Reject Per-Test Lengths Over a Numeric Test Code

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Summary

EditUnder reviewWhat this benchmark means

README.md

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

Goal: turn each collected sample's glucose and creatinine results into one laboratory record per test, identified by the test code in LBTESTCD and carrying the collected result in LBORRES.

Input: collected laboratory results with one record per subject sample, carrying the glucose (GLUC) and creatinine (CREAT) results as collected.

Variables:

LBTESTCD would be the laboratory's code for the test: 1001 for glucose and 1002 for creatinine.
LBORRES would be the result as collected, at most four characters long for glucose and three for creatinine.

Note: each test states its own maximum result length, which applies to the records carrying that test's code. A test code is text, but the test code here is declared as an integer, so no record can carry the code a length names and the lengths would check nothing. The run is rejected before any data is read and no artifact is accepted.

How to fix

Declare the test code as text, even though the laboratory's codes are digits:

- name: LBTESTCD
  type: str
  label: Lab Test or Examination Short Name

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: value_level_where_invalid
rule: SUB-12

expected/error.yaml

phase: validation
condition: value_level_where_invalid
spec_paths:
  - columns.LBORRES.submission.value_level.GLUC.where.LBTESTCD
rule: SUB-12
context:
  column: LBORRES
  entry: GLUC
  reason: not_str
  where_column: LBTESTCD

YAML specification

1 spec file

spec.yaml

Edit59 lines

1yamaa: "1.0"2type: spec3model: SDTM4domain: LB5keys: [STUDYID, USUBJID, LBTESTCD]6input:7  LB_RAW: input/lb_raw.csv89output:10  path: lb.csv11  columns: [STUDYID, USUBJID, LBTESTCD, LBORRES]1213columns:14  - name: STUDYID15    type: str16    label: Study Identifier17    derivation: LB_RAW.STUDYID1819  - name: USUBJID20    type: str21    label: Unique Subject Identifier22    derivation: LB_RAW.USUBJID2324  # The laboratory numbers its tests, so the test code was declared an25  # integer. Each test's result length below applies to the rows carrying26  # that test code, which an integer column never holds, so the27  # specification is rejected before any data is read.28  - name: LBTESTCD29    type: int30    label: Lab Test or Examination Short Name3132  # Each test states its own maximum result length.33  - name: LBORRES34    type: str35    label: Result or Finding in Original Units36    submission:37      length: 438      origins:39        - type: Collected40          source: Vendor41      value_level:42        - id: GLUC43          where: {LBTESTCD: ["1001"]}44          length: 445        - id: CREAT46          where: {LBTESTCD: ["1002"]}47          length: 34849rows:50  # One glucose and one creatinine record per collected sample.51  - id: glucose52    derivations:53      LBTESTCD: "'1001'"54      LBORRES: LB_RAW.GLUC5556  - id: creatinine57    derivations:58      LBTESTCD: "'1002'"59      LBORRES: LB_RAW.CREAT

Inputs

Under review1 source file

input/lb_raw.csv

Edit2 rows

input/lb_raw.csv
STUDYID	USUBJID	GLUC	CREAT
YAMAA-01		95	0.9
YAMAA-01		104	1.1

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	Length	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
LBTESTCD	Lab Test or Examination Short Name	Num		Derived	Set per constructed row; see the Row construction sheet.	SDTM	3
LBORRES	Result or Finding in Original Units	Char	4	Collected	Set per constructed row; see the Row construction sheet.	SDTM	4

Template	Include when	LBTESTCD	LBORRES
glucose		Constant "1001"	Copy LB_RAW.GLUC
creatinine		Constant "1002"	Copy LB_RAW.CREAT

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/lb_raw.csv

Your review

Mapping spec