Site Identifier with a Trailing Blank in Transport

Review ask

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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; one site identifier was entered with a trailing blank.

Variables:

SITEID is the collected site identifier, blank included.
AGE and SEX are as collected.

Note: a SAS transport file pads text with blanks, so a value ending in a blank cannot be read back as written and stops the submission.

How to fix

Correct the site identifier in the collected data. When the source cannot be corrected, remove trailing blanks explicitly:

  - name: SITEID
    type: str
    label: Study Site Identifier
    derivation:
      str_replace:
        source: DM_RAW.SITEID
        pattern: " +$"
        replacement: ""

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: output
condition: transport_text_invalid
rule: XPT-7

expected/error.yaml

phase: output
condition: transport_text_invalid
spec_paths:
  - datasets.DM.columns.SITEID
rule: XPT-7
context:
  dataset: DM
  column: SITEID
  row: 1
  value: 'UCSD '
  cause: trailing_blank

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: Sex98    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	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