Reject One Summary Over Exposure and Vital Signs Records Together

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Summary

EditUnder reviewWhat this benchmark means

README.md

Public entries: Python and R. Passing coverage requires an installed inventory.

Goal: give each subject's total dose per kilogram of body weight (DOSEKG) on the subject-level analysis dataset.

Input: subjects from the collected demographics, collected exposure records with the dose given (EXDOSE), and collected vital signs with the body weight (WEIGHT), several records per subject in each.

Variables:

DOSEKG would be the subject's total dose divided by the heaviest weight recorded for the subject.

Note: the total dose and the heaviest weight are summarized in one expression that reads the exposure records and the vital signs records together. Two sets of records have no single set of rows to summarize, so the run is rejected before any data is read and no artifact is accepted.

How to fix

Summarize each set of records into a column of its own, then combine the two columns:

- name: TOTDOSE
  type: float
  label: Total Dose
  derivation:
    aggregate: "SUM(EX.EXDOSE)"
- name: MAXWT
  type: float
  label: Maximum Weight (kg)
  derivation:
    aggregate: "MAX(VS.WEIGHT)"
- name: DOSEKG
  type: float
  label: Total Dose per kg Body Weight
  derivation: "TOTDOSE / MAXWT"

Keep the weight the statistical analysis plan names: the heaviest weight here, a baseline weight in many studies.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: mixed_relations
rule: LOOKUP-18

expected/error.yaml

phase: validation
condition: mixed_relations
spec_paths:
  - columns.DOSEKG.derivation.aggregate.expr
rule: LOOKUP-18
context:
  expr: "SUM(EX.EXDOSE) / MAX(VS.WEIGHT)"
  relations: [EX, VS]

YAML specification

1 spec file

spec.yaml

Edit35 lines

1yamaa: "1.0"2type: spec3model: ADaM4domain: ADSL5keys: [STUDYID, USUBJID]6input:7  DM: input/dm.csv8  EX: {path: input/ex.csv, types: {EXDOSE: float}}9  VS: {path: input/vs.csv, types: {WEIGHT: float}}10base: DM1112output:13  path: adsl.csv14  columns: [STUDYID, USUBJID, DOSEKG]1516columns:17  - name: STUDYID18    type: str19    label: Study Identifier20    derivation: DM.STUDYID2122  - name: USUBJID23    type: str24    label: Unique Subject Identifier25    derivation: DM.USUBJID2627  # The total dose over the heaviest recorded weight, written as one28  # reduction that reads the exposure and the vital signs records together.29  - name: DOSEKG30    type: float31    label: Total Dose per kg Body Weight32    derivation:33      aggregate:34        key: [STUDYID, USUBJID]35        expr: "SUM(EX.EXDOSE) / MAX(VS.WEIGHT)"

Inputs

Under review3 source files

input/dm.csv

Edit2 rows

input/dm.csv
STUDYID	USUBJID
YAMAA-01
YAMAA-01

input/ex.csv

Edit3 rows

input/ex.csv
STUDYID	EXSEQ	EXDOSE
YAMAA-01	1	200
YAMAA-01	2	200
YAMAA-01	1	150

input/vs.csv

Edit3 rows

input/vs.csv
STUDYID	VSSEQ	WEIGHT
YAMAA-01	1	80.0
YAMAA-01	2	78.5
YAMAA-01	1	61.0

Unexpected Output

Under reviewNo artifact is produced

No fixture files in this directory.

Shaded columns are derived— = missing value

Human review and assessment

Dataset Name	Variable Name	Variable Label	Type	Computational Method	Origin
ADSL	STUDYID	Study Identifier	character	Copy value from DM.STUDYID.	Predecessor
ADSL	USUBJID	Unique Subject Identifier	character	Copy value from DM.USUBJID.	Predecessor
ADSL	DOSEKG	Total Dose per kg Body Weight	numeric	Aggregate SUM(EX.EXDOSE) / MAX(VS.WEIGHT) over records matching on STUDYID and USUBJID.	Derived

Version	Date	Author	Description
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

How to fix

input/dm.csv

input/ex.csv

input/vs.csv

Your review

Mapping spec