Fail an Unnamed Count on Bad Data

Review ask

As a clinical trial statistician or programmer, challenge anything in this benchmark: describe a problem in Comments, or propose a fix with the Edit button on any source file.

Task: Is this a specification error a study team could realistically make, and should the build stop on it rather than continue?
Inputs: Do they trigger the failure for the reason the summary gives?
Expected failure: Is this the right error, raised at the right point, and would it tell the programmer what to fix?

The other tabs beside Comments are background for assessment, not under review.

Summary

EditUnder reviewWhat this benchmark means

README.md

Goal: carry the analysis date (ADT), the numeric result (AVAL), and the baseline flag (ABLFL) for each laboratory result, and check that each subject and parameter has exactly one flagged baseline result.

Input: collected laboratory results carrying analysis date (ADT), numeric result (AVAL), and baseline flag (ABLFL). One subject has two flagged records and another has none.

Variables:

ABLFL is the input baseline flag: Y on the record that serves as the baseline for the subject and parameter, blank on every other record.

Note: the grouped count has no id, and the declaration is valid. It runs and reports the failing subject-parameter groups at its specification path. The bounds remain available in the declaration at that path.

How to fix

Correct the baseline flags in the incoming records so each subject and parameter has exactly one record flagged Y.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: verification
condition: row_count_failed
requirement: REQ-0385

expected/error.yaml

phase: verification
condition: row_count_failed
spec_paths:
  - verifications[1].row_count
requirement: REQ-0385
context:
  failure_count: 2
  keys:
    - STUDYID: YAMAA-01
      USUBJID: YAMAA-01-101
      PARAMCD: ALT
    - STUDYID: YAMAA-01
      USUBJID: YAMAA-01-102
      PARAMCD: ALT
  counts:
    - 2
    - 0

YAML specification

1 spec file

spec.yaml

Edit50 lines

1schema_version: "1.0"2domain: ADLB3keys: [STUDYID, USUBJID, PARAMCD, ADT]4input:5  ADLB_RAW: {path: input/adlb_raw.csv, types: {AVAL: float, ADT: date}}67output:8  path: adlb.csv9  columns: [STUDYID, USUBJID, PARAMCD, ADT, AVAL, ABLFL]1011columns:12  - name: STUDYID13    type: str14    label: Study Identifier15    derivation: ADLB_RAW.STUDYID1617  - name: USUBJID18    type: str19    label: Unique Subject Identifier20    derivation: ADLB_RAW.USUBJID2122  - name: PARAMCD23    type: str24    label: Parameter Code25    derivation: ADLB_RAW.PARAMCD2627  - name: ADT28    type: date29    label: Analysis Date30    derivation: ADLB_RAW.ADT3132  - name: AVAL33    type: float34    label: Analysis Value35    derivation: ADLB_RAW.AVAL3637  - name: ABLFL38    type: str39    label: Baseline Record Flag40    derivation: ADLB_RAW.ABLFL4142verifications:43  - unique: [STUDYID, USUBJID, PARAMCD, ADT]44  # Exactly one baseline per subject and parameter, but this grouped count45  # has no id naming that rule.46  - row_count:47      group_by: [STUDYID, USUBJID, PARAMCD]48      filter: "ABLFL = 'Y'"49      min: 150      max: 1

Inputs

Under review1 source file

input/adlb_raw.csv

Edit3 rows

input/adlb_raw.csv
STUDYID	PARAMCD	ADT	AVAL	ABLFL
YAMAA-01	ALT	2025-01-01	10	Y
YAMAA-01	ALT	2025-01-08	15	Y
YAMAA-01	ALT	2025-01-01	8	—

Unexpected Output

Under review3 rows presented to the failing check - not an accepted artifact

expected/adlb.csv

Edit3 rows

expected/adlb.csv
STUDYID	PARAMCD	ADT	AVAL	ABLFL
YAMAA-01	ALT	2025-01-01	10	Y
YAMAA-01	ALT	2025-01-08	15	Y
YAMAA-01	ALT	2025-01-01	8	—

Shaded columns are derived— = missing value

Comments and assessment materials

Dataset Name	Variable Name	Variable Label	Type	Codelist/Controlled Terms	Computational Method	Origin
ADLB	STUDYID	Study Identifier	character		Copy value from ADLB_RAW.STUDYID.	Predecessor
ADLB	USUBJID	Unique Subject Identifier	character		Copy value from ADLB_RAW.USUBJID.	Predecessor
ADLB	PARAMCD	Parameter Code	character		Copy value from ADLB_RAW.PARAMCD.	Predecessor
ADLB	ADT	Analysis Date	numeric	ISO 8601	Copy value from ADLB_RAW.ADT.	Predecessor
ADLB	AVAL	Analysis Value	numeric		Copy value from ADLB_RAW.AVAL.	Predecessor
ADLB	ABLFL	Baseline Record Flag	character		Copy value from ADLB_RAW.ABLFL.	Predecessor

Version	Date	Author	Description
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/adlb_raw.csv

expected/adlb.csv

Comments

Mapping spec