yamaa / Benchmark

ADaM.ADSL

Share One Study's Project Between Two Submission Packages

input files
1
subjects
3
expected rows
3
Review ask

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Summary

Lifecycle: draftEditUnder reviewWhat this benchmark means
README.md

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

Goal: carry the planned treatment (TRT01P) and the reason for discontinuation from the study (DCSREAS) into ADSL for two submission packages of one study, with the second package's data-definition document.

Input: spec.yaml reads one pre-analysis row per subject, and three project files compose:

  • study/project.yaml holds what every package of the study shares: the study, its implementation guide, the vendor that prepared the metadata, the specification and study/codelists.yaml, the study's coded values;
  • pilot3/project.yaml, the first package, names the study's project as its parent and adds only where its document is written;
  • project.yaml, the second package, names the study's project as its parent too, lists the study's coded values and then codelists.yaml, its own discontinuation reasons, and removes the vendor, since the sponsor submits this package itself.

Variables:

  • TRT01P is the planned treatment, one of the study's coded values.
  • DCSREAS is the reason for discontinuation from the study.

Note: each package keeps every section of the study's project and changes only what it writes, field by field; a list it writes replaces the study's whole. A file the study's project names is read beside that project, so both packages build the one specification it lists. The second package's document cites the study and its guide from the study's project, decodes each reason as the package's coded values do, and names no originator.

Inputs

Under review1 source file

input/adsl_raw.csv

Edit3 rows
STUDYIDUSUBJIDTRT01PDCSREAS
CATHVITAMIN D3COMPLETED
CATHPLACEBOADVERSE EVENT
CATHPLACEBOWITHDRAWAL BY SUBJECT

Expected output

Under review3 expected rows

expected/adsl.csv

Edit3 rows
STUDYIDUSUBJIDTRT01PDCSREAS
CATHVITAMIN D3COMPLETED
CATHPLACEBOADVERSE EVENT
CATHPLACEBOWITHDRAWAL BY SUBJECT

expected/define.xml

EditDefine-XML

Define-XML 2.1.11: CATH

Example study resubmitting subject-level analysis data; CATH-01; ADaMIG 1.3

Datasets
DatasetDescriptionClassStructurePurposeKeysDocumentationLocation
ADSLSubject-Level Analysis DatasetSUBJECT LEVEL ANALYSIS DATASETOne record per subjectAnalysisSTUDYID, USUBJIDadsl.csv

