Reject a First Visit Window Taken From Records Not Yet 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 and add one follow-up record per subject, with the study day in VSDY, the record's category in VSCAT, the systolic blood pressure in VSSTRESN, and the visit window in VISIT.

Input: collected measurements carrying the study day (VSDY) and the systolic blood pressure (SYSBP), and a table of each subject's visit windows from a lowest (LO) to a highest (HI) study day.

Variables:

VSDY would be the measurement's study day, and on a follow-up record the subject's latest study day.
VSCAT would be COLLECTED on a measurement and FOLLOW-UP on the subject's follow-up record.
VSSTRESN would be the systolic blood pressure, blank on a follow-up record.
VISIT would name the window, both ends inclusive, that holds the study day of the subject's latest record already built.

Note: a record's window is found from the subject's latest record built before it. The collected measurements are the first records built, so for them no earlier record exists, and the run is rejected before any data is read and no artifact is accepted.

How to fix

Give the collected measurements the window of their own study day, and keep the latest-record window for the follow-up records, which are built after them:

intermediates:
  - id: OWNWIN
    dataset: WINDOWS
    key: [USUBJID]
    between: {value: VSDY, lower: LO, upper: HI}

- id: collected
  dataset: VITALS
  derivations:
    VISIT: OWNWIN.NAME

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: phase_boundary
rule: LOOKUP-7

expected/error.yaml

phase: validation
condition: phase_boundary
spec_paths:
  - rows.collected.derivations.VISIT.source
  - intermediates.LATESTWIN.between.value
rule: LOOKUP-7
context:
  identifier: LATEST.VSDY
  available_phase: completed_prior_row_template
  required_phase: row_construction

YAML specification

1 spec file

spec.yaml

Edit67 lines

1yamaa: "1.0"2type: spec3model: SDTM4domain: VS5keys: [USUBJID, VSDY, VSCAT]6input:7  VITALS: {path: input/vitals.csv, types: {VSDY: int, SYSBP: int}}8  WINDOWS: {path: input/windows.csv, types: {LO: int, HI: int}}910output:11  path: vs.csv12  columns: [USUBJID, VSDY, VSCAT, VSSTRESN, VISIT]1314intermediates:15  # The subject's latest record built so far.16  - id: LATEST17    dataset: SELF18    key: [USUBJID]19    order_by: [SELF.VSDY]20    keep: last2122  # The visit window holding the study day of that latest record.23  - id: LATESTWIN24    dataset: WINDOWS25    key: [USUBJID]26    between: {value: LATEST.VSDY, lower: LO, upper: HI}2728columns:29  - name: USUBJID30    type: str31    label: Unique Subject Identifier32    derivation: VITALS.USUBJID3334  - {name: VSDY, type: int, label: Study Day of Vital Signs}35  - {name: VSCAT, type: str, label: Category for Vital Signs}3637  - name: VSSTRESN38    type: int39    label: Numeric Result/Finding in Standard Units4041  - {name: VISIT, type: str, label: Visit Name}4243rows:44  # yamaa-lint: allow repeated_row_derivation -- the fault is in the row phase45  # Each collected measurement. Its visit is the window of the subject's46  # latest record built so far, but these are the first rows built, so no47  # such record exists yet, and the specification is rejected before any48  # data is read.49  - id: collected50    dataset: VITALS51    derivations:52      VSDY: VITALS.VSDY53      VSCAT: "'COLLECTED'"54      VSSTRESN: VITALS.SYSBP55      VISIT: LATESTWIN.NAME5657  # One follow-up record per subject, in the window of the subject's latest58  # collected measurement.59  - id: followup60    dataset: VITALS61    group_by: [VITALS.USUBJID]62    derivations:63      VSDY:64        aggregate: "MAX(VITALS.VSDY)"65      VSCAT: "'FOLLOW-UP'"66      VSSTRESN: null67      VISIT: LATESTWIN.NAME

Inputs

Under review2 source files

input/vitals.csv

Edit2 rows

input/vitals.csv
USUBJID	VSDY	SYSBP
	3	132
	10	128

input/windows.csv

Edit2 rows

input/windows.csv
USUBJID	LO	HI	NAME
	1	7	WEEK 1
	8	14	WEEK 2

Unexpected Output

Under reviewNo artifact is produced

No fixture files in this directory.

Shaded columns are derived— = missing value

Human review and assessment

Variable Name	Variable Label	Type	Origin	Conversion Definition	Variable Type	Variable Order
USUBJID	Unique Subject Identifier	Char	Collected	Copy value from VITALS.USUBJID.	SDTM	1
VSDY	Study Day of Vital Signs	Num	Derived	Set per constructed row; see the Row construction sheet.	SDTM	2
VSCAT	Category for Vital Signs	Char	Derived	Set per constructed row; see the Row construction sheet.	SDTM	3
VSSTRESN	Numeric Result/Finding in Standard Units	Num	Derived	Set per constructed row; see the Row construction sheet.	SDTM	4
VISIT	Visit Name	Char	Derived	Set per constructed row; see the Row construction sheet.	SDTM	5

Template	Include when	VSDY	VSCAT	VSSTRESN	VISIT
collected		Copy VITALS.VSDY	Constant "COLLECTED"	Copy VITALS.SYSBP	Copy NAME from the WINDOWS record matching on USUBJID, where LATEST.VSDY falls within LO to HI, and no match yields blank
followup		Aggregate MAX(VITALS.VSDY) over records matching on the shared output keys	Constant "FOLLOW-UP"	Constant "None"	Copy NAME from the WINDOWS record matching on USUBJID, where LATEST.VSDY falls within LO to HI, 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/vitals.csv

input/windows.csv

Your review

Mapping spec