Reject a Device Matched on a Record Some Rows Do Not Have

Review ask

As a clinical trial statistician or programmer, answer two short questions in Your review: the task and the inputs. Agreeing with both approves this benchmark; disagreeing with either needs a comment. Propose a fix with the Edit button on any source file, or add it to your comments.

We suggest spending no more than 5 minutes on a review. The other tabs beside Your review are background for assessment, not under review.

Summary

EditUnder reviewWhat this benchmark means

README.md

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

Goal: combine blood pressure measurements taken at the clinic and at home, with the study day in VSDY, where the measurement was taken in VSCAT, the systolic blood pressure in VSSTRESN, and the method in VSMETHOD.

Input: clinic measurements carrying the study day (VSDY), the systolic blood pressure (SYSBP) and the device number (DEVICEID), home measurements carrying the study day and the systolic blood pressure, and a device list giving each device's method (METHOD).

Variables:

VSCAT would be CLINIC or HOME.
VSSTRESN would be the systolic blood pressure.
VSMETHOD would be the method of the device the measurement was taken with.

Note: every record's method is found from the clinic measurement's device number. The home measurements build some of the records, and a home measurement has no clinic measurement of its own, so the run is rejected before any data is read and no artifact is accepted.

How to fix

Find the method only for the clinic measurements, and leave it blank for the home measurements, which carry no device number:

- id: clinic
  dataset: CLINIC
  derivations:
    VSMETHOD: DEVICE.METHOD

- id: home
  dataset: HOME
  derivations:
    VSMETHOD: null

Then remove the column-level derivation of VSMETHOD.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: unknown_field
rule: LOOKUP-5

expected/error.yaml

phase: validation
condition: unknown_field
spec_paths:
  - intermediates.DEVICE.key
rule: LOOKUP-5
context:
  identifier: CLINIC.DEVICEID
  intermediate: DEVICE

YAML specification

1 spec file

spec.yaml

Edit54 lines

1yamaa: "1.0"2type: spec3model: SDTM4domain: VS5keys: [USUBJID, VSDY, VSCAT]6input:7  CLINIC: {path: input/clinic.csv, types: {VSDY: int, SYSBP: int}}8  HOME: {path: input/home.csv, types: {VSDY: int, SYSBP: int}}9  DEVICES: input/devices.csv1011output:12  path: vs.csv13  columns: [USUBJID, VSDY, VSCAT, VSSTRESN, VSMETHOD]1415intermediates:16  # The device a measurement was taken with, matched on the clinic record's17  # device number.18  - id: DEVICE19    dataset: DEVICES20    key: {DEVICEID: CLINIC.DEVICEID}2122columns:23  - {name: USUBJID, type: str, label: Unique Subject Identifier}24  - {name: VSDY, type: int, label: Study Day of Vital Signs}25  - {name: VSCAT, type: str, label: Category for Vital Signs}2627  - name: VSSTRESN28    type: int29    label: Numeric Result/Finding in Standard Units3031  # Every record's method comes from its device, but home records build32  # some of the rows and have no clinic record, so the specification is33  # rejected before any data is read.34  - name: VSMETHOD35    type: str36    label: Method of Test or Examination37    derivation: DEVICE.METHOD3839rows:40  - id: clinic41    dataset: CLINIC42    derivations:43      USUBJID: CLINIC.USUBJID44      VSDY: CLINIC.VSDY45      VSCAT: "'CLINIC'"46      VSSTRESN: CLINIC.SYSBP4748  - id: home49    dataset: HOME50    derivations:51      USUBJID: HOME.USUBJID52      VSDY: HOME.VSDY53      VSCAT: "'HOME'"54      VSSTRESN: HOME.SYSBP

Inputs

Under review3 source files

input/clinic.csv

Edit2 rows

input/clinic.csv
USUBJID	VSDY	SYSBP	DEVICEID
	1	132	D01
	15	128	D02

input/devices.csv

Edit2 rows

input/devices.csv
DEVICEID	METHOD
D01	AUTOMATED
D02	MANUAL

input/home.csv

Edit1 row

input/home.csv
USUBJID	VSDY	SYSBP
	8	130

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	Derived	Set per constructed row; see the Row construction sheet.	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
VSMETHOD	Method of Test or Examination	Char	Derived	Take METHOD from the DEVICES record whose DEVICEID equals CLINIC.DEVICEID, and no match yields blank.	SDTM	5

Template	Include when	USUBJID	VSDY	VSCAT	VSSTRESN
clinic		Copy CLINIC.USUBJID	Copy CLINIC.VSDY	Constant "CLINIC"	Copy CLINIC.SYSBP
home		Copy HOME.USUBJID	Copy HOME.VSDY	Constant "HOME"	Copy HOME.SYSBP

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/clinic.csv

input/devices.csv

input/home.csv

Your review

Mapping spec