Reject a Sponsor-Added Epoch That Claims a Published 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: build the trial arms domain, one record per planned element of each arm, with its epoch (EPOCH) restricted to the study's epoch codelist.

Input: the protocol's planned arms and elements, and the study's codelists in the project file: the published epoch list, which admits sponsor additions, with the extension epoch added by the sponsor.

Variables:

DOMAIN is TA on every record.
EPOCH would be the epoch of the element, one of the codelist's values.

Note: the extension epoch is marked as a sponsor addition, yet it carries a published code, the one the treatment epoch carries. A sponsor addition has no published code, so the code claims a concept the published list does not assign to it, and the run is rejected before any data is read; no artifact is accepted.

How to fix

Remove the code from the sponsor addition, and keep the mark that it was added:

- value: EXTENSION
  extended: true

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: codelist_extended_alias
rule: CT-6

expected/error.yaml

phase: validation
condition: codelist_extended_alias
spec_paths:
  - codelists[0].codelists[0].items[2].alias
rule: CT-6
context:
  codelist: EPOCH
  value: EXTENSION
  alias: C101526

YAML specification

1 spec file

spec.yaml

Edit118 lines

1yamaa: "1.0"2type: spec3model: SDTM4domain: TA5keys: [STUDYID, ARMCD, TAETORD]6input:7  DESIGN: {path: input/design.csv, types: {TAETORD: int}}89output:10  path: ta.csv11  columns: [DOMAIN, STUDYID, ARMCD, ARM, TAETORD, ETCD, ELEMENT, EPOCH]1213columns:14  - name: DOMAIN15    type: str16    label: Domain Abbreviation17    derivation: "'TA'"18    submission:19      core: Req20      role: Identifier21      length: 222      origins:23        - type: Assigned24          source: Sponsor2526  - name: STUDYID27    type: str28    label: Study Identifier29    derivation: DESIGN.STUDYID30    submission:31      core: Req32      role: Identifier33      length: 834      origins:35        - type: Protocol36          source: Sponsor3738  - name: ARMCD39    type: str40    label: Planned Arm Code41    derivation: DESIGN.ARMCD42    submission:43      core: Req44      role: Topic45      length: 846      origins:47        - type: Protocol48          source: Sponsor4950  - name: ARM51    type: str52    label: Description of Planned Arm53    derivation: DESIGN.ARM54    submission:55      core: Req56      role: Synonym Qualifier57      length: 4058      origins:59        - type: Protocol60          source: Sponsor6162  - name: TAETORD63    type: int64    label: Planned Order of Element within Arm65    derivation: DESIGN.TAETORD66    submission:67      core: Req68      role: Timing69      length: 870      origins:71        - type: Protocol72          source: Sponsor7374  - name: ETCD75    type: str76    label: Element Code77    derivation: DESIGN.ETCD78    submission:79      core: Req80      role: Record Qualifier81      length: 882      origins:83        - type: Protocol84          source: Sponsor8586  - name: ELEMENT87    type: str88    label: Description of Element89    derivation: DESIGN.ELEMENT90    submission:91      core: Perm92      role: Synonym Qualifier93      length: 4094      origins:95        - type: Protocol96          source: Sponsor9798  # The open-label extension epoch is a sponsor addition to the published99  # epoch list, which the project declares as an extended item.100  - name: EPOCH101    type: str102    label: Epoch103    derivation: DESIGN.EPOCH104    submission:105      core: Req106      role: Timing107      length: 20108      codelist: EPOCH109      origins:110        - type: Protocol111          source: Sponsor112113submission:114  label: Trial Arms115  class: TRIAL DESIGN116  structure: One record per planned element per arm117  repeating: false118  reference_data: true

Inputs

Under review1 source file

input/design.csv

Edit3 rows

input/design.csv
STUDYID	ARMCD	ARM	TAETORD	ETCD	ELEMENT	EPOCH
YAMAA-01	PBO	Placebo	1	SCRN	Screening	SCREENING
YAMAA-01	PBO	Placebo	2	PBO	Placebo	TREATMENT
YAMAA-01	PBO	Placebo	3	OLE	Open-label active drug	EXTENSION

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	Controlled Terms or Format	Origin	Core	Conversion Definition	Variable Type	Variable Order
DOMAIN	Domain Abbreviation	Char	2		Assigned	Req	Set constant value "TA".	SDTM	1
STUDYID	Study Identifier	Char	8		Protocol	Req	Copy value from DESIGN.STUDYID.	SDTM	2
ARMCD	Planned Arm Code	Char	8		Protocol	Req	Copy value from DESIGN.ARMCD.	SDTM	3
ARM	Description of Planned Arm	Char	40		Protocol	Req	Copy value from DESIGN.ARM.	SDTM	4
TAETORD	Planned Order of Element within Arm	Num	8		Protocol	Req	Copy value from DESIGN.TAETORD.	SDTM	5
ETCD	Element Code	Char	8		Protocol	Req	Copy value from DESIGN.ETCD.	SDTM	6
ELEMENT	Description of Element	Char	40		Protocol	Perm	Copy value from DESIGN.ELEMENT.	SDTM	7
EPOCH	Epoch	Char	20	Epoch	Protocol	Req	Copy value from DESIGN.EPOCH.	SDTM	8

Codelist ID	Name	Value	Codelist NCI alias	Value NCI alias	Extensible	Extended value
EPOCH	Epoch	SCREENING	C99079	C48262	Yes
EPOCH	Epoch	TREATMENT	C99079	C101526	Yes
EPOCH	Epoch	EXTENSION	C99079	C101526	Yes	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/design.csv

Your review

Mapping spec