HEADACHE | Headache | |
| YAMAA-01 | 2 | BACK PAIN | — | |
| YAMAA-01 | 1 | — | — | |
| YAMAA-01 | 1 | RASH | Rash |
Unexpected Output
Under reviewNo artifact is producedNo fixture files in this directory.
Human review and assessment
| Variable Name | Variable Label | Type | Length | Controlled Terms or Format | Origin | Core | Conversion Definition | Variable Type | Variable Order | Comments for Define |
|---|---|---|---|---|---|---|---|---|---|---|
| STUDYID | Study Identifier | Char | Collected | Copy value from AE_RAW.STUDYID. | SDTM | 1 | ||||
| USUBJID | Unique Subject Identifier | Char | Collected | Copy value from AE_RAW.USUBJID. | SDTM | 2 | ||||
| AESEQ | Sequence Number | Num | Collected | Copy value from AE_RAW.AESEQ. | SDTM | 3 | ||||
| AETERM | Reported Term for the Adverse Event | Char | Collected | Copy value from AE_RAW.AETERM. | SDTM | 4 | ||||
| AEDECOD | Dictionary-Derived Term | Char | Collected | Copy value from AE_RAW.AEDECOD. | SDTM | 5 |
| 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 |