Refuse a Data Definition of a Variable Without Its Metadata

Review ask

As a clinical trial statistician or programmer, answer two short questions in Your review: the task and the inputs. Agreeing with both approves this benchmark; disagreeing with either needs a comment. Propose a fix with the Edit button on any source file, or add it to your comments.

We suggest spending no more than 5 minutes on a review. The other tabs beside Your review are background for assessment, not under review.

Summary

EditUnder reviewWhat this benchmark means

README.md

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

Goal: submit the demographics domain with its data definition, including each subject's study site (SITEID).

Input: collected demographics, one record per subject.

Variables:

DOMAIN is DM on every record.
SITEID is the identifier of the subject's study site.

Note: the study site was added to the domain late, with a label but without the metadata a data definition describes a variable by: its core designation, role, length and origin. The document cannot describe it, so the submission is refused before any document is written; the dataset itself still builds.

How to fix

Give the variable its submission metadata:

- name: SITEID
  type: str
  label: Study Site Identifier
  derivation: RAW.SITEID
  submission:
    core: Req
    role: Record Qualifier
    length: 3
    origins:
      - type: Assigned
        source: Sponsor

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: submission_metadata_missing
rule: DEFINE-7

expected/error.yaml

phase: validation
condition: submission_metadata_missing
spec_paths:
  - sdtm.specs[0].columns.SITEID.submission
rule: DEFINE-7

YAML specification

1 spec file

spec.yaml

Edit60 lines

1yamaa: "1.0"2type: spec3model: SDTM4domain: DM5keys: [STUDYID, USUBJID]6input:7  RAW: input/dm_raw.csv89output:10  path: dm.csv11  columns: [DOMAIN, STUDYID, USUBJID, SITEID]1213columns:14  - name: DOMAIN15    type: str16    label: Domain Abbreviation17    derivation: "'DM'"18    submission:19      core: Req20      role: Identifier21      length: 222      origins:23        - type: Assigned24          source: Sponsor2526  - name: STUDYID27    type: str28    label: Study Identifier29    derivation: RAW.STUDYID30    submission:31      core: Req32      role: Identifier33      length: 534      origins:35        - type: Protocol36          source: Sponsor3738  - name: USUBJID39    type: str40    label: Unique Subject Identifier41    derivation: RAW.USUBJID42    submission:43      core: Req44      role: Identifier45      length: 946      origins:47        - type: Assigned48          source: Sponsor4950  # Added late, with a label but without its submission metadata.51  - name: SITEID52    type: str53    label: Study Site Identifier54    derivation: RAW.SITEID5556submission:57  label: Demographics58  class: SPECIAL PURPOSE59  structure: One record per subject60  repeating: false

Inputs

Under review1 source file

input/dm_raw.csv

Edit2 rows

input/dm_raw.csv
STUDYID	USUBJID	SITEID
PAR01		101
PAR01		102

Unexpected Output

Under review2 rows presented to the failing check - not an accepted artifact

expected/dm.csv

Edit2 rows

expected/dm.csv
DOMAIN	STUDYID	USUBJID	SITEID
DM	PAR01		101
DM	PAR01		102

Shaded columns are derived— = missing value

Human review and assessment

Variable Name	Variable Label	Type	Length	Origin	Core	Conversion Definition	Variable Type	Variable Order
DOMAIN	Domain Abbreviation	Char	2	Assigned	Req	Set constant value "DM".	SDTM	1
STUDYID	Study Identifier	Char	5	Protocol	Req	Copy value from RAW.STUDYID.	SDTM	2
USUBJID	Unique Subject Identifier	Char	9	Assigned	Req	Copy value from RAW.USUBJID.	SDTM	3
SITEID	Study Site Identifier	Char		Collected		Copy value from RAW.SITEID.	SDTM	4

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/dm_raw.csv

expected/dm.csv

Your review

Mapping spec