Reject a Planned Dose Found While the Records Are Still Being Built

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Summary

EditUnder reviewWhat this benchmark means

README.md

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

Goal: carry each administration with its study day in ASTDY, its number among the subject's administrations in ADOSENUM, the dose given in AVAL, and the dose the schedule plans for that administration in PLANDOSE.

Input: exposure records, one per administration, carrying the study day (EXSTDY) and the dose given (EXDOSE), and a dosing schedule giving the planned dose (PLANDOSE) of each administration number (DOSENUM).

Variables:

ADOSENUM would number each subject's administrations from 1, by study day.
PLANDOSE would be the planned dose of the administration's number, and blank when the schedule plans none.

Note: an administration's number counts all of the subject's administrations, so it is numbered only after every record is built. The planned dose is looked up while each record is being built, before any administration has a number, so the run is rejected before any data is read and no artifact is accepted.

How to fix

Look the planned dose up after the records are built, by deriving PLANDOSE for every record once ADOSENUM is numbered:

- name: PLANDOSE
  type: float
  label: Planned Dose
  derivation: PLANNED.PLANDOSE

Then remove PLANDOSE from the row template's derivations.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: phase_boundary
rule: LOOKUP-2

expected/error.yaml

phase: validation
condition: phase_boundary
spec_paths:
  - rows.administered.derivations.PLANDOSE.source
rule: LOOKUP-2
context:
  identifier: ADOSENUM
  intermediate: PLANNED
  row: administered
  available_phase: column_derivation
  required_phase: row_construction

YAML specification

1 spec file

spec.yaml

Edit51 lines

1yamaa: "1.0"2type: spec3model: ADaM4domain: ADEX5keys: [STUDYID, USUBJID, ASTDY]6input:7  EX: {path: input/ex.csv, types: {EXSTDY: int, EXDOSE: float}}8  SCHEDULE: {path: input/schedule.csv, types: {DOSENUM: int, PLANDOSE: float}}910output:11  path: adex.csv12  columns: [STUDYID, USUBJID, ASTDY, ADOSENUM, AVAL, PLANDOSE]1314intermediates:15  # The scheduled dose of the administration's number among the subject's16  # administrations.17  - id: PLANNED18    dataset: SCHEDULE19    key: {DOSENUM: ADOSENUM}2021columns:22  - {name: STUDYID, type: str, label: Study Identifier}23  - {name: USUBJID, type: str, label: Unique Subject Identifier}24  - {name: ASTDY, type: int, label: Analysis Start Relative Day}2526  # The administration's number among the subject's administrations, by27  # study day. It is numbered once every record is built.28  - name: ADOSENUM29    type: int30    label: Administration Number31    derivation:32      row_number:33        window:34          group_by: [STUDYID, USUBJID]35          order_by: [ASTDY]3637  - {name: AVAL, type: float, label: Analysis Value}38  - {name: PLANDOSE, type: float, label: Planned Dose}3940rows:41  # Each administration. Its planned dose is found from its number, which is42  # numbered only after the records are built, so the specification is43  # rejected before any data is read.44  - id: administered45    dataset: EX46    derivations:47      STUDYID: EX.STUDYID48      USUBJID: EX.USUBJID49      ASTDY: EX.EXSTDY50      AVAL: EX.EXDOSE51      PLANDOSE: PLANNED.PLANDOSE

Inputs

Under review2 source files

input/ex.csv

Edit3 rows

input/ex.csv
STUDYID	EXSTDY	EXDOSE
YAMAA-01	1	50
YAMAA-01	15	100
YAMAA-01	1	50

input/schedule.csv

Edit2 rows

input/schedule.csv
DOSENUM	PLANDOSE
1	50
2	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	Set per constructed row; see the Row construction sheet.	Derived
ADEX	USUBJID	Unique Subject Identifier	character	Set per constructed row; see the Row construction sheet.	Derived
ADEX	ASTDY	Analysis Start Relative Day	numeric	Set per constructed row; see the Row construction sheet.	Derived
ADEX	ADOSENUM	Administration Number	numeric	Row number within each group of STUDYID, USUBJID, ordered by ASTDY.	Derived
ADEX	AVAL	Analysis Value	numeric	Set per constructed row; see the Row construction sheet.	Derived
ADEX	PLANDOSE	Planned Dose	numeric	Set per constructed row; see the Row construction sheet.	Derived

Template	Include when	STUDYID	USUBJID	ASTDY	AVAL	PLANDOSE
administered		Copy EX.STUDYID	Copy EX.USUBJID	Copy EX.EXSTDY	Copy EX.EXDOSE	Copy PLANDOSE from the SCHEDULE record whose DOSENUM equals ADOSENUM, and no match yields blank

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

input/schedule.csv

Your review

Mapping spec