yamaa / Benchmark

ADaM.ADAE

Reject a Qualifier Record Whose Name Is Not Declared

result
Rejected
input files
2
subjects
2
Review ask

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Summary

Lifecycle: draftEditUnder reviewWhat this benchmark means
README.md

Public 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; one record carries a reaction size, which the analysis does not declare.

Variables:

  • AEXSITE would contain the value of the event's AEXSITE qualifier.
  • AEXCAUS would contain the value of the event's AEXCAUS qualifier.

Note: the declared qualifier names are the complete list of what an event's qualifier records may carry. A record named otherwise, here the reaction size of the first event, has no column to go to, so the run is rejected with no artifact accepted rather than dropping the value silently.

How to fix

Decide whether the qualifier belongs in the analysis. When it does, list it and give it a column:

output:
  path: adae.csv
  columns: [STUDYID, USUBJID, AESEQ, AEXSITE, AEXCAUS, AEXSIZE]

intermediates:
  - id: QUAL
    dataset: SUPPAE
    key: {STUDYID: AE.STUDYID, USUBJID: AE.USUBJID, IDVARVAL: AE.AESEQ}
    filter: "SUPPAE.RDOMAIN = 'AE' AND SUPPAE.IDVAR = 'AESEQ'"
    pivot: {name: QNAM, value: QVAL, fields: [AEXSITE, AEXCAUS, AEXSIZE]}

columns:
  - name: AEXSIZE
    type: int
    label: Reaction Size (mm)
    derivation: QUAL.AEXSIZE

When it is left out on purpose, narrow the filter to the names the analysis reads, so the record is never a candidate:

    filter: >-
      SUPPAE.RDOMAIN = 'AE' AND SUPPAE.IDVAR = 'AESEQ'
      AND SUPPAE.QNAM IN ('AEXSITE', 'AEXCAUS')

Expected failure

Editthe run is rejected; no artifact is accepted
expected/error.yaml
phase
join
condition
unlisted_pivot_name
rule
LOOKUP-28
expected/error.yaml 
phase: join
condition: unlisted_pivot_name
spec_paths:
  - intermediates.QUAL
rule: LOOKUP-28
context:
  intermediate: QUAL
  dataset: SUPPAE
  name: QNAM
  value: AEXSIZE
  fields:
    - AEXSITE
    - AEXCAUS
  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 files

input/ae.csv

Edit2 rows
STUDYIDUSUBJIDAESEQ
YAMAA-011
YAMAA-011

input/suppae.csv

Edit3 rows
STUDYIDRDOMAINUSUBJIDIDVARIDVARVALQNAMQLABELQVAL
YAMAA-01AEAESEQ1AEXSITELocation DetailLEFT TEMPLE
YAMAA-01AEAESEQ1AEXSIZEReaction Size (mm)12
YAMAA-01AEAESEQ1AEXCAUSSuspected CauseSTRESS

Unexpected Output

Under reviewNo artifact is produced

No fixture files in this directory.

Shaded columns are derived— = missing value

Human review and assessment

Your review

2 questions and your comments · View benchmark discussions

Mapping spec

Generated from the benchmark YAML; do not edit by hand

Dataset NameVariable NameVariable LabelTypeCodelist/Controlled TermsCoreComputational MethodOrigin
ADAESTUDYIDStudy IdentifiercharacterCopy value from AE.STUDYID.Predecessor
ADAEUSUBJIDUnique Subject IdentifiercharacterCopy value from AE.USUBJID.Predecessor
ADAEAESEQSequence NumbernumericCopy value from AE.AESEQ.Predecessor
ADAEAEXSITELocation DetailcharacterTake 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
ADAEAEXCAUSSuspected CausecharacterTake 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
VersionDateAuthorDescriptionReviewerSign-off
1.72026-10-20yamaa docs buildRead 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
1.62026-10-17yamaa docs buildDescribe collected date parts written as ISO 8601 date text and times of day counted in seconds since midnight
1.52026-10-17yamaa docs buildName 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
1.42026-10-15yamaa docs buildState datetime precision codes through the hour and minute, and complete only the time parts a collected datetime lacks
1.32026-09-29yamaa docs buildShow study codelist names, external dictionaries, and ISO 8601 formats in variable rows; list the document's codelist values and metadata
1.22026-09-29yamaa docs buildClassify ADaM copies from a declared input as Predecessor and recodes as Derived, and SDTM recodes of locally derived columns as Derived
1.12026-09-29yamaa docs buildResolve lookups into the donor record they select, and give every derivation shape a plain-language rule instead of its raw YAML
1.0yamaa docs buildInitial generation from spec.yaml