ADSL

ADSL variables
VariableLabel / DescriptionTypeLength or Display FormatControlled Terms or ISO FormatOrigin / Source / Method / Comment
STUDYIDStudy Identifiertext4Predecessor; ADSL_RAW.STUDYID
USUBJIDUnique Subject Identifiertext9Predecessor; ADSL_RAW.USUBJID
TRT01PPlanned Treatment for Period 01text10Planned Treatment for Period 01 (CL.TRT01P) PLACEBO = Placebo VITAMIN D3 = Vitamin D3 5000 IU dailyPredecessor; ADSL_RAW.TRT01P
DCSREASReason for Discontinuation from Studytext21Reason for Discontinuation from Study (CL.DCSREAS) ADVERSE EVENT = ADVERSE EVENT COMPLETED = COMPLETED LOST TO FOLLOW-UP = LOST TO FOLLOW-UP WITHDRAWAL BY SUBJECT = WITHDRAWAL BY SUBJECTPredecessor; ADSL_RAW.DCSREAS
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/v2.1" xmlns:xlink="http://www.w3.org/1999/xlink" ODMVersion="1.3.2" FileType="Snapshot" FileOID="CATH.adam.Define-XML_2.1" CreationDateTime="2026-09-11T00:00:00" SourceSystem="yamaa" SourceSystemVersion="1.0" def:Context="Other">
  <Study OID="STDY.CATH">
    <GlobalVariables>
      <StudyName>CATH</StudyName>
      <StudyDescription>Example study resubmitting subject-level analysis data</StudyDescription>
      <ProtocolName>CATH-01</ProtocolName>
    </GlobalVariables>
    <MetaDataVersion OID="MDV.CATH.adam" Name="CATH adam metadata" def:DefineVersion="2.1.11">
      <def:Standards>
        <def:Standard OID="STD.ADaMIG" Name="ADaMIG" Type="IG" Version="1.3" Status="Final"/>
      </def:Standards>
      <ItemGroupDef OID="IG.ADSL" Name="ADSL" Purpose="Analysis" SASDatasetName="ADSL" Repeating="No" IsReferenceData="No" def:Structure="One record per subject" def:ArchiveLocationID="LF.ADSL" def:StandardOID="STD.ADaMIG">
        <Description>
          <TranslatedText xml:lang="en">Subject-Level Analysis Dataset</TranslatedText>
        </Description>
        <ItemRef ItemOID="IT.ADSL.STUDYID" OrderNumber="1" Mandatory="Yes" KeySequence="1"/>
        <ItemRef ItemOID="IT.ADSL.USUBJID" OrderNumber="2" Mandatory="Yes" KeySequence="2"/>
        <ItemRef ItemOID="IT.ADSL.TRT01P" OrderNumber="3" Mandatory="Yes"/>
        <ItemRef ItemOID="IT.ADSL.DCSREAS" OrderNumber="4" Mandatory="Yes"/>
        <def:Class Name="SUBJECT LEVEL ANALYSIS DATASET"/>
        <def:leaf ID="LF.ADSL" xlink:href="adsl.csv">
          <def:title>adsl.csv</def:title>
        </def:leaf>
      </ItemGroupDef>
      <ItemDef OID="IT.ADSL.STUDYID" Name="STUDYID" DataType="text" Length="4" SASFieldName="STUDYID">
        <Description>
          <TranslatedText xml:lang="en">Study Identifier</TranslatedText>
        </Description>
        <def:Origin Type="Predecessor">
          <Description>
            <TranslatedText xml:lang="en">ADSL_RAW.STUDYID</TranslatedText>
          </Description>
        </def:Origin>
      </ItemDef>
      <ItemDef OID="IT.ADSL.USUBJID" Name="USUBJID" DataType="text" Length="9" SASFieldName="USUBJID">
        <Description>
          <TranslatedText xml:lang="en">Unique Subject Identifier</TranslatedText>
        </Description>
        <def:Origin Type="Predecessor">
          <Description>
            <TranslatedText xml:lang="en">ADSL_RAW.USUBJID</TranslatedText>
          </Description>
        </def:Origin>
      </ItemDef>
      <ItemDef OID="IT.ADSL.TRT01P" Name="TRT01P" DataType="text" Length="10" SASFieldName="TRT01P">
        <Description>
          <TranslatedText xml:lang="en">Planned Treatment for Period 01</TranslatedText>
        </Description>
        <CodeListRef CodeListOID="CL.TRT01P"/>
        <def:Origin Type="Predecessor">
          <Description>
            <TranslatedText xml:lang="en">ADSL_RAW.TRT01P</TranslatedText>
          </Description>
        </def:Origin>
      </ItemDef>
      <ItemDef OID="IT.ADSL.DCSREAS" Name="DCSREAS" DataType="text" Length="21" SASFieldName="DCSREAS">
        <Description>
          <TranslatedText xml:lang="en">Reason for Discontinuation from Study</TranslatedText>
        </Description>
        <CodeListRef CodeListOID="CL.DCSREAS"/>
        <def:Origin Type="Predecessor">
          <Description>
            <TranslatedText xml:lang="en">ADSL_RAW.DCSREAS</TranslatedText>
          </Description>
        </def:Origin>
      </ItemDef>
      <CodeList OID="CL.TRT01P" Name="Planned Treatment for Period 01" DataType="text" def:IsNonStandard="Yes">
        <CodeListItem CodedValue="PLACEBO">
          <Decode>
            <TranslatedText xml:lang="en">Placebo</TranslatedText>
          </Decode>
        </CodeListItem>
        <CodeListItem CodedValue="VITAMIN D3">
          <Decode>
            <TranslatedText xml:lang="en">Vitamin D3 5000 IU daily</TranslatedText>
          </Decode>
        </CodeListItem>
      </CodeList>
      <CodeList OID="CL.DCSREAS" Name="Reason for Discontinuation from Study" DataType="text" def:IsNonStandard="Yes">
        <CodeListItem CodedValue="ADVERSE EVENT">
          <Decode>
            <TranslatedText xml:lang="en">ADVERSE EVENT</TranslatedText>
          </Decode>
        </CodeListItem>
        <CodeListItem CodedValue="COMPLETED">
          <Decode>
            <TranslatedText xml:lang="en">COMPLETED</TranslatedText>
          </Decode>
        </CodeListItem>
        <CodeListItem CodedValue="LOST TO FOLLOW-UP">
          <Decode>
            <TranslatedText xml:lang="en">LOST TO FOLLOW-UP</TranslatedText>
          </Decode>
        </CodeListItem>
        <CodeListItem CodedValue="WITHDRAWAL BY SUBJECT">
          <Decode>
            <TranslatedText xml:lang="en">WITHDRAWAL BY SUBJECT</TranslatedText>
          </Decode>
        </CodeListItem>
      </CodeList>
    </MetaDataVersion>
  </Study>
</ODM>
Shaded columns are derived— = missing value

