Reject a Dose per Kilogram From a Zero Weight

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Summary

EditUnder reviewWhat this benchmark means

README.md

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

Goal: derive each subject's first dose per kilogram of body weight (DOSEKG) with the study's own calculation.

Input: one record per subject with the first dose in milligrams (DOSEMG) and the baseline weight in kilograms (WEIGHTKG).

Variables:

DOSEMG and WEIGHTKG are the dose and the weight as collected.
DOSEKG would be the dose divided by the weight, from the study's dose_per_kg calculation.

One subject's weight was recorded as 0 kg. The study's calculation refuses a weight that is not positive and stops with an error, rather than return a dose per kilogram that means nothing. Its error stops the run, and no artifact is accepted.

How to fix

Find the subject's baseline weight in the source. A weight of zero is a recording error, most often a measurement that was never entered; correct it and export the record again:

STUDYID,USUBJID,DOSEMG,WEIGHTKG
CTX,CTX-81,150,60.0
CTX,CTX-82,200,74.0
CTX,CTX-83,100,50.0

If the study decides that an impossible weight gives no dose per kilogram, change the calculation to return a missing value for it, and declare may_return_missing: true in its function file.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: derivation
condition: function_call_failed
rule: FUNC-8

expected/error.yaml

phase: derivation
condition: function_call_failed
spec_paths:
  - columns.DOSEKG.derivation.function
rule: FUNC-8
context:
  function: dose_per_kg

YAML specification

1 spec file

spec.yaml

Edit44 lines

1yamaa: "1.0"2type: spec3model: ADaM4domain: ADSL5keys: [STUDYID, USUBJID]6input:7  # One baseline weight was recorded as zero.8  EX: {path: input/ex.csv, types: {DOSEMG: float, WEIGHTKG: float}}910output:11  path: adsl.csv12  columns: [STUDYID, USUBJID, DOSEMG, WEIGHTKG, DOSEKG]1314columns:15  - name: STUDYID16    type: str17    label: Study Identifier18    derivation: EX.STUDYID1920  - name: USUBJID21    type: str22    label: Unique Subject Identifier23    derivation: EX.USUBJID2425  - name: DOSEMG26    type: float27    label: First Dose (mg)28    derivation: EX.DOSEMG2930  - name: WEIGHTKG31    type: float32    label: Baseline Weight (kg)33    derivation: EX.WEIGHTKG3435  # The project function refuses a weight that is not positive.36  - name: DOSEKG37    type: float38    label: First Dose per Body Weight (mg/kg)39    derivation:40      function:41        name: dose_per_kg42        args:43          dose_mg: DOSEMG44          weight_kg: WEIGHTKG

Inputs

Under review1 source file

input/ex.csv

Edit3 rows

input/ex.csv
STUDYID	DOSEMG	WEIGHTKG
CTX	150	60.0
CTX	200	0
CTX	100	50.0

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 EX.STUDYID.	Predecessor
ADSL	USUBJID	Unique Subject Identifier	character	Copy value from EX.USUBJID.	Predecessor
ADSL	DOSEMG	First Dose (mg)	numeric	Copy value from EX.DOSEMG.	Predecessor
ADSL	WEIGHTKG	Baseline Weight (kg)	numeric	Copy value from EX.WEIGHTKG.	Predecessor
ADSL	DOSEKG	First Dose per Body Weight (mg/kg)	numeric	Call project function dose_per_kg with dose_mg = DOSEMG and weight_kg = WEIGHTKG.	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/ex.csv

Your review

Mapping spec