Reject a Value Stated as Both a Total and a Single Dose

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Summary

EditUnder reviewWhat this benchmark means

README.md

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

Goal: keep one record per study drug administration, with the dose in AVAL.

Input: collected exposure records, one per administration, with the dose given (EXDOSE).

Variables:

EXSEQ is the collected sequence number of the administration.
AVAL would be the analysis value of the record.

Note: the value of AVAL is stated twice: once as each subject's total dose over all administrations, and once, for each administration record, as the dose given on that record. A total is computed from all of a subject's records, so it cannot be replaced record by record, and the run is rejected before any data is read; no artifact is accepted.

How to fix

Decide what AVAL holds on an administration record. When it is the dose given, state only that, in the column itself:

- name: AVAL
  type: float
  label: Analysis Value
  derivation: EX.EXDOSE

When the subject's total dose is needed as well, give it a column of its own, such as a cumulative dose, rather than replacing it record by record.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: duplicate_derivation
rule: SPEC-6

expected/error.yaml

phase: validation
condition: duplicate_derivation
spec_paths:
  - columns.AVAL.derivation
rule: SPEC-6
context:
  column: AVAL
  rows: [administration]
  not_row_local: aggregate

YAML specification

1 spec file

spec.yaml

Edit45 lines

1yamaa: "1.0"2type: spec3model: ADaM4domain: ADEX5keys: [STUDYID, USUBJID, EXSEQ]6input:7  EX:8    path: input/ex.csv9    types: {EXSEQ: int, EXDOSE: float}10    key: [STUDYID, USUBJID]1112output:13  path: adex.csv14  columns: [STUDYID, USUBJID, EXSEQ, AVAL]1516columns:17  - name: STUDYID18    type: str19    label: Study Identifier20    derivation: EX.STUDYID2122  - name: USUBJID23    type: str24    label: Unique Subject Identifier25    derivation: EX.USUBJID2627  - name: EXSEQ28    type: int29    label: Sequence Number30    derivation: EX.EXSEQ3132  # Each subject's total dose over all of their administrations.33  - name: AVAL34    type: float35    label: Analysis Value36    derivation:37      aggregate: "SUM(EX.EXDOSE)"3839rows:40  # One record per administration, which states the dose given on that41  # record for the same column.42  - id: administration43    dataset: EX44    derivations:45      AVAL: EX.EXDOSE

Inputs

Under review1 source file

input/ex.csv

Edit3 rows

input/ex.csv
STUDYID	EXSEQ	EXDOSE
YAMAA-01	1	100
YAMAA-01	2	150
YAMAA-01	1	100

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
ADEX	STUDYID	Study Identifier	character	Copy value from EX.STUDYID.	Predecessor
ADEX	USUBJID	Unique Subject Identifier	character	Copy value from EX.USUBJID.	Predecessor
ADEX	EXSEQ	Sequence Number	numeric	Copy value from EX.EXSEQ.	Predecessor
ADEX	AVAL	Analysis Value	numeric	Aggregate SUM(EX.EXDOSE) over records matching on the shared output keys.	Derived

Template	Include when	AVAL
administration		Copy EX.EXDOSE

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