Reject an Age Band Chosen by Another Dataset's Age

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Summary

EditUnder reviewWhat this benchmark means

README.md

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

Goal: attach the reference range limits (LBSTNRLO, LBSTNRHI) to each laboratory result from the age band that holds the subject's age.

Input: laboratory results carrying a test code (LBTESTCD) and a numeric result (LBSTRESN), demographics carrying each subject's age (AGE), and a range table giving each test code's lower and upper limits for an age band from a lowest (AGELO) to a highest (AGEHI) age.

Variables:

LBSTNRLO and LBSTNRHI would be the limits of the band for the result's test code whose ages, both ends inclusive, hold the subject's age, and blank when no band does.

Note: a band is chosen by a value of the laboratory row itself: a field of the laboratory record the row was built from, or a column built for that row. The age is taken directly from demographics, a different dataset, so it is not a value of the laboratory row. The run is rejected before any data is read; no artifact is accepted.

How to fix

Decide which age selects the band; usually it is the subject's age as recorded in demographics. Bring that age onto each laboratory row as its own column, matched to the result by study and subject and declared before the range limits, and choose the band by that column:

columns:
  - name: AGE
    type: int
    label: Age
    derivation: DM.AGE

between: {value: AGE, lower: AGELO, upper: AGEHI}

Leave AGE out of the published columns when the artifact should not carry it.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: unknown_field
rule: LOOKUP-9

expected/error.yaml

phase: validation
condition: unknown_field
spec_paths:
  - intermediates.REFRANGE.between.value
rule: LOOKUP-9
context:
  identifier: DM.AGE
  intermediate: REFRANGE

YAML specification

1 spec file

spec.yaml

Edit66 lines

1yamaa: "1.0"2type: spec3model: SDTM4domain: LB5keys: [STUDYID, USUBJID, LBSEQ]6input:7  LB_RAW:8    path: input/lb_raw.csv9    types: {LBSEQ: int, LBSTRESN: float}10  DM:11    path: input/dm.csv12    types: {AGE: int}13  LBRANGE:14    path: input/lbrange.csv15    types: {AGELO: int, AGEHI: int, LBSTNRLO: float, LBSTNRHI: float}16base: LB_RAW1718output:19  path: lb.csv20  columns: [STUDYID, USUBJID, LBSEQ, LBTESTCD, LBSTRESN, LBSTNRLO, LBSTNRHI]2122intermediates:23  # The reference range for the result's test code whose age band holds the24  # subject's age. DM.AGE names a demographics record, and a laboratory row is25  # built from a laboratory record, so the specification is rejected before26  # any data is read.27  - id: REFRANGE28    dataset: LBRANGE29    key: [LBTESTCD]30    between: {value: DM.AGE, lower: AGELO, upper: AGEHI}3132columns:33  - name: STUDYID34    type: str35    label: Study Identifier36    derivation: LB_RAW.STUDYID3738  - name: USUBJID39    type: str40    label: Unique Subject Identifier41    derivation: LB_RAW.USUBJID4243  - name: LBSEQ44    type: int45    label: Sequence Number46    derivation: LB_RAW.LBSEQ4748  - name: LBTESTCD49    type: str50    label: Lab Test or Examination Short Name51    derivation: LB_RAW.LBTESTCD5253  - name: LBSTRESN54    type: float55    label: Numeric Result/Finding in Standard Units56    derivation: LB_RAW.LBSTRESN5758  - name: LBSTNRLO59    type: float60    label: Reference Range Lower Limit-Std Units61    derivation: REFRANGE.LBSTNRLO6263  - name: LBSTNRHI64    type: float65    label: Reference Range Upper Limit-Std Units66    derivation: REFRANGE.LBSTNRHI

Inputs

Under review3 source files

input/dm.csv

Edit2 rows

input/dm.csv
STUDYID	USUBJID	AGE
YAMAA-01		45
YAMAA-01		71

input/lb_raw.csv

Edit2 rows

input/lb_raw.csv
STUDYID	USUBJID	LBSEQ	LBTESTCD	LBSTRESN
YAMAA-01		1	ALT	38
YAMAA-01		1	ALT	38

input/lbrange.csv

Edit2 rows

input/lbrange.csv
LBTESTCD	AGELO	AGEHI	LBSTNRLO	LBSTNRHI
ALT	18	64	0	40
ALT	65	120	0	35

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
STUDYID	Study Identifier	Char	Collected	Copy value from LB_RAW.STUDYID.	SDTM	1
USUBJID	Unique Subject Identifier	Char	Collected	Copy value from LB_RAW.USUBJID.	SDTM	2
LBSEQ	Sequence Number	Num	Collected	Copy value from LB_RAW.LBSEQ.	SDTM	3
LBTESTCD	Lab Test or Examination Short Name	Char	Collected	Copy value from LB_RAW.LBTESTCD.	SDTM	4
LBSTRESN	Numeric Result/Finding in Standard Units	Num	Collected	Copy value from LB_RAW.LBSTRESN.	SDTM	5
LBSTNRLO	Reference Range Lower Limit-Std Units	Num	Derived	Take LBSTNRLO from the LBRANGE record matching on LBTESTCD, where DM.AGE falls within AGELO to AGEHI, and no match yields blank.	SDTM	6
LBSTNRHI	Reference Range Upper Limit-Std Units	Num	Derived	Take LBSTNRHI from the LBRANGE record matching on LBTESTCD, where DM.AGE falls within AGELO to AGEHI, and no match yields blank.	SDTM	7

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/dm.csv

input/lb_raw.csv

input/lbrange.csv

Your review

Mapping spec