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.

  1. Task: Is this a specification error a study team could realistically make, and should the build stop on it rather than continue?
  2. Inputs: Do they trigger the failure for the reason the summary gives?
  3. Expected failure: Is this the right error, raised at the right point, and would it tell the programmer what to fix?

The other tabs beside Comments are background for assessment, not under review.

Summary

Lifecycle: draftEditUnder review
What this benchmark means
README.md

Goal: attempt one supplemental Demographics (SUPPDM) record per reported race (QVAL) for each subject who marked more than one race, deciding "more than one" by counting the subject's race rows.

Input: EDC output in long form, one row per collected item; each race option a subject marks contributes one race row.

Variables:

  • QVAL: would be one race the subject marked, kept only for a subject with several.

Each record being built stands for one subject and one race, so a count taken while building it sees only that race's rows: a subject with two different races would count one for each and be dropped, while a race marked twice would count two and be kept. Asking the count to span the whole subject does not widen it, so the run is rejected before any data is read.

How to fix

Decide which record already says that a subject marked several races, and read it instead of recounting inside the record being built. When the same run builds DM, its RACE is MULTIPLE exactly then: read DM through an input with schema: and filter on DMRACE = 'MULTIPLE', as sdtm-dm-race-ethnicity does.

Without DM, select the subject's lowest and highest race with keyed lookups and keep the record when they differ. Unlike a row count, this does not mistake a race marked twice for two races:

intermediates:
  - id: RACELOW
    dataset: ODM
    key: {StudyOID: STUDYID, SubjectKey: USUBJID}
    filter: "ODM.ItemOID = 'IT.DM.RACE' AND ODM.Value IS NOT NULL"
    order_by: [ODM.Value]
    keep: first
  # RACEHIGH: the same lookup with keep: last
rows:
  - id: reported_race
    group_by: [ODM.StudyOID, ODM.SubjectKey, ODM.ItemOID, ODM.Value]
    filter: "ITEMOID = 'IT.DM.RACE' AND RACELOWV < RACEHIGHV"
    derivations:
      # STUDYID, USUBJID, ITEMOID and QVAL as before
      RACELOWV: RACELOW.Value
      RACEHIGHV: RACEHIGH.Value

Declare RACELOWV and RACEHIGHV as text columns in place of RACECOUNT, and leave them out of the output.

Expected failure

Edit
the run is rejected; no artifact is accepted
expected/error.yaml
phase
validation
condition
invalid_aggregate_context
requirement
REQ-0142
expected/error.yaml
phase: validation
condition: invalid_aggregate_context
spec_paths:
  - rows[0].derivations.RACECOUNT.aggregate.key
requirement: REQ-0142
context:
  expr: "COUNT(ODM.*)"
  reason: a grouped row aggregate reads its own group and declares no key pairs

Inputs

Under review
1 source file

input/odm.csv

Edit
5 rows
input/odm.csv
StudyOIDMetaDataVersionOIDSubjectKeyStudyEventOIDStudyEventRepeatKeyItemGroupOIDItemGroupRepeatKeyItemOIDValue
STUDY01MDV.1001SCREENING1IG.DM1IT.DM.RACEWhite
STUDY01MDV.1002SCREENING1IG.DM1IT.DM.RACEAsian
STUDY01MDV.1002SCREENING1IG.DM1IT.DM.RACEBlack or African American
STUDY01MDV.1003SCREENING1IG.DM1IT.DM.RACEWhite
STUDY01MDV.1003SCREENING1IG.DM1IT.DM.RACEWhite

Unexpected Output

Under review
No artifact is produced

No fixture files in this directory.

Shaded columns are derived— = missing value

Comments and assessment materials

Comments

Signed in with GitHub; saved in repository Discussions

Mapping spec

Generated from the benchmark YAML; do not edit by hand

Variable NameVariable LabelTypeLengthControlled Terms or FormatOriginCoreConversion DefinitionVariable TypeVariable OrderComments for Define
STUDYIDStudy IdentifierCharDerivedSet per constructed row; see the Row construction sheet.SUPP1
USUBJIDUnique Subject IdentifierCharDerivedSet per constructed row; see the Row construction sheet.SUPP2
QVALData ValueCharDerivedSet per constructed row; see the Row construction sheet.SUPP3
TemplateInclude whenSTUDYIDUSUBJIDITEMOIDQVALRACECOUNT
reported_raceITEMOID = 'IT.DM.RACE' AND RACECOUNT > 1Copy ODM.StudyOIDCopy ODM.SubjectKeyCopy ODM.ItemOIDCopy ODM.ValueAggregate COUNT(ODM.*) over records whose StudyOID equals STUDYID and SubjectKey equals USUBJID, where ODM.ItemOID = 'IT.DM.RACE'
VersionDateAuthorDescriptionReviewerSign-off
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