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Summary
EditUnder reviewWhat this benchmark meansREADME.mdPublic entries: Python and R. Passing coverage requires an installed inventory.
Goal: carry the location detail (AEXSITE) and the suspected cause
(AEXCAUS) of each adverse event onto its analysis row.
Input: adverse event records and the supplemental qualifier records of the AE domain, each naming the parent event by its sequence number, the qualifier name and its value.
Variables:
AEXSITEwould contain the value of the event's oneAEXSITEqualifier.AEXCAUSwould contain the value of the event's oneAEXCAUSqualifier.
Note: each qualifier name is answered by one record of that name, and
nothing says which of two to take, so an event with two AEXSITE records
has no single answer, and the run is rejected with no artifact accepted. The
other qualifier name of the same event takes no part in the rejection.
How to fix
Decide which record answers. When the later record of a name supersedes the earlier, keep the last in stored order by a field that orders them, such as a sequence number read as an integer:
input:
SUPPAE: {path: input/suppae.csv, types: {IDVARVAL: int, QSEQ: int}}
intermediates:
- id: QUAL
dataset: SUPPAE
key: {STUDYID: AE.STUDYID, USUBJID: AE.USUBJID, IDVARVAL: AE.AESEQ}
filter: "SUPPAE.RDOMAIN = 'AE' AND SUPPAE.IDVAR = 'AESEQ'"
order_by: [SUPPAE.QSEQ]
keep: last
pivot: {name: QNAM, value: QVAL, fields: [AEXSITE, AEXCAUS]}
When a repeated qualifier is a data error, leave the declaration as it is and correct the supplemental records.
Expected failure
Editthe run is rejected; no artifact is acceptedexpected/error.yaml- phase
- join
- condition
- multiple_matches
- rule
- LOOKUP-10
expected/error.yaml
phase: join
condition: multiple_matches
spec_paths:
- intermediates.QUAL
rule: LOOKUP-10
context:
intermediate: QUAL
dataset: SUPPAE
field: AEXSITE
match_count: 2
key:
- STUDYID
- USUBJID
- IDVARVAL
intermediate_key:
STUDYID: YAMAA-01
USUBJID: YAMAA-01-001
IDVARVAL: 1
keys:
- STUDYID: YAMAA-01
USUBJID: YAMAA-01-001
AESEQ: 1
Inputs
Under review2 source filesinput/ae.csv
Edit2 rows| STUDYID | USUBJID | AESEQ |
|---|---|---|
| YAMAA-01 | 1 | |
| YAMAA-01 | 1 |
input/suppae.csv
Edit4 rows| STUDYID | RDOMAIN | USUBJID | IDVAR | IDVARVAL | QNAM | QLABEL | QVAL |
|---|---|---|---|---|---|---|---|
| YAMAA-01 | AE | AESEQ | 1 | AEXSITE | Location Detail | LEFT TEMPLE | |
| YAMAA-01 | AE | AESEQ | 1 | AEXCAUS | Suspected Cause | STRESS | |
| YAMAA-01 | AE | AESEQ | 1 | AEXSITE | Location Detail | RIGHT TEMPLE | |
| YAMAA-01 | AE | AESEQ | 1 | AEXSITE | Location Detail | UPPER BACK |
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 | AESEQ | Sequence Number | numeric | Copy value from AE.AESEQ. | Predecessor | ||
| ADAE | AEXSITE | Location Detail | character | Take AEXSITE from the SUPPAE record whose STUDYID equals AE.STUDYID, USUBJID equals AE.USUBJID and IDVARVAL equals AE.AESEQ, where SUPPAE.RDOMAIN = 'AE' AND SUPPAE.IDVAR = 'AESEQ', and no match yields blank. | Derived | ||
| ADAE | AEXCAUS | Suspected Cause | character | Take AEXCAUS from the SUPPAE record whose STUDYID equals AE.STUDYID, USUBJID equals AE.USUBJID and IDVARVAL equals AE.AESEQ, where SUPPAE.RDOMAIN = 'AE' AND SUPPAE.IDVAR = 'AESEQ', and no match yields blank. | 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 |