Reject Duplicate Baselines

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 over the analysis value (AVAL) and the baseline record flag (ABLFL) for each laboratory record.

Input: pre-derived laboratory records carrying study, subject, and parameter identifiers, the analysis date (ADT), the analysis value (AVAL), and the baseline record flag (ABLFL). One subject carries two Y flags for a parameter; another subject carries 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: each subject and parameter must have exactly one record flagged Y; a combination with none is rejected as well. Two flagged records leave the change from baseline undefined, and neither record can be preferred without inventing a rule the study did not state. The run is rejected and no artifact is accepted. The expected output records the completed rows presented to that check.

How to fix

Correct the flag in the incoming records so that one record carries it, choosing the record the study's baseline definition selects, ordinarily the latest result on or before the first exposure. When the flag should be derived here instead of trusted from the input, derive it and let a tie be reported where it arises:

- name: ABLFL
  type: str
  label: Baseline Record Flag
  derivation:
    baseline_flag:
      window:
        group_by: [STUDYID, USUBJID, PARAMCD]
      date: ADT
      reference_date: TRTSDT

Do not widen the count to accept two records; a second baseline is a defect in the data rather than a policy the analysis can adopt.

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:
  verification_id: one-baseline-record-per-subject-and-parameter
  failure_count: 2
  keys:
    - STUDYID: YAMAA-01
      USUBJID: YAMAA-01-101
      PARAMCD: ALT
    - STUDYID: YAMAA-01
      USUBJID: YAMAA-01-103
      PARAMCD: ALT
  counts:
    - 2
    - 0

YAML specification

1 spec file

spec.yaml

Edit55 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.ABLFL41    verifications:42      allowed_values:43        values: [Y]4445verifications:46  - unique:47      columns: [STUDYID, USUBJID, PARAMCD, ADT]48  # Exactly one record flagged Y per subject and parameter: a combination49  # with no flagged record fails min just as two flagged records fail max.50  - row_count:51      id: one-baseline-record-per-subject-and-parameter52      group_by: [STUDYID, USUBJID, PARAMCD]53      filter: "ABLFL = 'Y'"54      min: 155      max: 1

Inputs

Under review1 source file

input/adlb_raw.csv

Edit7 rows

input/adlb_raw.csv
STUDYID	PARAMCD	ADT	AVAL	ABLFL
YAMAA-01	ALT	2025-01-01	10	Y
YAMAA-01	ALT	2025-01-02	12	Y
YAMAA-01	ALT	2025-01-08	15	—
YAMAA-01	ALT	2025-01-01	8	Y
YAMAA-01	ALT	2025-01-08	12	—
YAMAA-01	ALT	2025-01-01	9	—
YAMAA-01	ALT	2025-01-08	11	—

Unexpected Output

Under review7 rows presented to the failing check - not an accepted artifact

expected/adlb.csv

Edit7 rows

expected/adlb.csv
STUDYID	PARAMCD	ADT	AVAL	ABLFL
YAMAA-01	ALT	2025-01-01	10	Y
YAMAA-01	ALT	2025-01-02	12	Y
YAMAA-01	ALT	2025-01-08	15	—
YAMAA-01	ALT	2025-01-01	8	Y
YAMAA-01	ALT	2025-01-08	12	—
YAMAA-01	ALT	2025-01-01	9	—
YAMAA-01	ALT	2025-01-08	11	—

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	Y	Copy value from ADLB_RAW.ABLFL.	Predecessor

Variable	Permitted values
ABLFL	Y

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