Human review and assessment

Your review

2 questions and your comments · View benchmark discussions

Mapping spec

Generated from the benchmark YAML; do not edit by hand

Dataset NameVariable NameVariable LabelTypeCodelist/Controlled TermsCoreComputational MethodOrigin
ADSLSTUDYIDStudy IdentifiercharacterReqCopy value from ADSL_RAW.STUDYID.Predecessor
ADSLUSUBJIDUnique Subject IdentifiercharacterReqCopy value from ADSL_RAW.USUBJID.Predecessor
ADSLTRT01PPlanned Treatment for Period 01characterPlanned Treatment for Period 01ReqCopy value from ADSL_RAW.TRT01P.Predecessor
ADSLDCSREASReason for Discontinuation from StudycharacterReason for Discontinuation from StudyPermCopy value from ADSL_RAW.DCSREAS.Predecessor
Codelist IDNameValueDecodeCodelist NCI aliasValue NCI aliasExtensibleExtended valueSAS formatDictionaryVersion
DCSREASReason for DiscontinuationADVERSE EVENTAdverse EventNo
DCSREASReason for DiscontinuationCOMPLETEDCompletedNo
DCSREASReason for DiscontinuationWITHDRAWAL BY SUBJECTWithdrawal by SubjectNo
TRT01PPlanned Treatment for Period 01PLACEBOPlaceboNo
TRT01PPlanned Treatment for Period 01VITAMIN D3Vitamin D3 5000 IU dailyNo
DCSREASReason for Discontinuation from StudyADVERSE EVENTADVERSE EVENTNo
DCSREASReason for Discontinuation from StudyCOMPLETEDCOMPLETEDNo
DCSREASReason for Discontinuation from StudyLOST TO FOLLOW-UPLOST TO FOLLOW-UPNo
DCSREASReason for Discontinuation from StudyWITHDRAWAL BY SUBJECTWITHDRAWAL BY SUBJECTNo
VersionDateAuthorDescriptionReviewerSign-off
1.72026-10-20yamaa docs buildRead 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
1.62026-10-17yamaa docs buildDescribe collected date parts written as ISO 8601 date text and times of day counted in seconds since midnight
1.52026-10-17yamaa docs buildName 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
1.42026-10-15yamaa docs buildState datetime precision codes through the hour and minute, and complete only the time parts a collected datetime lacks
1.32026-09-29yamaa docs buildShow study codelist names, external dictionaries, and ISO 8601 formats in variable rows; list the document's codelist values and metadata
1.22026-09-29yamaa docs buildClassify ADaM copies from a declared input as Predecessor and recodes as Derived, and SDTM recodes of locally derived columns as Derived
1.12026-09-29yamaa docs buildResolve lookups into the donor record they select, and give every derivation shape a plain-language rule instead of its raw YAML
1.0yamaa docs buildInitial generation from spec.yaml

yamaa code

Public calls generated from benchmark.yaml; results must match the expected output

R

Edit4 lines
library(yamaa)yamaa_project("pilot3/project.yaml")$spec("ADSL")$run()$save()yamaa_project("project.yaml")$spec("ADSL")$run()$output

Python

Edit4 lines
import yamaayamaa.project("pilot3/project.yaml").spec("ADSL").run().save()yamaa.project("project.yaml").spec("ADSL").run().output