Sex Label Too Long for Transport

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 DM in a SAS transport file.

Input: one row per subject carrying the site, age and sex.

Variables:

SITEID, AGE and SEX are as collected.

Note: a submitted variable label has at most 40 characters, so the submission stops before any file is written; no label is shortened.

How to fix

Use the label the implementation guide publishes, Sex, and keep any longer explanation in a comment, which the data-definition document carries in full:

  - name: SEX
    type: str
    label: Sex

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: transport_label_invalid
rule: XPT-5

expected/error.yaml

phase: validation
condition: transport_label_invalid
spec_paths:
  - sdtm.specs[0].columns.SEX.label
rule: XPT-5
context:
  dataset: DM
  column: SEX
  label: Sex of the Subject as Collected on the Form
  cause: length

YAML specification

1 spec file

spec.yaml

Edit114 lines

1yamaa: "1.0"2type: spec3model: SDTM4domain: DM5keys: [STUDYID, USUBJID]6input:7  DM_RAW: input/dm_raw.csv89output:10  path: dm.csv11  columns: [DOMAIN, STUDYID, USUBJID, SUBJID, SITEID, AGE, SEX]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: DM_RAW.STUDYID30    submission:31      core: Req32      role: Identifier33      length: 2034      origins:35        - type: Protocol36          source: Sponsor3738  - name: USUBJID39    type: str40    label: Unique Subject Identifier41    derivation: DM_RAW.USUBJID42    submission:43      core: Req44      role: Identifier45      length: 3046      origins:47        - type: Assigned48          source: Sponsor4950  - name: SUBJID51    type: str52    label: Subject Identifier for the Study53    derivation: DM_RAW.SUBJID54    submission:55      core: Req56      role: Topic57      length: 1058      origins:59        - type: Collected60          source: Investigator61          documents:62            - document: acrf63              pages: {type: PhysicalRef, refs: "1"}6465  - name: SITEID66    type: str67    label: Study Site Identifier68    derivation: DM_RAW.SITEID69    submission:70      core: Req71      role: Record Qualifier72      length: 1073      origins:74        - type: Collected75          source: Investigator76          documents:77            - document: acrf78              pages: {type: PhysicalRef, refs: "1"}7980  - name: AGE81    type: int82    label: Age83    derivation: DM_RAW.AGE84    submission:85      core: Exp86      role: Record Qualifier87      length: 388      origins:89        - type: Collected90          source: Investigator91          documents:92            - document: acrf93              pages: {type: PhysicalRef, refs: "1"}9495  - name: SEX96    type: str97    label: Sex of the Subject as Collected on the Form98    derivation: DM_RAW.SEX99    submission:100      core: Req101      role: Record Qualifier102      length: 1103      origins:104        - type: Collected105          source: Investigator106          documents:107            - document: acrf108              pages: {type: PhysicalRef, refs: "1"}109110submission:111  label: Demographics112  class: SPECIAL PURPOSE113  structure: One record per subject114  repeating: false

Inputs

Under review1 source file

input/dm_raw.csv

Edit2 rows

input/dm_raw.csv
STUDYID	USUBJID	SUBJID	SITEID	AGE	SEX
CATH		0001	UCSD	34	F
CATH		0002	UCSD	67	M

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	SUBJID	SITEID	AGE	SEX
DM	CATH		0001	UCSD	34	F
DM	CATH		0002	UCSD	67	M

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	20	Protocol	Req	Copy value from DM_RAW.STUDYID.	SDTM	2
USUBJID	Unique Subject Identifier	Char	30	Assigned	Req	Copy value from DM_RAW.USUBJID.	SDTM	3
SUBJID	Subject Identifier for the Study	Char	10	Collected	Req	Copy value from DM_RAW.SUBJID.	SDTM	4
SITEID	Study Site Identifier	Char	10	Collected	Req	Copy value from DM_RAW.SITEID.	SDTM	5
AGE	Age	Num	3	Collected	Exp	Copy value from DM_RAW.AGE.	SDTM	6
SEX	Sex of the Subject as Collected on the Form	Char	1	Collected	Req	Copy value from DM_RAW.SEX.	SDTM	7

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