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Summary

EditUnder reviewWhat this benchmark means

README.md

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

Goal: show a resubmission level that changes only the list of published variables and the dataset file its data definition names, inheriting every other part of the dataset's layout and of its received description from the original package.

Dataset: dm.csv, SDTM demographics. One record per subject.

Input: two spec files, read root-first:

spec_package.yaml carries the original package: the age, its units and the sex collected for each subject, published in subject order to dm.csv, and the dataset's description as the package received it, a special-purpose demographics dataset of one record per subject held in the SAS transport file dm.xpt;
spec_resubmission.yaml is the entry: it names the original package as its parent, publishes its variables without the age units, and names its dataset file dm.json. It writes nothing else.

Variables:

DOMAIN is always DM.
AGE is the subject's collected age in years.
SEX is the subject's collected sex.

Note: a level that changes one part of the published layout or of the received description writes that part alone, and every part it leaves out keeps its inherited value. The resubmission therefore keeps the original file name and subject order, and its data definition describes the shorter variable list with the received description and the new dataset file.

YAML specification

2 spec files

spec_package.yaml
Edit79 lines
1yamaa: "1.0"2type: spec3model: SDTM4domain: DM5keys: [STUDYID, USUBJID]6input:7  RAW: {path: input/dm.csv, types: {AGE: int}}89# The original package publishes every subject in subject order.10output:11  path: dm.csv12  columns: [DOMAIN, STUDYID, USUBJID, AGE, AGEU, SEX]13  order_by: [USUBJID]1415columns:16  - name: DOMAIN17    type: str18    label: Domain Abbreviation19    derivation: "'DM'"20    submission:21      data_type: text22      length: 223      mandatory: true2425  - name: STUDYID26    type: str27    label: Study Identifier28    derivation: RAW.STUDYID29    submission:30      data_type: text31      length: 532      mandatory: true33      key_sequence: 13435  - name: USUBJID36    type: str37    label: Unique Subject Identifier38    derivation: RAW.USUBJID39    submission:40      data_type: text41      length: 942      mandatory: true43      key_sequence: 24445  - name: AGE46    type: int47    label: Age48    derivation: RAW.AGE49    submission:50      data_type: integer51      length: 352      mandatory: false5354  - name: AGEU55    type: str56    label: Age Units57    derivation: RAW.AGEU58    submission:59      data_type: text60      length: 561      mandatory: false6263  - name: SEX64    type: str65    label: Sex66    derivation: RAW.SEX67    submission:68      data_type: text69      length: 170      mandatory: true7172# The dataset's metadata as the original package received it, written once.73submission:74  mode: historical75  artifact: dm.xpt76  label: Demographics77  class: SPECIAL PURPOSE78  structure: One record per subject79  repeating: false
spec_resubmission.yaml
Edit13 lines
1yamaa: "1.0"2type: spec3parent: spec_package.yaml45# The resubmission publishes the variables without the age units; the path6# and the subject order come from the original package.7output:8  columns: [DOMAIN, STUDYID, USUBJID, AGE, SEX]910# The resubmitted dataset file; the rest of the received metadata is the11# original package's.12submission:13  artifact: dm.json

Inputs

Under review1 source file

input/dm.csv

Edit3 rows

input/dm.csv
STUDYID	AGE	AGEU	SEX
PKG01	71	YEARS	F
PKG01	34	YEARS	M
PKG01	58	YEARS	F

Expected output

Under review3 expected rows

expected/define.xml

EditDefine-XML

Define-XML 2.0.0: PKG01

Example study resubmitting its demographics dataset; PKG-01; SDTM-IG 3.4

Datasets
Dataset	Description	Class	Structure	Purpose	Keys	Documentation	Location
DM	Demographics	SPECIAL PURPOSE	One record per subject	Tabulation	STUDYID, USUBJID		dm.json

DM

DM variables
Variable	Label / Description	Type	Length or Display Format
DOMAIN	Domain Abbreviation	text	2
STUDYID	Study Identifier	text	5
USUBJID	Unique Subject Identifier	text	9
AGE	Age	integer	3
SEX	Sex	text	1

