Reject an Epoch the Study Never Declared

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Summary

EditUnder reviewWhat this benchmark means

README.md

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

Goal: carry each vital-signs record's trial period (EPOCH), coded with the study's epoch terminology.

Input: collected vital-signs records with the study and subject identifiers, a sequence number and the recorded epoch.

Variables:

EPOCH would be the trial period of the record, one of the epochs the terminology lists: SCREENING, TREATMENT or FOLLOW-UP; blank when no epoch was recorded.

Note: the published epoch list admits sponsor additions, but an addition counts only once the study declares it. A record carrying RUN-IN, an epoch the study's terminology never lists, rejects the run once the epochs are complete, so no artifact is accepted. A blank epoch passes.

How to fix

Decide whether RUN-IN is a real trial period of this study. When it is, add it to the study's epoch list. RUN-IN is a published epoch term, so it is an ordinary item:

- id: EPOCH
  name: Epoch
  extensible: true
  items:
    - {value: SCREENING}
    - {value: RUN-IN}
    - {value: TREATMENT}
    - {value: FOLLOW-UP}

Only a period the published list lacks is a sponsor addition, declared as an item with extended: true and no NCI code, which the data-definition document shows as an extended value. When RUN-IN is not a period of this study, correct the collected epoch at its source and rerun.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: verification
condition: allowed_values_failed
rule: CT-7

expected/error.yaml

phase: verification
condition: allowed_values_failed
spec_paths:
  - columns.EPOCH.submission.codelist
rule: CT-7
context:
  column: EPOCH
  codelist: EPOCH
  failure_count: 1
  keys:
    - STUDYID: YAMAA-01
      USUBJID: YAMAA-01-101
      VSSEQ: 2
  values: [RUN-IN]

YAML specification

1 spec file

spec.yaml

Edit39 lines

1yamaa: "1.0"2type: spec3model: SDTM4domain: VS5keys: [STUDYID, USUBJID, VSSEQ]6input:7  VS_RAW: input/vs_raw.csv89output:10  path: vs.csv11  columns: [STUDYID, USUBJID, VSSEQ, EPOCH]1213columns:14  - name: STUDYID15    type: str16    label: Study Identifier17    derivation: VS_RAW.STUDYID1819  - name: USUBJID20    type: str21    label: Unique Subject Identifier22    derivation: VS_RAW.USUBJID2324  - name: VSSEQ25    type: int26    label: Sequence Number27    derivation: VS_RAW.VSSEQ2829  # The epoch list is extensible, and its declared items are still the30  # whole set of accepted values.31  - name: EPOCH32    type: str33    label: Epoch34    derivation: VS_RAW.EPOCH35    submission:36      codelist: EPOCH37      origins:38        - type: Assigned39          source: Sponsor

Inputs

Under review1 source file

input/vs_raw.csv

Edit4 rows

input/vs_raw.csv
STUDYID	VSSEQ	EPOCH
YAMAA-01	1	SCREENING
YAMAA-01	2	RUN-IN
YAMAA-01	3	TREATMENT
YAMAA-01	4	—

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	Controlled Terms or Format	Origin	Conversion Definition	Variable Type	Variable Order
STUDYID	Study Identifier	Char		Collected	Copy value from VS_RAW.STUDYID.	SDTM	1
USUBJID	Unique Subject Identifier	Char		Collected	Copy value from VS_RAW.USUBJID.	SDTM	2
VSSEQ	Sequence Number	Num		Collected	Copy value from VS_RAW.VSSEQ.	SDTM	3
EPOCH	Epoch	Char	Epoch	Assigned	Copy value from VS_RAW.EPOCH.	SDTM	4

Codelist ID	Name	Value	Extensible
EPOCH	Epoch	SCREENING	Yes
EPOCH	Epoch	TREATMENT	Yes
EPOCH	Epoch	FOLLOW-UP	Yes

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/vs_raw.csv

Your review

Mapping spec