Reject a Period 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 collected blood pressure measurement with the study day in ADY, the record's position among the subject's records in ASEQ, the systolic blood pressure in AVAL, and the period in APERIODC.

Input: collected measurements carrying the study day (VSDY) and the systolic blood pressure (VSSTRESN), and the study's periods, each running from a first (FIRST) to a last (LAST) record position.

Variables:

ASEQ would number each subject's records from 1, by study day.
APERIODC would name the period, both ends inclusive, that holds the record's position, and be blank when no period does.

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

How to fix

Look the period up after the records are built, by deriving APERIODC for every record once ASEQ is numbered:

- name: APERIODC
  type: str
  label: Period (C)
  derivation: PERIOD.APERIODC

Then remove APERIODC 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.collected.derivations.APERIODC.source
rule: LOOKUP-2
context:
  identifier: ASEQ
  intermediate: PERIOD
  row: collected
  available_phase: column_derivation
  required_phase: row_construction

YAML specification

1 spec file

spec.yaml

Edit52 lines

1yamaa: "1.0"2type: spec3model: ADaM4domain: ADVS5keys: [STUDYID, USUBJID, ADY]6input:7  VS: {path: input/vs.csv, types: {VSDY: int, VSSTRESN: float}}8  PERIODS: {path: input/periods.csv, types: {FIRST: int, LAST: int}}910output:11  path: advs.csv12  columns: [STUDYID, USUBJID, ADY, ASEQ, AVAL, APERIODC]1314intermediates:15  # The period holding the record's position among the subject's records:16  # the first record is the run-in, the next eight the treatment.17  - id: PERIOD18    dataset: PERIODS19    key: [STUDYID]20    between: {value: ASEQ, lower: FIRST, upper: LAST}2122columns:23  - {name: STUDYID, type: str, label: Study Identifier}24  - {name: USUBJID, type: str, label: Unique Subject Identifier}25  - {name: ADY, type: int, label: Analysis Relative Day}2627  # The record's position among the subject's records, by study day. It is28  # numbered once every record is built.29  - name: ASEQ30    type: int31    label: Analysis Sequence Number32    derivation:33      row_number:34        window:35          group_by: [STUDYID, USUBJID]36          order_by: [ADY]3738  - {name: AVAL, type: float, label: Analysis Value}39  - {name: APERIODC, type: str, label: Period (C)}4041rows:42  # Each collected measurement. Its period is found from its position, which43  # is numbered only after the records are built, so the specification is44  # rejected before any data is read.45  - id: collected46    dataset: VS47    derivations:48      STUDYID: VS.STUDYID49      USUBJID: VS.USUBJID50      ADY: VS.VSDY51      AVAL: VS.VSSTRESN52      APERIODC: PERIOD.APERIODC

Inputs

Under review2 source files

input/periods.csv

Edit2 rows

input/periods.csv
STUDYID	FIRST	LAST	APERIODC
YAMAA-01	1	1	RUN-IN
YAMAA-01	2	9	TREATMENT

input/vs.csv

Edit3 rows

input/vs.csv
STUDYID	VSDY	VSSTRESN
YAMAA-01	1	132
YAMAA-01	8	128
YAMAA-01	15	126

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
ADVS	STUDYID	Study Identifier	character	Set per constructed row; see the Row construction sheet.	Derived
ADVS	USUBJID	Unique Subject Identifier	character	Set per constructed row; see the Row construction sheet.	Derived
ADVS	ADY	Analysis Relative Day	numeric	Set per constructed row; see the Row construction sheet.	Derived
ADVS	ASEQ	Analysis Sequence Number	numeric	Row number within each group of STUDYID, USUBJID, ordered by ADY.	Derived
ADVS	AVAL	Analysis Value	numeric	Set per constructed row; see the Row construction sheet.	Derived
ADVS	APERIODC	Period (C)	character	Set per constructed row; see the Row construction sheet.	Derived

Template	Include when	STUDYID	USUBJID	ADY	AVAL	APERIODC
collected		Copy VS.STUDYID	Copy VS.USUBJID	Copy VS.VSDY	Copy VS.VSSTRESN	Copy APERIODC from the PERIODS record matching on STUDYID, where ASEQ falls within FIRST to LAST, 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/periods.csv

input/vs.csv

Your review

Mapping spec