Original source

<?xml version="1.0" encoding="UTF-8"?>
<ODM xmlns="http://www.cdisc.org/ns/odm/v1.3" xmlns:def="http://www.cdisc.org/ns/def/v2.0" xmlns:xlink="http://www.w3.org/1999/xlink" ODMVersion="1.3.2" FileType="Snapshot" FileOID="PKG01.sdtm.Define-XML_2.0" CreationDateTime="2026-10-28T00:00:00" SourceSystem="yamaa" SourceSystemVersion="1.0">
  <Study OID="STDY.PKG01">
    <GlobalVariables>
      <StudyName>PKG01</StudyName>
      <StudyDescription>Example study resubmitting its demographics dataset</StudyDescription>
      <ProtocolName>PKG-01</ProtocolName>
    </GlobalVariables>
    <MetaDataVersion OID="MDV.PKG01.sdtm" Name="PKG01 sdtm metadata" def:DefineVersion="2.0.0" def:StandardName="SDTM-IG" def:StandardVersion="3.4">
      <ItemGroupDef OID="IG.DM" Name="DM" Domain="DM" Purpose="Tabulation" SASDatasetName="DM" Repeating="No" IsReferenceData="No" def:Structure="One record per subject" def:Class="SPECIAL PURPOSE" def:ArchiveLocationID="LF.DM">
        <Description>
          <TranslatedText xml:lang="en">Demographics</TranslatedText>
        </Description>
        <ItemRef ItemOID="IT.DM.DOMAIN" OrderNumber="1" Mandatory="Yes"/>
        <ItemRef ItemOID="IT.DM.STUDYID" OrderNumber="2" Mandatory="Yes" KeySequence="1"/>
        <ItemRef ItemOID="IT.DM.USUBJID" OrderNumber="3" Mandatory="Yes" KeySequence="2"/>
        <ItemRef ItemOID="IT.DM.AGE" OrderNumber="4" Mandatory="No"/>
        <ItemRef ItemOID="IT.DM.SEX" OrderNumber="5" Mandatory="Yes"/>
        <def:leaf ID="LF.DM" xlink:href="dm.json">
          <def:title>dm.json</def:title>
        </def:leaf>
      </ItemGroupDef>
      <ItemDef OID="IT.DM.DOMAIN" Name="DOMAIN" DataType="text" Length="2" SASFieldName="DOMAIN">
        <Description>
          <TranslatedText xml:lang="en">Domain Abbreviation</TranslatedText>
        </Description>
      </ItemDef>
      <ItemDef OID="IT.DM.STUDYID" Name="STUDYID" DataType="text" Length="5" SASFieldName="STUDYID">
        <Description>
          <TranslatedText xml:lang="en">Study Identifier</TranslatedText>
        </Description>
      </ItemDef>
      <ItemDef OID="IT.DM.USUBJID" Name="USUBJID" DataType="text" Length="9" SASFieldName="USUBJID">
        <Description>
          <TranslatedText xml:lang="en">Unique Subject Identifier</TranslatedText>
        </Description>
      </ItemDef>
      <ItemDef OID="IT.DM.AGE" Name="AGE" DataType="integer" Length="3" SASFieldName="AGE">
        <Description>
          <TranslatedText xml:lang="en">Age</TranslatedText>
        </Description>
      </ItemDef>
      <ItemDef OID="IT.DM.SEX" Name="SEX" DataType="text" Length="1" SASFieldName="SEX">
        <Description>
          <TranslatedText xml:lang="en">Sex</TranslatedText>
        </Description>
      </ItemDef>
    </MetaDataVersion>
  </Study>
</ODM>

expected/dm.csv

Edit3 rows

expected/dm.csv
DOMAIN	STUDYID	AGE	SEX
DM	PKG01	34	M
DM	PKG01	58	F
DM	PKG01	71	F

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	Comments for Define

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

R

Edit3 lines

1library(yamaa)23yamaa_project("project.yaml")$spec("DM")$run()$output

Python

Edit3 lines

1import yamaa23yamaa.project("project.yaml").spec("DM").run().output

input/dm.csv

expected/define.xml

Define-XML 2.0.0: PKG01

DM

expected/dm.csv

Your review

Mapping spec

yamaa code

R

Python