Reject Post-CR PR

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 each collected tumor assessment into an analysis record holding the assessment date (ADT) and the recorded response (AVALC), rejecting a partial response (PR) recorded directly after a complete response (CR).

Input: collected tumor assessments with the assessment date (RSDTC) and the assessed response (RSSTRESC), identified by study, subject, and sequence number.

Variables:

ADT is the assessment date, taken directly from RSDTC.
AVALC is the response recorded at that assessment, taken directly from RSSTRESC: CR, PR, stable disease (SD), NON-CR/NON-PD, progressive disease (PD), or not evaluable (NE).

Note: assessments are compared in date order within a subject. A complete response leaves no measurable disease to respond partly, so an assessment recording PR directly after CR for the same subject is a fault in the collected data: the whole run is rejected and no artifact is accepted, and the expected output records the completed rows presented to that check. A partial response that later becomes complete is ordinary and passes.

How to fix

Review the response sequence and correct the assessment that is inconsistent with the study definition. If the protocol genuinely permits a partial response after a complete response, revise the clinical rule and its check together; do not remove the check merely to accept an unexplained sequence.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: verification
condition: assert_failed
requirement: REQ-0384

expected/error.yaml

phase: verification
condition: assert_failed
spec_paths:
  - verifications[2].assert
requirement: REQ-0384
context:
  verification_id: response-does-not-fall-back-after-a-complete-response
  failure_count: 1
  keys:
    - STUDYID: PILOT7
      USUBJID: P7-962
      RSSEQ: 2

YAML specification

1 spec file

spec.yaml

Edit69 lines

1schema_version: "1.0"2domain: ADRS3keys: [STUDYID, USUBJID, RSSEQ]4input:5  RS: {path: input/rs.csv, types: {RSDTC: date}}67output:8  path: adrs.csv9  columns: [STUDYID, USUBJID, RSSEQ, PARAMCD, ADT, AVALC]1011columns:12  - name: STUDYID13    type: str14    label: Study Identifier15    derivation: RS.STUDYID1617  - name: USUBJID18    type: str19    label: Unique Subject Identifier20    derivation: RS.USUBJID2122  - name: RSSEQ23    type: int24    label: Sequence Number25    derivation: RS.RSSEQ2627  - name: PARAMCD28    type: str29    label: Parameter Code30    derivation: {literal: OVR}3132  - name: ADT33    type: date34    label: Analysis Date35    derivation: RS.RSDTC3637  - name: AVALC38    type: str39    label: Analysis Value (C)40    derivation: RS.RSSTRESC41    verifications:42      allowed_values:43        values: [CR, PR, SD, NON-CR/NON-PD, PD, NE]4445  # The subject's previous response in date order (sequence number breaks46  # a same-day tie); missing on the subject's first assessment.47  - name: PREVAVALC48    type: str49    label: Previous Analysis Value (C)50    derivation:51      row_value:52        source: AVALC53        offset: -154        window:55          group_by: [STUDYID, USUBJID]56          order_by: [ADT, RSSEQ]5758verifications:59  - unique:60      columns: [STUDYID, USUBJID, RSSEQ]61  - row_count:62      min: 663      max: 664  # A PR directly after a CR fails. The IS NOT NULL keeps a PR on the65  # first assessment passing: without it that row would be UNKNOWN and fail.66  - assert:67      id: response-does-not-fall-back-after-a-complete-response68      require: "NOT (AVALC = 'PR' AND PREVAVALC IS NOT NULL69        AND PREVAVALC = 'CR')"

Inputs

Under review1 source file

input/rs.csv

Edit6 rows

input/rs.csv
STUDYID	RSSEQ	RSDTC	RSSTRESC
PILOT7	1	2025-02-17	CR
PILOT7	2	2025-04-07	CR
PILOT7	1	2025-02-24	CR
PILOT7	2	2025-04-14	PR
PILOT7	1	2025-03-03	PR
PILOT7	2	2025-05-05	CR

Unexpected Output

Under review6 rows presented to the failing check - not an accepted artifact

expected/adrs.csv

Edit6 rows

expected/adrs.csv
STUDYID	RSSEQ	PARAMCD	ADT	AVALC
PILOT7	1	OVR	2025-02-17	CR
PILOT7	2	OVR	2025-04-07	CR
PILOT7	1	OVR	2025-02-24	CR
PILOT7	2	OVR	2025-04-14	PR
PILOT7	1	OVR	2025-03-03	PR
PILOT7	2	OVR	2025-05-05	CR

Shaded columns are derived— = missing value

Comments and assessment materials

Dataset Name	Variable Name	Variable Label	Type	Codelist/Controlled Terms	Computational Method	Origin
ADRS	STUDYID	Study Identifier	character		Copy value from RS.STUDYID.	Predecessor
ADRS	USUBJID	Unique Subject Identifier	character		Copy value from RS.USUBJID.	Predecessor
ADRS	RSSEQ	Sequence Number	numeric		Copy value from RS.RSSEQ.	Predecessor
ADRS	PARAMCD	Parameter Code	character		Set constant value "OVR".	Assigned
ADRS	ADT	Analysis Date	numeric	ISO 8601	Copy value from RS.RSDTC.	Predecessor
ADRS	AVALC	Analysis Value (C)	character	CR, PR, SD, NON-CR/NON-PD, PD, NE	Copy value from RS.RSSTRESC.	Predecessor

Variable	Permitted values
AVALC	CR, PR, SD, NON-CR/NON-PD, PD, NE

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/rs.csv

expected/adrs.csv

Comments

Mapping spec